diff --git a/articles/available-data.html b/articles/available-data.html
index 62a1775..c2aa0f0 100644
--- a/articles/available-data.html
+++ b/articles/available-data.html
@@ -72,7 +72,7 @@ <h1>Available data</h1>
 <code><a href="../reference/search_data.html">appliedepidata::search_data()</a></code> to search for data sets in
 other languages available in the package.</p>
 <div class="reactable html-widget html-fill-item" id="htmlwidget-ac96cb3ee4656e2e9ec3" style="width:auto;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-ac96cb3ee4656e2e9ec3">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"name":["AJS_AmTiman","AJS_AmTiman_population","Blocksshape","Quartiersshape","mortality_survey_data","mortality_survey_dict","fulton_data","fulton_data_clean","fulton_population","mpox_linelist","mpox_aggregate_table","stegentira_data"],"description":["Linelist data from a real outbreak of Hepatitis E virus (HEV) infection which occurred in the town of Am Timan, Chad, between October 2016 and April 2017.","Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016","Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016","Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016","Fake data for a mortality survey","Fake data dictionary for a mortality survey","Jittered COVID-19 linelist data from Fulton County","Jittered COVID-19 linelist data from Fulton County","County-level population data","Fictional mpox case linelist in five European countries","Fictional cumulative mpox case counts in five European countries","Fictional linelist of salmonella outbreak in Stegen, Germany"],"language":["<a href=\"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html\" target=\"_blank\">en<\/a>, <a href=\"https://appliedepi.github.io/appliedepidata/reference/franglais_AJS_AmTiman.html\" target=\"_blank\">fr<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html\" target=\"_blank\">en<\/a>"],"group_identifier":["acutejaundicesyndrome_outbreak_tcd_2016","acutejaundicesyndrome_outbreak_tcd_2016","acutejaundicesyndrome_outbreak_tcd_2016","acutejaundicesyndrome_outbreak_tcd_2016","mortality_survey_zzz_2021","mortality_survey_zzz_2021","covid-19_outbreak_usa_2020","covid-19_outbreak_usa_2020","covid-19_outbreak_usa_2020","mpox_outbreak_eue_2022","mpox_outbreak_eue_2022","salmonella_outbreak_de_1998"]},"columns":[{"id":"name","name":"name","type":"character"},{"id":"description","name":"description","type":"character"},{"id":"language","name":"language","type":"character","html":true},{"id":"group_identifier","name":"group_identifier","type":"character"}],"filterable":true,"defaultPageSize":10,"dataKey":"0404d034f946d6c60f4726ede4b12520"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script></main>
+<script type="application/json" data-for="htmlwidget-ac96cb3ee4656e2e9ec3">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"name":["AJS_AmTiman","AJS_AmTiman_population","Blocksshape","Quartiersshape","mortality_survey_data","mortality_survey_dict","fulton_data","fulton_data_clean","fulton_population","mpox_linelist","mpox_aggregate_table","stegentira_data","fluH7N9_China_2013","linelist_raw","linelist_cleaned_excel","linelist_cleaned_rds","hospital_linelists","linelist_cleaned_with_adm3","cleaning_dict","sle_adm3","sle_admpop_adm3_2020","epinow_res","epinow_res_small","generation_time","incubation_period","cases_clean","contacts_clean","followups_clean","relationships_clean","district_weekly_count_data","malaria_facility_count_data","Shigella_tree","sample_data_Shigella_tree","Shigella_subtree_2","country_demographics","country_demographics_2","deaths_countryA","deaths_countryB","world_standard_population_by_sex","likert_data","survey_data","survey_dict","population","campylobacter_germany","germany_weather"],"description":["Linelist data from a real outbreak of Hepatitis E virus (HEV) infection which occurred in the town of Am Timan, Chad, between October 2016 and April 2017.","Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016","Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016","Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016","Fake data for a mortality survey","Fake data dictionary for a mortality survey","Jittered COVID-19 linelist data from Fulton County","Jittered COVID-19 linelist data from Fulton County","County-level population data","Fictional mpox case linelist in five European countries","Fictional cumulative mpox case counts in five European countries","Fictional linelist of salmonella outbreak in Stegen, Germany","Linelist data from an outbreak of influenza A H7N9 in China 2013.","Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014","Excel clean version of fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014","R-dataset clean version of fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014","Subset of excel clean version of fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014","Subset with additional spatial data of rds clean version of fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014","Short example cleaning dictionary for the raw linelist","Shapefile at admin level  3 for Sierra Leone from Humanitarian Data Exchange","Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange","Outputs from {epinow2} based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014","Outputs from {epinow2} based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014","Outputs from {epinow2} based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2015","Outputs from {epinow2} based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2015","Fictional case data for a generic disease to demonstrate contact tracing","Fictional case data for a generic disease to demonstrate contact tracing","Fictional case data for a generic disease to demonstrate contact tracing","Fictional case data for a generic disease to demonstrate contact tracing","Fictional counts of malaria cases from Mozambique","Fictional counts of malaria cases from Mozambique","Next generation sequencing data of Shigella surveillance samples from Belgium","Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019","Analysis output from next generation sequencing data of Shigella surveillance samples from Belgium","Fictional country demographic and mortality data to demonstrate standardisation","Fictional country demographic and mortality data to demonstrate standardisation","Fictional country demographic and mortality data to demonstrate standardisation","Fictional country demographic and mortality data to demonstrate standardisation","World “standard population” by sex","Fictional likert data for demonstration purposes","Fictional data for a mortality survey","Fictional data dictionary for a mortality survey","Fictional population data for a mortality survey","Campylobacter surveillance data from Germany","Weather data for Germany from 2001-2011"],"language":["<a href=\"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html\" target=\"_blank\">en<\/a>, <a href=\"https://appliedepi.github.io/appliedepidata/reference/franglais_AJS_AmTiman.html\" target=\"_blank\">fr<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/fluH7N9_China_2013.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/linelist_raw.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_excel.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_rds.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/hospital_linelists.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_with_adm3.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/cleaning_dict.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/sle_adm3.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/sle_admpop_adm3_2020.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/epinow_res.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/epinow_res_small.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/generation_time.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/incubation_period.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/cases_clean.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/contacts_clean.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/followups_clean.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/relationships_clean.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/district_weekly_count_data.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/malaria_facility_count_data.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/Shigella_tree.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/sample_data_Shigella_tree.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/Shigella_subtree_2.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/country_demographics.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/country_demographics_2.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/deaths_countryA.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/deaths_countryB.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/world_standard_population_by_sex.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/likert_data.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/survey_data.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/survey_dict.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/population.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/campylobacter_germany.html\" target=\"_blank\">en<\/a>","<a href=\"https://appliedepi.github.io/appliedepidata/reference/germany_weather.html\" target=\"_blank\">en<\/a>"],"group_identifier":["acutejaundicesyndrome_outbreak_tcd_2016","acutejaundicesyndrome_outbreak_tcd_2016","acutejaundicesyndrome_outbreak_tcd_2016","acutejaundicesyndrome_outbreak_tcd_2016","mortality_survey_zzz_2021","mortality_survey_zzz_2021","covid-19_outbreak_usa_2020","covid-19_outbreak_usa_2020","covid-19_outbreak_usa_2020","mpox_outbreak_eue_2022","mpox_outbreak_eue_2022","salmonella_outbreak_deu_1998","influenza_outbreak_chn_2013","ebola_outbreak_sle_2014","ebola_outbreak_sle_2014","ebola_outbreak_sle_2014","ebola_outbreak_sle_2014","ebola_outbreak_sle_2014","ebola_outbreak_sle_2014","ebola_outbreak_sle_2014","ebola_outbreak_sle_2020","ebola_outbreak_sle_2014","ebola_outbreak_sle_2014","ebola_outbreak_sle_2014","ebola_outbreak_sle_2014","contacttracing_outbreak_zzz_2020","contacttracing_outbreak_zzz_2020","contacttracing_outbreak_zzz_2020","contacttracing_outbreak_zzz_2020","malaria_outbreak_moz_2019","malaria_outbreak_moz_2019","shigella_surveillance_bel_2013","shigella_surveillance_bel_2013","shigella_surveillance_bel_2013","mortality_surveillance_zzz_2020","mortality_surveillance_zzz_2020","mortality_surveillance_zzz_2020","mortality_surveillance_zzz_2020","mortality_surveillance_zzz_2020","likert_other_zzz_2020","mortality_survey_zzz_2021","mortality_survey_zzz_2021","mortality_survey_zzz_2021","campylobacter_surveillance_deu_2001","weather_other_deu_2001"]},"columns":[{"id":"name","name":"name","type":"character"},{"id":"description","name":"description","type":"character"},{"id":"language","name":"language","type":"character","html":true},{"id":"group_identifier","name":"group_identifier","type":"character"}],"filterable":true,"defaultPageSize":10,"dataKey":"52ff56d2876fcbdbe8a60654cdfac1d3"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script></main>
 </div>
 
 
diff --git a/pkgdown.yml b/pkgdown.yml
index d6803f5..c491250 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   adding-data: adding-data.html
   available-data: available-data.html
   data-dictionaries: data-dictionaries.html
-last_built: 2024-11-06T06:49Z
+last_built: 2024-11-09T02:43Z
 urls:
   reference: https://appliedepi.github.io/appliedepidata/reference
   article: https://appliedepi.github.io/appliedepidata/articles
diff --git a/reference/AJS_AmTiman.html b/reference/AJS_AmTiman.html
index 9a56a27..5ee9359 100644
--- a/reference/AJS_AmTiman.html
+++ b/reference/AJS_AmTiman.html
@@ -55,374 +55,8 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A data frame with 1477 rows and 122 columns:</p><dl><dt>Number</dt>
-<dd><p>a numeric denoting HEV  Count</p></dd>
-
-<dt>HEVID</dt>
-<dd><p>a numeric denoting HEV Case ID</p></dd>
-
-<dt>Sex</dt>
-<dd><p>a character denoting Sexe M=Male; F=Femelle</p></dd>
-
-<dt>Age</dt>
-<dd><p>a character denoting Age</p></dd>
-
-<dt>Agegroup</dt>
-<dd><p>a character denoting Groupe D'age 1=0 to 4; 2= 5 to 14; 3=15 to 44; 4==45</p></dd>
-
-<dt>dateentry</dt>
-<dd><p>a character denoting Initial Entry into Database (either Questionnaire or Medical Assessment)</p></dd>
-
-<dt>epiquestdate</dt>
-<dd><p>a character denoting Date de Questionnaire</p></dd>
-
-<dt>team</dt>
-<dd><p>a character denoting Equipe</p></dd>
-
-<dt>chw</dt>
-<dd><p>a character denoting AC</p></dd>
-
-<dt>block</dt>
-<dd><p>a character denoting Bloc</p></dd>
-
-<dt>hh</dt>
-<dd><p>a character denoting Menage</p></dd>
-
-<dt>referredby</dt>
-<dd><p>a character denoting Referer par: (1=Hôpital ; 2 = Superviseur Agent Communitaire)</p></dd>
-
-<dt>quartier</dt>
-<dd><p>a character denoting Quartier/Village</p></dd>
-
-<dt>interviewee</dt>
-<dd><p>a character denoting Statut interroge Patient ou Parent</p></dd>
-
-<dt>hhpers</dt>
-<dd><p>a character denoting Nombre de personnes dan le menage</p></dd>
-
-<dt>hhmale</dt>
-<dd><p>a character denoting Nombre masculin</p></dd>
-
-<dt>hhfemale</dt>
-<dd><p>a character denoting Nombre feminin</p></dd>
-
-<dt>hhu5</dt>
-<dd><p>a character denoting Nombre d'enfant &lt; 5 ans</p></dd>
-
-<dt>hpreferral</dt>
-<dd><p>a character denoting Référé à l’hôpital par Agent Com?  (O = Oui, N = Non)</p></dd>
-
-<dt>hprefpos</dt>
-<dd><p>a character denoting Si oui, le patient est-allé?</p></dd>
-
-<dt>patientpresent</dt>
-<dd><p>a character denoting Est-ce que le patient est présent ?</p></dd>
-
-<dt>ptjaundice</dt>
-<dd><p>a character denoting Est-ce que le patient a la jaunisse?</p></dd>
-
-<dt>ptvomit</dt>
-<dd><p>a character denoting Vomissements ?</p></dd>
-
-<dt>mtmental</dt>
-<dd><p>a character denoting Etat mental altéré ?</p></dd>
-
-<dt>ptpregnant</dt>
-<dd><p>a character denoting Enceinte?</p></dd>
-
-<dt>ptu1</dt>
-<dd><p>a character denoting Agée moins d’un an ?</p></dd>
-
-<dt>referring</dt>
-<dd><p>a character denoting 15. Allez-vous référer à l’hôpital?</p></dd>
-
-<dt>otherajs</dt>
-<dd><p>a character denoting Autre patient dans le foyer?</p></dd>
-
-<dt>otherajsnum</dt>
-<dd><p>a character denoting Si oui, combien?</p></dd>
-
-<dt>borehole</dt>
-<dd><p>a character denoting Forage?</p></dd>
-
-<dt>comtap</dt>
-<dd><p>a character denoting Bonne Fontaine?</p></dd>
-
-<dt>river</dt>
-<dd><p>a character denoting Riviere?</p></dd>
-
-<dt>citywater</dt>
-<dd><p>a character denoting Eau de la ville?</p></dd>
-
-<dt>otherwater</dt>
-<dd><p>a character denoting Autre</p></dd>
-
-<dt>otherwatersp</dt>
-<dd><p>a character denoting Si autre…</p></dd>
-
-<dt>watersourcefreq</dt>
-<dd><p>a character denoting Quel point utilisez-vous le plus souvent?</p></dd>
-
-<dt>ceramicjar</dt>
-<dd><p>a character denoting Jarre</p></dd>
-
-<dt>jerrycan</dt>
-<dd><p>a character denoting Jerrycan</p></dd>
-
-<dt>oildrum</dt>
-<dd><p>a character denoting Fut</p></dd>
-
-<dt>reserother</dt>
-<dd><p>a character denoting Autre?</p></dd>
-
-<dt>reserothersp</dt>
-<dd><p>a character denoting Si autre….</p></dd>
-
-<dt>resertype</dt>
-<dd><p>a character denoting 20. Type de stockage</p></dd>
-
-<dt>chlorination</dt>
-<dd><p>a character denoting 21. Ajouté  chlore la derniere fois?</p></dd>
-
-<dt>volumreser</dt>
-<dd><p>a character denoting 22a. Combien de stockage?</p></dd>
-
-<dt>handreser</dt>
-<dd><p>a character denoting 22b. Entrer la main dans le stockage?</p></dd>
-
-<dt>hweating</dt>
-<dd><p>a character denoting 23. Laver les mains avant de manger?</p></dd>
-
-<dt>hwwater</dt>
-<dd><p>a character denoting 24a. Est-ce qu'il y a de l'eau?</p></dd>
-
-<dt>hwsoap</dt>
-<dd><p>a character denoting 24b. Est-ce qu'il y a du savon?</p></dd>
-
-<dt>treatwater</dt>
-<dd><p>a character denoting Traitez vous l'eau?</p></dd>
-
-<dt>tptreatwater</dt>
-<dd><p>a character denoting Type de traitement</p></dd>
-
-<dt>tptreatwaterother</dt>
-<dd><p>a character denoting Autre traitment</p></dd>
-
-<dt>nottreatwhy</dt>
-<dd><p>a character denoting Si non, pourquoi</p></dd>
-
-<dt>defecriver</dt>
-<dd><p>a character denoting Riviere?.1</p></dd>
-
-<dt>defecair</dt>
-<dd><p>a character denoting L'air libre?</p></dd>
-
-<dt>defeclatrine</dt>
-<dd><p>a character denoting Latrine?</p></dd>
-
-<dt>numlatrine</dt>
-<dd><p>a character denoting 26-Combin de personnes qui utilise le latrine?</p></dd>
-
-<dt>dtmedical</dt>
-<dd><p>a character denoting Date of Medical Assessment</p></dd>
-
-<dt>hpid</dt>
-<dd><p>a character denoting 1. Numero de Clinique/Hopital</p></dd>
-
-<dt>outreachscreened</dt>
-<dd><p>a character denoting Outreach screening? Y/N/U</p></dd>
-
-<dt>evaljaundice</dt>
-<dd><p>a character denoting 7. Deja Evalué pour la Jaunisse?</p></dd>
-
-<dt>jaundiceid</dt>
-<dd><p>a character denoting Si Oui, Numero de Cas?</p></dd>
-
-<dt>referredbychw</dt>
-<dd><p>a character denoting 8. Référé par l’Agent Communautaire?</p></dd>
-
-<dt>jaundiceid2</dt>
-<dd><p>a character denoting Si Oui, Numero de Cas?.1</p></dd>
-
-<dt>medjaundice</dt>
-<dd><p>a character denoting 9. Le patient a la jaunisse?</p></dd>
-
-<dt>dtjaundice</dt>
-<dd><p>a character denoting 10. Date de début de la jaunisse ?</p></dd>
-
-<dt>medfever</dt>
-<dd><p>a character denoting 11a. Fievre?</p></dd>
-
-<dt>mednausea</dt>
-<dd><p>a character denoting 11b. Nausées/Anorexie </p></dd>
-
-<dt>medvomit</dt>
-<dd><p>a character denoting 11c. Vomissements?</p></dd>
-
-<dt>medepigastric</dt>
-<dd><p>a character denoting 11d. Douleur epigastrique?</p></dd>
-
-<dt>meditching</dt>
-<dd><p>a character denoting 11e. Démangeaisons ?</p></dd>
-
-<dt>medheadache</dt>
-<dd><p>a character denoting 11f. Mal de tete?</p></dd>
-
-<dt>medarthralgia</dt>
-<dd><p>a character denoting 11g. Arthralgies?</p></dd>
-
-<dt>meddiar</dt>
-<dd><p>a character denoting 11h. Diarrhées</p></dd>
-
-<dt>medbleeding</dt>
-<dd><p>a character denoting 11i. Saignements?</p></dd>
-
-<dt>medfev38</dt>
-<dd><p>a character denoting 12. Fièvre = 38.0°C?</p></dd>
-
-<dt>medmental</dt>
-<dd><p>a character denoting 13. Etat Mental?</p></dd>
-
-<dt>medother</dt>
-<dd><p>a character denoting Other symptoms (free text)</p></dd>
-
-<dt>medothhhajs</dt>
-<dd><p>a character denoting 14. Autre avec jaunisse dans le menage?</p></dd>
-
-<dt>medothhhajsnum</dt>
-<dd><p>a character denoting 14a. Combien?</p></dd>
-
-<dt>othercaseid</dt>
-<dd><p>a character denoting 14b. Numero de cas</p></dd>
-
-<dt>medpreg</dt>
-<dd><p>a character denoting 15. Enceinte?</p></dd>
-
-<dt>medpregtri</dt>
-<dd><p>a character denoting 15a. Trimestre? 1/2/3</p></dd>
-
-<dt>medpp</dt>
-<dd><p>a character denoting 16. Post-Partum?</p></dd>
-
-<dt>medppdays</dt>
-<dd><p>a character denoting 16a. Si postpartum, combien de jours?</p></dd>
-
-<dt>medppoutcome</dt>
-<dd><p>a character denoting 16b. Resultat de la grossesse?</p></dd>
-
-<dt>matdeathdt</dt>
-<dd><p>a character denoting Si décès maternelle, date de décès</p></dd>
-
-<dt>medppga</dt>
-<dd><p>a character denoting Gestation weeks of delivery</p></dd>
-
-<dt>medblood</dt>
-<dd><p>a character denoting 17. Prelevements de sang?</p></dd>
-
-<dt>medblooddt</dt>
-<dd><p>a character denoting Si oui, date de prelevement</p></dd>
-
-<dt>medmalrdt</dt>
-<dd><p>a character denoting 18a. Malaria RDT</p></dd>
-
-<dt>medhepb</dt>
-<dd><p>a character denoting 18b. Hep B</p></dd>
-
-<dt>medhepc</dt>
-<dd><p>a character denoting 18c. Hep C</p></dd>
-
-<dt>medhevrdt</dt>
-<dd><p>a character denoting 18d. Hep E RDT</p></dd>
-
-<dt>medhevelisa</dt>
-<dd><p>a character denoting Hep E confiramtion ELISA      MOH  / MSF</p></dd>
-
-<dt>hevrecent</dt>
-<dd><p>a character denoting Confirmed 'recent' case based on ELISA enter 1 if IgM+</p></dd>
-
-<dt>hevpcr</dt>
-<dd><p>a character denoting Hep E confirmation PCR      MOH/MSF</p></dd>
-
-<dt>hevgenotest</dt>
-<dd><p>a character denoting Genotype peformed? Y/N/unk</p></dd>
-
-<dt>hevgenotype</dt>
-<dd><p>a character denoting If yes, what type?</p></dd>
-
-<dt>medhavelisa</dt>
-<dd><p>a character denoting Hep A ELISA</p></dd>
-
-<dt>medhbvelisa</dt>
-<dd><p>a character denoting Hep Bc ELISA</p></dd>
-
-<dt>medhcvelisa</dt>
-<dd><p>a character denoting Hep C ELISA</p></dd>
-
-<dt>arbovpcr</dt>
-<dd><p>a character denoting ARBO PCR (YF, Rift, Chik, DEN, WN, ZIK)</p></dd>
-
-<dt>yf</dt>
-<dd><p>a character denoting Yellow Fever Elisa</p></dd>
-
-<dt>zika</dt>
-<dd><p>a character denoting Zika Elisa</p></dd>
-
-<dt>dengue</dt>
-<dd><p>a character denoting Dengue Elisa</p></dd>
-
-<dt>wnv</dt>
-<dd><p>a character denoting West Nile Elisa</p></dd>
-
-<dt>rvf</dt>
-<dd><p>a character denoting Rift Valley Elisa</p></dd>
-
-<dt>chik</dt>
-<dd><p>a character denoting Chikungunya Elisa</p></dd>
-
-<dt>hospitalised</dt>
-<dd><p>a character denoting 19. Hospitalised?</p></dd>
-
-<dt>dthospitalisation</dt>
-<dd><p>a character denoting Date de hopitalisation?</p></dd>
-
-<dt>outcomehp</dt>
-<dd><p>a character denoting 20. Resultat Clinique</p></dd>
-
-<dt>dtdeath</dt>
-<dd><p>a character denoting (Si décès la date de décès)</p></dd>
-
-<dt>epiwajs</dt>
-<dd><p>a character denoting EpiWeek Jaundice Onset</p></dd>
-
-<dt>epiwhevelisa</dt>
-<dd><p>a character denoting EpiWeek Confirmed (IgM+)</p></dd>
-
-<dt>epiwoutreach</dt>
-<dd><p>a character denoting EpiWeek FIRST Assessment (Community or Medical)</p></dd>
-
-<dt>epiwmed</dt>
-<dd><p>a character denoting EpiWeek MEDICAL  Assessment</p></dd>
-
-<dt>epiwepiquest</dt>
-<dd><p>a character denoting EpiWeek Assessment QUESTIONNAIRE</p></dd>
-
-<dt>epiwhp</dt>
-<dd><p>a character denoting EpiWeek HOSPITALIZATION</p></dd>
-
-<dt>epiwdeath</dt>
-<dd><p>a character denoting EpiWeek DEATH</p></dd>
-
-<dt>caseclass</dt>
-<dd><p>a character denoting Suspected/Confirmed/Not A Case (based on HEV RDT)</p></dd>
-
-<dt>Longitude</dt>
-<dd><p>a numeric denoting Jittered GPS coordinates</p></dd>
-
-<dt>Latitude</dt>
-<dd><p>a numeric denoting Jittered GPS coordinates</p></dd>
-
-
-</dl></div>
+    <p>A data frame with 1477 rows and 122 columns</p>
+    </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
     <p>This data was collected as part of Doctors Without Borders (MSF) outbreak
diff --git a/reference/AJS_AmTiman_population.html b/reference/AJS_AmTiman_population.html
index aa4810b..a301251 100644
--- a/reference/AJS_AmTiman_population.html
+++ b/reference/AJS_AmTiman_population.html
@@ -55,14 +55,8 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A data frame with 648 rows and 3 columns:</p><dl><dt>variable1</dt>
-<dd><p>explanation of a variable</p></dd>
-
-<dt>variable2</dt>
-<dd><p>more explanation of variables</p></dd>
-
-
-</dl></div>
+    <p>A data frame with 648 rows and 3 columns:</p>
+    </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
     <p>This data was collected as part of Doctors Without Borders (MSF) outbreak
diff --git a/reference/Blocksshape.html b/reference/Blocksshape.html
index 054b32e..86f4768 100644
--- a/reference/Blocksshape.html
+++ b/reference/Blocksshape.html
@@ -55,14 +55,8 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A data frame with 650 rows and 3 columns:</p><dl><dt>variable1</dt>
-<dd><p>explanation of a variable</p></dd>
-
-<dt>variable2</dt>
-<dd><p>more explanation of variables</p></dd>
-
-
-</dl></div>
+    <p>A data frame with 650 rows and 3 columns</p>
+    </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
     <p>This data was collected as part of Doctors Without Borders (MSF) outbreak
diff --git a/reference/Quartiersshape.html b/reference/Quartiersshape.html
index 7709db6..8cced41 100644
--- a/reference/Quartiersshape.html
+++ b/reference/Quartiersshape.html
@@ -55,14 +55,8 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A data frame with 34 rows and 3 columns:</p><dl><dt>variable1</dt>
-<dd><p>explanation of a variable</p></dd>
-
-<dt>variable2</dt>
-<dd><p>more explanation of variables</p></dd>
-
-
-</dl></div>
+    <p>A data frame with 34 rows and 3 columns</p>
+    </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
     <p>This data was collected as part of Doctors Without Borders (MSF) outbreak
diff --git a/reference/Shigella_subtree_2.html b/reference/Shigella_subtree_2.html
new file mode 100644
index 0000000..6134dcf
--- /dev/null
+++ b/reference/Shigella_subtree_2.html
@@ -0,0 +1,91 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_subtree_2 • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_subtree_2"><meta name="description" content="Outputs of analysis with next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019"><meta property="og:description" content="Outputs of analysis with next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
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+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019</h1>
+
+      <div class="d-none name"><code>Shigella_subtree_2.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Outputs of analysis with next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">Shigella_subtree_2</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A List of class "phylo"</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was posted on the <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB40097?show=xrefs" class="external-link">European Nucleotide Archive</a></p>
+<p>The original dataset is Shigella_subtree_2.txt</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" class="external-link">CC by-NC-SA 4.0</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is based on sequencing data from routine surveillance samples collected in Belgium between 2013 and 2019.
+It was produced using used together with <a href="sample_data_Shigella_tree.html">sample_data_Shigella_tree</a> and <a href="Shigella_tree.html">Shigella_tree</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>Fischer, N. et al. Genomic epidemiology of persistently circulating MDR Shigella sonnei strains associated with men who have sex with men (MSM) in Belgium (2013-19) <a href="https://doi.org/10.1093/jac/dkab377" class="external-link">doi:10.1093/jac/dkab377</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/Shigella_tree.html b/reference/Shigella_tree.html
new file mode 100644
index 0000000..daf4779
--- /dev/null
+++ b/reference/Shigella_tree.html
@@ -0,0 +1,91 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_tree • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_tree"><meta name="description" content="Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019"><meta property="og:description" content="Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
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+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
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+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019</h1>
+
+      <div class="d-none name"><code>Shigella_tree.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">Shigella_tree</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A List of class "phylo"</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was posted on the <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB40097?show=xrefs" class="external-link">European Nucleotide Archive</a></p>
+<p>The original dataset is Shigella_Tree.txt</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" class="external-link">CC by-NC-SA 4.0</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is sequencing data from routine surveillance samples collected in Belgium between 2013 and 2019.
+It can be used together with <a href="sample_data_Shigella_tree.html">sample_data_Shigella_tree</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>Fischer, N. et al. Genomic epidemiology of persistently circulating MDR Shigella sonnei strains associated with men who have sex with men (MSM) in Belgium (2013-19) <a href="https://doi.org/10.1093/jac/dkab377" class="external-link">doi:10.1093/jac/dkab377</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/campylobacter_germany.html b/reference/campylobacter_germany.html
new file mode 100644
index 0000000..6ca7952
--- /dev/null
+++ b/reference/campylobacter_germany.html
@@ -0,0 +1,94 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Linelist data of Campylobacter surveillance in Germany 2001-2011. — campylobacter_germany • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Linelist data of Campylobacter surveillance in Germany 2001-2011. — campylobacter_germany"><meta name="description" content="Linelist data of Campylobacter surveillance in Germany 2001-2011."><meta property="og:description" content="Linelist data of Campylobacter surveillance in Germany 2001-2011."></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
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+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Linelist data of Campylobacter surveillance in Germany 2001-2011.</h1>
+
+      <div class="d-none name"><code>campylobacter_germany.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Linelist data of Campylobacter surveillance in Germany 2001-2011.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">campylobacter_germany</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 509 rows and 2 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was originally added to the surveillance package, we have
+removed the last 13 rows of data and only kept date and cases variables.
+The data on campylobacteriosis cases have been queried from the "SurvstatRKI"
+database of the German Robert Koch Institute (https://survstat.rki.de/).</p>
+<p>The original dataset can be accessed using data("CampyDe"). Within
+this package the original dataset is campylobacter_germany.xlsx</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://www.gnu.org/licenses/gpl-3.0.html" class="external-link">GPL3</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>Weekly number of reported campylobacteriosis cases in Germany, 2002-2011.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>Manitz, J. and Höhle, M. (2013): Bayesian outbreak detection algorithm for monitoring reported cases of campylobacteriosis in Germany. Biometrical Journal, 55(4), 509-526 <a href="https://doi.org/10.1002/bimj.201200141" class="external-link">doi:10.1002/bimj.201200141</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/cases_clean.html b/reference/cases_clean.html
new file mode 100644
index 0000000..92b9d89
--- /dev/null
+++ b/reference/cases_clean.html
@@ -0,0 +1,98 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fictional case data for a generic disease to demonstrate contact tracing — cases_clean • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fictional case data for a generic disease to demonstrate contact tracing — cases_clean"><meta name="description" content="Fictional case data for a generic disease to demonstrate contact tracing"><meta property="og:description" content="Fictional case data for a generic disease to demonstrate contact tracing"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
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+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Fictional case data for a generic disease to demonstrate contact tracing</h1>
+
+      <div class="d-none name"><code>cases_clean.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Fictional case data for a generic disease to demonstrate contact tracing</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">cases_clean</span></span>
+<span></span>
+<span><span class="va">contacts_clean</span></span>
+<span></span>
+<span><span class="va">followups_clean</span></span>
+<span></span>
+<span><span class="va">relationships_clean</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 56 rows and 86 columns</p>
+<p>An object of class <code>data.frame</code> with 66 rows and 62 columns.</p>
+<p>An object of class <code>data.frame</code> with 437 rows and 53 columns.</p>
+<p>An object of class <code>data.frame</code> with 100 rows and 21 columns.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was originally sample contact tracing data from the
+<a href="https://worldhealthorganization.github.io/godata/" class="external-link">Go.Data</a> platform</p>
+<p>The original datasets are cases_clean.rds, contacts_clean.rds, followups_clean.rds,
+relationships_clean.rds</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://www.gnu.org/licenses/gpl-3.0.html" class="external-link">GPL3</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is fictional case-linelist which contains de-indentified individual level data,
+based on go.data format.</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/cleaning_dict.html b/reference/cleaning_dict.html
new file mode 100644
index 0000000..fbc84ba
--- /dev/null
+++ b/reference/cleaning_dict.html
@@ -0,0 +1,94 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — cleaning_dict • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — cleaning_dict"><meta name="description" content="Incomplete data dictionary used for demonstrating cleaning of raw version of fictional Ebola Virus
+Disease data simulating properties from the West African Ebola outbreak of 2014"><meta property="og:description" content="Incomplete data dictionary used for demonstrating cleaning of raw version of fictional Ebola Virus
+Disease data simulating properties from the West African Ebola outbreak of 2014"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
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+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</h1>
+
+      <div class="d-none name"><code>cleaning_dict.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Incomplete data dictionary used for demonstrating cleaning of raw version of fictional Ebola Virus
+Disease data simulating properties from the West African Ebola outbreak of 2014</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">cleaning_dict</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 9 rows and 3 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This has been created as an example for use with  <a href="linelist_raw.html">linelist_raw</a>,
+which is cleaned using code in the <a href="https://epirhandbook.com/en/new_pages/cleaning.html" class="external-link">epiRhandbook cleaning chapter</a>.</p>
+<p>The original dataset is cleaning_dict.csv</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://opensource.org/license/MIT" class="external-link">MIT</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is fictional data dictionary which contains recoding information.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>WHO Ebola Response Team. 2014. Ebola virus disease in West Africa–the first 9 months of the epidemic and forward projections. The New England journal of medicine 371:1481–1495 <a href="https://doi.org/10.1056/NEJMoa1411100" class="external-link">doi:10.1056/NEJMoa1411100</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/contacts_clean.html b/reference/contacts_clean.html
new file mode 100644
index 0000000..1dfb1a9
--- /dev/null
+++ b/reference/contacts_clean.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://appliedepi.github.io/appliedepidata/reference/cases_clean.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://appliedepi.github.io/appliedepidata/reference/cases_clean.html">
+  </head>
+</html>
+
diff --git a/reference/country_demographics.html b/reference/country_demographics.html
new file mode 100644
index 0000000..fd508b4
--- /dev/null
+++ b/reference/country_demographics.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fictional country demographic and mortality data to demonstrate standardisation — country_demographics • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fictional country demographic and mortality data to demonstrate standardisation — country_demographics"><meta name="description" content="Fictional country demographic and mortality data to demonstrate standardisation"><meta property="og:description" content="Fictional country demographic and mortality data to demonstrate standardisation"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Fictional country demographic and mortality data to demonstrate standardisation</h1>
+
+      <div class="d-none name"><code>country_demographics.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Fictional country demographic and mortality data to demonstrate standardisation</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">country_demographics</span></span>
+<span></span>
+<span><span class="va">country_demographics_2</span></span>
+<span></span>
+<span><span class="va">deaths_countryA</span></span>
+<span></span>
+<span><span class="va">deaths_countryB</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>Dataframes</p>
+<p>An object of class <code>data.frame</code> with 18 rows and 3 columns.</p>
+<p>An object of class <code>data.frame</code> with 18 rows and 4 columns.</p>
+<p>An object of class <code>data.frame</code> with 18 rows and 4 columns.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was created for training purposes</p>
+<p>The original dataset is country_demographics.csv</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" class="external-link">CC by-NC-SA 4.0</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>Fictional country demographic and mortality data to demonstrate standardisation</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/country_demographics_2.html b/reference/country_demographics_2.html
new file mode 100644
index 0000000..97058b9
--- /dev/null
+++ b/reference/country_demographics_2.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://appliedepi.github.io/appliedepidata/reference/country_demographics.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://appliedepi.github.io/appliedepidata/reference/country_demographics.html">
+  </head>
+</html>
+
diff --git a/reference/deaths_countryA.html b/reference/deaths_countryA.html
new file mode 100644
index 0000000..97058b9
--- /dev/null
+++ b/reference/deaths_countryA.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://appliedepi.github.io/appliedepidata/reference/country_demographics.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://appliedepi.github.io/appliedepidata/reference/country_demographics.html">
+  </head>
+</html>
+
diff --git a/reference/deaths_countryB.html b/reference/deaths_countryB.html
new file mode 100644
index 0000000..97058b9
--- /dev/null
+++ b/reference/deaths_countryB.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://appliedepi.github.io/appliedepidata/reference/country_demographics.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://appliedepi.github.io/appliedepidata/reference/country_demographics.html">
+  </head>
+</html>
+
diff --git a/reference/district_weekly_count_data.html b/reference/district_weekly_count_data.html
new file mode 100644
index 0000000..6d1c967
--- /dev/null
+++ b/reference/district_weekly_count_data.html
@@ -0,0 +1,86 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fictional counts of malaria cases from Mozambique in 2019 — district_weekly_count_data • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fictional counts of malaria cases from Mozambique in 2019 — district_weekly_count_data"><meta name="description" content="Fictional counts of malaria cases from Mozambique in 2019"><meta property="og:description" content="Fictional counts of malaria cases from Mozambique in 2019"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Fictional counts of malaria cases from Mozambique in 2019</h1>
+
+      <div class="d-none name"><code>district_weekly_count_data.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Fictional counts of malaria cases from Mozambique in 2019</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">district_weekly_count_data</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 9628 rows and 4 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data is fictional based on data from Mozambique.</p>
+<p>The original dataset district_weekly_count_data.xlsx.</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" class="external-link">CC by-NC-SA 4.0</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is fictional aggregate data with counts by date and region.</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/epinow_res.html b/reference/epinow_res.html
new file mode 100644
index 0000000..fb6b034
--- /dev/null
+++ b/reference/epinow_res.html
@@ -0,0 +1,96 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — epinow_res • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — epinow_res"><meta name="description" content="Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014"><meta property="og:description" content="Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</h1>
+
+      <div class="d-none name"><code>epinow_res.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">epinow_res</span></span>
+<span></span>
+<span><span class="va">epinow_res_small</span></span>
+<span></span>
+<span><span class="va">generation_time</span></span>
+<span></span>
+<span><span class="va">incubation_period</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A large list</p>
+<p>An object of class <code>epinow</code> (inherits from <code>list</code>) of length 3.</p>
+<p>An object of class <code>list</code> of length 5.</p>
+<p>An object of class <code>list</code> of length 5.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This is direct output from use with <a href="linelist_cleaned_rds.html">linelist_cleaned_rds</a>.</p>
+<p>The original datasets are epinow_res.rds, epinow_res_small.rds,
+generation_time.rds and incubation_period.rds</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://opensource.org/license/MIT" class="external-link">MIT</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>These outputs are produced using <a href="linelist_cleaned_rds.html">linelist_cleaned_rds</a> with <a href="https://epiforecasts.io/EpiNow2/" class="external-link">epinow2</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/epinow_res_small.html b/reference/epinow_res_small.html
new file mode 100644
index 0000000..c2ed653
--- /dev/null
+++ b/reference/epinow_res_small.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://appliedepi.github.io/appliedepidata/reference/epinow_res.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://appliedepi.github.io/appliedepidata/reference/epinow_res.html">
+  </head>
+</html>
+
diff --git a/reference/fluH7N9_China_2013.html b/reference/fluH7N9_China_2013.html
new file mode 100644
index 0000000..edd6192
--- /dev/null
+++ b/reference/fluH7N9_China_2013.html
@@ -0,0 +1,96 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Linelist data from an outbreak of influenza A H7N9 in China 2013. — fluH7N9_China_2013 • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Linelist data from an outbreak of influenza A H7N9 in China 2013. — fluH7N9_China_2013"><meta name="description" content="Linelist data from a real outbreak of influenza A H7N9 in China 2013."><meta property="og:description" content="Linelist data from a real outbreak of influenza A H7N9 in China 2013."></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Linelist data from an outbreak of influenza A H7N9 in China 2013.</h1>
+
+      <div class="d-none name"><code>fluH7N9_China_2013.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Linelist data from a real outbreak of influenza A H7N9 in China 2013.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">fluH7N9_China_2013</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 136 rows and 8 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was originally added to the outbreaks package, no edits
+were made here.
+The data was collated by Adam Kucharski et al. from ProMed, WHO, FluTrackers, news
+reports and research articles. Transfer to R and documentation by Simon
+Frost (sdwfrost@gmail.com).</p>
+<p>The original dataset can be accessed using outbreaks::fluH7N9_China_2013. Within
+this package the original dataset is fluH7N9_China_2013.csv</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://opensource.org/license/MIT" class="external-link">MIT</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is a case-linelist which contains de-indentified individual level data
+on clinical outcome, demographics and region.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>A. Kucharski, H. Mills, A. Pinsent, C. Fraser, M. Van Kerkhove, C. A. Donnelly, and S. Riley. 2014. Distinguishing between reservoir exposure and human-to-human transmission for emerging pathogens using case onset data. PLOS Currents Outbreaks. Mar 7, edition 1 <a href="https://doi.org/10.1371/currents.outbreaks.e1473d9bfc99d080ca242139a06c455f" class="external-link">doi:10.1371/currents.outbreaks.e1473d9bfc99d080ca242139a06c455f</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/followups_clean.html b/reference/followups_clean.html
new file mode 100644
index 0000000..1dfb1a9
--- /dev/null
+++ b/reference/followups_clean.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://appliedepi.github.io/appliedepidata/reference/cases_clean.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://appliedepi.github.io/appliedepidata/reference/cases_clean.html">
+  </head>
+</html>
+
diff --git a/reference/generation_time.html b/reference/generation_time.html
new file mode 100644
index 0000000..c2ed653
--- /dev/null
+++ b/reference/generation_time.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://appliedepi.github.io/appliedepidata/reference/epinow_res.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://appliedepi.github.io/appliedepidata/reference/epinow_res.html">
+  </head>
+</html>
+
diff --git a/reference/germany_weather.html b/reference/germany_weather.html
new file mode 100644
index 0000000..90eb436
--- /dev/null
+++ b/reference/germany_weather.html
@@ -0,0 +1,89 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Weather data for Germany from 2001-2011 — germany_weather • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Weather data for Germany from 2001-2011 — germany_weather"><meta name="description" content="Weather data for Germany from 2001-2011"><meta property="og:description" content="Weather data for Germany from 2001-2011"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Weather data for Germany from 2001-2011</h1>
+
+      <div class="d-none name"><code>germany_weather.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Weather data for Germany from 2001-2011</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">germany_weather</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A list</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was obtained using the ecmwfr package as described in the
+epiRhandbook chapter on timeseries. This data was originally collected with the
+European Union Copernicus satelite and made available on their
+<a href="https://cds.climate.copernicus.eu/datasets/derived-era5-land-daily-statistics?tab=overview" class="external-link">climate data store</a></p>
+<p>The original dataset is germany_weather.zip</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://www.gnu.org/licenses/gpl-3.0.html" class="external-link">GPL3</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>Weather data for Germany from 2001-2011</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/get_data.html b/reference/get_data.html
index 603c605..3207fe7 100644
--- a/reference/get_data.html
+++ b/reference/get_data.html
@@ -69,6 +69,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  name <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  language <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  group_identifier <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  usage <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  unique_identifier <span class="op">=</span> <span class="cn">NULL</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
@@ -93,6 +94,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 unless further criteria are given.</p></dd>
 
 
+<dt id="arg-usage">usage<a class="anchor" aria-label="anchor" href="#arg-usage"></a></dt>
+<dd><p>(optional) A string representing where the datasets are used.
+If provided, the function will return all datasets within the group unless
+further criteria are given.</p></dd>
+
+
 <dt id="arg-unique-identifier">unique_identifier<a class="anchor" aria-label="anchor" href="#arg-unique-identifier"></a></dt>
 <dd><p>(optional) A string representing the unique identifier
 for a dataset.</p></dd>
@@ -116,6 +123,12 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 <li><p><strong>Post-Processing Based on Object Type:</strong> Once the dataset is loaded,
 the function checks the type of object and handles it accordingly:</p><ul><li><p><strong>Data frames</strong> are directly assigned to the global environment without
 any further processing.</p></li>
+<li><p><strong>Phylo objects</strong> (<code>phylo</code> class) are directly assigned to the global
+environment without any further processing.</p></li>
+<li><p><strong>Stars objects</strong> (<code>stars</code> class) are directly assigned to the global
+environment without any further processing.</p></li>
+<li><p><strong>Epinow objects</strong> (<code>epinow</code> class) are directly assigned to the global
+environment without any further processing.</p></li>
 <li><p><strong>Spatial objects</strong> (<code>sf</code> class) are processed using <code><a href="https://r-spatial.github.io/sf/reference/st_as_sf.html" class="external-link">sf::st_as_sf()</a></code> to
 ensure correct handling of spatial data, and then assigned to the global
 environment.</p></li>
diff --git a/reference/hospital_linelists.html b/reference/hospital_linelists.html
new file mode 100644
index 0000000..dd867f0
--- /dev/null
+++ b/reference/hospital_linelists.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — hospital_linelists • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — hospital_linelists"><meta name="description" content="Subset of cleaned version of fictional Ebola Virus Disease data simulating
+properties from the West African Ebola outbreak of 2014"><meta property="og:description" content="Subset of cleaned version of fictional Ebola Virus Disease data simulating
+properties from the West African Ebola outbreak of 2014"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</h1>
+
+      <div class="d-none name"><code>hospital_linelists.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Subset of cleaned version of fictional Ebola Virus Disease data simulating
+properties from the West African Ebola outbreak of 2014</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">hospital_linelists</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 454 rows and 30 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data is a subset version of <a href="linelist_cleaned_excel.html">linelist_cleaned_excel</a>, which is cleaned
+using code in the <a href="https://epirhandbook.com/en/new_pages/cleaning.html" class="external-link">epiRhandbook cleaning chapter</a>.</p>
+<p>The original dataset is hospital_linelist.xlsx</p>
+<p>This is version 4.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://opensource.org/license/MIT" class="external-link">MIT</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is fictional case-linelist which contains de-indentified individual level data
+on clinical outcome, demographics and region.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>WHO Ebola Response Team. 2014. Ebola virus disease in West Africa–the first 9 months of the epidemic and forward projections. The New England journal of medicine 371:1481–1495 <a href="https://doi.org/10.1056/NEJMoa1411100" class="external-link">doi:10.1056/NEJMoa1411100</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/incubation_period.html b/reference/incubation_period.html
new file mode 100644
index 0000000..c2ed653
--- /dev/null
+++ b/reference/incubation_period.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://appliedepi.github.io/appliedepidata/reference/epinow_res.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://appliedepi.github.io/appliedepidata/reference/epinow_res.html">
+  </head>
+</html>
+
diff --git a/reference/index.html b/reference/index.html
index 650ce3c..c6a9ab5 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -210,6 +210,249 @@ <h3 id="fictional-linelist-data-from-salmonella-outbreak-in-stegen-germany-engli
 
         </dt>
         <dd>Linelist for fictionalized salmonella outbreak in Stegen, Germany</dd>
+      </dl></div><div class="section level2">
+
+      <h3 id="influenza-a-h-n-data-in-china-english">Influenza A H7N9 data in China (2013) - English<a class="anchor" aria-label="anchor" href="#influenza-a-h-n-data-in-china-english"></a></h3>
+
+
+
+    </div><div class="section level2">
+
+
+
+
+      <dl><dt>
+
+          <code><a href="fluH7N9_China_2013.html">fluH7N9_China_2013</a></code>
+
+        </dt>
+        <dd>Linelist data from an outbreak of influenza A H7N9 in China 2013.</dd>
+      </dl></div><div class="section level2">
+
+      <h3 id="fictional-linelist-data-from-ebola-outbreak-in-sierra-leone-english">Fictional linelist data from Ebola outbreak in Sierra Leone (2014) - English<a class="anchor" aria-label="anchor" href="#fictional-linelist-data-from-ebola-outbreak-in-sierra-leone-english"></a></h3>
+
+
+
+    </div><div class="section level2">
+
+
+
+
+      <dl><dt>
+
+          <code><a href="linelist_raw.html">linelist_raw</a></code>
+
+        </dt>
+        <dd>Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</dd>
+      </dl><dl><dt>
+
+          <code><a href="linelist_cleaned_excel.html">linelist_cleaned_excel</a></code>
+
+        </dt>
+        <dd>Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</dd>
+      </dl><dl><dt>
+
+          <code><a href="linelist_cleaned_rds.html">linelist_cleaned_rds</a></code>
+
+        </dt>
+        <dd>Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</dd>
+      </dl><dl><dt>
+
+          <code><a href="hospital_linelists.html">hospital_linelists</a></code>
+
+        </dt>
+        <dd>Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</dd>
+      </dl><dl><dt>
+
+          <code><a href="linelist_cleaned_with_adm3.html">linelist_cleaned_with_adm3</a></code>
+
+        </dt>
+        <dd>Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</dd>
+      </dl><dl><dt>
+
+          <code><a href="cleaning_dict.html">cleaning_dict</a></code>
+
+        </dt>
+        <dd>Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</dd>
+      </dl><dl><dt>
+
+          <code><a href="sle_adm3.html">sle_adm3</a></code>
+
+        </dt>
+        <dd>Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange</dd>
+      </dl><dl><dt>
+
+          <code><a href="sle_admpop_adm3_2020.html">sle_admpop_adm3_2020</a></code>
+
+        </dt>
+        <dd>Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange</dd>
+      </dl><dl><dt>
+
+          <code><a href="epinow_res.html">epinow_res</a></code> <code><a href="epinow_res.html">epinow_res_small</a></code> <code><a href="epinow_res.html">generation_time</a></code> <code><a href="epinow_res.html">incubation_period</a></code>
+
+        </dt>
+        <dd>Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</dd>
+      </dl></div><div class="section level2">
+
+      <h3 id="fictional-case-data-for-a-generic-disease-to-demonstrate-contact-tracing-english">Fictional case data for a generic disease to demonstrate contact tracing (2020) - English<a class="anchor" aria-label="anchor" href="#fictional-case-data-for-a-generic-disease-to-demonstrate-contact-tracing-english"></a></h3>
+
+
+
+    </div><div class="section level2">
+
+
+
+
+      <dl><dt>
+
+          <code><a href="cases_clean.html">cases_clean</a></code> <code><a href="cases_clean.html">contacts_clean</a></code> <code><a href="cases_clean.html">followups_clean</a></code> <code><a href="cases_clean.html">relationships_clean</a></code>
+
+        </dt>
+        <dd>Fictional case data for a generic disease to demonstrate contact tracing</dd>
+      </dl></div><div class="section level2">
+
+      <h3 id="fictional-counts-of-malaria-cases-from-mozambique-english">Fictional counts of malaria cases from Mozambique (2019) - English<a class="anchor" aria-label="anchor" href="#fictional-counts-of-malaria-cases-from-mozambique-english"></a></h3>
+
+
+
+    </div><div class="section level2">
+
+
+
+
+      <dl><dt>
+
+          <code><a href="district_weekly_count_data.html">district_weekly_count_data</a></code>
+
+        </dt>
+        <dd>Fictional counts of malaria cases from Mozambique in 2019</dd>
+      </dl><dl><dt>
+
+          <code><a href="malaria_facility_count_data.html">malaria_facility_count_data</a></code>
+
+        </dt>
+        <dd>Fictional counts of malaria cases from Mozambique in 2019</dd>
+      </dl></div><div class="section level2">
+
+      <h3 id="next-generation-sequencing-data-of-shigella-surveillance-samples-from-belgium-english">Next generation sequencing data of Shigella surveillance samples from Belgium (2013-2019) - English<a class="anchor" aria-label="anchor" href="#next-generation-sequencing-data-of-shigella-surveillance-samples-from-belgium-english"></a></h3>
+
+
+
+    </div><div class="section level2">
+
+
+
+
+      <dl><dt>
+
+          <code><a href="Shigella_tree.html">Shigella_tree</a></code>
+
+        </dt>
+        <dd>Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019</dd>
+      </dl><dl><dt>
+
+          <code><a href="sample_data_Shigella_tree.html">sample_data_Shigella_tree</a></code>
+
+        </dt>
+        <dd>Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019</dd>
+      </dl><dl><dt>
+
+          <code><a href="Shigella_subtree_2.html">Shigella_subtree_2</a></code>
+
+        </dt>
+        <dd>Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019</dd>
+      </dl></div><div class="section level2">
+
+      <h3 id="fictional-country-demographic-and-mortality-data-to-demonstrate-standardisation-english">Fictional country demographic and mortality data to demonstrate standardisation (2020) - English<a class="anchor" aria-label="anchor" href="#fictional-country-demographic-and-mortality-data-to-demonstrate-standardisation-english"></a></h3>
+
+
+
+    </div><div class="section level2">
+
+
+
+
+      <dl><dt>
+
+          <code><a href="country_demographics.html">country_demographics</a></code> <code><a href="country_demographics.html">country_demographics_2</a></code> <code><a href="country_demographics.html">deaths_countryA</a></code> <code><a href="country_demographics.html">deaths_countryB</a></code>
+
+        </dt>
+        <dd>Fictional country demographic and mortality data to demonstrate standardisation</dd>
+      </dl><dl><dt>
+
+          <code><a href="world_standard_population_by_sex.html">world_standard_population_by_sex</a></code>
+
+        </dt>
+        <dd>World “standard population” by sex</dd>
+      </dl></div><div class="section level2">
+
+      <h3 id="other-fictional-example-data">Other fictional example data<a class="anchor" aria-label="anchor" href="#other-fictional-example-data"></a></h3>
+
+
+
+    </div><div class="section level2">
+
+
+
+
+      <dl><dt>
+
+          <code><a href="likert_data.html">likert_data</a></code>
+
+        </dt>
+        <dd>Fictional likert data for demonstration purposes</dd>
+      </dl></div><div class="section level2">
+
+      <h3 id="fictional-data-for-a-mortality-survey-english">Fictional data for a mortality survey - English<a class="anchor" aria-label="anchor" href="#fictional-data-for-a-mortality-survey-english"></a></h3>
+
+
+
+    </div><div class="section level2">
+
+
+
+
+      <dl><dt>
+
+          <code><a href="survey_data.html">survey_data</a></code>
+
+        </dt>
+        <dd>Fake data for a mortality survey</dd>
+      </dl><dl><dt>
+
+          <code><a href="survey_dict.html">survey_dict</a></code>
+
+        </dt>
+        <dd>Fake data dictionary for a mortality survey</dd>
+      </dl><dl><dt>
+
+          <code><a href="population.html">population</a></code>
+
+        </dt>
+        <dd>Fake population data for a mortality survey</dd>
+      </dl></div><div class="section level2">
+
+      <h3 id="campylobacter-surveillance-data-from-germany-english">Campylobacter surveillance data from Germany (2001-2011) - English<a class="anchor" aria-label="anchor" href="#campylobacter-surveillance-data-from-germany-english"></a></h3>
+
+
+
+    </div><div class="section level2">
+
+
+
+
+      <dl><dt>
+
+          <code><a href="campylobacter_germany.html">campylobacter_germany</a></code>
+
+        </dt>
+        <dd>Linelist data of Campylobacter surveillance in Germany 2001-2011.</dd>
+      </dl><dl><dt>
+
+          <code><a href="germany_weather.html">germany_weather</a></code>
+
+        </dt>
+        <dd>Weather data for Germany from 2001-2011</dd>
       </dl></div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
diff --git a/reference/likert_data.html b/reference/likert_data.html
new file mode 100644
index 0000000..5314350
--- /dev/null
+++ b/reference/likert_data.html
@@ -0,0 +1,86 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fictional likert data for demonstration purposes — likert_data • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fictional likert data for demonstration purposes — likert_data"><meta name="description" content="Fictional likert data for demonstration purposes"><meta property="og:description" content="Fictional likert data for demonstration purposes"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Fictional likert data for demonstration purposes</h1>
+
+      <div class="d-none name"><code>likert_data.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Fictional likert data for demonstration purposes</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">likert_data</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>Dataframes</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was created for training purposes</p>
+<p>The original dataset is likert_data.csv</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" class="external-link">CC by-NC-SA 4.0</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>Fictional likert data for demonstration purposes</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/linelist_cleaned_excel.html b/reference/linelist_cleaned_excel.html
new file mode 100644
index 0000000..4c5e0cd
--- /dev/null
+++ b/reference/linelist_cleaned_excel.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_excel • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_excel"><meta name="description" content="Excel file with cleaned version of fictional Ebola Virus Disease data simulating
+properties from the West African Ebola outbreak of 2014"><meta property="og:description" content="Excel file with cleaned version of fictional Ebola Virus Disease data simulating
+properties from the West African Ebola outbreak of 2014"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</h1>
+
+      <div class="d-none name"><code>linelist_cleaned_excel.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Excel file with cleaned version of fictional Ebola Virus Disease data simulating
+properties from the West African Ebola outbreak of 2014</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">linelist_cleaned_excel</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 5888 rows and 30 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data is a cleaned version of <a href="linelist_raw.html">linelist_raw</a>, which is cleaned
+using code in the <a href="https://epirhandbook.com/en/new_pages/cleaning.html" class="external-link">epiRhandbook cleaning chapter</a>.</p>
+<p>The original dataset is linelist_cleaned_excel.xlsx</p>
+<p>This is version 2.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://opensource.org/license/MIT" class="external-link">MIT</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is fictional case-linelist which contains de-indentified individual level data
+on clinical outcome, demographics and region.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>WHO Ebola Response Team. 2014. Ebola virus disease in West Africa–the first 9 months of the epidemic and forward projections. The New England journal of medicine 371:1481–1495 <a href="https://doi.org/10.1056/NEJMoa1411100" class="external-link">doi:10.1056/NEJMoa1411100</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/linelist_cleaned_rds.html b/reference/linelist_cleaned_rds.html
new file mode 100644
index 0000000..d9c4563
--- /dev/null
+++ b/reference/linelist_cleaned_rds.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_rds • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_rds"><meta name="description" content="R-dataset file with cleaned version of fictional Ebola Virus Disease data simulating
+properties from the West African Ebola outbreak of 2014"><meta property="og:description" content="R-dataset file with cleaned version of fictional Ebola Virus Disease data simulating
+properties from the West African Ebola outbreak of 2014"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</h1>
+
+      <div class="d-none name"><code>linelist_cleaned_rds.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>R-dataset file with cleaned version of fictional Ebola Virus Disease data simulating
+properties from the West African Ebola outbreak of 2014</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">linelist_cleaned_rds</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 5888 rows and 30 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data is a cleaned version of <a href="linelist_raw.html">linelist_raw</a>, which is cleaned
+using code in the <a href="https://epirhandbook.com/en/new_pages/cleaning.html" class="external-link">epiRhandbook cleaning chapter</a>.</p>
+<p>The original dataset is linelist_cleaned_rds.rds</p>
+<p>This is version 3.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://opensource.org/license/MIT" class="external-link">MIT</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is fictional case-linelist which contains de-indentified individual level data
+on clinical outcome, demographics and region.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>WHO Ebola Response Team. 2014. Ebola virus disease in West Africa–the first 9 months of the epidemic and forward projections. The New England journal of medicine 371:1481–1495 <a href="https://doi.org/10.1056/NEJMoa1411100" class="external-link">doi:10.1056/NEJMoa1411100</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/linelist_cleaned_with_adm3.html b/reference/linelist_cleaned_with_adm3.html
new file mode 100644
index 0000000..d1839bb
--- /dev/null
+++ b/reference/linelist_cleaned_with_adm3.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_with_adm3 • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_with_adm3"><meta name="description" content="Subset with additional spatial data of rds clean version of fictional Ebola Virus
+Disease data simulating properties from the West African Ebola outbreak of 2014"><meta property="og:description" content="Subset with additional spatial data of rds clean version of fictional Ebola Virus
+Disease data simulating properties from the West African Ebola outbreak of 2014"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</h1>
+
+      <div class="d-none name"><code>linelist_cleaned_with_adm3.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Subset with additional spatial data of rds clean version of fictional Ebola Virus
+Disease data simulating properties from the West African Ebola outbreak of 2014</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">linelist_cleaned_with_adm3</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 454 rows and 30 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data is a cleaned version of <a href="linelist_cleaned_rds.html">linelist_cleaned_rds</a>, which is cleaned
+using code in the <a href="https://epirhandbook.com/en/new_pages/cleaning.html" class="external-link">epiRhandbook cleaning chapter</a>.</p>
+<p>The original dataset is linelist_cleaned_with_adm3.rds</p>
+<p>This is version 4.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://opensource.org/license/MIT" class="external-link">MIT</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is fictional case-linelist which contains de-indentified individual level data
+on clinical outcome, demographics and region.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>WHO Ebola Response Team. 2014. Ebola virus disease in West Africa–the first 9 months of the epidemic and forward projections. The New England journal of medicine 371:1481–1495 <a href="https://doi.org/10.1056/NEJMoa1411100" class="external-link">doi:10.1056/NEJMoa1411100</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/linelist_raw.html b/reference/linelist_raw.html
new file mode 100644
index 0000000..16c3d3e
--- /dev/null
+++ b/reference/linelist_raw.html
@@ -0,0 +1,99 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_raw • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_raw"><meta name="description" content="Fictional Ebola Virus Disease data simulating properties from the West African
+Ebola outbreak of 2014"><meta property="og:description" content="Fictional Ebola Virus Disease data simulating properties from the West African
+Ebola outbreak of 2014"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014</h1>
+
+      <div class="d-none name"><code>linelist_raw.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Fictional Ebola Virus Disease data simulating properties from the West African
+Ebola outbreak of 2014</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">linelist_raw</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 136 rows and 8 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was originally added to the outbreaks package, extensive
+edits have been made for teaching purposes.
+The data was originally simulated to match properties of the
+West African Ebola outbreak of 2014-2015 (see outbreaks package documentation
+for details).</p>
+<p>The original dataset can be accessed using outbreaks::ebola_sim. Within this
+package the original dataset is linelist_raw.xlsx.</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://opensource.org/license/MIT" class="external-link">MIT</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is fictional case-linelist which contains de-indentified individual level data
+on clinical outcome, demographics and region.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>WHO Ebola Response Team. 2014. Ebola virus disease in West Africa–the first 9 months of the epidemic and forward projections. The New England journal of medicine 371:1481–1495 <a href="https://doi.org/10.1056/NEJMoa1411100" class="external-link">doi:10.1056/NEJMoa1411100</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/lookup_dataset.html b/reference/lookup_dataset.html
index 7354068..590c72d 100644
--- a/reference/lookup_dataset.html
+++ b/reference/lookup_dataset.html
@@ -66,6 +66,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  name <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  language <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  group_identifier <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  usage <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  unique_identifier <span class="op">=</span> <span class="cn">NULL</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
@@ -90,6 +91,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 unless further criteria are given.</p></dd>
 
 
+<dt id="arg-usage">usage<a class="anchor" aria-label="anchor" href="#arg-usage"></a></dt>
+<dd><p>(optional) A string representing where the datasets are used.
+If provided, the function will return all datasets within the group unless
+further criteria are given.</p></dd>
+
+
 <dt id="arg-unique-identifier">unique_identifier<a class="anchor" aria-label="anchor" href="#arg-unique-identifier"></a></dt>
 <dd><p>(optional) A string representing the unique identifier
 for a dataset.</p></dd>
@@ -117,6 +124,9 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 <li><p><strong>Searching by <code>group_identifier</code>:</strong></p><ul><li><p>If a <code>group_identifier</code> is provided, the function returns all datasets
 within the group unless further refinement by <code>language</code> is necessary.</p></li>
 </ul></li>
+<li><p><strong>Searching by <code>usage</code>:</strong></p><ul><li><p>If a <code>usage</code> is provided, the function returns all datasets
+within the group unless further refinement by <code>language</code> is necessary.</p></li>
+</ul></li>
 <li><p><strong>Searching by <code>unique_identifier</code>:</strong></p><ul><li><p>If a <code>unique_identifier</code> is provided, the function will attempt to find
 a dataset by that identifier and apply further filtering by <code>language</code>
 or <code>name</code> if needed.</p></li>
diff --git a/reference/malaria_facility_count_data.html b/reference/malaria_facility_count_data.html
new file mode 100644
index 0000000..94e6a51
--- /dev/null
+++ b/reference/malaria_facility_count_data.html
@@ -0,0 +1,87 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fictional counts of malaria cases from Mozambique in 2019 — malaria_facility_count_data • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fictional counts of malaria cases from Mozambique in 2019 — malaria_facility_count_data"><meta name="description" content="Fictional counts of malaria cases from Mozambique in 2019"><meta property="og:description" content="Fictional counts of malaria cases from Mozambique in 2019"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Fictional counts of malaria cases from Mozambique in 2019</h1>
+
+      <div class="d-none name"><code>malaria_facility_count_data.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Fictional counts of malaria cases from Mozambique in 2019</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">malaria_facility_count_data</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frame with 3038 rows and 10 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data is fictional based on data from Mozambique. It has been adapted
+from <a href="district_weekly_count_data.html">district_weekly_count_data</a>.</p>
+<p>The original dataset malaria_facility_count_Data.rds.</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" class="external-link">CC by-NC-SA 4.0</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is fictional aggregate data with counts by date, region and age group.</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/mortality_survey_data.html b/reference/mortality_survey_data.html
index b92f37d..75a90cf 100644
--- a/reference/mortality_survey_data.html
+++ b/reference/mortality_survey_data.html
@@ -54,30 +54,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
     <p>Two data frames, 'Mortality Survey' with 424 rows and 16 columns, and
 'hh_member' with 2874 rows and 24 columns:</p>
-<dl><dt>Mortality Survey</dt>
-<dd><p>A data frame with 424 rows and 16 columns:</p><dl><dt>variable1</dt>
-<dd><p>Description of variable1</p></dd>
-
-<dt>variable2</dt>
-<dd><p>Description of variable2</p></dd>
-
-# Add more variables as needed
-
-</dl></dd>
-
-<dt>hh_member</dt>
-<dd><p>A data frame with 2874 rows and 24 columns:</p><dl><dt>variable1</dt>
-<dd><p>Description of variable1</p></dd>
-
-<dt>variable2</dt>
-<dd><p>Description of variable2</p></dd>
-
-# Add more variables as needed
-
-</dl></dd>
-
-
-</dl></div>
+    </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
     <p>This data was generated with functions from the
diff --git a/reference/population.html b/reference/population.html
new file mode 100644
index 0000000..61db09c
--- /dev/null
+++ b/reference/population.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fake population data for a mortality survey — population • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fake population data for a mortality survey — population"><meta name="description" content="This is an example fake population data for a mortality survey which was generated
+using epidict package functions."><meta property="og:description" content="This is an example fake population data for a mortality survey which was generated
+using epidict package functions."></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Fake population data for a mortality survey</h1>
+
+      <div class="d-none name"><code>population.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>This is an example fake population data for a mortality survey which was generated
+using <a href="https://r4epi.github.io/epidict/index.html" class="external-link">epidict</a> package functions.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">population</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A dataframe with 20 rows and 5 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was generated with functions from the
+<a href="https://r4epi.github.io/epidict/index.html" class="external-link">epidict</a> package which was created
+as part of the R4Epis project funded by the Doctors Without Borders (MSF)
+sappling nursery.</p>
+<p>The original dataset is 'population.xlsx'</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://www.gnu.org/licenses/gpl-3.0.html" class="external-link">GPL3</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is a fake population data for the <a href="survey_data.html">survey_data</a> dataset.
+Please note, that this data is entirely fictional created based on the
+Doctors without Borders (MSF) ethical review board pre-approved survey
+dictionaries. They have been generated here exclusively for training purposes.</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/relationships_clean.html b/reference/relationships_clean.html
new file mode 100644
index 0000000..1dfb1a9
--- /dev/null
+++ b/reference/relationships_clean.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://appliedepi.github.io/appliedepidata/reference/cases_clean.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://appliedepi.github.io/appliedepidata/reference/cases_clean.html">
+  </head>
+</html>
+
diff --git a/reference/sample_data_Shigella_tree.html b/reference/sample_data_Shigella_tree.html
new file mode 100644
index 0000000..9da0214
--- /dev/null
+++ b/reference/sample_data_Shigella_tree.html
@@ -0,0 +1,91 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — sample_data_Shigella_tree • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — sample_data_Shigella_tree"><meta name="description" content="Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019"><meta property="og:description" content="Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019</h1>
+
+      <div class="d-none name"><code>sample_data_Shigella_tree.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">sample_data_Shigella_tree</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A dataframe with 299 rows and 13 columns.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was posted on the <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB40097?show=xrefs" class="external-link">European Nucleotide Archive</a></p>
+<p>The original dataset is sample_data_Shigella_Tree.txt</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" class="external-link">CC by-NC-SA 4.0</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This linelist data to accompany sequencing data from routine surveillance samples collected in Belgium between 2013 and 2019.
+It can be used together with <a href="Shigella_tree.html">Shigella_tree</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>Fischer, N. et al. Genomic epidemiology of persistently circulating MDR Shigella sonnei strains associated with men who have sex with men (MSM) in Belgium (2013-19) <a href="https://doi.org/10.1093/jac/dkab377" class="external-link">doi:10.1093/jac/dkab377</a></p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/save_data.html b/reference/save_data.html
index 7223dc9..5971409 100644
--- a/reference/save_data.html
+++ b/reference/save_data.html
@@ -60,6 +60,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  name <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  language <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  group_identifier <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  usage <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  unique_identifier <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  path <span class="op">=</span> <span class="fu">rstudioapi</span><span class="fu">::</span><span class="fu"><a href="https://rstudio.github.io/rstudioapi/reference/file-dialogs.html" class="external-link">selectDirectory</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="op">)</span></span></code></pre></div>
@@ -85,6 +86,12 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 unless further criteria are given.</p></dd>
 
 
+<dt id="arg-usage">usage<a class="anchor" aria-label="anchor" href="#arg-usage"></a></dt>
+<dd><p>(optional) A string representing where the datasets are used.
+If provided, the function will return all datasets within the group unless
+further criteria are given.</p></dd>
+
+
 <dt id="arg-unique-identifier">unique_identifier<a class="anchor" aria-label="anchor" href="#arg-unique-identifier"></a></dt>
 <dd><p>(optional) A string representing the unique identifier
 for a dataset.</p></dd>
@@ -107,7 +114,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 directory of the <code>appliedepidata</code> package.
 The function follows these steps:</p><ol><li><p><strong>Dataset Lookup</strong>: It looks up dataset information using <code>lookup_dataset</code>
 based on the provided search criteria (<code>name</code>, <code>language</code>, <code>group_identifier</code>,
-or <code>unique_identifier</code>).</p></li>
+<code>usage</code> or <code>unique_identifier</code>).</p></li>
 <li><p><strong>File Existence Check</strong>: It checks if all required dataset files exist
 using the <code>list_data</code> function. If any files are missing, an error message
 lists them.</p></li>
diff --git a/reference/sle_adm3.html b/reference/sle_adm3.html
new file mode 100644
index 0000000..37d73b9
--- /dev/null
+++ b/reference/sle_adm3.html
@@ -0,0 +1,91 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange — sle_adm3 • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange — sle_adm3"><meta name="description" content="Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange"><meta property="og:description" content="Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange</h1>
+
+      <div class="d-none name"><code>sle_adm3.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">sle_adm3</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A shapefile with 167 rows and 20 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This shapefile was downloaded from
+<a href="https://data.humdata.org/dataset/cod-ab-sle" class="external-link">Humanitarian Data Exchange</a>.
+No edits were made to this.</p>
+<p>This is the original dataset is sle_adm3.shp</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://data.humdata.org/faqs/licenses" class="external-link">CC by-IGO</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This shapefile can be used together with <a href="linelist_cleaned_with_adm3.html">linelist_cleaned_with_adm3</a>.
+Data collected from the government of Sierra Leone and cleaned and pcoded by UNOCHA and ITOS
+Admin4 : Data provided by OCHA, attribute fields and geometries have been
+checked by UNMEER IM (Ghana) Will be replaced if/when official Government data is provided</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/sle_admpop_adm3_2020.html b/reference/sle_admpop_adm3_2020.html
new file mode 100644
index 0000000..4e72020
--- /dev/null
+++ b/reference/sle_admpop_adm3_2020.html
@@ -0,0 +1,89 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange — sle_admpop_adm3_2020 • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange — sle_admpop_adm3_2020"><meta name="description" content="Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange"><meta property="og:description" content="Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange</h1>
+
+      <div class="d-none name"><code>sle_admpop_adm3_2020.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">sle_admpop_adm3_2020</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A shapefile with 167 rows and 20 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This population data was downloaded from
+<a href="https://data.humdata.org/dataset/cod-ps-sle" class="external-link">Humanitarian Data Exchange</a>
+No edits were made to this.</p>
+<p>This is the original dataset is sle_admpop_adm3_2020.csv</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://data.humdata.org/faqs/licenses" class="external-link">CC by-IGO</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This population data can be used with <a href="linelist_cleaned_with_adm3.html">linelist_cleaned_with_adm3</a> and
+<a href="sle_adm3.html">sle_adm3</a>.</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/stegentira_data.html b/reference/stegentira_data.html
index 6a8fca0..248f7bf 100644
--- a/reference/stegentira_data.html
+++ b/reference/stegentira_data.html
@@ -52,7 +52,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>Linelist with 291 rows and 20 columns</p>
+    <p>A data frame with 291 rows and 20 columns</p>
     </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
diff --git a/reference/survey_data.html b/reference/survey_data.html
new file mode 100644
index 0000000..377b655
--- /dev/null
+++ b/reference/survey_data.html
@@ -0,0 +1,98 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fake data for a mortality survey — survey_data • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fake data for a mortality survey — survey_data"><meta name="description" content="This is an example fake dataset of a mortality survey which was generated
+using epidict package functions."><meta property="og:description" content="This is an example fake dataset of a mortality survey which was generated
+using epidict package functions."></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Fake data for a mortality survey</h1>
+
+      <div class="d-none name"><code>survey_data.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>This is an example fake dataset of a mortality survey which was generated
+using <a href="https://r4epi.github.io/epidict/index.html" class="external-link">epidict</a> package functions.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">survey_data</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A data frames with 1000 rows and 55 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was generated with functions from the
+<a href="https://r4epi.github.io/epidict/index.html" class="external-link">epidict</a> package which was created
+as part of the R4Epis project funded by the Doctors Without Borders (MSF)
+sappling nursery.</p>
+<p>The original dataset is 'survey_data.xlsx'</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://www.gnu.org/licenses/gpl-3.0.html" class="external-link">GPL3</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is a fake survey dataset. This data has been merge, and differs from the
+original which data comes in two parts: a household level dataset ('Mortality Survey')
+and an individual level dataset ('hh_member').
+It can be used together with <a href="survey_dict.html">survey_dict</a>.
+Please note, that this data is entirely fictional created based on the
+Doctors without Borders (MSF) ethical review board pre-approved survey
+dictionaries. They have been generated here exclusively for training purposes.</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/survey_dict.html b/reference/survey_dict.html
new file mode 100644
index 0000000..e1e4aff
--- /dev/null
+++ b/reference/survey_dict.html
@@ -0,0 +1,99 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fake data dictionary for a mortality survey — survey_dict • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fake data dictionary for a mortality survey — survey_dict"><meta name="description" content="This is an example fake data dictionary for a mortality survey which was generated
+using epidict package functions."><meta property="og:description" content="This is an example fake data dictionary for a mortality survey which was generated
+using epidict package functions."></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/adding-data.html">Adding data</a></li>
+    <li><a class="dropdown-item" href="../articles/available-data.html">Available data</a></li>
+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
+
+
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>Fake data dictionary for a mortality survey</h1>
+
+      <div class="d-none name"><code>survey_dict.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>This is an example fake data dictionary for a mortality survey which was generated
+using <a href="https://r4epi.github.io/epidict/index.html" class="external-link">epidict</a> package functions.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">survey_dict</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>A dataframe with 46 rows and 14 columns</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data was generated with functions from the
+<a href="https://r4epi.github.io/epidict/index.html" class="external-link">epidict</a> package which was created
+as part of the R4Epis project funded by the Doctors Without Borders (MSF)
+sappling nursery.</p>
+<p>The original dataset is 'mortality_survey_dict.xlsx'</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://www.gnu.org/licenses/gpl-3.0.html" class="external-link">GPL3</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>This is a fake data dictionary for the <a href="survey_data.html">survey_data</a> dataset.
+This data dictionary was originally in ODK excel format and using functions
+from <a href="https://r4epi.github.io/epidict/index.html" class="external-link">epidict</a> was transformed in
+to long format, so that it can be used for recoding using the
+<a href="https://www.repidemicsconsortium.org/matchmaker/" class="external-link">matchmaker</a> package.
+Please note, that this data is entirely fictional created based on the
+Doctors without Borders (MSF) ethical review board pre-approved survey
+dictionaries. They have been generated here exclusively for training purposes.</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+    </footer></div>
+
+
+
+
+
+  </body></html>
+
diff --git a/reference/world_standard_population_by_sex.html b/reference/world_standard_population_by_sex.html
new file mode 100644
index 0000000..f7a5c4b
--- /dev/null
+++ b/reference/world_standard_population_by_sex.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>World “standard population” by sex — world_standard_population_by_sex • appliedepidata</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="World “standard population” by sex — world_standard_population_by_sex"><meta name="description" content="This is reference population counts which can be used together with country_demographics"><meta property="og:description" content="This is reference population counts which can be used together with country_demographics"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+    <a class="navbar-brand me-2" href="../index.html">appliedepidata</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
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+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item dropdown">
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+    <li><a class="dropdown-item" href="../articles/data-dictionaries.html">Data dictionaries</a></li>
+  </ul></li>
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+      </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
+      </ul></div>
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+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+
+      <h1>World “standard population” by sex</h1>
+
+      <div class="d-none name"><code>world_standard_population_by_sex.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>This is reference population counts which can be used together with <a href="country_demographics.html">country_demographics</a></p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">world_standard_population_by_sex</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
+    <p>Dataframes</p>
+    </div>
+    <div class="section level2">
+    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
+    <p>This data is made available by <a href="https://www.opendata.nhs.scot/dataset/4dd86111-7326-48c4-8763-8cc4aa190c3e/resource/2f493d21-fd39-48f9-ad6a-9b2c95b32e30/download/world_standard_population_by_sex.csv" class="external-link">Public Health Scotland</a></p>
+<p>The original dataset is country_demographics.csv</p>
+<p>This is version 1.0.</p>
+<p>This dataset is English.</p>
+<p>This dataset is licensed under <a href="https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/" class="external-link">OGL</a></p>
+    </div>
+    <div class="section level2">
+    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+    <p>The World standard population is based on the populations of 46 countries and
+was developed in 1960. It is used to produce world standardised rates. It is
+a much ‘younger’ population compared to the population of Scotland
+(and other Western European countries). Also, like the European standard
+population, the World standard population has equal numbers of males and females
+within an age band.
+However, as the World standard population is a very ‘young’ population, it is
+generally less appropriate for Scottish data than the European standard population
+and is only be used for particular purposes.
+This file is split by five year age groups and sex</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
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+  <p>Developed by Alexander Spina.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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+
+  </body></html>
+
diff --git a/search.json b/search.json
index b9630d0..ab71ce9 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":[]},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"overview","dir":"Articles","previous_headings":"Guide to contributing new datasets > PACKAGE FOLDER STRUCTURE","what":"Overview","title":"Adding data","text":"diagram descriptions simplified explanation R packages data chapter. fuller understanding, read chapter.","code":". ├── appliedepidata.Rproj ├── _pkgdown.yml ├── data │   └── newdata.rda (note: internalised) ├── data-raw │   └── newdata.R ├── inst │   └── extdata │       └── tableoftables.xlsx │       └── newdata.xlsx ├── R │   └── newdata_doc.R └── man     └── newdata.Rd"},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"folders-you-will-edit","dir":"Articles","previous_headings":"Guide to contributing new datasets > PACKAGE FOLDER STRUCTURE","what":"Folders you will edit","title":"Adding data","text":"inst/extdata: Newly added datasets go original filetype, e.g. .xlsx, .csv, also .rds files. files downloaded save_data() function. data-raw: Contains R scripts used processing internalizing datasets (making efficient storage), .e. turning newly added datasets inst/extdata .rda files R: Contains R scripts Roxygen2 format define functions datasets. run creates R documentation files (.Rd files) saved man folder. Multiple datasets can defined one script, sensible grouped together (e.g. part outbreak) vignettes: Contains detailed instructions use particular functions. complement function-level documentation man folder giving broader explanation.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"folders-you-will-not-edit","dir":"Articles","previous_headings":"Guide to contributing new datasets > PACKAGE FOLDER STRUCTURE","what":"Folders you will not edit","title":"Adding data","text":"contain files outputted running code folders . data: Contains internalised processed R datasets (.rda files). created internalizing data (running code data-raw folder), makes efficient file storage. man: Contains R documentation files package functions datasets (created running code R folder). .Rd file information specific function dataset. tests: Contains test files developer use .","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"adding-data","dir":"Articles","previous_headings":"Guide to contributing new datasets","what":"ADDING DATA","title":"Adding data","text":"describes process adding file repo. Note original datasets need added inst/exta folder, even already .rda format. adding dataset existing R package, can skip step 3 . Name file appropriately . can name whatever want, stick basic naming conventions. B. Ensure already file tableoftables.xlsx named . C. Avoid generic names like: linelist_cleaned.xlsx survey_data.xlsx. D. Use consistent descriptive names without spaces (e.g., AJS_AmTiman, sitrep_mortality_survey). E. Name files group (e.g. outbreak case study) prefix. E.g: examplename_data examplename_population case linelist corresponding denominator table respectively. Place file correct folder . Add inst/extdata folder. downloaded running save_data() function. shapefile, zip first. Build package added data . Press Ctrl + Shift + B build package newly added data. mean data recognized next step. Reproducibly edit dataset internalize (see data-raw/AJS_AmTiman.R example) . console run usethis::use_data_raw(\"<name file without extension>\"). B. creates R script data-raw folder. already contain comment top saying “code prepare  data goes ” usethis::use_data() function internalise dataset (.e. produce rda file) C. Edit R script correctly read file using system.file(), . Necessary edits dataset also go . run script internalise data, close. D. NOTE want process raw data create dataset also accessible users (e.g. via get_data() save_data() functions), make sure processed data also gets saved inst/extdata version 2. Make sure internalise (use_data) versions data. Add dataset tablesoftables.xlsx described . Add documentation dataset added . Create new R script R folder, one file datasets group. file name group name generated tableoftables (column P), suffix ‘_doc’. Note easiest copy edit existing R script folder. B. Ensure clearly document source license dataset. C. Ensure put correct name dataset bottom dataset description (@docType). E.g. examplename_linelist. D. Run devtools::document() create actual R documentation. .Rd file man folder, file name corresponding dataset name (e.g. examplename_linelist.Rd) Add datasets _pkgdown.yml . Subtitle: Describe group linelists. State year brackets language end B. Contents: List datasets. , names correspond name dataset without extension, e.g “examplename_linelist”. C. Make sure correct indentation use dashes. See prior examples file.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"adding-dataset-metadata-adding-to-tablesoftables-xlsx","dir":"Articles","previous_headings":"Guide to contributing new datasets","what":"ADDING DATASET METADATA (adding to tablesoftables.xlsx)","title":"Adding data","text":"table explaining fill variable dataset metadata Excel sheet (tablesoftables.xlsx). guide helps ensure consistency completeness adding new datasets collection. name: filename dataset appears inst/extdata directory, without file extension. unique within dataset group, ideally also within tableoftables (.e. avoid generic names like: linelist_cleaned.xlsx survey_data.xlsx). Use consistent descriptive names without spaces (e.g., AJS_AmTiman, mortality_survey). type: category type dataset (e.g., linelist, population, shape, survey, dictionary). extension: file extension (e.g., xlsx, zip). type_version: Used identify original dataset associated child data. Increment format variables change. multiple linelists one group, increment type. data_version: Used identify original dataset associated child data. Increment format variables change. Ensure document changes appropriate ‘data-raw’ file. language: Language code using ISO 639-1 codes (e.g., en, fr). country: Country code using ISO 3166-1 alpha-3 codes (e.g., tcd). scale: Geographic scale (e.g., subnational, national, international). subject: Main subject dataset (e.g., acute jaundice syndrome). context: Context data (e.g., outbreak, survey). fictional: dataset fictional (yes) real ()? year: Year data collected (e.g., 2016). earliest year dataset (even fictional). description: Brief description dataset. Ideally, copy roxygen documentation. usage: Intended usage (e.g., {sitrep} walkthroughs, training). license: License dataset (e.g., gpl3, mit). group_identifier: EDIT - Created concatinating function excel. High-level identifier combining subject, context, country, year (e.g.,acute_jaundice_syndrome_outbreak_tcd_2016). unique_identifier: EDIT - Combines group_identifier, type, type_version, data_version, context, year create unique identifier (e.g. acute_jaundice_syndrome_outbreak_tcd_2016_linelist_1). example, adding Ebola dataset, enter information shown . original dataset (whether ’s {outbreaks} another source) considered type_version 1. ’s linelist group, remains type_version 1. completely different linelist added (just edited version), increment type_version accordingly. changes data (cleaning changing nums rows columns), increment data_version (e.g., data_version 2), type_version remains indicate ’s derivative (“child”) original. child dataset gets entry. dataset translated different language, create new entry translated version keeping data_version type_version , editing language column accordingly. ensures can trace back parent-child relationship datasets.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Alexander Spina. Author, maintainer.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Spina (2024). appliedepidata: Datasets used Applied Epi courses resources. R package version 0.0.0.9000, https://appliedepi.github.io/appliedepidata/.","code":"@Manual{,   title = {appliedepidata: Datasets used in Applied Epi courses and resources},   author = {Alexander Spina},   year = {2024},   note = {R package version 0.0.0.9000},   url = {https://appliedepi.github.io/appliedepidata/}, }"},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"appliedepidata","dir":"","previous_headings":"","what":"Datasets used in Applied Epi courses and resources","title":"Datasets used in Applied Epi courses and resources","text":"package stores Applied Epi data across courses resources. includes courses, tutorials, case studies books (EpiRhandbook Applied Epi Manual).","code":""},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Datasets used in Applied Epi courses and resources","text":"can install development version appliedepidata GitHub :","code":"# install.packages(\"pak\") pak::pak(\"appliedepi/appliedepidata\")"},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Datasets used in Applied Epi courses and resources","text":"can see available datasets available data table well depth descriptions reference section. Within RStudio can use search_data browse available datasets. Using information can either load data RStudio environment using get_data save copy data computer using save_data.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":null,"dir":"Reference","previous_headings":"","what":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"Linelist data real outbreak Hepatitis E virus (HEV) infection occurred town Timan, Chad, October 2016 April 2017.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"","code":"AJS_AmTiman"},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"data frame 1477 rows 122 columns: Number numeric denoting HEV  Count HEVID numeric denoting HEV Case ID Sex character denoting Sexe M=Male; F=Femelle Age character denoting Age Agegroup character denoting Groupe D'age 1=0 4; 2= 5 14; 3=15 44; 4==45 dateentry character denoting Initial Entry Database (either Questionnaire Medical Assessment) epiquestdate character denoting Date de Questionnaire team character denoting Equipe chw character denoting AC block character denoting Bloc hh character denoting Menage referredby character denoting Referer par: (1=Hôpital ; 2 = Superviseur Agent Communitaire) quartier character denoting Quartier/Village interviewee character denoting Statut interroge Patient ou Parent hhpers character denoting Nombre de personnes dan le menage hhmale character denoting Nombre masculin hhfemale character denoting Nombre feminin hhu5 character denoting Nombre d'enfant < 5 ans hpreferral character denoting Référé à l’hôpital par Agent Com?  (O = Oui, N = Non) hprefpos character denoting Si oui, le patient est-allé? patientpresent character denoting Est-ce que le patient est présent ? ptjaundice character denoting Est-ce que le patient la jaunisse? ptvomit character denoting Vomissements ? mtmental character denoting Etat mental altéré ? ptpregnant character denoting Enceinte? ptu1 character denoting Agée moins d’un  ? referring character denoting 15. Allez-vous référer à l’hôpital? otherajs character denoting Autre patient dans le foyer? otherajsnum character denoting Si oui, combien? borehole character denoting Forage? comtap character denoting Bonne Fontaine? river character denoting Riviere? citywater character denoting Eau de la ville? otherwater character denoting Autre otherwatersp character denoting Si autre… watersourcefreq character denoting Quel point utilisez-vous le plus souvent? ceramicjar character denoting Jarre jerrycan character denoting Jerrycan oildrum character denoting Fut reserother character denoting Autre? reserothersp character denoting Si autre…. resertype character denoting 20. Type de stockage chlorination character denoting 21. Ajouté  chlore la derniere fois? volumreser character denoting 22a. Combien de stockage? handreser character denoting 22b. Entrer la main dans le stockage? hweating character denoting 23. Laver les mains avant de manger? hwwater character denoting 24a. Est-ce qu'il y de l'eau? hwsoap character denoting 24b. Est-ce qu'il y du savon? treatwater character denoting Traitez vous l'eau? tptreatwater character denoting Type de traitement tptreatwaterother character denoting Autre traitment nottreatwhy character denoting Si non, pourquoi defecriver character denoting Riviere?.1 defecair character denoting L'air libre? defeclatrine character denoting Latrine? numlatrine character denoting 26-Combin de personnes qui utilise le latrine? dtmedical character denoting Date Medical Assessment hpid character denoting 1. Numero de Clinique/Hopital outreachscreened character denoting Outreach screening? Y/N/U evaljaundice character denoting 7. Deja Evalué pour la Jaunisse? jaundiceid character denoting Si Oui, Numero de Cas? referredbychw character denoting 8. Référé par l’Agent Communautaire? jaundiceid2 character denoting Si Oui, Numero de Cas?.1 medjaundice character denoting 9. Le patient la jaunisse? dtjaundice character denoting 10. Date de début de la jaunisse ? medfever character denoting 11a. Fievre? mednausea character denoting 11b. Nausées/Anorexie  medvomit character denoting 11c. Vomissements? medepigastric character denoting 11d. Douleur epigastrique? meditching character denoting 11e. Démangeaisons ? medheadache character denoting 11f. Mal de tete? medarthralgia character denoting 11g. Arthralgies? meddiar character denoting 11h. Diarrhées medbleeding character denoting 11i. Saignements? medfev38 character denoting 12. Fièvre = 38.0°C? medmental character denoting 13. Etat Mental? medother character denoting symptoms (free text) medothhhajs character denoting 14. Autre avec jaunisse dans le menage? medothhhajsnum character denoting 14a. Combien? othercaseid character denoting 14b. Numero de cas medpreg character denoting 15. Enceinte? medpregtri character denoting 15a. Trimestre? 1/2/3 medpp character denoting 16. Post-Partum? medppdays character denoting 16a. Si postpartum, combien de jours? medppoutcome character denoting 16b. Resultat de la grossesse? matdeathdt character denoting Si décès maternelle, date de décès medppga character denoting Gestation weeks delivery medblood character denoting 17. Prelevements de sang? medblooddt character denoting Si oui, date de prelevement medmalrdt character denoting 18a. Malaria RDT medhepb character denoting 18b. Hep B medhepc character denoting 18c. Hep C medhevrdt character denoting 18d. Hep E RDT medhevelisa character denoting Hep E confiramtion ELISA      MOH  / MSF hevrecent character denoting Confirmed 'recent' case based ELISA enter 1 IgM+ hevpcr character denoting Hep E confirmation PCR      MOH/MSF hevgenotest character denoting Genotype peformed? Y/N/unk hevgenotype character denoting yes, type? medhavelisa character denoting Hep ELISA medhbvelisa character denoting Hep Bc ELISA medhcvelisa character denoting Hep C ELISA arbovpcr character denoting ARBO PCR (YF, Rift, Chik, DEN, WN, ZIK) yf character denoting Yellow Fever Elisa zika character denoting Zika Elisa dengue character denoting Dengue Elisa wnv character denoting West Nile Elisa rvf character denoting Rift Valley Elisa chik character denoting Chikungunya Elisa hospitalised character denoting 19. Hospitalised? dthospitalisation character denoting Date de hopitalisation? outcomehp character denoting 20. Resultat Clinique dtdeath character denoting (Si décès la date de décès) epiwajs character denoting EpiWeek Jaundice Onset epiwhevelisa character denoting EpiWeek Confirmed (IgM+) epiwoutreach character denoting EpiWeek FIRST Assessment (Community Medical) epiwmed character denoting EpiWeek MEDICAL  Assessment epiwepiquest character denoting EpiWeek Assessment QUESTIONNAIRE epiwhp character denoting EpiWeek HOSPITALIZATION epiwdeath character denoting EpiWeek DEATH caseclass character denoting Suspected/Confirmed/Case (based HEV RDT) Longitude numeric denoting Jittered GPS coordinates Latitude numeric denoting Jittered GPS coordinates","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"data collected part Doctors Without Borders (MSF) outbreak response Ministry Health (MoH) Chad approved use data training purposes. original dataset AJS_AmTiman.xlsx. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"case-linelist contains de-indentified individual level data clinical, laboratory epidemiological information. can used together AJS_AmTiman_population, Blocksshape Quartiersshape. Please note, data adapted order best achieve training objectives. Also, GPS coordinates included dataset correspond real cases identified outbreak. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"Spina , Lenglet , et al. (2017) large outbreak Hepatitis E virus genotype 1 infection urban setting Chad likely linked household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240 doi:10.1371/journal.pone.0188240","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"Population data real outbreak Hepatitis E virus (HEV) infection occurred town Timan, Chad, October 2016 April 2017.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"","code":"AJS_AmTiman_population"},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"data frame 648 rows 3 columns: variable1 explanation variable variable2 explanation variables","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"data collected part Doctors Without Borders (MSF) outbreak response Ministry Health (MoH) Chad approved use data training purposes. original dataset 'AJS_AmTiman_population.xlsx'. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"contains population counts houses individuals housing blocks found Blocksshape can also used together AJS_AmTiman.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"Spina , Lenglet , et al. (2017) large outbreak Hepatitis E virus genotype 1 infection urban setting Chad likely linked household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240 doi:10.1371/journal.pone.0188240","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":null,"dir":"Reference","previous_headings":"","what":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"Shapefile data real outbreak Hepatitis E virus (HEV) infection occurred town Timan, Chad, October 2016 April 2017.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"","code":"Blocksshape"},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"data frame 650 rows 3 columns: variable1 explanation variable variable2 explanation variables","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"data collected part Doctors Without Borders (MSF) outbreak response Ministry Health (MoH) Chad approved use data training purposes. original dataset 'Blocksshape.zip' (contains necessary Shapefile components). version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"contains shapefile housing blocks correspond population counts found AJS_AmTiman_population can also used together AJS_AmTiman.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"Spina , Lenglet , et al. (2017) large outbreak Hepatitis E virus genotype 1 infection urban setting Chad likely linked household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240 doi:10.1371/journal.pone.0188240","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":null,"dir":"Reference","previous_headings":"","what":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"Shapefile data real outbreak Hepatitis E virus (HEV) infection occurred town Timan, Chad, October 2016 April 2017.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"","code":"Quartiersshape"},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"data frame 34 rows 3 columns: variable1 explanation variable variable2 explanation variables","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"data collected part Doctors Without Borders (MSF) outbreak response Ministry Health (MoH) Chad approved use data training purposes. original dataset 'Blocksshape.zip' (contains necessary Shapefile components). version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"contains shapefile neighbourhoods correspond population counts found AJS_AmTiman_population can also used together AJS_AmTiman.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"Spina , Lenglet , et al. (2017) large outbreak Hepatitis E virus genotype 1 infection urban setting Chad likely linked household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240 doi:10.1371/journal.pone.0188240","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Description of Variables for Roxygen Documentation — create_desc","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"function uses data frame (data dictionary format) create description section 'format' data set documentation Roxygen package.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"","code":"create_desc(   dictionary,   variable_name,   type = NULL,   description,   copy_to_clipboard = TRUE )"},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"dictionary data frame listing minimum variable name, variable type description column. variable_name column listing names variables type column listing type variable description column explaining variable contains copy_to_clipboard TRUE (default), description text copied user's clipboard clipr::write_clip(). FALSE, printed user's console.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"character string can pasted documentation file","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"","code":"if (FALSE) { # \\dontrun{ # Create description text for ...  create_desc(data_dict, \"variable_name\", \"type\", \"description\") } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"Anonymized jittered linelist data real emergence COVID-19 Fulton County, sample dates early 2020 July 2021.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"","code":"fulton_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"object class data.frame 82101 rows 31 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"data collected Fulton County surveillance purposes, anonymized jittered training. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"case-linelist contains de-indentified individual level data clinical, laboratory epidemiological information. can used together fulton_population (population data county). Please note, data adapted order best achieve training objectives. Also, GPS coordinates included dataset correspond real cases identified outbreak. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"Anonymized jittered linelist data real emergence COVID-19 Fulton County, sample dates early 2020 July 2021. data cleaned standardise column names content, format column classes, remove erroneous data.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"","code":"fulton_data_clean"},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"object class data.frame 81757 rows 40 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"data collected Fulton County surveillance purposes, anonymized jittered training. version 2.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"case-linelist contains de-indentified individual level data clinical, laboratory epidemiological information. clean version fulton_data can used together fulton_population(population data county). Please note, data adapted order best achieve training objectives. Also, GPS coordinates included dataset correspond real cases identified outbreak. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Zip-code population data Fulton County (USA), 2020 — fulton_population","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"Table population size per zip code Fulton County (USA), 2020","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"","code":"fulton_population"},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"object class data.frame 49 rows 2 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"population data provided Fulton County training purposes. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"aggregate dataset population size per zip code Fulton County (USA), 2020. can used together fulton_data fulton_data_clean, raw clean versions COVID-19 linelist data Fulton County respectively. Please note, data adapted order best achieve training objectives.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve and Load Datasets — get_data","title":"Retrieve and Load Datasets — get_data","text":"get_data function designed load specific datasets appliedepidata package based search criteria name, language, group_identifier, unique_identifier. function performs internal lookup identify appropriate dataset(s), loads assigns global environment. Depending type dataset (e.g., regular data frame, spatial data (sf), list), appropriate post-processing done ensure proper handling loading.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve and Load Datasets — get_data","text":"","code":"get_data(   name = NULL,   language = NULL,   group_identifier = NULL,   unique_identifier = NULL )"},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve and Load Datasets — get_data","text":"name (optional) string specifying name dataset load. language (optional) string specifying language dataset. used name, group_identifier, unique_identifier, function filter datasets based language. group_identifier (optional) string identifying group related datasets. provided, function return datasets within group unless criteria given. unique_identifier (optional) string representing unique identifier dataset.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve and Load Datasets — get_data","text":"dataset(s) loaded global environment. Depending structure #' dataset, data frame, spatial object, individual list elements loaded separate objects.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve and Load Datasets — get_data","text":"function operates follows: Dataset Lookup: performs internal lookup identify datasets matching search criteria provided. Loading Datasets: dataset found: attempts load dataset using data() function appliedepidata package. dataset loaded temporary environment avoid global environment clutter loading process. Post-Processing Based Object Type: dataset loaded, function checks type object handles accordingly: Data frames directly assigned global environment without processing. Spatial objects (sf class) processed using sf::st_as_sf() ensure correct handling spatial data, assigned global environment. Lists data frames split individual objects assigned global environment separate entities. dataset found loaded, function raise error.","code":""},{"path":[]},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve and Load Datasets — get_data","text":"","code":"if (FALSE) { # \\dontrun{ # Load a dataset by name get_data(name = \"AJS_AmTiman\")  # Load a dataset by name and language get_data(name = \"AJS_AmTiman\", language = \"en\")  # Load datasets by group identifier get_data(group_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016\")  } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":null,"dir":"Reference","previous_headings":"","what":"List Datasets in a Package — list_data","title":"List Datasets in a Package — list_data","text":"function lists files data,inst/extdata internal binaries directories specified R package.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List Datasets in a Package — list_data","text":"","code":"list_data(package_name = \"appliedepidata\")"},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List Datasets in a Package — list_data","text":"package_name character string specifying name R package list files. Defaults \"appliedepidata\".","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List Datasets in a Package — list_data","text":"data frame four columns: directory directory (data,extdata, intdata) file located. name name dataset found directories. extension file extension dataset found directories duplicate Logical vector (TRUE/FALSE) file name (extension) exists . flags second occurrence. useful packages built making .rda files internal","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List Datasets in a Package — list_data","text":"","code":"if (FALSE) { # \\dontrun{ # List all files in the directories of the \"ggplot2\" package files <- list_data(package_name = \"ggplot2\") print(files) } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Lookup Dataset Information — lookup_dataset","title":"Lookup Dataset Information — lookup_dataset","text":"function internal function used within get_data.R save_data.R functions. function helps retrieve information (tableoftables.xlsx) datasets based provided search criteria name, language, group_identifier, unique_identifier. returns dataset matches specified criteria suggests alternatives mismatches found.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lookup Dataset Information — lookup_dataset","text":"","code":"lookup_dataset(   name = NULL,   language = NULL,   group_identifier = NULL,   unique_identifier = NULL )"},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lookup Dataset Information — lookup_dataset","text":"name (optional) string specifying name dataset search . language (optional) string specifying language dataset. used name, group_identifier, unique_identifier, function filter datasets based language. group_identifier (optional) string identifying group related datasets. provided, function return datasets within group unless criteria given. unique_identifier (optional) string representing unique identifier dataset.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lookup Dataset Information — lookup_dataset","text":"data.frame containing dataset information matching dataset found. dataset found multiple datasets found details required (unless group), error message returned suggestions search refinement.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Lookup Dataset Information — lookup_dataset","text":"function performs searches following order: Searching name: single dataset found name, function checks parameters like language group_identifier match dataset. match, suggests alternatives. multiple datasets found, additional filtering done based language group_identifier (specified). Handling incorrect language group_identifier: dataset found name, specified language group_identifier match, alternative datasets suggested based unique_identifier. Searching group_identifier: group_identifier provided, function returns datasets within group unless refinement language necessary. Searching unique_identifier: unique_identifier provided, function attempt find dataset identifier apply filtering language name needed.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lookup Dataset Information — lookup_dataset","text":"","code":"if (FALSE) { # \\dontrun{ # Search by name lookup_dataset(name = \"AJS_AmTiman\")  # Search by name and language lookup_dataset(name = \"AJS_AmTiman\", language = \"en\")  # Search by group identifier and language lookup_dataset(group_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016\", language = \"fr\")  # Search by unique identifier lookup_dataset(unique_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016_linelist_1_1_outbreak_2016\")  # Search by name and group identifier lookup_dataset(name = \"AJS_AmTiman\", group_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016\") } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Fake data for a mortality survey — mortality_survey_data","title":"Fake data for a mortality survey — mortality_survey_data","text":"example fake dataset mortality survey generated using epidict package functions.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fake data for a mortality survey — mortality_survey_data","text":"","code":"mortality_survey_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fake data for a mortality survey — mortality_survey_data","text":"Two data frames, 'Mortality Survey' 424 rows 16 columns, 'hh_member' 2874 rows 24 columns: Mortality Survey data frame 424 rows 16 columns: variable1 Description variable1 variable2 Description variable2 hh_member data frame 2874 rows 24 columns: variable1 Description variable1 variable2 Description variable2","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fake data for a mortality survey — mortality_survey_data","text":"data generated functions epidict package created part R4Epis project funded Doctors Without Borders (MSF) sappling nursery. original dataset 'mortality_survey_data.xlsx' version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fake data for a mortality survey — mortality_survey_data","text":"fake survey dataset. data comes two parts: household level dataset ('Mortality Survey') individual level dataset ('hh_member'). can used together mortality_survey_dict. Please note, data entirely fictional created based Doctors without Borders (MSF) ethical review board pre-approved survey dictionaries. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":null,"dir":"Reference","previous_headings":"","what":"Fake data dictionary for a mortality survey — mortality_survey_dict","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"example fake data dictionary mortality survey generated using epidict package functions.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"","code":"mortality_survey_dict"},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"Two data frames, 'Mortality Survey' 424 rows 16 columns, 'hh_member' 2874 rows 24 columns:","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"data generated functions epidict package created part R4Epis project funded Doctors Without Borders (MSF) sappling nursery. original dataset 'mortality_survey_dict.xlsx' version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"fake data dictionary mortality_survey_data dataset. data dictionary originally ODK excel format using functions epidict transformed long format, can used recoding using matchmaker package. Please note, data entirely fictional created based Doctors without Borders (MSF) ethical review board pre-approved survey dictionaries. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"Fictional case counts based real emergence Mpox Europe 2022.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"","code":"mpox_aggregate_table"},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"object class data.frame 101 rows 3 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"Fictional data provided ECDC EI Group training purposes version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"table cumulative mpox case totals date country (country - E). intended use part Mpox case study, alongside mpox_linelist (case linelist fictional case-level information data five countries).","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"Fictional linelist data based real emergence mpox Europe 2022.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"","code":"mpox_linelist"},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"object class data.frame 2000 rows 13 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"Fictional data provided ECDC EI Group training purposes version 1.0. data English. data licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"case linelist contains fictional individual level data five countries (country - E) clinical, laboratory epidemiological information. intended use part mpox case study, alongside mpox_aggregate_table (cumulative case totals date country).","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Save Data Files to a Specified Directory — save_data","title":"Save Data Files to a Specified Directory — save_data","text":"save_data function saves dataset files (unzips necessary) based search criteria dataset name, language, group_identifier, unique_identifier. checks existence required files, files exist, either copied unzipped specified directory.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Save Data Files to a Specified Directory — save_data","text":"","code":"save_data(   name = NULL,   language = NULL,   group_identifier = NULL,   unique_identifier = NULL,   path = rstudioapi::selectDirectory() )"},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Save Data Files to a Specified Directory — save_data","text":"name (optional) string specifying name dataset save. language (optional) string specifying language dataset. used name, group_identifier, unique_identifier, function filter datasets based language. group_identifier (optional) string identifying group related datasets. provided, function return datasets within group unless criteria given. unique_identifier (optional) string representing unique identifier dataset. path (optional) string specifying directory dataset files saved. provided, function prompt user select directory via rstudioapi::selectDirectory() function.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Save Data Files to a Specified Directory — save_data","text":"return value. function saves specified dataset files chosen directory. success failure message printed upon completion.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Save Data Files to a Specified Directory — save_data","text":"function assumes dataset files available \"extdata\" directory appliedepidata package. function follows steps: Dataset Lookup: looks dataset information using lookup_dataset based provided search criteria (name, language, group_identifier, unique_identifier). File Existence Check: checks required dataset files exist using list_data function. files missing, error message lists . File Copying Unzipping: files found, function copies files specified directory. files zipped (.zip), unzipped saved.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Save Data Files to a Specified Directory — save_data","text":"","code":"if (FALSE) { # \\dontrun{ # Save a dataset by name to a chosen directory save_data(name = \"AJS_AmTiman\", path = \"/path/to/save/directory\")  # Save a dataset by group identifier and language save_data(group_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016\", language = \"fr\")  # Save a dataset by unique identifier save_data(unique_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016_linelist_1_1_outbreak_2016\") } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Search and Filter Datasets Available in appliedepidata — search_data","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"Search Filter Datasets Available appliedepidata","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"","code":"search_data()"},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"Shiny application object. function open Shiny app web browser executed.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"Launches interactive Shiny application allows users filter search dataset. Users can select language dropdown menu enter search query filter data displayed reactive table.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"","code":"if (FALSE) { # \\dontrun{ # Launch the interactive data search application search_data() } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"Linelist data fictionalized salmonella outbreak occured highschool Stegen, Germany (1998)","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"","code":"stegentira_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"Linelist 291 rows 20 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"case study first designed Alain Moren Gilles Desve EPIET. based investigation conducted Anja Hauri, RKI, Berlin, 1998. Data fictional inspired Nygren et al. Tick-borne encephalitis: acute clinical manifestations severity 581 cases Germany, 2018-2020. Journal Infection. 2023 Apr 1;86(4):369-75 version 1.0 (appliedepidata package. Earlier data versions used EPIET considered) dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"fake case linelist individual level data clinical epidemiological information, focus foods eaten cafeteria (exposures)","code":""},{"path":"https://appliedepi.github.io/appliedepidata/news/index.html","id":"appliedepidata-development-version","dir":"Changelog","previous_headings":"","what":"appliedepidata (development version)","title":"appliedepidata (development version)","text":"Initial CRAN submission.","code":""}]
+[{"path":[]},{"path":[]},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"overview","dir":"Articles","previous_headings":"Guide to contributing new datasets > PACKAGE FOLDER STRUCTURE","what":"Overview","title":"Adding data","text":"diagram descriptions simplified explanation R packages data chapter. fuller understanding, read chapter.","code":". ├── appliedepidata.Rproj ├── _pkgdown.yml ├── data │   └── newdata.rda (note: internalised) ├── data-raw │   └── newdata.R ├── inst │   └── extdata │       └── tableoftables.xlsx │       └── newdata.xlsx ├── R │   └── newdata_doc.R └── man     └── newdata.Rd"},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"folders-you-will-edit","dir":"Articles","previous_headings":"Guide to contributing new datasets > PACKAGE FOLDER STRUCTURE","what":"Folders you will edit","title":"Adding data","text":"inst/extdata: Newly added datasets go original filetype, e.g. .xlsx, .csv, also .rds files. files downloaded save_data() function. data-raw: Contains R scripts used processing internalizing datasets (making efficient storage), .e. turning newly added datasets inst/extdata .rda files R: Contains R scripts Roxygen2 format define functions datasets. run creates R documentation files (.Rd files) saved man folder. Multiple datasets can defined one script, sensible grouped together (e.g. part outbreak) vignettes: Contains detailed instructions use particular functions. complement function-level documentation man folder giving broader explanation.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"folders-you-will-not-edit","dir":"Articles","previous_headings":"Guide to contributing new datasets > PACKAGE FOLDER STRUCTURE","what":"Folders you will not edit","title":"Adding data","text":"contain files outputted running code folders . data: Contains internalised processed R datasets (.rda files). created internalizing data (running code data-raw folder), makes efficient file storage. man: Contains R documentation files package functions datasets (created running code R folder). .Rd file information specific function dataset. tests: Contains test files developer use .","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"adding-data","dir":"Articles","previous_headings":"Guide to contributing new datasets","what":"ADDING DATA","title":"Adding data","text":"describes process adding file repo. Note original datasets need added inst/exta folder, even already .rda format. adding dataset existing R package, can skip step 3 . Name file appropriately . can name whatever want, stick basic naming conventions. B. Ensure already file tableoftables.xlsx named . C. Avoid generic names like: linelist_cleaned.xlsx survey_data.xlsx. D. Use consistent descriptive names without spaces (e.g., AJS_AmTiman, sitrep_mortality_survey). E. Name files group (e.g. outbreak case study) prefix. E.g: examplename_data examplename_population case linelist corresponding denominator table respectively. Place file correct folder . Add inst/extdata folder. downloaded running save_data() function. shapefile, zip first. Build package added data . Press Ctrl + Shift + B build package newly added data. mean data recognized next step. Reproducibly edit dataset internalize (see data-raw/AJS_AmTiman.R example) . console run usethis::use_data_raw(\"<name file without extension>\"). B. creates R script data-raw folder. already contain comment top saying “code prepare  data goes ” usethis::use_data() function internalise dataset (.e. produce rda file) C. Edit R script correctly read file using system.file(), . Necessary edits dataset also go . run script internalise data, close. D. NOTE want process raw data create dataset also accessible users (e.g. via get_data() save_data() functions), make sure processed data also gets saved inst/extdata version 2. Make sure internalise (use_data) versions data. Add dataset tablesoftables.xlsx described . Add documentation dataset added . Create new R script R folder, one file datasets group. file name group name generated tableoftables (column P), suffix ‘_doc’. Note easiest copy edit existing R script folder. B. Ensure clearly document source license dataset. C. Ensure put correct name dataset bottom dataset description (@docType). E.g. examplename_linelist. D. Run devtools::document() create actual R documentation. .Rd file man folder, file name corresponding dataset name (e.g. examplename_linelist.Rd) Add datasets _pkgdown.yml . Subtitle: Describe group linelists. State year brackets language end B. Contents: List datasets. , names correspond name dataset without extension, e.g “examplename_linelist”. C. Make sure correct indentation use dashes. See prior examples file.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"adding-dataset-metadata-adding-to-tablesoftables-xlsx","dir":"Articles","previous_headings":"Guide to contributing new datasets","what":"ADDING DATASET METADATA (adding to tablesoftables.xlsx)","title":"Adding data","text":"table explaining fill variable dataset metadata Excel sheet (tablesoftables.xlsx). guide helps ensure consistency completeness adding new datasets collection. name: filename dataset appears inst/extdata directory, without file extension. unique within dataset group, ideally also within tableoftables (.e. avoid generic names like: linelist_cleaned.xlsx survey_data.xlsx). Use consistent descriptive names without spaces (e.g., AJS_AmTiman, mortality_survey). type: category type dataset (e.g., linelist, population, shape, survey, dictionary). extension: file extension (e.g., xlsx, zip). type_version: Used identify original dataset associated child data. Increment format variables change. multiple linelists one group, increment type. data_version: Used identify original dataset associated child data. Increment format variables change. Ensure document changes appropriate ‘data-raw’ file. language: Language code using ISO 639-1 codes (e.g., en, fr). country: Country code using ISO 3166-1 alpha-3 codes (e.g., tcd). scale: Geographic scale (e.g., subnational, national, international). subject: Main subject dataset (e.g., acute jaundice syndrome). context: Context data (e.g., outbreak, survey). fictional: dataset fictional (yes) real ()? year: Year data collected (e.g., 2016). earliest year dataset (even fictional). description: Brief description dataset. Ideally, copy roxygen documentation. usage: Intended usage (e.g., {sitrep} walkthroughs, training). license: License dataset (e.g., gpl3, mit). group_identifier: EDIT - Created concatinating function excel. High-level identifier combining subject, context, country, year (e.g.,acute_jaundice_syndrome_outbreak_tcd_2016). unique_identifier: EDIT - Combines group_identifier, type, type_version, data_version, context, year create unique identifier (e.g. acute_jaundice_syndrome_outbreak_tcd_2016_linelist_1). example, adding Ebola dataset, enter information shown . original dataset (whether ’s {outbreaks} another source) considered type_version 1. ’s linelist group, remains type_version 1. completely different linelist added (just edited version), increment type_version accordingly. changes data (cleaning changing nums rows columns), increment data_version (e.g., data_version 2), type_version remains indicate ’s derivative (“child”) original. child dataset gets entry. dataset translated different language, create new entry translated version keeping data_version type_version , editing language column accordingly. ensures can trace back parent-child relationship datasets.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Alexander Spina. Author, maintainer.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Spina (2024). appliedepidata: Datasets used Applied Epi courses resources. R package version 0.0.0.9000, https://appliedepi.github.io/appliedepidata/.","code":"@Manual{,   title = {appliedepidata: Datasets used in Applied Epi courses and resources},   author = {Alexander Spina},   year = {2024},   note = {R package version 0.0.0.9000},   url = {https://appliedepi.github.io/appliedepidata/}, }"},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"appliedepidata","dir":"","previous_headings":"","what":"Datasets used in Applied Epi courses and resources","title":"Datasets used in Applied Epi courses and resources","text":"package stores Applied Epi data across courses resources. includes courses, tutorials, case studies books (EpiRhandbook Applied Epi Manual).","code":""},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Datasets used in Applied Epi courses and resources","text":"can install development version appliedepidata GitHub :","code":"# install.packages(\"pak\") pak::pak(\"appliedepi/appliedepidata\")"},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Datasets used in Applied Epi courses and resources","text":"can see available datasets available data table well depth descriptions reference section. Within RStudio can use search_data browse available datasets. Using information can either load data RStudio environment using get_data save copy data computer using save_data.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":null,"dir":"Reference","previous_headings":"","what":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"Linelist data real outbreak Hepatitis E virus (HEV) infection occurred town Timan, Chad, October 2016 April 2017.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"","code":"AJS_AmTiman"},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"data frame 1477 rows 122 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"data collected part Doctors Without Borders (MSF) outbreak response Ministry Health (MoH) Chad approved use data training purposes. original dataset AJS_AmTiman.xlsx. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"case-linelist contains de-indentified individual level data clinical, laboratory epidemiological information. can used together AJS_AmTiman_population, Blocksshape Quartiersshape. Please note, data adapted order best achieve training objectives. Also, GPS coordinates included dataset correspond real cases identified outbreak. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman","text":"Spina , Lenglet , et al. (2017) large outbreak Hepatitis E virus genotype 1 infection urban setting Chad likely linked household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240 doi:10.1371/journal.pone.0188240","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"Population data real outbreak Hepatitis E virus (HEV) infection occurred town Timan, Chad, October 2016 April 2017.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"","code":"AJS_AmTiman_population"},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"data frame 648 rows 3 columns:","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"data collected part Doctors Without Borders (MSF) outbreak response Ministry Health (MoH) Chad approved use data training purposes. original dataset 'AJS_AmTiman_population.xlsx'. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"contains population counts houses individuals housing blocks found Blocksshape can also used together AJS_AmTiman.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/AJS_AmTiman_population.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — AJS_AmTiman_population","text":"Spina , Lenglet , et al. (2017) large outbreak Hepatitis E virus genotype 1 infection urban setting Chad likely linked household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240 doi:10.1371/journal.pone.0188240","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":null,"dir":"Reference","previous_headings":"","what":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"Shapefile data real outbreak Hepatitis E virus (HEV) infection occurred town Timan, Chad, October 2016 April 2017.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"","code":"Blocksshape"},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"data frame 650 rows 3 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"data collected part Doctors Without Borders (MSF) outbreak response Ministry Health (MoH) Chad approved use data training purposes. original dataset 'Blocksshape.zip' (contains necessary Shapefile components). version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"contains shapefile housing blocks correspond population counts found AJS_AmTiman_population can also used together AJS_AmTiman.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Blocksshape.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Blocksshape","text":"Spina , Lenglet , et al. (2017) large outbreak Hepatitis E virus genotype 1 infection urban setting Chad likely linked household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240 doi:10.1371/journal.pone.0188240","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":null,"dir":"Reference","previous_headings":"","what":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"Shapefile data real outbreak Hepatitis E virus (HEV) infection occurred town Timan, Chad, October 2016 April 2017.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"","code":"Quartiersshape"},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"data frame 34 rows 3 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"data collected part Doctors Without Borders (MSF) outbreak response Ministry Health (MoH) Chad approved use data training purposes. original dataset 'Blocksshape.zip' (contains necessary Shapefile components). version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"contains shapefile neighbourhoods correspond population counts found AJS_AmTiman_population can also used together AJS_AmTiman.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Shapefile of neighbourhoods (fr: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016 — Quartiersshape","text":"Spina , Lenglet , et al. (2017) large outbreak Hepatitis E virus genotype 1 infection urban setting Chad likely linked household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240 doi:10.1371/journal.pone.0188240","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_subtree_2.html","id":null,"dir":"Reference","previous_headings":"","what":"Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_subtree_2","title":"Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_subtree_2","text":"Outputs analysis next generation sequencing data Shigella surveillance samples Belgium 2013-2019","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_subtree_2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_subtree_2","text":"","code":"Shigella_subtree_2"},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_subtree_2.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_subtree_2","text":"List class \"phylo\"","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_subtree_2.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_subtree_2","text":"data posted European Nucleotide Archive original dataset Shigella_subtree_2.txt version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_subtree_2.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_subtree_2","text":"based sequencing data routine surveillance samples collected Belgium 2013 2019. produced using used together sample_data_Shigella_tree Shigella_tree","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_subtree_2.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Phylogenetic tree produced from next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_subtree_2","text":"Fischer, N. et al. Genomic epidemiology persistently circulating MDR Shigella sonnei strains associated men sex men (MSM) Belgium (2013-19) doi:10.1093/jac/dkab377","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_tree","title":"Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_tree","text":"Next generation sequencing data Shigella surveillance samples Belgium 2013-2019","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_tree","text":"","code":"Shigella_tree"},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_tree.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_tree","text":"List class \"phylo\"","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_tree.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_tree","text":"data posted European Nucleotide Archive original dataset Shigella_Tree.txt version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_tree.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_tree","text":"sequencing data routine surveillance samples collected Belgium 2013 2019. can used together sample_data_Shigella_tree","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/Shigella_tree.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — Shigella_tree","text":"Fischer, N. et al. Genomic epidemiology persistently circulating MDR Shigella sonnei strains associated men sex men (MSM) Belgium (2013-19) doi:10.1093/jac/dkab377","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/campylobacter_germany.html","id":null,"dir":"Reference","previous_headings":"","what":"Linelist data of Campylobacter surveillance in Germany 2001-2011. — campylobacter_germany","title":"Linelist data of Campylobacter surveillance in Germany 2001-2011. — campylobacter_germany","text":"Linelist data Campylobacter surveillance Germany 2001-2011.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/campylobacter_germany.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Linelist data of Campylobacter surveillance in Germany 2001-2011. — campylobacter_germany","text":"","code":"campylobacter_germany"},{"path":"https://appliedepi.github.io/appliedepidata/reference/campylobacter_germany.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Linelist data of Campylobacter surveillance in Germany 2001-2011. — campylobacter_germany","text":"data frame 509 rows 2 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/campylobacter_germany.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Linelist data of Campylobacter surveillance in Germany 2001-2011. — campylobacter_germany","text":"data originally added surveillance package, removed last 13 rows data kept date cases variables. data campylobacteriosis cases queried \"SurvstatRKI\" database German Robert Koch Institute (https://survstat.rki.de/). original dataset can accessed using data(\"CampyDe\"). Within package original dataset campylobacter_germany.xlsx version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/campylobacter_germany.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Linelist data of Campylobacter surveillance in Germany 2001-2011. — campylobacter_germany","text":"Weekly number reported campylobacteriosis cases Germany, 2002-2011.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/campylobacter_germany.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Linelist data of Campylobacter surveillance in Germany 2001-2011. — campylobacter_germany","text":"Manitz, J. Höhle, M. (2013): Bayesian outbreak detection algorithm monitoring reported cases campylobacteriosis Germany. Biometrical Journal, 55(4), 509-526 doi:10.1002/bimj.201200141","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/cases_clean.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional case data for a generic disease to demonstrate contact tracing — cases_clean","title":"Fictional case data for a generic disease to demonstrate contact tracing — cases_clean","text":"Fictional case data generic disease demonstrate contact tracing","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/cases_clean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional case data for a generic disease to demonstrate contact tracing — cases_clean","text":"","code":"cases_clean  contacts_clean  followups_clean  relationships_clean"},{"path":"https://appliedepi.github.io/appliedepidata/reference/cases_clean.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional case data for a generic disease to demonstrate contact tracing — cases_clean","text":"data frame 56 rows 86 columns object class data.frame 66 rows 62 columns. object class data.frame 437 rows 53 columns. object class data.frame 100 rows 21 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/cases_clean.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional case data for a generic disease to demonstrate contact tracing — cases_clean","text":"data originally sample contact tracing data Go.Data platform original datasets cases_clean.rds, contacts_clean.rds, followups_clean.rds, relationships_clean.rds version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/cases_clean.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional case data for a generic disease to demonstrate contact tracing — cases_clean","text":"fictional case-linelist contains de-indentified individual level data, based go.data format.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/cleaning_dict.html","id":null,"dir":"Reference","previous_headings":"","what":"Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — cleaning_dict","title":"Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — cleaning_dict","text":"Incomplete data dictionary used demonstrating cleaning raw version fictional Ebola Virus Disease data simulating properties West African Ebola outbreak 2014","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/cleaning_dict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — cleaning_dict","text":"","code":"cleaning_dict"},{"path":"https://appliedepi.github.io/appliedepidata/reference/cleaning_dict.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — cleaning_dict","text":"data frame 9 rows 3 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/cleaning_dict.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — cleaning_dict","text":"created example use  linelist_raw, cleaned using code epiRhandbook cleaning chapter. original dataset cleaning_dict.csv version 1.0. dataset English. dataset licensed MIT","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/cleaning_dict.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — cleaning_dict","text":"fictional data dictionary contains recoding information.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/cleaning_dict.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Example data dictionary for fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — cleaning_dict","text":"Ebola Response Team. 2014. Ebola virus disease West Africa–first 9 months epidemic forward projections. New England journal medicine 371:1481–1495 doi:10.1056/NEJMoa1411100","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/country_demographics.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional country demographic and mortality data to demonstrate standardisation — country_demographics","title":"Fictional country demographic and mortality data to demonstrate standardisation — country_demographics","text":"Fictional country demographic mortality data demonstrate standardisation","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/country_demographics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional country demographic and mortality data to demonstrate standardisation — country_demographics","text":"","code":"country_demographics  country_demographics_2  deaths_countryA  deaths_countryB"},{"path":"https://appliedepi.github.io/appliedepidata/reference/country_demographics.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional country demographic and mortality data to demonstrate standardisation — country_demographics","text":"Dataframes object class data.frame 18 rows 3 columns. object class data.frame 18 rows 4 columns. object class data.frame 18 rows 4 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/country_demographics.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional country demographic and mortality data to demonstrate standardisation — country_demographics","text":"data created training purposes original dataset country_demographics.csv version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/country_demographics.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional country demographic and mortality data to demonstrate standardisation — country_demographics","text":"Fictional country demographic mortality data demonstrate standardisation","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Description of Variables for Roxygen Documentation — create_desc","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"function uses data frame (data dictionary format) create description section 'format' data set documentation Roxygen package.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"","code":"create_desc(   dictionary,   variable_name,   type = NULL,   description,   copy_to_clipboard = TRUE )"},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"dictionary data frame listing minimum variable name, variable type description column. variable_name column listing names variables type column listing type variable description column explaining variable contains copy_to_clipboard TRUE (default), description text copied user's clipboard clipr::write_clip(). FALSE, printed user's console.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"character string can pasted documentation file","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/create_desc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Description of Variables for Roxygen Documentation — create_desc","text":"","code":"if (FALSE) { # \\dontrun{ # Create description text for ...  create_desc(data_dict, \"variable_name\", \"type\", \"description\") } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/district_weekly_count_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional counts of malaria cases from Mozambique in 2019 — district_weekly_count_data","title":"Fictional counts of malaria cases from Mozambique in 2019 — district_weekly_count_data","text":"Fictional counts malaria cases Mozambique 2019","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/district_weekly_count_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional counts of malaria cases from Mozambique in 2019 — district_weekly_count_data","text":"","code":"district_weekly_count_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/district_weekly_count_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional counts of malaria cases from Mozambique in 2019 — district_weekly_count_data","text":"data frame 9628 rows 4 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/district_weekly_count_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional counts of malaria cases from Mozambique in 2019 — district_weekly_count_data","text":"data fictional based data Mozambique. original dataset district_weekly_count_data.xlsx. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/district_weekly_count_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional counts of malaria cases from Mozambique in 2019 — district_weekly_count_data","text":"fictional aggregate data counts date region.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/epinow_res.html","id":null,"dir":"Reference","previous_headings":"","what":"Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — epinow_res","title":"Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — epinow_res","text":"Outputs epinow2 based fictional Ebola Virus Disease data simulating properties West African Ebola outbreak 2014","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/epinow_res.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — epinow_res","text":"","code":"epinow_res  epinow_res_small  generation_time  incubation_period"},{"path":"https://appliedepi.github.io/appliedepidata/reference/epinow_res.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — epinow_res","text":"large list object class epinow (inherits list) length 3. object class list length 5. object class list length 5.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/epinow_res.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — epinow_res","text":"direct output use linelist_cleaned_rds. original datasets epinow_res.rds, epinow_res_small.rds, generation_time.rds incubation_period.rds version 1.0. dataset English. dataset licensed MIT","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/epinow_res.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Outputs from epinow2 based on fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — epinow_res","text":"outputs produced using linelist_cleaned_rds epinow2","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fluH7N9_China_2013.html","id":null,"dir":"Reference","previous_headings":"","what":"Linelist data from an outbreak of influenza A H7N9 in China 2013. — fluH7N9_China_2013","title":"Linelist data from an outbreak of influenza A H7N9 in China 2013. — fluH7N9_China_2013","text":"Linelist data real outbreak influenza H7N9 China 2013.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fluH7N9_China_2013.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Linelist data from an outbreak of influenza A H7N9 in China 2013. — fluH7N9_China_2013","text":"","code":"fluH7N9_China_2013"},{"path":"https://appliedepi.github.io/appliedepidata/reference/fluH7N9_China_2013.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Linelist data from an outbreak of influenza A H7N9 in China 2013. — fluH7N9_China_2013","text":"data frame 136 rows 8 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fluH7N9_China_2013.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Linelist data from an outbreak of influenza A H7N9 in China 2013. — fluH7N9_China_2013","text":"data originally added outbreaks package, edits made . data collated Adam Kucharski et al. ProMed, , FluTrackers, news reports research articles. Transfer R documentation Simon Frost (sdwfrost@gmail.com). original dataset can accessed using outbreaks::fluH7N9_China_2013. Within package original dataset fluH7N9_China_2013.csv version 1.0. dataset English. dataset licensed MIT","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fluH7N9_China_2013.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Linelist data from an outbreak of influenza A H7N9 in China 2013. — fluH7N9_China_2013","text":"case-linelist contains de-indentified individual level data clinical outcome, demographics region.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fluH7N9_China_2013.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Linelist data from an outbreak of influenza A H7N9 in China 2013. — fluH7N9_China_2013","text":". Kucharski, H. Mills, . Pinsent, C. Fraser, M. Van Kerkhove, C. . Donnelly, S. Riley. 2014. Distinguishing reservoir exposure human--human transmission emerging pathogens using case onset data. PLOS Currents Outbreaks. Mar 7, edition 1 doi:10.1371/currents.outbreaks.e1473d9bfc99d080ca242139a06c455f","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"Anonymized jittered linelist data real emergence COVID-19 Fulton County, sample dates early 2020 July 2021.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"","code":"fulton_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"object class data.frame 82101 rows 31 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"data collected Fulton County surveillance purposes, anonymized jittered training. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data","text":"case-linelist contains de-indentified individual level data clinical, laboratory epidemiological information. can used together fulton_population (population data county). Please note, data adapted order best achieve training objectives. Also, GPS coordinates included dataset correspond real cases identified outbreak. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"Anonymized jittered linelist data real emergence COVID-19 Fulton County, sample dates early 2020 July 2021. data cleaned standardise column names content, format column classes, remove erroneous data.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"","code":"fulton_data_clean"},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"object class data.frame 81757 rows 40 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"data collected Fulton County surveillance purposes, anonymized jittered training. version 2.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_data_clean.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Clean anonymized COVID-19 linelist data from Fulton County (USA), 2020 — fulton_data_clean","text":"case-linelist contains de-indentified individual level data clinical, laboratory epidemiological information. clean version fulton_data can used together fulton_population(population data county). Please note, data adapted order best achieve training objectives. Also, GPS coordinates included dataset correspond real cases identified outbreak. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Zip-code population data Fulton County (USA), 2020 — fulton_population","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"Table population size per zip code Fulton County (USA), 2020","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"","code":"fulton_population"},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"object class data.frame 49 rows 2 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"population data provided Fulton County training purposes. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/fulton_population.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Zip-code population data Fulton County (USA), 2020 — fulton_population","text":"aggregate dataset population size per zip code Fulton County (USA), 2020. can used together fulton_data fulton_data_clean, raw clean versions COVID-19 linelist data Fulton County respectively. Please note, data adapted order best achieve training objectives.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/germany_weather.html","id":null,"dir":"Reference","previous_headings":"","what":"Weather data for Germany from 2001-2011 — germany_weather","title":"Weather data for Germany from 2001-2011 — germany_weather","text":"Weather data Germany 2001-2011","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/germany_weather.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Weather data for Germany from 2001-2011 — germany_weather","text":"","code":"germany_weather"},{"path":"https://appliedepi.github.io/appliedepidata/reference/germany_weather.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Weather data for Germany from 2001-2011 — germany_weather","text":"list","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/germany_weather.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Weather data for Germany from 2001-2011 — germany_weather","text":"data obtained using ecmwfr package described epiRhandbook chapter timeseries. data originally collected European Union Copernicus satelite made available climate data store original dataset germany_weather.zip version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/germany_weather.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Weather data for Germany from 2001-2011 — germany_weather","text":"Weather data Germany 2001-2011","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve and Load Datasets — get_data","title":"Retrieve and Load Datasets — get_data","text":"get_data function designed load specific datasets appliedepidata package based search criteria name, language, group_identifier, unique_identifier. function performs internal lookup identify appropriate dataset(s), loads assigns global environment. Depending type dataset (e.g., regular data frame, spatial data (sf), list), appropriate post-processing done ensure proper handling loading.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve and Load Datasets — get_data","text":"","code":"get_data(   name = NULL,   language = NULL,   group_identifier = NULL,   usage = NULL,   unique_identifier = NULL )"},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve and Load Datasets — get_data","text":"name (optional) string specifying name dataset load. language (optional) string specifying language dataset. used name, group_identifier, unique_identifier, function filter datasets based language. group_identifier (optional) string identifying group related datasets. provided, function return datasets within group unless criteria given. usage (optional) string representing datasets used. provided, function return datasets within group unless criteria given. unique_identifier (optional) string representing unique identifier dataset.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve and Load Datasets — get_data","text":"dataset(s) loaded global environment. Depending structure #' dataset, data frame, spatial object, individual list elements loaded separate objects.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve and Load Datasets — get_data","text":"function operates follows: Dataset Lookup: performs internal lookup identify datasets matching search criteria provided. Loading Datasets: dataset found: attempts load dataset using data() function appliedepidata package. dataset loaded temporary environment avoid global environment clutter loading process. Post-Processing Based Object Type: dataset loaded, function checks type object handles accordingly: Data frames directly assigned global environment without processing. Phylo objects (phylo class) directly assigned global environment without processing. Stars objects (stars class) directly assigned global environment without processing. Epinow objects (epinow class) directly assigned global environment without processing. Spatial objects (sf class) processed using sf::st_as_sf() ensure correct handling spatial data, assigned global environment. Lists data frames split individual objects assigned global environment separate entities. dataset found loaded, function raise error.","code":""},{"path":[]},{"path":"https://appliedepi.github.io/appliedepidata/reference/get_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve and Load Datasets — get_data","text":"","code":"if (FALSE) { # \\dontrun{ # Load a dataset by name get_data(name = \"AJS_AmTiman\")  # Load a dataset by name and language get_data(name = \"AJS_AmTiman\", language = \"en\")  # Load datasets by group identifier get_data(group_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016\")  } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/hospital_linelists.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — hospital_linelists","title":"Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — hospital_linelists","text":"Subset cleaned version fictional Ebola Virus Disease data simulating properties West African Ebola outbreak 2014","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/hospital_linelists.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — hospital_linelists","text":"","code":"hospital_linelists"},{"path":"https://appliedepi.github.io/appliedepidata/reference/hospital_linelists.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — hospital_linelists","text":"data frame 454 rows 30 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/hospital_linelists.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — hospital_linelists","text":"data subset version linelist_cleaned_excel, cleaned using code epiRhandbook cleaning chapter. original dataset hospital_linelist.xlsx version 4.0. dataset English. dataset licensed MIT","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/hospital_linelists.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — hospital_linelists","text":"fictional case-linelist contains de-indentified individual level data clinical outcome, demographics region.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/hospital_linelists.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Subset of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — hospital_linelists","text":"Ebola Response Team. 2014. Ebola virus disease West Africa–first 9 months epidemic forward projections. New England journal medicine 371:1481–1495 doi:10.1056/NEJMoa1411100","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/likert_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional likert data for demonstration purposes — likert_data","title":"Fictional likert data for demonstration purposes — likert_data","text":"Fictional likert data demonstration purposes","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/likert_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional likert data for demonstration purposes — likert_data","text":"","code":"likert_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/likert_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional likert data for demonstration purposes — likert_data","text":"Dataframes","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/likert_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional likert data for demonstration purposes — likert_data","text":"data created training purposes original dataset likert_data.csv version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/likert_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional likert data for demonstration purposes — likert_data","text":"Fictional likert data demonstration purposes","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_excel.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_excel","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_excel","text":"Excel file cleaned version fictional Ebola Virus Disease data simulating properties West African Ebola outbreak 2014","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_excel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_excel","text":"","code":"linelist_cleaned_excel"},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_excel.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_excel","text":"data frame 5888 rows 30 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_excel.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_excel","text":"data cleaned version linelist_raw, cleaned using code epiRhandbook cleaning chapter. original dataset linelist_cleaned_excel.xlsx version 2.0. dataset English. dataset licensed MIT","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_excel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_excel","text":"fictional case-linelist contains de-indentified individual level data clinical outcome, demographics region.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_excel.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_excel","text":"Ebola Response Team. 2014. Ebola virus disease West Africa–first 9 months epidemic forward projections. New England journal medicine 371:1481–1495 doi:10.1056/NEJMoa1411100","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_rds.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_rds","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_rds","text":"R-dataset file cleaned version fictional Ebola Virus Disease data simulating properties West African Ebola outbreak 2014","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_rds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_rds","text":"","code":"linelist_cleaned_rds"},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_rds.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_rds","text":"data frame 5888 rows 30 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_rds.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_rds","text":"data cleaned version linelist_raw, cleaned using code epiRhandbook cleaning chapter. original dataset linelist_cleaned_rds.rds version 3.0. dataset English. dataset licensed MIT","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_rds.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_rds","text":"fictional case-linelist contains de-indentified individual level data clinical outcome, demographics region.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_rds.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_rds","text":"Ebola Response Team. 2014. Ebola virus disease West Africa–first 9 months epidemic forward projections. New England journal medicine 371:1481–1495 doi:10.1056/NEJMoa1411100","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_with_adm3.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_with_adm3","title":"Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_with_adm3","text":"Subset additional spatial data rds clean version fictional Ebola Virus Disease data simulating properties West African Ebola outbreak 2014","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_with_adm3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_with_adm3","text":"","code":"linelist_cleaned_with_adm3"},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_with_adm3.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_with_adm3","text":"data frame 454 rows 30 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_with_adm3.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_with_adm3","text":"data cleaned version linelist_cleaned_rds, cleaned using code epiRhandbook cleaning chapter. original dataset linelist_cleaned_with_adm3.rds version 4.0. dataset English. dataset licensed MIT","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_with_adm3.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_with_adm3","text":"fictional case-linelist contains de-indentified individual level data clinical outcome, demographics region.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_cleaned_with_adm3.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Subset with additional spatial data of cleaned fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_cleaned_with_adm3","text":"Ebola Response Team. 2014. Ebola virus disease West Africa–first 9 months epidemic forward projections. New England journal medicine 371:1481–1495 doi:10.1056/NEJMoa1411100","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_raw.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_raw","title":"Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_raw","text":"Fictional Ebola Virus Disease data simulating properties West African Ebola outbreak 2014","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_raw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_raw","text":"","code":"linelist_raw"},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_raw.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_raw","text":"data frame 136 rows 8 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_raw.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_raw","text":"data originally added outbreaks package, extensive edits made teaching purposes. data originally simulated match properties West African Ebola outbreak 2014-2015 (see outbreaks package documentation details). original dataset can accessed using outbreaks::ebola_sim. Within package original dataset linelist_raw.xlsx. version 1.0. dataset English. dataset licensed MIT","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_raw.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_raw","text":"fictional case-linelist contains de-indentified individual level data clinical outcome, demographics region.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/linelist_raw.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Fictional Ebola Virus Disease data simulating properties from the West African Ebola outbreak of 2014 — linelist_raw","text":"Ebola Response Team. 2014. Ebola virus disease West Africa–first 9 months epidemic forward projections. New England journal medicine 371:1481–1495 doi:10.1056/NEJMoa1411100","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":null,"dir":"Reference","previous_headings":"","what":"List Datasets in a Package — list_data","title":"List Datasets in a Package — list_data","text":"function lists files data,inst/extdata internal binaries directories specified R package.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List Datasets in a Package — list_data","text":"","code":"list_data(package_name = \"appliedepidata\")"},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List Datasets in a Package — list_data","text":"package_name character string specifying name R package list files. Defaults \"appliedepidata\".","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List Datasets in a Package — list_data","text":"data frame four columns: directory directory (data,extdata, intdata) file located. name name dataset found directories. extension file extension dataset found directories duplicate Logical vector (TRUE/FALSE) file name (extension) exists . flags second occurrence. useful packages built making .rda files internal","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List Datasets in a Package — list_data","text":"","code":"if (FALSE) { # \\dontrun{ # List all files in the directories of the \"ggplot2\" package files <- list_data(package_name = \"ggplot2\") print(files) } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Lookup Dataset Information — lookup_dataset","title":"Lookup Dataset Information — lookup_dataset","text":"function internal function used within get_data.R save_data.R functions. function helps retrieve information (tableoftables.xlsx) datasets based provided search criteria name, language, group_identifier, unique_identifier. returns dataset matches specified criteria suggests alternatives mismatches found.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lookup Dataset Information — lookup_dataset","text":"","code":"lookup_dataset(   name = NULL,   language = NULL,   group_identifier = NULL,   usage = NULL,   unique_identifier = NULL )"},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lookup Dataset Information — lookup_dataset","text":"name (optional) string specifying name dataset search . language (optional) string specifying language dataset. used name, group_identifier, unique_identifier, function filter datasets based language. group_identifier (optional) string identifying group related datasets. provided, function return datasets within group unless criteria given. usage (optional) string representing datasets used. provided, function return datasets within group unless criteria given. unique_identifier (optional) string representing unique identifier dataset.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lookup Dataset Information — lookup_dataset","text":"data.frame containing dataset information matching dataset found. dataset found multiple datasets found details required (unless group), error message returned suggestions search refinement.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Lookup Dataset Information — lookup_dataset","text":"function performs searches following order: Searching name: single dataset found name, function checks parameters like language group_identifier match dataset. match, suggests alternatives. multiple datasets found, additional filtering done based language group_identifier (specified). Handling incorrect language group_identifier: dataset found name, specified language group_identifier match, alternative datasets suggested based unique_identifier. Searching group_identifier: group_identifier provided, function returns datasets within group unless refinement language necessary. Searching usage: usage provided, function returns datasets within group unless refinement language necessary. Searching unique_identifier: unique_identifier provided, function attempt find dataset identifier apply filtering language name needed.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/lookup_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lookup Dataset Information — lookup_dataset","text":"","code":"if (FALSE) { # \\dontrun{ # Search by name lookup_dataset(name = \"AJS_AmTiman\")  # Search by name and language lookup_dataset(name = \"AJS_AmTiman\", language = \"en\")  # Search by group identifier and language lookup_dataset(group_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016\", language = \"fr\")  # Search by unique identifier lookup_dataset(unique_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016_linelist_1_1_outbreak_2016\")  # Search by name and group identifier lookup_dataset(name = \"AJS_AmTiman\", group_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016\") } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/malaria_facility_count_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional counts of malaria cases from Mozambique in 2019 — malaria_facility_count_data","title":"Fictional counts of malaria cases from Mozambique in 2019 — malaria_facility_count_data","text":"Fictional counts malaria cases Mozambique 2019","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/malaria_facility_count_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional counts of malaria cases from Mozambique in 2019 — malaria_facility_count_data","text":"","code":"malaria_facility_count_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/malaria_facility_count_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional counts of malaria cases from Mozambique in 2019 — malaria_facility_count_data","text":"data frame 3038 rows 10 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/malaria_facility_count_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional counts of malaria cases from Mozambique in 2019 — malaria_facility_count_data","text":"data fictional based data Mozambique. adapted district_weekly_count_data. original dataset malaria_facility_count_Data.rds. version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/malaria_facility_count_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional counts of malaria cases from Mozambique in 2019 — malaria_facility_count_data","text":"fictional aggregate data counts date, region age group.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Fake data for a mortality survey — mortality_survey_data","title":"Fake data for a mortality survey — mortality_survey_data","text":"example fake dataset mortality survey generated using epidict package functions.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fake data for a mortality survey — mortality_survey_data","text":"","code":"mortality_survey_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fake data for a mortality survey — mortality_survey_data","text":"Two data frames, 'Mortality Survey' 424 rows 16 columns, 'hh_member' 2874 rows 24 columns:","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fake data for a mortality survey — mortality_survey_data","text":"data generated functions epidict package created part R4Epis project funded Doctors Without Borders (MSF) sappling nursery. original dataset 'mortality_survey_data.xlsx' version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fake data for a mortality survey — mortality_survey_data","text":"fake survey dataset. data comes two parts: household level dataset ('Mortality Survey') individual level dataset ('hh_member'). can used together mortality_survey_dict. Please note, data entirely fictional created based Doctors without Borders (MSF) ethical review board pre-approved survey dictionaries. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":null,"dir":"Reference","previous_headings":"","what":"Fake data dictionary for a mortality survey — mortality_survey_dict","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"example fake data dictionary mortality survey generated using epidict package functions.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"","code":"mortality_survey_dict"},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"Two data frames, 'Mortality Survey' 424 rows 16 columns, 'hh_member' 2874 rows 24 columns:","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"data generated functions epidict package created part R4Epis project funded Doctors Without Borders (MSF) sappling nursery. original dataset 'mortality_survey_dict.xlsx' version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fake data dictionary for a mortality survey — mortality_survey_dict","text":"fake data dictionary mortality_survey_data dataset. data dictionary originally ODK excel format using functions epidict transformed long format, can used recoding using matchmaker package. Please note, data entirely fictional created based Doctors without Borders (MSF) ethical review board pre-approved survey dictionaries. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"Fictional case counts based real emergence Mpox Europe 2022.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"","code":"mpox_aggregate_table"},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"object class data.frame 101 rows 3 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"Fictional data provided ECDC EI Group training purposes version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_aggregate_table.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional cumulative mpox case totals from five European countries, 2022 — mpox_aggregate_table","text":"table cumulative mpox case totals date country (country - E). intended use part Mpox case study, alongside mpox_linelist (case linelist fictional case-level information data five countries).","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":null,"dir":"Reference","previous_headings":"","what":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"Fictional linelist data based real emergence mpox Europe 2022.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"","code":"mpox_linelist"},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"object class data.frame 2000 rows 13 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"Fictional data provided ECDC EI Group training purposes version 1.0. data English. data licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/mpox_linelist.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fictional mpox linelist data from five European countries, 2022 — mpox_linelist","text":"case linelist contains fictional individual level data five countries (country - E) clinical, laboratory epidemiological information. intended use part mpox case study, alongside mpox_aggregate_table (cumulative case totals date country).","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/population.html","id":null,"dir":"Reference","previous_headings":"","what":"Fake population data for a mortality survey — population","title":"Fake population data for a mortality survey — population","text":"example fake population data mortality survey generated using epidict package functions.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fake population data for a mortality survey — population","text":"","code":"population"},{"path":"https://appliedepi.github.io/appliedepidata/reference/population.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fake population data for a mortality survey — population","text":"dataframe 20 rows 5 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/population.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fake population data for a mortality survey — population","text":"data generated functions epidict package created part R4Epis project funded Doctors Without Borders (MSF) sappling nursery. original dataset 'population.xlsx' version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/population.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fake population data for a mortality survey — population","text":"fake population data survey_data dataset. Please note, data entirely fictional created based Doctors without Borders (MSF) ethical review board pre-approved survey dictionaries. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sample_data_Shigella_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — sample_data_Shigella_tree","title":"Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — sample_data_Shigella_tree","text":"Linelist data accompany next generation sequencing data Shigella surveillance samples Belgium 2013-2019","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sample_data_Shigella_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — sample_data_Shigella_tree","text":"","code":"sample_data_Shigella_tree"},{"path":"https://appliedepi.github.io/appliedepidata/reference/sample_data_Shigella_tree.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — sample_data_Shigella_tree","text":"dataframe 299 rows 13 columns.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sample_data_Shigella_tree.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — sample_data_Shigella_tree","text":"data posted European Nucleotide Archive original dataset sample_data_Shigella_Tree.txt version 1.0. dataset English. dataset licensed CC -NC-SA 4.0","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sample_data_Shigella_tree.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — sample_data_Shigella_tree","text":"linelist data accompany sequencing data routine surveillance samples collected Belgium 2013 2019. can used together Shigella_tree","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sample_data_Shigella_tree.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Linelist data to accompany next generation sequencing data of Shigella surveillance samples from Belgium 2013-2019 — sample_data_Shigella_tree","text":"Fischer, N. et al. Genomic epidemiology persistently circulating MDR Shigella sonnei strains associated men sex men (MSM) Belgium (2013-19) doi:10.1093/jac/dkab377","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Save Data Files to a Specified Directory — save_data","title":"Save Data Files to a Specified Directory — save_data","text":"save_data function saves dataset files (unzips necessary) based search criteria dataset name, language, group_identifier, unique_identifier. checks existence required files, files exist, either copied unzipped specified directory.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Save Data Files to a Specified Directory — save_data","text":"","code":"save_data(   name = NULL,   language = NULL,   group_identifier = NULL,   usage = NULL,   unique_identifier = NULL,   path = rstudioapi::selectDirectory() )"},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Save Data Files to a Specified Directory — save_data","text":"name (optional) string specifying name dataset save. language (optional) string specifying language dataset. used name, group_identifier, unique_identifier, function filter datasets based language. group_identifier (optional) string identifying group related datasets. provided, function return datasets within group unless criteria given. usage (optional) string representing datasets used. provided, function return datasets within group unless criteria given. unique_identifier (optional) string representing unique identifier dataset. path (optional) string specifying directory dataset files saved. provided, function prompt user select directory via rstudioapi::selectDirectory() function.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Save Data Files to a Specified Directory — save_data","text":"return value. function saves specified dataset files chosen directory. success failure message printed upon completion.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Save Data Files to a Specified Directory — save_data","text":"function assumes dataset files available \"extdata\" directory appliedepidata package. function follows steps: Dataset Lookup: looks dataset information using lookup_dataset based provided search criteria (name, language, group_identifier, usage unique_identifier). File Existence Check: checks required dataset files exist using list_data function. files missing, error message lists . File Copying Unzipping: files found, function copies files specified directory. files zipped (.zip), unzipped saved.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/save_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Save Data Files to a Specified Directory — save_data","text":"","code":"if (FALSE) { # \\dontrun{ # Save a dataset by name to a chosen directory save_data(name = \"AJS_AmTiman\", path = \"/path/to/save/directory\")  # Save a dataset by group identifier and language save_data(group_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016\", language = \"fr\")  # Save a dataset by unique identifier save_data(unique_identifier = \"acutejaundicesyndrome_outbreak_tcd_2016_linelist_1_1_outbreak_2016\") } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Search and Filter Datasets Available in appliedepidata — search_data","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"Search Filter Datasets Available appliedepidata","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"","code":"search_data()"},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"Shiny application object. function open Shiny app web browser executed.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"Launches interactive Shiny application allows users filter search dataset. Users can select language dropdown menu enter search query filter data displayed reactive table.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search and Filter Datasets Available in appliedepidata — search_data","text":"","code":"if (FALSE) { # \\dontrun{ # Launch the interactive data search application search_data() } # }"},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_adm3.html","id":null,"dir":"Reference","previous_headings":"","what":"Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange — sle_adm3","title":"Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange — sle_adm3","text":"Shapefile admin 3 level Sierra Leone Humanitarian Data Exchange","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_adm3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange — sle_adm3","text":"","code":"sle_adm3"},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_adm3.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange — sle_adm3","text":"shapefile 167 rows 20 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_adm3.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange — sle_adm3","text":"shapefile downloaded Humanitarian Data Exchange. edits made . original dataset sle_adm3.shp version 1.0. dataset English. dataset licensed CC -IGO","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_adm3.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Shapefile at admin 3 level for Sierra Leone from Humanitarian Data Exchange — sle_adm3","text":"shapefile can used together linelist_cleaned_with_adm3. Data collected government Sierra Leone cleaned pcoded UNOCHA ITOS Admin4 : Data provided OCHA, attribute fields geometries checked UNMEER IM (Ghana) replaced /official Government data provided","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_admpop_adm3_2020.html","id":null,"dir":"Reference","previous_headings":"","what":"Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange — sle_admpop_adm3_2020","title":"Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange — sle_admpop_adm3_2020","text":"Population data admin level 3 Sierra Leone Humanitarian Data Exchange","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_admpop_adm3_2020.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange — sle_admpop_adm3_2020","text":"","code":"sle_admpop_adm3_2020"},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_admpop_adm3_2020.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange — sle_admpop_adm3_2020","text":"shapefile 167 rows 20 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_admpop_adm3_2020.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange — sle_admpop_adm3_2020","text":"population data downloaded Humanitarian Data Exchange edits made . original dataset sle_admpop_adm3_2020.csv version 1.0. dataset English. dataset licensed CC -IGO","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/sle_admpop_adm3_2020.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Population data at admin level 3 for Sierra Leone from Humanitarian Data Exchange — sle_admpop_adm3_2020","text":"population data can used linelist_cleaned_with_adm3 sle_adm3.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"Linelist data fictionalized salmonella outbreak occured highschool Stegen, Germany (1998)","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"","code":"stegentira_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"data frame 291 rows 20 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"case study first designed Alain Moren Gilles Desve EPIET. based investigation conducted Anja Hauri, RKI, Berlin, 1998. Data fictional inspired Nygren et al. Tick-borne encephalitis: acute clinical manifestations severity 581 cases Germany, 2018-2020. Journal Infection. 2023 Apr 1;86(4):369-75 version 1.0 (appliedepidata package. Earlier data versions used EPIET considered) dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/stegentira_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Linelist for fictionalized salmonella outbreak in Stegen, Germany — stegentira_data","text":"fake case linelist individual level data clinical epidemiological information, focus foods eaten cafeteria (exposures)","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Fake data for a mortality survey — survey_data","title":"Fake data for a mortality survey — survey_data","text":"example fake dataset mortality survey generated using epidict package functions.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fake data for a mortality survey — survey_data","text":"","code":"survey_data"},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fake data for a mortality survey — survey_data","text":"data frames 1000 rows 55 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fake data for a mortality survey — survey_data","text":"data generated functions epidict package created part R4Epis project funded Doctors Without Borders (MSF) sappling nursery. original dataset 'survey_data.xlsx' version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fake data for a mortality survey — survey_data","text":"fake survey dataset. data merge, differs original data comes two parts: household level dataset ('Mortality Survey') individual level dataset ('hh_member'). can used together survey_dict. Please note, data entirely fictional created based Doctors without Borders (MSF) ethical review board pre-approved survey dictionaries. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_dict.html","id":null,"dir":"Reference","previous_headings":"","what":"Fake data dictionary for a mortality survey — survey_dict","title":"Fake data dictionary for a mortality survey — survey_dict","text":"example fake data dictionary mortality survey generated using epidict package functions.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_dict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fake data dictionary for a mortality survey — survey_dict","text":"","code":"survey_dict"},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_dict.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Fake data dictionary for a mortality survey — survey_dict","text":"dataframe 46 rows 14 columns","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_dict.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Fake data dictionary for a mortality survey — survey_dict","text":"data generated functions epidict package created part R4Epis project funded Doctors Without Borders (MSF) sappling nursery. original dataset 'mortality_survey_dict.xlsx' version 1.0. dataset English. dataset licensed GPL3","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/survey_dict.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fake data dictionary for a mortality survey — survey_dict","text":"fake data dictionary survey_data dataset. data dictionary originally ODK excel format using functions epidict transformed long format, can used recoding using matchmaker package. Please note, data entirely fictional created based Doctors without Borders (MSF) ethical review board pre-approved survey dictionaries. generated exclusively training purposes.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/world_standard_population_by_sex.html","id":null,"dir":"Reference","previous_headings":"","what":"World “standard population” by sex — world_standard_population_by_sex","title":"World “standard population” by sex — world_standard_population_by_sex","text":"reference population counts can used together country_demographics","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/world_standard_population_by_sex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"World “standard population” by sex — world_standard_population_by_sex","text":"","code":"world_standard_population_by_sex"},{"path":"https://appliedepi.github.io/appliedepidata/reference/world_standard_population_by_sex.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"World “standard population” by sex — world_standard_population_by_sex","text":"Dataframes","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/world_standard_population_by_sex.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"World “standard population” by sex — world_standard_population_by_sex","text":"data made available Public Health Scotland original dataset country_demographics.csv version 1.0. dataset English. dataset licensed OGL","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/world_standard_population_by_sex.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"World “standard population” by sex — world_standard_population_by_sex","text":"World standard population based populations 46 countries developed 1960. used produce world standardised rates. much ‘younger’ population compared population Scotland (Western European countries). Also, like European standard population, World standard population equal numbers males females within age band. However, World standard population ‘young’ population, generally less appropriate Scottish data European standard population used particular purposes. file split five year age groups sex","code":""},{"path":"https://appliedepi.github.io/appliedepidata/news/index.html","id":"appliedepidata-development-version","dir":"Changelog","previous_headings":"","what":"appliedepidata (development version)","title":"appliedepidata (development version)","text":"Initial CRAN submission.","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index a9dad01..08a95bf 100644
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