From 09403f999fb3894640ac92d5dd3feeccea7f66cb Mon Sep 17 00:00:00 2001 From: aspina7 Date: Mon, 9 Sep 2024 14:08:55 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20appliede?= =?UTF-8?q?pi/appliedepidata@19e5d7abef7434f13e2e0bccc95be6033954ead5=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/adding-data.html | 7 +-- pkgdown.yml | 2 +- reference/index.html | 4 +- reference/list_data.html | 107 +++++++++++++++++++++++++++++++++++++ reference/search_data.html | 88 ++++++++++++++++++++++++++++++ search.json | 2 +- sitemap.xml | 4 +- 7 files changed, 205 insertions(+), 9 deletions(-) create mode 100644 reference/list_data.html create mode 100644 reference/search_data.html diff --git a/articles/adding-data.html b/articles/adding-data.html index 6796441..1abeebf 100644 --- a/articles/adding-data.html +++ b/articles/adding-data.html @@ -77,6 +77,8 @@

Adding a new dataset to the package

repo folder structure

+

Read this r packages +chapter for details.

.
 ├── appliedepidata.Rproj
 ├── data
@@ -110,8 +112,7 @@ 
repo folder structure)’. Read this r packages chapter for
-details.
+folder e.g. ‘rio()’.
 
 
  • 
 data-raw usually contains R scripts which are used
@@ -317,7 +318,7 @@ 
    Data Entry Guide for Dataset Meta
 
 
 unique_identifier
-ebola_outbreak_lbr_2014_linelist_1| |                       | 1_outbreak_2014
+ebola_outbreak_lbr_2014_linelist_1_1_outbreak_2014
 
 
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 3613c48..a62a7b6 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   adding-data: adding-data.html
   available-data: available-data.html
-last_built: 2024-09-09T08:58Z
+last_built: 2024-09-09T14:08Z
 urls:
   reference: https://appliedepi.github.io/appliedepidata/reference
   article: https://appliedepi.github.io/appliedepidata/articles
diff --git a/reference/index.html b/reference/index.html
index 88dcd3f..d032330 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -47,13 +47,13 @@ 
    Functionslist_datasets()
+          list_data()
 
         
         
    List Datasets in a Package
    
       
    
 
-          search_datasets()
+          search_data()
 
         
    
         
    Search and Filter Datasets Available in appliedepidata
    
diff --git a/reference/list_data.html b/reference/list_data.html
new file mode 100644
index 0000000..abfea89
--- /dev/null
+++ b/reference/list_data.html
@@ -0,0 +1,107 @@
+
+List Datasets in a Package — list_data • appliedepidata
+    Skip to contents
+
+
+    
    
+
    
+  
    
+
+      
    List Datasets in a Package
    
+
+      
    list_data.Rd
    
+    
    
+
+    
    
+    
    This function lists all the files in the data,inst/extdata and
+internal binaries directories of a specified R package.
    
+    
    
+
+    
    
+    
    Usage
    
+    
    list_data(package_name = "appliedepidata")
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    package_name
    
+
    A character string specifying the name of the R package
+for which to list files. Defaults to "appliedepidata".
    
+
+
    
+    
    
+    
    Value
    
+    
    A data frame with two columns:
    directory
    
+
    The directory (data,extdata, intdata) where the
+file is located.
    
+
+
    file
    
+
    The name and file extension for each dataset found in
+directories.
    
+
+
    duplicate
    
+
    Logical vector (TRUE/FALSE) if the file name exists
+more than once. Only flags from the second occurrence. This is useful for
+packages which have not been built making .rda files internal
    
+
+
+
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# List all files in the directories of the "ggplot2" package
+files <- list_data(package_name = "ggplot2")
+print(files)
+} # }
+
+
    
+    
    
+  
    
+
+
+    
    
+  
    Developed by Alexander Spina.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+    
    
+
+
+
+
+
+  
+
diff --git a/reference/search_data.html b/reference/search_data.html
new file mode 100644
index 0000000..d390cc0
--- /dev/null
+++ b/reference/search_data.html
@@ -0,0 +1,88 @@
+
+Search and Filter Datasets Available in appliedepidata — search_data • appliedepidata
+    Skip to contents
+
+
+    
    
+
    
+  
    
+
+      
    Search and Filter Datasets Available in appliedepidata
    
+
+      
    search_data.Rd
    
+    
    
+
+    
    
+    
    Search and Filter Datasets Available in appliedepidata
    
+    
    
+
+    
    
+    
    Usage
    
+    
    search_data()
    
+    
    
+
+    
    
+    
    Value
    
+    
    A Shiny application object. This function will open the Shiny app in a web browser when executed.
    
+    
    
+    
    
+    
    Details
    
+    
    Launches an interactive Shiny application that allows users to filter and
+search a dataset.
+Users can select a language from a dropdown menu and enter a search query to
+filter the data displayed in a reactive table.
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# Launch the interactive data search application
+search_data()
+} # }
+
+
    
+    
    
+  
    
+
+
+    
    
+  
    Developed by Alexander Spina.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+    
    
+
+
+
+
+
+  
+
diff --git a/search.json b/search.json
index 5b57799..aa9601f 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"adding-a-new-dataset-to-the-package","dir":"Articles","previous_headings":"","what":"Adding a new dataset to the package","title":"adding-data","text":"guideline contributing datasets similar tidytuesday","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"repo-folder-structure","dir":"Articles","previous_headings":"","what":"repo folder structure","title":"adding-data","text":"data R datasets go data folder option adding messy datasets. However internalised .rda version described . internal data additional complication build package, can make Rda datasets (data folder) “internal” (efficient file storage, become part binary), access package::dataset. can also imported directly github using link file data folder e.g. ‘rio()’. Read r packages chapter details. data-raw usually contains R scripts used creating exported internal data (e.g. edited dataset, {usethis} internalises dataset) sysdata probably tableoftables just stay extdata alternatively go sysdata exported (.e. just package usage)","code":". ├── appliedepidata.Rproj ├── data │   └── newdata.rda ├── 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":"if-a-non-r-not--rda-file","dir":"Articles","previous_headings":"repo folder structure","what":"if a non-R (not .rda) file","title":"adding-data","text":"","code":"- name file what want but stick to guidelines described in metadata below - versioning of datasets (and edits thereof, e.g. same data for diff  bits of course) - define overarching source file and resulting child files (as per metadata below) - place file in 'inst/extdata' folder   - if adding a shapefile then zip it  - in console run 'usethis::use_data_raw() - read in the file with 'rio' and 'system.file' - make edits as needed - save with usethis::usedata() - add documentation for each data set added (ideally group these within the  same file if part of the same group of datasets)   - ideally: data dictionary used to fill in the *man* files for each (link to    function)   - probably do the same way [alison horst](https://github.com/lter/lterdatasampler/) does   - licensing: while the overall package repo will be GPL3, it is possible that individual datasets will come under a different license (so there needs to be a license section in documentation for each dataset)"},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"if-adding-an--rda-file","dir":"Articles","previous_headings":"repo folder structure","what":"if adding an .rda file:","title":"adding-data","text":"link appropriate part non-R onwards relevant","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"data-entry-guide-for-dataset-metadata","dir":"Articles","previous_headings":"","what":"Data Entry Guide for Dataset Metadata","title":"adding-data","text":"table explaining fill variable dataset metadata Excel sheet (1tablesoftables.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. 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/articles/available-data.html","id":"available-datasets","dir":"Articles","previous_headings":"","what":"Available datasets","title":"available-data","text":"can see available 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":[]},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"functions","dir":"","previous_headings":"stuff to consider","what":"functions","title":"Datasets used in Applied Epi courses and resources","text":"list available datasets needs tests (point idea ) ?necessary - rather new users freakout different ways accessing data) download/save dataset locally function (based tableoftables) decide help w/ {datadict} {epidict} just become fake data generator. odk example dictionary xlsxform function uses data dict create description section roxygen dataset phase 2 build helper functions create description file tableoftables (user just needs edit excel file) ?pull snapshots bit {gapminder} re changes datasets","code":""},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"documentation","dir":"","previous_headings":"stuff to consider","what":"Documentation","title":"Datasets used in Applied Epi courses and resources","text":"readme/pkgdown table (adapted tableoftables) listing available datasets, versions, languages, source, used (e.g. case study, course, tutorial, epirhandbook) ?pkgdown separated heading dictionaries actual datasets, cross-links two","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 GPL3","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 GPL3","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 GPL3","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 GPL3","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/list_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"List Datasets in a Package — list_datasets","title":"List Datasets in a Package — list_datasets","text":"function lists files data,inst/extdata internal binaries directories specified R package.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List Datasets in a Package — list_datasets","text":"","code":"list_datasets(package_name = \"appliedepidata\")"},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List Datasets in a Package — list_datasets","text":"package_name character string specifying name R package list files. Defaults \"appliedepidata\".","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List Datasets in a Package — list_datasets","text":"data frame two columns: directory directory (data,extdata, intdata) file located. file name file extension dataset found directories. duplicate Logical vector (TRUE/FALSE) file name exists . flags second occurrence. useful packages built making .rda files internal","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/list_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List Datasets in a Package — list_datasets","text":"","code":"if (FALSE) { # \\dontrun{ # List all files in the directories of the \"ggplot2\" package files <- list_datasets(package_name = \"ggplot2\") print(files) } # }"},{"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/search_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Search and Filter Datasets Available in appliedepidata — search_datasets","title":"Search and Filter Datasets Available in appliedepidata — search_datasets","text":"Search Filter Datasets Available appliedepidata","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search and Filter Datasets Available in appliedepidata — search_datasets","text":"","code":"search_datasets()"},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search and Filter Datasets Available in appliedepidata — search_datasets","text":"Shiny application object. function open Shiny app web browser executed.","code":""},{"path":"https://appliedepi.github.io/appliedepidata/reference/search_datasets.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Search and Filter Datasets Available in appliedepidata — search_datasets","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_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search and Filter Datasets Available in appliedepidata — search_datasets","text":"","code":"if (FALSE) { # \\dontrun{ # Launch the interactive data search application search_available_data() } # }"}]
+[{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"adding-a-new-dataset-to-the-package","dir":"Articles","previous_headings":"","what":"Adding a new dataset to the package","title":"adding-data","text":"guideline contributing datasets similar tidytuesday","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"repo-folder-structure","dir":"Articles","previous_headings":"","what":"repo folder structure","title":"adding-data","text":"Read r packages chapter details. data R datasets go data folder option adding messy datasets. However internalised .rda version described . internal data additional complication build package, can make Rda datasets (data folder) “internal” (efficient file storage, become part binary), access package::dataset. can also imported directly github using link file data folder e.g. ‘rio()’. data-raw usually contains R scripts used creating exported internal data (e.g. edited dataset, {usethis} internalises dataset) sysdata probably tableoftables just stay extdata alternatively go sysdata exported (.e. just package usage)","code":". ├── appliedepidata.Rproj ├── data │   └── newdata.rda ├── 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":"if-a-non-r-not--rda-file","dir":"Articles","previous_headings":"repo folder structure","what":"if a non-R (not .rda) file","title":"adding-data","text":"","code":"- name file what want but stick to guidelines described in metadata below - versioning of datasets (and edits thereof, e.g. same data for diff  bits of course) - define overarching source file and resulting child files (as per metadata below) - place file in 'inst/extdata' folder   - if adding a shapefile then zip it  - in console run 'usethis::use_data_raw() - read in the file with 'rio' and 'system.file' - make edits as needed - save with usethis::usedata() - add documentation for each data set added (ideally group these within the  same file if part of the same group of datasets)   - ideally: data dictionary used to fill in the *man* files for each (link to    function)   - probably do the same way [alison horst](https://github.com/lter/lterdatasampler/) does   - licensing: while the overall package repo will be GPL3, it is possible that individual datasets will come under a different license (so there needs to be a license section in documentation for each dataset)"},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"if-adding-an--rda-file","dir":"Articles","previous_headings":"repo folder structure","what":"if adding an .rda file:","title":"adding-data","text":"link appropriate part non-R onwards relevant","code":""},{"path":"https://appliedepi.github.io/appliedepidata/articles/adding-data.html","id":"data-entry-guide-for-dataset-metadata","dir":"Articles","previous_headings":"","what":"Data Entry Guide for Dataset Metadata","title":"adding-data","text":"table explaining fill variable dataset metadata Excel sheet (1tablesoftables.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. 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/articles/available-data.html","id":"available-datasets","dir":"Articles","previous_headings":"","what":"Available datasets","title":"available-data","text":"can see available 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":[]},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"functions","dir":"","previous_headings":"stuff to consider","what":"functions","title":"Datasets used in Applied Epi courses and resources","text":"list available datasets needs tests (point idea ) ?necessary - rather new users freakout different ways accessing data) download/save dataset locally function (based tableoftables) decide help w/ {datadict} {epidict} just become fake data generator. odk example dictionary xlsxform function uses data dict create description section roxygen dataset phase 2 build helper functions create description file tableoftables (user just needs edit excel file) ?pull snapshots bit {gapminder} re changes datasets","code":""},{"path":"https://appliedepi.github.io/appliedepidata/index.html","id":"documentation","dir":"","previous_headings":"stuff to consider","what":"Documentation","title":"Datasets used in Applied Epi courses and resources","text":"readme/pkgdown table (adapted tableoftables) listing available datasets, versions, languages, source, used (e.g. case study, course, tutorial, epirhandbook) ?pkgdown separated heading dictionaries actual datasets, cross-links two","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 GPL3","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 GPL3","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 GPL3","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 GPL3","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/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 two columns: directory directory (data,extdata, intdata) file located. file name file extension dataset found directories. duplicate Logical vector (TRUE/FALSE) file name 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/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/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() } # }"}]
diff --git a/sitemap.xml b/sitemap.xml
index a7945ba..8789497 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -12,9 +12,9 @@
 https://appliedepi.github.io/appliedepidata/reference/Quartiersshape.html
 https://appliedepi.github.io/appliedepidata/reference/create_desc.html
 https://appliedepi.github.io/appliedepidata/reference/index.html
-https://appliedepi.github.io/appliedepidata/reference/list_datasets.html
+https://appliedepi.github.io/appliedepidata/reference/list_data.html
 https://appliedepi.github.io/appliedepidata/reference/mortality_survey_data.html
 https://appliedepi.github.io/appliedepidata/reference/mortality_survey_dict.html
-https://appliedepi.github.io/appliedepidata/reference/search_datasets.html
+https://appliedepi.github.io/appliedepidata/reference/search_data.html