ausmisten

R/AJS_chad_doc.R

@@ -1,28 +1,143 @@
-#' @title Data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016
+#' @title Linelist data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016
 #'
 #' @description
-#' Data from a real outbreak of Hepatitis E virus (HEV) infection which
+#' 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. 
 #'  
 #' @details
+#' This is a case-linelist which contains de-indentified individual level data 
+#' on clinical, laboratory and epidemiological information. It can be used 
+#' together with \link{AJS_AmTiman_population}, \link{Blocksshape} and 
+#' \link{Quartiersshape}. 
 #' Please note, that some data has been adapted in order to best achieve
 #' training objectives. Also, the GPS coordinates included in the dataset
 #' do not correspond to real cases identified during this outbreak.
 #' They have been generated exclusively for training purposes.
 #'  
 #' @source This data was collected as part of Doctors Without Borders (MSF) outbreak 
 #' response and the the Ministry of Health (MoH) in Chad has approved the use 
-#' of this data for training purposes.
+#' of this data for training purposes. 
+#'  
+#' This is version 1.0.  
+#' 
+#' This dataset is English.   
+#' 
 #' This dataset is licensed under [GPL3](https://www.gnu.org/licenses/gpl-3.0.html) 
 #' 
 #' @references {Spina A, Lenglet A, et al. (2017) A large outbreak of Hepatitis E virus genotype 1 infection in an urban setting in Chad likely linked to household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240} \doi{10.1371/journal.pone.0188240}
+#' 
 #' @format A data frame with 1477 rows and 122 columns:
 #' \describe{
-#'   \item{blabla}{explanation of a variable}
-#'   \item{blabla}{more explanation of variables}
+#'   \item{variable1}{explanation of a variable}
+#'   \item{variable2}{more explanation of variables}
 #' }
 #' 
 #' @docType data
-#' @name AJS_chad
 "AJS_AmTiman"
+
+
+
+
+
+#' @title Population data from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016
+#'
+#' @description
+#' Population 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. 
+#'  
+#' @details
+#' This contains population counts for houses and individuals in each of 
+#' the housing blocks found in \link{Blocksshape} and can also be used together 
+#' with \link{AJS_AmTiman}. 
+#'  
+#' @source This data was collected as part of Doctors Without Borders (MSF) outbreak 
+#' response and the the Ministry of Health (MoH) in Chad has approved the use 
+#' of this data for training purposes. 
+#'  
+#' This is version 1.0.  
+#' 
+#' This dataset is English.   
+#' 
+#' This dataset is licensed under [GPL3](https://www.gnu.org/licenses/gpl-3.0.html) 
+#' 
+#' @references {Spina A, Lenglet A, et al. (2017) A large outbreak of Hepatitis E virus genotype 1 infection in an urban setting in Chad likely linked to household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240} \doi{10.1371/journal.pone.0188240}
+#' 
+#' @format A data frame with 648 rows and 3 columns:
+#' \describe{
+#'   \item{variable1}{explanation of a variable}
+#'   \item{variable2}{more explanation of variables}
+#' }
+#' 
+#' @docType data
+"AJS_AmTiman_population"
+
+
+#' @title Shapefile of housing blocks from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016
+#'
+#' @description
+#' Shapefile 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. 
+#'  
+#' @details
+#' This contains a shapefile for housing blocks which correspond with the population
+#' counts found in \link{AJS_AmTiman_population} and can also be used together 
+#' with \link{AJS_AmTiman}. 
+#'  
+#' @source This data was collected as part of Doctors Without Borders (MSF) outbreak 
+#' response and the the Ministry of Health (MoH) in Chad has approved the use 
+#' of this data for training purposes. 
+#'  
+#' This is version 1.0.  
+#' 
+#' This dataset is English.   
+#' 
+#' This dataset is licensed under [GPL3](https://www.gnu.org/licenses/gpl-3.0.html) 
+#' 
+#' @references {Spina A, Lenglet A, et al. (2017) A large outbreak of Hepatitis E virus genotype 1 infection in an urban setting in Chad likely linked to household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240} \doi{10.1371/journal.pone.0188240}
+#' 
+#' @format A data frame with 650 rows and 3 columns:
+#' \describe{
+#'   \item{variable1}{explanation of a variable}
+#'   \item{variable2}{more explanation of variables}
+#' }
+#' 
+#' @docType data
+"Blocksshape"
+
+
+
+#' @title Shapefile of neighbourhoods (*fr*: quartiers) from an outbreak of Acute Jaundice Syndrome (AJS) in Chad 2016
+#'
+#' @description
+#' Shapefile 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. 
+#'  
+#' @details
+#' This contains a shapefile for neighbourhoods which correspond with the population
+#' counts found in \link{AJS_AmTiman_population} and can also be used together 
+#' with \link{AJS_AmTiman}. 
+#'  
+#' @source This data was collected as part of Doctors Without Borders (MSF) outbreak 
+#' response and the the Ministry of Health (MoH) in Chad has approved the use 
+#' of this data for training purposes. 
+#'  
+#' This is version 1.0.  
+#' 
+#' This dataset is English.   
+#' 
+#' This dataset is licensed under [GPL3](https://www.gnu.org/licenses/gpl-3.0.html) 
+#' 
+#' @references {Spina A, Lenglet A, et al. (2017) A large outbreak of Hepatitis E virus genotype 1 infection in an urban setting in Chad likely linked to household level transmission factors, 2016-2017. PLoS ONE 12(11): e0188240} \doi{10.1371/journal.pone.0188240}
+#' 
+#' @format A data frame with 34 rows and 3 columns:
+#' \describe{
+#'   \item{variable1}{explanation of a variable}
+#'   \item{variable2}{more explanation of variables}
+#' }
+#' 
+#' @docType data
+"Quartiersshape"

R/list_datasets.R

@@ -1,4 +1,4 @@
-#' @title List Files in a Package
+#' @title List Datasets in a Package
 #'
 #' @description
 #' This function lists all the files in the `data`,`inst/extdata` and 
@@ -20,7 +20,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' # List all files in the data and inst directories of the "ggplot2" package
+#' # List all files in the directories of the "ggplot2" package
 #' files <- list_datasets(package_name = "ggplot2")
 #' print(files)
 #' }

R/sitrep_surveys_doc.R

@@ -0,0 +1,44 @@
+#' @title Fake data for a mortality survey
+#'
+#' @description
+#' This is an example fake dataset of a mortality survey which was generated 
+#' using \pkg{epidict} functions. 
+#'  
+#' @details
+#' This is a fake survey dataset . This data comes in two parts: 
+#' a household level dataset ('Mortality Survey') and an individual 
+#' level dataset ('hh_member'). It can be used together with \link{mortality_survey_dict}. 
+#' 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.
+#'  
+#' @source This data was generated with functions from the 
+#' [epidict](https://r4epi.github.io/epidict/index.html) package which was created 
+#' as part of the R4Epis project funded by the Doctors Without Borders (MSF) 
+#' sappling nursery.
+#'  
+#' This is version 1.0.  
+#' 
+#' This dataset is English.   
+#' 
+#' This dataset is licensed under [GPL3](https://www.gnu.org/licenses/gpl-3.0.html) 
+#' 
+#' @format Two data frames, 'Mortality Survey' with 424 rows and 16 columns, and 
+#' 'hh_member' with 2874 rows and 24 columns:
+#' 
+#' \strong{Mortality Survey}
+#' \describe{
+#'   \item{variable1}{Description of variable1}
+#'   \item{variable2}{Description of variable2}
+#'   # Add more variables as needed
+#' }
+#' 
+#' \strong{hh_member}
+#' \describe{
+#'   \item{variable1}{Description of variable1}
+#'   \item{variable2}{Description of variable2}
+#'   # Add more variables as needed
+#' }
+#' 
+#' @docType data
+"mortality_survey_data"

_pkgdown.yml

@@ -10,4 +10,11 @@ reference:
 
 - title: Data 
   contents: 
-  - AJS_AmTiman
+
+  - subtitle: AJS in Am Timan, Chad (2016) - English 
+    contents:
+    - AJS_AmTiman
+    - AJS_AmTiman_population
+
+  - subtitle: {Sitrep} example datasets - English
+    - mortality_survey_data

data-raw/mortality_survey_data.R

@@ -1,6 +1,10 @@
 ## code to prepare `mortality_survey_data` dataset goes here
 # This creates an .rda format of the mortality_survey_data.xlsx file
 
+
+### NOTE: these datasets were created using epidict::gen_data and msf_dict_survey
+# eventually this script should be updated to reflect that 
+
 # Define the path to the Excel file in inst/extdata
 file_path <- system.file("extdata", "mortality_survey_data.xlsx", package = "appliedepidata")
 

data-raw/mortality_survey_dict.R

@@ -1,6 +1,9 @@
 ## code to prepare `mortality_survey_dict` dataset goes here
 # This creates an .rda format of the mortality_survey_dict.xlsx file
 
+### NOTE: these datasets were created using epidict::gen_data and msf_dict_survey
+# eventually this script should be updated to reflect that 
+
 # Define the path to the Excel file in inst/extdata
 file_path <- system.file("extdata", "mortality_survey_dict.xlsx", package = "appliedepidata")