Merge pull request #305 from R4EPI/nb_outbreakWalk

Nb outbreak walk

DESCRIPTION

@@ -44,6 +44,7 @@ Imports:
     binom,
     broom,
     clipr,
+    cli,
     dplyr (>= 0.8.0),
     epitabulate (>= 0.0.0.9007),
     epidict (>= 0.0.0.9001),
@@ -68,6 +69,7 @@ Imports:
     rio,
     rlang (>= 0.4.0),
     rmarkdown,
+    rstudioapi,
     scales,
     sf,
     slider,
@@ -103,7 +105,8 @@ Collate:
     'epidict_exports.R'
     'epikit_exports.R'
     'epitabulate_exports.R'
-    'AJS_linelist.R'
-    'AJS_pop.R'
-    'quartier_shape.R'
-    'block_shape.R'
+    'AJS_linelist_internal.R'
+    'AJS_pop_internal.R'
+    'shape_quartier_internal.R'
+    'shape_block_internal.R'
+    'download_datasets.R'

NAMESPACE

@@ -18,6 +18,12 @@ export(check_sitrep_templates)
 export(constrain_dates)
 export(data_frame_from_2x2)
 export(dots_to_charlist)
+export(download_kobo)
+export(download_outbreak_linelist)
+export(download_outbreak_pop)
+export(download_shape_block)
+export(download_shape_quartier)
+export(download_survey)
 export(fac_from_num)
 export(find_breaks)
 export(find_date_cause)
@@ -47,6 +53,7 @@ export(tab_univariate)
 export(unite_ci)
 export(zcurve)
 importFrom(apyramid,age_pyramid)
+importFrom(cli,cli_alert_success)
 importFrom(dplyr,count)
 importFrom(epidict,gen_data)
 importFrom(epidict,msf_dict)
@@ -105,6 +112,7 @@ importFrom(glue,glue)
 importFrom(rlang,"!!")
 importFrom(rlang,":=")
 importFrom(rlang,.data)
+importFrom(rstudioapi,selectDirectory)
 importFrom(scales,percent_format)
 importFrom(stats,setNames)
 importFrom(tibble,as_tibble)

R/AJS_linelist.R → R/AJS_linelist_internal.R

@@ -11,7 +11,7 @@
 #'
 #' @docType data
 #'
-#' @usage data(AJS_linelist)
+#' @usage data(AJS_linelist_internal)
 #'
 #' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
 #'
@@ -23,6 +23,6 @@
 #' @source \href{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188240}{Article}
 #'
 #' @examples
-#' data(AJS_linelist)
-#' head(AJS_linelist)
-"AJS_linelist"
+#' data(AJS_linelist_internal)
+#' head(AJS_linelist_internal)
+"AJS_linelist_internal"

R/AJS_pop.R → R/AJS_pop_internal.R

@@ -1,6 +1,6 @@
 #' Example population data for Hepatatis E virus or Acute Jaundice Syndrome (AJS)
 #'
-#' Data from a real outbreak of Hepatitis E virus (HEV) infection which
+#' Population data from a real outbreak of Hepatitis E virus (HEV) infection which
 #' occurred in the Chadian town of Am Timan between October 2016 and
 #' April 2017. The Chadian Ministry of Health (MoH) has approved the use
 #'  of this data for training purposes.
@@ -11,7 +11,7 @@
 #'
 #' @docType data
 #'
-#' @usage data(AJS_pop)
+#' @usage data(AJS_pop_internal)
 #'
 #' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
 #'
@@ -23,6 +23,6 @@
 #' @source \href{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188240}{Article}
 #'
 #' @examples
-#' data(AJS_pop)
-#' head(AJS_pop)
-"AJS_pop"
+#' data(AJS_pop_internal)
+#' head(AJS_pop_internal)
+"AJS_pop_internal"

R/download_datasets.R

@@ -0,0 +1,118 @@
+#' @title Internal function (not exported - i.e. not userfacing) to reduce code duplication
+#'
+#' @param path **Run with no arguments to pick a directory interactively**. Path on your computer where the file(s) should be saved to *string*
+#' @param dataset The name of the file to save
+#'
+#' @importFrom rstudioapi selectDirectory
+#' @importFrom cli cli_alert_success
+
+generic_download <- function(path = rstudioapi::selectDirectory(), dataset){
+
+  ## normalise in case given manually
+  path <- normalizePath(path)
+
+  file_to_copy <- system.file(package = "sitrep", "extdata", dataset)
+
+  success <- lapply(file_to_copy, file.copy, to = path, overwrite = TRUE)
+
+  if(all(as.logical(success))) cli::cli_alert_success("File successfully saved here: {path}")
+
+}
+
+
+#' @title Access kobo data dictionary
+#'
+#' @param path **Run with no arguments to pick a directory interactively**. Path on your computer where the file(s) should be saved to *string*
+#'
+#' @importFrom rstudioapi selectDirectory
+#' @importFrom cli cli_alert_success
+#'
+#' @export
+download_kobo <- function(path = rstudioapi::selectDirectory()){
+
+  generic_download(path = path, dataset = "mortality_survey_dict.xlsx")
+
+}
+
+
+#' @title Access AJS outbreak linelist
+#'
+#' @param path **Run with no arguments to pick a directory interactively**. Path on your computer where the file(s) should be saved to *string*
+#'
+#' @importFrom rstudioapi selectDirectory
+#' @importFrom cli cli_alert_success
+#'
+#' @export
+download_outbreak_linelist <- function(path = rstudioapi::selectDirectory()){
+
+  generic_download(path = path, dataset = "AJS_AmTiman.xlsx")
+
+}
+
+
+#' @title Access AJS outbreak population data
+#'
+#' @param path **Run with no arguments to pick a directory interactively**. Path on your computer where the file(s) should be saved to *string*
+#'
+#' @importFrom rstudioapi selectDirectory
+#' @importFrom cli cli_alert_success
+#'
+#' @export
+download_outbreak_pop <- function(path = rstudioapi::selectDirectory()){
+
+  generic_download(path = path, dataset = "AJS_AmTiman_population.xlsx")
+
+}
+
+
+#' @title Access Am Timan blocks shapefile
+#'
+#' @param path **Run with no arguments to pick a directory interactively**. Path on your computer where the file(s) should be saved to *string*
+#'
+#' @importFrom rstudioapi selectDirectory
+#' @importFrom cli cli_alert_success
+#'
+#' @export
+download_shape_block <- function(path = rstudioapi::selectDirectory()){
+
+  included_files <- list.files(system.file(package = "sitrep", "extdata"))
+
+  dataset <- included_files[grep("Blocksshape", included_files)]
+
+  generic_download(path = path, dataset = dataset)
+
+}
+
+
+#' @title Access Am Timan quartier shapefile
+#'
+#' @param path **Run with no arguments to pick a directory interactively**. Path on your computer where the file(s) should be saved to *string*
+#'
+#' @importFrom rstudioapi selectDirectory
+#' @importFrom cli cli_alert_success
+#'
+#' @export
+download_shape_quartier <- function(path = rstudioapi::selectDirectory()){
+
+  included_files <- list.files(system.file(package = "sitrep", "extdata"))
+
+  dataset <- included_files[grep("Quartiersshape", included_files)]
+
+  generic_download(path = path, dataset = dataset)
+
+}
+
+
+#' @title Access fake mortality survey data
+#'
+#' @param path **Run with no arguments to pick a directory interactively**. Path on your computer where the file(s) should be saved to *string*
+#'
+#' @importFrom rstudioapi selectDirectory
+#' @importFrom cli cli_alert_success
+#'
+#' @export
+download_survey <- function(path = rstudioapi::selectDirectory()){
+
+  generic_download(path = path, dataset = "mortality_survey_data.xlsx")
+
+}

R/block_shape.R → R/shape_block_internal.R

@@ -11,7 +11,7 @@
 #'
 #' @docType data
 #'
-#' @usage data(block_shape)
+#' @usage data(shape_block_internal)
 #'
 #' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
 #'
@@ -23,6 +23,6 @@
 #' @source \href{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188240}{Article}
 #'
 #' @examples
-#' data(block_shape)
-#' head(block_shape)
-"block_shape"
+#' data(shape_block_internal)
+#' head(shape_block_internal)
+"shape_block_internal"

R/quartier_shape.R → R/shape_quartier_internal.R

@@ -11,7 +11,7 @@
 #'
 #' @docType data
 #'
-#' @usage data(quartier_shape)
+#' @usage data(shape_quartier_internal)
 #'
 #' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
 #'
@@ -23,6 +23,6 @@
 #' @source \href{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188240}{Article}
 #'
 #' @examples
-#' data(quartier_shape)
-#' head(quartier_shape)
-"quartier_shape"
+#' data(shape_quartier_internal)
+#' head(shape_quartier_internal)
+"shape_quartier_internal"