Refactor data wrangling for wrangling age and enhance unit test

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mwanaApp
 Title: mwana GUI
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: 
     person(given = "Tomás", 
             family = "Zaba",

NEWS.md

@@ -1,3 +1,23 @@
+# mwanaApp 0.2.0
+
+### New features ✨
+
++ Enabled estimation of age in months from the date of data collection and the 
+child’s date of birth, and added a corresponding note in the user guide.
+
+### General updates 
+
++ Revised the documentation for the app’s user‑interface and server modules.
+
+### Bug fixes 
+
++ Resolved an issue in which the app’s user interface failed to display the input
+ field for supplying survey weights in the weight‑for‑height- and combined‑prevalence 
+ tabs.
+
++ Resolved an issue where hyperlinks in the app were directing users to a 
+non‑existent page.
+
 ## mwanaApp v0.1.0
 
-+ First release of a feature-complete app.
++ First release of a feature-complete app.

R/module-data-upload.R

@@ -5,9 +5,10 @@
 #'
 #'
 #' @param id Module ID
-#'
+#' @rdname module-id
+#' 
 #' @keywords internal
-#'
+#' 
 #'
 module_ui_upload <- function(id) {
   ## Namespace ID's ----
@@ -94,9 +95,10 @@ module_ui_upload <- function(id) {
 #'
 #' Module server for data upload
 #'
+#' @rdname module-id
 #'
-#' @param id Module ID
-#'
+#' @returns A reactive data object to be used in data wrangling tab.
+#' 
 #' @keywords internal
 #'
 #'

R/module-data-wrangling.R

@@ -6,8 +6,7 @@
 #'
 #' Module UI for data wrangling
 #'
-#' @param id Module ID
-#'
+#' @rdname module-id
 #'
 #' @keywords internal
 #'
@@ -64,7 +63,7 @@ module_ui_wrangling <- function(id) {
           style = "font-size: 15px; font-weight: bold;"
         )),
 
-        #### A Placehoder for wrangled data and embed user feedback ----
+        #### A Placeholder for wrangled data and embed user feedback ----
         shinycssloaders::withSpinner(
           ui_element = DT::DTOutput(outputId = ns("wrangled")),
           type = 8,
@@ -82,7 +81,7 @@ module_ui_wrangling <- function(id) {
           )
         ),
 
-        #### Placeholder for donwload button ----
+        #### Placeholder for download button ----
         shiny::uiOutput(outputId = ns("download_wrangled_data"))
       )
     )
@@ -98,7 +97,11 @@ module_ui_wrangling <- function(id) {
 #' Module server for data wrangling
 #'
 #' @param id Module ID
-#'
+#' 
+#' @param data An output and reactive data object from previous tab.
+#' 
+#' @returns A reactive data object wrangled and ready to be used in plausibility 
+#' checks and prevalence analysis tabs.
 #'
 #' @keywords internal
 #'
@@ -175,31 +178,67 @@ module_server_wrangling <- function(id, data) {
             w <- switch(EXPR = input$wrangle,
               "wfhz" = {
                 shiny::req(input$sex, input$weight, input$height)
-                data() |>
-                  dplyr::rename(
+
+                ### Wrangle age dynamically ----
+                df <- if (nzchar(input$dos)) {
+                  dplyr::mutate(
+                    .data = data(),
+                    dos = as.Date(!!rlang::sym(input$dos), format = "%d/%m/%Y"),
+                    dob = as.Date(!!rlang::sym(input$dob), format = "%d/%m/%Y"),
+                    age = as.numeric(!!rlang::sym(input$age)),
                     sex = !!rlang::sym(input$sex),
                     weight = !!rlang::sym(input$weight),
                     height = !!rlang::sym(input$height)
                   ) |>
+                    mwana::mw_wrangle_age(.data$dos, .data$dob, .data$age)
+                } else {
+                  dplyr::mutate(
+                    .data = data(), 
+                    dos = NULL, 
+                    dob = NULL,
+                    sex = !!rlang::sym(input$sex),
+                    weight = !!rlang::sym(input$weight),
+                    height = !!rlang::sym(input$height)
+                  )
+                }
+
+                 ### Wrangle WFHZ data ----
+                df |>
                   mwana::mw_wrangle_wfhz(
                     sex = .data$sex,
                     .recode_sex = TRUE,
                     weight = .data$weight,
                     height = .data$height
                   )
               },
+
               "mfaz" = {
                 shiny::req(input$age, input$sex, input$muac)
 
-                data() |>
+                ### Wrangle age dynamically ----
+                df <- if (nzchar(input$dos)) {
                   dplyr::mutate(
-                    muac = mwana::recode_muac(x = !!rlang::sym(input$muac), .to = "cm")
+                    .data = data(),
+                    muac = mwana::recode_muac(!!rlang::sym(input$muac), "cm"),
+                    dos = as.Date(!!rlang::sym(input$dos), format = "%d/%m/%Y"),
+                    dob = as.Date(!!rlang::sym(input$dob), format = "%d/%m/%Y"),
+                    age = as.numeric(!!rlang::sym(input$age)),
+                    sex = !!rlang::sym(input$sex)
                   ) |>
-                  dplyr::rename(
-                    age = !!rlang::sym(input$age),
+                    mwana::mw_wrangle_age(.data$dos, .data$dob, .data$age)
+                } else {
+                  dplyr::mutate(
+                    .data = data(),
+                    muac = mwana::recode_muac(!!rlang::sym(input$muac), "cm"),
+                    dos = NULL,
+                    dob = NULL,
                     sex = !!rlang::sym(input$sex)
                   ) |>
-                  mwana::mw_wrangle_age(dos = NULL, dob = NULL, age = .data$age) |>
+                    mwana::mw_wrangle_age(NULL, NULL, .data$age)
+                }
+
+                ### Wrangle MUAC ----
+                df |>
                   mwana::mw_wrangle_muac(
                     sex = .data$sex,
                     .recode_sex = TRUE,
@@ -232,23 +271,40 @@ module_server_wrangling <- function(id, data) {
                   input$muac
                 )
 
-                data() |>
+                ### Wrangle age dynamically ----
+                df <- if (nzchar(input$dos)) {
                   dplyr::mutate(
-                    muac = mwana::recode_muac(x = !!rlang::sym(input$muac), .to = "cm")
+                    .data = data(),
+                    muac = mwana::recode_muac(!!rlang::sym(input$muac), "cm"),
+                    dos = as.Date(!!rlang::sym(input$dos), format = "%d/%m/%Y"),
+                    dob = as.Date(!!rlang::sym(input$dob), format = "%d/%m/%Y"),
+                    age = as.numeric(!!rlang::sym(input$age)),
+                    sex = !!rlang::sym(input$sex),
+                    weight = !!rlang::sym(input$weight),
+                    height = !!rlang::sym(input$height)
                   ) |>
-                  dplyr::rename(
-                    age = !!rlang::sym(input$age),
+                    mwana::mw_wrangle_age(.data$dos, .data$dob, .data$age)
+                } else {
+                  dplyr::mutate(
+                    .data = data(),
+                    muac = mwana::recode_muac(!!rlang::sym(input$muac), "cm"),
+                    dos = NULL,
+                    dob = NULL,
                     sex = !!rlang::sym(input$sex),
                     weight = !!rlang::sym(input$weight),
                     height = !!rlang::sym(input$height)
                   ) |>
+                    mwana::mw_wrangle_age(NULL, NULL, .data$age)
+                }
+
+                ### Wrangle WHZ and MUAC data ----
+                df |>
                   mwana::mw_wrangle_wfhz(
                     sex = .data$sex,
                     .recode_sex = TRUE,
                     weight = .data$weight,
                     height = .data$height
                   ) |>
-                  mwana::mw_wrangle_age(dos = NULL, dob = NULL, age = .data$age) |>
                   mwana::mw_wrangle_muac(
                     sex = .data$sex,
                     .recode_sex = FALSE,

R/module-helpers-data-wrangling.R

@@ -5,8 +5,17 @@
 #'
 #'
 #' Display input variables dynamically, according to UI for screening
-#'
-#'
+#' 
+#' @param vars An object holding the data variable names. This is used to display
+#' all the variables in the input variable of the ui. 
+#' 
+#' @param method User-selected method for data wrangling.
+#' 
+#' @param ns A placeholder for Shiny module namespace.
+#' 
+#' @returns A set of input variables specific for the user-selected data-wrangling 
+#' method.
+#' 
 #' @keywords internal
 #'
 #'

R/module-helpers-ipc-check.R

@@ -8,8 +8,18 @@
 #'
 #'
 #' Display input variables dynamically, according to UI for screening
+#' 
+#' @param vars An object holding the data variable names. This is used to display
+#' all the variables in the input variable of the UI. 
+#' 
+#' @param source User-selected source of data. As in the underlying method 
+#' used to collect the data. Choices are survey, screening and sentinel.
 #'
-#'
+#' @param ns A placeholder for Shiny module namespace.
+#' 
+#' @returns A set of input variables specific for the user-selected source of 
+#' data.
+#' 
 #' @keywords internal
 #'
 #'
@@ -103,7 +113,14 @@ mod_ipccheck_display_input_variables <- function(vars, source, ns) {
 #' Invoke mwana's IPC Acute Malnutrition minimum sample size requirement checker
 #' from within the module server
 #'
-#'
+#' @param df,cluster,source,area1,area2 Input variables collected from the UI
+#' and required to pass to mwana::mw_check_ipcamn_ssreq() function.
+#' 
+#' @returns A summary tibble containing check results for:
+#' + n_clusters - the total number of unique clusters or screening or site identifiers;
+#' + n_obs - the corresponding total number of children in the dataset; and,
+#' + meet_ipc - whether the IPC AMN requirements were met.
+#' 
 #' @keywords internal
 #'
 #'

R/module-helpers-plausibility-check.R

@@ -6,7 +6,8 @@
 #'
 #' Display input variables dynamically, according to UI for screening
 #'
-#' @keywords internal
+#' @inheritParams mod_data_wrangling_display_input_variables
+#' 
 #'
 mod_plausibility_display_input_variables <- function(vars, method, ns) {
   ### Base inputs always shown
@@ -132,16 +133,21 @@ mod_plausibility_display_input_variables <- function(vars, method, ns) {
   inputs_vars
 }
 
+
 #'
 #'
 #' Invoke mwana's plausibility checkers dynamically from within module server,
 #' according to user specifications in the UI
 #'
-#'
+#' @param df,age,sex,muac,weight,height,flags,area1,area2,area3,.for Input 
+#' variables collected from the UI and required to pass to 
+#' mwana::mw_plausibility_check_wfhz().
+#' 
+#' @returns A single-row summary tibble with columns containing the plausibility 
+#' check results.
+#' 
 #' @keywords internal
 #'
-#'
-#'
 mod_plausibility_call_checker <- function(
     df, age = NULL, sex, muac = NULL, weight = NULL,
     height = NULL, flags, area1, area2, area3, .for = c("wfhz", "muac", "mfaz")) {