Increase test coverage

README.md

@@ -1,6 +1,6 @@
 
 
-# mwanaApp: A seamless graphical interface to the mwana R package for data wrangling, plausibility checks, and prevalence estimation
+# mwanaApp: A graphical interface to the `mwana` R package for data wrangling, plausibility checks, and prevalence estimation of wasting
 
 <!-- badges: start -->
 
@@ -33,7 +33,7 @@ The App can be installed from GitHub:
 
 ``` r
 # First install remotes package with: install.package("remotes")
-# The install mwana package from GitHub with: 
+# The install mwana package from GitHub with:
 remotes::install_github(repo = "mphimo/mwanaApp", dependencies = TRUE)
 ```
 

README.qmd

@@ -2,7 +2,7 @@
 format: gfm
 ---
 
-# mwanaApp: A seamless graphical interface to the mwana R package for data wrangling, plausibility checks, and prevalence estimation
+# mwanaApp: A graphical interface to the `mwana` R package for data wrangling, plausibility checks, and prevalence estimation of wasting
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/mphimo/mwanaApp/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mphimo/mwanaApp/actions/workflows/R-CMD-check.yaml)
@@ -32,7 +32,7 @@ The App can be installed from GitHub:
 #| eval: false
 
 # First install remotes package with: install.package("remotes")
-# The install mwana package from GitHub with: 
+# The install mwana package from GitHub with:
 remotes::install_github(repo = "mphimo/mwanaApp", dependencies = TRUE)
 ```
 

tests/testthat/fixtures/anthro-03.csv

@@ -0,0 +1,45 @@
+survey_area,survdate,cluster,team,id,hh,sex,birthdat,age,months,weight,height,oedema
+District A,03/04/2026,2,2,,2,m,04/07/2023,,32.99,16.4,94.3,n
+District A,03/04/2026,2,2,,2,f,01/05/2025,,11.07,9.7,76.2,n
+District A,03/04/2026,2,2,,6,m,03/08/2023,,32,13.3,95.6,n
+District A,03/04/2026,2,2,,5,m,22/08/2025,,7.36,8.2,65,n
+District A,03/04/2026,2,2,,10,f,02/04/2023,,36.04,13.1,97.4,n
+District A,03/04/2026,2,2,,10,f,20/05/2024,,22.44,9.4,81.5,n
+District A,03/04/2026,2,2,,14,f,10/04/2025,,11.76,8.4,75.7,n
+District A,03/04/2026,3,3,,5,m,23/11/2023,,28.32,11.1,85,n
+District A,03/04/2026,3,3,,5,m,17/03/2025,,12.55,7.7,69.7,n
+District A,03/04/2026,4,4,,2,f,02/08/2022,,44.02,11.7,97.1,n
+District A,03/04/2026,4,4,,2,f,10/06/2024,,21.75,9.2,80,n
+District A,03/04/2026,4,4,,4,m,20/09/2025,,6.41,5.6,64.4,n
+District A,03/04/2026,4,4,,8,f,09/06/2024,,21.78,9.1,76.6,n
+District A,04/04/2026,6,2,,9,f,21/09/2025,,6.41,6.5,65.7,n
+District A,04/04/2026,4,4,,2,f,09/02/2025,,13.77,6.4,63,n
+District A,05/04/2026,9,1,,1,m,02/09/2025,,7.06,7.2,67,n
+District A,05/04/2026,9,1,,2,m,06/05/2025,,10.97,6.9,67,n
+District A,05/04/2026,12,4,,2,m,05/05/2025,,11.01,7.4,72.5,n
+District A,05/04/2026,12,4,,14,f,11/08/2025,,7.79,5.8,65,n
+District A,05/04/2026,12,4,,16,m,09/03/2025,,12.88,5.5,65,n
+District A,05/04/2026,12,4,,19,m,07/03/2025,,12.94,5.9,65.3,n
+District A,06/04/2026,14,2,,5,f,10/09/2025,,6.83,6.5,64,n
+District A,06/04/2026,14,2,,14,f,22/03/2025,,12.48,5,65.2,n
+District A,06/04/2026,16,4,,2,m,07/02/2025,,13.9,10.1,73.5,n
+District A,06/04/2026,16,4,,6,f,10/04/2025,,11.86,9.1,78.5,n
+District A,06/04/2026,16,4,,10,f,03/12/2022,,40.08,13.8,90,n
+District A,06/04/2026,16,4,,10,f,03/05/2025,,11.1,7.3,77.2,n
+District A,06/04/2026,16,4,,14,m,06/08/2025,,7.98,8,70,n
+District A,07/04/2026,20,4,,2,f,10/07/2025,,8.9,6.1,65.7,n
+District A,07/04/2026,20,4,,6,f,05/02/2025,,14,6.9,65.9,n
+District A,07/04/2026,20,4,,14,f,10/07/2025,,8.9,5.6,65.5,n
+District A,08/04/2026,24,4,,2,f,12/07/2025,,8.87,7.3,70.4,n
+District A,08/04/2026,24,4,,8,f,10/09/2025,,6.9,7.5,68.4,n
+District A,08/04/2026,24,4,,10,m,04/08/2025,,8.11,6.7,66.6,n
+District A,08/04/2026,24,4,,12,m,06/07/2025,,9.07,5.6,65.1,n
+District A,09/04/2026,28,4,,4,f,07/04/2025,,12.06,7.8,74.5,n
+District A,09/04/2026,28,4,,9,f,12/07/2025,,8.9,5.3,66.3,n
+District A,09/04/2026,28,4,,16,m,10/06/2025,,9.95,6.5,69,n
+District A,09/04/2026,28,4,,17,m,13/09/2025,,6.83,4.9,60.1,n
+District A,10/04/2026,29,1,,5,f,04/08/2025,,8.18,6.3,64.4,n
+District A,10/04/2026,32,4,,2,m,04/04/2025,,12.19,7.3,70.5,n
+District A,10/04/2026,32,4,,8,f,08/04/2025,,12.06,5.3,66.5,n
+District A,10/04/2026,32,4,,14,m,11/06/2025,,9.95,6.7,69.5,n
+District A,11/04/2026,33,1,,17,f,27/08/2025,,7.46,6,63.6,n

tests/testthat/test-module-prevalence.R

@@ -69,6 +69,9 @@ testthat::test_that(desc = "Module works well to estimate weighted-WFHZ prevalen
   ### Click on Estime Prevalence button ----
   app$click(input = "prevalence-estimate")
   app$wait_for_value(output = "prevalence-results", timeout = 40000)
+  #### Donwload results ----
+  app$wait_for_idle(timeout = 40000)
+  results <- app$get_download(output = "prevalence-download_results")
 
   ### Capture JavaScript expressions to return results's cols and values ----
   js_cols <- "$('#prevalence-results thead th').map(function()
@@ -90,6 +93,15 @@ testthat::test_that(desc = "Module works well to estimate weighted-WFHZ prevalen
   testthat::expect_equal(length(app$get_js(js_cols)[1:19]), 19)
   testthat::expect_equal(as.numeric(weighted_pop), 292611)
   testthat::expect_equal(as.numeric(gam_prev), 6.1)
+  testthat::expect_equal(
+    object = basename(results),
+    paste0(
+      "mwana-amn-prevalence-survey-wfhz_",
+      Sys.Date(),
+      ".xlsx",
+      sep = ""
+    )
+  )
 
   ### Stop the app ----
   app$stop()
@@ -161,6 +173,9 @@ testthat::test_that(desc = "Module works well to estimate unweighted-WFHZ preval
   ### Click on Estime Prevalence button ----
   app$click(input = "prevalence-estimate")
   app$wait_for_value(output = "prevalence-results", timeout = 40000)
+  #### Donwload results ----
+  app$wait_for_idle(timeout = 40000)
+  results <- app$get_download(output = "prevalence-download_results")
 
   ### Capture JavaScript expressions to return results's cols and values ----
   js_cols <- "$('#prevalence-results thead th').map(function()
@@ -178,6 +193,15 @@ testthat::test_that(desc = "Module works well to estimate unweighted-WFHZ preval
   testthat::expect_equal(length(app$get_js(js_cols)[1:19]), 19)
   testthat::expect_equal(as.numeric(pop), 280)
   testthat::expect_equal(as.numeric(gam_prev), 6.1)
+  testthat::expect_equal(
+    object = basename(results),
+    paste0(
+      "mwana-amn-prevalence-survey-wfhz_",
+      Sys.Date(),
+      ".xlsx",
+      sep = ""
+    )
+  )
 
   ### Stop the app ----
   app$stop()
@@ -254,6 +278,9 @@ testthat::test_that(desc = "Module works well to estimate weighted-MUAC prevalen
   ### Click on Estime Prevalence button ----
   app$click(input = "prevalence-estimate")
   app$wait_for_value(output = "prevalence-results", timeout = 40000)
+  #### Donwload results ----
+  app$wait_for_idle(timeout = 40000)
+  results <- app$get_download(output = "prevalence-download_results")
 
   ### Capture JavaScript expressions to return results's cols and values ----
   js_cols <- "$('#prevalence-results thead th').map(function()
@@ -283,6 +310,15 @@ testthat::test_that(desc = "Module works well to estimate weighted-MUAC prevalen
   testthat::expect_equal(length(app$get_js(js_cols)[1:19]), 19)
   testthat::expect_equal(as.numeric(prev[2]), 7.7) # GAM
   testthat::expect_equal(as.numeric(weighted_pop), 307395)
+  testthat::expect_equal(
+    object = basename(results),
+    paste0(
+      "mwana-amn-prevalence-survey-muac_",
+      Sys.Date(),
+      ".xlsx",
+      sep = ""
+    )
+  )
 
   ### Stop the app ----
   app$stop()
@@ -359,6 +395,9 @@ testthat::test_that(desc = "Module works well to estimate unweighted-MUAC preval
   ### Click on Estime Prevalence button ----
   app$click(input = "prevalence-estimate")
   app$wait_for_value(output = "prevalence-results", timeout = 40000)
+  #### Donwload results ----
+  app$wait_for_idle(timeout = 40000)
+  results <- app$get_download(output = "prevalence-download_results")
 
   ### Capture JavaScript expressions to return results's cols and values ----
   js_cols <- "$('#prevalence-results thead th').map(function()
@@ -384,6 +423,15 @@ testthat::test_that(desc = "Module works well to estimate unweighted-MUAC preval
   testthat::expect_equal(length(app$get_js(js_cols)[1:19]), 19)
   testthat::expect_equal(as.numeric(prev), 8.0) # GAM
   testthat::expect_equal(as.numeric(pop), 300)
+  testthat::expect_equal(
+    object = basename(results),
+    paste0(
+      "mwana-amn-prevalence-survey-muac_",
+      Sys.Date(),
+      ".xlsx",
+      sep = ""
+    )
+  )
 
   ### Stop the app ----
   app$stop()
@@ -460,6 +508,9 @@ testthat::test_that(desc = "Module works well to estimate weighted-combined prev
   ### Click on Estime Prevalence button ----
   app$click(input = "prevalence-estimate")
   app$wait_for_value(output = "prevalence-results", timeout = 40000)
+  #### Donwload results ----
+  app$wait_for_idle(timeout = 40000)
+  results <- app$get_download(output = "prevalence-download_results")
 
   ### Capture JavaScript expressions to return results's cols and values ----
   js_cols <- "$('#prevalence-results thead th').map(function()
@@ -481,6 +532,15 @@ testthat::test_that(desc = "Module works well to estimate weighted-combined prev
   testthat::expect_equal(length(app$get_js(js_cols)[1:19]), 19)
   testthat::expect_equal(as.numeric(prev[2]), 10.8) # GAM
   testthat::expect_equal(as.numeric(weighted_pop), 288534)
+  testthat::expect_equal(
+    object = basename(results),
+    paste0(
+      "mwana-amn-prevalence-survey-combined_",
+      Sys.Date(),
+      ".xlsx",
+      sep = ""
+    )
+  )
 
   ### Stop the app ----
   app$stop()
@@ -557,6 +617,9 @@ testthat::test_that(desc = "Module works well to estimate unweighted-combined pr
   ### Click on Estime Prevalence button ----
   app$click(input = "prevalence-estimate")
   app$wait_for_value(output = "prevalence-results", timeout = 40000)
+  #### Donwload results ----
+  app$wait_for_idle(timeout = 40000)
+  results <- app$get_download(output = "prevalence-download_results")
 
   ### Capture JavaScript expressions to return results's cols and values ----
   js_cols <- "$('#prevalence-results thead th').map(function()
@@ -574,6 +637,15 @@ testthat::test_that(desc = "Module works well to estimate unweighted-combined pr
   testthat::expect_equal(length(app$get_js(js_cols)[1:19]), 19)
   testthat::expect_equal(as.numeric(prev), 10.5) # GAM
   testthat::expect_equal(as.numeric(pop), 276)
+  testthat::expect_equal(
+    object = basename(results),
+    paste0(
+      "mwana-amn-prevalence-survey-combined_",
+      Sys.Date(),
+      ".xlsx",
+      sep = ""
+    )
+  )
 
   ### Stop the app ----
   app$stop()
@@ -656,6 +728,9 @@ testthat::test_that(desc = "Module works well to estimate prevalence from screen
   ### Click on Estime Prevalence button ----
   app$click(input = "prevalence-estimate")
   app$wait_for_value(output = "prevalence-results", timeout = 40000)
+  #### Donwload results ----
+  app$wait_for_idle(timeout = 40000)
+  results <- app$get_download(output = "prevalence-download_results")
 
   ### Capture JavaScript expressions to return results's cols and values ----
   js_cols <- "$('#prevalence-results thead th').map(function()
@@ -685,6 +760,15 @@ testthat::test_that(desc = "Module works well to estimate prevalence from screen
   testthat::expect_equal(as.numeric(prev_unit_a)[2], 1.2) # SAM
   testthat::expect_equal(as.numeric(prev_unit_a)[3], 5.3) # MAM
   testthat::expect_equal(as.numeric(prev_unit_b), 12.4) # Age-weighted GAM
+  testthat::expect_equal(
+    object = basename(results),
+    paste0(
+      "mwana-amn-prevalence-screening-age-avail_",
+      Sys.Date(),
+      ".xlsx",
+      sep = ""
+    )
+  )
 
   ### Stop the app ----
   app$stop()
@@ -767,6 +851,9 @@ testthat::test_that(desc = "Prevalence tab works as expected when age is given i
   app$click(input = "prevalence-estimate")
   #### Wait until output has been rendered ----
   app$wait_for_value(output = "prevalence-results", timeout = 40000)
+  #### Donwload results ----
+  app$wait_for_idle(timeout = 40000)
+  results <- app$get_download(output = "prevalence-download_results")
 
   ### Capture JavaScript expressions to return results's cols and values ----
   js_cols <- "$('#prevalence-results thead th').map(function()
@@ -796,6 +883,15 @@ testthat::test_that(desc = "Prevalence tab works as expected when age is given i
   testthat::expect_equal(as.numeric(prev_unit_a)[2], 1.1) # SAM
   testthat::expect_equal(as.numeric(prev_unit_a)[3], 5.2) # MAM
   testthat::expect_equal(as.numeric(prev_unit_b), 12.6) # Age-weighted GAM
+  testthat::expect_equal(
+    object = basename(results),
+    paste0(
+      "mwana-amn-prevalence-screening-age-notavail_",
+      Sys.Date(),
+      ".xlsx",
+      sep = ""
+    )
+  )
 
   ### Stop the app ----
   app$stop()