add wrapper function

mrc-ide · Oct 29, 2024 · 47b9e69 · 47b9e69
1 parent 5fdb573
commit 47b9e69
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Showing 2 changed files with 41 additions and 4 deletions.
diff --git a/R/input-time-series.R b/R/input-time-series.R
@@ -689,10 +689,45 @@ prepare_anc_spectrum_comparison <- function(anc, shape, pjnz) {
   dat |>
     dplyr::mutate(
       sex = "female", age_group = "Y015_049",
-      group = indicator,
+      group = "anc_adult_female",
       difference = value_spectrum - value_naomi) |>
     dplyr::select(indicator, area_name, year, group,
                   value_spectrum, value_naomi, difference)
 
 }
 
+##' Compare aggregated subnational Naomi + spectrum totals for comparison table
+##'
+##' @param art Path to file containing ART data or ART data object
+##' @param anc Path to file containing ART data or ART data object
+##' @param shape Path to file containing geojson areas data or areas data object
+##' @param pjnz Path to zip file containing spectrum pjnz file/s
+##' @keywords internal
+
+prepare_spectrum_naomi_comparison <- function(art, anc, shape, pjnz){
+
+
+  ## Check if shape is object or file path
+  if(!inherits(shape, "sf")) {
+    shape <- read_area_merged(shape) }
+
+  ## Check if anc is object or file path
+  if(!inherits(anc, c("spec_tbl_df","tbl_df","tbl","data.frame" ))) {
+    anc <- read_anc_testing(anc)
+  }
+
+  ## Check if art is object or file path
+  if(!inherits(art, c("spec_tbl_df","tbl_df","tbl","data.frame" ))) {
+    art <- read_art_number(art, all_columns = TRUE)}
+
+  ## PJNZ either object or file path
+  if (!inherits(pjnz, "spec_program_data")) {
+    pjnz <- extract_pjnz_program_data(pjnz) }
+
+  art_comparison <- prepare_art_spectrum_comparison(art, shape, pjnz)
+  anc_comparison <- prepare_anc_spectrum_comparison(anc, shape, pjnz)
+
+  rbind(art_comparison, anc_comparison)
+
+}
+
diff --git a/tests/testthat/test-input-time-series.R b/tests/testthat/test-input-time-series.R
@@ -813,8 +813,9 @@ test_that("ANC data is properly aggreagted for Spectrum comparison table", {
 
   x <- prepare_anc_spectrum_comparison(anc, shape, pjnz)
 
-  expect_equal(unique(x$group), c("anc_already_art", "anc_clients",
-                                  "anc_known_pos", "anc_tested" , "anc_tested_pos"))
+  expect_equal(unique(x$indicator), c("anc_already_art", "anc_clients",
+                                      "anc_known_pos", "anc_tested" , "anc_tested_pos"))
+  expect_equal(unique(x$group), c("anc_adult_female"))
   expect_equal(unique(x$area_name), c("Northern", "Central", "Southern"))
 
   # Test that aggregation works with national pjnz
@@ -824,8 +825,9 @@ test_that("ANC data is properly aggreagted for Spectrum comparison table", {
   x <- prepare_anc_spectrum_comparison(anc, shape, pjnz)
 
 
-  expect_equal(unique(x$group), c("anc_already_art", "anc_clients",
+  expect_equal(unique(x$indicator), c("anc_already_art", "anc_clients",
                                   "anc_known_pos", "anc_tested" , "anc_tested_pos"))
+  expect_equal(unique(x$group), c("anc_adult_female"))
   expect_equal(unique(x$area_name), c("Malawi - Demo"))
 
 })