From d07a38f9b902dfc249cdf7cafb17e0e60f362ee5 Mon Sep 17 00:00:00 2001
From: rtesra <70330391+rtesra@users.noreply.github.com>
Date: Wed, 11 Dec 2024 11:42:38 +0200
Subject: [PATCH] remove naomi-spectrum comparison check from navigator code

---
 R/model.R                     | 65 ++---------------------------------
 R/unaids-navigator.R          |  4 ---
 tests/testthat/test-outputs.R |  4 +--
 3 files changed, 3 insertions(+), 70 deletions(-)

diff --git a/R/model.R b/R/model.R
index a21d8f6e..7a1a5650 100644
--- a/R/model.R
+++ b/R/model.R
@@ -570,7 +570,7 @@ naomi_model_frame <- function(area_merged,
                       spec_unaware_untreated_prop_t4 = unaware_untreated_prop,
                       asfr_t4 = asfr,
                       frr_plhiv_t4 = frr_plhiv,
-                      frr_already_art_t4 = frr_already_art                      
+                      frr_already_art_t4 = frr_already_art
                     ),
              by = c("spectrum_region_code", "sex", "age_group")
            ) %>%
@@ -881,65 +881,6 @@ select_naomi_data <- function(
 
   stopifnot(methods::is(naomi_mf, "naomi_mf"))
 
-  ## Check anc_testing and art_number against Spectrum inputs.
-  ## Return NA if spec_program_data not provided
-  anc_testing_spectrum_aligned <- NA
-  art_number_spectrum_aligned <- NA
-
-  if (!is.null(spec_program_data)) {
-    stopifnot(methods::is(spec_program_data, "spec_program_data"))
-
-    if (!is.null(anc_testing)) {
-
-      anc_merged <- anc_testing %>%
-        dplyr::left_join(
-          dplyr::select(naomi_mf$mf_areas, area_id, spectrum_region_code),
-          by = "area_id"
-        ) %>%
-        tidyr::pivot_longer(dplyr::starts_with("anc"),
-                            names_to = "indicator",
-                            values_to = "value_naomi") %>%
-        dplyr::count(spectrum_region_code, year, indicator,
-                     wt = value_naomi, name = "value_naomi") %>%
-        dplyr::inner_join(
-          spec_program_data$anc_testing %>%
-          dplyr::rename("value_spectrum" = "value"),
-          by = c("spectrum_region_code", "indicator", "year")
-        )
-
-      anc_testing_spectrum_aligned <- all(anc_merged$value_naomi == anc_merged$value_spectrum)
-
-    } else {
-      ## If no ANC testing data, return TRUE
-      anc_testing_spectrum_aligned <- TRUE
-    }
-
-    if (!is.null(art_number)) {
-
-      art_merged <- art_number %>%
-        dplyr::left_join(
-          dplyr::select(naomi_mf$mf_areas, area_id, spectrum_region_code),
-          by = "area_id"
-        ) %>%
-        dplyr::count(spectrum_region_code, sex, age_group, calendar_quarter,
-                     wt = art_current, name = "art_current_naomi") %>%
-        dplyr::inner_join(
-          spec_program_data$art_dec31 %>%
-          dplyr::mutate(
-            calendar_quarter = paste0("CY", year, "Q4"),
-            year = NULL
-          ),
-          by = c("spectrum_region_code", "sex", "age_group", "calendar_quarter")
-        )
-
-      art_number_spectrum_aligned <- all(art_merged$art_current_naomi == art_merged$art_dec31)
-
-    } else {
-      ## If no ANC testing data, return TRUE
-      art_number_spectrum_aligned <- TRUE
-    }
-  }
-
   common_surveys <- intersect(artcov_survey_ids, vls_survey_ids)
   if (length(common_surveys)) {
     stop(t_("ART_COV_AND_VLS_SAME_SURVEY",
@@ -1101,9 +1042,7 @@ select_naomi_data <- function(
                        artnum_calendar_quarter_t1 = artnum_calendar_quarter_t1,
                        artnum_calendar_quarter_t2 = artnum_calendar_quarter_t2,
                        anc_prev_year_t1 = anc_artcov_year_t1,
-                       anc_prev_year_t2 = anc_artcov_year_t2,
-                       art_number_spectrum_aligned = art_number_spectrum_aligned,
-                       anc_testing_spectrum_aligned = anc_testing_spectrum_aligned)
+                       anc_prev_year_t2 = anc_artcov_year_t2)
 
   naomi_mf$data_options <- data_options
 
diff --git a/R/unaids-navigator.R b/R/unaids-navigator.R
index dfc4292d..e538d453 100644
--- a/R/unaids-navigator.R
+++ b/R/unaids-navigator.R
@@ -91,10 +91,6 @@ write_navigator_checklist <- function(naomi_output,
 
   if (!is.null(data_options)) {
 
-    ## Compare aggregated naomi inputs to national Spectrum totals
-    v$TrueFalse[v$NaomiCheckPermPrimKey == "ART_is_Spectrum"] <- data_options$art_number_spectrum_aligned
-    v$TrueFalse[v$NaomiCheckPermPrimKey == "ANC_is_Spectrum"] <- data_options$anc_testing_spectrum_aligned
-
     ## Check that all surveys used are from most recent quarter available
     most_recent_survey_available  <- max(data_options$prev_survey_available_quarters)
     v$TrueFalse[v$NaomiCheckPermPrimKey == "Opt_recent_survey_only"] <-
diff --git a/tests/testthat/test-outputs.R b/tests/testthat/test-outputs.R
index 2bcf7ad8..afb75217 100644
--- a/tests/testthat/test-outputs.R
+++ b/tests/testthat/test-outputs.R
@@ -165,7 +165,7 @@ test_that("subset_output_package() saves expected output package", {
 
 
   ## Test that can **drop** selected indicators (rather than keep)
-  
+
   sub_drop_file <- tempfile(fileext = ".zip")
 
   expect_warning(
@@ -328,8 +328,6 @@ test_that("navigator checklist returns expected results", {
 
   adj_output$fit$data_options$prev_survey_ids <- "DEMO2020PHIA"
   adj_output$fit$data_options$prev_survey_quarters <- "CY2020Q3"
-  adj_output$fit$data_options$art_number_spectrum_aligned <- TRUE
-  adj_output$fit$data_options$anc_testing_spectrum_aligned <- TRUE
 
   adj_output$fit$calibration_options$spectrum_population_calibration <- "subnational"
   adj_output$fit$calibration_options$spectrum_artnum_calibration_level <- "subnational"