Update metadata to include new input comparison indicators, export fu…

…nction and format output

NAMESPACE

@@ -51,6 +51,7 @@ export(hintr_prepare_comparison_report_download)
 export(hintr_prepare_spectrum_download)
 export(hintr_prepare_summary_report_download)
 export(hintr_run_model)
+export(hintr_validate_programme_data)
 export(interpolate_population_agesex)
 export(log_linear_interp)
 export(map_outputs)
@@ -61,6 +62,7 @@ export(output_package)
 export(pop_pyramid_outputs)
 export(prepare_input_time_series_anc)
 export(prepare_input_time_series_art)
+export(prepare_spectrum_naomi_comparison)
 export(prepare_tmb_inputs)
 export(quarter_id_to_calendar_quarter)
 export(quarter_labels)

R/input-comparison.R

@@ -8,7 +8,6 @@
 ##' @keywords internal
 prepare_art_spectrum_comparison <- function(art, shape, pjnz) {
 
-
   ## Check if shape is object or file path
   if(!inherits(shape, "sf")) {
     shape <- read_area_merged(shape) }
@@ -132,8 +131,7 @@ prepare_anc_spectrum_comparison <- function(anc, shape, pjnz) {
 ##' @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
-
+##' @export
 prepare_spectrum_naomi_comparison <- function(art, anc, shape, pjnz){
 
   null_df <- setNames(data.frame(matrix(ncol = 7, nrow = 0)),
@@ -171,7 +169,12 @@ prepare_spectrum_naomi_comparison <- function(art, anc, shape, pjnz){
     comparison_df <- rbind(art_comparison, anc_comparison)
   }
 
-  comparison_df
-
+  comparison_df |>
+    dplyr::select(indicator, area_name, year, group,
+                  spectrum = value_spectrum, naomi = value_naomi, difference) |>
+    tidyr::pivot_longer(
+      c(spectrum, naomi, difference),
+      names_to = "data_source"
+    ) |>
+    tidyr::drop_na(value)
 }
-

inst/metadata/meta_indicator.csv

@@ -1,37 +1,39 @@
-indicator,indicator_label,description,parameter,indicator_sort_order,anc_indicator,format,scale
-population,t_(POPULATION),t_(INDICATOR_LABEL_POPULATION),population_out,1,FALSE,,
-prevalence,t_(HIV_PREVALENCE),t_(INDICATOR_LABEL_PREVALENCE),rho_out,2,FALSE,,
-plhiv,t_(PLHIV),t_(INDICATOR_LABEL_PLHIV),plhiv_out,3,FALSE,,
-art_coverage,t_(ART_COVERAGE),t_(INDICATOR_LABEL_ART_COVERAGE),alpha_out,4,FALSE,,
-art_current_residents,t_(ART_NUMBER_RESIDENTS),t_(INDICATOR_LABEL_ART_NUM_RESIDENTS),artnum_out,5,FALSE,,
-art_current,t_(ART_NUMBER_ATTENDING),t_(INDICATOR_LABEL_ART_NUM_ATTENDING),artattend_out,6,FALSE,,
-untreated_plhiv_num,t_(UNTREATED_PLHIV_NUM),t_(INDICATOR_LABEL_UNTREATED_PLHIV_NUM),untreated_plhiv_num_out,7,FALSE,,
-aware_plhiv_prop,t_(AWARE_PLHIV_PROP),t_(INDICATOR_LABEL_AWARE_PLHIV_PROP),aware_plhiv_prop_out,8,FALSE,,
-unaware_plhiv_num,t_(UNAWARE_PLHIV_NUM),t_(INDICATOR_LABEL_UNAWARE_PLHIV_NUM),unaware_plhiv_num_out,9,FALSE,,
-aware_plhiv_num,t_(AWARE_PLHIV_NUM),t_(INDICATOR_LABEL_AWARE_PLHIV_NUM),aware_plhiv_num_out,10,FALSE,,
-plhiv_attend,t_(PLHIV_ATTEND),t_(INDICATOR_LABEL_PLHIV_ATTEND),plhiv_attend_out,11,FALSE,,
-untreated_plhiv_attend,t_(UNTREATED_PLHIV_ATTEND),t_(INDICATOR_LABEL_UNTREATED_PLHIV_ATTEND),untreated_plhiv_attend_out,12,FALSE,,
-aware_plhiv_attend,t_(AWARE_PLHIV_ATTEND),t_(INDICATOR_LABEL_AWARE_PLHIV_ATTEND),aware_plhiv_attend_out,13,FALSE,,
-unaware_plhiv_attend,t_(UNAWARE_PLHIV_ATTEND),t_(INDICATOR_LABEL_UNAWARE_PLHIV_ATTEND),unaware_plhiv_attend_out,14,FALSE,,
-incidence,t_(INCIDENCE),t_(INDICATOR_LABEL_INCIDENCE),lambda_out,15,FALSE,,
-infections,t_(NEW_INFECTIONS),t_(INDICATOR_LABEL_INFECTIONS),infections_out,16,FALSE,,
-anc_prevalence,t_(ANC_HIV_PREVALENCE),t_(INDICATOR_LABEL_ANC_PREVALENCE),anc_rho_out,17,TRUE,,
-anc_art_coverage,t_(ANC_PRIOR_ART_COVERAGE),t_(INDICATOR_LABEL_ANC_ART_COVERAGE),anc_alpha_out,18,TRUE,,
-anc_clients,t_(ANC_CLIENTS),t_(INDICATOR_LABEL_ANC_CLIENTS),anc_clients_out,19,TRUE,,
-anc_plhiv,t_(ANC_PLHIV),t_(INDICATOR_LABEL_ANC_PLHIV),anc_plhiv_out,20,TRUE,,
-anc_already_art,t_(ANC_ALREADY_ART),t_(INDICATOR_LABEL_ANC_ALREADY_ART),anc_already_art_out,21,TRUE,,
-anc_art_new,t_(ANC_ART_NEW),t_(INDICATOR_LABEL_ANC_ART_NEW),anc_art_new_out,22,TRUE,,
-anc_known_pos,t_(ANC_KNOWN_POS),t_(INDICATOR_LABEL_ANC_KNOWN_POS),anc_known_pos_out,23,TRUE,,
-anc_tested_pos,t_(ANC_TESTED_POS),t_(INDICATOR_LABEL_ANC_TESTED_POS),anc_tested_pos_out,24,TRUE,,
-anc_tested_neg,t_(ANC_TESTED_NEG),t_(INDICATOR_LABEL_ANC_TESTED_NEG),anc_tested_neg_out,25,TRUE,,
-population_ratio,t_(POPULATION_RATIO),,,26,FALSE,,
-plhiv_ratio,t_(PLHIV_RATIO),,,27,FALSE,,
-infections_ratio,t_(NEW_INFECTIONS_RATIO),,,28,FALSE,,
-art_current_ratio,t_(ART_NUMBER_ATTENDING_RATIO),,,29,FALSE,,
-unaware_plhiv_num_ratio,t_(UNAWARE_PLHIV_NUM_RATIO),,,30,FALSE,,
-prevalence_ratio,t_(HIV_PREVALENCE_RATIO),,,31,FALSE,,
-art_coverage_ratio,t_(ART_COVERAGE_RATIO),,,32,FALSE,,
-aware_plhiv_prop_ratio,t_(AWARE_PLHIV_PROP_RATIO),,,33,FALSE,,
-incidence_ratio,t_(INCIDENCE_RATIO),,,34,FALSE,,
-anc_prevalence_age_matched,t_(ANC_PREVALENCE_AGE_MATCHED),,,35,TRUE,,
-anc_art_coverage_age_matched,t_(ANC_ART_COVERAGE_AGE_MATCHED),,,36,TRUE,,
+indicator,indicator_label,description,parameter,indicator_sort_order,anc_indicator,format,scale
+population,t_(POPULATION),t_(INDICATOR_LABEL_POPULATION),population_out,1,FALSE,,
+prevalence,t_(HIV_PREVALENCE),t_(INDICATOR_LABEL_PREVALENCE),rho_out,2,FALSE,,
+plhiv,t_(PLHIV),t_(INDICATOR_LABEL_PLHIV),plhiv_out,3,FALSE,,
+art_coverage,t_(ART_COVERAGE),t_(INDICATOR_LABEL_ART_COVERAGE),alpha_out,4,FALSE,,
+art_current_residents,t_(ART_NUMBER_RESIDENTS),t_(INDICATOR_LABEL_ART_NUM_RESIDENTS),artnum_out,5,FALSE,,
+art_current,t_(ART_NUMBER_ATTENDING),t_(INDICATOR_LABEL_ART_NUM_ATTENDING),artattend_out,6,FALSE,,
+untreated_plhiv_num,t_(UNTREATED_PLHIV_NUM),t_(INDICATOR_LABEL_UNTREATED_PLHIV_NUM),untreated_plhiv_num_out,7,FALSE,,
+aware_plhiv_prop,t_(AWARE_PLHIV_PROP),t_(INDICATOR_LABEL_AWARE_PLHIV_PROP),aware_plhiv_prop_out,8,FALSE,,
+unaware_plhiv_num,t_(UNAWARE_PLHIV_NUM),t_(INDICATOR_LABEL_UNAWARE_PLHIV_NUM),unaware_plhiv_num_out,9,FALSE,,
+aware_plhiv_num,t_(AWARE_PLHIV_NUM),t_(INDICATOR_LABEL_AWARE_PLHIV_NUM),aware_plhiv_num_out,10,FALSE,,
+plhiv_attend,t_(PLHIV_ATTEND),t_(INDICATOR_LABEL_PLHIV_ATTEND),plhiv_attend_out,11,FALSE,,
+untreated_plhiv_attend,t_(UNTREATED_PLHIV_ATTEND),t_(INDICATOR_LABEL_UNTREATED_PLHIV_ATTEND),untreated_plhiv_attend_out,12,FALSE,,
+aware_plhiv_attend,t_(AWARE_PLHIV_ATTEND),t_(INDICATOR_LABEL_AWARE_PLHIV_ATTEND),aware_plhiv_attend_out,13,FALSE,,
+unaware_plhiv_attend,t_(UNAWARE_PLHIV_ATTEND),t_(INDICATOR_LABEL_UNAWARE_PLHIV_ATTEND),unaware_plhiv_attend_out,14,FALSE,,
+incidence,t_(INCIDENCE),t_(INDICATOR_LABEL_INCIDENCE),lambda_out,15,FALSE,,
+infections,t_(NEW_INFECTIONS),t_(INDICATOR_LABEL_INFECTIONS),infections_out,16,FALSE,,
+anc_prevalence,t_(ANC_HIV_PREVALENCE),t_(INDICATOR_LABEL_ANC_PREVALENCE),anc_rho_out,17,TRUE,,
+anc_art_coverage,t_(ANC_PRIOR_ART_COVERAGE),t_(INDICATOR_LABEL_ANC_ART_COVERAGE),anc_alpha_out,18,TRUE,,
+anc_clients,t_(ANC_CLIENTS),t_(INDICATOR_LABEL_ANC_CLIENTS),anc_clients_out,19,TRUE,,
+anc_plhiv,t_(ANC_PLHIV),t_(INDICATOR_LABEL_ANC_PLHIV),anc_plhiv_out,20,TRUE,,
+anc_already_art,t_(ANC_ALREADY_ART),t_(INDICATOR_LABEL_ANC_ALREADY_ART),anc_already_art_out,21,TRUE,,
+anc_art_new,t_(ANC_ART_NEW),t_(INDICATOR_LABEL_ANC_ART_NEW),anc_art_new_out,22,TRUE,,
+anc_known_pos,t_(ANC_KNOWN_POS),t_(INDICATOR_LABEL_ANC_KNOWN_POS),anc_known_pos_out,23,TRUE,,
+anc_tested_pos,t_(ANC_TESTED_POS),t_(INDICATOR_LABEL_ANC_TESTED_POS),anc_tested_pos_out,24,TRUE,,
+anc_tested_neg,t_(ANC_TESTED_NEG),t_(INDICATOR_LABEL_ANC_TESTED_NEG),anc_tested_neg_out,25,TRUE,,
+population_ratio,t_(POPULATION_RATIO),,,26,FALSE,,
+plhiv_ratio,t_(PLHIV_RATIO),,,27,FALSE,,
+infections_ratio,t_(NEW_INFECTIONS_RATIO),,,28,FALSE,,
+art_current_ratio,t_(ART_NUMBER_ATTENDING_RATIO),,,29,FALSE,,
+unaware_plhiv_num_ratio,t_(UNAWARE_PLHIV_NUM_RATIO),,,30,FALSE,,
+prevalence_ratio,t_(HIV_PREVALENCE_RATIO),,,31,FALSE,,
+art_coverage_ratio,t_(ART_COVERAGE_RATIO),,,32,FALSE,,
+aware_plhiv_prop_ratio,t_(AWARE_PLHIV_PROP_RATIO),,,33,FALSE,,
+incidence_ratio,t_(INCIDENCE_RATIO),,,34,FALSE,,
+anc_prevalence_age_matched,t_(ANC_PREVALENCE_AGE_MATCHED),,,35,TRUE,,
+anc_art_coverage_age_matched,t_(ANC_ART_COVERAGE_AGE_MATCHED),,,36,TRUE,,
+number_on_art,t_(NUMBER_ON_ART),t_(NUMBER_ON_ART_DESC),,37,TRUE,,
+anc_tested,t_(ANC_TESTED),t_(ANC_TESTED_DESC),,38,TRUE,,

inst/metadata/metadata.csv

@@ -82,3 +82,9 @@ comparison,barchart,art_coverage,mean,lower,upper,indicator,art_coverage,t_(ART_
 comparison,barchart,art_current,mean,lower,upper,indicator,art_current,t_(ART_NUMBER_ATTENDING),1,100,"""0,0"""
 comparison,barchart,anc_prevalence_age_matched,mean,lower,upper,indicator,anc_prevalence_age_matched,t_(ANC_PREVALENCE_AGE_MATCHED),1,,"""0.0%"""
 comparison,barchart,anc_art_coverage_age_matched,mean,lower,upper,indicator,anc_art_coverage_age_matched,t_(ANC_ART_COVERAGE_AGE_MATCHED),1,,"""0.0%"""
+input_comparison,barchart,number_on_art,value,,,,number_on_art,t_(NUMBER_ON_ART),1,,"""0,0"""
+input_comparison,barchart,anc_already_art,value,,,,anc_already_art,t_(ANC_ALREADY_ART),1,10,"""0,0"""
+input_comparison,barchart,anc_clients,value,,,,anc_clients,t_(ANC_CLIENTS),1,10,"""0,0"""
+input_comparison,barchart,anc_known_pos,value,,,,anc_known_pos,t_(ANC_KNOWN_POS),1,10,"""0,0"""
+input_comparison,barchart,anc_tested,value,,,,anc_tested,t_(ANC_TESTED),1,10,"""0,0"""
+input_comparison,barchart,anc_tested_pos,value,,,,anc_tested_pos,t_(ANC_TESTED_POS),1,10,"""0,0"""

inst/traduire/en-translation.json

@@ -273,5 +273,7 @@
     "DOWNLOAD_OUTPUT_DESCRIPTION": "Naomi output uploaded from Naomi web app",
     "DOWNLOAD_SUMMARY_DESCRIPTION": "Naomi summary report uploaded from Naomi web app",
     "DOWNLOAD_COMPARISON_DESCRIPTION": "Naomi comparison report uploaded from Naomi web app",
-    "DOWNLOAD_AGYW_DESCRIPTION": "Naomi AGYW tool uploaded from Naomi web app"
+    "DOWNLOAD_AGYW_DESCRIPTION": "Naomi AGYW tool uploaded from Naomi web app",
+    "NUMBER_ON_ART": "Number on ART",
+    "NUMBER_ON_ART_DESC": "Number on ART description"
 }

inst/traduire/fr-translation.json

@@ -272,5 +272,7 @@
     "BIRTHS_FACILITY_DESC": "Nombre de naissances dans les établissements de santé",
     "DOWNLOAD_OUTPUT_DESCRIPTION": "Paquet Naomi téléchargée depuis l'application web Naomi",
     "DOWNLOAD_SUMMARY_DESCRIPTION": "Rapport de synthèse Naomi téléchargé depuis l'application web Naomi",
-    "DOWNLOAD_COMPARISON_DESCRIPTION": "Rapport de comparaison Naomi téléchargé à partir de l'application web Naomi"
+    "DOWNLOAD_COMPARISON_DESCRIPTION": "Rapport de comparaison Naomi téléchargé à partir de l'application web Naomi",
+    "NUMBER_ON_ART": "Nombre de personnes sous TARV",
+    "NUMBER_ON_ART_DESC": "Number on ART description"
 }

inst/traduire/pt-translation.json

@@ -272,5 +272,7 @@
     "BIRTHS_FACILITY_DESC": "Número de nascimentos em estabelecimentos de saúde",
     "DOWNLOAD_OUTPUT_DESCRIPTION": "Pacote Naomi descarregado a partir da aplicação web Naomi",
     "DOWNLOAD_SUMMARY_DESCRIPTION": "Relatório de síntese da Naomi carregado da aplicação web Naomi",
-    "DOWNLOAD_COMPARISON_DESCRIPTION": "Relatório de comparação Naomi carregado a partir da aplicação web Naomi"
+    "DOWNLOAD_COMPARISON_DESCRIPTION": "Relatório de comparação Naomi carregado a partir da aplicação web Naomi",
+    "NUMBER_ON_ART": "Nombre de personnes sous TARV",
+    "NUMBER_ON_ART_DESC": "Number on ART description"
 }