R/global_summary.R

In pepfar-datim/daa-analytics: Utilities for Compiling and Analyzing PEPFAR Data Alignment Activity Data

#' Prepare Global Summary Table of DAA Data
#'
#' @inheritParams daa_analytics_params
#'
#' @return Summary table dataframe
#' @export
#'
global_summary <- function(combined_data) {
    combined_data |>
    dplyr::group_by(OU, period, indicator) |>
    dplyr::summarize(
      CountOfFacilities_ReportedByBoth = length(Facility_UID[reported_by == "Both"]),
      CountOfFacilities_ReportedByMOH = length(Facility_UID[reported_by %in% c("Both", "MOH")]),
      CountOfFacilities_ReportedByPEPFAR = length(Facility_UID[reported_by %in% c("Both", "PEPFAR")]),
      CountOfFacilities_ReportedByPEPFAROnly = length(Facility_UID[reported_by == "PEPFAR"]),
      CountOfFacilities_ReportedByBoth_WithEMR = length(Facility_UID[reported_by == "Both" & emr_present == TRUE & !is.na(emr_present)]),
      Pct_PEPFAR_Reported_Facilities_ReportedByMOH = length(Facility_UID[reported_by == "Both"]) / length(Facility_UID[reported_by %in% c("Both", "PEPFAR")]),
      Pct_MOH_Facilities_SupportedBy_PEPFAR = length(Facility_UID[reported_by == "Both"]) / length(Facility_UID[reported_by %in% c("Both", "MOH")]),
      Pct_PEPFAR_Facilities_WithEMR = length(Facility_UID[emr_present == TRUE & !is.na(emr_present) & reported_by %in% c("PEPFAR", "Both")]) / length(Facility_UID[reported_by %in% c("PEPFAR", "Both")]),
      Pct_PEPFAR_Facilities_ReportedByBoth_WithEMR = length(Facility_UID[emr_present == TRUE & !is.na(emr_present) & reported_by == "Both"]) / length(Facility_UID[reported_by == "Both"]),
      MOH_Results_Total = sum(moh[reported_by %in% c("Both", "MOH")], na.rm = TRUE),
      PEPFAR_Results_Total = sum(pepfar[reported_by %in% c("Both", "PEPFAR")], na.rm = TRUE),
      MOH_Results_FacilitiesReportedByBoth = sum(moh[reported_by == "Both"], na.rm = TRUE),
      PEPFAR_Results_FacilitiesReportedByBoth = sum(pepfar[reported_by == "Both"], na.rm = TRUE),
      PEPFAR_Results_FacilitiesReportedByPEPFAROnly = sum(pepfar[reported_by == "PEPFAR"], na.rm = TRUE),
      SumOfPEPFARResults_ReportedByBoth_WithEMR = sum(pepfar[reported_by == "Both" & emr_present == TRUE & !is.na(emr_present)], na.rm = TRUE),
      Concordance = sum(OU_Concordance[reported_by == "Both"], na.rm = TRUE),
      ConcordanceOfFacilitiesWithEMR = sum(EMR_Concordance[reported_by == "Both" & emr_present == TRUE & !is.na(emr_present)], na.rm = TRUE),
      ConcordanceOfFacilitiesWithOutEMR = sum(EMR_Concordance[reported_by == "Both" & emr_present == FALSE & !is.na(emr_present)], na.rm = TRUE),
      Absolute_Difference = sum(absolute_difference[reported_by == "Both"], na.rm = TRUE),
      Average_Absolute_Difference = round(Absolute_Difference / CountOfFacilities_ReportedByBoth),
    ) |>
    dplyr::mutate(
      dplyr::across(
        c(MOH_Results_FacilitiesReportedByBoth,
          PEPFAR_Results_FacilitiesReportedByBoth,
          Pct_PEPFAR_Facilities_ReportedByBoth_WithEMR,
          Concordance,
          ConcordanceOfFacilitiesWithEMR,
          ConcordanceOfFacilitiesWithOutEMR,
          Absolute_Difference,
          Average_Absolute_Difference),
        ~ ifelse(CountOfFacilities_ReportedByBoth == 0, NA, .x))) |>
    dplyr::mutate(
      dplyr::across(
        c(Pct_PEPFAR_Reported_Facilities_ReportedByMOH,
          Pct_MOH_Facilities_SupportedBy_PEPFAR),
        ~ ifelse(CountOfFacilities_ReportedByPEPFAR == 0 | CountOfFacilities_ReportedByMOH == 0, NA, .x))) |>
    dplyr::mutate(
      ConcordanceOfFacilitiesWithEMR = ifelse(Pct_PEPFAR_Facilities_ReportedByBoth_WithEMR == 0, NA, ConcordanceOfFacilitiesWithEMR),
      ConcordanceOfFacilitiesWithOutEMR = ifelse(Pct_PEPFAR_Facilities_ReportedByBoth_WithEMR == 1, NA, ConcordanceOfFacilitiesWithOutEMR)
    ) |>
    dplyr::mutate(
      dplyr::across(c(MOH_Results_Total,
               MOH_Results_FacilitiesReportedByBoth),
             ~ ifelse(CountOfFacilities_ReportedByMOH == 0, NA, .x))) |>
    dplyr::mutate(
      dplyr::across(c(PEPFAR_Results_Total,
               PEPFAR_Results_FacilitiesReportedByBoth,
               Pct_PEPFAR_Facilities_WithEMR),
             ~ ifelse(CountOfFacilities_ReportedByPEPFAR == 0, NA, .x)))

  # nolint end
}