Adjust PEPFAR Data Pack export for 2021 specification

adjust_datapack_export2021.R

#' This function saves an updated data pack export CSV in the same directory as
#' the Naomi output package file
#'
#' Example:
#'
#' file <- "~/Downloads/MWI_20210308-090536_naomi_spectrum_digest.zip"  ## !! REPLACE HERE
#' adjust_datapack_export2021(file)
#' 

adjust_datapack_export2021 <- function(naomi_output_package) {

  tmpd <- tempfile()
  on.exit(unlink(tmpd, recursive = TRUE, force = TRUE))
  unzip(naomi_output_package, file = "pepfar_datapack_indicators_2021.csv", exdir = tmpd)
  
  dp <- readr::read_csv(file.path(tmpd, "pepfar_datapack_indicators_2021.csv"))
  
  
  #' Add dataelement_uid column
  
  datapack_indicators <- readr::read_csv("https://raw.githubusercontent.com/mrc-ide/naomi/master/inst/datapack/datapack_indicator_mapping.csv")
  
  dp <- dplyr::left_join(dp,
                         dplyr::select(datapack_indicators,
                                       indicator_code = datapack_indicator_code,
                                       dataelement_uid = datapack_indicator_id),
                         by = "indicator_code"
                         )
  dp <- dplyr::mutate(dp, 
                      dataelement_uid = dplyr::if_else(indicator_code == "TX_CURR_SUBNAT.R",
                                                       "MktYDp33kd6", dataelement_uid)
                      )
  dp <- dplyr::select(dp, psnu, psnu_uid, area_id, indicator_code, dataelement_uid, everything())

  #' Change age column to =""<01""
  
  dp$age <- paste0("=\"", dp$age, "\"")
  
  outfile <- sub("naomi-output", "datapack-export", naomi_output_package)
  outfile <- sub("zip$", "csv", outfile)
  
  readr::write_csv(dp, outfile, na = "")
}