In Thaliehln/timci: Data management and visualisation for the TIMCI project

library(timci)
library(magrittr)
knitr::opts_chunk$set(echo = FALSE,
                      warning = FALSE,
                      message = FALSE)

is_india <- Sys.getenv('TIMCI_COUNTRY') == 'India'
is_tanzania <- Sys.getenv('TIMCI_COUNTRY') == 'Tanzania'
is_kenya <- Sys.getenv('TIMCI_COUNTRY') == 'Kenya'
is_senegal <- Sys.getenv('TIMCI_COUNTRY') == 'Senegal'
is_rct <- is_tanzania | is_india

path_dir <- params$path_dir
facility_data <- NULL
wfa_data <- NULL
research_facilities <- NULL

facility_data <- params$facility_data
wfa_data <- params$wfa_data
research_facilities <- params$research_facilities

facility_data <- facility_data %>%
  merge(y = research_facilities[,c("facility_id", "rollout_date")] %>% distinct(),
        by.x = 'fid',
        by.y = 'facility_id',
        all.x = TRUE) %>%
  dplyr::filter(!is.na(rollout_date) & as.Date(date_visit) >= as.Date(rollout_date))

stats <- timci::get_summary_by_fid(facility_data)

stats <- merge(x = stats,
               y = research_facilities[, c("facility_id", "facility_name", "lvl2")] %>% distinct(),
               by.x = 'fid_from_device',
               by.y = 'facility_id',
               all = FALSE)
tmp <- timci::export_df2xlsx(stats,
                             path_dir,
                             paste0("facility_stats_", Sys.Date()))

if (!is.null(wfa_data)) {

  if (nrow(wfa_data) > 0) {

    tmp <- timci::export_df2xlsx(wfa_data,
                                 path_dir,
                                 paste0("weekly_facility_assessment_", Sys.Date()))

    last_data <- timci::extract_last_fa_data(wfa_data,
                                             stats)
    soc_data <- last_data[last_data$arm == 0,]
    pox_data <- last_data[last_data$arm == 1,]
    cdsa_data <- last_data[last_data$arm == 2,]

    if (nrow(pox_data) > 0) {
      cat("\\newpage")
      cat('# Facilities with pulse oximetry alone\n\n')
      display_weekly_fa_data_per_facility(pox_data,
                                          wfa_data)
    }
    if (nrow(cdsa_data) > 0) {
      cat("\\newpage")
      cat('# Facilities with pulse oximetry and CDSA\n\n')
      display_weekly_fa_data_per_facility(cdsa_data,
                                          wfa_data)
    }

    last_data2 <- timci::extract_last_fa_data(wfa_data,
                                              stats)
    out <- format_weekly_fa_data_for_export(last_data2)
    out <- out[out$facility_id %in% research_facilities$facility_id, ]
    tmp <- timci::export_df2xlsx(out,
                                 path_dir,
                                 paste0("TIMCI_M&E_RA_data_for_PATH_", Sys.Date()))

  }

}