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

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

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat("## Soumissions par poste de santé\n\n")
} else {
  cat("## Submissions by facility\n\n")
}

if (nrow(facility_data) > 0) {
  stats <- timci::get_summary_by_deviceid(facility_data)
  stats <- merge(x = stats, y = params$research_facilities, by.x = 'device_id', by.y = 'deviceid', all.x = TRUE)
  stats$screened <- stats$screened / days_nb
  stats$children <- stats$children / days_nb
}

if (Sys.getenv('TIMCI_COUNTRY') == 'Tanzania') {
  min_target_day <- 5
  max_target_day <- 8
} else {
  min_target_day <- 0.6 * enrolment_target
  max_target_day <- enrolment_target
}

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat(paste0("### Moyenne quotidienne de recrutements par poste de santé\n\n"))
} else {
  cat(paste0("### Enrolment daily average by facility\n\n"))
}
timci::generate_enrolment_hist(stats, facility_label, children, min_target_day, max_target_day, "Daily average of children enrolled", "facilities")

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat(paste0("### Moyenne quotidienne de screenings par poste de santé\n\n"))
} else {
  cat(paste0("### Screening daily average by facility\n\n"))
}
timci::generate_enrolment_hist(stats, facility_label, screened, min_target_day+1, max_target_day, "Daily average of children screened", "facilities")

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat(paste0("### Moyenne quotidienne d'appels téléphoniques à jour 7 par poste de santé\n\n"))
  cat(paste0("A compléter\n\n"))
} else {
  cat(paste0("### Day 7 phone calls by facility\n\n"))
  cat(paste0("To be completed\n\n"))
}
#timci::generate_enrolment_hist(stats, facility_label, children, 5, 15, "Number of children enrolled", "facilities")