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

write(formats2h2("Context"),stderr())
write("Write contextual information including dates, study facilities, facility and device correspondence", stderr())

Context

end_date <- NULL
facility_data_is_not_null <- !is.null(facility_data)
facility_data_is_not_empty <- timci::is_not_empty(facility_data)

end_date <- max(facility_data$date_visit)
if (is.null(lock_date)) {
  lock_date <- end_date
}
week_nb <- ceiling(difftime(as.Date(lock_date), as.Date(start_date) - 1,units = "weeks"))
if (is_senegal) {
  cat(paste0("* Début de la collecte de données pour l'étude longitudinale : **", start_date, "**"))
} else {
  cat(paste0("* Study start: **", start_date, "**"))
}

if (is_senegal) {
  cat(paste0("* Clôture de la base de données : **", lock_date, "** (semaine **", week_nb,"** de la collecte)"))
} else {
  cat(paste0("* Database lock: **", lock_date, "** (week **", week_nb,"** of the data collection)"))
}

timci::generate_calendar_heatmap2(facility_data %>%
                                    dplyr::filter(date_visit >= as.Date(start_date, "%Y-%m-%d") & date_visit <= as.Date(lock_date, "%Y-%m-%d")),
                                  date_visit,
                                  legendtitle = "Calendar heatmap of facility screenings")

Study facilities

cat("### Included facilities")

cat(paste0("Data collection was conducted in **", facility_nb, "** facilities."))

facility_disp %>%
  knitr::kable()

cat("### Excluded facilities")

cat("Data from the facilities listed in the table hereafter are present in the database despite the fact that these facilities are not part of the current study. The data from these facilities will therefore be deleted in subsequent data cleaning stages.")

excluded_facility_disp %>%
  knitr::kable()

Facility / device correspondence

facility_device <- facility_data[facility_data$fid %in% research_facilities$facility_id, ] %>%
  dplyr::select(c('device_id',
                  'fid')) %>%
  unique()
facility_device <- facility_device %>%
  merge(research_facilities,
        by.x = 'fid',
        by.y = 'facility_id',
        all.x = TRUE) %>%
  dplyr::select(c('device_id',
                  'fid',
                  'facility_name'))

if (is_senegal){
  # Remove device identification row for Senegal (RA used wrong QR codes)
  facility_device <- facility_device[!(facility_device$device_id  == "collect:Qrefi36S3VGHH9VP" & facility_device$fid == "F0059"),]
}

cat(paste0("Data collection has been done using **", nrow(facility_device), "** tablets."))

facility_device %>%
  knitr::kable(col.names = c("Device ID", "Facility ID", "Facility name"))

Thaliehln/timci documentation built on April 8, 2024, 3:38 p.m.