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

\newpage

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat(paste0("# Suivi des visites à l'hôpital\n\n"))
} else {
  cat(paste0("# Hospital follow-up\n\n"))
}

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat(paste0("## Visite à l'hôpital\n\n"))
} else {
  cat(paste0("## Hospital visit\n\n"))
}

if (!is.null(raw_hospit_data)) {
  if (nrow(raw_hospit_data) > 0) {
    p <- timci::generate_week_bar_plot(date_vec = raw_hospit_data$date,
                                       date_min = as.Date(start_date),
                                       date_max = as.Date(Sys.Date() + 7),
                                       ylbl = submission_str)
    plot(p)
  } else{
    cat('0 hospital submissions since the start of the study.\n\n')
  }
} else{
  cat('0 hospital submissions since the start of the study.\n\n')
}

cat(calendar_heatmap_title_str)

if (!is.null(raw_hospit_data)) {
  if (nrow(raw_hospit_data) > 0) {
    timci::generate_calendar_heatmap2(raw_hospit_data,
                                      date,
                                      legendtitle = "Number of hospital submissions")
  } else{
    cat('N/A\n\n')
  }
} else{
    cat('N/A\n\n')
  }

if (!is.null(raw_hospit_data)) {
  if (nrow(raw_hospit_data) > 0) {

    all <- timci::format_hospital_data(raw_hospit_data)
    all$hospit[is.na(all$hospit)] <- 0

    hospit_summary <- list(
      "summary" = list(
        "Found" = ~qwraps2::n_perc(found == 1, prec, na_rm = TRUE),
        "Hospitalisation" = ~qwraps2::n_perc(hospit == 1, prec, na_rm = TRUE)
        )
      )
    out <- format_summary_table(all, hospit_summary) 
    out %>% 
      kableExtra::kbl(booktabs = TRUE,
                      longtable = TRUE,
                      linesep = "") %>% 
      kableExtra::kable_styling(latex_options = c("HOLD_position", "repeat_header"), font_size = table_fs) %>%
      kableExtra::row_spec(0, bold = TRUE)
  }
}