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

\newpage

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat(paste0("# Suivi à Jour 7\n\n"))
  cat(paste0("La période valable pour le suivi à Jour 7 est de **", day7_wmin, "** à **", day7_wmax, "** jours.\n\n"))
  if (n_due_day7fu > 0) {
    cat(paste0("**", n_due_day7fu, "** participants devraient avoir complété leur suivi à Jour 7.\n\n"))
    cat(paste0("**", n_completed_day7fu, "** participants (", n_day7fu_rate100,"%) ont complété leur suivi à Jour 7."))
  }
} else {
  cat(paste0("# Day 7 follow-up\n\n"))
  cat(paste0("The valid Day 7 follow-up period is **", day7_wmin, "** to **", day7_wmax, "** days.\n\n"))
  if (n_due_day7fu > 0) {
    cat(paste0("**", n_due_day7fu, "** participants should have completed their Day 7 follow-up.\n\n"))
    cat(paste0("**", n_completed_day7fu, "** participants (", n_day7fu_rate100,"%) completed their Day 7 follow-up."))
  }
}

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat("## Appels hebdomadaires\n\n")
} else {
  cat("## Weekly calls\n\n")
}

if (!is.null(raw_day7fu_data) & length(raw_day7fu_data) > 0 & nrow(raw_day7fu_data) > 0) {
  p <- timci::generate_week_bar_plot(date_vec = raw_day7fu_data$date,
                                     date_min = as.Date(start_date),
                                     date_max = as.Date(Sys.Date() + 7),
                                     ylbl = paste0(enrolment_str),
                                     date_vec_ref = as.Date(as.Date(baseline_data$date_visit) + 7))
  plot(p)
}

raw_day7fu_data %>%
  dplyr::mutate(week = lubridate::floor_date(as.Date(raw_day7fu_data$date),
                                             "week",
                                             week_start = getOption("lubridate.week.start", 1))) %>%
  dplyr::group_by(week) %>%
  dplyr::tally() %>%
  dplyr::rename('N' = 'n') %>%
  kableExtra::kbl(booktabs = TRUE,
                  longtable = TRUE,
                  linesep = "") %>% 
  kableExtra::kable_styling(latex_options = c("striped", "HOLD_position", "repeat_header"), font_size = table_fs) %>%
  kableExtra::row_spec(0, bold = TRUE)

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat("## Nombre de soumissions au cours des 30 derniers jours\n\n")
} else {
  cat("## Number of submissions during the last 30 days\n\n")
}

if (!is.null(raw_day7fu_data)) {
  if (nrow(raw_day7fu_data) > 0) {

    p <- timci::generate_day_bar_plot(raw_day7fu_data$date,
                                      as.Date(Sys.Date() - w),
                                      as.Date(Sys.Date() + 1),
                                      ylbl = submission_str,
                                      date_vec_ref = as.Date(as.Date(baseline_data$date_visit) + 7))
    plot(p)
  } else{
    cat('0 submissions since the start of the study.\n\n')
  }
} else {
  cat('0 submissions since the start of the study.\n\n')
  }

cat(calendar_heatmap_title_str)

if (!is.null(raw_day7fu_data)) {
  if (nrow(raw_day7fu_data) > 0) {
    timci::generate_calendar_heatmap2(raw_day7fu_data,
                                      date,
                                      legendtitle = "Number of day 7 follow-up phone calls")
  } else{
    cat('N/A\n\n')
  }
} else{
    cat('N/A\n\n')
  }

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat("## Tentatives d'appel enregistrées")
} else {
  cat("## Recorded attempts")
}

# Add facility generic information to the RCT/LS facility data
day7fu_data <- merge(x = day7fu_data,
                     y = params$research_facilities[, c("facility_id", "facility_name")],
                     by.x = 'fid',
                     by.y = 'facility_id',
                     all = FALSE)

if (!is.null(day7fu_data)) {
  if (nrow(day7fu_data) > 0) {

    all <- data.frame(day7fu_data)
    all$cg_ok[is.na(all$cg_ok)] <- 0

    day7_call_stats <- list(
      "District" = list(
        "Successful phone attempt" = ~qwraps2::n_perc(call_ok == 1, prec, na_rm = TRUE),
        "Completed follow-up" = ~qwraps2::n_perc(proceed_day7 == 1, prec, na_rm = TRUE)
        )
    )

    out <- format_summary_table(all, day7_call_stats, facility_name) 
    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) %>%
      kableExtra::row_spec(1, color = total_row_ft2, background = total_row_bg2, bold = TRUE) %>%
      kableExtra::row_spec(1:(nrow(out)/2) * 2, background = striped_row_bg) %>%
      kableExtra::footnote(general = "denominator = all Day 7 call attempts that have been recorded.")

  }
}

if (!is.null(day7fu_data)) {
  if (nrow(day7fu_data) > 0) {

    all <- data.frame(day7fu_data)

    day7_call_stats <- list(
      "District" = list(
        "Call attempted" = ~qwraps2::n_perc(fu_type == 1, prec, na_rm = TRUE),
        "Physical attempted" = ~qwraps2::n_perc(fu_type == 2, prec, na_rm = TRUE),
        "Completed follow-up" = ~qwraps2::n_perc(proceed_day7 == 1, prec, na_rm = TRUE)
        )
    )

    out <- format_summary_table(all, day7_call_stats, facility_name) 
    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) %>%
      kableExtra::row_spec(1, color = total_row_ft2, background = total_row_bg2, bold = TRUE) %>%
      kableExtra::row_spec(1:(nrow(out)/2) * 2, background = striped_row_bg) %>%
      kableExtra::footnote(general = "denominator = all Day 7 call attempts that have been recorded.")

  }
}

if (!is.null(day7fu_data)) {
  if (nrow(day7fu_data) > 0) {

    all$cg_reached[is.na(all$cg_reached)] <- 0

    day7_call_stats <- list(
      "District" = list(
        "Caregiver reached" = ~qwraps2::n_perc(cg_reached == 1, prec, na_rm = TRUE),
        "Caregiver OK" = ~qwraps2::n_perc(cg_ok == 1, prec, na_rm = TRUE)
        )
    )

    out <- format_summary_table(all, day7_call_stats, facility_name) 
    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) %>%
      kableExtra::row_spec(1, color = total_row_ft2, background = total_row_bg2, bold = TRUE) %>%
      kableExtra::row_spec(1:(nrow(out)/2) * 2, background = striped_row_bg) %>%
      kableExtra::footnote(general = "denominator = all Day 7 call attempts that have been recorded.")

  }
}

if (!is.null(day7fu_data)) {
  if (nrow(day7fu_data) > 0) {

    all$respondent_ok[is.na(all$respondent_ok)] <- 0
    all$cg_reached[is.na(all$cg_reached)] <- 0

    day7_call_stats <- list(
      "District" = list(
        "Caregiver reached" = ~qwraps2::n_perc(cg_reached == 1, prec, na_rm = TRUE),
        "Caregiver OK" = ~qwraps2::n_perc(cg_ok == 1, prec, na_rm = TRUE),
        "Other OK" = ~qwraps2::n_perc(respondent_ok == 1, prec, na_rm = TRUE)
        )
    )

    out <- format_summary_table(all, day7_call_stats, facility_name) 
    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) %>%
      kableExtra::row_spec(1, color = total_row_ft2, background = total_row_bg2, bold = TRUE) %>%
      kableExtra::row_spec(1:(nrow(out)/2) * 2, background = striped_row_bg) %>%
      kableExtra::footnote(general = "denominator = all Day 7 call attempts that have been recorded.")

  }
}

if (!is.null(day7fu_data)) {
  if (nrow(day7fu_data) > 0) {

    all$respondent_ok[is.na(all$respondent_ok)] <- 0
    all$cg_reached[is.na(all$cg_reached)] <- 0

    day7_call_stats <- list(
      "District" = list(
        "Caregiver reached" = ~qwraps2::n_perc(cg_reached == 1, prec, na_rm = TRUE),
        "Caregiver OK" = ~qwraps2::n_perc(successful_phone_fu == 1, prec, na_rm = TRUE),
        "Other OK" = ~qwraps2::n_perc(respondent_ok == 1, prec, na_rm = TRUE)
        )
    )

    out <- format_summary_table(all, day7_call_stats, facility_name) 
    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) %>%
      kableExtra::row_spec(1, color = total_row_ft2, background = total_row_bg2, bold = TRUE) %>%
      kableExtra::row_spec(1:(nrow(out)/2) * 2, background = striped_row_bg) %>%
      kableExtra::footnote(general = "denominator = all Day 7 call attempts that have been recorded.")

  }
}

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat("## Suivis réalisés")
} else {
  cat("## Completed follow-ups")
}

if (!is.null(day7fu_data)) {
  if (nrow(day7fu_data) > 0) {
    succ_day7fu_data <- merge(x = succ_day7fu_data,
                              y = params$research_facilities[, c("facility_id", "facility_name")],
                              by.x = 'fid',
                              by.y = 'facility_id',
                              all = FALSE)
  }
}

if (!is.null(day7fu_data)) {
  if (nrow(day7fu_data) > 0) {

    all <- data.frame(succ_day7fu_data)

    day7_outcome_ss <- list(
      "summary" = list(
        "Before day 7" = ~qwraps2::n_perc(days <= 6, prec, na_rm = TRUE),
        "Day 7-10" = ~qwraps2::n_perc(days >= 7 & days <= 10, prec, na_rm = TRUE),
        "Above day 10" = ~qwraps2::n_perc(days > 10, prec, na_rm = TRUE),
        "Median" = ~qwraps2::median_iqr(days, na_rm = TRUE)
        )
      )
    out <- format_summary_table(all, day7_outcome_ss, facility_name) 
    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) %>%
      # kableExtra::column_spec(2, color = ifelse(as.numeric(gsub("\\(([^()]*)%\\)|.", "\\1", x = out[, 1], perl = TRUE)) > 0,
      #                                           "red",
      #                                           "black")) %>%
      kableExtra::row_spec(1, color = total_row_ft2, background = total_row_bg2, bold = TRUE) %>%
      kableExtra::row_spec(1:(nrow(out)/2) * 2, background = striped_row_bg) %>%
      kableExtra::footnote(general = "Mean and inner quartile range (IQR) are represented by the format \\\\textit{median (Q1, Q3)}.",
                           escape = FALSE)
  }
}

if (!is.null(day7fu_data)) {
  if (nrow(day7fu_data) > 0) {

    all <- data.frame(succ_day7fu_data)
    all$cure_day7[is.na(all$cure_day7)] <- 0
    all$all_hf_visit_day7 <- ifelse(all$status_day7 == 2 | (all$status_day7 != 2 & all$hf_visit_day7 == 1 & all$hf_visit_type == hospit_value), 1, 0)
    all$admission[is.na(all$admission)] <- 0

    day7_outcome_ss <- list(
      "summary" = list(
        "Cure" = ~qwraps2::n_perc(cure_day7 == 1 | cure_day7 == 2, prec, na_rm = TRUE),
        "Death" = ~qwraps2::n_perc(status_day7 == 3, prec, na_rm = TRUE),
        "Higher level visit" = ~qwraps2::n_perc(all_hf_visit_day7 == 1, prec, na_rm = TRUE),
        "Admission" = ~qwraps2::n_perc(admission == 1, prec, na_rm = TRUE)
        )
      )
    out <- format_summary_table(all, day7_outcome_ss, facility_name) 
    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) %>%
      # kableExtra::column_spec(3, color = ifelse(as.numeric(gsub("\\(([^()]*)%\\)|.", "\\1", x = out[, 2], perl = TRUE)) > 0,
      #                                           "red",
      #                                           "black")) %>%
      # kableExtra::column_spec(4, color = ifelse(as.numeric(gsub("\\(([^()]*)%\\)|.", "\\1", x = out[, 3], perl = TRUE)) > 0,
      #                                           "red",
      #                                           "black")) %>%
      kableExtra::row_spec(1, color = total_row_ft2, background = total_row_bg2, bold = TRUE) %>%
      kableExtra::row_spec(1:(nrow(out)/2) * 2, background = striped_row_bg)
  }
}