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

library(magrittr)
library(readxl)
library(ggplot2)
library(lubridate)
library(gridExtra)
library(kableExtra)
knitr::opts_chunk$set(echo = FALSE,
                      warning = FALSE,
                      message = FALSE,
                      fig.pos='!H')
options(qwraps2_markup = 'markdown')

# Qwraps2 parameters
prec <- 1

#kableExtra table parameters
table_fs <- 7
figsize <- 3
total_row_ft <- "gray"
total_row_ft2 <- "white"
striped_row_bg <- "gray!10"
total_row_bg2 <- "gray"

\fancypagestyle{plain}{\pagestyle{fancy}} \pagestyle{fancy} \fancyhf{} \setlength{\headheight}{32pt} \renewcommand{\headrulewidth}{0pt} \fancyhead[C]{\includegraphics[width=10cm]{banner.png}} \fancyfoot[R]{Page \thepage\ of \pageref{LastPage}} \fancyfoot[L]{TIMCI SPA Operational Report v1.0}

\setcounter{tocdepth}{2} \tableofcontents

\newpage

r notice_str

r intro_str

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
is_ls <- is_kenya | is_senegal

spa_sco_data <- params$spa_sco_data
spa_cgei_data <- params$spa_cgei_data
spa_fa_data <- params$spa_fa_data
spa_hcpi_data <- params$spa_hcpi_data

spa_sco_is_not_null <- !is.null(spa_sco_data)
if(spa_sco_is_not_null) {
  spa_sco_is_not_null <- (nrow(spa_sco_data) > 0) & (length(spa_sco_data) > 0)
}
spa_cgei_is_not_null <- !is.null(spa_cgei_data)
if(spa_cgei_is_not_null) {
  spa_cgei_is_not_null <- (nrow(spa_cgei_data) > 0) & (length(spa_cgei_data) > 0)
}
spa_fa_is_not_null <- !is.null(spa_fa_data)
if(spa_fa_is_not_null) {
  spa_fa_is_not_null <- (nrow(spa_fa_data) > 0) & (length(spa_fa_data) > 0)
}
spa_hcpi_is_not_null <- !is.null(spa_hcpi_data)
if(spa_hcpi_is_not_null) {
  spa_hcpi_is_not_null <- (nrow(spa_hcpi_data) > 0) & (length(spa_hcpi_data) > 0)
}
spa_is_not_null <- spa_sco_is_not_null | spa_cgei_is_not_null | spa_fa_is_not_null | spa_hcpi_is_not_null

start_date <- NULL
end_date <- NULL

sco_start_date <- NULL
sco_end_date <- NULL
if (spa_sco_is_not_null) {
  sco_start_date <- min(spa_sco_data$date)
  sco_end_date <- max(spa_sco_data$date)
}

cgei_start_date <- NULL
cgei_end_date <- NULL
if (spa_cgei_is_not_null) {
  if (nrow(spa_cgei_data) > 0) {
    cgei_start_date <- min(spa_cgei_data$date)
    cgei_end_date <- max(spa_cgei_data$date)
  }
}

fa_start_date <- NULL
fa_end_date <- NULL
if (spa_fa_is_not_null) {
  if (nrow(spa_fa_data) > 0) {
    fa_start_date <- min(spa_fa_data$date)
    fa_end_date <- max(spa_fa_data$date)
  }
}

hcpi_start_date <- NULL
hcpi_end_date <- NULL
if (spa_hcpi_is_not_null) {
  if (nrow(spa_hcpi_data) > 0) {
    hcpi_start_date <- min(spa_hcpi_data$date)
    hcpi_end_date <- max(spa_hcpi_data$date)
  }
}

start_date <- min(sco_start_date, cgei_start_date, fa_start_date, hcpi_start_date)
end_date <- max(sco_end_date, cgei_end_date, fa_end_date, hcpi_end_date)

if (Sys.getenv('TIMCI_COUNTRY') == 'Senegal') {
  cat(paste0("Ce rapport couvre la période du **", start_date, "** (début de l'étude) au **", end_date, "** pour le **Sénégal**."))
} else {
  cat(paste0("This report covers the period from **", start_date, "** (study start) to **", end_date, "** for **", Sys.getenv('TIMCI_COUNTRY'), "**."))
}

# obs_count <- all %>%                       
#   dplyr::group_by(facility_name) %>%
#   dplyr::summarise("Observed children" = n_distinct(child_id),
#                    "Observed providers" = n_distinct(hcp_id)) %>%
#   bind_rows(dplyr::summarise(.,
#                              across(where(is.numeric), sum),
#                              across(where(is.character), ~"Total"))) %>%
#   rowwise() %>% 
#   dplyr::mutate(Total = sum(c_across(where(is.numeric)), na.rm = TRUE))
# 
# obs_count %>% 
#   kableExtra::kbl(booktabs = TRUE,
#                   linesep = "",
#                   align = c("c", "c", "c"),
#                   caption = "Number of consultation observations") %>% 
#   kableExtra::kable_styling(latex_options = c("HOLD_position", "repeat_header"), font_size = table_fs) %>%
#   kableExtra::row_spec(0, bold = TRUE) %>%
#   kableExtra::row_spec(1:(nrow(obs_count)/2) * 2, background = striped_row_bg)