In SwissTPH/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"

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

\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 PM \& T-F Operational Report v1.0}

\setcounter{tocdepth}{2} \tableofcontents

\newpage

r notice_str

r intro_str

if (!is.null(params$facility_data)) {

  facility_data <- params$facility_data
  tf_data <- params$tf_data
  pm_data <- params$pm_data
  raw_withdrawal_data <- params$raw_withdrawal_data

}

# Extract personally identifiable data
pii <- timci::extract_enrolled_participants(facility_data)[[2]]

# Merge facility generic info with facility data
facility_data <- merge(facility_data, params$research_facilities[, c("deviceid", "facility_name")], by.x = 'device_id', by.y = 'deviceid', all.x = TRUE)

start_date <- NULL
end_date <- NULL
if (nrow(tf_data) > 0) {
  start_date <- min(tf_data$date)
  end_date <- max(tf_data$date)
  week_nb <- ceiling(difftime(as.Date(end_date), as.Date(start_date) - 1,units = "weeks"))
  days_nb <- sum(!lubridate::wday(seq(as.Date(start_date), as.Date(end_date), "days")) %in% c("7", "1"))
  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'), "**."))
  }
}

pm_is_not_null <- !is.null(pm_data)
if (pm_is_not_null) {
  pm_is_not_null <- length(pm_data) > 0
}

tf_is_not_null <- !is.null(tf_data)
if (tf_is_not_null) {
  tf_is_not_null <- length(tf_data) > 0
}

\newpage \listoftables

\newpage \listoffigures

SwissTPH/timci documentation built on April 11, 2024, 8:31 a.m.