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

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

# 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

if (is_india) {
  hospit_value <- 13
} else{
  hospit_value <- 1
}

day7_wmin <- 7
day7_wmax <- 10
day28_wmin <- 28
day28_wmax <- 32

\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 Data Monitoring Report v1.0}

\setcounter{tocdepth}{2} \tableofcontents

\clearpage

r notice_str

r intro_str

start_date <- params$start_date
end_date <- params$end_date
sample_target <- params$sample_target

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

  facility_data <- params$facility_data
  raw_day7fu_data <- params$raw_day7fu_data
  raw_hospit_data <- params$raw_hospit_data
  raw_day28fu_data <- params$raw_day28fu_data
  raw_withdrawal_data <- params$raw_withdrawal_data
  wfa_data <- params$wfa_data

}

facility_data <- timci::correct_day0_all(facility_data)

if (nrow(facility_data) > 0) {
  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') {
    date_boundary_str <- paste0("Ce rapport couvre la période du **", start_date, "** (début de l'étude) au **", end_date, "** (semaine **", week_nb, "** de l'étude) pour le **Sénégal**.")
  } else {
    date_boundary_str <- paste0("This report covers the period from **", start_date, "** (study start) to **", end_date, "** (week **", week_nb,"** of the study) for **", Sys.getenv('TIMCI_COUNTRY'), "**.")
  }
  cat(date_boundary_str)
}

write(timci::formats2h2("Generate context maps"), stderr())

library(sf)     # classes and functions for vector data
library(raster) # classes and functions for raster data
library(spData)        # load geographic data
library(ggplot2)
library(gridExtra)
library(graphics)

out <- lapply(1:nrow(facilities),
              function(i) {
                knitr::knit_child('maps.Rmd',
                    envir = environment(),
                    quiet = TRUE)
                })
cat(unlist(out), sep = '\n')

detach("package:raster", unload=TRUE)
detach("package:spData", unload=TRUE)
detach("package:sf", unload=TRUE)
tmp <- gc() # garbage collection

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