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
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