In shug0131/cctu: In-house Functions for Report Writing at Cambridge Clinical Trials Unit

library(cctu)
library(magrittr)

PATH_figure <- file.path(getwd(),"Output","Figures")

meta_table <- read.csv(file=file.path("Output","meta_table.csv"), stringsAsFactors = FALSE)
index <- order_dewey(meta_table$number)
meta_table <- meta_table[index,]
rm(index)

sections <- unique(meta_table$section)
src <- as.character(NULL)
for(sect in sections){
  src <- c(src, paste("\n#", sect)) 
  subtab <- subset(meta_table, section==sect)
  for(row in 1:nrow(subtab)){
    src <- c(src, paste("\n##", subtab[row,"number"], subtab[row,"title"], "\nPopulation:", subtab[row,"population"]))
    if( !is.na(subtab[row,"subtitle"])){ src <- c(src, paste("\nSubtitle:",subtab[row,"subtitle"]))}

    if( subtab[row,"item"] %>% tolower=="table"){
          file_name <- file.path("Output","Core",paste0("table_",subtab[row,"number"],".xml") )
        # knit exapnd really doesn't like absolute paths or \ or \\
        if( file.exists(file_name)){
          src <- c(src, 
               knitr::knit_expand(file=file.path("Progs","table.Rmd") %>% normalizePath(),
                           chunk_name=paste0("table",subtab[row,"number"]),
                           file_name=file_name 
                           )
          )}
    }


    if( subtab[row,"item"] %>% tolower=="text"){
          file_name <- paste0("Output/Core/text_",subtab[row,"number"],".xml") 
        # knit exapnd really doesn't like absolute paths or \ or \\
        if( file.exists(file_name)){
          src <- c(src, 
               knitr::knit_expand(file="Progs/text.Rmd" %>% normalizePath(),
                           chunk_name=paste0("text",subtab[row,"number"]),
                           file_name=file_name 
                           )
          )}
    }


    if(subtab[row,"item"] %>% tolower=="figure" ){
      file_name <- file.path(PATH_figure,paste0("fig_",subtab[row,"number"],".png"))
      if( file.exists(file_name)) src <- c(src, paste0("![](",file_name,") \n" ))
    }
    if( !is.na(subtab[row,"footnote1"])){ src <- c(src, paste("\n",subtab[row,"footnote1"]))}
    if( !is.na(subtab[row,"footnote1"])){ src <- c(src, paste("\n",subtab[row,"footnote2"]))}
  }
}

r knitr::knit_child(text=src, envir=parent.frame())

Actual implimentation

This would typically be called from main.R like, to achieve a html version of the main report.

rmarkdown::render(file.path("Progs","rmarkdown_report.Rmd"),
       output_file ="Vignette Report.html",output_dir = file.path("Output","Reports"),
       params=list(my_author="Simon Bond",
                   my_title= "Vignette Report")
)

NB use the file /scripts/Progs/rmarkdown_report.Rmd and not the similarly named one within /scripts . Building vignettes requires these two slighlty different versions.

shug0131/cctu documentation built on Nov. 10, 2023, 12:03 p.m.