Using roxygen2 and doxygen on the same package? [closed]

I personally use the following code in a "dataManagement" package I call in all my scripts. It has roxygen documentation and examples. You actually simply call document()and have doxygen ran on the C code, in src/. The doc is put in inst/doxygenSo that your package is CRAN ready.

The R documentation being designed for R end users not supposed to look at the C code I didn't integrate the C code documentation in the classic R documentation but it would probably be a good practice to copy the resulting C documentation as a "vignette".

    library("testthat")    library("devtools")    #' @title Replace a value for a given tag on file in memory    #' @description Scan the lines and change the value for the named tag if one line has this tag,     #'    add a line at the end if no line has this tag and return a warning if several lines    #'    matching the tag    #' @param fileStrings A vector with each string containing a line of the file    #' @param tag The tag to be searched for     #' @param newVal The new value for the tag    #' @return The vector of strings with the new value    #' @examples    #' fakeFileStrings <- c("Hello = world","SURE\t= indeed","Hello = you")    #'     #' expect_warning(ReplaceTag(fakeFileStrings,"Hello","me"))    #'     #' newFake <- ReplaceTag(fakeFileStrings,"SURE","me")    #' expect_equal(length(newFake), length(fakeFileStrings))    #' expect_equal(length(grep("SURE",newFake)), 1)    #' expect_equal(length(grep("me",newFake)), 1)    #'     #' newFake <- ReplaceTag(fakeFileStrings,"Bouh","frightened?")    #' expect_equal(length(newFake), length(fakeFileStrings)+1)    #' expect_equal(length(grep("Bouh",newFake)), 1)    #' expect_equal(length(grep("frightened?",newFake)), 1)    ReplaceTag <- function(fileStrings,tag,newVal){        iLine <- grep(paste0("^",tag,"\\>"),fileStrings)        nLines <- length(iLine)        if(nLines == 0){            line <- paste0(tag,"\t= ",newVal)            iLine <- length(fileStrings)+1        }else if (nLines > 0){            line <- gsub("=.*",paste0("= ",newVal),fileStrings[iLine])            if(nLines >1){                warning(paste0("File has",nLines,"for key",tag,"check it up manually"))            }        }        fileStrings[iLine] <- line        return(fileStrings)    }    #' Prepares the R package structure for use with doxygen    #' @description Makes a configuration file in inst/doxygen    #'     and set a few options:     #'     \itemize{    #'        \item{EXTRACT_ALL = YES}    #'        \item{INPUT = src/}    #'        \item{OUTPUT_DIRECTORY = inst/doxygen/}    #'     }    #' @param rootFolder The root of the R package    #' @return NULL    #' @examples     #' \dontrun{    #' DoxInit()    #' }    #' @export    DoxInit <- function(rootFolder="."){        doxyFileName <- "Doxyfile"        initFolder <- getwd()        if(rootFolder != "."){            setwd(rootFolder)        }        rootFileYes <- length(grep("DESCRIPTION",dir()))>0        # prepare the doxygen folder        doxDir <- "inst/doxygen"        if(!file.exists(doxDir)){            dir.create(doxDir,recursive=TRUE)        }        setwd(doxDir)        # prepare the doxygen configuration file        system(paste0("doxygen -g ",doxyFileName))        doxyfile <- readLines("Doxyfile")        doxyfile <- ReplaceTag(doxyfile,"EXTRACT_ALL","YES")        doxyfile <- ReplaceTag(doxyfile,"INPUT","src/")        doxyfile <- ReplaceTag(doxyfile,"OUTPUT_DIRECTORY","inst/doxygen/")        cat(doxyfile,file=doxyFileName,sep="\n")        setwd(initFolder)        return(NULL)    }    #' devtools document function when using doxygen    #' @description Overwrites devtools::document() to include the treatment of     #'    doxygen documentation in src/    #' @param doxygen A boolean: should doxygen be ran on documents in src?    #'     the default is TRUE if a src folder exist and FALSE if not    #' @return The value returned by devtools::document()    #' @example    #' \dontrun{    #' document()    #' }    #' @export    document <- function(doxygen=file.exists("src")){        if(doxygen){            doxyFileName<-"inst/doxygen/Doxyfile"            if(!file.exists(doxyFileName)){                DoxInit()            }            system(paste("doxygen",doxyFileName))        }        devtools::document()    }