R/rmd_setup.R

In MikhaelManurung/mdmisc: MDM's Miscellaneous

#All output (including figures/cache/objects/.html) will be generated in a subdirectory of "wd" named "subdir".
# Need to adapt this with here::here
rmd_setup <- function(proj_dir, sub_dir, ...) {
    library("knitr")

    # Set knitr
    if (grepl("/dla_mm", getwd())) {
        proj_wd <- paste("/hpc/dla_mm/bogaert", proj_dir, "wd", paste0(sub_dir, "/"), sep="/")
    } else {
        proj_wd <- paste("/Users/Wouter/Documents/Research_Folder/projects", proj_dir, "wd", paste0(sub_dir, "/"), sep="/")
    }

    opts_knit$set(aliases=c(h = "fig.height", w = "fig.width", ow = "out.width", fa="fig.asp"),
                  root.dir = proj_wd)

    # Create directories if these do not exist yet
    if(!dir.exists(opts_knit$get("root.dir")))  {
        dir.create(paste0(opts_knit$get("root.dir"), "figures"), recursive = TRUE)
        dir.create(paste0(opts_knit$get("root.dir"), "RData"))
    }

    # Set environment working directory
    setwd(opts_knit$get("root.dir"))

    # Figures will be saved in a subdirectory
    knitr::opts_chunk$set(warning = FALSE,
                          message = FALSE,
                          keep_md = FALSE,
                          results = "markup",
                          dpi = 150,
                          # depreciated because svg does not render as beautiful as pdf
                          dev = c("png", "pdf"),
                          fig.path = paste0(getwd(), "/figures/"),
                          ow='70%', w=7, fa=0.618, fig.align = "center")
    #,tidy = FALSE,
    #tidy.opts=list(blank = TRUE, width.cutoff = 60), ...)

    message(paste0("Working directory is set to: ", getwd(), "."))
}