Rmarkdown

For some reason, the filename extension either needs to be .rmd or can't be .txt.

I first tried this downloaded file which arrived as .txt and it didn't execute any of the R code.

R -e "rmarkdown::render('example-r-markdown.rmd',output_file='example-r-markdown.rmd.html')"

open example-r-markdown.rmd.html 

I don't think that it needs to be broken up into smaller blocks unless you want to. I think that rmarkdown will break it up if anything is output. Of course, if you need to add your own text, you will need to do it manually.

Self executable ...

Start your myfile.Rmd with ...

#!/usr/bin/env Rscript

args <- commandArgs()
fname <- normalizePath(sub("--file=", "", args[grepl("--file=", args)]))
thisfile <- readLines(fname)
newfname <- paste0(tempdir(), "/", basename(fname))
writeLines(thisfile[-1:-which(thisfile == "q(\"no\")")], newfname)

args = commandArgs(trailingOnly=TRUE)
#output_file = paste(basename(fname),basename(args[2]),"html", sep=".")
output_file = paste(basename(fname),"html", sep=".")
print(output_file)

rmarkdown::render(newfname, output_dir = dirname(fname), output_file = output_file )
q("no")

Anything after the q("no") line will be part of the actual rmarkdown.

This also allows for the use of positional arguments. In this case, I use one in the initial script and later on I ...

meta=args[1]
ifile=args[2]

I still don't get the difference between = and <- in R. I've used them interchangeably with no obvious issues.

Rmarkdown example

Complete example of self executing script that takes command line arguments, that could be used to control the output file, includes a table of contents, 2 different tab sets and could use python.

#!/usr/bin/env Rscript

args <- commandArgs()
fname <- normalizePath(sub("--file=", "", args[grepl("--file=", args)]))
thisfile <- readLines(fname)
newfname <- paste0(tempdir(), "/", basename(fname))
writeLines(thisfile[-1:-which(thisfile == "q(\"no\")")], newfname)

args = commandArgs(trailingOnly=TRUE)
#output_file = paste(basename(fname),basename(args[2]),"html", sep=".")
output_file = paste(basename(fname),"html", sep=".")
print(output_file)

rmarkdown::render(newfname, output_dir = dirname(fname), output_file = output_file )
q("no")


---
title: RMD TEST
author: Jake
date: 20221122
output: 
  html_document:
    toc: true # table of content true
    toc_depth: 3  # upto three depths of headings (specified by #, ## and ###)
    number_sections: true  ## if you want number sections at each table header
    theme: united  # many options for theme, this one is my favorite.
    highlight: tango
---


#	Description

This Rmd is self executed.

Take command line arguments.

Build a Table of Contents.

And demonstrates tab sets.


# Load libraries and read data {.tabset .tabset-fade .tabset-pills}

<!--

THAT MUST BE FIRST TO BE USEFUL!

-->

```{r "Figure Settings", include = FALSE}
knitr::opts_chunk$set(fig.width=12, fig.height=8) 
```


# Tabset example {.tabset .tabset-fade .tabset-pills}

##	One
```{r setup}
library('reticulate')
```

##	Two
```{r python}
use_python('/opt/local/bin/python')
```

##	Three
```{r args}
args
```

##	Four
```{python pyargs}
r.args
```


# Another different style {.tabset .tabset-fade}

##	One

Content for One

##	Two

Content for Two

##	Three

Content for Three

Note that using the self-executing script will require that file parameters include a full path as it will be run in the temp dir and a file in the current directory won't be in the current directory when executed.