For typical R scripts the shebang syntax can be used to run the code within. With a file file.R
#!/usr/bin/env Rscript
<some R code here>
Running ./file.R will execute the code.
But can somehow the same be done with R-markdown? So that with a file named file.Rmd:
#!/usr/bin/env <some command>
<some markdown>
<some R code here>
<some markdown again>
Running ./file.Rmd would produce file.md?
You can treat an Rmd file as an Rscript. For instance, assume that your Rmd file looks like this
---
title: "Untitled"
author: "ekoam"
date: "`r Sys.Date()`"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
You can then prepend the following code to that Rmd file
#!/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)
rmarkdown::render(newfname, output_dir = dirname(fname))
q("no")
The trick here is q("no"). This line terminates the R session, and, thus, whatever written after it will be ignored. Such an effect also means high flexibility for coding because you can write almost any valid R code before that q("no"). The code above simply creates another temporary Rmd file with the same content as what is after q("no"). Then, we rmarkdown::render that temporary file and dump the output to the current directory.
The complete Rmd file looks like this
#!/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)
rmarkdown::render(newfname, output_dir = dirname(fname))
q("no")
---
title: "Untitled"
author: "ekoam"
date: "`r Sys.Date()`"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.