You may use Rscript to run a .Rmd file and include any "R code" within the command line to keep your code chunks intact.

Rscript -e "library(knitr); opts_knit\$set(root.dir='~'); knit('test.Rmd')" is an example bash command to run the test.Rmd file below. You may change the root.dir to suit your needs.

make directories```{r mkdir, engine='bash'}mkdir mytestmkdir mytest2```create one file in the 1st dir```{r create, engine='bash'}cd mytesttouch myfile```create another file in the 2nd dir```{r create2, engine='bash'}cd mytest2touch myfile2```check contents```{r ls, engine='bash'}ls mytest*```

The output:

```## mytest:## myfile#### mytest2:## myfile2```

Another way of looking at it would be to create every folder and file from where you are, and not move around with cd.

Create a directory tree

mkdir accepts more than one argument

mkdir -p 'plots/scatter' 'plots/box'# creates plots folder in the working directory,# and then creates scatter and box folders in it.

Create files in there

touch 'plots/scatter/firstfile.txt' 'plots/scatter/secondfile.txt'# single quotes mean literals

Keep key parts as variables

To easily change the folder structure from a one central variable:

scatter_folder=plots/scattertouch "$scatter_folder/third_file.txt" "$scatter_folder/fourth_file.txt"# double quotes allow for variable substitution.