When you are creating an R package, you will have a directory tree containing the following (among others) in the root directory of the package: DESCRIPTION, NAMESPACE, and the R/ directory. If you also have an inst/ directory, then everything within that directory is copied verbatim to within your package directory, excluding the inst/.
For instance, if your package directory looks like this:
+- DESCRIPTION
+- NAMESPACE
+- inst/
| \- rmd/
| \- file.Rmd
\- R/
+- file1.R
+- file2.R
\- file3.R
Then when you build the package and install it, you'll find in the following in your package library:
+- DESCRIPTION
+- INDEX
+- NAMESPACE
+- rmd/
| \- file.Rmd
\- R/
+- packagename
+- packagename.rdb
\- packagename.rdx
(Other files/directories are created during the process, I'm ignoring them for simplicity.)
The last piece of information you need to know is "how do I access this file once it is installed?" Since some systems install the R library in different directories, and on top of that users often install packages within a personal R library, you cannot know a priori where to look Enter system.file:
system.file("rmd", "file.Rmd", package = "packagename")
## [1] "c:/R/R-3.1.3/library/packagename/rmd/file.Rmd"
This can be used for the whole Rmd file. I use it for company-specific templates for Rmd-rendered documents. That is, I look for "include" files to personalize the LaTeX so that the rendered PDF has headers/footers and is styled the way we want. This step requires writing a function that replaces the pdf_document (for example) in the Rmd YAML header, but that's covered well at rmarkdown.rstudio.com.
