I'm comfortable with package basics, but now I'd like to create a package containing functions that create html reports from Rmd files and user inputs.
Outside of a package I can just make a function including a render call with input = mypath.Rmd. How can I integrate this in a package ? Where do I put my Rmd files ? how do I call them ?
Files that don't fall into the usual directories of an R package can go in the inst directory. Hadley Wickham gives a good overview of the purpose and usage for that directory in his R Packages text. In short:
A package should only have standard files in the top directory.
Files that don't go in the top level or usual directories can go in the inst directory.
When creating a built package, everything from inst is copied to the top level of the bundle.
You can get the path to any file in a package using the system.file() function.
For your case, I'd suggest a directory structure like this (items ending with / are directories):