r modify and rebuild package

Question

I'm trying to use the SemiMarkov package and I want to change one small line of code in there. I've done some digging via:

getAnywhere("semiMarkov")

& I've identified that I want to change this line:

hessian <- diag(ginv(hessian(V, solution)))

to try something like:

hessian <- diag(ginv(pracma::hessian(V, solution)))

How do I go about this? Do I need to rebuild the package from scratch, and if so do I need rTools etc for this, or is there a simple-ish workaround (I'm a relevant R novice)? I've done some searching online and can't find anything obvious. Any ideas/pointers gratefully appreciated.

Answer 1

Linux environment

Starting with downloading the package source from CRAN.

• This is the landing page: https://cran.r-project.org/web/packages/SemiMarkov/index.html
• This is the package source: https://cran.r-project.org/src/contrib/SemiMarkov_1.4.2.tar.gz

Download and extract the source:

wget https://cran.r-project.org/src/contrib/SemiMarkov_1.4.2.tar.gz
tar -xvzf SemiMarkov_1.4.2.tar.gz

This should result in a directory named SemiMarkov. Open up the source (cd SemiMarkov), and modify as necessary.

Next, build the changes:

cd ..
R CMD build SemiMarkov/

This will result in a new archive file named SemiMarkov_1.4.2.tar.gz.

Lastly, install your modified archive:

R CMD INSTALL SemiMarkov_1.4.2.tar.gz

Windows environment

I'm less familiar with the Windows platform. *nix tooling is available in Cygwin, but it's painful. Instead, as Josh O'Brien points out, you should follow the Windows-specific instructions in the R Installation and Administration manual.

Answer 2

If you'd like to simply test out the effect of that change in an interactive R session, you can do so using trace(). Here's how:

1. Type trace("semiMarkov", edit=TRUE)
2. In the text editor that that launches, edit the line of interest.
3. Save the modified file.
4. Close the text editor
5. Back in R, use the modified function.