Is Graphviz needed when using R's pcalg?

My question is related to these explanations about the pcalg package in R. I am currently installing the required packages to run CDT’s graph-related PC.py. As the plotting is done using networkx, I figured Graphviz would not be needed.

Am I guessing correctly? Is there anything more I should know about these R requirements (say, about the path to the packages or some environment variables…)

Thanks, A.V

[Diviyan-Kalainathan]

Hi, D2C is not required at the moment; I planned to add the algorithm, so I added the requirement in advance, but it isn’t used at the moment.

So maybe skip D2C. The R requirements are managed independently for each algorithm so no issues there. To run PC, you only need to have pcalg, kpcalg and RCIT:

and install RCIT from my fork repo, it contains an adaptation of the author’s code to make it work with CDT

from cdt.causality.graph.PC:

    def __init__(self, CItest="gaussian", method_indep='corr', alpha=0.01,
                 njobs=None, verbose=None):
        """Init the model and its available arguments."""
        if not (RPackages.pcalg and RPackages.kpcalg and RPackages.RCIT):
            raise ImportError("R Package (k)pcalg/RCIT is not available. "
                              "RCIT has to be installed from "
                              "https://github.com/Diviyan-Kalainathan/RCIT")

I should add in the documentation the required R packages for each algorithm.

Best, Diviyan

[Diviyan-Kalainathan]

It should be done ! I will close this issue, don’t hesitate to reopen it if an issue arises.