[Feature Request] Group present/Contradicted (GC) calculation

[HS6986]

Dear @ms609,

I think that it would be very useful if Group present/Contradicted (GC) values (Goloboff et al., 2005) could be calculated in TreeTools, for example from resampling results of TreeSearch. I would greatly appreciate it if you could implement it when you are available.

Thank you very much for your time and support.

[HS6986]

Since it will be almost exclusively for use for results produced by TreeSearch, I'm starting to think it might be better implemented directly in TreeSearch, like TreeSearch::JackLabels(). But of course, I’ll leave the decision up to you.

[ms609]

Nice idea – I've had a sprint and put together a draft implementation at TreeSearch::PresCont(). You will need to install development versions of TreeTools from the "split-contradict" branch (install_github("ms606/TreeTools", ref = "split-contradict")) and TreeSearch via install_github("ms606/TreeSearch", ref = "groups-present-contra").

It might be a while before I can test this rigorously: please let me know if you encounter any glitches or spot any potential improvements.

[HS6986]

Thank you very much for implementing those features.

I tested them using the examples, but the following error message occured:

Error in PresCont(tree, jackTrees) : object 'reference' not found

[ms609]

d'oh – missed a replacement during a final change to parameter names. Thanks for catching – didn't have time to implement test cases last night. Should be fixed if you update TreeSearch.

[HS6986]

Thank you for fixing the code. I updated TreeSearch, and the function worked properly.