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macroevolution / bamm

A program for multimodel inference on speciation and trait evolution
GNU General Public License v2.0
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Check BAMMtools for upload to CRAN #89

Closed drabosky closed 10 years ago

drabosky commented 10 years ago

We need to have at least two people (other than me) go through all functions for BAMMtools and try to run all the examples to make sure all is well and that things make sense. Ideally, you will also have a look over R help files to look for:

1) Major formatting issues 2) Obvious errors (e.g., the arguments to the function listed in the help file do not match the actual arguments specified as defaults in the function definition) 3) Make sure examples run (this will be checked automatically when uploading to CRAN, so it is critical that they work) 4) Please flag any documentation that really is not clear - at this point is has been written by a number of us collectively.

redcurry commented 10 years ago

I volunteer to be one of those people.

ptitle commented 10 years ago

I can do this too.

drabosky commented 10 years ago

That will be great!

drabosky commented 10 years ago

If you haven't looked at this yet, I am going to update a couple of things this evening. Somewhat annoyingly, I thought of a way to make a couple of functions much better….

drabosky commented 10 years ago

I finished the changes I wanted to make. I think we can move forward with reviewing the package and the documentation together.

ptitle commented 10 years ago

Posting this here so that this can be confirmed as something to fix: In the BAMMtools help, 3 functions, getCohortMatrix, getBAMMCorrelationMatrix and getMacroevolutionaryCohortMatrix all point to the same help file, but only getCohortMatrix seems to exist as a function.

drabosky commented 10 years ago

ok, we can delete references to that. I think it was an earlier version of marginalShiftProbsTree

On Mar 3, 2014, at 2:43 PM, ptitle wrote:

The BAMMtools help index lists a function called ShiftProbsTree which does not seem to exist anymore.

— Reply to this email directly or view it on GitHub.

ptitle commented 10 years ago

Actually, I think I was mistaken. It's the name of the help file, but not the functions in the help file.