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thibautjombart / apex

Phylogenetic Methods for Multiple Gene Data
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Add extra arguments to further address #2 #3

Closed zkamvar closed 9 years ago

zkamvar commented 9 years ago

This appears to pass check.

mlst = TRUE will render the resulting genind object with the number of loci equal to the number of genes.

gapIsNA = TRUE will turn genes that are all gaps to NAs.

Both of these are off by default.

thibautjombart commented 9 years ago

Looks great!

On Fri, Mar 20, 2015 at 7:50 PM, Zhian N. Kamvar notifications@github.com wrote:

This appears to pass check.

mlst = TRUE will render the resulting genind object with the number of loci equal to the number of genes.

gapIsNA = TRUE will turn genes that are all gaps to NAs.

Both of these are off by default.

You can view, comment on, or merge this pull request online at:

https://github.com/thibautjombart/apex/pull/3 Commit Summary

  • Add export for mslt. Not documented.
  • add mlst and gapIsNA options to multidna2genind.
  • add insignificant comma
  • merge master from thibaut

File Changes

Patch Links:

— Reply to this email directly or view it on GitHub https://github.com/thibautjombart/apex/pull/3.

zkamvar commented 9 years ago

Can this branch be merged?

thibautjombart commented 9 years ago

I am merging it but there are problems. Your branch is fine, but @KlausVigo pushed changes on the master branch which break the package.

thibautjombart commented 9 years ago

Can't easily re-merge into an older state without messing around. I'll push as is and disable stuff that's broken.