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feedback #2
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hi @sckott, be good to check with @skembel on this. I think most of the functionality got ported to https://github.com/skembel/picante , and there are some newer methods for some of the stuff in phylocom , but I don't have a complete overview. |
Thanks @wcornwell - Im not up on how much of phylocom functionaluty is in picante. And I assume picante is pure R? So possibly speed improvement wrapping the C library? And I don't think phylomatic or bladj are in picante |
also good to check with @camwebb :) Hi Cam! |
Some but not all of the functionality in phylocom was ported to the picante package in R.
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Thanks for |
@skembel thanks! I'll make notes in the docs letting users know where using |
@camwebb thanks for
Any features/behavior you know about already? Is the API to Do you have a target date for release yet?
What kinds of things are you looking for? |
Main thing to fix on Not sure what you mean by the API. The CLI flags, arguments won't change though there might be some new flags. No release date yet. Just starting to think about this! Thx |
The user facing methods (e.g., aot, ecovolve, etc.). I ask because in an ideal world we wouldn't want to release this to CRAN and then a lot changes in the next version of |
I will commit to leaving all CLI interactions (and executable names) unchanged. See: phylocom/phylocom#22 |
thanks @camwebb |
@cboettig @fmichonneau @Pakillo @wcornwell (and let anyone else know that uses phylocom a lot)
curious to get feedback on this - if you use Phylocom that is, if not, nevermind :)
Jeroen was good enough to wrap Phylocom in R for us, - that is, it ships with the package, so works across operating systems. - no need to require users to install it separately. unfortunately, it's not ideal situation since we don't link to it via Rcpp like a proper C library, we just call the executables, but its best we can do, and better than shelling out separately.
I've been working on higher level interfaces to each of the things one can do with Phylocom. Look at the readme https://github.com/ropensci/phylocomr#phylocomr for some examples. Not all higher level things are done yet
Thoughts? Feedback?
one usecase I need it for right now is in the
brranching
package to call phylomatic locally for when users have massive species lists https://github.com/ropensci/brranching/blob/master/R/phylomatic_local.RThe text was updated successfully, but these errors were encountered: