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I'm having a problem when I run rarefaction, it never finishes, it stays at 2679/2680.
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Hi !
I get this error and I can't debug why it happens, the input files look good to me
`TypeError: Population must be a sequence. For dicts or sets, use sorted(d).`
I'm using ppanggolin li…
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`rarefy_even_depth()` does not scale well. While rarefying is [problematic for some things](https://doi.org/10.1371/journal.pcbi.1003531), the subsampling approach still has its uses.
A simple way …
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Hello,
I acknowledge that I have submitted several posts to this GitHub Discussions in the past few weeks, and I always appreciate your prompt and helpful replies! This package and your replies have …
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Add support for subsampling BAM files to determine if sequencing was performed sufficiently. More specifically, the final goal is to determine metrics like %genome coverage or % 5x genome coverage as …
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- [x] I have the most recent version of poppr and R
- [ ] I have found a bug
- [x] I have searched for solutions on this site and the [poppr forum](https://groups.google.com/group/poppr)
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Until this is integrated, downstream analysis of core metrics calculations must be conducted separately after a manual rarefaction step.
Consider various techniques for automation:
* Good's coverage …
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Need to implement efficient rarefaction function based on [RTK](https://github.com/hildebra/Rarefaction).
vmikk updated
6 years ago
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## code refactoring
- [ ] `get_mob_stats` --> 316776f introduced `calc_comm_div` which accomplishes some of these (`get_mob_stats` is obsolete`)
- [x] output needs to be in as a `tibble` or `dat…
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As Sydne noted from reading the FAQ for hypervolume (see #14), it might be a problem if the overlaps are calculated across species with very different numbers of data points. This might be a problem f…