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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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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…
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I want to rarefy my samples to the first quartile.
i don't understand how `mp_cal_rarecurve()` works with this?
```
mouse.time.mpse %%
mp_cal_rarecurve(
.abundance = RareAbundance,
…
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- [ ] smooth out sSBR by averaging it over at a minimum 20 runs. Currently the sSBR looks very jagged which largely reflects the particulars of the random walk that it took in sampling. By doing this …
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Should we switch using [vegan::rrafefy](https://rdrr.io/cran/vegan/man/rarefy.html) (it is fast since it is programmed with C)? One downside is that it does not support `replace`. Moreover, one thing …
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**Improvement Description**
A forum user [suggested](https://forum.qiime2.org/t/seeding-the-rarefaction-algorithm/76) that we add support for seeding rarefaction, which is an interesting idea for sup…
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it would make it easier for users to compute the non-spatial sampled based rarefaction curve if they only have to input the reference density and not the argument `dens_ratio` which is the ratio of t…
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hello
thank you for all these great tools.
would it be possible to generate rarefaction curve to assess sampling depth (e.g. by subsampling data without replacement at XXX sequence increments, and…
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Hi,SourceTracker team,
I used my otu_table and the corresponding map-file to run the code
`sourcetracker2 gibbs -i otu_table.biom -m map-file.txt -o try1/`
And an error raised:
**ValueError: Inva…