Leo Lahti

Currently `mapTaxonomy` is slow for longer taxa vectors. This seems be because it maps every entry along taxa vector separately, instead of mapping unique entries and then mapping back to...

Rarified beta diversity calculations

10

Would be nice to have beta diversity calculations with rarefaction, as described in [Pat Schloss recent preprint](https://www.biorxiv.org/content/10.1101/2023.06.23.546313v1). Now, this can be achieved by using `vegan::avgdist` function as follows. I am...

Regarding the latest developments in `addAlpha()` in #460 I realized that we could also need `getAlpha()` as an exported function. For instance in altExp mechanism one might like to retrieve...

readQZA fails

3

I tried to load example files "distance.qza" and "ordination.qza" from [QIIME/DEICODE tutorial](https://library.qiime2.org/plugins/deicode/19/). After downloading them I did in R: ``` distance.qiime

We co-authored a fast Faith index calculation, potentially this could be called from R: https://genome.cshlp.org/content/31/11/2131 Ideally, we could utilize the same fast solution by calling it from mia. This might...

Rarefaction as optional strategy for alpha diversity

2

Ref: Pat Schloss' [recent analyses](https://www.biorxiv.org/content/10.1101/2023.06.23.546313v1.full.pdf) on rarefaction in alpha & beta diversity. This addressess well some of the long debates and controversies surrounding rarefaction in microbial ecology. Based on this...

Bray-Curtis issue

5

It was reported by @nuorenarra that the _vegan_ "bray" dissimilarity default does not correspond to the standard version of the widely known Bray-Curtis dissimilarity. TODO: let us consider how the...

Clean up the manpages

3

The html manpages do not always render well, see e.g. https://microbiome.github.io/mia/reference/getExperimentCrossAssociation.html

loadFrom* documentation

4

The function `loadFromBiom` has outdated example section: - refers to `se` (not `tse`) as function output, although the function seems to return TreeSE - converts SE to TreeSE although the...

Critical issue with mergeFeaturesByPrevalence

13

Unexpected and potentially critical behavior with `mergeFeaturesByPrevalence`. Let's first prepare example data. ``` library(mia) data(GlobalPatterns, package="mia") tse 0.5/100) > 0.2) #>26 sum(rowMeans(assay(altExp(tse, "Family2"), "relabundance") > 0.5/100) > 0.2) #>19 ```...