Vladimir Mikryukov
Vladimir Mikryukov
Dear PGLMM gurus, Unfortunately, currently there is no `predict(object, newdata = ...)` method for `communityPGLMM` class, and it is only possible to extract the fitted values with `fitted.communityPGLMM`. In particular,...
This PR adds `sourmash` as an additional profiler. Related to https://github.com/nf-core/taxprofiler/issues/112 NOTES: 1. Database Sourmash supports several [types of databases](https://sourmash.readthedocs.io/en/latest/databases.html#types-of-databases). For taxprofiler, I propose to use a single ZIP file...
**Metaxa2**: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data https://microbiology.se/software/metaxa2/ [doi:10.1111/1755-0998.12399](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12399)
It seems that `dissimilarity_to_distance` function (which transforms non-metric dissimilarity matrix to a weighted Euclidean distance) works only with data where number of samples > number of species. Otherwise, `smacof::smacofConstraint` returns...
- [ ] Implement Knijnenburg et al. 2009 approach (as a robust alternative to SES) in phylogenetic diversity estimation. See: - Botta-Dukát Z. 2018: https://akademiai.com/doi/abs/10.1556/168.2018.19.1.8 - Knijnenburg et al. 2009:...
Should we switch from [plyr](https://github.com/hadley/plyr) to [purrr](https://github.com/tidyverse/purrr)? Check also [multidplyr](https://github.com/hadley/multidplyr) (a backend for dplyr) to parallelize the code. + see [the comprehensive tutorial on this topic by Jenny Bryan](https://jennybc.github.io/purrr-tutorial/bk01_base-functions.html) and...
Need to implement efficient rarefaction function based on [RTK](https://github.com/hildebra/Rarefaction).
It should be quite easy to parallelize plyr-dependent functions to speed up processing of data. Functions that could be modified to accept parallel option: - [x] `phyloseq_mult_raref` - [ ]...
Currently, no tests other than examples in the manual are part of the package. See [testthat](https://github.com/hadley/testthat) package (+[test workflow example](http://r-pkgs.had.co.nz/tests.html)).