metagMisc
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vmikk
Miscellaneous functions for metagenomic analysis.
I believe dependencies in phyloseq_inext may be compromised. The function was working for me beautifully maybe a week ago, and now the example code associated with this function is no...
**My Code:** ``` # Merge seq and tree OTU otu_tree Phylogenetic tree with 17 tips and 15 internal nodes. Tip labels: Amblychaeturichthys_hexanema, Chaeturichthys_stigmatias, Ctenotrypauchen_chinensis, Odontamblyopus_lacepedii, Hexagrammos_otakii, Pholis_fangi, ... Unrooted; includes...
this error: Errore in sort.list(bx[m$xi]) : 'x' dev'essere atomico per 'sort.list', metodo "shell" e "quick" Si è chiamato 'sort' su una lista? In aggiunta: Messaggi di avvertimento: 1: : ......
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)).