Leo Lahti

Informative error messages

1

The plot_landscape() and other functions fail if the named metadata variable is not present in the metadata (for instance color = "nationality" when the metadata does not have nationality). This...

Deprecate write_phyloseq

2

This function is now marked deprecated. Instead, add an example in the tutorial.

BMI categories differ by population. group_bmi function could have multiple options

read_mothur2phyloseq example broken

3

The read_mothur2phyloseq example is currently broken. The inst/extdata datasets will need to be moved to a separate data package or tutorial.

aggregate_taxa: add top argument

1

Had to remove the merge top taxa ("top" argument) functionality for now. Implement it back as the time allows.

Prepare microbiome cheat sheet. For a template, check [this](https://github.com/rOpenGov/eurostat/tree/master/inst/extras/cheatsheet)

Add Smith-Wilson evenness index.

Consider adding local, permanence and individual-based stability methods for competitive types: https://www.ncbi.nlm.nih.gov/pubmed/26542567

otu naming

1

Thanks to XXX: " - - This solution does not resolve all duplicates in the strain level data, so in the profile-level phyloseq object taxa rownames are simply indexes ‘sp’...