Salix Dubois

Since ids aren't used at all in the current function, I wanted to check how many binom+sequences were duplicated. Turns out, there's quite a few, the duplicates represent ~ 32%...

Sequences with binominal species aren't in silva_species_assignment_v138.1.fa.gz

1

I was looking at the function making the silva_species_assignment_v138.1.fa.gz file from SILVA_138_SSURef_tax_silva.fasta.gz. I noticed that since only sequences with 7 taxonomy fields are chosen, some sequences who do have binomial...

Update to bold::bold_tax_id()

1

Not so much an issue with taxize, but I made an update to {bold} and if using the dev version (or when it pass to CRAN) the classification using the...

I had some issues trying to use the 'color_by' argument in `plot_weight`. When using a character vector, I got the error: ``` Error in if ((length(color_by) == 1) && is.character(color_by)...

The single & at line [393 of 'utils.R'](https://github.com/bioFAM/MOFA2/blob/e605bf285bfa3ed98b3ebfb3b2e9d2b7a68c2717/R/utils.R#L393) and at line [604 of 'plot_weigths.R'](https://github.com/bioFAM/MOFA2/blob/e605bf285bfa3ed98b3ebfb3b2e9d2b7a68c2717/R/plot_weights.R#L604) was preventing the use of a character vector for the argument `color_by` since it wouldn't stop...

Discrepancies between Taxonomy API and Public API

2

# Availability of taxa Some species can't be found by name or id using the Taxonomy API (`bold_tax_name()`|`bold_tax_id()`) but still have public records ("Moraea elsiae", for example). `bold_stats(ids = "GBVC3127-11")`...

fix for cran

Issue #107 made me see things I wanted to change for tests so making an issue so I don't forget to do them.