CRAN release 2.1

[zachary-foster]

I think I have made all the changes I want for a minor version release. Its actually been a while and a lot of changes have accumulated. Here is the news for this version so far:

Improvements

• parse_tax_data can now incorperate rank information which can be accessed by result$taxon_ranks() (issue #113).
• taxmap print methods now have more information and color (issue #124).
• Added leaves_apply function that works like subtaxa_apply, but on leaves (issue #126).
• Functions with a value option now return named taxon indexes by default, instead of unnamed taxon indexes (issue #128).
• lookup_tax_data and extract_tax_data can now use "fuzzy" matching when looking up taxon names, so taxon names can be mispelled and still be founds.
• lookup_tax_data and extract_tax_data now only look up unique sequence IDs, improving download speed.
• filter_obs now can filter out observations in non-target data sets that are assocaited with taxa that are removed when drop_taxa = TRUE (issue #143). This is done using filter_taxa, so the supertaxa, subtaxa, and reassign_obs options are now available to filter_obs to control how taxon removal is done.
• lookup_tax_data and extract_tax_data now have progress bars instead of printing lots of text when downloading information.
• mutate_obs now creates new vector/tables if the data set specified does not exist (issue #121).
• Add filter_taxa option keep_order that preserves input taxon order. It is TRUE by default, which changes how it used to work. Set to FALSE for old behavior.
• Using NSE with an ambiguous name (appears in multiple datasets) now produces a warning (issue #153).

Changes

• The simplify option in many functions is now always handled the same way: If all vectors in a list are names, then unique key-value pairs are returned. Otherwise, names are ignored and unique values are returned.
• The leaves option now behaves like subtaxa, returning all leaves for each taxon. The old behavior can be replicated by setting the new simplify option to TRUE (issue #127).

Bug fixes

• filter_taxa now has better error messages for invalid inputs (issue #117).
• Fix a bug that caused an error in filter_taxa when no taxa pass filter (issue #116).
• Fixed a bug in parse_tax_data when class_key was not named (issue #131).
• Fixed bug in hierarchy print method with taxon_id class was not used (issue #138).
• Fixed bug in parse_tax_data when all classification data is NA.
• Fixed bug in taxmap print method when printing zero-length lists and vectors (issue #148).

@sckott, is there anything you want done before another release to CRAN? I can think of the folllowing:

• [x] make sure news is up to date
• [x] make me maintainer (Thanks @sckott!)
• [x] update version number

anything else? Thanks

[sckott]

not that I can think of, though should these two issues https://github.com/ropensci/taxa/milestone/3?closed=1 be included in this milestone since they are closed ?

[zachary-foster]

The one about how to handle filtering datasets with no taxon IDs is done. datasets without valid taxon IDs are not modified by filter_taxa.

The other one will be implemented as discussed in #139, but I want to for the next release for that since it will involve changing a lot of code.

They can be included in this milestone, although I have not been using this milestone until very recently so there are probably a lot of other issues with no milestone that were closed but will be implemented in this release.

[sckott]

okay, just trying to check if any closed issues should go in here that didn't get this milestone label.

[zachary-foster]

Ahh ok, I will go through the recently closed ones and add them to this milestone

[zachary-foster]

I think everything is read for a release now. @sckott, do you need to email CRAN about the change of maintainer or did you already do that?

[sckott]

already did, see email from Feb 1

Then please resubmit with yourself as the maintakner citing this message in the submisison comments.

[zachary-foster]

For some reason I cant find that email. Can you forward it to me please?

[sckott]

done

[zachary-foster]

got it, thanks