fishtree 0.3.4
CRAN release: 2021-01-30
- This release fixes some tests, and has no new user-facing features.
fishtree 0.3.3
CRAN release: 2020-10-31
The internal
.get()function now avoids a build-time dependency onmemoise::memoise(), per https://github.com/r-lib/memoise/issues/76Vignettes and citations have been updated to use the latest versions, where relevant.
fishtree 0.3.2
CRAN release: 2019-12-17
fishtree_alignment()now works correctly withspecies = ...arguments.The internal
.name_checkfunction now emits structured warning output. This means that users supplying species names to e.g.,fishtree_phylogenythat do not have matches in the taxonomy may use functions that capture warning messages to programmatically determine which species are missing, without parsing error messages.Converted some warnings to messages.
Minor documentation changes.
fishtree 0.3.0
CRAN release: 2019-04-03
New function:
fishtree_complete_phylogeny, gets complete phylogenies where unsampled taxa were placed using stochastic polytomy resolution.Use package
memoiseinstead of rolling our own caching functionality.New global option
fishtree.quiet: when set toFALSE, be more verbose during downloads (can help with debugging issues).Some internal reorganization.
fishtree 0.2.0
CRAN release: 2019-02-26
New function:
fishtree_rogues, identifies rogue/intruder taxa that break the monophyly of a selected group.fishtree_phylogenynow permits downloads of MRCA trees for paraphyletic groups. Suggested by an anonymous reviewer.fishtree_taxonomyrevamped. It now takes a single argumentranks = ...where you can retrieve taxonomic information for any valid taxonomic rank in our taxonomy. Calling it without arguments returns a data frame of all valid taxa names. Suggested by an anonymous reviewer.