NEWS.md

In jonchang/fishtree: Interface to the Fish Tree of Life API

fishtree (development version)

fishtree 0.3.4

• This release fixes some tests, and has no new user-facing features.

fishtree 0.3.3

• The internal .get() function now avoids a build-time dependency on memoise::memoise(), per https://github.com/r-lib/memoise/issues/76

• Vignettes and citations have been updated to use the latest versions, where relevant.

fishtree 0.3.2

• fishtree_alignment() now works correctly with species = ... arguments.

• The internal .name_check function now emits structured warning output. This means that users supplying species names to e.g., fishtree_phylogeny that 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 0.3.1

• fishtree_tip_rates now warns on missing / invalid species.

fishtree 0.3.0

• New function: fishtree_complete_phylogeny, gets complete phylogenies where unsampled taxa were placed using stochastic polytomy resolution.

• Use package memoise instead of rolling our own caching functionality.

• New global option fishtree.quiet: when set to FALSE, be more verbose during downloads (can help with debugging issues).

• Some internal reorganization.

fishtree 0.2.0

• New function: fishtree_rogues, identifies rogue/intruder taxa that break the monophyly of a selected group.

• fishtree_phylogeny now permits downloads of MRCA trees for paraphyletic groups. Suggested by an anonymous reviewer.

• fishtree_taxonomy revamped. It now takes a single argument ranks = ... 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.

fishtree 0.1.0

• Initial release.

jonchang/fishtree documentation built on Dec. 18, 2024, 8:48 p.m.