fishtree 0.3.4 2021-01-30

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

fishtree 0.3.3 2020-10-31

fishtree 0.3.2 2019-12-17

  • 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 2019-05-31

  • fishtree_tip_rates now warns on missing / invalid species.

fishtree 0.3.0 2019-04-03

  • 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 2019-02-26

  • 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 2018-11-30

  • Initial release.