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_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_tip_rates now warns on missing / invalid
species.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.
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.