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.