fishtree_alignment() now works correctly with
species = ... arguments.
.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 programatically determine which species are missing, without parsing error messages.
Converted some warnings to messages.
Minor documentation changes.
fishtree_complete_phylogeny, gets complete phylogenies where unsampled taxa were placed using stochastic polytomy resolution.
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_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.