Skip to contents

Changelog

Source: NEWS.md

fishtree (development version)

  • taxon replaces rank as the argument that names a taxon, e.g., fishtree_phylogeny(taxon = "Acanthuridae"), and replaces ranks in fishtree_taxonomy(). rank and ranks still work, with a warning, and will be removed in fishtree 1.0.

  • fishtree_taxonomy() documents the fields that future versions will keep: species, sampled_species, unsampled_species and taxonomy for each taxon, and the rank and name columns of the table of taxa. Its other fields are deprecated and will be removed in fishtree 1.0. Look up ranks in taxonomy by name, not position.

  • New fishtree_releases() and fishtree_release() list the tree releases on the Fish Tree of Life and describe one: how to cite it, its license, and its files with their URLs, sizes and SHA-256 checksums.

  • Every function has a new release argument, which defaults to getOption("fishtree.release", "R2018"). The default is fixed for each version of fishtree, so a new release on the website never changes your results. Looking up a taxon is only available for "R2018".

  • fishtree now finds its files through the data manifest at https://fishtreeoflife.org/data/manifest.json. Set options(fishtree.manifest = ...) to use another copy.

  • Downloads are checked against their size and, on R 4.5.0 and later, their SHA-256 checksum in the manifest. They’re kept in a cache that lasts between sessions; see fishtree_cache_info() and fishtree_cache_clear().

  • Downloads now wait at least 10 minutes before timing out.

  • Taxa with spaces in their names (e.g., “Incertae sedis in Carangaria”) now work with fishtree_taxonomy() and all functions that take a taxon = ... argument.

fishtree 0.3.4

CRAN release: 2021-01-30

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

fishtree 0.3.3

CRAN release: 2020-10-31

fishtree 0.3.2

CRAN release: 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

CRAN release: 2019-05-31

  • fishtree_tip_rates now warns on missing / invalid species.

fishtree 0.3.0

CRAN release: 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

CRAN release: 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

CRAN release: 2018-11-30

  • Initial release.