An interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information for ray-finned fishes.
The goal of
fishtree is to provide an easy interface to the Fish Tree
of Life API, to download taxonomies, phylogenies, diversification rate
information, and other data for ray-finned fishes.
See a list of taxa available to download.
library(fishtree)tax <- fishtree_taxonomy()head(tax)#> rank name#> 1 class Actinopteri#> 2 class Cladistia#> 3 subclass Chondrostei#> 4 subclass Neopterygii#> 5 infraclass Holostei#> 6 infraclass Teleostei
Retrieve a phylogeny for the surgeonfishes and plot the phylogeny and lineage through time plot.
library(ape)phy <- fishtree_phylogeny(rank = "Acanthuridae")phy#>#> Phylogenetic tree with 67 tips and 66 internal nodes.#>#> Tip labels:#> Acanthurus_mata, Acanthurus_blochii, Acanthurus_xanthopterus, Acanthurus_bariene, Acanthurus_dussumieri, Acanthurus_leucocheilus, ...#>#> Rooted; includes branch lengths.
par(mfrow=c(2, 1))plot(phy, show.tip.label = FALSE)ltt.plot(phy)
You can install the released version of fishtree from CRAN with:
Alternatively, download the development version with devtools:
The manuscript for this package is currently in review.
withr::with_envvar(c("NOT_CRAN" = "true"), devtools::release())
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.