Interface to the Fish Tree of Life API

An interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information for ray-finned fishes.


BuildStatus CRANstatus

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.

Example

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)

Installation

You can install the released version of fishtree from CRAN with:

install.packages("fishtree")

Alternatively, download the development version with devtools:

devtools::install_github("jonchang/fishtree")

References

The manuscript for this package is currently in review.

Releasing

withr::with_envvar(c("NOT_CRAN" = "true"), devtools::release())

News

fishtree 0.2.0

  • 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

Initial release.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("fishtree")

0.2.0 by Jonathan Chang, 21 days ago


https://fishtreeoflife.org/


Report a bug at https://github.com/jonchang/fishtree/issues


Browse source code at https://github.com/cran/fishtree


Authors: Jonathan Chang [aut, cre] , Michael E Alfaro [ctb] , Daniel L Rabosky [ctb] , Stephen A Smith [ctb]


Documentation:   PDF Manual  


BSD_2_clause + file LICENSE license


Imports ape, rlang, jsonlite, utils

Suggests rfishbase, hisse, geiger, knitr, rmarkdown, picante, spelling


See at CRAN