The goal of fishtree
is to provide an easy interface in R to the Fish Tree of Life API, to download taxonomies, phylogenies, diversification rate information, and other data for ray-finned fishes. It should seamlessly integrate with the rest of the R ecosystem, especially the package ape
.
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.
You can also check out the vignettes for more detailed examples.
Installation
You can install the released version of fishtree from CRAN with:
install.packages("fishtree")
Alternatively, download the development version with devtools:
if (!requireNamespace("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("jonchang/fishtree")
References
To cite fishtree
in publications use:
Chang, J., Rabosky, D. L., Smith, S. A., & Alfaro, M. E. (2019). An R package and online resource for macroevolutionary studies using the ray‐finned fish tree of life. Methods in Ecology and Evolution, 10(7) 1118-1124. doi: 10.1111/2041-210x.13182
The primary data source for fishtree
was published as a part of:
Rabosky, D. L., Chang, J., Title, P. O., Cowman, P. F., Sallan, L., Friedman, M., Kaschner, K., Garilao, C., Near, T. J., Coll, M., Alfaro, M. E. (2018). An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559(7714), 392–395. doi: 10.1038/s41586-018-0273-1
License
The fishtree
package is licensed under a 2-clause BSD license.
Sponsorship
Please consider sponsoring the maintenance of fishtree
via GitHub Sponsors.