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
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.
You can install the released version of fishtree from CRAN with:
Alternatively, download the development version with devtools:
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
fishtree package is licensed under a 2-clause BSD license.
Please consider sponsoring the maintenance of
fishtree via GitHub Sponsors.