GitHub - jonchang/fishtree: The R interface to the Fish Tree of Life (original) (raw)

fishtree

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.

par(mfrow=c(2, 1)) plot(phy, show.tip.label = FALSE) ltt.plot(phy)

You can also check out the vignettes for more detailed examples.

Installation

You can install the released version of fishtree fromCRAN 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.

Releasing

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