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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 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.

Releasing

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.