https://github.com/jonchang/fishtree
The R interface to the Fish Tree of Life
https://github.com/jonchang/fishtree
cran phylogeny r
Last synced: 26 days ago
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The R interface to the Fish Tree of Life
- Host: GitHub
- URL: https://github.com/jonchang/fishtree
- Owner: jonchang
- License: other
- Created: 2018-08-14T21:59:27.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2025-04-30T20:13:26.000Z (about 1 month ago)
- Last Synced: 2025-05-05T05:06:39.796Z (26 days ago)
- Topics: cran, phylogeny, r
- Language: R
- Homepage: https://fishtree.fishtreeoflife.org
- Size: 12.2 MB
- Stars: 11
- Watchers: 3
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
out.width = "100%"
)
library(fishtree)
```
[](https://cran.r-project.org/package=fishtree)
[](https://cran.r-project.org/package=fishtree)
[](https://doi.org/10.1111/2041-210x.13182)
# 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.
```{r}
library(fishtree)
tax <- fishtree_taxonomy()
head(tax)
```
Retrieve a phylogeny for the surgeonfishes and plot the phylogeny and lineage through time plot.
```{r}
library(ape)
phy <- fishtree_phylogeny(rank = "Acanthuridae")
phy
```
```r
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](https://CRAN.R-project.org) with:
```r
install.packages("fishtree")
```
Alternatively, download the development version with devtools:
```r
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](https://doi.org/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](https://doi.org/10.1038/s41586-018-0273-1)
## License
The `fishtree` package is licensed under a [2-clause BSD license](https://opensource.org/licenses/BSD-2-Clause).
## Sponsorship
Please consider sponsoring the maintenance of `fishtree` via [GitHub Sponsors](https://github.com/sponsors/jonchang).
## Releasing
```
withr::with_envvar(c("NOT_CRAN" = "true"), devtools::release())
```