https://github.com/brunomioto/fishtree
The R interface to the Fish Tree of Life
Science Score: 23.0%
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○CITATION.cff file
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○codemeta.json file
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✓DOI references
Found 9 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Scientific vocabulary similarity
Low similarity (15.2%) to scientific vocabulary
Keywords from Contributors
projection
interactive
archival
generic
phylogeny
sequences
observability
autograding
hacking
shellcodes
Last synced: 6 months ago
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Repository
The R interface to the Fish Tree of Life
Basic Info
- Host: GitHub
- Owner: brunomioto
- License: other
- Default Branch: master
- Homepage: https://fishtree.fishtreeoflife.org
- Size: 4.73 MB
Statistics
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 0
Fork of jonchang/fishtree
Created about 3 years ago
· Last pushed about 3 years ago
Metadata Files
Readme
License
README.Rmd
---
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())
```
Owner
- Name: Bruno Mioto
- Login: brunomioto
- Kind: user
- Website: www.brunomioto.com
- Repositories: 44
- Profile: https://github.com/brunomioto
GitHub Events
Total
Last Year
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jonathan Chang | j****1@g****m | 174 |
| Jonathan Chang | me@j****g | 31 |
| dependabot[bot] | 4****] | 4 |
| lbreedy | 9****y | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 2 years ago
All Time
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- Total pull requests: 0
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- Bot pull requests: 0
Past Year
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- Pull requests: 0
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- Average comments per issue: 0
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