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fishtree

The R interface to the Fish Tree of Life

https://github.com/jonchang/fishtree

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.2%) to scientific vocabulary

Keywords

cran phylogeny r

Keywords from Contributors

interactive serializer packaging network-simulation shellcodes hacking autograding observability genomics embedded
Last synced: 6 months ago · JSON representation

Repository

The R interface to the Fish Tree of Life

Basic Info
Statistics
  • Stars: 12
  • Watchers: 3
  • Forks: 2
  • Open Issues: 3
  • Releases: 7
Topics
cran phylogeny r
Created over 7 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)
library(fishtree)
```

![Build status](https://github.com/jonchang/fishtree/workflows/CI/badge.svg)
[![CRAN status](https://www.r-pkg.org/badges/version/fishtree)](https://cran.r-project.org/package=fishtree)
[![CRANlogs downloads count](https://cranlogs.r-pkg.org/badges/fishtree)](https://cran.r-project.org/package=fishtree)
[![Digital object identifier](https://zenodo.org/badge/DOI/10.1111/2041-210x.13182.svg)](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: Jonathan Chang
  • Login: jonchang
  • Kind: user
  • Location: Los Angeles

GitHub Events

Total
  • Push event: 49
  • Pull request event: 1
  • Create event: 1
Last Year
  • Push event: 49
  • Pull request event: 1
  • Create event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 212
  • Total Committers: 4
  • Avg Commits per committer: 53.0
  • Development Distribution Score (DDS): 0.179
Past Year
  • Commits: 2
  • Committers: 2
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
Jonathan Chang j****1@g****m 174
Jonathan Chang me@j****g 32
dependabot[bot] 4****] 5
lbreedy 9****y 1
Committer Domains (Top 20 + Academic)
jonathanchang.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 11
  • Total pull requests: 14
  • Average time to close issues: 12 days
  • Average time to close pull requests: 11 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 2.27
  • Average comments per pull request: 0.07
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 14 days
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • jonchang (9)
  • jpwrobinson (1)
  • sarevalo7 (1)
Pull Request Authors
  • jonchang (7)
  • dependabot[bot] (6)
  • lbreedy (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (6) github_actions (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 340 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 3
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: fishtree

Interface to the Fish Tree of Life API

  • Versions: 7
  • Dependent Packages: 2
  • Dependent Repositories: 3
  • Downloads: 340 Last month
Rankings
Dependent packages count: 13.7%
Dependent repos count: 16.5%
Forks count: 17.0%
Stargazers count: 17.4%
Average: 20.4%
Downloads: 37.7%
Maintainers (1)
me@jonathanchang.org
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • ape >= 5.2 imports
  • jsonlite >= 1.5 imports
  • memoise * imports
  • parallel * imports
  • rlang >= 0.4.1 imports
  • utils * imports
  • diversitree * suggests
  • geiger * suggests
  • hisse >= 1.9.10 suggests
  • knitr * suggests
  • markdown * suggests
  • phytools * suggests
  • picante * suggests
  • rfishbase * suggests
  • rmarkdown * suggests
  • spelling * suggests
  • testthat * suggests
.github/workflows/ci.yml actions
  • Homebrew/actions/git-user-config master composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite