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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Make sure to edit the .Rmd file and not the .md -->
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
results = "asis",
echo = TRUE,
comment = "#>",
fig.path = "vignettes/figures/README-",
out.width = "100%"
)
library(OpenTreeChronograms)
if (!requireNamespace("versions")) {
install.packages("versions")
}
```
<!-- <img src='https://github.com/phylotastic/datelife/raw/master/man/figures/datelife-hexsticker-ai.png' align='right' style='width:150px' />
[![CRAN status](https://www.r-pkg.org/badges/version/datelife)](https://CRAN.R-project.org/package=datelife)
-->
![GitHub R package version](https://img.shields.io/github/r-package/v/phylotastic/OpenTreeChronograms?color=green&label=GitHub)
[![R-CMD-check](https://github.com/phylotastic/OpenTreeChronograms/workflows/R-CMD-check/badge.svg)](https://github.com/phylotastic/OpenTreeChronograms/actions)
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# OpenTreeChronograms: a database of phylogenetic trees with branch lengths proportional to time
Welcome to `OpenTreeChronograms` GitHub repository!
`OpenTreeChronograms` is an R package that hosts a chronogram database assembled with data from the Open Tree of Life phylogenetic database, the [Phylesystem](https://github.com/OpenTreeOfLife/phylesystem-1).
`OpenTreeChronograms` has been developed to work along with the
[`datelife` R package](http://phylotastic.org/datelife/index.html).
## README topics:
- [Installation](#local)
- [Loading](#loading)
- [Citation](#citing)
- [License](#license)
- [Funding](#funding)
## Local installation of the `OpenTreeChronograms` R package
`OpenTreeChronograms`'s most recent stable version can be installed with:
```{r, eval = FALSE}
install.packages("OpenTreeChronograms")
```
`OpenTreeChronograms`'s previous stable versions are available for installation from the CRAN repository.
For example, to install `version 2022.01.28`, you can run:
```{r eval = FALSE}
devtools::install_version("OpenTreeChronograms", version="2022.01.28")
```
You can install `OpenTreeChronograms`'s development version from its GitHub repository with:
```{r eval = FALSE}
devtools::install_github("phylotastic/OpenTreeChronograms")
```
## Loading the database
```{r, eval = FALSE}
data("opentree_chronograms", package = "OpenTreeChronograms")
```
```{r, eval = TRUE}
opentree_chronograms$version
opentree_chronograms$update
```
## Citing `OpenTreeChronograms`
If you use `OpenTreeChronograms` for a publication, please cite the Open Tree of Life database Phylesystem, the `OpenTreeChronograms` R package, the accompanying paper, and all chronograms used.
## License
This package is free and open source software, licensed under GPL.
## Funding
`OpenTreeChronograms` was developed and is maintained as part of the Datelife project, funded by the [phylotastic](http://phylotastic.org/) and the [Open Tree of Life](https://tree.opentreeoflife.org/about/open-tree-of-life) projects.