README.Rmd

---
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")
}
```

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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.