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https://github.com/fmichonneau/phylobase
An R package that provides a base S4 class for comparative methods, incorporating one or more trees and trait data
https://github.com/fmichonneau/phylobase
phylogenetics r
Last synced: 2 months ago
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An R package that provides a base S4 class for comparative methods, incorporating one or more trees and trait data
- Host: GitHub
- URL: https://github.com/fmichonneau/phylobase
- Owner: fmichonneau
- Created: 2014-06-14T23:34:50.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2024-01-30T09:28:56.000Z (11 months ago)
- Last Synced: 2024-09-14T11:18:49.491Z (3 months ago)
- Topics: phylogenetics, r
- Language: R
- Homepage:
- Size: 5.91 MB
- Stars: 17
- Watchers: 4
- Forks: 0
- Open Issues: 6
-
Metadata Files:
- Readme: README.Rmd
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# phylobase
[](https://github.com/fmichonneau/phylobase/actions/workflows/R-CMD-check.yaml)
[![codecov.io][(https://app.codecov.io/github/fmichonneau/phylobase?branch=master)](https://app.codecov.io/github/fmichonneau/phylobase?branch=master)
[](https://cran.r-project.org/package=phylobase)
## About this package
`phylobase` provides classes and methods to easily associate, manipulate,
explore, and plot phylogenetic trees and data about the species they
include. The goal of this package is to provide a base set of tools likely to be
shared by all packages designed for phylogenetic analysis. This standardization
will benefit both *end-users* by allowing them to move results across packages
and keep data associated with the phylogenetic trees; and *developers* by
focusing on method development instead of having to rewrite the base functions.
- Authors: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler,
Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut
Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara,
Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
- Maintainer: Francois Michonneau
- Licence: GPL (>= 2)
- Issues, bug reports, feature requests, discussion:
https://github.com/fmichonneau/phylobase/issues
## Installation
### Stable version
The stable version (the minor and patch version numbers are even, e.g., 0.6.8)
can be downloaded from CRAN.
```{r, eval=FALSE}
install.packages("phylobase")
```
### Development version
The development version (the patch version number is odd, e.g., 0.6.9) is
available on GitHub (https://github.com/fmichonneau/phylobase), and can be
installed using the [`devtools`](https://cran.r-project.org/package=devtools)
package.
```{r, eval=FALSE}
pak::install_github("fmichonneau/phylobase")
library(phylobase)
```
### Getting started
```{r, echo=FALSE}
library(phylobase)
```
`phylobase` comes with example data sets `geospiza` and `geospiza_raw`.
- `geospiza` is a `phylo4d` object (the `phylobase` class that holds together a
phylogenetic tree and associated data, the `phylo4` class is for phylogenetic
trees only).
- `geospiza_raw` is a list that contains the tree `geospiza_raw$tree` (as an
`ape::phylo` object) and the data `geospiza_raw$data` (as a `data.frame`) that
were used to build the `geospiza` object.
Now we'll take the \emph{Geospiza} data from \verb+geospiza_raw$data+ and merge
it with the tree. However, since \emph{G. olivacea} is included in the tree but
not in the data set, we will initially run into some trouble:
```{r, error=TRUE}
data(geospiza_raw)
g1 <- as(geospiza_raw$tree, "phylo4")
geodata <- geospiza_raw$data
g2 <- phylo4d(g1, geodata)
```
To deal with _G. olivacea_ missing from the data, we have a few choices. The
easiest is to use `missing.data="warn"` to allow `R` to create the new object
with a warning (you can also use `missing.data="OK"` to proceed without
warnings):
```{r, warn=TRUE}
g2 <- phylo4d(g1, geodata, missing.data="warn")
head(g2)
```
### Importing data
#### From NEXUS files
`phylobase` has a robust parser for NEXUS files (it uses the NEXUS Class Library
from Paul Lewis and Mark Holder,
[NCL](https://sourceforge.net/projects/ncl/files/)). It can be used to import
simultaneously tree and species data.
```{r}
myrmeFile <- system.file("nexusfiles/treeWithDiscreteData.nex", package="phylobase")
myrme <- readNexus(file=myrmeFile)
head(myrme)
```
#### From NeXML
```{r}
library(RNeXML)
nxmlFile <- system.file("nexmlfiles/comp_analysis.xml", package="phylobase")
nxml <- nexml_read(nxmlFile)
nxmlEx <- phylo4(nxml)
```