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README.Rmd
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---
title: "treespace readme"
author: "Michelle Kendall"
date: "`r Sys.Date()`"
output: md_document
---
```{r setup, echo=FALSE}
# set global chunk options: images will be 7x7 inches
knitr::opts_chunk$set(fig.width=7, fig.height=7, fig.path="figs/", cache=FALSE, dpi=96)
options(digits = 4)
```
[](https://ci.appveyor.com/project/thibautjombart/treespace/branch/master)
[](https://cran.r-project.org/package=treespace)
[](https://cran.r-project.org/package=treespace)
*treespace*: exploration of landscapes of phylogenetic trees
============================================================
*treespace* implements new methods for the exploration and analysis of
distributions of phylogenetic trees for a given set of taxa.
Installing *treespace*
-------------
To install the development version from github:
```{r install, eval=FALSE}
library(devtools)
install_github("thibautjombart/treespace")
```
The stable version can be installed from CRAN using:
```{r install2, eval=FALSE}
install.packages("treespace")
```
Then, to load the package, use:
```{r load}
library("treespace")
```
Content overview
----------------
The main functions implemented in *treespace* are:
* __`treespace`__: explore landscapes of phylogenetic trees
* __`treespaceServer`__: open up an application in a web browser for an
interactive exploration of the diversity in a set of trees
* __`findGroves`__: identify clusters of similar trees
* __`plotGroves`__: scatterplot of groups of trees, and __`plotGrovesD3`__ which
enables interactive plotting based on d3.js
* __`medTree`__: find geometric median tree(s) to summarise a group of trees
* __`wiwTreeDist`__: find the distance between transmission trees by comparing their MRCI depth matrices
* __`wiwMedTree`__: find the median of a list of transmission scenarios
* __`relatedTreeDist`__: calculate the distances between trees whose tips belong to the same categories but are not necessarily identically labelled
* __`treeConcordance`__: calculate the concordance between a category tree and an individuals tree
Other functions are central to the computations of distances between trees:
* __`treeVec`__: characterise a tree by a vector
* __`treeDist`__: find the distance between two tree vectors
* __`multiDist`__: find the pairwise distances of a list of trees
* __`refTreeDist`__: find the distances of a list of trees from a reference tree
* __`tipDiff`__: for a pair of trees, list the tips with differing ancestry
* __`plotTreeDiff`__: plot a pair of trees, highlighting the tips with differing
ancestry
* __`findMRCIs`__: find the most recent common infector (MRCI) matrix from "who infected whom" information
* __`tipsMRCAdepths`__: similar to `treeVec` but the output is a matrix where columns 1 and 2 correspond to tip labels and column 3 gives the depth of the MRCA of that pair of tips
Distributed datasets include:
* __`woodmiceTrees`__: illustrative set of 201 trees built using the
neighbour-joining and bootstrapping example from the *woodmice* dataset in the
*ape* documentation.
* __`DengueTrees`__: 500 trees sampled from a BEAST posterior set of trees from
(Drummond and Rambaut, 2007)
* __`DengueSeqs`__: 17 dengue virus serotype 4 sequences from (Lanciotti *et
al.*, 1997), from which the `DengueTrees` were inferred.
* __`DengueBEASTMCC`__: the maximum clade credibility (MCC) tree from the
`DengueTrees`.
Documentation
-------------
*treespace* comes with the following vignettes:
-
[*introduction*](https://cran.r-project.org/package=treespace/vignettes/introduction.html):
general introduction using a worked example.
- [*Dengue
example*](https://cran.r-project.org/package=treespace/vignettes/DengueVignette.html):
worked example using a Dengue dataset, used in the *treespace* publication.
- [*transmission
trees*](https://cran.r-project.org/package=treespace/vignettes/TransmissionTreesVignette.html):
worked example using transmission trees.
- [*tip categories*](https://cran.r-project.org/package=treespace/vignettes/tipCategories.html): introduction to the measures for comparing trees with shared tip label "categories"
Contributing / asking a question
--------------------------------
Contributions are welcome via **pull requests**.
Please note that this project is released with a [Contributor Code of
Conduct](https://thibautjombart.github.io/treespace/CONDUCT.html). By participating in this project you agree to abide by its
terms.
Questions, feature requests and bugs can be reported using the package's [issue
system](https://github.com/thibautjombart/treespace/issues).
Authors
-------
Authors:
* [Thibaut Jombart](https://thibautjombart.netlify.app/)
* [Michelle Kendall](https://michellekendall.github.io/)
Contributors:
* [Jacob Almagro-Garcia](http://biotop.co/people/jacob-almagro/)
* [Caroline Colijn](https://www.sfu.ca/math/people/faculty/ccolijn/)
Maintainer of the CRAN version:
* [Michelle Kendall](https://michellekendall.github.io/)
See details of contributions on: <br>
https://github.com/thibautjombart/treespace/graphs/contributors