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**phytools**: Phylogenetic Tools for Comparative Biology (and Other Things)**edgeProbs**: Compute the relative frequencies of state changes along edges

# Compute the relative frequencies of state changes along edges

### Description

This function computes the relative frequencies of character state changes along edges from a sample of stochastically mapped character histories. This function assumes that all trees in the sample differ only in their mapped histories & not at all in topology or branch lengths. Note that it only asks whether the starting and ending states of the edge differ in a particular way, and thus ignores multiple-hits along a single edge.

### Usage

1 | ```
edgeProbs(trees)
``` |

### Arguments

`trees` |
an object of class |

### Value

The object that is returned is a matrix with the state changes & the relative frequency of each state change. Rows are in the order of the matrix `edge`

for any of the mapped trees.

### Author(s)

Liam Revell liam.revell@umb.edu

### References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). *Methods Ecol. Evol.*, **3**, 217-223.

### See Also

`plotSimmap`

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- collapseTree: Interactive tree visualizer
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- fitMk: Fits Mk model
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- mapped.states: Returns a vector, matrix, or list of the mapped states on a...
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- optim.phylo.ls: Phylogeny inference using the least squares method
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- paste.tree: Paste two trees together
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- phylANOVA: Phylogenetic ANOVA and post-hoc tests
- phyl.cca: Phylogenetic canonical correlation analysis
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- phylomorphospace: Creates phylomorphospace plot
- phylomorphospace3d: Creates tree-dimensional phylomorphospace plot
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- phylo.to.map: Plot tree with tips linked to geographic coordinates
- phyl.pairedttest: Phylogenetic paired t-test
- phyl.pca: Phylogenetic principal components analysis
- phyl.resid: Phylogenetic size-correction via GLS regression
- phyl.RMA: Phylogenetic reduced major axis (RMA) regression
- phyl.vcv: Compute evolutionary VCV matrix for a tree & dataset
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- plot.backbonePhylo: Plots backbone tree with triangles as clades
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- plotThresh: Tree plotting with posterior probabilities of ancestral...
- plotTree: Plots rooted phylogenetic tree
- plotTree.wBars: Plot a tree with bars at the tips
- posterior.evolrate: Analysis of the posterior sample from evol.rate.mcmc
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- read.newick: Robust Newick style tree reader
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- rep.phylo: Replicate a tree or set of trees
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- splitTree: Split tree at a point
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- threshDIC: Deviance Information Criterion from the threshold model
- threshState: Computes value for a threshold character from a liability and...
- to.matrix: Convert a character vector to a binary matrix
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- untangle: Attempts to untangle crossing branches for plotting
- vcvPhylo: Calculates cophenetic (i.e., phylogenetic VCV) matrix
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- write.simmap: Write a stochastic character mapped tree to file