evolCCM

R package for CCM (Community Coevolution Model).

Introduction

This is the R implementation for CCM (Community Coevolution Model) from the paper The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles. This package was written in R v4.0.2 and includes the main functions for profiles simulation, profiles visualization and CCM estimation.

Dependencies

evolCCM requires the following R packages:

• ape

• gplots

# install.packages("ape")
# install.packages("gplots")
library(ape)
library(gplots)

Installation

Install the package evolCCM from github using devtools:

# install.packages("devtools")
library(devtools)
devtools::install_github("beiko-lab/evolCCM")
library(evolCCM)

List of functions

• TreeToDen(): Convert tree to dendrogram for plotting.
• ProfilePlot(): Plot the profiles along with the tree.
• SimulateProfile(): Simulate binary profiles.
• EstimateCCM(): Estimate parameters in CCM model.
• ProcessAE(): Calculate the standard errors of parameter estimates.

Documentation

For detailed instructions and examples, please see the package manual.

A brief tutorial can also be found here.

A parallel version of the EvolCCM is available here.