simCophy: Generate simulated cophylogeny event counts

In DEEPR: Dirichlet-multinomial Evolutionary Event Profile Randomization (DEEPR) test

Description

This command provides a way to generate simulated matrices representing sets of cophylogeny event counts.

Usage

simCophy(group_alphas = c(1,1,1,1), cophy_number = 20, mean_event_count = 33)

Arguments

group_alphas	Set of Dirichlet alpha parameter for cophylogeny group
cophy_number	Number of simulated cophylogeny event profiles to be generated in the group
mean_event_count	The expected number of total event counts per simulated cophylogeny

Details

From specified Dirichlet parameters, a set of multinomial probabilities are generated. A total number of co-evolutionary events are generated from a Poisson distribution in order to introduce variation in the number of events per cophylogeny. These events are then distributed among the sets of multinomial probabilities previously generated.

Value

group_events

A matrix of cophylogeny event counts. Each row represents a single reconstructed cophylogeny and each column represents specific event type counts.

Author(s)

Mark T Merilo <[e-mail]>

Examples

#Generate a simulated event count set with specified Dirichlet parameters
#and desired number of simulated cophylogenies
simCophy(c(1,1,1,5), 20)

DEEPR documentation built on May 2, 2019, 3:47 p.m.