SimulateProfiles: Simulate profiles

In beiko-lab/evolCCM: R package for Community Coevolution Model

Simulate profiles

Description

Simulate binary profiles based on the Community Coevolution Model using the input tree and user-defined parameters.

Usage

SimulateProfiles(phytree, alpha, B, root=F)

Arguments

phytree	a phylogenetic tree.
alpha	a vector of the intrinsic rates (\alpha) in CCM. The length of the vector decides how many profiles to simulate.
B	a symmetric association matrix (B) in CCM. If the input matrix is not symmetric, the upper triangle of the matrix will be used.
root	a vector of states at root node. 'root=F' as default (random states will be assigned at root).

Value

a matrix containing simulated profiles.

Examples

set.seed(123)
# generate a random 50-tip tree
t <- rtree(50)
# simulate 5 profiles
n <- 5
# assigning parameter values.
# The parameters should be in a reasonable scale otherwise the simulated profiles may have all 0s or 1s.
alpha <- runif(n, -0.5, 1) # assign n random intrinsic rates.
association matrix B
B <- matrix(0,n,n)
B[1:3,1:3] <- 1 # first 3 genes are correlated. The other 2 have no interaction with others
diag(B) <- runif(n, -0.5,0.5) # assign half the difference between gain and loss rates for each gene
# simulate 5 random profiles
simDF <- SimulateProfiles(t, alpha, B)
# plot the profiles
d <- TreeToDend(t) # convert the tree to dendrogram
ProfilePlot(simDF, d)

beiko-lab/evolCCM documentation built on Feb. 26, 2024, 5:21 p.m.