Function_ComputeDistances_1Network_1Tree: Function_ComputeDistances_1Network_1Tree: function to compute...

In radamsRHA/PRDATR: Computing probabilistic distances between phylogenetic models of continuous trait evolution

Description

This function returns a vector containing the Hellinger and KL distances between two tree models

Usage

Function_ComputeDistances_1Network_1Tree(
  list.Model_01_Network,
  list.Model_02_Tree
)

Arguments

list.Model_01_Network	List containing the following (1) handle.Phylogeny, (2) string.Model = "BM", "OU", "EB", "lambda", "kappa", "delta", (3) vector.Z = vector of mean (ancestral) state values, and (4) vector.Model_01_Theta = vector containing relevant parameters for the models
list.Model_02_Tree	List containing the following (1) handle.Phylogeny, (2) string.Model = "BM", "OU", "EB", "lambda", "kappa", "delta", (3) vector.Z = vector of mean (ancestral) state values, and (4) vector.Model_01_Theta = vector containing relevant parameters for the models

Value

vector.Distances Vector containing the distances computed between the two focal tree models

Examples

################
# Load depends #
################
library(ape)
library(geiger)
library(gaussDiff)
library(BMhyd)

######################
# Simulate a network #
######################
handle.SimulatedNetwork <- SimulateNetwork(ntax.nonhybrid=5, ntax.hybrid=3,
                                           flow.proportion=0.5, origin.type='clade', birth = 1, death = 0.5, sample.f = 0.5,
                                           tree.height = 1, allow.ghost=FALSE)

###############################
# Set the first network model #
###############################
list.Model01_BM <- list(handle.Phylogeny = handle.SimulatedNetwork$phy,
                        handle.Flow = handle.SimulatedNetwork$flow,
                        string.Model = "BM",
                        vector.Z = rep(0, 8),
                        numeric.Sig2 = 1)

#############################
# Set the second tree model #
#############################
list.Model02_BM <- list(handle.Phylogeny = handle.SimulatedNetwork$phy,
                        string.Model = "BM",
                        vector.Z = rep(0, 8),
                        numeric.Sig2 = 1)


#####################
# Compute distances #
#####################
Function_ComputeDistances_1Network_1Tree(list.Model_01_Network = list.Model01_BM, list.Model_02_Tree = list.Model02_BM)

radamsRHA/PRDATR documentation built on Dec. 25, 2021, 11:44 a.m.