ratematrix (version 1.2)

extractCorrelation: Extract the posterior distribution of evolutionary correlation

Description

Function extracts the posterior distribution of evolutionary correlation among traits.

Usage

extractCorrelation(post)

Arguments

post

a posterior distribution object as returned by the function 'readMCMC' or a merged posterior generated by 'mergePosterior'.

Value

a list with the posterior distribution of evolutionary correlations among traits.

Details

Returns a list with length equal to the number of regimes. Each list element is composed by a matrix with trait correlation types in the columns and the evolutionary correlations for each sample at the rows.

One can plot the correlation values using boxplots and compare their distribution. Pairwise statistical tests across the samples is also possible.

Examples

# NOT RUN {
data( centrarchidae )
dt.range <- t( apply( centrarchidae$data, 2, range ) )
## The step size for the root value can be set given the range we need to sample from:
w_mu <- ( dt.range[,2] - dt.range[,1] ) / 10
par.sd <- cbind(c(0,0), sqrt( c(10,10) ))
prior <- makePrior(r=2, p=2, den.mu="unif", par.mu=dt.range, den.sd="unif", par.sd=par.sd)
handle <- ratematrixMCMC(data=centrarchidae$data, phy=centrarchidae$phy.map, prior=prior
                         , gen=10000, w_mu=w_mu, dir=tempdir())
posterior <- readMCMC(handle, burn = 0.2, thin = 10)
## Get the correlations:
cor.list <- extractCorrelation(post = posterior)
## Plot the results:
boxplot(cor.list[[1]], main = "Regime 1") ## Regime 1
boxplot(cor.list[[2]], main = "Regime 2") ## Regime 2
# }