evolqg (version 0.2-2)

MonteCarloRep: Parametric repeatabilities with covariance or correlation matrices

Description

Using a multivariate normal model, random populations are generated using the suplied covariance matrix. A statistic is calculated on the random population and compared to the statistic calculated on the original matrix.

Usage

MonteCarloRep(cov.matrix, sample.size, ComparisonFunc, ..., iterations = 1000,
  correlation = FALSE, parallel = FALSE)

Arguments

cov.matrix

Covariance matrix.

sample.size

Size of the random populations.

ComparisonFunc

comparison function.

...

Aditional arguments passed to ComparisonFunc.

iterations

Number of random populations.

correlation

If TRUE, correlation matrix is used, else covariance matrix. MantelCor and MatrixCor should always uses correlation matrix.

parallel

If is TRUE and list is passed, computations are done in parallel. Some foreach backend must be registered, like doParallel or doMC.

Value

• returns the mean repeatability, or mean value of comparisons from samples to original statistic.

Details

Since this function uses multivariate normal model to generate populations, only covariance matrices should be used, even when computing repeatabilities for covariances matrices.

See Also

BootstrapRep, AlphaRep

Examples

cov.matrix <- RandomMatrix(5, 1, 1, 10)

MonteCarloRep(cov.matrix, sample.size = 30, RandomSkewers, iterations = 20)
MonteCarloRep(cov.matrix, sample.size = 30, RandomSkewers, num.vectors = 100, 
              iterations = 20, correlation = TRUE)
MonteCarloRep(cov.matrix, sample.size = 30, MatrixCor, correlation = TRUE)
MonteCarloRep(cov.matrix, sample.size = 30, KrzCor, iterations = 20)
MonteCarloRep(cov.matrix, sample.size = 30, KrzCor, correlation = TRUE)

#Creating repeatability vector for a list of matrices
mat.list <- RandomMatrix(5, 3, 1, 10)
laply(mat.list, MonteCarloRep, 30, KrzCor, correlation = TRUE)

##Multiple threads can be used with doMC library
#library(doParallel)
##Windows:
#cl <- makeCluster(2)
#registerDoParallel(cl)
##Mac and Linux:
#registerDoParallel(cores = 2)
#MonteCarloRep(cov.matrix, 30, RandomSkewers, iterations = 100, parallel = TRUE)