MonteCarloRep: Parametric repeatabilities with covariance or correlation...

In evolqg: Evolutionary Quantitative Genetics

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.

Details

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

Value

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

Author(s)

Diogo Melo Guilherme Garcia

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)


## Not run: 
#Multiple threads can be used with some foreach backend library, like doMC or doParallel
library(doMC)
registerDoMC(cores = 2)
MonteCarloRep(cov.matrix, 30, RandomSkewers, iterations = 100, parallel = TRUE)

## End(Not run)

evolqg documentation built on May 29, 2024, 6:35 a.m.