evolqg: MonteCarloRep – R documentation

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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.

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

Examples

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

MonteCarloRep(cov.matrix, sample.size = 30, RandomSkewers, iterations = 20)

## Not run: 
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

##Windows:
#cl <- makeCluster(2)
#registerDoParallel(cl)
##Mac and Linux:
library(doParallel)
registerDoParallel(cores = 2)

MonteCarloRep(cov.matrix, 30, RandomSkewers, iterations = 100, parallel = TRUE)

## End(Not run)

evolqg

Tools for Evolutionary Quantitative Genetics

v0.2-8

MIT + file LICENSE

Authors

Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Andrade Machado, Guilherme Garcia

Initial release

2020-11-14