defineModelsSpecifications: Define _mcmcglmm_ (Bayesian Phylogenetic Mixed Models)...

In pablosanchezmart/TrEvol: What the Package Does (One Line, Title Case)

Define mcmcglmm (Bayesian Phylogenetic Mixed Models) specifications

Description

Return an object containing the specifications that can be used as in the argument "model_specifications" of the functions computeVariancePartition, computeCovariancePartition and computeVarianceCovariancePartition. See "MCMCglmm" R package documentation for further information.

Usage

defineModelsSpecifications(
  number_iterations = 100,
  burning = 10,
  thinning = 2,
  uniresponse_prior = list(R = list(V = 1, nu = 0.002), G = list(G1 = list(V = 1, nu =
    0.002))),
  biresponse_prior = list(R = list(V = diag(2)/2, nu = 2), G = list(G1 = list(V =
    diag(2)/2, nu = 2))),
  triresponse_prior = list(R = list(V = diag(3)/2, nu = 2), G = list(G1 = list(V =
    diag(3)/2, nu = 2)))
)

Arguments

number_iterations	(integer) Number of iterations of the MCMCglmm model.
burning	(integer) Number of burning iterations. This initial iterations will be excluded from when estimating the posterior distribution. It allows achieving convergence.
thinning	(integer) Number of thinning iterations. Number of iterations that will be discarded after a sampled one. It allows to deal with autocorrelation.
uniresponse_prior	(list) Parameters for the random effects for uni-response models. Default is set to an inverse-Gamma distribution, which is canonical and considered non-informative.
biresponse_prior	(list) Parameters for the random effects of bi-response models. Normally, these are the models including two traits. Default is set to an inverse-Gamma distribution, which is canonical and considered non-informative.
triresponse_prior	(list) Parameters for the random effects of tri-response models. Normally, these are the models including two traits and one environmental variable. Default is set to an inverse-Gamma distribution, which is canonical and considered non-informative.

Value

List of mcmcglmm model specifications.

pablosanchezmart/TrEvol documentation built on April 23, 2024, 4:05 p.m.