jagsAMmv: Animal model (multivariate)

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Animal model (multivariate)

Description

Given T traits, I genotypes, Q covariates and N=I*Q phenotypes per trait, fit an "animal model" with the rstan package via the following likelihood: Y = W C + Z G_A + Z G_D + E, where Y is NxT; W is NxQ; Z is NxI; G_A ~ Normal_IxT(0, A, V_G_A) with A the known matrix of additive genetic relationships; G_D ~ Normal_IxT(0, D, V_G_D) with D the known matrix of dominant genetic relationships; E ~ Normal_NxT(0, Id_N, V_E); Missing phenotypes are jointly imputed with the other unknown variables, and the errors can follow a Student's t distribution to handle outliers.

Usage

jagsAMmv(
  data,
  relmat,
  inits = NULL,
  nb.chains = 1,
  nb.adapt = 10^3,
  burnin = 10^2,
  nb.iters = 10^3,
  thin = 10,
  progress.bar = NULL,
  rm.jags.file = TRUE,
  verbose = 0
)

Arguments

data	data.frame containing the data corresponding to relmat; should have columns grep-able for "response" as well as a column "geno.add" used with matrix A; if a column "geno.dom" exists, it will be used with matrix D; any other column will be interpreted as corresponding to "fixed effects"
relmat	list containing the matrices of genetic relationships (see estimGenRel); additive relationships (matrix A) are compulsory, with name "geno.add"; dominant relationships (matrix D) are optional, with name "geno.dom"; can be in the "matrix" class (base) or the "dsCMatrix" class (Matrix package)
inits	list of initial values (possible to use 1 sub-list per chain, see jags.model); if NULL, JAGS will choose typical values (usually mean, median, or mode of the prior)
nb.chains	number of independent chains to run (see jags.model)
nb.adapt	number of iterations for adaptation (see jags.model)
burnin	number of initial iterations to discard (see the update function of the rjags package)
nb.iters	number of iterations to monitor (see coda.samples)
thin	thinning interval for monitored iterations (see coda.samples)
progress.bar	type of progress bar (text/gui/none or NULL)
rm.jags.file	remove the file specifying the model written in the JAGS-dialect of the BUGS language
verbose	verbosity level (0/1)

Author(s)

Timothee Flutre, inspired by code from Najla Saad Elhezzani (arXiv:1507.08638)

See Also

jagsAM

timflutre/rutilstimflutre documentation built on Feb. 12, 2025, 11:35 p.m.