diallel.gibbs: Gibbs sampler that specifies a form of the BayesDiallel...

In gkeele/DIDACT: Diallel Informed Decision theoretic Approach for Crosses Tool (DIDACT)

Description

This function runs the BayesDiallel Gibbs Sampler for diallel cross data.

Usage

diallel.gibbs(phenotype, sex = NULL, is.female = TRUE, mother.str,
  father.str, n.iter = 1000, burn.in = 10000, multi.chain = 1,
  thin = 1, sigma.2.starter = 5, tau_add.starter = 2,
  tau_inbred.starter = 2, tau_mat.starter = 2,
  tau_epi_sym.starter = 2, tau_epi_asym.starter = 2,
  strains.reorder = c("AJ", "B6", "129", "NOD", "NZO", "CAST", "PWK",
  "WSB"), strains.rename = c("AJ", "B6", "129", "NOD", "NZO", "CAST",
  "PWK", "WSB"), use.constraint = TRUE, use.progress.bar = TRUE,
  hyper.ga.alpha = 0.002, hyper.ga.beta = 2)

Arguments

phenotype	Vector of the phenotypes. Expects a quantitative phenotype.
sex	Binary vector for females and males. By default, expects females to be coded as 1 and males as 0.
is.female	DEFAULT: TRUE. If TRUE, then sex expects female=1 and male=0. If FALSE, then female=0 and male=1.
mother.str	Vector of strain identities of mother/dam.
father.str	Vector of strain identities of father/sire.
n.iter	DEFAULT: 1000. The number of samples to be collected.
burn.in	DEFAULT: 10000. The number of samples run as a burn-in, which are not stored.
multi.chain	DEFAULT: 1. The number of MCMC chains to run.
thin	DEFAULT: 1. If 1, no thinning is used. If 2, then every other sample is stored. If 3, then every third observation is stored. And so on.
tau_add.starter	DEFAULT: 2. Starting value for the variance parameter of the additive effects in the Gibbs Sampler.
tau_inbred.starter	DEFAULT: 2. Starting value for the variance parameter of the inbred effects in the Gibbs Sampler.
tau_mat.starter	DEFAULT: 2. Starting value for the variance parameter of the maternal effects in the Gibbs Sampler.
tau_epi_sym.starter	DEFAULT: 2. Starting value for the variance parameter of the symmetric epistatic effects in the Gibbs Sampler.
tau_epi_asym.starter	DEFAULT: 2. Starting value for the variance parameter of the asymmetric epistatic effects in the Gibbs Sampler.
strains.reorder	DEFAULT: c("AJ", "B6", "129", "NOD", "NZO", "CAST", "PWK", "WSB"). Orders the strains based on the standard ordering of Collaborative Cross founders
strains.rename	DEFAULT: c("AJ", "B6", "129", "NOD", "NZO", "CAST", "PWK", "WSB"). Renames the strains. By default, expects the founders of the Collaborative Cross.
use.constraint	DEFAULT: TRUE. Use a rotation matrix to reduce the dimension of strain matrices because the system is linearly dependent. Can result in narrower posterior intervals.
use.progress.bar	DEFAULT: TRUE. A progress bar shows how sampling is progressing.
sigma2.starter	DEFAULT: 5. Starting value for the residual error variance parameter in the Gibbs Sampler.

Examples

diallel.gibbs()

gkeele/DIDACT documentation built on Jan. 1, 2020, 2:58 a.m.