simul.replace: Simulation phase for the P-SIMEX with misassignment error.

In PSIMEX: SIMEX Algorithm on Pedigree Structures

Description

This function calls the proper simulation function for the parameter of interest with misassigned paternities.

Usage

simul.replace(pedigree, lambda, lambda0, B, data, 
model, parameter, way, prior, nitt, thin, burnin)

Arguments

pedigree	A dataset containing the initial pedigree structure. It must have three columns: id, parent1, parent2.
lambda	A vector of real numbers specifying the error proportion to be generated.
lambda0	A real number specifying the initial error rate.
B	An integer specifying the number of simulations to be run for each error level.
data	A dataset containing the phenotypic measurements on the population and the covariates which are included in the model. The trait shoul be named differently than 'trait' (see MCMCglmm)
model	An object specifying the model to calculate the parameter of interest. It can be a lm or glm for inbreeding depression and a MCMCglmm for heritability.
parameter	A string specifying the parameter of interest. It must be 'inbreeding' or 'heritability'.
way	A string specifying how errors are generated. It must be 'uniform' or 'similar'.
prior	Prior distribution for MCMCglmm model
nitt	Number of iterations for MCMCglmm model
thin	Thinning interval for MCMCglmm model
burnin	Burn in period for MCMCglmm model

Value

For inbreeding a list:

inb	A dataset containing all the simulated values for inbreeding depression
se_inb	A dataset containing all the simulated standard errors for inbreeding depression
pval	A dataset containing all the simulated p-values for inbreeding depression
mean_inb	A dataset containing all the simulated values for inbreeding coefficient mean
median_inb	A dataset containing all the simulated values for inbreeding coefficient median
var_inb	A dataset containing all the simulated values for inbreeding coefficient variance

For heritability a list:

h	A dataset containing all the simulated values for heritability
se_h	A dataset containing all the simulated standard errors for heritability
VA	A dataset containing all the simulated values for additive variance
VE	A dataset containing all the simulated values for environmental variance

Author(s)

Erica Ponzi

PSIMEX documentation built on May 2, 2019, 3:34 p.m.