estVC: Estimate Variance Component Parameters

In QTLRel: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

Estimate Variance Component Parameters

Description

Estimate model parameters for covariates, genetic variance components and residual effect.

Usage

estVC(y, x, v = list(E=diag(length(y))), initpar, nit = 25,
   method = c("ML", "REML"), control = list(), hessian = FALSE)

Arguments

y	A numeric vector or a numeric matrix of one column (representing a phenotype for instance).
x	A data frame or matrix, representing covariates if not missing.
v	A list of matrices representing variance components of interest. Note: E is reserved for residual (or environmental) variance and can be missed in v; it is considered to be an identify matrix if it is missing. v can be provided as a single matrix, representing a variance component other than E.
initpar	Optional initial parameter values. When provided, optim will be called for optimization, which may take time but is good for checking of the result (see details for more).
nit	Maximum number of iterations for optimization. Ignored if there are not more than two variance components.
method	Either maximum likelihood (ML) or restricted maximum likelihood (REML).
control	A list of control parameters to be passed to optim.
hessian	Logical. Should a numerically differentiated Hessian matrix be returned?

Details

The optimization function optim is adopted in the above function to estimate the parameters and maximum likelihood. Several optimization methods are available for the optimization algorithm in optim, but we recommend "Nelder-Mead" for the sake of stability. Alternatively, one may choose other options, e.g., "BFGS" to initialize and speed up the estimation procedure and then the procedure will automatically turn to "Nelder-Mead" for final results. If there is only one variance component (other than E), optimize will be used for optimization unless initpar is provided.

Normality is assumed for the random effects. Input data should be free of missing values.

Value

par	estimates of the model parameters.
value	log-likelihood of the model.
y	y used.
x	associated with x used.
v	variance component matrices v used.
...	other information.

Note

Hessian matrix, if requested, pertains to -log-likelihood function.

See Also

optim and rem.

Examples

data(miscEx)

## Not run: 
# no sex effect
pheno<- pdatF8[!is.na(pdatF8$bwt) & !is.na(pdatF8$sex),]
ii<- match(rownames(pheno), rownames(gmF8$AA))
v<- list(A=gmF8$AA[ii,ii], D=gmF8$DD[ii,ii])

o<- estVC(y=pheno$bwt, v=v)
o

# sex as fixed effect
fo<- estVC(y=pheno$bwt, x=pheno$sex, v=v)
fo
2*(fo$value-o$value) # log-likelihood test statistic

# sex as random effect
SM<- rem(~sex, data=pheno)
ro<- estVC(y=pheno$bwt, v=c(v,list(Sex=SM$sex)))
ro
2*(ro$value-o$value) # log-likelihood test statistic

## End(Not run)

QTLRel documentation built on Aug. 9, 2023, 1:07 a.m.