lmerUvcov-class

ranef,lmerUvcov-method

A mixed-effects model fit by <code>lmerUvcov</code>.
 This class extends class <code>"<a href="/link/merMod?package=lme4GS&version=0.1" data-mini-rdoc="lme4GS::merMod">merMod</a>"</code> class and includes one
 additional slot, <code>relfac</code>, which is a list of (left) Cholesky
 factors of the relationship matrices derived from 
 user provided variance covariance matrixes.

classes

Flexible functions that use 'lme4' as computational engine for
fitting models used in Genomic Selection (GS). GS is a technology used for genetic
improvement, and it has many advantages over phenotype-based selection. There
are several statistical models that adequately approach the statistical
challenges in GS, such as in linear mixed models (LMMs). The 'lme4' is the
standard package for fitting linear and generalized LMMs in the R-package,
but its use for genetic analysis is limited because it does not allow the
correlation between individuals or groups of individuals to be defined. The
'lme4GS' package is focused on fitting LMMs with covariance structures defined
by the user, bandwidth selection, and genomic prediction. The new package is
focused on genomic prediction of the models used in GS and can fit LMMs using
different variance-covariance matrices. Several examples of GS models are
presented using this package as well as the analysis using real data. For more
details see Caamal-Pat et.al. (2021) <doi:10.3389/fgene.2021.680569>.

Paulino Rodriguez

lme4GS

'lme4' for Genomic Selection

Diana Yanira Caamal Pat

Paulino Perez Rodriguez

Erick Javier Suarez Sanchez

lmerUvcov-class function

Objects are created by calls to the
 <code>lmerUvcov</code> function.

Objects from the Class

Class <code>"<a href="/link/merMod?package=lme4GS&version=0.1" data-mini-rdoc="lme4GS::merMod">merMod</a>"</code>, directly.

Extends

<dl>
 <dt>ranef</dt>
<dd><code>signature(object = "lmerUvcov")</code>: incorporates
 the user defined variance covariance matrix into the random effects as returned for the object
 viewed as a <code>"<a href="/link/merMod?package=lme4GS&version=0.1" data-mini-rdoc="lme4GS::merMod">merMod</a>"</code> object.</dd> 
</dl>

Methods

A mixed-effects model fit by <code>lmerUvcov</code>.
 This class extends class <code>"<a href='https://rdrr.io/pkg/lme4/man/merMod-class.html'>merMod</a>"</code> class and includes one
 additional slot, <code>relfac</code>, which is a list of (left) Cholesky
 factors of the relationship matrices derived from 
 user provided variance covariance matrixes.

User defined variance covariance  mixed-effects model fits — lmerUvcov-class

Class <code>"<a href='https://rdrr.io/pkg/lme4/man/merMod-class.html'>merMod</a>"</code>, directly.

<dl>
 <dt>ranef</dt>
<dd><code>signature(object = "lmerUvcov")</code>: incorporates
 the user defined variance covariance matrix into the random effects as returned for the object
 viewed as a <code>"<a href='https://rdrr.io/pkg/lme4/man/merMod-class.html'>merMod</a>"</code> object.</dd>

 
</dl>

lmerUvcov-class: User defined variance covariance mixed-effects model fits

Description

Arguments

Objects from the Class

Extends

Methods

See Also

Examples