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lme4breeding (version 1.0.63)

Relationship-Based Mixed-Effects Models

Description

Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the 'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.

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Version

Install

install.packages('lme4breeding')

Monthly Downloads

588

Version

1.0.63

License

GPL (>= 2)

Maintainer

Giovanny Covarrubias-Pazaran

Last Published

May 16th, 2025

Functions in lme4breeding (1.0.63)

DT_polyploid

Genotypic and Phenotypic data for a potato polyploid population
DT_rice

Rice lines dataset
DT_halfdiallel

half diallel data for corn hybrids
DT_legendre

Simulated data for random regression
DT_technow

Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
DT_sleepstudy

Reaction times in a sleep deprivation study
DT_wheat

wheat lines dataset
DT_mohring

Full diallel data for corn hybrids
DT_ige

Data to fit indirect genetic effects.
DT_yatesoats

Yield of oats in a split-block experiment
add.diallel.vars

add.diallel.vars
leg

Legendre polynomial matrix
lme4breeding-package

Linear mixed equations 4 Breeding
imputev

Imputing a numeric or character vector
getMME

Build the mixed model equations from a lmebreed object
fillData

Filling gaps for a dataset to balance
build.HMM

Build a hybrid marker matrix using parental genotypes from inbred individuals
adjBeta

Adjusting fixed effects for intercept
lmebreed-class

Relationship-based mixed-effects model fits
rrm

reduced rank matrix
atcg1234

Letter to number converter
bbasis

Function for creating B-spline basis functions (Eilers & Marx, 2010)
redmm

Reduced Model Matrix
umat

Rotation matrix UDU' decomposition
overlay

Overlay Matrix
tps

Get Tensor Product Spline Mixed Model Incidence Matrices
lmebreed

Fit mixed-effects models incorporating relationships
simage

Image of sparsity between two variables
smm

sparse model matrix
stackTrait

Stacking traits in a dataset
DT_cpdata

Genotypic and Phenotypic data for a CP population
DT_expdesigns

Data for different experimental designs
A.mat

Additive relationship matrix
DT_cornhybrids

Corn crosses and markers
DT_example

Broad sense heritability calculation.
DT_gryphon

Gryphon data from the Journal of Animal Ecology
DT_btdata

Blue Tit Data for a Quantitative Genetic Experiment
DT_fulldiallel

Full diallel data for corn hybrids
DT_h2

Broad sense heritability calculation.
DT_augment

DT_augment design example.