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lme4breeding (version 1.0.80)

Breeding-Related 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

605

Version

1.0.80

License

GPL (>= 2)

Maintainer

Giovanny Covarrubias-Pazaran

Last Published

September 22nd, 2025

Functions in lme4breeding (1.0.80)

DT_wheat

wheat lines dataset
add.diallel.vars

add.diallel.vars
build.HMM

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

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

Build the mixed model equations from a lmebreed object
fillData

Filling gaps for a dataset to balance
DT_yatesoats

Yield of oats in a split-block experiment
I.mat

Identity relationship matrix
overlay

Overlay Matrix
atcg1234

Letter to number converter
lmebreed

Fit breeding-related mixed-effects models
leg

Legendre polynomial matrix
imputev

Imputing a numeric or character vector
balanceData

Balance a dataset
lme4breeding-package

Linear mixed equations 4 Breeding
lmebreed-class

Relationship-based mixed-effects model fits
simage2

Shortcut to sparse matrix image
simage

Image of sparsity between two variables
rrm

reduced rank matrix
umat

Rotation matrix UDU' decomposition
adjBeta

Adjusting fixed effects for intercept
redmm

Reduced Model Matrix
smm

sparse model matrix
tps

Get Tensor Product Spline Mixed Model Incidence Matrices
DT_fulldiallel

Full diallel data for corn hybrids
A.mat

Additive relationship matrix
DT_expdesigns

Data for different experimental designs
DT_cornhybrids

Corn crosses and markers
DT_mohring

Full diallel data for corn hybrids
DT_big

Big GxE Quantitative Genetic Simulation
DT_example

Broad sense heritability calculation.
DT_btdata

Blue Tit Data for a Quantitative Genetic Experiment
DT_ige

Data to fit indirect genetic effects.
DT_cpdata

Genotypic and Phenotypic data for a CP population
DT_gryphon

Gryphon data from the Journal of Animal Ecology
DT_rice

Rice lines dataset
DT_augment

DT_augment design example.
DT_h2

Broad sense heritability calculation.
DT_polyploid

Genotypic and Phenotypic data for a potato polyploid population
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