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lme4breeding (version 1.0.50)

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

277

Version

1.0.50

License

GPL (>= 2)

Maintainer

Giovanny Covarrubias-Pazaran

Last Published

January 18th, 2025

Functions in lme4breeding (1.0.50)

DT_yatesoats

Yield of oats in a split-block experiment
DT_polyploid

Genotypic and Phenotypic data for a potato polyploid population
leg

Legendre polynomial matrix
DT_ige

Data to fit indirect genetic effects.
imputev

Imputing a numeric or character vector
atcg1234

Letter to number converter
fillData

Filling gaps for a dataset to balance
add.diallel.vars

add.diallel.vars
bbasis

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

Adjusting fixed effects for intercept
getMME

Build the mixed model equations from a lmebreed object
build.HMM

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

Overlay Matrix
stackTrait

Stacking traits in a dataset
smm

sparse model matrix
redmm

Reduced Model Matrix
lme4breeding-package

Linear mixed equations 4 Breeding
tps

Get Tensor Product Spline Mixed Model Incidence Matrices
umat

Rotation matrix UDU' decomposition
lmebreed-class

Relationship-based mixed-effects model fits
rrm

reduced rank matrix
simage

Image of sparsity between two variables
lmebreed

Fit mixed-effects models incorporating relationships
DT_expdesigns

Data for different experimental designs
DT_augment

DT_augment design example.
A.mat

Additive relationship matrix
DT_btdata

Blue Tit Data for a Quantitative Genetic Experiment
DT_cornhybrids

Corn crosses and markers
DT_gryphon

Gryphon data from the Journal of Animal Ecology
DT_halfdiallel

half diallel data for corn hybrids
DT_rice

Rice lines dataset
DT_legendre

Simulated data for random regression
DT_fulldiallel

Full diallel data for corn hybrids
DT_h2

Broad sense heritability calculation.
DT_mohring

Full diallel data for corn hybrids
DT_cpdata

Genotypic and Phenotypic data for a CP population
DT_example

Broad sense heritability calculation.
DT_sleepstudy

Reaction times in a sleep deprivation study
DT_technow

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

wheat lines dataset