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lme4breeding (version 1.0.31)

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

681

Version

1.0.31

License

GPL (>= 2)

Maintainer

Giovanny Covarrubias-Pazaran

Last Published

August 19th, 2024

Functions in lme4breeding (1.0.31)

DT_legendre

Simulated data for random regression
DT_mohring

Full diallel data for corn hybrids
leg

Legendre polynomial matrix
add.diallel.vars

add.diallel.vars
adjBeta

Adjusting fixed effects for intercept
build.HMM

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

Build the mixed model equations from a lmebreed object
imputev

Imputing a numeric or character vector
bbasis

Function for creating B-spline basis functions (Eilers & Marx, 2010)
atcg1234

Letter to number converter
lme4breeding-package

Linear mixed equations 4 Breeding
lmebreed-class

Relationship-based mixed-effects model fits
umat

Rotation matrix UDU' decomposition
smm

sparse model matrix
overlay

Overlay Matrix
tps

Get Tensor Product Spline Mixed Model Incidence Matrices
rrm

reduced rank matrix
lmebreed

Fit mixed-effects models incorporating relationships
stackTrait

Stacking traits in a dataset
redmm

Reduced Model Matrix
A.mat

Additive relationship matrix
DT_augment

DT_augment design example.
DT_expdesigns

Data for different experimental designs
DT_yatesoats

Yield of oats in a split-block experiment
DT_example

Broad sense heritability calculation.
DT_wheat

wheat lines dataset
DT_h2

Broad sense heritability calculation.
DT_technow

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

Blue Tit Data for a Quantitative Genetic Experiment
DT_sleepstudy

Reaction times in a sleep deprivation study
DT_cornhybrids

Corn crosses and markers
DT_cpdata

Genotypic and Phenotypic data for a CP population
DT_halfdiallel

half diallel data for corn hybrids
DT_gryphon

Gryphon data from the Journal of Animal Ecology
DT_fulldiallel

Full diallel data for corn hybrids
DT_ige

Data to fit indirect genetic effects.
DT_rice

Rice lines dataset
DT_polyploid

Genotypic and Phenotypic data for a potato polyploid population