Relationship-Based Mixed-Effects Models

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Documentation for package ‘lme4breeding’ version 1.0.31

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A.mat Additive relationship matrix
add.diallel.vars add.diallel.vars
adjBeta Adjusting fixed effects for intercept
Ad_technow Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
Af_technow Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
atcg1234 Letter to number converter
A_example Broad sense heritability calculation.
A_gryphon Gryphon data from the Journal of Animal Ecology
A_ige Data to fit indirect genetic effects.
bbasis Function for creating B-spline basis functions (Eilers & Marx, 2010)
build.HMM Build a hybrid marker matrix using parental genotypes from inbred individuals
DTi_cornhybrids Corn crosses and markers
DT_augment DT_augment design example.
DT_btdata Blue Tit Data for a Quantitative Genetic Experiment
DT_cornhybrids Corn crosses and markers
DT_cpdata Genotypic and Phenotypic data for a CP population
DT_example Broad sense heritability calculation.
DT_expdesigns Data for different experimental designs
DT_fulldiallel Full diallel data for corn hybrids
DT_gryphon Gryphon data from the Journal of Animal Ecology
DT_h2 Broad sense heritability calculation.
DT_halfdiallel half diallel data for corn hybrids
DT_ige Data to fit indirect genetic effects.
DT_legendre Simulated data for random regression
DT_mohring Full diallel data for corn hybrids
DT_polyploid Genotypic and Phenotypic data for a potato polyploid population
DT_rice Rice lines dataset
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
DT_yatesoats Yield of oats in a split-block experiment
fitted-method Relationship-based mixed-effects model fits
getMME Build the mixed model equations from a lmebreed object
GTn_rice Rice lines dataset
GT_cornhybrids Corn crosses and markers
GT_cpdata Genotypic and Phenotypic data for a CP population
GT_polyploid Genotypic and Phenotypic data for a potato polyploid population
GT_rice Rice lines dataset
GT_wheat wheat lines dataset
imputev Imputing a numeric or character vector
leg Legendre polynomial matrix
lme4breeding *L*inear *m*ixed *e*quations *4* *B*reeding
lmebreed Fit mixed-effects models incorporating relationships
lmebreed-class Relationship-based mixed-effects model fits
Md_technow Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
Mf_technow Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
MP_cpdata Genotypic and Phenotypic data for a CP population
MP_polyploid Genotypic and Phenotypic data for a potato polyploid population
overlay Overlay Matrix
P_gryphon Gryphon data from the Journal of Animal Ecology
ranef-method Relationship-based mixed-effects model fits
redmm Reduced Model Matrix
residuals-method Relationship-based mixed-effects model fits
rrm reduced rank matrix
smm sparse model matrix
stackTrait Stacking traits in a dataset
tps Get Tensor Product Spline Mixed Model Incidence Matrices
umat Rotation matrix UDU' decomposition