Relationship-Based Mixed-Effects Models


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Documentation for package ‘lme4breeding’ version 1.0.40

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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
simage Image of sparsity between two variables
smm sparse model matrix
spl2Dmats Get Tensor Product Spline Mixed Model Incidence Matrices
stackTrait Stacking traits in a dataset
tps Get Tensor Product Spline Mixed Model Incidence Matrices
umat Rotation matrix UDU' decomposition