# Breeding-Related Mixed-Effects Models

## Documentation for package ‘lme4breeding’ version 1.0.90

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.
balanceData | Balance a dataset
bbasis | Function for creating B-spline basis functions (Eilers & Marx, 2010)
build.HMM | Build a hybrid marker matrix using parental genotypes from inbred individuals
Dtable | Get the hypertable for predictions
DTi_cornhybrids | Corn crosses and markers
DT_augment | DT_augment design example.
DT_big | Big GxE Quantitative Genetic Simulation
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
getCi | Get the inverse coefficient matrix
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
I.mat | Identity relationship matrix
imputev | Imputing a numeric or character vector
leg | Legendre polynomial matrix
lme4breeding | *L*inear *m*ixed *e*quations *4* *B*reeding
lmebreed | Fit breeding-related mixed-effects models
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)
mkMmeIndex | Table to track effects
MP_cpdata | Genotypic and Phenotypic data for a CP population
MP_polyploid | Genotypic and Phenotypic data for a potato polyploid population
M_big | Big GxE Quantitative Genetic Simulation
overlay | Overlay Matrix
predict-method | Relationship-based mixed-effects model fits
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
simage2 | Shortcut to sparse matrix image
smm | sparse model matrix
tps | Get Tensor Product Spline Mixed Model Incidence Matrices
umat | Rotation matrix UDU' decomposition