Solving Mixed Model Equations in R

Documentation for package ‘sommer’ version 4.3.1

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A B C D E F G H I J L M N O P R S T U V W

-- A --

A.mat	Additive relationship matrix
add.diallel.vars	add.diallel.vars
adiag1	Binds arrays corner-to-corner
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)
AI	Average Information Algorithm
anova.mmec	anova form a GLMM fitted with mmec
anova.mmer	anova form a GLMM fitted with mmer
AR1	Autocorrelation matrix of order 1.
ARMA	Autocorrelation Moving average.
atc	atc covariance structure
atcg1234	Letter to number converter
atr	atr covariance structure
A_example	Broad sense heritability calculation.
A_gryphon	Gryphon data from the Journal of Animal Ecology
A_ige	Data to fit indirect genetic effects.

-- B --

bathy.colors	Generate a sequence of colors for plotting bathymetric data.
bbasis	Function for creating B-spline basis functions (Eilers & Marx, 2010)
bivariateRun	bivariateRun functionality
build.HMM	Build a hybrid marker matrix using parental genotypes from inbred individuals

-- C --

coef.mmec	coef form a GLMM fitted with mmec
coef.mmer	coef form a GLMM fitted with mmer
corImputation	Imputing a matrix using correlations
CS	Compound symmetry matrix
csc	customized covariance structure
csr	customized covariance structure

-- D --

D.mat	Dominance relationship matrix
dfToMatrix	data frame to matrix
dsc	diagonal covariance structure
dsr	diagonal covariance structure
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

-- E --

E.mat	Epistatic relationship matrix
EM	Expectation Maximization Algorithm

-- F --

fcm	fixed effect constraint indication matrix
fitted.mmec	fitted form a LMM fitted with mmec
fitted.mmer	fitted form a LMM fitted with mmer
fixm	fixed indication matrix

-- G --

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
gvsr	general variance structure specification
GWAS	Genome wide association study analysis

-- H --

H.mat

Combined relationship matrix H

-- I --

imputev	Imputing a numeric or character vector
isc	identity covariance structure

-- J --

jet.colors

Generate a sequence of colors alog the jet colormap.

-- L --

LD.decay	Calculation of linkage disequilibrium decay
leg	Legendre polynomial matrix
list2usmat	list or vector to unstructured matrix
logspace	Decreasing logarithmic trend

-- M --

manhattan	Creating a manhattan plot
map.plot	Creating a genetic map plot
Md_technow	Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
MEMMA	Multivariate Efficient Mixed Model Association Algorithm
Mf_technow	Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
mmec	mixed model equations for c coefficients
mmer	mixed model equations for r records
MP_cpdata	Genotypic and Phenotypic data for a CP population
MP_polyploid	Genotypic and Phenotypic data for a potato polyploid population

-- N --

neMarker

Effective population size based on marker matrix

-- O --

overlay

Overlay Matrix

-- P --

plot.mmec	plot form a LMM plot with mmec
plot.mmer	plot form a LMM plot with mmer
pmonitor	plot the change of VC across iterations
predict.mmec	Predict form of a LMM fitted with mmec
predict.mmer	Predict form of a LMM fitted with mmer
print.mmec	summary form a GLMM fitted with mmec
print.mmer	summary form a GLMM fitted with mmer
print.summary.mmec	summary form a GLMM fitted with mmec
print.summary.mmer	summary form a GLMM fitted with mmer
print.wald.test	Wald Test for Model Coefficients
P_gryphon	Gryphon data from the Journal of Animal Ecology

-- R --

r2	Reliability
randef	extracting random effects
redmm	Reduced Model Matrix
residuals.mmec	Residuals form a GLMM fitted with mmec
residuals.mmer	Residuals form a GLMM fitted with mmer
rrc	reduced rank covariance structure

-- S --

simGECorMat	Create a GE correlation matrix for simulation purposes.
sommer	Solving Mixed Model Equations in R
spl2Da	Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Db	Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Dc	Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Dmats	Get Tensor Product Spline Mixed Model Incidence Matrices
stackTrait	Stacking traits in a dataset
summary.mmec	summary form a GLMM fitted with mmec
summary.mmer	summary form a GLMM fitted with mmer

-- T --

tpsmmbwrapper	Get Tensor Product Spline Mixed Model Incidence Matrices
transformConstraints	transformConstraints
transp	Creating color with transparency

-- U --

unsm	unstructured indication matrix
usc	unstructured covariance structure
usr	unstructured covariance structure

-- V --

vpredict	vpredict form of a LMM fitted with mmer
vpredict.mmer	vpredict form of a LMM fitted with mmer
vs	variance structure specification
vsc	variance structure specification
vsr	variance structure specification

-- W --

wald.test

Wald Test for Model Coefficients