Solving Mixed Model Equations in R


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Documentation for package ‘sommer’ version 4.4.1

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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)
anova.mmes anova form a GLMM fitted with mmes
AR1 Autocorrelation matrix of order 1.
ARMA Autocorrelation Moving average.
atcg1234 Letter to number converter
atcg1234BackTransform Letter to number converter
atm atm 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)
build.HMM Build a hybrid marker matrix using parental genotypes from inbred individuals

-- C --

coef.mmes coef form a GLMM fitted with mmes
corImputation Imputing a matrix using correlations
covm covariance between random effects
CS Compound symmetry matrix
csm customized covariance structure

-- D --

D.mat Dominance relationship matrix
dfToMatrix data frame to matrix
dsm 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

-- F --

fitted.mmes fitted form a LMM fitted with mmes
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
GWAS Genome wide association study analysis

-- H --

H.mat Combined relationship matrix H

-- I --

imputev Imputing a numeric or character vector
ism 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
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)
Mf_technow Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
mmer *m*ixed *m*odel *e*quations for *r* records
mmes *m*ixed *m*odel *e*quations *s*olver
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.mmes plot form a LMM plot with mmes
pmonitor plot the change of VC across iterations
predict.mmes Predict form of a LMM fitted with mmes
print.mmer summary form a GLMM fitted with mmer
print.mmes summary form a GLMM fitted with mmes
print.summary.mmer summary form a GLMM fitted with mmer
print.summary.mmes summary form a GLMM fitted with mmes
print.wald.test Wald Test for Model Coefficients
propMissing Proportion of missing data
P_gryphon Gryphon data from the Journal of Animal Ecology

-- R --

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

-- S --

simGECorMat Create a GE correlation matrix for simulation purposes.
sommer *So*lving *M*ixed *M*odel *E*quations in *R*
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.mmer summary form a GLMM fitted with mmer
summary.mmes summary form a GLMM fitted with mmes

-- T --

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

-- U --

unsm unstructured indication matrix
usm unstructured covariance structure

-- V --

vpredict vpredict form of a LMM fitted with mmes
vpredict.mmes vpredict form of a LMM fitted with mmes
vs variance structure specification
vsm variance structure specification
vsr variance structure specification

-- W --

wald.test Wald Test for Model Coefficients