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sommer: Solving Mixed Model Equations in R

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects and unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016; Maier et al., 2015). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) and dense known covariance structures for levels of random effects. Spatial models can also be fitted using i.e. the two-dimensional spline functionality available in sommer.

Installation

You can install the development version of sommer from GitHub:

devtools::install_github('covaruber/sommer')

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Version

Install

install.packages('sommer')

Monthly Downloads

7,425

Version

4.1.4

License

GPL (>= 2)

Maintainer

Giovanny Covarrubias-Pazaran

Last Published

July 29th, 2021

Functions in sommer (4.1.4)

A.mat

Additive relationship matrix
ARMA

Autocorrelation Moving average.
DT_btdata

Blue Tit Data for a Quantitative Genetic Experiment
DT_cpdata

Genotypic and Phenotypic data for a CP population
CS

Compound symmetry matrix
AR1

Autocorrelation matrix of order 1.
D.mat

Dominance relationship matrix
DT_augment

DT_augment design example.
DT_cornhybrids

Corn crosses and markers
DT_example

Broad sense heritability calculation.
DT_halfdiallel

half diallel data for corn hybrids
DT_gryphon

Gryphon data from the Journal of Animal Ecology
DT_h2

Broad sense heritability calculation.
DT_expdesigns

Data for different experimental designs
DT_yatesoats

Yield of oats in a split-block experiment
DT_fulldiallel

Full diallel data for corn hybrids
MEMMA

Multivariate Efficient Mixed Model Association Algorithm
DT_ige

Data to fit indirect genetic effects.
DT_technow

Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
DT_legendre

Simulated data for random regression
at

at covariance structure
DT_sleepstudy

Reaction times in a sleep deprivation study
DT_wheat

wheat lines dataset
build.HMM

Build a hybrid marker matrix using parental genotypes from inbred individuals
coef.mmer

coef form a GLMM fitted with mmer
DT_polyploid

Genotypic and Phenotypic data for a potato polyploid population
atcg1234

Letter to number converter
dfToMatrix

data frame to matrix
cs

customized covariance structure
H.mat

Combined relationship matrix H
DT_rice

Rice lines dataset
LD.decay

Calculation of linkage disequilibrium decay
GWAS2

Genome wide association study
GWAS

Genome wide association study analysis
add.diallel.vars

add.diallel.vars
anova.mmer

anova form a GLMM fitted with mmer
adiag1

Binds arrays corner-to-corner
ds

diagonal covariance structure
DT_mohring

Full diallel data for corn hybrids
simGECorMat

Create a GE correlation matrix for simulation purposes.
fcm

fixed effect constraint indication matrix
residuals.mmer

Residuals form a GLMM fitted with mmer
jet.colors

Generate a sequence of colors alog the jet colormap.
imputev

Imputing a numeric or character vector
randef

extracting random effects
summary.mmer

summary form a GLMM fitted with mmer
gvs

general variance structure specification
E.mat

Epistatic relationship matrix
transformConstraints

transformConstraints
predict.mmer

Predict form of a LMM fitted with mmer
bathy.colors

Generate a sequence of colors for plotting bathymetric data.
EM

Expectation Maximization Algorithm
bivariateRun

bivariateRun functionality
fitted.mmer

fitted form a LMM fitted with mmer
fixm

fixed indication matrix
overlay

Overlay Matrix
transp

Creating color with transparency
leg

Legendre polynomial matrix
plot.mmer

plot form a LMM plot with mmer
manhattan

Creating a manhattan plot
map.plot

Creating a genetic map plot
uncm

unconstrained indication matrix
list2usmat

list or vector to unstructured matrix
unsm

unstructured indication matrix
spl2D

Two-dimensional penalised tensor-product of marginal B-Spline basis.
sommer-package

Solving Mixed Model Equations in R Figure: mai.png
us

unstructured covariance structure
h2.fun

Obtain heritabilities with three different methods
mmer2

mixed model equations in R
mmer

mixed model equations in R
vpredict

vpredict form of a LMM fitted with mmer
vs

variance structure specification
wald.test

Wald Test for Model Coefficients