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sommer (version 3.0)

Solving Mixed Model Equations in R

Description

Structural multivariate-univariate linear mixed model solver for multiple random effects allowing the specification of variance-covariance structures for random effects and allowing the fit of heterogeneous variance models. ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson, and Efficient Mixed Model Association algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures, but also functional as a regular mixed model program.

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Version

Install

install.packages('sommer')

Monthly Downloads

4,273

Version

3.0

License

GPL-3

Maintainer

Giovanny Covarrubias-Pazaran

Last Published

August 24th, 2017

Functions in sommer (3.0)

D.mat

Dominance relationship matrix
E.mat

Epistatic relationship matrix
F1geno

Genotypes from an F1(CP) cross to show phasing
FDdata

Full diallel data for corn hybrids
A.mat

Additive relationship matrix
AI

Average Information Algorithm
BTdata

Blue Tit Data for a Quantitative Genetic Experiment
CPdata

Genotypic and Phenotypic data for a CP population
EM

Expectation Maximization Algorithm
ExpDesigns

Data for different experimental designs
RICE

Rice lines dataset
Technow_data

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

half diallel data for corn hybrids
MEMMA

Multivariate Efficient Mixed Model Association Algorithm
atcg1234

Letter to number converter
augment

augment design example.
MNR

Multivariate Newton-Raphson Algorithm
PolyData

Genotypic and Phenotypic data for a potato polyploid population
anova.MMERM

anova form a GLMM fitted with mmer
adiag1

Binds arrays corner-to-corner
and

and functionality
bathy.colors

Generate a sequence of colors for plotting bathymetric data.
big.peaks.col

Peak search by first derivatives
at

at functionality
fdr2

False Discovery Rate calculation
fill.design

Filling the design of an experiment
grp

grouping functionality
GWAS

Genome Wide Association Analysis
GWAS2

Genome Wide Association Analysis
blockerT

Applying transversal postblocking in a field
brewer.pal

Generate a sequence of colors for groups.
example

Broad sense heritability calculation.
fdr

False Discovery Rate calculation
is.square.matrix

Test for square matrix
gryphondata

Gryphon data from the Journal of Animal Ecology
manhattan

Creating a manhattan plot
map.plot

Creating a genetic map plot
randef

extracting random effects
jet.colors

Generate a sequence of colors alog the jet colormap.
matrix.trace

The trace of a matrix
maxi.qtl

Peak search by first derivatives
pin

pin functionality
plot.MMERM

plot form a LMM plot with mmer
residuals.MMERM

Residuals form a GLMM fitted with mmer
yates.oats

Yield of oats in a split-block experiment
blocker

Applying postblocking in a field
blockerL

Applying linear postblocking in a field
coef.MMERM

coef form a GLMM fitted with mmer
cornHybrid

Corn crosses and markers
imputev

Imputing a numeric or character vector
design.score

design score for the model to be tested
eig

eigen decomposition functionality
hdm

Half Diallel Matrix
hits

Creating a fixed effect matrix with significant GWAS markers
is.diagonal.matrix

Test for diagonal square matrix
overlay

Overlay Matrix
phase.F1

Phasing F1 (CP) data in biparental populations
my.colors

All typical colors in R easy to access.
nna

Nearest neighbour adjustment
us

us functionality
vctable

vctable functionality
fitted.MMERM

fitted form a GLMM fitted with mmer
g

g functionality
h2

Broad sense heritability calculation.
hadamard.prod

Hadamard product of two matrices
mmer

mixed model equations in R
mmer2

mixed model equations in R
score.calcMV

Score calculation for markers
sommer-package

Solving Mixed Model Equations in R
summary.MMERM

summary form a GLMM fitted with mmer
transp

Creating color with transparency
vctable.help

vctable.help functionality
wheatLines

wheat lines dataset