sommer: Solving Mixed Model Equations in R
Version 2.7

Multivariate linear mixed-effect model solver for multiple random effects allowing the specification of variance covariance structures. ML/REML estimates are obtained using the Direct-Inversion Newton-Raphson (NR), Direct-Inversion Average Information (AI), Expectation-Maximization (EM), or Efficient Mixed Model Association (EMMA) algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program. Multivariate models (multiple responses) can be fitted currently with NR, AI and EMMA algorithms allowing multiple random effects as well. Covariance structures for the residual component are no longer supported.

Browse man pages Browse package API and functions Browse package files

AuthorGiovanny Covarrubias-Pazaran
Date of publication2017-04-15 13:53:09 UTC
MaintainerGiovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
LicenseGPL-3
Version2.7
URL http://www.wisc.edu
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sommer")

Man pages

adiag1: Binds arrays corner-to-corner
AI: Average Information Algorithm
ai2help: Average Information Algorithm
A.mat: Additive relationship matrix
and: and functionality
anova.mmer: anova form a GLMM fitted with mmer
anova.mmerM: anova form a GLMM fitted with mmer
anova.MMERM1: anova form a GLMM fitted with mmer
at: at functionality
atcg1234: Letter to number converter
augment: augment design example.
bathy.colors: Generate a sequence of colors for plotting bathymetric data.
big.peaks.col: Peak search by first derivatives
brewer.pal: Generate a sequence of colors for groups.
coef.mmer: coef form a GLMM fitted with mmer
coef.mmerM: coef form a GLMM fitted with mmer
coef.MMERM1: coef form a GLMM fitted with mmer
cornHybrid: Corn crosses and markers
CPdata: Genotypic and Phenotypic data for a CP population
design.score: design score for the model to be tested
D.mat: Dominance relationship matrix
eigenGWAS: Unraveling selection signatures with eigenGWAS
EM: Expectation Maximization Algorithm
EM2: Expectation Maximization Algorithm
E.mat: Epistatic relationship matrix
EMMA: Efficient Mixed Model Association Algorithm
ExpDesigns: Data for different experimental designs
F1geno: Genotypes from an F1(CP) cross to show phasing
FDdata: Full diallel data for corn hybrids
fdr: False Discovery Rate calculation
fdr2: False Discovery Rate calculation
fitted.mmer: fitted form a GLMM fitted with mmer
fitted.mmerM: fitted form a GLMM fitted with mmer
fitted.MMERM1: fitted form a GLMM fitted with mmer
g: g functionality
gryphondata: Gryphon data from the Journal of Animal Ecology
h2: Broad sense heritability calculation.
hadamard.prod: Hadamard product of two matrices
HDdata: half diallel data for corn hybrids
hdm: Half Diallel Matrix
hits: Creating a fixed effect matrix with significant GWAS markers
impute: Imputing a numeric or character vector
is.diagonal.matrix: Test for diagonal square matrix
is.square.matrix: Test for square matrix
jet.colors: Generate a sequence of colors alog the jet colormap.
LD.decay: Calculation of linkage disequilibrium decay
MAI: Multivariate Average Information Algorithm
MAI2: Multivariate Average Information Algorithm
manhattan: Creating a manhattan plot
map.plot: Creating a genetic map plot
matrix.trace: The trace of a matrix
maxi.qtl: Peak search by first derivatives
MEMMA: Multivariate Efficient Mixed Model Association Algorithm
mmer: Mixed Model Equations in R
mmer2: Mixed Model Equations in R v2
MMERM: Multivariate mixed model solver to be called inside mmer
mmerSNOW: Mixed Model Equations in R univariate
MNR: Multivariate Newton-Raphson Algorithm
my.colors: All typical colors in R easy to access.
name.change: renaming a vector by adding zeros
nna: Nearest neighbour adjustment
NR: Newton-Raphson Algorithm
NR22: Newton-Raphson Algorithm
overlay: Overlay Matrix
PEV: Selecting the best training population for genomic selection
phase.F1: Phasing F1 (CP) data in biparental populations
plot.mmer: plot form a GLMM plot with mmer
plot.mmerM: plot form a GLMM plot with mmer
plot.MMERM1: plot form a GLMM plot with mmer
poe: Short poems from Latin America, and other places why not?
PolyData: Genotypic and Phenotypic data for a potato polyploid...
randef: extracting random effects
residuals.mmer: Residuals form a GLMM fitted with mmer
residuals.mmerM: Residuals form a GLMM fitted with mmer
residuals.MMERM1: Residuals form a GLMM fitted with mmer
RICE: Rice lines dataset
score.calc: Score calculation for markers
score.calcMV: Score calculation for markers
sommer-package: Solving Mixed Model Equations in R
summary.mmer: summary form a GLMM fitted with mmer
summary.mmerM: summary form a GLMM fitted with mmer
summary.MMERM1: summary form a GLMM fitted with mmer
Technow_data: Genotypic and Phenotypic data from single cross hybrids...
TP.prep: Selecting the best training population for genomic selection
transp: Creating color with transparency
us: us functionality
wheatLines: wheat lines dataset
yates.oats: Yield of oats in a split-block experiment

Functions

A.mat Man page Source code
AI Man page Source code
CPdata Man page
D.mat Man page Source code
E.mat Man page Source code
EM Man page Source code
EM2 Man page Source code
EMMA Man page Source code
ExpDesigns Man page
F1geno Man page
FDdata Man page
HDdata Man page
LD.decay Man page Source code
MAI Man page Source code
MAI2 Man page Source code
MAIhelp Source code
MEMMA Man page Source code
MMERM Man page Source code
MNR Man page Source code
NR Man page Source code
NR22 Man page Source code
PEV Man page Source code
PolyData Man page
RICE Man page
TP.prep Man page Source code
Technow_data Man page
adiag1 Man page Source code
ai2help Man page Source code
and Man page Source code
anova.MMERM Man page Source code
anova.mmer Man page Source code
anova.mmerM Man page Source code
at Man page Source code
atcg1234 Man page Source code
augment Man page
bathy.colors Man page Source code
big.peaks.col Man page Source code
brewer.pal Man page Source code
coef.MMERM Man page
coef.mmer Man page
coef.mmerM Man page
cornHybrid Man page
design.score Man page Source code
eigenGWAS Man page Source code
fdr Man page Source code
fdr2 Man page Source code
fitted.MMERM Man page
fitted.mmer Man page
fitted.mmerM Man page
g Man page Source code
gryphondata Man page
h2 Man page
hadamard.prod Man page Source code
hdm Man page Source code
hits Man page Source code
imputev Man page Source code
is.diagonal.matrix Man page Source code
is.square.matrix Man page Source code
jet.colors Man page Source code
manhattan Man page Source code
map.plot Man page Source code
matrix.trace Man page Source code
maxi.qtl Man page Source code
mmer Man page Source code
mmer2 Man page Source code
mmerSNOW Man page Source code
my.colors Man page
name.change Man page Source code
nna Man page Source code
onAttach Source code
overlay Man page Source code
phase.F1 Man page Source code
plot.MMERM Man page Source code
plot.mmer Man page Source code
plot.mmerM Man page Source code
poe Man page Source code
print.MMERM Man page
print.mmer Man page
print.mmerM Man page
print.summary.MMERM Man page
print.summary.mmer Man page
print.summary.mmerM Man page
randef Man page
residuals.MMERM Man page
residuals.mmer Man page
residuals.mmerM Man page
score.calc Man page Source code
score.calcMV Man page Source code
sommer Man page
summary.MMERM Man page
summary.mmer Man page
summary.mmerM Man page
transp Man page Source code
us Man page Source code
wheatLines Man page
yates.oats Man page

Files

inst
inst/CITATION
inst/doc
inst/doc/sommer.R
inst/doc/sommer.pdf
inst/doc/sommer.Rmd
NAMESPACE
CHANGELOG
data
data/PolyData.RData
data/gryphondata.RData
data/Technow_data.RData
data/augment.RData
data/HDdata.RData
data/RICE.RData
data/yates.oats.RData
data/ExpDesigns.RData
data/h2.RData
data/FDdata.RData
data/cornHybrid.RData
data/CPdata.RData
data/datalist
data/my.colors.RData
data/wheatLines.RData
data/F1geno.RData
R
R/MMERM.R
R/formula_func.R
R/fdr2.R
R/design.score.R
R/D.mat.R
R/mmer.R
R/MAIhelp.R
R/poe.R
R/score.calcMV.R
R/maxi.qtl.R
R/impute.R
R/hits.R
R/MNR.R
R/TP.prep.R
R/A.mat.R
R/adiag.R
R/MEMMA.R
R/jet.colors.R
R/EM.R
R/ai2help.R
R/NR22.R
R/PEV.R
R/map.plot.R
R/NR.R
R/hdm.R
R/overlay.R
R/mmerSNOW.R
R/fdr.R
R/big.peaks.col.R
R/EM2.R
R/transp.R
R/phase.F1.R
R/manhattan.R
R/matrix.calculations.R
R/mmer2.R
R/E.mat.R
R/brewer.pal.R
R/score.calc.R
R/LD.decay.R
R/EMMA.R
R/AI.R
R/name.change.R
R/atcg1234.R
R/eigenGWAS.R
R/MAI.R
R/MAI2.R
R/nna.R
vignettes
vignettes/sommer.html
vignettes/sommer.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/anova.MMERM1.Rd
man/MAI.Rd
man/RICE.Rd
man/nna.Rd
man/PEV.Rd
man/EMMA.Rd
man/MAI2.Rd
man/cornHybrid.Rd
man/fitted.mmer.Rd
man/us.Rd
man/h2.Rd
man/mmerSNOW.Rd
man/mmer.Rd
man/eigenGWAS.Rd
man/residuals.mmerM.Rd
man/EM.Rd
man/MEMMA.Rd
man/residuals.mmer.Rd
man/MNR.Rd
man/Technow_data.Rd
man/AI.Rd
man/plot.mmerM.Rd
man/MMERM.Rd
man/fitted.MMERM1.Rd
man/poe.Rd
man/hadamard.prod.Rd
man/summary.MMERM1.Rd
man/phase.F1.Rd
man/fdr2.Rd
man/gryphondata.Rd
man/fitted.mmerM.Rd
man/plot.mmer.Rd
man/anova.mmer.Rd
man/coef.MMERM1.Rd
man/ai2help.Rd
man/FDdata.Rd
man/coef.mmerM.Rd
man/g.Rd
man/hdm.Rd
man/summary.mmerM.Rd
man/PolyData.Rd
man/at.Rd
man/big.peaks.col.Rd
man/transp.Rd
man/D.mat.Rd
man/is.diagonal.matrix.Rd
man/NR22.Rd
man/adiag1.Rd
man/manhattan.Rd
man/bathy.colors.Rd
man/EM2.Rd
man/F1geno.Rd
man/anova.mmerM.Rd
man/map.plot.Rd
man/coef.mmer.Rd
man/score.calc.Rd
man/and.Rd
man/augment.Rd
man/summary.mmer.Rd
man/mmer2.Rd
man/TP.prep.Rd
man/my.colors.Rd
man/impute.Rd
man/A.mat.Rd
man/name.change.Rd
man/ExpDesigns.Rd
man/matrix.trace.Rd
man/NR.Rd
man/wheatLines.Rd
man/sommer-package.Rd
man/HDdata.Rd
man/residuals.MMERM1.Rd
man/atcg1234.Rd
man/brewer.pal.Rd
man/jet.colors.Rd
man/is.square.matrix.Rd
man/overlay.Rd
man/LD.decay.Rd
man/fdr.Rd
man/hits.Rd
man/design.score.Rd
man/plot.MMERM1.Rd
man/score.calcMV.Rd
man/maxi.qtl.Rd
man/yates.oats.Rd
man/CPdata.Rd
man/randef.Rd
man/E.mat.Rd
sommer documentation built on May 19, 2017, 1:35 p.m.