sommer: Solving Mixed Model Equations in R

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Multivariate mixed model solver for multiple random effects allowing the specification of variance covariance structures. ML/REML estimates are obtained using the Average Information (AI), Expectation-Maximization (EM), Newton-Raphson (NR), 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 is currently supported only for balanced univariate Newton Raphson models.

Author
Giovanny Covarrubias-Pazaran
Date of publication
2016-12-01 21:12:53
Maintainer
Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
License
GPL-3
Version
2.4
URLs

View on CRAN

Man pages

adiag1
Binds arrays corner-to-corner
AI
Average Information Algorithm
ai2help
Average Information Algorithm
A.mat
Additive relationship matrix
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
AR1.mat
Autocorrelation matrix of order 1.
ARMA.mat
Autorregressive moving average matrix
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
CS.mat
Compound symmetry matrix
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
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
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
NRR
Newton-Raphson Algorithm including Residual structures
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
wheatLines
wheat lines dataset
yates.oats
Yield of oats in a split-block experiment

Files in this package

sommer
sommer/inst
sommer/inst/CITATION
sommer/inst/doc
sommer/inst/doc/sommer.R
sommer/inst/doc/sommer.pdf
sommer/inst/doc/sommer.Rmd
sommer/NAMESPACE
sommer/CHANGELOG
sommer/data
sommer/data/PolyData.RData
sommer/data/gryphondata.RData
sommer/data/Technow_data.RData
sommer/data/augment.RData
sommer/data/HDdata.RData
sommer/data/RICE.RData
sommer/data/yates.oats.RData
sommer/data/ExpDesigns.RData
sommer/data/h2.RData
sommer/data/FDdata.RData
sommer/data/cornHybrid.RData
sommer/data/CPdata.RData
sommer/data/datalist
sommer/data/my.colors.RData
sommer/data/wheatLines.RData
sommer/data/F1geno.RData
sommer/R
sommer/R/MMERM.R
sommer/R/design.score.R
sommer/R/D.mat.R
sommer/R/mmer.R
sommer/R/MAIhelp.R
sommer/R/poe.R
sommer/R/score.calcMV.R
sommer/R/maxi.qtl.R
sommer/R/impute.R
sommer/R/hits.R
sommer/R/MNR.R
sommer/R/TP.prep.R
sommer/R/A.mat.R
sommer/R/adiag.R
sommer/R/MEMMA.R
sommer/R/jet.colors.R
sommer/R/EM.R
sommer/R/ai2help.R
sommer/R/NR22.R
sommer/R/Rstructures.R
sommer/R/PEV.R
sommer/R/map.plot.R
sommer/R/NR.R
sommer/R/hdm.R
sommer/R/NRR.R
sommer/R/mmerSNOW.R
sommer/R/fdr.R
sommer/R/big.peaks.col.R
sommer/R/EM2.R
sommer/R/transp.R
sommer/R/phase.F1.R
sommer/R/manhattan.R
sommer/R/matrix.calculations.R
sommer/R/mmer2.R
sommer/R/E.mat.R
sommer/R/brewer.pal.R
sommer/R/score.calc.R
sommer/R/LD.decay.R
sommer/R/EMMA.R
sommer/R/AI.R
sommer/R/name.change.R
sommer/R/atcg1234.R
sommer/R/eigenGWAS.R
sommer/R/MAI.R
sommer/R/MAI2.R
sommer/R/nna.R
sommer/vignettes
sommer/vignettes/sommer.html
sommer/vignettes/sommer.Rmd
sommer/MD5
sommer/build
sommer/build/vignette.rds
sommer/DESCRIPTION
sommer/man
sommer/man/anova.MMERM1.Rd
sommer/man/MAI.Rd
sommer/man/RICE.Rd
sommer/man/nna.Rd
sommer/man/PEV.Rd
sommer/man/EMMA.Rd
sommer/man/MAI2.Rd
sommer/man/cornHybrid.Rd
sommer/man/fitted.mmer.Rd
sommer/man/h2.Rd
sommer/man/mmerSNOW.Rd
sommer/man/mmer.Rd
sommer/man/eigenGWAS.Rd
sommer/man/residuals.mmerM.Rd
sommer/man/EM.Rd
sommer/man/MEMMA.Rd
sommer/man/residuals.mmer.Rd
sommer/man/MNR.Rd
sommer/man/Technow_data.Rd
sommer/man/AI.Rd
sommer/man/plot.mmerM.Rd
sommer/man/MMERM.Rd
sommer/man/ARMA.mat.Rd
sommer/man/fitted.MMERM1.Rd
sommer/man/poe.Rd
sommer/man/hadamard.prod.Rd
sommer/man/summary.MMERM1.Rd
sommer/man/phase.F1.Rd
sommer/man/gryphondata.Rd
sommer/man/fitted.mmerM.Rd
sommer/man/plot.mmer.Rd
sommer/man/anova.mmer.Rd
sommer/man/AR1.mat.Rd
sommer/man/coef.MMERM1.Rd
sommer/man/ai2help.Rd
sommer/man/CS.mat.Rd
sommer/man/FDdata.Rd
sommer/man/coef.mmerM.Rd
sommer/man/hdm.Rd
sommer/man/summary.mmerM.Rd
sommer/man/PolyData.Rd
sommer/man/big.peaks.col.Rd
sommer/man/NRR.Rd
sommer/man/transp.Rd
sommer/man/D.mat.Rd
sommer/man/is.diagonal.matrix.Rd
sommer/man/NR22.Rd
sommer/man/adiag1.Rd
sommer/man/manhattan.Rd
sommer/man/bathy.colors.Rd
sommer/man/EM2.Rd
sommer/man/F1geno.Rd
sommer/man/anova.mmerM.Rd
sommer/man/map.plot.Rd
sommer/man/coef.mmer.Rd
sommer/man/score.calc.Rd
sommer/man/augment.Rd
sommer/man/summary.mmer.Rd
sommer/man/mmer2.Rd
sommer/man/TP.prep.Rd
sommer/man/my.colors.Rd
sommer/man/impute.Rd
sommer/man/A.mat.Rd
sommer/man/name.change.Rd
sommer/man/ExpDesigns.Rd
sommer/man/matrix.trace.Rd
sommer/man/NR.Rd
sommer/man/wheatLines.Rd
sommer/man/sommer-package.Rd
sommer/man/HDdata.Rd
sommer/man/residuals.MMERM1.Rd
sommer/man/atcg1234.Rd
sommer/man/brewer.pal.Rd
sommer/man/jet.colors.Rd
sommer/man/is.square.matrix.Rd
sommer/man/LD.decay.Rd
sommer/man/fdr.Rd
sommer/man/hits.Rd
sommer/man/design.score.Rd
sommer/man/plot.MMERM1.Rd
sommer/man/score.calcMV.Rd
sommer/man/maxi.qtl.Rd
sommer/man/yates.oats.Rd
sommer/man/CPdata.Rd
sommer/man/randef.Rd
sommer/man/E.mat.Rd