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sommer (version 1.9)

Solving Mixed Model Equations in R

Description

Mixed model equation solver allowing the specification of variance covariance structures for random effects. ML/REML estimates are obtained using the Average Information, Expectation-Maximization, Newton-Raphson, or 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 in R, but also functional as a regular mixed model program. Multivariate models can be fitted for mixed models with a single random effect.

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Version

Install

install.packages('sommer')

Monthly Downloads

4,370

Version

1.9

License

GPL-3

Maintainer

Giovanny CovarrubiasPazaran

Last Published

July 1st, 2016

Functions in sommer (1.9)

anova.mmer

anova form a GLMM fitted with mmer
anova.mmerM

anova form a GLMM fitted with mmer
AI3

Average Information Algorithm
AI

Average Information Algorithm
augment

augment design example.
AI2

Average Information Algorithm
A.mat

Additive relationship matrix
adiag1

Binds arrays corner-to-corner
atcg1234

Letter to number converter
cornHybrid

Corn crosses and markers
big.peaks.col

Peak search by first derivatives
D.mat

Dominance relationship matrix
bathy.colors

Generate a sequence of colors for plotting bathymetric data.
design.score

design score for the model to be tested
CPdata

Genotypic and Phenotypic data for a CP population
coef.MMERM

coef form a GLMM fitted with mmer
coef.mmer

coef form a GLMM fitted with mmer
brewer.pal

Generate a sequence of colors for groups.
fitted.mmer

fitted form a GLMM fitted with mmer
EM2

Expectation Maximization Algorithm
eigenGWAS

Unraveling selection signatures with eigenGWAS
E.mat

Epistatic relationship matrix
EMMA

Efficient Mixed Model Association Algorithm
EMMAM

Multivariate Efficient Mixed Model Association Algorithm
EM

Expectation Maximization Algorithm
F1geno

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

half diallel data for corn hybrids
fdr

False Discovery Rate calculation
h2

Broad sense heritability calculation.
HDdata

half diallel data for corn hybrids
hdm

Half Diallel Matrix
hadamard.prod

Hadamard product of two matrices
fitted.MMERM

fitted form a GLMM fitted with mmer
jet.colors

Generate a sequence of colors alog the jet colormap.
is.square.matrix

Test for square matrix
hits

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

Test for diagonal square matrix
PEV

Selecting the best training population for genomic selection
NR22

Newton-Raphson Algorithm
matrix.trace

The trace of a matrix
map.plot

Creating a genetic map
my.colors

All typical colors in R easy to access.
mmerSNOW

Mixed Model Equations in R univariate
phase.F1

Phasing F1 (CP) data in biparental populations
maxi.qtl

Peak search by first derivatives
manhattan

Creating a manhattan plot
NR

Newton-Raphson Algorithm
plot.MMERM

plot form a GLMM plot with mmer
RICE

Rice lines dataset
randef

extracting random effects
poe

Short poems from Latin America, and other places why not?
PolyData

Genotypic and Phenotypic data for a potato polyploid population
plot.mmer

plot form a GLMM plot with mmer
residuals.MMERM

Residuals form a GLMM fitted with mmer
residuals.mmer

Residuals form a GLMM fitted with mmer
summary.MMERM

summary form a GLMM fitted with mmer
Technow_data

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

summary form a GLMM fitted with mmer
S.mat

Spatial relationship matrix
score.calc

Score calculation for markers
transp

Creating color with transparency
TP.prep

Selecting the best training population for genomic selection
wheatLines

wheat lines dataset