Learn R Programming
⚠️There's a newer version (4.4.1) of this package.Take me there.

sommer (version 1.3)

Solving Mixed Model Equations in R

Description

Mixed model equation solver allowing the specification of variance covariance structures of random effects and residual structures. ML/REML estimates are obtained using the Average Information and/or Expectation-Maximization algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominant and epistatic relationship structures.

Copy Link

Version

Install

install.packages('sommer')

Monthly Downloads

4,273

Version

1.3

License

GPL-3

Maintainer

Giovanny CovarrubiasPazaran

Last Published

March 9th, 2016

Functions in sommer (1.3)

cornHybrid

Corn crosses and markers
PolyData

Genotypic and Phenotypic data for a potato polyploid population
E.mat

Epistatic relationship matrix
A.mat

Additive relationship matrix
AI

Average Information Algorithm
mmer2

Mixed Model Equations in R 2
residuals.mmer

Residuals form a GLMM fitted with mmer
poe

Short poems from Latin America, and other places why not?
fitted.mmer

fitted form a GLMM fitted with mmer
CPdata

Genotypic and Phenotypic data for a CP population (F1; cross between 2 highly heterozygote individuals; i.e. humans, fruit crops, bredding populations in recurrent selection).
design.score

design score for the model to be tested
bathy.colors

Generate a sequence of colors for plotting bathymetric data.
atcg1234

Letter to number converter
summary.mmer

summary form a GLMM fitted with mmer
wheatLines

wheat lines dataset
AI2

Average Information Algorithm
AI3

Average Information Algorithm
hdm

Half Diallel Matrix
bag

Creating a fixed effect matrix with significant GWAS markers
adiag1

Binds arrays corner-to-corner
D.mat

Dominance relationship matrix
randef

extracting random effects
mmer

Mixed Model Equations in R
EM

Expectation Maximization Algorithm
sommer-package

Solving Mixed Model Equations in R
coef.mmer

coef form a GLMM fitted with mmer
jet.colors

Generate a sequence of colors alog the jet colormap.
map.plot2

Creating a genetic map
anova.mmer

anova form a GLMM fitted with mmer
score.calc

Score calculation for markers
plot.mmer

plot form a GLMM plot with mmer
transp

Creating color with transparency
HDdata

half diallel data for corn hybrids
EMMA

Efficient Mixed Model Association Algorithm
fdr

False Discovery Rate calculation