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sommer (version 1.2)

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.

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Version

Install

install.packages('sommer')

Monthly Downloads

4,995

Version

1.2

License

GPL-3

Maintainer

Giovanny CovarrubiasPazaran

Last Published

February 7th, 2016

Functions in sommer (1.2)

Additive relationship matrix

plot form a GLMM plot with mmer

Mixed Model Equations in R

Score calculation for markers

Letter to number converter

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).

Average Information Algorithm

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

Solving Mixed Model Equations in R

half diallel data for corn hybrids

Dominance relationship matrix

Mixed Model Equations in R 2

Corn crosses and markers

extracting random effects

Residuals form a GLMM fitted with mmer

Epistatic relationship matrix

Half Diallel Matrix

summary form a GLMM fitted with mmer

Creating a genetic map

Genotypic and Phenotypic data for a potato polyploid population

design score for the model to be tested

Efficient Mixed Model Association Algorithm

wheat lines dataset

Average Information Algorithm

anova form a GLMM fitted with mmer

fitted form a GLMM fitted with mmer

Average Information Algorithm

Creating color with transparency

Binds arrays corner-to-corner

False Discovery Rate calculation

coef form a GLMM fitted with mmer

Expectation Maximization Algorithm