Function reference • statgenGxE

Mixed model analysis of GxE table of means

gxeVarComp(): Mixed model analysis of GxE table of means

plot(<varComp>): Plot function for class varComp

predict(<varComp>): Predictions based on a fitted varComp model.

vc(): Extract variance components

herit(): Calculate heritability

CRDR(): Calculate the correlated response to selection

correlations(): Compute different types of correlations.

diagnostics(): Get diagnostics for an object of class varComp

Finlay-Wilkinson

gxeFw(): Finlay-Wilkinson analysis

plot(<FW>): Plot function for class FW

report(<FW>): Report method for class FW

fitted(<FW>): Extract fitted values.

residuals(<FW>): Extract residuals.

AMMI

gxeAmmi(): AMMI analysis

plot(<AMMI>): Plot function for class AMMI

report(<AMMI>): Report method for class AMMI

fitted(<AMMI>): Extract fitted values.

residuals(<AMMI>): Extract residuals.

GGE

gxeGGE(): GGE analysis

Identifying mega environments

gxeMegaEnv(): Form mega environments based on fitted values from an AMMI model

plot(<megaEnv>): Plot function for class megaEnv

predict(<megaEnv>): Compute BLUPS based on a set of mega environments

Stability measures

gxeStability(): Calculate stability coefficients for genotype-by-environment data

plot(<stability>): Plot function for class stability

report(<stability>): Report method for class stability

Modeling of heterogeneity of genetic variances and correlations

gxeVarCov(): Selects the best variance-covariance model for a set of trials

plot(<varCov>): Plot function for class varCov

report(<varCov>): Report method for class varCov

fitted(<varCov>): Extract fitted values.

residuals(<varCov>): Extract residuals.

Example data

dropsPheno: DROPS data set

TDMaize: Field data for a maize experiment in Tlaltizapan, Mexico

Internal helper functions

multMissing(): Estimate missing values in multivariate data