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statgenGxE

statgenGxE is an R package providing functions for Genotype by Environment (GxE) analysis for data of plant breeding experiments.

The following types of analysis can be done using statgenGxE:

  • Mixed model analysis of GxE table of means
  • Finlay-Wilkinson Analysis
  • AMMI Analysis
  • GGE Analysis
  • Identifying mega environments
  • Stability measures
  • Modeling of heterogeneity of genetic variances and correlations

statgenGxE has extensive options for summarizing and visualizing the results of the analyses. For a full overview of all options it is best to read the vignette

Installation

  • Install from CRAN:
install.packages("statgenGxE")
  • Install latest development version from GitHub (requires remotes package):
remotes::install_github("Biometris/statgenGxE", ref = "develop", dependencies = TRUE)

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Version

Install

install.packages('statgenGxE')

Monthly Downloads

393

Version

1.0.2

License

GPL

Maintainer

Bart-Jan van Rossum

Last Published

October 1st, 2020

Functions in statgenGxE (1.0.2)

fitted.AMMI

Extract fitted values.
fitted.FW

Extract fitted values.
herit

Calculate heritability
AMMI

S3 class AMMI
CRDR

Calculate the correlated response to selection
diagnostics

Get diagnostics for an object of class varComp
gxeVarComp

Mixed model analysis of GxE table of means
dropsPheno

DROPS data set
plot.varCov

Plot function for class varCov
gxeVarCov

Selects the best variance-covariance model for a set of trials
gxeFw

Finlay-Wilkinson analysis
megaEnv

S3 class megaEnv
gxeGGE

GGE analysis
plot.AMMI

Plot function for class AMMI
multMissing

Estimate missing values in multivariate data
plot.megaEnv

Plot function for class megaEnv
plot.FW

Plot function for class FW
vc

Extract variance components
report.AMMI

Report method for class AMMI
report.FW

Report method for class FW
predict.megaEnv

Compute BLUPS based on a set of mega environments
report.stability

Report method for class stability
statgenGxE-package

statgenGxE: Genotype by Environment (GxE) Analysis
report.varCov

Report method for class varCov
varCov

S3 class varCov
fitted.varCov

Extract fitted values.
gxeAmmi

AMMI analysis
TDMaize

Field data for a maize experiment in Tlaltizapan, Mexico
plot.stability

Plot function for class stability
FW

S3 class FW
plot.varComp

Plot function for class varComp
residuals.FW

Extract residuals.
residuals.AMMI

Extract residuals.
gxeMegaEnv

Form mega environments based on fitted values from an AMMI model
predict.varComp

Predictions based on a fitted varComp model.
gxeStability

Calculate stability coefficients for genotype-by-environment data
reexports

Objects exported from other packages
residuals.varCov

Extract residuals.
stability

S3 class stability
correlations

Compute different types of correlations.
createVarComp

S3 class varComp