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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

1.0.9

License

GPL

Issues

Pull Requests

Stars

Forks

Maintainer

Bart-Jan van Rossum

Last Published

September 18th, 2024

Functions in statgenGxE (1.0.9)

gxeFw

Finlay-Wilkinson analysis
correlations

Compute different types of correlations.
diagnostics

Get diagnostics for an object of class varComp
createVarComp

S3 class varComp
gxeGGE

GGE analysis
CRDR

Calculate the correlated response to selection
statgenGxE-package

statgenGxE: Genotype by Environment (GxE) Analysis
predict.varComp

Predictions based on a fitted varComp model.
FW

S3 class FW
reexports

Objects exported from other packages
fitted.varCov

Extract fitted values.
TDMaize

Field data for a maize experiment in Tlaltizapan, Mexico
herit

Calculate heritability
multMissing

Estimate missing values in multivariate data
varCov

S3 class varCov
megaEnv

S3 class megaEnv
gxeAmmi

AMMI analysis
fitted.AMMI

Extract fitted values.
plot.varCov

Plot function for class varCov
fitted.FW

Extract fitted values.
plot.stability

Plot function for class stability
plot.varComp

Plot function for class varComp
gxeMegaEnv

Form mega environments based on fitted values from an AMMI model
gxeStability

Calculate stability coefficients for genotype-by-environment data
predict.megaEnv

Compute BLUPS based on a set of mega environments
residuals.AMMI

Extract residuals.
gxeVarComp

Mixed model analysis of GxE table of means
gxeVarCov

Selects the best variance-covariance model for a set of trials
plot.AMMI

Plot function for class AMMI
report.AMMI

Report method for class AMMI
plot.FW

Plot function for class FW
report.FW

Report method for class FW
plot.megaEnv

Plot function for class megaEnv
residuals.FW

Extract residuals.
report.stability

Report method for class stability
residuals.varCov

Extract residuals.
report.varCov

Report method for class varCov
stability

S3 class stability
vc

Extract variance components
dropsPheno

DROPS data set
AMMI

S3 class AMMI