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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

359

Version

1.0.3

License

GPL

Issues

2

Pull Requests

0

Stars

11

Forks

7

Maintainer

Bart-Jan van Rossum

Last Published

November 9th, 2020

Functions in statgenGxE (1.0.3)

fitted.FW

Extract fitted values.
createVarComp

S3 class varComp
diagnostics

Get diagnostics for an object of class varComp
fitted.AMMI

Extract fitted values.
correlations

Compute different types of correlations.
CRDR

Calculate the correlated response to selection
AMMI

S3 class AMMI
TDMaize

Field data for a maize experiment in Tlaltizapan, Mexico
FW

S3 class FW
dropsPheno

DROPS data set
fitted.varCov

Extract fitted values.
gxeVarCov

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

Plot function for class varCov
gxeVarComp

Mixed model analysis of GxE table of means
plot.FW

Plot function for class FW
gxeAmmi

AMMI analysis
plot.megaEnv

Plot function for class megaEnv
predict.megaEnv

Compute BLUPS based on a set of mega environments
plot.varComp

Plot function for class varComp
plot.stability

Plot function for class stability
multMissing

Estimate missing values in multivariate data
herit

Calculate heritability
plot.AMMI

Plot function for class AMMI
megaEnv

S3 class megaEnv
report.varCov

Report method for class varCov
report.stability

Report method for class stability
gxeFw

Finlay-Wilkinson analysis
gxeGGE

GGE analysis
residuals.varCov

Extract residuals.
stability

S3 class stability
gxeMegaEnv

Form mega environments based on fitted values from an AMMI model
statgenGxE-package

statgenGxE: Genotype by Environment (GxE) Analysis
gxeStability

Calculate stability coefficients for genotype-by-environment data
varCov

S3 class varCov
report.FW

Report method for class FW
report.AMMI

Report method for class AMMI
predict.varComp

Predictions based on a fitted varComp model.
residuals.AMMI

Extract residuals.
reexports

Objects exported from other packages
residuals.FW

Extract residuals.
vc

Extract variance components