biometris / statgengxe

See https://biometris.github.io/statgenGxE for a full description

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)

statgengxe's Issues

Models for the VCOV structure in the vignette

Hello,

Just want to report a mistake in the vignette.
I had compared the model table to the original reference (Boer et al. 2007)
In the table of section"Modeling of heterogeneity of genetic variances and correlations",
var(gij) of the identity model should be σ2GE, and cov(gij;gik) in the compound symmetry model should be σ2G.

Best regards,
YCL

plot.AMMI overwritten by agricolae

Dear developers,
I wanted to report an issue I encountered while trying AMMI analysis with your package.
I am working on R version 4.0.4 and among my packages I have agricolae version 1.3-3. When I load statgenGxE I get the following message:

Registered S3 method overwritten by 'agricolae':
method from
plot.AMMI statgenGxE

Indeed, the plot function does not work with the gxeAmmi() output, giving me the following list of error/warnings:
Error in plot.window(...) : need finite 'xlim' values
Inoltre: Warning messages:
1: In min(x, na.rm = na.rm) :
no non-missing arguments to min; returning Inf
2: In max(x, na.rm = na.rm) :
no non-missing arguments to max; returning -Inf
3: In min(x, na.rm = na.rm) :
no non-missing arguments to min; returning Inf
4: In max(x, na.rm = na.rm) :
no non-missing arguments to max; returning -Inf
5: In plot.window(...) : invalid graphic parameter "plotType"
6: In plot.window(...) : invalid graphic parameter "scale"

Kind regards,
Chiara