RGxEStat

Interactive Genotype × Environment Statistical Analysis

RGxEStat is an R/Shiny package, providing a user-friendly web interface for performing:

• Analysis of Significance based on mixed effect model
• Univariate Stability Analysis including group regression slope and deviation, Shukla's σ², Wricke's ecovalence, Kang's yield stability, etc.
• Multivariate Stability Analysis by analysis of variance, principal component analysis, and singular value decomposition.
• Export of tables and figures

---

📦 Installation

Install the released version from CRAN:

if (getRversion() <= "4.4.0") {
  install.packages("RGxEStat")
} else {
  message("Detected R > 4.4.0. Manually install dependencies and RGxEStat from GitHub.")

or from GitHub:

if (!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}

if (getRversion() <= "4.4.0") {
  devtools::install_github("mason-ching/RGxEStat@main")
} else {
  devtools::install_github("cran/GGEBiplotGUI@master")
  install.packages("klaR")
  install.packages("https://cran.r-project.org/src/contrib/Archive/agricolae/agricolae_1.3-6.tar.gz", repos = NULL, type = "source")
  devtools::install_github("mason-ching/RGxEStat@main")
}

---

🚀 Launching the App

library(RGxEStat)
run_app()

This will open an interactive app in your browser with three main tabs:

1. Significance Analyzer
2. Univariate Analyzer
3. Multivariate Analyzer

---

🔍 1. Significance Analyzer

Select your dataset and trait, then choose one of five different cases to perform ANOSI:

• Fixed/Random effect combinations of Genotype (CLT), Year (YR), Location (LC) and Replication (RP).

Results include the ANOSI tables of random and fixed effects and BLUP estimates for each genotype.

---

📈 2. Univariate Analyzer

2.1 Descriptive and stability statistics for each genotype:

• Coefficient of Variation
• Trait Means over various factors
• Group Regression Slope and Deviation
• Shukla's σ², Wricke's Ecovalence, Kang's Yield Stability

Click Execute or Compute under each section to update the results table on the right.

2.2 Discriminative and representative location & environment

• Location: genotype F ratio for each location and correlation among location and average location
• Environment: genotype F ratio for each environment and correlation among environment and average environment

When the mean of all genotypes are equal, then the F ratio will be close to 1. If analysis of variance is run by location, then high genotype F ratio indicates high discriminating ability for that location. High and significant Pearson correlation of each location with the mean of all locations indicates strong representation of mean location performance.

2.3 Cluster analysis & Export results

• Cluster dendrogram groups similar locations
• Save & Export panel:
  • Choose which results to export
  • Select file format: csv, txt, xlsx, doc
  • Click Export to download

---

📊 3. Multivariate Analyzer

3.1 Additive main effect and multiplicative interaction

• Select principal components (PC1, PC2, PC3, PC4) and render a biplot or triplot

3.2 Gene main effect plus gene-environment interaction effect

• Interactive window for model selection and various biplot explorations

---

⚙️ API

If you prefer to integrate RGxEStat into your own scripts, you can call:

# Launch the interactive app
RGxEStat::run_app()

---

📝 NEWS

See NEWS.md for the full changelog.

---

🖥️ Standalone Application

The RGxEStat has been packaged as a standalone desktop application using Electron. You do not need to install R or any R packages to run it. Just simply download the release from: Google Drive, unzip it, and double-click RGxEStat.exe to launch the application.

Note:

• Currently, only Windows systems are supported. For any questions or issues, feel free to contact mengenching@gmail.com.
• Use YR, LC, CLT and RP as the column names of years, locations, cultivars (genotypes) and replications in your data file.

---

📄 License

The project and application are licensed under the MIT License.