geneticae

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# geneticae <img src="man/figures/baseplot.png" align="right" alt="" width="160"/>

## Statistical Tools for the Analysis of Multi Environment Agronomic Trials

Web: <https://jangelini.github.io/geneticae/>

CRAN: <https://CRAN.R-project.org/package=geneticae/index.html>

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Understanding the relationship between crops performance and environment
is a key problem for plant breeders and geneticists. In advanced stages
of breeding programs, in which few genotypes are evaluated,
multi-environmental trials (MET) are one of the most used experiments.
Such studies test a number of genotypes in multiple environments in
order to identify the superior genotypes according to their performance.
In these experimentes, crop performance is modeled as a function of
genotype (G), environment (E) and genotype-environment interaction
(GEI). The presence of GEI generates differential genotypic responses in
the different environments. Therefore appropriate statistical methods
should be used to obtain an adequate GEI analysis, which is essential
for plant breeders.

The average performance of genotypes through different environments can
only be considered in the absence of GEI. However, GEI is almost always
present and the comparison of the mean performance between genotypes is
not enough. The most widely used methods to analyze MET data are based
on regression models, analysis of variance (ANOVA) and multivariate
techniques. In particular, two statistical models are widely used among
plant breeders as they provide useful graphical tools for the study of
GEI: the Additive Main effects and Multiplicative Interaction model
(AMMI) and the Site Regression Model (SREG). However, these models are
not always efficient enough to analyze MET data structure of plant
breeding programs. They present serious limitations in the presence of
atypical observations and missing values, which occur very frequently.
To overcome this, several imputation alternatives (Angelini et al.,
2024) and a robust AMMI and a SREG model were recently proposed in
literature (Rodrigues et al., 2016; Angelini et al., 2022).

The `geneticae` package was created to gather in one place the most
useful functions for this type of analysis and it also implements new
methodology which can be found in recent literature. More importantly,
`geneticae` is the first package to implement the robust AMMI models
proposed by Rodrigues et al. (2016), the robusts SREG proposed by
Angelini et al. (2022) and new imputation methods proposed by Angelini
et al. (2024). In addition, there is no need to preprocess the data to
use the `geneticae` package, as it the case of some previous packages
which require a data frame or matrix containing genotype by environment
means with the genotypes in rows and the environments in columns. In
this package, data in long format is required. There is no restriction
on columns names of genotypes, environments, repetitions (if any) and
phenotypic traits of interest. Also, extra information that will not be
used in the analysis may be present in the dataset. Finally, `geneticae`
offers a wide variety of options to customize the biplots, which are
part of the graphical output of these methods.

This package can be used through
[this](https://geneticae.shinyapps.io/geneticae-shiny-web-app/) Shiny
app, making it available not only for R programmers.

## Installation

You can install the released version of `geneticae` from
[CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("geneticae")
```

You can install the development version from our [GitHub
repo](https://github.com/jangelini/geneticae) with:

``` r
# install.packages("devtools")
devtools::install_github("jangelini/geneticae")
```

## Shiny app

You can use `geneticae` through
[this](https://geneticae.shinyapps.io/geneticae-shiny-web-app/) Shiny
app. Source code is in [GitHub
repo](https://github.com/jangelini/Geneticae-Shiny-Web-APP).

## Getting Started

If you are just getting started with `geneticae` we recommend visiting
the vignettes and exploring the examples throughout the package
documentation.

Here we present a small example.

The dataset `yan.winterwheat` has information about the yield of 18
winter wheat varieties grown in nine environments in Ontario at 1993.
The function `GGEPlot()` builds several GGE biplots views. The basic
biplot is produced with the argument `type="Biplot"`. If the function is
used with the argument `type = "Selected Environment"` and the name of
one environment is provided in `selectedE`, a line that passes through
the environment marker (i.e. OA93), and the biplot origin is added. The
most suitable cultivars for that particular environment can be
identified looking at their projection onto this axis. Thus, at the
environment OA93, the highest-yielding cultivar was *Zav*, and the
lowest-yielding cultivar was *Luc*. The perpendicular line to the OA93
axis separates genotypes that yielded above and below the mean in this
environment.

``` r
library(geneticae)
library(agridat)
data(yan.winterwheat)


GGE1 <- rSREGModel(yan.winterwheat, genotype = "gen", environment = "env", 
                   response = "yield",  model = "SREG")

rSREGPlot(GGE1, type = "Selected Environment", selectedE = "OA93", footnote = FALSE, titles = FALSE)
```

<div class="figure" style="text-align: center">

<img src="man/figures/README-unnamed-chunk-4-1.png" alt="Figure: comparison of cultivar performance in a selected environment." width="45%" />
<p class="caption">

Figure: comparison of cultivar performance in a selected environment.
</p>

</div>