Description Usage Arguments Value References Examples

The Site Regression model (also called genotype +
genotype-by-environment (GGE) model) is a powerful tool for effective
analysis and interpretation of data from multi-environment trials in
breeding programs. This function is a wrapper for
`GGEModel`

from the
GGEBiplots package,
with the following enhacements:

It can be used for data from trials with repetitions (there is no need to calculate means beforehand)

Other variables not used in the analysis can be present in the dataset.

Variables can be in any order in the dataset.

1 2 3 4 5 6 7 8 9 10 | ```
GGEmodel(
Data,
genotype = "gen",
environment = "env",
response = "yield",
rep = NULL,
centering = "tester",
scaling = "none",
SVP = "symmetrical"
)
``` |

`Data` |
dataframe with genotypes, environments, repetitions (if any) and the phenotypic trait of interest. Variables can be in any order, even additional variables that will not be used in the model may be present in the data. |

`genotype` |
column name for genotypes. |

`environment` |
column name for environments. |

`response` |
column name for the phenotypic trait. |

`rep` |
column name for replications. If this argument is NULL, there are no replications in the data. Defaults to NULL. |

`centering` |
centering method. Either '"tester"' for tester centered (G+GE), '"global"' for global centered (E+G+GE), '"double"' for double centered (GE) or '"none"' for no centering. Defaults to '"tester"'. |

`scaling` |
scaling method. Either '"sd"' for standard deviation or '"none"' for no scaling. Defaults to '"none"'. |

`SVP` |
method for singular value partitioning. Either '"row"', '"column"', '"dual"' or '"symmetrical"'. Defaults to '"symmetrical"'. |

A list of class `GGE_Model`

containing:

`coordgenotype` |
plotting coordinates for each genotype in every component. |

`coordenviroment` |
plotting coordinates for each environment in every component. |

`eigenvalues` |
vector of eigenvalues for each component. |

`vartotal` |
overall variance. |

`varexpl` |
percentage of variance explained by each component. |

`labelgen` |
genotype names. |

`labelenv` |
environment names. |

`axes` |
axis labels. |

`Data` |
scaled and centered input data. |

`centering` |
name of centering method. |

`scaling` |
name of scaling method. |

`SVP` |
name of SVP method. |

Sam Dumble (2017). GGEBiplots: GGE Biplots with 'ggplot2'. R package version 0.1.1. https://CRAN.R-project.org/package=GGEBiplots

Yan W, Kang M (2003). *GGE Biplot Analysis: A Graphical Tool
for Breeders, Geneticists, and Agronomists*. CRC Press.

Yan W, Kang M (2002). *Singular-Value Partitioning in Biplot
Analysis of Multienvironment Trial Data*. Agronomy Journal, 94, 990-996.
doi: 10.2134/agronj2002.0990

1 2 3 4 5 6 7 8 9 10 11 | ```
library(geneticae)
# Data without replication
library(agridat)
data(yan.winterwheat)
GGE1 <- GGEmodel(yan.winterwheat, genotype = "gen", environment = "env",
response = "yield", centering = "tester")
# Data with replication
data(plrv)
GGE2 <- GGEmodel(plrv, genotype = "Genotype", environment = "Locality",
response = "Yield", rep = "Rep", centering = "tester")
``` |

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