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Additive Main Effects and Multiplicative Interaction (AMMI)

Source: R/ammi.R
ammi.Rd

Performs Additive Main Effects and Multiplicative Interaction (AMMI) Analysis for Genotypes by Environment Interaction (GEI)

Usage

ammi(.data, .y, .rep, .gen, .env)

# Default S3 method
ammi(.data, .y, .rep, .gen, .env)

Arguments

.data

data.frame

.y

Response Variable

.rep

Replication Factor

.gen

Genotypes Factor

.env

Environment Factor

Value

Stability Measures

References

Singh, R. K. and Chaudhary, B. D. (2004) Biometrical Methods in Quantitative Genetic Analysis. New Delhi: Kalyani.

Author

  1. Muhammad Yaseen (myaseen208@gmail.com)

  2. Kent M. Edkridge (keskridge1@unl.edu)

Examples


data(ge_data)
Yield.ammi <-
     ammi(
            .data = ge_data
          , .y    = Yield
          , .rep  = Rep
          , .gen  = Gen
          , .env  = Env
      )
Yield.ammi
#> $anova
#> Analysis of Variance Table
#> 
#> Response: .data[[Y]]
#>            Df    Sum Sq  Mean Sq F value    Pr(>F)    
#> Env        10 263940496 26394050 68.0551 1.995e-08 ***
#> Rep(Env)   11   4266167   387833                      
#> Gen        59  71662431  1214617 12.2482 < 2.2e-16 ***
#> Gen:Env   590 201336476   341248  3.4411 < 2.2e-16 ***
#> Residuals 649  64359568    99167                      
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#> 
#> $pc.anova
#> # A tibble: 11 × 9
#>    PC     SingVal  Percent accumPerc    Df       SS  Mean.Sq  F.value   Pr..F.
#>    <chr>    <dbl>    <dbl>     <dbl> <dbl>    <dbl>    <dbl>    <dbl>    <dbl>
#>  1 PC1   4.50e+ 3 2.01e+ 1      20.1    68 4.04e+ 7 5.95e+ 5 6.00e+ 0 0       
#>  2 PC2   4.17e+ 3 1.73e+ 1      37.4    66 3.49e+ 7 5.28e+ 5 5.33e+ 0 0       
#>  3 PC3   4.05e+ 3 1.63e+ 1      53.7    64 3.27e+ 7 5.12e+ 5 5.16e+ 0 0       
#>  4 PC4   3.49e+ 3 1.21e+ 1      65.8    62 2.44e+ 7 3.93e+ 5 3.96e+ 0 0       
#>  5 PC5   3.38e+ 3 1.13e+ 1      77.1    60 2.29e+ 7 3.81e+ 5 3.84e+ 0 0       
#>  6 PC6   3.11e+ 3 9.63e+ 0      86.7    58 1.94e+ 7 3.34e+ 5 3.37e+ 0 4.02e-14
#>  7 PC7   2.30e+ 3 5.25e+ 0      92.0    56 1.06e+ 7 1.89e+ 5 1.90e+ 0 1.45e- 4
#>  8 PC8   2.03e+ 3 4.10e+ 0      96.1    54 8.25e+ 6 1.53e+ 5 1.54e+ 0 9.52e- 3
#>  9 PC9   1.52e+ 3 2.30e+ 0      98.4    52 4.63e+ 6 8.91e+ 4 8.98e- 1 6.77e- 1
#> 10 PC10  1.28e+ 3 1.63e+ 0     100      50 3.27e+ 6 6.55e+ 4 6.60e- 1 9.66e- 1
#> 11 PC11  2.08e-11 4.32e-28     100      48 8.69e-22 1.81e-23 1.83e-28 1   e+ 0
#>