Predict the means of a performs_ammi object considering a specific number of axis.
Usage
# S3 method for performs_ammi
predict(object, naxis = 2, ...)Arguments
- object
An object of class performs_ammi
- naxis
The the number of axis to be use in the prediction. If
objecthas more than one variable, thennaxismust be a vector.- ...
Additional parameter for the function
Details
This function is used to predict the response variable of a two-way table
(for examples the yielding of the i-th genotype in the j-th environment)
based on AMMI model. This prediction is based on the number of multiplicative
terms used. If naxis = 0, only the main effects (AMMI0) are used. In
this case, the predicted mean will be the predicted value from OLS
estimation. If naxis = 1 the AMMI1 (with one multiplicative term) is
used for predicting the response variable. If naxis = min(gen-1;env-1), the AMMIF is fitted and the predicted value will be the
cell mean, i.e. the mean of R-replicates of the i-th genotype in the j-th
environment. The number of axis to be used must be carefully chosen.
Procedures based on Postdictive success (such as Gollobs's d.f.) or
Predictive success (such as cross-validation) should be used to do this. This
package provide both. performs_ammi() function compute
traditional AMMI analysis showing the number of significant axis. On the
other hand, cv_ammif() function provide a cross-validation,
estimating the RMSPD of all AMMI-family models, based on resampling
procedures.
Author
Tiago Olivoto tiagoolivoto@gmail.com
Examples
# \donttest{
library(metan)
model <- performs_ammi(data_ge, ENV, GEN, REP,
resp = c(GY, HM))
#> variable GY
#> ---------------------------------------------------------------------------
#> AMMI analysis table
#> ---------------------------------------------------------------------------
#> Source Df Sum Sq Mean Sq F value Pr(>F) Proportion Accumulated
#> ENV 13 279.574 21.5057 62.33 0.00e+00 NA NA
#> REP(ENV) 28 9.662 0.3451 3.57 3.59e-08 NA NA
#> GEN 9 12.995 1.4439 14.93 2.19e-19 NA NA
#> GEN:ENV 117 31.220 0.2668 2.76 1.01e-11 NA NA
#> PC1 21 10.749 0.5119 5.29 0.00e+00 34.4 34.4
#> PC2 19 9.924 0.5223 5.40 0.00e+00 31.8 66.2
#> PC3 17 4.039 0.2376 2.46 1.40e-03 12.9 79.2
#> PC4 15 3.074 0.2049 2.12 9.60e-03 9.8 89.0
#> PC5 13 1.446 0.1113 1.15 3.18e-01 4.6 93.6
#> PC6 11 0.932 0.0848 0.88 5.61e-01 3.0 96.6
#> PC7 9 0.567 0.0630 0.65 7.53e-01 1.8 98.4
#> PC8 7 0.362 0.0518 0.54 8.04e-01 1.2 99.6
#> PC9 5 0.126 0.0252 0.26 9.34e-01 0.4 100.0
#> Residuals 252 24.367 0.0967 NA NA NA NA
#> Total 536 389.036 0.7258 NA NA NA NA
#> ---------------------------------------------------------------------------
#>
#> variable HM
#> ---------------------------------------------------------------------------
#> AMMI analysis table
#> ---------------------------------------------------------------------------
#> Source Df Sum Sq Mean Sq F value Pr(>F) Proportion Accumulated
#> ENV 13 5710.32 439.255 57.22 1.11e-16 NA NA
#> REP(ENV) 28 214.93 7.676 2.70 2.20e-05 NA NA
#> GEN 9 269.81 29.979 10.56 7.41e-14 NA NA
#> GEN:ENV 117 1100.73 9.408 3.31 1.06e-15 NA NA
#> PC1 21 381.13 18.149 6.39 0.00e+00 34.6 34.6
#> PC2 19 319.43 16.812 5.92 0.00e+00 29.0 63.6
#> PC3 17 114.26 6.721 2.37 2.10e-03 10.4 74.0
#> PC4 15 81.96 5.464 1.92 2.18e-02 7.4 81.5
#> PC5 13 68.11 5.240 1.84 3.77e-02 6.2 87.7
#> PC6 11 59.07 5.370 1.89 4.10e-02 5.4 93.0
#> PC7 9 46.69 5.188 1.83 6.33e-02 4.2 97.3
#> PC8 7 26.65 3.808 1.34 2.32e-01 2.4 99.7
#> PC9 5 3.41 0.682 0.24 9.45e-01 0.3 100.0
#> Residuals 252 715.69 2.840 NA NA NA NA
#> Total 536 9112.21 17.000 NA NA NA NA
#> ---------------------------------------------------------------------------
#>
#> All variables with significant (p < 0.05) genotype-vs-environment interaction
#> Done!
# Predict GY with 3 IPCA and HM with 1 IPCA
predict <- predict(model, naxis = c(3, 1))
# }