Performs Additive Main Effects and Multiplication Interaction Analysis of Genotype by Environment Interaction Model
References
Crossa, J., Perez-Elizalde, S., Jarquin, D., Cotes, J.M., Viele, K., Liu, G., and Cornelius, P.L. (2011) Bayesian Estimation of the Additive Main Effects and Multiplicative Interaction Model Crop Science, 51, 1458–1469. (doi: 10.2135/cropsci2010.06.0343)
Author
Muhammad Yaseen (myaseen208@gmail.com)
Examples
data(Maiz)
fm1 <-
ge_ammi(
.data = Maiz
, .y = Yield
, .gen = Gen
, .env = Env
, .rep = Rep
)
fm1
#> $g
#> [1] 9
#>
#> $e
#> [1] 20
#>
#> $Rep
#> [1] 4
#>
#> $k
#> [1] 8
#>
#> $ge_means
#> $ge_means$ge_means
#> 1 2 3 4 5 6 7 8
#> [1,] 3621.550 3728.325 5554.025 4565.575 4379.800 6436.725 2832.400 6011.400
#> [2,] 3426.450 3918.650 4936.675 4962.575 5201.475 6036.275 2514.600 5277.700
#> [3,] 3445.850 4082.125 5117.025 5136.275 4177.925 6458.800 3529.075 4730.750
#> [4,] 3719.900 4539.175 4542.500 6029.500 5672.250 6677.800 2997.600 2516.225
#> [5,] 3164.625 4078.850 6172.525 5831.000 5413.550 6881.700 3555.600 2731.600
#> [6,] 4116.075 4877.550 5204.825 5979.900 5591.350 6915.950 3948.875 2982.575
#> [7,] 3354.025 4767.025 5389.025 4342.275 4277.175 6744.550 3536.875 4205.575
#> [8,] 4528.775 3393.250 5248.075 4441.500 4476.400 4986.250 3087.675 4483.900
#> [9,] 3135.525 4500.050 3779.600 5781.375 5407.150 5609.700 3061.375 3309.425
#> 9 10 11 12 13 14 15 16
#> [1,] 4646.700 3099.875 4432.850 6873.275 6720.550 5848.575 4600.925 5009.675
#> [2,] 4713.900 2971.750 4348.525 7570.900 5626.975 5932.475 4125.825 5196.450
#> [3,] 5447.500 2785.375 4526.200 7727.025 6293.875 5886.475 4537.400 5455.475
#> [4,] 4863.925 2843.325 7117.225 8385.050 7331.725 6439.375 6331.175 6351.100
#> [5,] 5588.350 2688.000 5995.175 8105.600 7173.575 6358.975 6327.975 6069.800
#> [6,] 5602.725 3023.500 6150.275 7636.575 7261.925 6380.225 5961.350 5730.175
#> [7,] 4318.200 2888.925 5051.575 7443.575 5543.850 5819.775 4345.925 5013.425
#> [8,] 4001.050 3353.125 3712.975 5815.825 4116.550 5522.450 4321.200 4551.000
#> [9,] 5553.450 2773.950 6429.925 8090.675 6919.875 6282.350 4889.475 5278.375
#> 17 18 19 20
#> [1,] 4414.850 3344.475 1632.000 4587.025
#> [2,] 4210.550 4415.200 2281.750 4396.475
#> [3,] 4749.175 4294.600 3059.175 5018.175
#> [4,] 5160.850 5617.700 2232.600 4987.975
#> [5,] 5454.375 4497.800 3072.525 5775.875
#> [6,] 5807.050 5333.025 3011.025 5088.475
#> [7,] 3861.575 5276.350 3210.550 4056.075
#> [8,] 5243.000 2940.375 2634.350 4806.175
#> [9,] 4988.775 5244.400 2734.950 4822.275
#>
#> $ge_means$grand_mean
#> [1] 4858.138
#>
#>
#> $mu
#> [1] 4858.138
#>
#> $sigma2
#> [1] 602844.8
#>
#> $tau
#> [1] 1.658802e-06
#>
#> $tao
#> GEffs
#> [1,] -241.10903
#> [2,] -254.87903
#> [3,] -35.22403
#> [4,] 359.71097
#> [5,] 388.73597
#> [6,] 472.03347
#> [7,] -185.82153
#> [8,] -574.94278
#> [9,] 71.49597
#>
#> $delta
#> $delta$e_effects
#> EEffs
#> [1,] -1245.60722
#> [2,] -648.69333
#> [3,] 246.78167
#> [4,] 371.85944
#> [5,] 97.09278
#> [6,] 1447.16778
#> [7,] -1628.79611
#> [8,] -830.45444
#> [9,] 112.50667
#> [10,] -1921.71278
#> [11,] 449.05389
#> [12,] 2658.36222
#> [13,] 1473.96222
#> [14,] 1194.15944
#> [15,] 190.89000
#> [16,] 548.02611
#> [17,] 18.55111
#> [18,] -306.59056
#> [19,] -2206.03500
#> [20,] -20.52389
#>
#>
#> $lambdas
#> [1] 5922.8913 3070.4543 2552.4065 2320.2216 1758.6707 1313.4148 792.6324
#> [8] 757.0277
#>
#> $alphas
#> [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,] -0.3812275 0.226376853 0.640917402 0.06276348 -0.27443433 0.37189646
#> [2,] -0.2475437 0.318181602 0.006538921 0.28188493 -0.01561052 -0.59051506
#> [3,] -0.1646604 0.148474658 0.057621352 -0.20971703 0.57150726 0.10396503
#> [4,] 0.5150500 -0.003274222 0.055897289 0.19678126 -0.53669368 -0.15093898
#> [5,] 0.2830484 -0.342584150 0.367812867 -0.48923056 0.20120360 -0.40537436
#> [6,] 0.2711150 -0.219555439 -0.091312330 -0.08018815 -0.03226380 0.54258480
#> [7,] -0.1187550 0.378875355 -0.568803868 -0.51368905 -0.26377705 0.03780326
#> [8,] -0.4791048 -0.693744264 -0.287949071 0.23087508 -0.08707764 -0.04170396
#> [9,] 0.3220780 0.187249608 -0.180722562 0.52052004 0.43714616 0.13228281
#> [,7] [,8]
#> [1,] -0.02847968 0.25131927
#> [2,] 0.46762033 -0.28151218
#> [3,] -0.45151147 -0.50113650
#> [4,] -0.44908389 -0.26316390
#> [5,] 0.11832901 0.31298999
#> [6,] 0.57650833 -0.35300400
#> [7,] -0.04118176 0.26668701
#> [8,] -0.16110446 0.08106783
#> [9,] -0.03109641 0.48675248
#>
#> $gammas
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] -0.2247956069 -0.268762762 -0.180394316 0.222348371 -0.30092049
#> [2,] 0.0175838398 0.177687532 -0.298911720 -0.041784559 -0.09111097
#> [3,] -0.2576076055 -0.175443927 0.178717786 -0.529519189 -0.18043272
#> [4,] 0.1479472725 -0.088454266 0.069163882 0.217056712 0.16726564
#> [5,] 0.0858940079 -0.087735308 -0.015520307 0.332760370 -0.13388850
#> [6,] -0.0062634265 0.202736159 0.119096124 -0.436497716 -0.22923737
#> [7,] -0.0811124294 -0.104663893 -0.205425713 -0.255736793 0.15108197
#> [8,] -0.6729482134 0.417876989 0.208225840 0.270178727 -0.01642642
#> [9,] 0.0379649453 0.044739257 0.120116710 0.036624299 0.56157302
#> [10,] -0.2181054837 -0.067854487 -0.114378161 0.181480140 -0.15899739
#> [11,] 0.3893229450 0.068645984 -0.059924965 0.161721122 -0.23021612
#> [12,] 0.1599691886 0.315491388 0.024223837 -0.006684231 0.17771568
#> [13,] 0.2494794721 0.243512687 0.502522098 -0.008462921 0.05281381
#> [14,] -0.0066476422 0.023585491 -0.005191355 0.104224942 -0.02038511
#> [15,] 0.2075844883 -0.282722634 0.217172457 -0.120945134 -0.27658890
#> [16,] 0.0789946673 0.002229003 0.112568804 -0.036351911 -0.09773665
#> [17,] 0.0000971901 -0.429651688 0.026360843 0.176686594 0.13223547
#> [18,] 0.2171860426 0.341218990 -0.436647122 -0.014493154 -0.12508018
#> [19,] -0.0881298634 -0.075990205 -0.423893917 -0.250725603 0.37341100
#> [20,] -0.0364137885 -0.256444309 0.162119195 -0.001880067 0.24492422
#> [,6] [,7] [,8]
#> [1,] 0.22504209 -0.130319195 -0.346996059
#> [2,] 0.23675510 0.123777955 0.075854726
#> [3,] -0.24701208 0.236917971 0.284672769
#> [4,] -0.08520769 0.086797272 -0.253419484
#> [5,] -0.35236840 0.648776843 0.103439840
#> [6,] 0.08901469 0.141215583 -0.340199773
#> [7,] 0.35496791 -0.055017924 0.028131793
#> [8,] 0.01828035 -0.105003681 0.082344453
#> [9,] 0.11756614 0.209431533 -0.061495518
#> [10,] 0.01349805 -0.095472591 0.181030943
#> [11,] 0.10857575 -0.305245881 0.533888082
#> [12,] -0.40955254 -0.254230128 -0.098681803
#> [13,] 0.44305168 0.095962075 0.073725166
#> [14,] -0.08463012 0.007199696 0.162724818
#> [15,] -0.02802126 -0.117949268 -0.009900736
#> [16,] -0.28799008 -0.338596778 -0.376137186
#> [17,] 0.20513432 0.072427393 -0.133836476
#> [18,] -0.03944587 0.128626906 -0.181451526
#> [19,] -0.09573202 -0.080505313 0.157417883
#> [20,] -0.18192604 -0.268792467 0.118888087
#>