Genotype by Environment Interaction Effects
ge_eff.RdCalcuates Genotype by Environment Interaction Effects
References
Perez-Elizalde, S., Jarquin, D., and Crossa, J. (2011) A General Bayesian Estimation Method of Linear–Bilinear Models Applied to Plant Breeding Trials With Genotype × Environment Interaction. Journal of Agricultural, Biological, and Environmental Statistics, 17, 15–37. (doi:10.1007/s13253-011-0063-9)
Author
Muhammad Yaseen (myaseen208@gmail.com)
Examples
data(cultivo2008)
ge_eff(
.data = cultivo2008
, .y = y
, .gen = entry
, .env = site
)
#> $ge_effects
#> 1 2 3 4 5 6
#> [1,] 537.33311 -11.81553 164.73911 1607.60156 -887.0130 -1020.17182
#> [2,] -389.00019 -184.74550 -706.64566 478.34846 -726.9542 -231.83519
#> [3,] -389.45869 -292.29659 175.54232 361.76604 -1993.6862 -294.46728
#> [4,] -12.73747 512.89009 142.85894 -89.11561 -393.0486 301.28754
#> [5,] 143.71554 -205.08010 -83.14126 64.10512 537.1250 941.77247
#> [6,] 564.27841 194.85331 233.98909 -34.11080 498.7520 -187.44145
#> [7,] 29.14697 -601.61640 152.75344 -617.39351 483.5983 -135.96402
#> [8,] -209.99777 337.59019 144.95344 -286.85124 661.5514 840.60377
#> [9,] -259.90219 313.73404 -328.90078 -317.21946 293.2612 241.78442
#> [10,] -179.00020 516.46396 -232.31279 -376.11301 138.0560 130.27147
#> [11,] -31.08584 -74.38475 46.36576 -690.12759 579.9726 -634.73937
#> [12,] 196.70831 -505.59273 289.79839 -100.88996 808.3854 48.89945
#> 7 8 9 10 11 12
#> [1,] -736.54360 -198.63737 1347.1799 -115.89769 313.48611 242.127342
#> [2,] 434.37680 -1061.70381 -1198.2633 -477.05966 61.70895 -353.991894
#> [3,] 1239.94418 -588.96797 882.1704 907.46059 -322.02849 820.335947
#> [4,] -709.45976 45.00365 497.1633 -131.12320 1083.05361 -290.736170
#> [5,] 609.06795 393.15859 494.4314 184.23374 -693.84352 97.346769
#> [6,] 92.78645 428.93913 -104.0367 -823.34238 285.29982 70.668514
#> [7,] 861.85143 -599.20804 221.2493 945.46684 -337.43556 250.248272
#> [8,] -1234.22993 524.76062 -136.5551 -1805.62443 370.99883 281.520667
#> [9,] -697.75482 -339.00954 -225.2018 518.95129 1481.68666 -525.161952
#> [10,] -584.58211 1296.89792 -926.5270 112.20881 -375.43178 -260.353501
#> [11,] 765.33208 -833.08012 -1128.0805 99.50803 -663.54493 -7.057741
#> [12,] -40.78868 931.84696 276.4702 585.21805 -1203.94970 -324.946253
#> 13 14 15 16 17 18
#> [1,] 523.50790 -146.415457 159.636589 301.78062 -629.27483 216.8436
#> [2,] -910.20628 754.958751 -357.330023 1391.70328 -72.97119 624.2481
#> [3,] -82.53552 -20.652148 280.752435 -149.17592 755.41259 500.6782
#> [4,] 301.03737 -174.927770 31.988875 -750.30844 827.16135 241.6887
#> [5,] -135.15863 -2.212446 9.513278 410.11588 302.78948 -800.8867
#> [6,] -271.40448 551.136766 235.000624 405.29725 -213.01668 -705.3567
#> [7,] -910.53914 162.010802 -455.828014 1014.25527 -229.69145 155.2331
#> [8,] 74.78175 -331.414067 -368.179371 -1281.12544 155.51061 588.9227
#> [9,] 161.58367 4.731590 -15.968402 -927.61740 256.09743 -614.3305
#> [10,] 500.06832 -365.767239 459.278366 30.96089 15.14061 -187.1007
#> [11,] 461.03420 -224.409159 -153.010517 -95.27180 -232.56850 454.3998
#> [12,] 287.83085 -207.039624 174.146160 -350.61419 -934.58943 -474.3396
#> 19 20 21 22 23 24
#> [1,] -146.093235 -93.9213 552.54335 258.9858 -865.70433 369.04134
#> [2,] -174.949672 17.9379 -143.67826 1048.9861 2487.05563 -933.23309
#> [3,] 389.430436 199.8570 -42.56721 -750.0386 -943.17052 97.16381
#> [4,] 73.733586 594.8381 -51.62653 -424.7009 35.27516 -477.54217
#> [5,] -152.979609 393.6986 -495.19032 579.9369 -933.71857 -921.10243
#> [6,] 371.396070 120.3167 -647.36011 697.0945 -896.60709 -709.63869
#> [7,] 214.867627 -704.4389 305.66209 432.3326 -700.62833 566.58261
#> [8,] 245.997422 -1046.5096 610.05607 155.4940 533.99793 507.35153
#> [9,] -158.077864 347.0065 508.62269 -224.3869 861.93598 -563.75902
#> [10,] -195.914145 590.8982 -378.79878 -922.3661 910.03996 -340.06690
#> [11,] -476.940585 -101.2554 -20.44728 489.4121 134.04892 1816.22586
#> [12,] 9.529969 -318.4278 -197.21569 -1340.7494 -622.52473 588.97715
#> 25
#> [1,] -1743.3182
#> [2,] 623.2439
#> [3,] -741.4688
#> [4,] -1182.6536
#> [5,] -737.6970
#> [6,] -157.4935
#> [7,] -502.5153
#> [8,] 666.3961
#> [9,] 207.8951
#> [10,] 624.0497
#> [11,] 519.7047
#> [12,] 2423.8569
#>
#> $ge_svd
#> $ge_svd$d
#> [1] 5.306015e+03 4.692968e+03 4.516310e+03 3.460385e+03 3.277681e+03
#> [6] 2.689057e+03 2.304612e+03 2.070916e+03 1.501113e+03 1.253564e+03
#> [11] 7.273420e+02 3.519674e-12
#>
#> $ge_svd$u
#> [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,] -0.49639709 -0.01350060 -0.21115093 -0.30390933 -0.16341192 -0.60756798
#> [2,] 0.19898029 0.74698082 0.35429464 0.07885691 0.07154442 -0.31184167
#> [3,] -0.48872991 -0.06983089 0.12486219 -0.10120628 0.53685319 0.13621756
#> [4,] -0.13996223 0.11055868 -0.45687833 0.01497988 0.15525861 0.24431296
#> [5,] -0.17336967 -0.10896668 0.03986944 0.53428801 -0.25796797 0.19481846
#> [6,] -0.04821528 -0.02161613 -0.03525923 0.36068343 -0.45296257 -0.08963435
#> [7,] -0.18667504 -0.06091344 0.41106965 -0.06638193 -0.24407477 0.33133829
#> [8,] 0.35226134 -0.02207961 -0.36647640 -0.43142270 -0.35184232 0.07709388
#> [9,] 0.17180821 0.17130570 -0.31123735 0.04682435 0.21682462 0.30524281
#> [10,] 0.31768461 -0.05495220 -0.12644476 0.25505065 0.33915693 -0.18552887
#> [11,] 0.16738710 -0.06768044 0.38848066 -0.46075398 -0.04171364 0.23702799
#> [12,] 0.32522767 -0.60930521 0.18887041 0.07299097 0.19233543 -0.33147908
#> [,7] [,8] [,9] [,10] [,11] [,12]
#> [1,] 0.29774691 -0.056901713 -0.168310552 0.08208238 0.101633842 -0.2886751
#> [2,] -0.17915784 -0.117962367 -0.009017575 0.10491124 -0.166990703 -0.2886751
#> [3,] -0.46576653 0.088788032 0.248797486 0.01646866 0.230955306 -0.2886751
#> [4,] 0.06478569 0.100171564 -0.023517202 -0.13344160 -0.748001677 -0.2886751
#> [5,] -0.09809391 0.139462508 -0.372112111 0.55991945 0.046168247 -0.2886751
#> [6,] 0.01612038 0.157745684 0.679233742 -0.27825269 0.073504663 -0.2886751
#> [7,] 0.05798743 -0.369209382 -0.334565247 -0.53267366 0.003609535 -0.2886751
#> [8,] -0.55175611 -0.003415016 -0.105783460 0.02546885 0.160121357 -0.2886751
#> [9,] 0.41280992 -0.490250556 0.182262320 0.19391807 0.370100330 -0.2886751
#> [10,] 0.12740878 0.434020104 -0.347606264 -0.41544336 0.290182991 -0.2886751
#> [11,] 0.38617325 0.476292338 0.144446728 0.25006810 -0.059588163 -0.2886751
#> [12,] -0.06825798 -0.358741196 0.106172138 0.12697458 -0.301695729 -0.2886751
#>
#> $ge_svd$v
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] -0.06149555 -0.095776540 -0.020085587 0.053485452 -0.192370102
#> [2,] 0.06382394 0.069265292 -0.223012831 0.007245669 0.016223148
#> [3,] -0.06234288 -0.161589114 -0.027877503 -0.066171798 -0.070226716
#> [4,] -0.22328258 0.087939952 -0.081894659 -0.029555421 0.004720508
#> [5,] 0.34015624 -0.221141350 0.019886545 0.115078408 -0.461294977
#> [6,] 0.13604635 -0.035575308 -0.152782983 0.216331097 -0.076064329
#> [7,] -0.17925443 -0.008220764 0.486389275 0.121012253 0.104457833
#> [8,] 0.16851341 -0.300923514 -0.237473292 0.283737969 -0.032484624
#> [9,] -0.37880548 -0.226245625 -0.190507450 -0.006295249 -0.031822410
#> [10,] -0.17631728 -0.156241264 0.241103123 0.136191994 0.439504584
#> [11,] -0.03856963 0.281021990 -0.396475650 -0.073858390 -0.018275981
#> [12,] -0.15048775 -0.057086221 0.042526139 -0.104295885 -0.046147779
#> [13,] 0.02779221 -0.166184921 -0.190075463 -0.120287697 0.136150568
#> [14,] -0.02562801 0.148316363 0.102464710 0.123843723 -0.087197216
#> [15,] -0.03306255 -0.080778240 -0.061970020 0.108056886 0.130615739
#> [16,] -0.13300819 0.199339099 0.403776537 0.247180138 -0.148457310
#> [17,] -0.08023974 0.128508018 -0.145447171 0.060490874 0.165334914
#> [18,] -0.02898784 0.148839007 0.059826858 -0.384608761 0.088386594
#> [19,] -0.05162250 -0.031424301 -0.032488782 0.025200029 -0.035049855
#> [20,] -0.05938773 0.067086940 -0.087996631 0.277716272 0.249867522
#> [21,] -0.01893186 0.031502095 -0.088510231 -0.299110591 -0.016775003
#> [22,] -0.06400466 0.313983895 0.146135268 -0.008686526 -0.519035687
#> [23,] 0.40742463 0.545310815 -0.001792043 -0.082554898 0.249830817
#> [24,] 0.03920025 -0.266644464 0.197570466 -0.610998999 -0.032598625
#> [25,] 0.58247162 -0.213281841 0.238711373 0.010853450 0.182708385
#> [,6] [,7] [,8] [,9] [,10] [,11]
#> [1,] -0.15214690 0.15936825 0.02067801 0.126559055 -0.04600328 -0.20881979
#> [2,] 0.02582939 0.08771757 0.23530231 0.070836581 -0.13570217 0.08000068
#> [3,] 0.02280977 -0.05349986 0.02454913 0.133676964 -0.14757687 -0.23892606
#> [4,] -0.54543626 -0.04520260 -0.09293229 -0.020241562 0.37994683 0.04265817
#> [5,] 0.22409172 0.30160539 -0.09899123 -0.165707098 0.03107112 -0.13188145
#> [6,] 0.30814563 -0.34916527 -0.06920767 -0.343382297 0.28753161 -0.06073450
#> [7,] 0.25985576 -0.13541484 0.13655494 0.203900197 0.17442733 0.06723694
#> [8,] -0.21860626 -0.13349828 0.20700594 -0.232207178 -0.32275704 0.19019793
#> [9,] -0.10808562 -0.16940009 -0.36894797 -0.116546014 0.16893393 -0.28240555
#> [10,] 0.20888556 0.37600777 -0.33079547 -0.245389950 -0.07280846 0.10994327
#> [11,] 0.19739773 0.23456919 -0.31248927 0.362129220 -0.21683619 0.03626185
#> [12,] 0.04287239 -0.27993677 0.12590257 0.020591297 -0.07414563 0.51539168
#> [13,] -0.11135653 0.25189464 0.30364543 0.005283518 0.29367201 0.04683575
#> [14,] -0.04796449 -0.04182344 -0.12835667 0.297411403 -0.07074139 -0.07630688
#> [15,] -0.11982140 0.06221173 0.16464386 0.151096451 -0.04843282 0.21704546
#> [16,] -0.27346497 0.08744810 0.01443431 -0.262979031 -0.35792745 -0.06952943
#> [17,] 0.39198486 -0.22701339 0.18965879 -0.008864584 0.05139047 -0.10811056
#> [18,] -0.03086566 -0.25303599 0.14822690 -0.166686920 -0.19828932 -0.42200963
#> [19,] 0.04214619 -0.24563312 -0.10146317 0.202523819 -0.31771755 0.02714807
#> [20,] 0.01996723 0.26699847 0.27545862 0.094863342 0.16727079 -0.20955229
#> [21,] 0.03220692 0.04047115 -0.31981348 -0.215064889 0.01427687 0.37989544
#> [22,] 0.06634486 0.07593417 0.09987921 0.049958773 0.29665035 0.17145966
#> [23,] -0.12256304 0.02002146 -0.03841030 -0.267679383 0.02126357 -0.01463869
#> [24,] 0.07461537 0.18130656 0.18402855 -0.040263913 -0.03871857 -0.04352811
#> [25,] -0.18684224 -0.21193079 -0.26856105 0.366182200 0.16122186 -0.01763195
#> [,12]
#> [1,] -0.230979169
#> [2,] -0.259316264
#> [3,] 0.068851826
#> [4,] -0.134291327
#> [5,] -0.162298956
#> [6,] 0.054556373
#> [7,] -0.169021773
#> [8,] -0.349083327
#> [9,] -0.190678147
#> [10,] -0.256434001
#> [11,] -0.213377198
#> [12,] -0.257377341
#> [13,] 0.027987539
#> [14,] -0.139632312
#> [15,] 0.024283775
#> [16,] -0.006448319
#> [17,] -0.205231739
#> [18,] -0.410785747
#> [19,] 0.224586137
#> [20,] -0.155096805
#> [21,] -0.113569212
#> [22,] -0.263449750
#> [23,] -0.003970044
#> [24,] -0.016615022
#> [25,] -0.272265195
#>
#>