ge_eff.RdCalcuates Genotype by Environment Interaction Effects
# S3 method for default ge_eff(.data, .y, .gen, .env)
| .data | data.frame |
|---|---|
| .y | Response Variable |
| .gen | Genotypes Factor |
| .env | Environment Factor |
Genotype by Environment Interaction Effects
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)
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 3.579408e-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,] -0.226956409 #> [2,] -0.269720206 #> [3,] 0.084933882 #> [4,] -0.124388801 #> [5,] -0.163555798 #> [6,] 0.065442884 #> [7,] -0.187837439 #> [8,] -0.354251042 #> [9,] -0.207805695 #> [10,] -0.243959738 #> [11,] -0.214053998 #> [12,] -0.249160634 #> [13,] 0.022744347 #> [14,] -0.132017371 #> [15,] 0.035013451 #> [16,] -0.008164594 #> [17,] -0.199473649 #> [18,] -0.405461177 #> [19,] 0.219232205 #> [20,] -0.155383185 #> [21,] -0.118858563 #> [22,] -0.259093124 #> [23,] -0.009718095 #> [24,] -0.015505754 #> [25,] -0.270962405 #> #>