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
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)
data(Maiz) ge_eff( .data = Maiz , .y = y , .gen = entry , .env = site )#> $ge_effects #> 1 2 3 4 5 6 #> [1,] 250.12847 -240.01042 690.21458 -423.31319 -334.32153 372.52847 #> [2,] 68.79847 -35.91542 86.63458 -12.54319 501.12347 -14.15153 #> [3,] -131.45653 -92.09542 47.32958 -58.49819 -742.08153 188.71847 #> [4,] -252.34153 -29.98042 -922.13042 439.79181 357.30847 12.78347 #> [5,] -836.64153 -519.33042 678.86958 212.26681 69.58347 187.65847 #> [6,] 31.51097 196.07208 -372.12792 277.86931 164.08597 138.61097 #> [7,] -72.68403 743.40208 469.92708 -701.90069 -492.23403 625.06597 #> [8,] 1491.18722 -241.25167 718.09833 -213.55444 96.11222 -744.11278 #> [9,] -548.50153 219.10958 -1396.81542 479.88181 380.42347 -767.10153 #> 7 8 9 10 11 12 #> [1,] -155.83264 2224.8257 -82.835417 404.5590 -633.23264 -402.1160 #> [2,] -459.86264 1504.8957 -1.865417 290.2040 -703.78764 309.2790 #> [3,] 334.95736 738.2907 512.079583 -115.8260 -745.76764 245.7490 #> [4,] -591.45264 -1871.1693 -466.430417 -452.8110 1450.32236 508.8390 #> [5,] -62.47764 -1684.8193 228.969583 -637.1610 299.24736 200.3640 #> [6,] 247.49986 -1517.1418 160.047083 -384.9585 371.04986 -351.9585 #> [7,] 493.35486 363.7132 -466.622917 138.3215 -69.79514 112.8965 #> [8,] 433.27611 1031.1594 -394.651667 991.6428 -1019.27389 -1125.7322 #> [9,] -239.46264 -789.7543 511.309583 -233.9710 1051.23736 502.6790 #> 13 14 15 16 17 18 #> [1,] 629.559028 37.38681 -206.9937 -155.37986 -220.72986 -965.9632 #> [2,] -450.245972 135.05681 -668.3237 45.16514 -411.25986 118.5318 #> [3,] -3.000972 -130.59819 -476.4037 84.53514 -92.28986 -221.7232 #> [4,] 639.914028 27.36681 922.4363 585.22514 -75.54986 706.4418 #> [5,] 452.739028 -82.05819 890.2113 274.90014 188.95014 -442.4832 #> [6,] 457.791528 -144.10569 440.2888 -148.02236 458.32764 309.4443 #> [7,] -602.428472 -46.70069 -517.2812 -206.91736 -829.29236 910.6243 #> [8,] -1640.607222 45.09556 -152.8850 -280.22111 941.25389 -1036.2294 #> [9,] 516.279028 158.55681 -231.0487 -199.28486 40.59014 621.3568 #> 19 20 #> [1,] -778.99375 -9.479861 #> [2,] -115.47375 -186.259861 #> [3,] 442.29625 215.785139 #> [4,] -779.21375 -209.349861 #> [5,] 31.68625 549.525139 #> [6,] -113.11125 -221.172361 #> [7,] 744.26875 -595.717361 #> [8,] 557.19000 543.503889 #> [9,] 11.35125 -86.834861 #> #> $ge_svd #> $ge_svd$d #> [1] 5.922891e+03 3.070454e+03 2.552407e+03 2.320222e+03 1.758671e+03 #> [6] 1.313415e+03 7.926324e+02 7.570277e+02 3.786282e-12 #> #> $ge_svd$u #> [,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] [,9] #> [1,] 0.02847968 0.25131927 0.3333333 #> [2,] -0.46762033 -0.28151218 0.3333333 #> [3,] 0.45151147 -0.50113650 0.3333333 #> [4,] 0.44908389 -0.26316390 0.3333333 #> [5,] -0.11832901 0.31298999 0.3333333 #> [6,] -0.57650833 -0.35300400 0.3333333 #> [7,] 0.04118176 0.26668701 0.3333333 #> [8,] 0.16110446 0.08106783 0.3333333 #> [9,] 0.03109641 0.48675248 0.3333333 #> #> $ge_svd$v #> [,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] [,9] #> [1,] -0.22504209 0.130319195 -0.346996059 0.23943472 #> [2,] -0.23675510 -0.123777955 0.075854726 0.27776716 #> [3,] 0.24701208 -0.236917971 0.284672769 0.02381551 #> [4,] 0.08520769 -0.086797272 -0.253419484 0.22708065 #> [5,] 0.35236840 -0.648776843 0.103439840 0.20189373 #> [6,] -0.08901469 -0.141215583 -0.340199773 0.18195799 #> [7,] -0.35496791 0.055017924 0.028131793 0.09622467 #> [8,] -0.01828035 0.105003681 0.082344453 0.28891463 #> [9,] -0.11756614 -0.209431533 -0.061495518 0.30977404 #> [10,] -0.01349805 0.095472591 0.181030943 0.01191561 #> [11,] -0.10857575 0.305245881 0.533888082 0.17717692 #> [12,] 0.40955254 0.254230128 -0.098681803 0.18591489 #> [13,] -0.44305168 -0.095962075 0.073725166 0.03394251 #> [14,] 0.08463012 -0.007199696 0.162724818 0.06595852 #> [15,] 0.02802126 0.117949268 -0.009900736 0.60208158 #> [16,] 0.28799008 0.338596778 -0.376137186 0.01521026 #> [17,] -0.20513432 -0.072427393 -0.133836476 -0.05532874 #> [18,] 0.03944587 -0.128626906 -0.181451526 -0.01933649 #> [19,] 0.09573202 0.080505313 0.157417883 0.33548427 #> [20,] 0.18192604 0.268792467 0.118888087 0.02244904 #> #>