This analysis tests the mean effect of breed composition in ALL MSUPRP meat quality traits. It does so by including a fixed effect for the estimated percentage of duroc. This is totally equivalent to what Andres called \(\theta_S\). Because \(\theta_S=2*(perc.duroc-0.5)\). Consequently, under linear transformation of a fixed effect, itsestimated value and its standard error will differ, but the p-value will be identical. Note: changing my file to produce IDENTICAL estimates to those from Andres and Sebastian would only require adding the column TITAS to the covar of my gpdata object.
rm(list=ls())
library(xlsx)## Loading required package: rJava## Loading required package: xlsxjarslibrary(synbreed)
library(regress)
library(gwaR)
#only run these two lines if you need to compute A
#if you will load A, just comment this lines and ignore them
setwd("C:/Users/steibelj/OneDrive/Documents/GWA/")
load("MSUPRP_meat.RData")
#compute A matrix and save it or load it if it has been previously saved
#(select by commenting the appropriate lines)
A_matrix<-kin(MSUPRP_meat,ret="add")
save(A_matrix,file="A_MSU.Rdata")
#load("A_MSU.Rdata")
#take a peak at a random diagonal block
A_matrix[100:105,100:105]## 1032 1033 1034 1035 1036 1037
## 1032 1.0000 0.0625 0.5000 0.0625 0.5000 0.0625
## 1033 0.0625 1.0000 0.0625 0.5000 0.0625 0.5000
## 1034 0.5000 0.0625 1.0000 0.0625 0.5000 0.0625
## 1035 0.0625 0.5000 0.0625 1.0000 0.0625 0.5000
## 1036 0.5000 0.0625 0.5000 0.0625 1.0000 0.0625
## 1037 0.0625 0.5000 0.0625 0.5000 0.0625 1.0000
## attr(,"class")
## [1] "relationshipMatrix" "matrix"Now let’s take advantage of the gwaR package flexibility to perform analyses on a gpData object. using a good old loop
traits<-colnames(MSUPRP_meat$pheno)
#fit animal model
system.time({
for(i in traits){
mod_res<-gblup(rsp = i,data = MSUPRP_meat, #response and dataset
design = c(y~sex+perc_duroc), #fixed effectsmodel
G=A_matrix) #var-cov for additive eff
#check estimation of variance components and h2
varcomp(mod_res) #notice h2=0.3017
#fixed effects
print(mod_res)
print(paste("end of results for trait:",mod_res$name))
print("--------------------------------------")
print("--------------------------------------")
}
})## gblup analysis of trait: wt_birth
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 650.9148 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 1.47570238 0.13669270 10.7957661 0.0000000000
## sexM 0.06935642 0.01926057 3.6009535 0.0003170523
## perc_duroc 0.03762537 0.18809689 0.2000319 0.8414556480
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.08239774 0.02131580 0.6591117
## In 0.04261558 0.01160312 0.3408883
## [1] "end of results for trait: wt_birth"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: wt_3wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -814.3316 converged in: 7 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 5.7884302 0.52255885 11.0770876 0.0000000
## sexM 0.1896442 0.09329719 2.0326895 0.0420839
## perc_duroc -0.6195441 0.86019237 -0.7202391 0.4713778
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.677024 0.2350235 0.2910352
## In 1.649238 0.1573046 0.7089648
## [1] "end of results for trait: wt_3wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: wt_6wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1400.229 converged in: 7 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 11.9842010 1.2174141 9.8439804 0.0000000
## sexM 0.1655761 0.1723297 0.9608098 0.3366478
## perc_duroc -0.7340040 1.6809789 -0.4366527 0.6623632
##
## estimated variance components:
## Estimate StdError prop.var
## G 6.486400 1.6842789 0.652049
## In 3.461318 0.9186228 0.347951
## [1] "end of results for trait: wt_6wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: wt_10wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1879.195 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 26.479180332 2.0091756 13.179127142 0.000000000
## sexM 0.832046686 0.2868911 2.900217578 0.003729037
## perc_duroc -0.004537628 2.7942472 -0.001623918 0.998704302
##
## estimated variance components:
## Estimate StdError prop.var
## G 17.393701 4.551622 0.6370935
## In 9.907947 2.492461 0.3629065
## [1] "end of results for trait: wt_10wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: bf10_10wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -932.6466 converged in: 4 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 7.0138259 0.6697564 10.472205 0.000000e+00
## sexM 0.5583778 0.1050674 5.314475 1.069653e-07
## perc_duroc 1.3535450 1.0023518 1.350369 1.768976e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 1.600738 0.4597743 0.4843186
## In 1.704396 0.2665716 0.5156814
## [1] "end of results for trait: bf10_10wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lma_10wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1249.987 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 13.232905 1.167350 11.335852 0.00000000
## sexM -0.310722 0.145330 -2.138044 0.03251318
## perc_duroc -2.073280 1.451433 -1.428437 0.15316602
##
## estimated variance components:
## Estimate StdError prop.var
## G 7.233879 1.719713 0.8642826
## In 1.135928 0.899526 0.1357174
## [1] "end of results for trait: lma_10wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lrf_10wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -495.3679 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 5.0357917 0.37239645 13.522663 0.000000000
## sexM 0.1894495 0.06637261 2.854332 0.004312740
## perc_duroc 1.8816264 0.61225816 3.073256 0.002117364
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.3459177 0.11946772 0.2934313
## In 0.8329534 0.07981623 0.7065687
## [1] "end of results for trait: lrf_10wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: wt_13wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2171.172 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 42.488925 2.9449439 14.4277535 0.000000e+00
## sexM 1.923468 0.3899528 4.9325666 8.115610e-07
## perc_duroc -1.588104 3.8534390 -0.4121263 6.802468e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 42.23934 10.429322 0.7623987
## In 13.16388 5.547106 0.2376013
## [1] "end of results for trait: wt_13wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: bf10_13wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1274.755 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 9.1219724 1.0231569 8.9155167 0.000000e+00
## sexM 1.0446585 0.1508008 6.9274062 4.286349e-12
## perc_duroc 0.2691645 1.4590590 0.1844782 8.536383e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 4.254806 1.1448278 0.5849338
## In 3.019189 0.6371896 0.4150662
## [1] "end of results for trait: bf10_13wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lma_13wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1538.959 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 19.59140112 1.4556673 13.4587084 0.00000000
## sexM 0.04138447 0.1989985 0.2079637 0.83525731
## perc_duroc -4.62597883 1.9548807 -2.3663740 0.01796329
##
## estimated variance components:
## Estimate StdError prop.var
## G 9.824409 2.482035 0.7093542
## In 4.025384 1.334657 0.2906458
## [1] "end of results for trait: lma_13wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lrf_13wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -715.2574 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 6.0907932 0.49727320 12.248384 0.000000e+00
## sexM 0.4696495 0.08365363 5.614216 1.974553e-08
## perc_duroc 1.5654781 0.78417502 1.996338 4.589719e-02
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.7394162 0.2324097 0.3767295
## In 1.2233082 0.1438606 0.6232705
## [1] "end of results for trait: lrf_13wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: wt_16wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2382.37 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 63.862552 3.5014402 18.2389385 0.000000e+00
## sexM 3.299083 0.4902413 6.7295082 1.702372e-11
## perc_duroc -3.843442 4.7936936 -0.8017705 4.226858e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 54.65365 14.068188 0.6696558
## In 26.96089 7.636825 0.3303442
## [1] "end of results for trait: wt_16wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: bf10_16wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1501.638 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 11.571026 1.2690117 9.11814005 0.0000000
## sexM 1.936253 0.1924475 10.06120103 0.0000000
## perc_duroc 0.082754 1.8503827 0.04472264 0.9643284
##
## estimated variance components:
## Estimate StdError prop.var
## G 6.184065 1.7109906 0.5385221
## In 5.299336 0.9687275 0.4614779
## [1] "end of results for trait: bf10_16wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lma_16wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1670.858 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 28.5790291 1.4671274 19.4795826 0.000000000
## sexM 0.1303409 0.2310608 0.5640979 0.572687479
## perc_duroc -6.6465640 2.2022773 -3.0180414 0.002544142
##
## estimated variance components:
## Estimate StdError prop.var
## G 7.612394 2.196702 0.4780997
## In 8.309796 1.277488 0.5219003
## [1] "end of results for trait: lma_16wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lrf_16wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1163.467 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 7.515569 0.8100583 9.277813 0.000000e+00
## sexM 1.061990 0.1348874 7.873157 3.552714e-15
## perc_duroc 3.098885 1.2678510 2.444203 1.451727e-02
##
## estimated variance components:
## Estimate StdError prop.var
## G 2.018586 0.6253519 0.3920314
## In 3.130456 0.3827779 0.6079686
## [1] "end of results for trait: lrf_16wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: wt_19wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2539.247 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 81.100023 4.1901137 19.3550890 0.000000e+00
## sexM 4.514672 0.5791269 7.7956524 6.439294e-15
## perc_duroc -2.632084 5.6771653 -0.4636264 6.429154e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 79.96968 20.38387 0.6911303
## In 35.73887 11.00631 0.3088697
## [1] "end of results for trait: wt_19wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: bf10_19wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1834.461 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 13.736849 1.9405018 7.0790190 1.451728e-12
## sexM 3.665187 0.2732836 13.4116616 0.000000e+00
## perc_duroc 2.238363 2.6691364 0.8386095 4.016885e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 16.620245 4.300037 0.659968
## In 8.563164 2.339973 0.340032
## [1] "end of results for trait: bf10_19wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lma_19wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1755.226 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 34.9208523 1.6607515 21.0271389 0.000000000
## sexM 0.1708023 0.2522864 0.6770177 0.498394750
## perc_duroc -6.3053928 2.4248001 -2.6003763 0.009312159
##
## estimated variance components:
## Estimate StdError prop.var
## G 10.553926 2.925258 0.5357598
## In 9.145064 1.658046 0.4642402
## [1] "end of results for trait: lma_19wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lrf_19wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1469.378 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 8.960947 1.2829193 6.984810 2.852385e-12
## sexM 2.108574 0.1853904 11.373696 0.000000e+00
## perc_duroc 3.802304 1.8012210 2.110959 3.477583e-02
##
## estimated variance components:
## Estimate StdError prop.var
## G 6.941086 1.835355 0.6173694
## In 4.301916 1.010858 0.3826306
## [1] "end of results for trait: lrf_19wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: wt_22wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2632.736 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 98.7162352 4.4542240 22.1623870 0.0000000
## sexM 5.8121512 0.6415176 9.0600030 0.0000000
## perc_duroc -0.7102156 6.2371920 -0.1138678 0.9093426
##
## estimated variance components:
## Estimate StdError prop.var
## G 84.18015 22.19290 0.6228805
## In 50.96639 12.20304 0.3771195
## [1] "end of results for trait: wt_22wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: bf10_22wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2046.605 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 18.2345773 2.1667404 8.4156724 0.0000000
## sexM 5.2337675 0.3452917 15.1575252 0.0000000
## perc_duroc -0.9298525 3.2816832 -0.2833462 0.7769115
##
## estimated variance components:
## Estimate StdError prop.var
## G 16.15204 4.726082 0.4595544
## In 18.99514 2.774985 0.5404456
## [1] "end of results for trait: bf10_22wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lma_22wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1877.563 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 41.744974 1.9874896 21.0038707 0.000000000
## sexM -0.194251 0.2865623 -0.6778664 0.497856426
## perc_duroc -8.627162 2.7854848 -3.0971851 0.001953679
##
## estimated variance components:
## Estimate StdError prop.var
## G 16.72669 4.409075 0.6210661
## In 10.20553 2.426172 0.3789339
## [1] "end of results for trait: lma_22wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: lrf_22wk
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1658.44 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 11.296998 1.4265494 7.919107 2.442491e-15
## sexM 3.367507 0.2282309 14.754824 0.000000e+00
## perc_duroc 3.186467 2.1670436 1.470421 1.414477e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 6.935839 2.038367 0.4534038
## In 8.361429 1.200983 0.5465962
## [1] "end of results for trait: lrf_22wk"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: Days
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2848.681 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 158.112904 5.6422296 28.0231245 0.0000000
## sexM -7.082236 0.8074742 -8.7708516 0.0000000
## perc_duroc 2.266750 7.8609766 0.2883547 0.7730752
##
## estimated variance components:
## Estimate StdError prop.var
## G 136.62157 35.80709 0.6333686
## In 79.08469 19.62999 0.3666314
## [1] "end of results for trait: Days"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: tofat
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1420.926 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 10.30445194 1.2557551 8.20578123 2.220446e-16
## sexM 2.22652598 0.1773587 12.55380235 0.000000e+00
## perc_duroc -0.02234883 1.8037335 -0.01239032 9.901142e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 6.843479 1.782480 0.6516371
## In 3.658500 0.971171 0.3483629
## [1] "end of results for trait: tofat"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: fftoln
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1080.649 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 18.4409666 0.8188681 22.520069 0.000000000
## sexM 0.3324072 0.1236887 2.687450 0.007199995
## perc_duroc -2.4035926 1.2405969 -1.937448 0.052690551
##
## estimated variance components:
## Estimate StdError prop.var
## G 2.526538 0.7016001 0.5357586
## In 2.189276 0.3973116 0.4642414
## [1] "end of results for trait: fftoln"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: mtfat
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -165.0397 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 6.9082135 0.30885618 22.3670885 0.000000e+00
## sexM 0.2230977 0.04633866 4.8145046 1.475655e-06
## perc_duroc -0.4250256 0.46547569 -0.9130995 3.611902e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.3650523 0.10062505 0.5473289
## In 0.3019183 0.05672481 0.4526711
## [1] "end of results for trait: mtfat"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: mtpro
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -934.5388 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 9.5892557 0.7048592 13.604498 0.0000000
## sexM 1.5548856 0.1057111 14.708826 0.0000000
## perc_duroc -0.6818459 1.0619677 -0.642059 0.5208349
##
## estimated variance components:
## Estimate StdError prop.var
## G 1.902972 0.5244274 0.5479979
## In 1.569618 0.2955441 0.4520021
## [1] "end of results for trait: mtpro"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: ADG
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -4716.706 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 859.32843 44.684082 19.2311979 0.0000000
## sexM 57.16509 6.050641 9.4477742 0.0000000
## perc_duroc -22.26316 61.999563 -0.3590858 0.7195309
##
## estimated variance components:
## Estimate StdError prop.var
## G 9343.705 2354.009 0.7243007
## In 3556.606 1260.275 0.2756993
## [1] "end of results for trait: ADG"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: dress_ptg
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1155.16 converged in: 7 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 74.434229 0.7607207 97.846982 0.00000000
## sexM -0.220297 0.1356312 -1.624235 0.10432556
## perc_duroc -2.648494 1.2486552 -2.121077 0.03391534
##
## estimated variance components:
## Estimate StdError prop.var
## G 1.454788 0.5020127 0.2966368
## In 3.449484 0.3342717 0.7033632
## [1] "end of results for trait: dress_ptg"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: color
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -266.4328 converged in: 7 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 2.9376030 0.2970411 9.8895512 0.00000000
## sexM -0.1067958 0.0522989 -2.0420281 0.04114875
## perc_duroc 0.4229535 0.4841477 0.8736043 0.38233379
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.2295512 0.07772979 0.3128731
## In 0.5041366 0.05088882 0.6871269
## [1] "end of results for trait: color"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: L
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1117.971 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 53.6918257 0.8853484 60.6448557 0.000000e+00
## sexM 0.6385600 0.1414395 4.5147233 6.339948e-06
## perc_duroc -0.5339857 1.3522194 -0.3948957 6.929198e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 2.620856 0.7751907 0.4678638
## In 2.980893 0.4554795 0.5321362
## [1] "end of results for trait: L"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: a
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -834.0479 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 16.9866888 0.8160040 20.8169179 0.000000000
## sexM -0.2645323 0.1008541 -2.6229203 0.008717968
## perc_duroc 0.8755444 1.0151508 0.8624771 0.388425003
##
## estimated variance components:
## Estimate StdError prop.var
## G 3.5268865 0.8375426 0.8987128
## In 0.3974889 0.4370275 0.1012872
## [1] "end of results for trait: a"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: b
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -729.42 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 9.4897032 0.7000615 13.555528 0.0000000
## sexM 0.1288981 0.0898256 1.434982 0.1512921
## perc_duroc -0.9331012 0.8984398 -1.038580 0.2990003
##
## estimated variance components:
## Estimate StdError prop.var
## G 2.4661685 0.5990673 0.8362098
## In 0.4830537 0.3154102 0.1637902
## [1] "end of results for trait: b"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: cook_yield
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1379.869 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 76.139809 1.0298587 73.932289 0.000000000
## sexM 0.539581 0.1759385 3.066873 0.002163107
## perc_duroc 2.251344 1.6383528 1.374151 0.169394833
##
## estimated variance components:
## Estimate StdError prop.var
## G 3.064345 0.9829967 0.3619081
## In 5.402845 0.6165908 0.6380919
## [1] "end of results for trait: cook_yield"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: WBS
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -80.32923 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 3.28665808 0.24738943 13.28536205 0.000000000
## sexM -0.13324282 0.04297984 -3.10012371 0.001934398
## perc_duroc -0.01754797 0.39874195 -0.04400833 0.964897766
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.1673331 0.05518053 0.336363
## In 0.3301446 0.03538333 0.663637
## [1] "end of results for trait: WBS"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: juiciness
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 32.02981 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 5.22815188 0.17903051 29.2025755 0.0000000
## sexM 0.04267834 0.03837984 1.1119987 0.2661387
## perc_duroc -0.04989270 0.33318721 -0.1497437 0.8809668
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.0260155 0.01637598 0.07437779
## In 0.3237597 0.01877009 0.92562221
## [1] "end of results for trait: juiciness"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: tenderness
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 19.62437 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 5.6399585 0.20711437 27.231130 0.000000000
## sexM 0.1189755 0.03860947 3.081511 0.002059529
## perc_duroc -0.3561252 0.35135995 -1.013562 0.310791664
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.09013823 0.03409429 0.2357592
## In 0.29219358 0.02457868 0.7642408
## [1] "end of results for trait: tenderness"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: overtend
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 114.8308 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 5.67556328 0.18568870 30.5649362 0.000000000
## sexM 0.09939338 0.03484625 2.8523412 0.004339848
## perc_duroc -0.25269698 0.31647670 -0.7984695 0.424598113
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.07038159 0.02703262 0.2270189
## In 0.23964372 0.01975285 0.7729811
## [1] "end of results for trait: overtend"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: conn_tiss
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 435.7618 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 6.26032461 0.12524657 49.9839996 0.000000000
## sexM 0.06691946 0.02469813 2.7094952 0.006738567
## perc_duroc 0.14771330 0.22082633 0.6689116 0.503551855
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.02490643 0.010933939 0.1649709
## In 0.12606821 0.009008501 0.8350291
## [1] "end of results for trait: conn_tiss"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: off_flavor
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 992.312 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 1.120004814 0.0602041 18.6034637 0.0000000
## sexM -0.008434035 0.0136248 -0.6190209 0.5359026
## perc_duroc 0.051248522 0.1156864 0.4429950 0.6577693
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.001161702 0.001278411 0.02684988
## In 0.042104837 0.002183663 0.97315012
## [1] "end of results for trait: off_flavor"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: farm_wt
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2425.061 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 109.647483 3.292374 33.3034667 0.000000e+00
## sexM 3.255247 0.527275 6.1737185 6.670227e-10
## perc_duroc 1.541453 4.995368 0.3085765 7.576437e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 37.08041 10.915185 0.4559254
## In 44.24958 6.422786 0.5440746
## [1] "end of results for trait: farm_wt"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: car_wt
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2224.331 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 81.844605 2.5619480 31.9462403 0.000000e+00
## sexM 2.108068 0.4259525 4.9490692 7.456923e-07
## perc_duroc -2.200845 3.9974988 -0.5505555 5.819384e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 20.41620 6.308940 0.3983176
## In 30.83988 3.845549 0.6016824
## [1] "end of results for trait: car_wt"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: marb
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -282.232 converged in: 7 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 2.0371638 0.29577078 6.887644 5.672351e-12
## sexM 0.2415586 0.05321775 4.539060 5.650550e-06
## perc_duroc 1.3233823 0.48986862 2.701504 6.902655e-03
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.2104024 0.07411247 0.2814461
## In 0.5371738 0.05023025 0.7185539
## [1] "end of results for trait: marb"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: firm
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -221.4692 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 2.50748222 0.26157951 9.585927 0.0000000
## sexM 0.05010507 0.05065467 0.989150 0.3225897
## perc_duroc 0.74137128 0.46007001 1.611431 0.1070857
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.1096224 0.04727316 0.1738152
## In 0.5210614 0.03820276 0.8261848
## [1] "end of results for trait: firm"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: driploss
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -584.3401 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 2.19041195 0.41878485 5.2303993 1.691443e-07
## sexM -0.01886318 0.07356741 -0.2564067 7.976368e-01
## perc_duroc -0.91187893 0.68174442 -1.3375671 1.810376e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.4588866 0.1547077 0.3152982
## In 0.9965187 0.1010736 0.6847018
## [1] "end of results for trait: driploss"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: temp_45m
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1167.924 converged in: 7 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 38.05204967 0.7959225 47.80873572 0.00000000
## sexM 0.01229205 0.1374959 0.08939941 0.92876449
## perc_duroc 2.83157452 1.2767961 2.21771864 0.02657402
##
## estimated variance components:
## Estimate StdError prop.var
## G 1.767298 0.5778340 0.3421588
## In 3.397843 0.3679995 0.6578412
## [1] "end of results for trait: temp_45m"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: temp_24h
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -590.6442 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 2.5748698 0.40457204 6.3644284 1.960183e-10
## sexM 0.3309417 0.07434709 4.4513062 8.534953e-06
## perc_duroc 0.3607179 0.67993932 0.5305149 5.957550e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.3635841 0.13351476 0.2532461
## In 1.0721106 0.09381664 0.7467539
## [1] "end of results for trait: temp_24h"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: ph_45m
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 932.1892 converged in: 7 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 6.42355531 0.07251642 88.5807013 0.0000000
## sexM 0.00464539 0.01438062 0.3230313 0.7466715
## perc_duroc -0.10382301 0.12787259 -0.8119254 0.4168344
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.008246676 0.003666931 0.1627659
## In 0.042419180 0.003032868 0.8372341
## [1] "end of results for trait: ph_45m"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: ph_24h
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 1361.515 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 5.43055853 0.04621476 117.507020 0.000000000
## sexM 0.02406171 0.00892326 2.696516 0.007006908
## perc_duroc 0.15584131 0.08060884 1.933303 0.053198897
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.003717104 0.001550845 0.189457
## In 0.015902671 0.001212607 0.810543
## [1] "end of results for trait: ph_24h"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: pH_dec
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 903.8624 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 0.95078871 0.06836120 13.908309 0.0000000
## sexM -0.01740501 0.01473661 -1.181073 0.2375737
## perc_duroc -0.17952310 0.12780637 -1.404649 0.1601257
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.003440981 0.002274261 0.06900101
## In 0.046427576 0.002700378 0.93099899
## [1] "end of results for trait: pH_dec"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: car_length
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1285.633 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 79.3445219 0.9545764 83.1201347 0.00000000
## sexM -0.3651991 0.1555112 -2.3483786 0.01885535
## perc_duroc -1.4034691 1.4666113 -0.9569468 0.33859408
##
## estimated variance components:
## Estimate StdError prop.var
## G 2.991661 0.8983316 0.4300006
## In 3.965681 0.5367763 0.5699994
## [1] "end of results for trait: car_length"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: num_ribs
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -196.7629 converged in: 4 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 15.24748749 0.38333660 39.775715 0.0000000
## sexM -0.08428508 0.06314161 -1.334858 0.1819228
## perc_duroc -0.62925000 0.62132886 -1.012749 0.3111802
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.4291249 0.13545137 0.5159872
## In 0.4025330 0.07925616 0.4840128
## [1] "end of results for trait: num_ribs"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: first_rib
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2024.057 converged in: 7 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 38.110764 2.4717405 15.4185942 0.000000e+00
## sexM 3.066717 0.4570835 6.7093136 1.955414e-11
## perc_duroc 1.060367 4.1896797 0.2530903 8.001985e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 12.64410 4.803189 0.2568805
## In 36.57761 3.387655 0.7431195
## [1] "end of results for trait: first_rib"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: last_rib
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2124.862 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 26.2731098 2.3353433 11.2502133 0.000000e+00
## sexM 3.0596363 0.3836015 7.9760797 1.554312e-15
## perc_duroc 0.4430944 3.6101640 0.1227353 9.023167e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 17.53305 5.323754 0.4173482
## In 24.47756 3.205758 0.5826518
## [1] "end of results for trait: last_rib"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: last_lum
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2084.263 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 17.420429 2.173489 8.014959 1.110223e-15
## sexM 3.351289 0.368952 9.083265 0.000000e+00
## perc_duroc 5.964736 3.441494 1.733182 8.306329e-02
##
## estimated variance components:
## Estimate StdError prop.var
## G 13.89950 4.416250 0.3684355
## In 23.82623 2.753578 0.6315645
## [1] "end of results for trait: last_lum"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: car_bf10
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -2134.84 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 20.7538107 2.3289354 8.91128650 0.0000000
## sexM 6.5375070 0.3959171 16.51231314 0.0000000
## perc_duroc 0.1645363 3.6866782 0.04462997 0.9644023
##
## estimated variance components:
## Estimate StdError prop.var
## G 15.96485 5.078002 0.3699668
## In 27.18727 3.163076 0.6300332
## [1] "end of results for trait: car_bf10"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: car_lma
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -1798.74 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 47.513746 1.6332500 29.091533 0.0000000000
## sexM -3.446340 0.2741713 -12.570021 0.0000000000
## perc_duroc -9.965215 2.5631164 -3.887929 0.0001011031
##
## estimated variance components:
## Estimate StdError prop.var
## G 8.114486 2.535741 0.3874231
## In 12.830278 1.559012 0.6125769
## [1] "end of results for trait: car_lma"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: ham
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -196.9641 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 9.716936280 0.26712048 36.3766056 0.0000000
## sexM -0.006640108 0.04854285 -0.1367886 0.8911979
## perc_duroc -0.258662531 0.44424735 -0.5822489 0.5603990
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.1677485 0.05991991 0.2710049
## In 0.4512387 0.04113230 0.7289951
## [1] "end of results for trait: ham"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: loin
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -274.4998 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 8.5840124 0.28818357 29.786613 0.000000e+00
## sexM -0.2376928 0.05278693 -4.502873 6.704091e-06
## perc_duroc -0.3047886 0.48193633 -0.632425 5.271092e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.1894678 0.06890787 0.2603323
## In 0.5383243 0.04790358 0.7396677
## [1] "end of results for trait: loin"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: boston
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 88.65665 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 3.83155724 0.21269514 18.0143146 0.0000000
## sexM 0.04931754 0.03553354 1.3879152 0.1651629
## perc_duroc 0.10928839 0.33295402 0.3282387 0.7427312
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.1390387 0.04322143 0.391659
## In 0.2159608 0.02647529 0.608341
## [1] "end of results for trait: boston"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: picnic
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 77.91436 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 3.86877632 0.2152968 17.969500 0.0000000
## sexM 0.04642663 0.0359450 1.291602 0.1964950
## perc_duroc -0.35415252 0.3368663 -1.051315 0.2931141
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.1427119 0.04432274 0.39263
## In 0.2207649 0.02713136 0.60737
## [1] "end of results for trait: picnic"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: belly
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -61.38161 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 4.90565496 0.24072990 20.37825346 0.000000e+00
## sexM 0.24307004 0.04185169 5.80789092 6.326471e-09
## perc_duroc -0.01112968 0.38795085 -0.02868837 9.771131e-01
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.1585106 0.05235265 0.3329595
## In 0.3175551 0.03362003 0.6670405
## [1] "end of results for trait: belly"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: spareribs
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: 1079.246 converged in: 4 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 1.43623429 0.07613259 18.8649085 0.0000000
## sexM 0.01198271 0.01219445 0.9826358 0.3257867
## perc_duroc 0.12939517 0.11543535 1.1209319 0.2623169
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.01987582 0.005846502 0.4584309
## In 0.02348037 0.003436939 0.5415691
## [1] "end of results for trait: spareribs"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: moisture
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -810.7136 converged in: 6 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 74.6010394 0.55190375 135.170380 0.000000000
## sexM -0.3120681 0.09509139 -3.281770 0.001031576
## perc_duroc -1.1483119 0.88627692 -1.295658 0.195093309
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.8455059 0.2763794 0.3451983
## In 1.6038281 0.1757924 0.6548017
## [1] "end of results for trait: moisture"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: fat
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -698.5738 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 1.8974923 0.52044279 3.645919 2.664377e-04
## sexM 0.5845773 0.08381917 6.974267 3.074652e-12
## perc_duroc 1.9862286 0.79488474 2.498763 1.246276e-02
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.9063554 0.2693728 0.4480301
## In 1.1166232 0.1593866 0.5519699
## [1] "end of results for trait: fat"
## [1] "--------------------------------------"
## [1] "--------------------------------------"
## gblup analysis of trait: protein
##
## fixed effects equation:
## y ~ sex + perc_duroc
##
## random effects equation:
## ~G + In
##
## log-likelihood: -527.8284 converged in: 5 iterations
##
## estimated fixed effects:
## Estimate StdError test.st p.value
## (Intercept) 23.6146186 0.40434989 58.4014474 0.000000000
## sexM -0.2708246 0.06999913 -3.8689703 0.000109296
## perc_duroc 0.2469994 0.65195865 0.3788575 0.704793685
##
## estimated variance components:
## Estimate StdError prop.var
## G 0.4463994 0.14709375 0.3380826
## In 0.8739863 0.09416662 0.6619174
## [1] "end of results for trait: protein"
## [1] "--------------------------------------"
## [1] "--------------------------------------"## user system elapsed
## 733.26 12.02 751.99