######################################################### ######################################################### # Accounting for genotype-by-environment interactions and residual genetic variation # in genomic selection for water-soluble carbohydrate concentration in wheat # # Supplementary File S5 # this script file contains # 1) Final Genomic Selection model (line 151) # 2) Cross validation of final Genomic Selection model (script starts on line 194) ######################################################### ######################################################### # Script for the final Genomic Selection model: ######################################################### # load required packages: require(myf) require(asreml) # This is the DIAG model from the E-BLUPs analysis: WSCCPrediction.asr.gblup <- asreml(WSCCPrediction ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ diag(IEXPT):giv(ID) + diag(IEXPT):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, data=wscc.am.with.markers,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=9.5e8), na.method.X='include', aom=F) # AIC file: Model.l.d <- summary(WSCCPrediction.asr.gblup,all=F)$loglik Model.v.d <- length(summary(WSCCPrediction.asr.gblup, all=F)$varcomp$constraint[summary(WSCCPrediction.asr.gblup, all=F)$varcomp$constraint != "Fixed"]) AIC.diag <- -2*Model.l.d + 2*Model.v.d #Write AIC to file sink("wscc.gblup.am.AIC.txt", append=TRUE,split=TRUE) cat("\n") cat("AIC.diag") cat("\n") AIC.diag cat("\n") sink() ######################################################### # START OF FACTOR ANALYSIS - FA1:FA1 # Get starting values: wscc.gblup.sv1.asr <- asreml(WSCCPrediction ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,1):giv(ID) + fa(IEXPT,1):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, start.values='wscc.gblup.sv.csv', data=wscc.am.with.markers,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), na.method.X='include', aom=F) ns <- length(unique(wscc.gblup.am$IEXPT)) #ns being no of sites wscc.gblup.sv1 <- read.csv('wscc.gblup.sv.csv') wscc.gblup.sv1$Value[1:ns] <- WSCCPrediction.asr.gblup$gammas[1] wscc.gblup.sv1$Value[(ns+1):(ns*2)] <- WSCCPrediction.asr.gblup$gammas[1:ns+1] write.csv(wscc.gblup.sv1,"wscc.gblup.fa1.sv.csv", row.names=F) #now that you have calculated starting values, you can run the model: wscc.gblup.fa1.asr <- asreml(WSCCPrediction ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,1):giv(ID) + fa(IEXPT,1):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.gblup.fa1.sv.csv', R.param='wscc.gblup.fa1.sv.csv', data=wscc.am.with.markers,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=1, stepsize=0.00001,na.method.X='include', aom=F) # 'for' loop to help the model converge: for(i in 1:20) { if(wscc.gblup.fa1.asr$converge==FALSE){ wscc.gblup.sv1$Value <- wscc.gblup.fa1.asr$gammas write.csv(wscc.gblup.sv1,"wscc.gblup.fa1.sv.csv", row.names=F) wscc.gblup.fa1.asr <- asreml(WSCCPrediction ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,1):giv(ID) + fa(IEXPT,1):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.gblup.fa1.sv.csv', R.param='wscc.gblup.fa1.sv.csv', data=wscc.am.with.markers,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), na.method.X='include', aom=F) } } # add FA1:FA1 values to AIC file Model.l.1 <- summary(wscc.gblup.fa1.asr,all=F)$loglik Model.v.1 <- length(summary(wscc.gblup.fa1.asr, all=F)$varcomp$constraint[summary(wscc.gblup.fa1.asr, all=F)$varcomp$constraint != "Fixed"]) names(wscc.gblup.fa1.asr) summary(wscc.gblup.fa1.asr, all=F)$varcomp$constraint AIC.fa1 <- -2*Model.l.1 + 2*Model.v.1 #Write AIC to file sink("wscc.gblup.am.AIC.txt", append=TRUE,split=TRUE) cat("\n") cat("AIC.fa1") cat("\n") AIC.fa1 cat("\n") sink() ######################################################### # FACTOR ANALYSIS - FA2:FA2 # Get starting values: wscc.gblup.sv2.asr <- asreml(WSCCPrediction ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, start.values='wscc.gblup.fa2.sv.csv', data=wscc.am.with.markers,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), na.method.X='include', aom=F) wscc.gblup.sv2 <- read.csv('wscc.gblup.fa2.sv.csv') wscc.gblup.sv2$Value[1:ns] <- wscc.gblup.fa1.asr$gammas[1] wscc.gblup.sv2$Value[(ns+1):(ns*2)] <- wscc.gblup.fa1.asr$gammas[(ns+1):(ns*2)] wscc.gblup.sv2$Value[(ns*2+1):(ns*3)] <- 0.1 # put in the average for FA1 gammas wscc.gblup.sv2$Value[(ns*3+1):(ns*4)] <- wscc.gblup.fa1.asr$gammas[1] wscc.gblup.sv2$Value[(ns*4+1):(ns*5)] <- wscc.gblup.fa1.asr$gammas[(ns+1):(ns*2)] wscc.gblup.sv2$Value[(ns*5+1):(ns*6)] <- 0.1 # put in the average for FA1 gammas write.csv(wscc.gblup.sv2,"wscc.gblup.fa2.sv.csv", row.names=F) #now that you have calculated starting values, you can run model: wscc.gblup.fa2.asr <- asreml(WSCCPrediction ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.gblup.fa2.sv.csv', R.param='wscc.gblup.fa2.sv.csv', data=wscc.am.with.markers,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=1, stepsize=0.00001,na.method.X='include', aom=F) # 'for' loop to help the model converge: for(i in 1:20) { if(wscc.gblup.fa2.asr$converge==FALSE){ wscc.gblup.sv2$Value <- wscc.gblup.fa2.asr$gammas write.csv(wscc.gblup.sv2,"wscc.gblup.fa2.sv.csv", row.names=F) wscc.gblup.fa2.asr <- asreml(WSCCPrediction ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.gblup.fa2.sv.csv', R.param='wscc.gblup.fa2.sv.csv', data=wscc.am.with.markers,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), na.method.X='include', aom=F) } } # AIC for FA2:FA2 Model.l.2 <- summary(wscc.gblup.fa2.asr,all=F)$loglik Model.v.2 <- length(summary(wscc.gblup.fa2.asr, all=F)$varcomp$constraint[summary(wscc.gblup.fa2.asr, all=F)$varcomp$constraint != "Fixed"]) AIC.fa2 <- -2*Model.l.2 + 2*Model.v.2 #Write AIC to file sink("wscc.gblup.am.AIC.txt", append=TRUE,split=TRUE) cat("\n") cat("AIC.fa2") cat("\n") AIC.fa2 cat("\n") sink() ######################################################### # summary.fa object: wscc.gblupFA2sum <- summary.fa(wscc.gblup.fa2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # here are the GVs, GEBVs and non-additive gblups by expt: write.csv(wscc.gblupFA2sum$blups$"fa(IEXPT, 2):giv(ID)"$blups, "wscc.gblup.FA2.giv.csv") write.csv(wscc.gblupFA2sum$blups$"fa(IEXPT, 2):ide(ID)"$blups, "wscc.gblup.FA2.ide.csv") write.csv(wscc.gblupFA2sum$blups$"IEXPT:ID-total"$blups.inmet, "wscc.gblup.FA2.total.csv") ######################################################### ######################################################### # Script for cross validation of final Genomic Selection model: ######################################################### # load required packages: require(asreml) # MonCheck function to identify variance components that change a lot between iterations: function(model, write = T, file = "mon.csv"){ mon <- model$monitor[,1:(length(model$monitor) - 2)] mon <- mon[4:dim(mon)[1],] vm <- length(mon) vper <- (abs(mon[,vm] - mon[,vm - 1]))/mon[,vm - 1] vmat <- cbind(rownames(mon), mon, vper) names(vmat) <- c("component", paste("iter " ,as.character(1:vm), sep =""), "percent") if(write) write.table(vmat, file = file, col.names = T, row.names = F, sep = ",") else vmat } ######################################################### # cross validation subsets were made in MS Excel: wscc.am.cross <- read.csv("File S6.csv") str(wscc.am.cross) #make factor columns 'factors' wscc.am.cross$IEXPT <- factor(wscc.am.cross$IEXPT) wscc.am.cross$YEAR <- factor(wscc.am.cross$YEAR) wscc.am.cross$ID <- factor(wscc.am.cross$ID) wscc.am.cross$FRANGE <- factor(wscc.am.cross$FRANGE) wscc.am.cross$FROW <- factor(wscc.am.cross$FROW) wscc.am.cross$FREP <- factor(wscc.am.cross$FREP) wscc.am.cross$FBAY <- factor(wscc.am.cross$FBAY) wscc.am.cross$LDAY <- factor(wscc.am.cross$LDAY) wscc.am.cross$LCAROUSEL <- factor(wscc.am.cross$LCAROUSEL) wscc.am.cross$LWELL <- factor(wscc.am.cross$LWELL) wscc.am.cross$WSCCPrediction <- as.numeric(wscc.am.cross$WSCCPrediction) str(wscc.am.cross) # expt order: wscc.am.cross <- wscc.am.cross[order(wscc.am.cross$YEAR, wscc.am.cross$LDAY, wscc.am.cross$LCAROUSEL, wscc.am.cross$LWELL),] ######################################################### # using the starting values from the converged FA2/FA2 full gblups model: wscc.crossval.sv <- read.csv("wscc.gblup.fa2.sv.csv") # crossval1_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet1_1.sv <- wscc.crossval.sv write.csv(wscc.CrossValSet1_1.sv,"wscc.CrossValSet1_1.sv.csv", row.names=F) wscc.gblup.CrossValSet1_1.asr <- asreml(CrossValSet1_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_1.sv.csv', R.param='wscc.CrossValSet1_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=1, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet1_1.asr$converge==FALSE){ wscc.CrossValSet1_1.sv$Value <- wscc.gblup.CrossValSet1_1.asr$gammas write.csv(wscc.CrossValSet1_1.sv,"wscc.CrossValSet1_1.sv.csv", row.names=F) wscc.gblup.CrossValSet1_1.asr <- asreml(CrossValSet1_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_1.sv.csv', R.param='wscc.CrossValSet1_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2, na.method.X='include', aom=F) } } # monCheck(wscc.gblup.CrossValSet1_1.asr) ######################################################### # CrossValSet1_2 require(asreml) # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet1_2.sv <- wscc.crossval.sv write.csv(wscc.CrossValSet1_2.sv,"wscc.CrossValSet1_2.sv.csv", row.names=F) wscc.gblup.CrossValSet1_2.asr <- asreml(CrossValSet1_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_2.sv.csv', R.param='wscc.CrossValSet1_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet1_2.asr$converge==FALSE){ wscc.CrossValSet1_2.sv$Value <- wscc.gblup.CrossValSet1_2.asr$gammas write.csv(wscc.CrossValSet1_2.sv,"wscc.CrossValSet1_2.sv.csv", row.names=F) wscc.gblup.CrossValSet1_2.asr <- asreml(CrossValSet1_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_2.sv.csv', R.param='wscc.CrossValSet1_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2,na.method.X='include', aom=F) } } ######################################################### # CrossValSet1_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet1_3.sv <- wscc.crossval.sv write.csv(wscc.CrossValSet1_3.sv,"wscc.CrossValSet1_3.sv.csv", row.names=F) wscc.gblup.CrossValSet1_3.asr <- asreml(CrossValSet1_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_3.sv.csv', R.param='wscc.CrossValSet1_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet1_3.asr$converge==FALSE){ wscc.CrossValSet1_3.sv$Value <- wscc.gblup.CrossValSet1_3.asr$gammas write.csv(wscc.CrossValSet1_3.sv,"wscc.CrossValSet1_3.sv.csv", row.names=F) wscc.gblup.CrossValSet1_3.asr <- asreml(CrossValSet1_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_3.sv.csv', R.param='wscc.CrossValSet1_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2,na.method.X='include', aom=F) } } ######################################################### # CrossValSet1_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet1_3.sv <- wscc.crossval.sv write.csv(wscc.CrossValSet1_3.sv,"wscc.CrossValSet1_3.sv.csv", row.names=F) wscc.gblup.CrossValSet1_3.asr <- asreml(CrossValSet1_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_3.sv.csv', R.param='wscc.CrossValSet1_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet1_3.asr$converge==FALSE){ wscc.CrossValSet1_3.sv$Value <- wscc.gblup.CrossValSet1_3.asr$gammas write.csv(wscc.CrossValSet1_3.sv,"wscc.CrossValSet1_3.sv.csv", row.names=F) wscc.gblup.CrossValSet1_3.asr <- asreml(CrossValSet1_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_3.sv.csv', R.param='wscc.CrossValSet1_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2,na.method.X='include', aom=F) } } # monCheck(wscc.gblup.CrossValSet1_3.asr) ######################################################### # CrossValSet1_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet1_4.sv <- wscc.crossval.sv write.csv(wscc.CrossValSet1_4.sv,"wscc.CrossValSet1_4.sv.csv", row.names=F) wscc.gblup.CrossValSet1_4.asr <- asreml(CrossValSet1_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_4.sv.csv', R.param='wscc.CrossValSet1_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet1_4.asr$converge==FALSE){ wscc.CrossValSet1_4.sv$Value <- wscc.gblup.CrossValSet1_4.asr$gammas write.csv(wscc.CrossValSet1_4.sv,"wscc.CrossValSet1_4.sv.csv", row.names=F) wscc.gblup.CrossValSet1_4.asr <- asreml(CrossValSet1_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_4.sv.csv', R.param='wscc.CrossValSet1_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2,na.method.X='include', aom=F) } } # monCheck(wscc.gblup.CrossValSet1_4.asr) ######################################################### # CrossValSet1_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet1_5.sv <- wscc.crossval.sv write.csv(wscc.CrossValSet1_5.sv,"wscc.CrossValSet1_5.sv.csv", row.names=F) wscc.gblup.CrossValSet1_5.asr <- asreml(CrossValSet1_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_5.sv.csv', R.param='wscc.CrossValSet1_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:10) { if(wscc.gblup.CrossValSet1_5.asr$converge==FALSE){ wscc.CrossValSet1_5.sv$Value <- wscc.gblup.CrossValSet1_5.asr$gammas write.csv(wscc.CrossValSet1_5.sv,"wscc.CrossValSet1_5.sv.csv", row.names=F) wscc.gblup.CrossValSet1_5.asr <- asreml(CrossValSet1_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet1_5.sv.csv', R.param='wscc.CrossValSet1_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet1_5.asr) ######################################################### # CrossValSet2_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet2_1.sv <- wscc.crossval.sv write.csv(wscc.CrossValSet2_1.sv,"wscc.CrossValSet2_1.sv.csv", row.names=F) wscc.gblup.CrossValSet2_1.asr <- asreml(CrossValSet2_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_1.sv.csv', R.param='wscc.CrossValSet2_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet2_1.asr$converge==FALSE){ wscc.CrossValSet2_1.sv$Value <- wscc.gblup.CrossValSet2_1.asr$gammas write.csv(wscc.CrossValSet2_1.sv,"wscc.CrossValSet2_1.sv.csv", row.names=F) wscc.gblup.CrossValSet2_1.asr <- asreml(CrossValSet2_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_1.sv.csv', R.param='wscc.CrossValSet2_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet2_1.asr) ######################################################### # CrossValSet2_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet2_2.sv <- wscc.crossval.sv write.csv(wscc.CrossValSet2_2.sv,"wscc.CrossValSet2_2.sv.csv", row.names=F) wscc.gblup.CrossValSet2_2.asr <- asreml(CrossValSet2_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_2.sv.csv', R.param='wscc.CrossValSet2_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet2_2.asr$converge==FALSE){ wscc.CrossValSet2_2.sv$Value <- wscc.gblup.CrossValSet2_2.asr$gammas write.csv(wscc.CrossValSet2_2.sv,"wscc.CrossValSet2_2.sv.csv", row.names=F) wscc.gblup.CrossValSet2_2.asr <- asreml(CrossValSet2_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_2.sv.csv', R.param='wscc.CrossValSet2_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet2_2.asr) ######################################################### # CrossValSet2_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet2_3.sv <- wscc.crossval.sv write.csv(wscc.CrossValSet2_3.sv,"wscc.CrossValSet2_3.sv.csv", row.names=F) wscc.gblup.CrossValSet2_3.asr <- asreml(CrossValSet2_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_3.sv.csv', R.param='wscc.CrossValSet2_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet2_3.asr$converge==FALSE){ wscc.CrossValSet2_3.sv$Value <- wscc.gblup.CrossValSet2_3.asr$gammas write.csv(wscc.CrossValSet2_3.sv,"wscc.CrossValSet2_3.sv.csv", row.names=F) wscc.gblup.CrossValSet2_3.asr <- asreml(CrossValSet2_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_3.sv.csv', R.param='wscc.CrossValSet2_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet2_3.asr) ######################################################### # CrossValSet2_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet2_4.sv <- wscc.crossval.sv wscc.CrossValSet2_4.sv <- read.csv("wscc.CrossValSet2_4.sv.csv") write.csv(wscc.CrossValSet2_4.sv,"wscc.CrossValSet2_4.sv.csv", row.names=F) wscc.gblup.CrossValSet2_4.asr <- asreml(CrossValSet2_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_4.sv.csv', R.param='wscc.CrossValSet2_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet2_4.asr$converge==FALSE){ wscc.CrossValSet2_4.sv$Value <- wscc.gblup.CrossValSet2_4.asr$gammas write.csv(wscc.CrossValSet2_4.sv,"wscc.CrossValSet2_4.sv.csv", row.names=F) wscc.gblup.CrossValSet2_4.asr <- asreml(CrossValSet2_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_4.sv.csv', R.param='wscc.CrossValSet2_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet2_4.asr) ######################################################### # CrossValSet2_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet2_5.sv <- wscc.crossval.sv #wscc.CrossValSet2_5.sv <- read.csv("wscc.CrossValSet2_5.sv.csv") write.csv(wscc.CrossValSet2_5.sv,"wscc.CrossValSet2_5.sv.csv", row.names=F) wscc.gblup.CrossValSet2_5.asr <- asreml(CrossValSet2_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_5.sv.csv', R.param='wscc.CrossValSet2_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet2_5.asr$converge==FALSE){ wscc.CrossValSet2_5.sv$Value <- wscc.gblup.CrossValSet2_5.asr$gammas write.csv(wscc.CrossValSet2_5.sv,"wscc.CrossValSet2_5.sv.csv", row.names=F) wscc.gblup.CrossValSet2_5.asr <- asreml(CrossValSet2_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet2_5.sv.csv', R.param='wscc.CrossValSet2_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet2_5.asr) ######################################################### # CrossValSet3_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet3_1.sv <- wscc.crossval.sv wscc.CrossValSet3_1.sv <- read.csv("wscc.CrossValSet3_1.sv.csv") write.csv(wscc.CrossValSet3_1.sv,"wscc.CrossValSet3_1.sv.csv", row.names=F) wscc.gblup.CrossValSet3_1.asr <- asreml(CrossValSet3_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_1.sv.csv', R.param='wscc.CrossValSet3_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet3_1.asr$converge==FALSE){ wscc.CrossValSet3_1.sv$Value <- wscc.gblup.CrossValSet3_1.asr$gammas write.csv(wscc.CrossValSet3_1.sv,"wscc.CrossValSet3_1.sv.csv", row.names=F) wscc.gblup.CrossValSet3_1.asr <- asreml(CrossValSet3_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_1.sv.csv', R.param='wscc.CrossValSet3_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=2, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet3_1.asr) ######################################################### # CrossValSet3_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet3_2.sv <- wscc.crossval.sv wscc.CrossValSet3_2.sv <- read.csv("wscc.CrossValSet3_2.sv.csv") write.csv(wscc.CrossValSet3_2.sv,"wscc.CrossValSet3_2.sv.csv", row.names=F) wscc.gblup.CrossValSet3_2.asr <- asreml(CrossValSet3_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_2.sv.csv', R.param='wscc.CrossValSet3_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:3) { if(wscc.gblup.CrossValSet3_2.asr$converge==FALSE){ wscc.CrossValSet3_2.sv$Value <- wscc.gblup.CrossValSet3_2.asr$gammas write.csv(wscc.CrossValSet3_2.sv,"wscc.CrossValSet3_2.sv.csv", row.names=F) wscc.gblup.CrossValSet3_2.asr <- asreml(CrossValSet3_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_2.sv.csv', R.param='wscc.CrossValSet3_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet3_2.asr) ######################################################### # CrossValSet3_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet3_3.sv <- wscc.crossval.sv #wscc.CrossValSet3_3.sv <- read.csv("wscc.CrossValSet3_3.sv.csv") write.csv(wscc.CrossValSet3_3.sv,"wscc.CrossValSet3_3.sv.csv", row.names=F) wscc.gblup.CrossValSet3_3.asr <- asreml(CrossValSet3_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_3.sv.csv', R.param='wscc.CrossValSet3_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet3_3.asr$converge==FALSE){ wscc.CrossValSet3_3.sv$Value <- wscc.gblup.CrossValSet3_3.asr$gammas write.csv(wscc.CrossValSet3_3.sv,"wscc.CrossValSet3_3.sv.csv", row.names=F) wscc.gblup.CrossValSet3_3.asr <- asreml(CrossValSet3_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_3.sv.csv', R.param='wscc.CrossValSet3_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet3_3.asr) ######################################################### # CrossValSet3_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet3_4.sv <- wscc.crossval.sv wscc.CrossValSet3_4.sv <- read.csv("wscc.CrossValSet3_4.sv.csv") write.csv(wscc.CrossValSet3_4.sv,"wscc.CrossValSet3_4.sv.csv", row.names=F) wscc.gblup.CrossValSet3_4.asr <- asreml(CrossValSet3_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_4.sv.csv', R.param='wscc.CrossValSet3_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet3_4.asr$converge==FALSE){ wscc.CrossValSet3_4.sv$Value <- wscc.gblup.CrossValSet3_4.asr$gammas write.csv(wscc.CrossValSet3_4.sv,"wscc.CrossValSet3_4.sv.csv", row.names=F) wscc.gblup.CrossValSet3_4.asr <- asreml(CrossValSet3_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_4.sv.csv', R.param='wscc.CrossValSet3_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet3_4.asr) ######################################################### # CrossValSet3_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet3_5.sv <- wscc.crossval.sv wscc.CrossValSet3_5.sv <- read.csv("wscc.CrossValSet3_5.sv.csv") write.csv(wscc.CrossValSet3_5.sv,"wscc.CrossValSet3_5.sv.csv", row.names=F) wscc.gblup.CrossValSet3_5.asr <- asreml(CrossValSet3_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_5.sv.csv', R.param='wscc.CrossValSet3_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet3_5.asr$converge==FALSE){ wscc.CrossValSet3_5.sv$Value <- wscc.gblup.CrossValSet3_5.asr$gammas write.csv(wscc.CrossValSet3_5.sv,"wscc.CrossValSet3_5.sv.csv", row.names=F) wscc.gblup.CrossValSet3_5.asr <- asreml(CrossValSet3_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet3_5.sv.csv', R.param='wscc.CrossValSet3_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet3_5.asr) ######################################################### # CrossValSet4_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet4_1.sv <- wscc.crossval.sv wscc.CrossValSet4_1.sv <- read.csv("wscc.CrossValSet4_1.sv.csv") write.csv(wscc.CrossValSet4_1.sv,"wscc.CrossValSet4_1.sv.csv", row.names=F) wscc.gblup.CrossValSet4_1.asr <- asreml(CrossValSet4_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_1.sv.csv', R.param='wscc.CrossValSet4_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=1, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet4_1.asr$converge==FALSE){ wscc.CrossValSet4_1.sv$Value <- wscc.gblup.CrossValSet4_1.asr$gammas write.csv(wscc.CrossValSet4_1.sv,"wscc.CrossValSet4_1.sv.csv", row.names=F) wscc.gblup.CrossValSet4_1.asr <- asreml(CrossValSet4_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_1.sv.csv', R.param='wscc.CrossValSet4_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=8e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet4_1.asr) ######################################################### # CrossValSet4_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet4_2.sv <- wscc.crossval.sv wscc.gblup.CrossValSet4_2.asr <- asreml(CrossValSet4_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_2.sv.csv', R.param='wscc.CrossValSet4_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet4_2.asr$converge==FALSE){ wscc.CrossValSet4_2.sv$Value <- wscc.gblup.CrossValSet4_2.asr$gammas write.csv(wscc.CrossValSet4_2.sv,"wscc.CrossValSet4_2.sv.csv", row.names=F) wscc.gblup.CrossValSet4_2.asr <- asreml(CrossValSet4_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_2.sv.csv', R.param='wscc.CrossValSet4_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet4_2.asr) ######################################################### # CrossValSet4_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet4_3.sv <- wscc.crossval.sv wscc.gblup.CrossValSet4_3.asr <- asreml(CrossValSet4_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_3.sv.csv', R.param='wscc.CrossValSet4_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet4_3.asr$converge==FALSE){ wscc.CrossValSet4_3.sv$Value <- wscc.gblup.CrossValSet4_3.asr$gammas write.csv(wscc.CrossValSet4_3.sv,"wscc.CrossValSet4_3.sv.csv", row.names=F) wscc.gblup.CrossValSet4_3.asr <- asreml(CrossValSet4_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_3.sv.csv', R.param='wscc.CrossValSet4_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet4_3.asr) ######################################################### # CrossValSet4_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet4_4.sv <- wscc.crossval.sv wscc.gblup.CrossValSet4_4.asr <- asreml(CrossValSet4_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_4.sv.csv', R.param='wscc.CrossValSet4_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet4_4.asr$converge==FALSE){ wscc.CrossValSet4_4.sv$Value <- wscc.gblup.CrossValSet4_4.asr$gammas write.csv(wscc.CrossValSet4_4.sv,"wscc.CrossValSet4_4.sv.csv", row.names=F) wscc.gblup.CrossValSet4_4.asr <- asreml(CrossValSet4_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_4.sv.csv', R.param='wscc.CrossValSet4_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } ######################################################### # CrossValSet4_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet4_5.sv <- wscc.crossval.sv wscc.gblup.CrossValSet4_5.asr <- asreml(CrossValSet4_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_5.sv.csv', R.param='wscc.CrossValSet4_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet4_5.asr$converge==FALSE){ wscc.CrossValSet4_5.sv$Value <- wscc.gblup.CrossValSet4_5.asr$gammas write.csv(wscc.CrossValSet4_5.sv,"wscc.CrossValSet4_5.sv.csv", row.names=F) wscc.gblup.CrossValSet4_5.asr <- asreml(CrossValSet4_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet4_5.sv.csv', R.param='wscc.CrossValSet4_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet4_5.asr) ######################################################### # CrossValSet5_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet5_1.sv <- wscc.crossval.sv wscc.gblup.CrossValSet5_1.asr <- asreml(CrossValSet5_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_1.sv.csv', R.param='wscc.CrossValSet5_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet5_1.asr$converge==FALSE){ wscc.CrossValSet5_1.sv$Value <- wscc.gblup.CrossValSet5_1.asr$gammas write.csv(wscc.CrossValSet5_1.sv,"wscc.CrossValSet5_1.sv.csv", row.names=F) wscc.gblup.CrossValSet5_1.asr <- asreml(CrossValSet5_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_1.sv.csv', R.param='wscc.CrossValSet5_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet5_1.asr) ######################################################### # CrossValSet5_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet5_2.sv <- wscc.crossval.sv wscc.gblup.CrossValSet5_2.asr <- asreml(CrossValSet5_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_2.sv.csv', R.param='wscc.CrossValSet5_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet5_2.asr$converge==FALSE){ wscc.CrossValSet5_2.sv$Value <- wscc.gblup.CrossValSet5_2.asr$gammas write.csv(wscc.CrossValSet5_2.sv,"wscc.CrossValSet5_2.sv.csv", row.names=F) wscc.gblup.CrossValSet5_2.asr <- asreml(CrossValSet5_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_2.sv.csv', R.param='wscc.CrossValSet5_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet5_2.asr) ######################################################### # CrossValSet5_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet5_3.sv <- wscc.crossval.sv wscc.gblup.CrossValSet5_3.asr <- asreml(CrossValSet5_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_3.sv.csv', R.param='wscc.CrossValSet5_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet5_3.asr$converge==FALSE){ wscc.CrossValSet5_3.sv$Value <- wscc.gblup.CrossValSet5_3.asr$gammas write.csv(wscc.CrossValSet5_3.sv,"wscc.CrossValSet5_3.sv.csv", row.names=F) wscc.gblup.CrossValSet5_3.asr <- asreml(CrossValSet5_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_3.sv.csv', R.param='wscc.CrossValSet5_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet5_3.asr) ######################################################### # CrossValSet5_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet5_4.sv <- wscc.crossval.sv wscc.gblup.CrossValSet5_4.asr <- asreml(CrossValSet5_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_4.sv.csv', R.param='wscc.CrossValSet5_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet5_4.asr$converge==FALSE){ wscc.CrossValSet5_4.sv$Value <- wscc.gblup.CrossValSet5_4.asr$gammas write.csv(wscc.CrossValSet5_4.sv,"wscc.CrossValSet5_4.sv.csv", row.names=F) wscc.gblup.CrossValSet5_4.asr <- asreml(CrossValSet5_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_4.sv.csv', R.param='wscc.CrossValSet5_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet5_4.asr) ######################################################### # CrossValSet5_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet5_5.sv <- wscc.crossval.sv wscc.gblup.CrossValSet5_5.asr <- asreml(CrossValSet5_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_5.sv.csv', R.param='wscc.CrossValSet5_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet5_5.asr$converge==FALSE){ wscc.CrossValSet5_5.sv$Value <- wscc.gblup.CrossValSet5_5.asr$gammas write.csv(wscc.CrossValSet5_5.sv,"wscc.CrossValSet5_5.sv.csv", row.names=F) wscc.gblup.CrossValSet5_5.asr <- asreml(CrossValSet5_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet5_5.sv.csv', R.param='wscc.CrossValSet5_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet5_5.asr) ######################################################### # CrossValSet6_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet6_1.sv <- wscc.crossval.sv wscc.gblup.CrossValSet6_1.asr <- asreml(CrossValSet6_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_1.sv.csv', R.param='wscc.CrossValSet6_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet6_1.asr$converge==FALSE){ wscc.CrossValSet6_1.sv$Value <- wscc.gblup.CrossValSet6_1.asr$gammas write.csv(wscc.CrossValSet6_1.sv,"wscc.CrossValSet6_1.sv.csv", row.names=F) wscc.gblup.CrossValSet6_1.asr <- asreml(CrossValSet6_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_1.sv.csv', R.param='wscc.CrossValSet6_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet6_1.asr) ######################################################### # CrossValSet6_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet6_2.sv <- wscc.crossval.sv wscc.gblup.CrossValSet6_2.asr <- asreml(CrossValSet6_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_2.sv.csv', R.param='wscc.CrossValSet6_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet6_2.asr$converge==FALSE){ wscc.CrossValSet6_2.sv$Value <- wscc.gblup.CrossValSet6_2.asr$gammas write.csv(wscc.CrossValSet6_2.sv,"wscc.CrossValSet6_2.sv.csv", row.names=F) wscc.gblup.CrossValSet6_2.asr <- asreml(CrossValSet6_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_2.sv.csv', R.param='wscc.CrossValSet6_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet6_2.asr) ######################################################### # CrossValSet6_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet6_3.sv <- wscc.crossval.sv wscc.gblup.CrossValSet6_3.asr <- asreml(CrossValSet6_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_3.sv.csv', R.param='wscc.CrossValSet6_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet6_3.asr$converge==FALSE){ wscc.CrossValSet6_3.sv$Value <- wscc.gblup.CrossValSet6_3.asr$gammas write.csv(wscc.CrossValSet6_3.sv,"wscc.CrossValSet6_3.sv.csv", row.names=F) wscc.gblup.CrossValSet6_3.asr <- asreml(CrossValSet6_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_3.sv.csv', R.param='wscc.CrossValSet6_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet6_3.asr) ######################################################### # CrossValSet6_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet6_4.sv <- wscc.crossval.sv wscc.gblup.CrossValSet6_4.asr <- asreml(CrossValSet6_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_4.sv.csv', R.param='wscc.CrossValSet6_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet6_4.asr$converge==FALSE){ wscc.CrossValSet6_4.sv$Value <- wscc.gblup.CrossValSet6_4.asr$gammas write.csv(wscc.CrossValSet6_4.sv,"wscc.CrossValSet6_4.sv.csv", row.names=F) wscc.gblup.CrossValSet6_4.asr <- asreml(CrossValSet6_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_4.sv.csv', R.param='wscc.CrossValSet6_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet6_4.asr) ######################################################### #CrossValSet6_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet6_5.sv <- wscc.crossval.sv wscc.gblup.CrossValSet6_5.asr <- asreml(CrossValSet6_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_5.sv.csv', R.param='wscc.CrossValSet6_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet6_5.asr$converge==FALSE){ wscc.CrossValSet6_5.sv$Value <- wscc.gblup.CrossValSet6_5.asr$gammas write.csv(wscc.CrossValSet6_5.sv,"wscc.CrossValSet6_5.sv.csv", row.names=F) wscc.gblup.CrossValSet6_5.asr <- asreml(CrossValSet6_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet6_5.sv.csv', R.param='wscc.CrossValSet6_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet6_5.asr) ######################################################### #CrossValSet7_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet7_1.sv <- wscc.crossval.sv wscc.gblup.CrossValSet7_1.asr <- asreml(CrossValSet7_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_1.sv.csv', R.param='wscc.CrossValSet7_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet7_1.asr$converge==FALSE){ wscc.CrossValSet7_1.sv$Value <- wscc.gblup.CrossValSet7_1.asr$gammas write.csv(wscc.CrossValSet7_1.sv,"wscc.CrossValSet7_1.sv.csv", row.names=F) wscc.gblup.CrossValSet7_1.asr <- asreml(CrossValSet7_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_1.sv.csv', R.param='wscc.CrossValSet7_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet7_1.asr) ######################################################### #CrossValSet7_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet7_2.sv <- wscc.crossval.sv wscc.gblup.CrossValSet7_2.asr <- asreml(CrossValSet7_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_2.sv.csv', R.param='wscc.CrossValSet7_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet7_2.asr$converge==FALSE){ wscc.CrossValSet7_2.sv$Value <- wscc.gblup.CrossValSet7_2.asr$gammas write.csv(wscc.CrossValSet7_2.sv,"wscc.CrossValSet7_2.sv.csv", row.names=F) wscc.gblup.CrossValSet7_2.asr <- asreml(CrossValSet7_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_2.sv.csv', R.param='wscc.CrossValSet7_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet7_2.asr) ######################################################### #CrossValSet7_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet7_2.sv <- wscc.crossval.sv wscc.gblup.CrossValSet7_2.asr <- asreml(CrossValSet7_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_2.sv.csv', R.param='wscc.CrossValSet7_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet7_2.asr$converge==FALSE){ wscc.CrossValSet7_2.sv$Value <- wscc.gblup.CrossValSet7_2.asr$gammas write.csv(wscc.CrossValSet7_2.sv,"wscc.CrossValSet7_2.sv.csv", row.names=F) wscc.gblup.CrossValSet7_2.asr <- asreml(CrossValSet7_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_2.sv.csv', R.param='wscc.CrossValSet7_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet7_2.asr) ######################################################### #CrossValSet7_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet7_3.sv <- wscc.crossval.sv wscc.gblup.CrossValSet7_3.asr <- asreml(CrossValSet7_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_3.sv.csv', R.param='wscc.CrossValSet7_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet7_3.asr$converge==FALSE){ wscc.CrossValSet7_3.sv$Value <- wscc.gblup.CrossValSet7_3.asr$gammas write.csv(wscc.CrossValSet7_3.sv,"wscc.CrossValSet7_3.sv.csv", row.names=F) wscc.gblup.CrossValSet7_3.asr <- asreml(CrossValSet7_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_3.sv.csv', R.param='wscc.CrossValSet7_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet7_3.asr) ######################################################### #CrossValSet7_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet7_4.sv <- wscc.crossval.sv wscc.gblup.CrossValSet7_4.asr <- asreml(CrossValSet7_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_4.sv.csv', R.param='wscc.CrossValSet7_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet7_4.asr$converge==FALSE){ wscc.CrossValSet7_4.sv$Value <- wscc.gblup.CrossValSet7_4.asr$gammas write.csv(wscc.CrossValSet7_4.sv,"wscc.CrossValSet7_4.sv.csv", row.names=F) wscc.gblup.CrossValSet7_4.asr <- asreml(CrossValSet7_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_4.sv.csv', R.param='wscc.CrossValSet7_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet7_4.asr) # # maxit=1, ######################################################### #CrossValSet7_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet7_5.sv <- wscc.crossval.sv wscc.gblup.CrossValSet7_5.asr <- asreml(CrossValSet7_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_5.sv.csv', R.param='wscc.CrossValSet7_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet7_5.asr$converge==FALSE){ wscc.CrossValSet7_5.sv$Value <- wscc.gblup.CrossValSet7_5.asr$gammas write.csv(wscc.CrossValSet7_5.sv,"wscc.CrossValSet7_5.sv.csv", row.names=F) wscc.gblup.CrossValSet7_5.asr <- asreml(CrossValSet7_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet7_5.sv.csv', R.param='wscc.CrossValSet7_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet7_5.asr) ######################################################### #CrossValSet8_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet8_1.sv <- wscc.crossval.sv wscc.gblup.CrossValSet8_1.asr <- asreml(CrossValSet8_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_1.sv.csv', R.param='wscc.CrossValSet8_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet8_1.asr$converge==FALSE){ wscc.CrossValSet8_1.sv$Value <- wscc.gblup.CrossValSet8_1.asr$gammas write.csv(wscc.CrossValSet8_1.sv,"wscc.CrossValSet8_1.sv.csv", row.names=F) wscc.gblup.CrossValSet8_1.asr <- asreml(CrossValSet8_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_1.sv.csv', R.param='wscc.CrossValSet8_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet8_1.asr) ######################################################### #CrossValSet8_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet8_2.sv <- wscc.crossval.sv wscc.gblup.CrossValSet8_2.asr <- asreml(CrossValSet8_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_2.sv.csv', R.param='wscc.CrossValSet8_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet8_2.asr$converge==FALSE){ wscc.CrossValSet8_2.sv$Value <- wscc.gblup.CrossValSet8_2.asr$gammas write.csv(wscc.CrossValSet8_2.sv,"wscc.CrossValSet8_2.sv.csv", row.names=F) wscc.gblup.CrossValSet8_2.asr <- asreml(CrossValSet8_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_2.sv.csv', R.param='wscc.CrossValSet8_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } # model check function: monCheck(wscc.gblup.CrossValSet8_2.asr) ######################################################### #CrossValSet8_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet8_3.sv <- wscc.crossval.sv wscc.gblup.CrossValSet8_3.asr <- asreml(CrossValSet8_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_3.sv.csv', R.param='wscc.CrossValSet8_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet8_3.asr$converge==FALSE){ wscc.CrossValSet8_3.sv$Value <- wscc.gblup.CrossValSet8_3.asr$gammas write.csv(wscc.CrossValSet8_3.sv,"wscc.CrossValSet8_3.sv.csv", row.names=F) wscc.gblup.CrossValSet8_3.asr <- asreml(CrossValSet8_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_3.sv.csv', R.param='wscc.CrossValSet8_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet8_3.asr) ######################################################### #CrossValSet8_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet8_4.sv <- wscc.crossval.sv wscc.gblup.CrossValSet8_4.asr <- asreml(CrossValSet8_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_4.sv.csv', R.param='wscc.CrossValSet8_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet8_4.asr$converge==FALSE){ wscc.CrossValSet8_4.sv$Value <- wscc.gblup.CrossValSet8_4.asr$gammas write.csv(wscc.CrossValSet8_4.sv,"wscc.CrossValSet8_4.sv.csv", row.names=F) wscc.gblup.CrossValSet8_4.asr <- asreml(CrossValSet8_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_4.sv.csv', R.param='wscc.CrossValSet8_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet8_4.asr) ######################################################### #CrossValSet8_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet8_5.sv <- wscc.crossval.sv wscc.gblup.CrossValSet8_5.asr <- asreml(CrossValSet8_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_5.sv.csv', R.param='wscc.CrossValSet8_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet8_5.asr$converge==FALSE){ wscc.CrossValSet8_5.sv$Value <- wscc.gblup.CrossValSet8_5.asr$gammas write.csv(wscc.CrossValSet8_5.sv,"wscc.CrossValSet8_5.sv.csv", row.names=F) wscc.gblup.CrossValSet8_5.asr <- asreml(CrossValSet8_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet8_5.sv.csv', R.param='wscc.CrossValSet8_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet8_5.asr) ######################################################### #CrossValSet9_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet9_1.sv <- wscc.crossval.sv wscc.gblup.CrossValSet9_1.asr <- asreml(CrossValSet9_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_1.sv.csv', R.param='wscc.CrossValSet9_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet9_1.asr$converge==FALSE){ wscc.CrossValSet9_1.sv$Value <- wscc.gblup.CrossValSet9_1.asr$gammas write.csv(wscc.CrossValSet9_1.sv,"wscc.CrossValSet9_1.sv.csv", row.names=F) wscc.gblup.CrossValSet9_1.asr <- asreml(CrossValSet9_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_1.sv.csv', R.param='wscc.CrossValSet9_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet9_1.asr) ######################################################### #CrossValSet9_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet9_2.sv <- wscc.crossval.sv wscc.gblup.CrossValSet9_2.asr <- asreml(CrossValSet9_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_2.sv.csv', R.param='wscc.CrossValSet9_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:20) { if(wscc.gblup.CrossValSet9_2.asr$converge==FALSE){ wscc.CrossValSet9_2.sv$Value <- wscc.gblup.CrossValSet9_2.asr$gammas write.csv(wscc.CrossValSet9_2.sv,"wscc.CrossValSet9_2.sv.csv", row.names=F) wscc.gblup.CrossValSet9_2.asr <- asreml(CrossValSet9_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_2.sv.csv', R.param='wscc.CrossValSet9_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet9_2.asr) ######################################################### #CrossValSet9_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet9_3.sv <- wscc.crossval.sv wscc.gblup.CrossValSet9_3.asr <- asreml(CrossValSet9_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_3.sv.csv', R.param='wscc.CrossValSet9_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet9_3.asr$converge==FALSE){ wscc.CrossValSet9_3.sv$Value <- wscc.gblup.CrossValSet9_3.asr$gammas write.csv(wscc.CrossValSet9_3.sv,"wscc.CrossValSet9_3.sv.csv", row.names=F) wscc.gblup.CrossValSet9_3.asr <- asreml(CrossValSet9_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_3.sv.csv', R.param='wscc.CrossValSet9_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=10, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet9_3.asr) ######################################################### #CrossValSet9_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet9_4.sv <- wscc.crossval.sv wscc.CrossValSet9_4.sv <- read.csv("wscc.CrossValSet9_4.sv.csv") write.csv(wscc.CrossValSet9_4.sv,"wscc.CrossValSet9_4.sv.csv", row.names=F) save.image("C:/Users/lislec/Desktop/140504_crossval/.RData") wscc.gblup.CrossValSet9_4.asr <- asreml(CrossValSet9_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_4.sv.csv', R.param='wscc.CrossValSet9_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:30) { if(wscc.gblup.CrossValSet9_4.asr$converge==FALSE){ wscc.CrossValSet9_4.sv$Value <- wscc.gblup.CrossValSet9_4.asr$gammas write.csv(wscc.CrossValSet9_4.sv,"wscc.CrossValSet9_4.sv.csv", row.names=F) wscc.gblup.CrossValSet9_4.asr <- asreml(CrossValSet9_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_4.sv.csv', R.param='wscc.CrossValSet9_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet9_4.asr) ######################################################### #CrossValSet9_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet9_5.sv <- wscc.crossval.sv wscc.gblup.CrossValSet9_5.asr <- asreml(CrossValSet9_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_5.sv.csv', R.param='wscc.CrossValSet9_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:10) { if(wscc.gblup.CrossValSet9_5.asr$converge==FALSE){ wscc.CrossValSet9_5.sv$Value <- wscc.gblup.CrossValSet9_5.asr$gammas write.csv(wscc.CrossValSet9_5.sv,"wscc.CrossValSet9_5.sv.csv", row.names=F) wscc.gblup.CrossValSet9_5.asr <- asreml(CrossValSet9_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet9_5.sv.csv', R.param='wscc.CrossValSet9_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet9_5.asr) ######################################################### #CrossValSet10_1 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet10_1.sv <- wscc.crossval.sv wscc.gblup.CrossValSet10_1.asr <- asreml(CrossValSet10_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_1.sv.csv', R.param='wscc.CrossValSet10_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:40) { if(wscc.gblup.CrossValSet10_1.asr$converge==FALSE){ wscc.CrossValSet10_1.sv$Value <- wscc.gblup.CrossValSet10_1.asr$gammas write.csv(wscc.CrossValSet10_1.sv,"wscc.CrossValSet10_1.sv.csv", row.names=F) wscc.gblup.CrossValSet10_1.asr <- asreml(CrossValSet10_1 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_1.sv.csv', R.param='wscc.CrossValSet10_1.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet10_1.asr) ######################################################### #CrossValSet10_2 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet10_2.sv <- wscc.crossval.sv wscc.gblup.CrossValSet10_2.asr <- asreml(CrossValSet10_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_2.sv.csv', R.param='wscc.CrossValSet10_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet10_2.asr$converge==FALSE){ wscc.CrossValSet10_2.sv$Value <- wscc.gblup.CrossValSet10_2.asr$gammas write.csv(wscc.CrossValSet10_2.sv,"wscc.CrossValSet10_2.sv.csv", row.names=F) wscc.gblup.CrossValSet10_2.asr <- asreml(CrossValSet10_2 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_2.sv.csv', R.param='wscc.CrossValSet10_2.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet10_2.asr) ######################################################### #CrossValSet10_3 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet10_3.sv <- wscc.crossval.sv wscc.gblup.CrossValSet10_3.asr <- asreml(CrossValSet10_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_3.sv.csv', R.param='wscc.CrossValSet10_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet10_3.asr$converge==FALSE){ wscc.CrossValSet10_3.sv$Value <- wscc.gblup.CrossValSet10_3.asr$gammas write.csv(wscc.CrossValSet10_3.sv,"wscc.CrossValSet10_3.sv.csv", row.names=F) wscc.gblup.CrossValSet10_3.asr <- asreml(CrossValSet10_3 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_3.sv.csv', R.param='wscc.CrossValSet10_3.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=4, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet10_3.asr) ######################################################### #CrossValSet10_4 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet10_4.sv <- wscc.crossval.sv wscc.gblup.CrossValSet10_4.asr <- asreml(CrossValSet10_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_4.sv.csv', R.param='wscc.CrossValSet10_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet10_4.asr$converge==FALSE){ wscc.CrossValSet10_4.sv$Value <- wscc.gblup.CrossValSet10_4.asr$gammas write.csv(wscc.CrossValSet10_4.sv,"wscc.CrossValSet10_4.sv.csv", row.names=F) wscc.gblup.CrossValSet10_4.asr <- asreml(CrossValSet10_4 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_4.sv.csv', R.param='wscc.CrossValSet10_4.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet10_4.asr) ######################################################### #CrossValSet10_5 # using the starting values from the converged FA2/FA2 model: wscc.CrossValSet10_5.sv <- wscc.crossval.sv wscc.gblup.CrossValSet10_5.asr <- asreml(CrossValSet10_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_5.sv.csv', R.param='wscc.CrossValSet10_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) # use this for loop to get the model to converge: ############## for(i in 1:50) { if(wscc.gblup.CrossValSet10_5.asr$converge==FALSE){ wscc.CrossValSet10_5.sv$Value <- wscc.gblup.CrossValSet10_5.asr$gammas write.csv(wscc.CrossValSet10_5.sv,"wscc.CrossValSet10_5.sv.csv", row.names=F) wscc.gblup.CrossValSet10_5.asr <- asreml(CrossValSet10_5 ~ 1 + IEXPT + at(YEAR,c("2010")):lcarousel + at(EXPT):lrow + at(EXPT,c(1)):lcol, random=~ fa(IEXPT,2):giv(ID) + fa(IEXPT,2):ide(ID) + at(EXPT):FREP + at(EXPT):FRANGE:FROW + at(EXPT):FBAY + at(YEAR):LDAY + at(YEAR):LDAY:LCAROUSEL + at(EXPT):Dehydrator + at(EXPT,c(4)):GrinderBatch, rcov=~ at(YEAR):units, G.param='wscc.CrossValSet10_5.sv.csv', R.param='wscc.CrossValSet10_5.sv.csv', data=wscc.am.cross,control=asreml.control(ginverse=list(ID=wscc.gmat.ginv),workspace=7e8), maxit=3, na.method.X='include', aom=F) } } monCheck(wscc.gblup.CrossValSet10_5.asr) ######################################################### # End of cross validation. # Write cross validation set to file: ######################################################### # CHECK IF MODELS ARE CONVERGED: # cross val set 1 wscc.gblup.CrossValSet1_1.asr$converge wscc.gblup.CrossValSet1_2.asr$converge wscc.gblup.CrossValSet1_3.asr$converge wscc.gblup.CrossValSet1_4.asr$converge wscc.gblup.CrossValSet1_5.asr$converge # cross val set 2 wscc.gblup.CrossValSet2_1.asr$converge wscc.gblup.CrossValSet2_2.asr$converge wscc.gblup.CrossValSet2_3.asr$converge wscc.gblup.CrossValSet2_4.asr$converge wscc.gblup.CrossValSet2_5.asr$converge # cross val set 3 wscc.gblup.CrossValSet3_1.asr$converge wscc.gblup.CrossValSet3_2.asr$converge wscc.gblup.CrossValSet3_3.asr$converge wscc.gblup.CrossValSet3_4.asr$converge wscc.gblup.CrossValSet3_5.asr$converge # cross val set 4 wscc.gblup.CrossValSet4_1.asr$converge wscc.gblup.CrossValSet4_2.asr$converge wscc.gblup.CrossValSet4_3.asr$converge wscc.gblup.CrossValSet4_4.asr$converge wscc.gblup.CrossValSet4_5.asr$converge # cross val set 5 wscc.gblup.CrossValSet5_1.asr$converge wscc.gblup.CrossValSet5_2.asr$converge wscc.gblup.CrossValSet5_3.asr$converge wscc.gblup.CrossValSet5_4.asr$converge wscc.gblup.CrossValSet5_5.asr$converge # cross val set 6 wscc.gblup.CrossValSet6_1.asr$converge wscc.gblup.CrossValSet6_2.asr$converge wscc.gblup.CrossValSet6_3.asr$converge wscc.gblup.CrossValSet6_4.asr$converge wscc.gblup.CrossValSet6_5.asr$converge # cross val set 7 wscc.gblup.CrossValSet7_1.asr$converge wscc.gblup.CrossValSet7_2.asr$converge wscc.gblup.CrossValSet7_3.asr$converge wscc.gblup.CrossValSet7_4.asr$converge wscc.gblup.CrossValSet7_5.asr$converge # cross val set 8 wscc.gblup.CrossValSet8_1.asr$converge wscc.gblup.CrossValSet8_2.asr$converge wscc.gblup.CrossValSet8_3.asr$converge wscc.gblup.CrossValSet8_4.asr$converge wscc.gblup.CrossValSet8_5.asr$converge # cross val set 9 wscc.gblup.CrossValSet9_1.asr$converge wscc.gblup.CrossValSet9_2.asr$converge wscc.gblup.CrossValSet9_3.asr$converge wscc.gblup.CrossValSet9_4.asr$converge wscc.gblup.CrossValSet9_5.asr$converge # cross val set 10 wscc.gblup.CrossValSet10_1.asr$converge wscc.gblup.CrossValSet10_2.asr$converge wscc.gblup.CrossValSet10_3.asr$converge wscc.gblup.CrossValSet10_4.asr$converge wscc.gblup.CrossValSet10_5.asr$converge #ok, so all are converged. ######################################################### # make summary objects for all cross val models: require(myf) # crossval set 1: wscc.gblup.CrossValSet1_1.sum <- summary.fa(wscc.gblup.CrossValSet1_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet1_2.sum <- summary.fa(wscc.gblup.CrossValSet1_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet1_3.sum <- summary.fa(wscc.gblup.CrossValSet1_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet1_4.sum <- summary.fa(wscc.gblup.CrossValSet1_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet1_5.sum <- summary.fa(wscc.gblup.CrossValSet1_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # crossval set 2: wscc.gblup.CrossValSet2_1.sum <- summary.fa(wscc.gblup.CrossValSet2_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet2_2.sum <- summary.fa(wscc.gblup.CrossValSet2_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet2_3.sum <- summary.fa(wscc.gblup.CrossValSet2_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet2_4.sum <- summary.fa(wscc.gblup.CrossValSet2_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet2_5.sum <- summary.fa(wscc.gblup.CrossValSet2_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # crossval set 3: wscc.gblup.CrossValSet3_1.sum <- summary.fa(wscc.gblup.CrossValSet3_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet3_2.sum <- summary.fa(wscc.gblup.CrossValSet3_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet3_3.sum <- summary.fa(wscc.gblup.CrossValSet3_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet3_4.sum <- summary.fa(wscc.gblup.CrossValSet3_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet3_5.sum <- summary.fa(wscc.gblup.CrossValSet3_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # crossval set 4: wscc.gblup.CrossValSet4_1.sum <- summary.fa(wscc.gblup.CrossValSet4_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet4_2.sum <- summary.fa(wscc.gblup.CrossValSet4_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet4_3.sum <- summary.fa(wscc.gblup.CrossValSet4_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet4_4.sum <- summary.fa(wscc.gblup.CrossValSet4_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet4_5.sum <- summary.fa(wscc.gblup.CrossValSet4_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # crossval set 5: wscc.gblup.CrossValSet5_1.sum <- summary.fa(wscc.gblup.CrossValSet5_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet5_2.sum <- summary.fa(wscc.gblup.CrossValSet5_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet5_3.sum <- summary.fa(wscc.gblup.CrossValSet5_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet5_4.sum <- summary.fa(wscc.gblup.CrossValSet5_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet5_5.sum <- summary.fa(wscc.gblup.CrossValSet5_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # crossval set 6: wscc.gblup.CrossValSet6_1.sum <- summary.fa(wscc.gblup.CrossValSet6_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet6_2.sum <- summary.fa(wscc.gblup.CrossValSet6_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet6_3.sum <- summary.fa(wscc.gblup.CrossValSet6_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet6_4.sum <- summary.fa(wscc.gblup.CrossValSet6_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet6_5.sum <- summary.fa(wscc.gblup.CrossValSet6_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # crossval set 7: wscc.gblup.CrossValSet7_1.sum <- summary.fa(wscc.gblup.CrossValSet7_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet7_2.sum <- summary.fa(wscc.gblup.CrossValSet7_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet7_3.sum <- summary.fa(wscc.gblup.CrossValSet7_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet7_4.sum <- summary.fa(wscc.gblup.CrossValSet7_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet7_5.sum <- summary.fa(wscc.gblup.CrossValSet7_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # crossval set 8: wscc.gblup.CrossValSet8_1.sum <- summary.fa(wscc.gblup.CrossValSet8_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet8_2.sum <- summary.fa(wscc.gblup.CrossValSet8_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet8_3.sum <- summary.fa(wscc.gblup.CrossValSet8_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet8_4.sum <- summary.fa(wscc.gblup.CrossValSet8_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet8_5.sum <- summary.fa(wscc.gblup.CrossValSet8_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # crossval set 9: wscc.gblup.CrossValSet9_1.sum <- summary.fa(wscc.gblup.CrossValSet9_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet9_2.sum <- summary.fa(wscc.gblup.CrossValSet9_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet9_3.sum <- summary.fa(wscc.gblup.CrossValSet9_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet9_4.sum <- summary.fa(wscc.gblup.CrossValSet9_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet9_5.sum <- summary.fa(wscc.gblup.CrossValSet9_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) # crossval set 10: wscc.gblup.CrossValSet10_1.sum <- summary.fa(wscc.gblup.CrossValSet10_1.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet10_2.sum <- summary.fa(wscc.gblup.CrossValSet10_2.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet10_3.sum <- summary.fa(wscc.gblup.CrossValSet10_3.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet10_4.sum <- summary.fa(wscc.gblup.CrossValSet10_4.asr,heatmap.ord='cluster',trunc.char=c(1,14)) wscc.gblup.CrossValSet10_5.sum <- summary.fa(wscc.gblup.CrossValSet10_5.asr,heatmap.ord='cluster',trunc.char=c(1,14)) ######################################################### # make a file : IEXPT_ID <- read.csv("iexpt_id.csv") # file with 2 columns: ID and IEXPT head(IEXPT_ID) # output CrossValSet1_1 wscc.gblup.CrossValSet1_1.giv <- wscc.gblup.CrossValSet1_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet1_1.giv) <- c("1_1.giv.blup","IEXPT","ID","1_1.giv.regblup") wscc.gblup.CrossValSet1_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_1.giv$IEXPT, wscc.gblup.CrossValSet1_1.giv$ID,sep="_") wscc.gblup.CrossValSet1_1.giv <- wscc.gblup.CrossValSet1_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_1.ide <- wscc.gblup.CrossValSet1_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet1_1.ide) <- c("1_1.ide.blup","IEXPT","ID","1_1.ide.regblup") wscc.gblup.CrossValSet1_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_1.ide$IEXPT, wscc.gblup.CrossValSet1_1.ide$ID,sep="_") wscc.gblup.CrossValSet1_1.ide <- wscc.gblup.CrossValSet1_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_1.total <- wscc.gblup.CrossValSet1_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet1_1.total) <- c("IEXPT","ID","1_1.total.pres","1_1.total.blup","1_1.total.regblup") wscc.gblup.CrossValSet1_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_1.total$IEXPT, wscc.gblup.CrossValSet1_1.total$ID,sep="_") wscc.gblup.CrossValSet1_1.total <- wscc.gblup.CrossValSet1_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_1.total,by="IEXPT_ID",all=TRUE) # head(wscc.gblup.CrossValSet1_1.giv) head(wscc.gblup.CrossValSet1_1.ide) head(wscc.gblup.CrossValSet1_1.total) # output CrossValSet1_2 wscc.gblup.CrossValSet1_2.giv <- wscc.gblup.CrossValSet1_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet1_2.giv) <- c("1_2.giv.blup","IEXPT","ID","1_2.giv.regblup") wscc.gblup.CrossValSet1_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_2.giv$IEXPT, wscc.gblup.CrossValSet1_2.giv$ID,sep="_") wscc.gblup.CrossValSet1_2.giv <- wscc.gblup.CrossValSet1_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_2.ide <- wscc.gblup.CrossValSet1_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet1_2.ide) <- c("1_2.ide.blup","IEXPT","ID","1_2.ide.regblup") wscc.gblup.CrossValSet1_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_2.ide$IEXPT, wscc.gblup.CrossValSet1_2.ide$ID,sep="_") wscc.gblup.CrossValSet1_2.ide <- wscc.gblup.CrossValSet1_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_2.total <- wscc.gblup.CrossValSet1_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet1_2.total) <- c("IEXPT","ID","1_2.total.pres","1_2.total.blup","1_2.total.regblup") wscc.gblup.CrossValSet1_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_2.total$IEXPT, wscc.gblup.CrossValSet1_2.total$ID,sep="_") wscc.gblup.CrossValSet1_2.total <- wscc.gblup.CrossValSet1_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet1_3 wscc.gblup.CrossValSet1_3.giv <- wscc.gblup.CrossValSet1_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet1_3.giv) <- c("1_3.giv.blup","IEXPT","ID","1_3.giv.regblup") wscc.gblup.CrossValSet1_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_3.giv$IEXPT, wscc.gblup.CrossValSet1_3.giv$ID,sep="_") wscc.gblup.CrossValSet1_3.giv <- wscc.gblup.CrossValSet1_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_3.ide <- wscc.gblup.CrossValSet1_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet1_3.ide) <- c("1_3.ide.blup","IEXPT","ID","1_3.ide.regblup") wscc.gblup.CrossValSet1_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_3.ide$IEXPT, wscc.gblup.CrossValSet1_3.ide$ID,sep="_") wscc.gblup.CrossValSet1_3.ide <- wscc.gblup.CrossValSet1_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_3.total <- wscc.gblup.CrossValSet1_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet1_3.total) <- c("IEXPT","ID","1_3.total.pres","1_3.total.blup","1_3.total.regblup") wscc.gblup.CrossValSet1_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_3.total$IEXPT, wscc.gblup.CrossValSet1_3.total$ID,sep="_") wscc.gblup.CrossValSet1_3.total <- wscc.gblup.CrossValSet1_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet1_4 wscc.gblup.CrossValSet1_4.giv <- wscc.gblup.CrossValSet1_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet1_4.giv) <- c("1_4.giv.blup","IEXPT","ID","1_4.giv.regblup") wscc.gblup.CrossValSet1_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_4.giv$IEXPT, wscc.gblup.CrossValSet1_4.giv$ID,sep="_") wscc.gblup.CrossValSet1_4.giv <- wscc.gblup.CrossValSet1_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_4.ide <- wscc.gblup.CrossValSet1_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet1_4.ide) <- c("1_4.ide.blup","IEXPT","ID","1_4.ide.regblup") wscc.gblup.CrossValSet1_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_4.ide$IEXPT, wscc.gblup.CrossValSet1_4.ide$ID,sep="_") wscc.gblup.CrossValSet1_4.ide <- wscc.gblup.CrossValSet1_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_4.total <- wscc.gblup.CrossValSet1_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet1_4.total) <- c("IEXPT","ID","1_4.total.pres","1_4.total.blup","1_4.total.regblup") wscc.gblup.CrossValSet1_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_4.total$IEXPT, wscc.gblup.CrossValSet1_4.total$ID,sep="_") wscc.gblup.CrossValSet1_4.total <- wscc.gblup.CrossValSet1_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet1_5 wscc.gblup.CrossValSet1_5.giv <- wscc.gblup.CrossValSet1_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet1_5.giv) <- c("1_5.giv.blup","IEXPT","ID","1_5.giv.regblup") wscc.gblup.CrossValSet1_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_5.giv$IEXPT, wscc.gblup.CrossValSet1_5.giv$ID,sep="_") wscc.gblup.CrossValSet1_5.giv <- wscc.gblup.CrossValSet1_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_5.ide <- wscc.gblup.CrossValSet1_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet1_5.ide) <- c("1_5.ide.blup","IEXPT","ID","1_5.ide.regblup") wscc.gblup.CrossValSet1_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_5.ide$IEXPT, wscc.gblup.CrossValSet1_5.ide$ID,sep="_") wscc.gblup.CrossValSet1_5.ide <- wscc.gblup.CrossValSet1_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet1_5.total <- wscc.gblup.CrossValSet1_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet1_5.total) <- c("IEXPT","ID","1_5.total.pres","1_5.total.blup","1_5.total.regblup") wscc.gblup.CrossValSet1_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet1_5.total$IEXPT, wscc.gblup.CrossValSet1_5.total$ID,sep="_") wscc.gblup.CrossValSet1_5.total <- wscc.gblup.CrossValSet1_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet1_5.total,by="IEXPT_ID",all=TRUE) # output CrossValSet2_1 wscc.gblup.CrossValSet2_1.giv <- wscc.gblup.CrossValSet2_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet2_1.giv) <- c("2_1.giv.blup","IEXPT","ID","2_1.giv.regblup") wscc.gblup.CrossValSet2_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_1.giv$IEXPT, wscc.gblup.CrossValSet2_1.giv$ID,sep="_") wscc.gblup.CrossValSet2_1.giv <- wscc.gblup.CrossValSet2_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_1.ide <- wscc.gblup.CrossValSet2_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet2_1.ide) <- c("2_1.ide.blup","IEXPT","ID","2_1.ide.regblup") wscc.gblup.CrossValSet2_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_1.ide$IEXPT, wscc.gblup.CrossValSet2_1.ide$ID,sep="_") wscc.gblup.CrossValSet2_1.ide <- wscc.gblup.CrossValSet2_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_1.total <- wscc.gblup.CrossValSet2_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet2_1.total) <- c("IEXPT","ID","2_1.total.pres","2_1.total.blup","2_1.total.regblup") wscc.gblup.CrossValSet2_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_1.total$IEXPT, wscc.gblup.CrossValSet2_1.total$ID,sep="_") wscc.gblup.CrossValSet2_1.total <- wscc.gblup.CrossValSet2_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_1.total,by="IEXPT_ID",all=TRUE) # output CrossValSet2_2 wscc.gblup.CrossValSet2_2.giv <- wscc.gblup.CrossValSet2_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet2_2.giv) <- c("2_2.giv.blup","IEXPT","ID","2_2.giv.regblup") wscc.gblup.CrossValSet2_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_2.giv$IEXPT, wscc.gblup.CrossValSet2_2.giv$ID,sep="_") wscc.gblup.CrossValSet2_2.giv <- wscc.gblup.CrossValSet2_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_2.ide <- wscc.gblup.CrossValSet2_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet2_2.ide) <- c("2_2.ide.blup","IEXPT","ID","2_2.ide.regblup") wscc.gblup.CrossValSet2_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_2.ide$IEXPT, wscc.gblup.CrossValSet2_2.ide$ID,sep="_") wscc.gblup.CrossValSet2_2.ide <- wscc.gblup.CrossValSet2_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_2.total <- wscc.gblup.CrossValSet2_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet2_2.total) <- c("IEXPT","ID","2_2.total.pres","2_2.total.blup","2_2.total.regblup") wscc.gblup.CrossValSet2_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_2.total$IEXPT, wscc.gblup.CrossValSet2_2.total$ID,sep="_") wscc.gblup.CrossValSet2_2.total <- wscc.gblup.CrossValSet2_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet2_3 wscc.gblup.CrossValSet2_3.giv <- wscc.gblup.CrossValSet2_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet2_3.giv) <- c("2_3.giv.blup","IEXPT","ID","2_3.giv.regblup") wscc.gblup.CrossValSet2_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_3.giv$IEXPT, wscc.gblup.CrossValSet2_3.giv$ID,sep="_") wscc.gblup.CrossValSet2_3.giv <- wscc.gblup.CrossValSet2_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_3.ide <- wscc.gblup.CrossValSet2_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet2_3.ide) <- c("2_3.ide.blup","IEXPT","ID","2_3.ide.regblup") wscc.gblup.CrossValSet2_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_3.ide$IEXPT, wscc.gblup.CrossValSet2_3.ide$ID,sep="_") wscc.gblup.CrossValSet2_3.ide <- wscc.gblup.CrossValSet2_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_3.total <- wscc.gblup.CrossValSet2_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet2_3.total) <- c("IEXPT","ID","2_3.total.pres","2_3.total.blup","2_3.total.regblup") wscc.gblup.CrossValSet2_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_3.total$IEXPT, wscc.gblup.CrossValSet2_3.total$ID,sep="_") wscc.gblup.CrossValSet2_3.total <- wscc.gblup.CrossValSet2_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet2_4 wscc.gblup.CrossValSet2_4.giv <- wscc.gblup.CrossValSet2_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet2_4.giv) <- c("2_4.giv.blup","IEXPT","ID","2_4.giv.regblup") wscc.gblup.CrossValSet2_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_4.giv$IEXPT, wscc.gblup.CrossValSet2_4.giv$ID,sep="_") wscc.gblup.CrossValSet2_4.giv <- wscc.gblup.CrossValSet2_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_4.ide <- wscc.gblup.CrossValSet2_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet2_4.ide) <- c("2_4.ide.blup","IEXPT","ID","2_4.ide.regblup") wscc.gblup.CrossValSet2_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_4.ide$IEXPT, wscc.gblup.CrossValSet2_4.ide$ID,sep="_") wscc.gblup.CrossValSet2_4.ide <- wscc.gblup.CrossValSet2_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_4.total <- wscc.gblup.CrossValSet2_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet2_4.total) <- c("IEXPT","ID","2_4.total.pres","2_4.total.blup","2_4.total.regblup") wscc.gblup.CrossValSet2_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_4.total$IEXPT, wscc.gblup.CrossValSet2_4.total$ID,sep="_") wscc.gblup.CrossValSet2_4.total <- wscc.gblup.CrossValSet2_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet2_5 wscc.gblup.CrossValSet2_5.giv <- wscc.gblup.CrossValSet2_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet2_5.giv) <- c("2_5.giv.blup","IEXPT","ID","2_5.giv.regblup") wscc.gblup.CrossValSet2_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_5.giv$IEXPT, wscc.gblup.CrossValSet2_5.giv$ID,sep="_") wscc.gblup.CrossValSet2_5.giv <- wscc.gblup.CrossValSet2_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_5.ide <- wscc.gblup.CrossValSet2_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet2_5.ide) <- c("2_5.ide.blup","IEXPT","ID","2_5.ide.regblup") wscc.gblup.CrossValSet2_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_5.ide$IEXPT, wscc.gblup.CrossValSet2_5.ide$ID,sep="_") wscc.gblup.CrossValSet2_5.ide <- wscc.gblup.CrossValSet2_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet2_5.total <- wscc.gblup.CrossValSet2_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet2_5.total) <- c("IEXPT","ID","2_5.total.pres","2_5.total.blup","2_5.total.regblup") wscc.gblup.CrossValSet2_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet2_5.total$IEXPT, wscc.gblup.CrossValSet2_5.total$ID,sep="_") wscc.gblup.CrossValSet2_5.total <- wscc.gblup.CrossValSet2_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet2_5.total,by="IEXPT_ID",all=TRUE) # output CrossValSet3_1 wscc.gblup.CrossValSet3_1.giv <- wscc.gblup.CrossValSet3_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet3_1.giv) <- c("3_1.giv.blup","IEXPT","ID","3_1.giv.regblup") wscc.gblup.CrossValSet3_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_1.giv$IEXPT, wscc.gblup.CrossValSet3_1.giv$ID,sep="_") wscc.gblup.CrossValSet3_1.giv <- wscc.gblup.CrossValSet3_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_1.ide <- wscc.gblup.CrossValSet3_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet3_1.ide) <- c("3_1.ide.blup","IEXPT","ID","3_1.ide.regblup") wscc.gblup.CrossValSet3_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_1.ide$IEXPT, wscc.gblup.CrossValSet3_1.ide$ID,sep="_") wscc.gblup.CrossValSet3_1.ide <- wscc.gblup.CrossValSet3_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_1.total <- wscc.gblup.CrossValSet3_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet3_1.total) <- c("IEXPT","ID","3_1.total.pres","3_1.total.blup","3_1.total.regblup") wscc.gblup.CrossValSet3_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_1.total$IEXPT, wscc.gblup.CrossValSet3_1.total$ID,sep="_") wscc.gblup.CrossValSet3_1.total <- wscc.gblup.CrossValSet3_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_1.total,by="IEXPT_ID",all=TRUE) # output CrossValSet3_2 wscc.gblup.CrossValSet3_2.giv <- wscc.gblup.CrossValSet3_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet3_2.giv) <- c("3_2.giv.blup","IEXPT","ID","3_2.giv.regblup") wscc.gblup.CrossValSet3_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_2.giv$IEXPT, wscc.gblup.CrossValSet3_2.giv$ID,sep="_") wscc.gblup.CrossValSet3_2.giv <- wscc.gblup.CrossValSet3_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_2.ide <- wscc.gblup.CrossValSet3_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet3_2.ide) <- c("3_2.ide.blup","IEXPT","ID","3_2.ide.regblup") wscc.gblup.CrossValSet3_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_2.ide$IEXPT, wscc.gblup.CrossValSet3_2.ide$ID,sep="_") wscc.gblup.CrossValSet3_2.ide <- wscc.gblup.CrossValSet3_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_2.total <- wscc.gblup.CrossValSet3_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet3_2.total) <- c("IEXPT","ID","3_2.total.pres","3_2.total.blup","3_2.total.regblup") wscc.gblup.CrossValSet3_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_2.total$IEXPT, wscc.gblup.CrossValSet3_2.total$ID,sep="_") wscc.gblup.CrossValSet3_2.total <- wscc.gblup.CrossValSet3_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet3_3 wscc.gblup.CrossValSet3_3.giv <- wscc.gblup.CrossValSet3_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet3_3.giv) <- c("3_3.giv.blup","IEXPT","ID","3_3.giv.regblup") wscc.gblup.CrossValSet3_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_3.giv$IEXPT, wscc.gblup.CrossValSet3_3.giv$ID,sep="_") wscc.gblup.CrossValSet3_3.giv <- wscc.gblup.CrossValSet3_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_3.ide <- wscc.gblup.CrossValSet3_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet3_3.ide) <- c("3_3.ide.blup","IEXPT","ID","3_3.ide.regblup") wscc.gblup.CrossValSet3_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_3.ide$IEXPT, wscc.gblup.CrossValSet3_3.ide$ID,sep="_") wscc.gblup.CrossValSet3_3.ide <- wscc.gblup.CrossValSet3_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_3.total <- wscc.gblup.CrossValSet3_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet3_3.total) <- c("IEXPT","ID","3_3.total.pres","3_3.total.blup","3_3.total.regblup") wscc.gblup.CrossValSet3_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_3.total$IEXPT, wscc.gblup.CrossValSet3_3.total$ID,sep="_") wscc.gblup.CrossValSet3_3.total <- wscc.gblup.CrossValSet3_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet3_4 wscc.gblup.CrossValSet3_4.giv <- wscc.gblup.CrossValSet3_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet3_4.giv) <- c("3_4.giv.blup","IEXPT","ID","3_4.giv.regblup") wscc.gblup.CrossValSet3_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_4.giv$IEXPT, wscc.gblup.CrossValSet3_4.giv$ID,sep="_") wscc.gblup.CrossValSet3_4.giv <- wscc.gblup.CrossValSet3_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_4.ide <- wscc.gblup.CrossValSet3_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet3_4.ide) <- c("3_4.ide.blup","IEXPT","ID","3_4.ide.regblup") wscc.gblup.CrossValSet3_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_4.ide$IEXPT, wscc.gblup.CrossValSet3_4.ide$ID,sep="_") wscc.gblup.CrossValSet3_4.ide <- wscc.gblup.CrossValSet3_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_4.total <- wscc.gblup.CrossValSet3_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet3_4.total) <- c("IEXPT","ID","3_4.total.pres","3_4.total.blup","3_4.total.regblup") wscc.gblup.CrossValSet3_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_4.total$IEXPT, wscc.gblup.CrossValSet3_4.total$ID,sep="_") wscc.gblup.CrossValSet3_4.total <- wscc.gblup.CrossValSet3_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet3_5 wscc.gblup.CrossValSet3_5.giv <- wscc.gblup.CrossValSet3_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet3_5.giv) <- c("3_5.giv.blup","IEXPT","ID","3_5.giv.regblup") wscc.gblup.CrossValSet3_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_5.giv$IEXPT, wscc.gblup.CrossValSet3_5.giv$ID,sep="_") wscc.gblup.CrossValSet3_5.giv <- wscc.gblup.CrossValSet3_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_5.ide <- wscc.gblup.CrossValSet3_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet3_5.ide) <- c("3_5.ide.blup","IEXPT","ID","3_5.ide.regblup") wscc.gblup.CrossValSet3_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_5.ide$IEXPT, wscc.gblup.CrossValSet3_5.ide$ID,sep="_") wscc.gblup.CrossValSet3_5.ide <- wscc.gblup.CrossValSet3_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet3_5.total <- wscc.gblup.CrossValSet3_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet3_5.total) <- c("IEXPT","ID","3_5.total.pres","3_5.total.blup","3_5.total.regblup") wscc.gblup.CrossValSet3_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet3_5.total$IEXPT, wscc.gblup.CrossValSet3_5.total$ID,sep="_") wscc.gblup.CrossValSet3_5.total <- wscc.gblup.CrossValSet3_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet3_5.total,by="IEXPT_ID",all=TRUE) # output CrossValSet4_1 wscc.gblup.CrossValSet4_1.giv <- wscc.gblup.CrossValSet4_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet4_1.giv) <- c("4_1.giv.blup","IEXPT","ID","4_1.giv.regblup") wscc.gblup.CrossValSet4_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_1.giv$IEXPT, wscc.gblup.CrossValSet4_1.giv$ID,sep="_") wscc.gblup.CrossValSet4_1.giv <- wscc.gblup.CrossValSet4_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_1.ide <- wscc.gblup.CrossValSet4_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet4_1.ide) <- c("4_1.ide.blup","IEXPT","ID","4_1.ide.regblup") wscc.gblup.CrossValSet4_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_1.ide$IEXPT, wscc.gblup.CrossValSet4_1.ide$ID,sep="_") wscc.gblup.CrossValSet4_1.ide <- wscc.gblup.CrossValSet4_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_1.total <- wscc.gblup.CrossValSet4_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet4_1.total) <- c("IEXPT","ID","4_1.total.pres","4_1.total.blup","4_1.total.regblup") wscc.gblup.CrossValSet4_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_1.total$IEXPT, wscc.gblup.CrossValSet4_1.total$ID,sep="_") wscc.gblup.CrossValSet4_1.total <- wscc.gblup.CrossValSet4_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_1.total,by="IEXPT_ID",all=TRUE) # output CrossValSet4_2 wscc.gblup.CrossValSet4_2.giv <- wscc.gblup.CrossValSet4_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet4_2.giv) <- c("4_2.giv.blup","IEXPT","ID","4_2.giv.regblup") wscc.gblup.CrossValSet4_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_2.giv$IEXPT, wscc.gblup.CrossValSet4_2.giv$ID,sep="_") wscc.gblup.CrossValSet4_2.giv <- wscc.gblup.CrossValSet4_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_2.ide <- wscc.gblup.CrossValSet4_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet4_2.ide) <- c("4_2.ide.blup","IEXPT","ID","4_2.ide.regblup") wscc.gblup.CrossValSet4_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_2.ide$IEXPT, wscc.gblup.CrossValSet4_2.ide$ID,sep="_") wscc.gblup.CrossValSet4_2.ide <- wscc.gblup.CrossValSet4_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_2.total <- wscc.gblup.CrossValSet4_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet4_2.total) <- c("IEXPT","ID","4_2.total.pres","4_2.total.blup","4_2.total.regblup") wscc.gblup.CrossValSet4_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_2.total$IEXPT, wscc.gblup.CrossValSet4_2.total$ID,sep="_") wscc.gblup.CrossValSet4_2.total <- wscc.gblup.CrossValSet4_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet4_3 wscc.gblup.CrossValSet4_3.giv <- wscc.gblup.CrossValSet4_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet4_3.giv) <- c("4_3.giv.blup","IEXPT","ID","4_3.giv.regblup") wscc.gblup.CrossValSet4_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_3.giv$IEXPT, wscc.gblup.CrossValSet4_3.giv$ID,sep="_") wscc.gblup.CrossValSet4_3.giv <- wscc.gblup.CrossValSet4_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_3.ide <- wscc.gblup.CrossValSet4_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet4_3.ide) <- c("4_3.ide.blup","IEXPT","ID","4_3.ide.regblup") wscc.gblup.CrossValSet4_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_3.ide$IEXPT, wscc.gblup.CrossValSet4_3.ide$ID,sep="_") wscc.gblup.CrossValSet4_3.ide <- wscc.gblup.CrossValSet4_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_3.total <- wscc.gblup.CrossValSet4_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet4_3.total) <- c("IEXPT","ID","4_3.total.pres","4_3.total.blup","4_3.total.regblup") wscc.gblup.CrossValSet4_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_3.total$IEXPT, wscc.gblup.CrossValSet4_3.total$ID,sep="_") wscc.gblup.CrossValSet4_3.total <- wscc.gblup.CrossValSet4_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet4_4 wscc.gblup.CrossValSet4_4.giv <- wscc.gblup.CrossValSet4_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet4_4.giv) <- c("4_4.giv.blup","IEXPT","ID","4_4.giv.regblup") wscc.gblup.CrossValSet4_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_4.giv$IEXPT, wscc.gblup.CrossValSet4_4.giv$ID,sep="_") wscc.gblup.CrossValSet4_4.giv <- wscc.gblup.CrossValSet4_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_4.ide <- wscc.gblup.CrossValSet4_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet4_4.ide) <- c("4_4.ide.blup","IEXPT","ID","4_4.ide.regblup") wscc.gblup.CrossValSet4_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_4.ide$IEXPT, wscc.gblup.CrossValSet4_4.ide$ID,sep="_") wscc.gblup.CrossValSet4_4.ide <- wscc.gblup.CrossValSet4_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_4.total <- wscc.gblup.CrossValSet4_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet4_4.total) <- c("IEXPT","ID","4_4.total.pres","4_4.total.blup","4_4.total.regblup") wscc.gblup.CrossValSet4_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_4.total$IEXPT, wscc.gblup.CrossValSet4_4.total$ID,sep="_") wscc.gblup.CrossValSet4_4.total <- wscc.gblup.CrossValSet4_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet4_5 wscc.gblup.CrossValSet4_5.giv <- wscc.gblup.CrossValSet4_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet4_5.giv) <- c("4_5.giv.blup","IEXPT","ID","4_5.giv.regblup") wscc.gblup.CrossValSet4_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_5.giv$IEXPT, wscc.gblup.CrossValSet4_5.giv$ID,sep="_") wscc.gblup.CrossValSet4_5.giv <- wscc.gblup.CrossValSet4_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_5.ide <- wscc.gblup.CrossValSet4_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet4_5.ide) <- c("4_5.ide.blup","IEXPT","ID","4_5.ide.regblup") wscc.gblup.CrossValSet4_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_5.ide$IEXPT, wscc.gblup.CrossValSet4_5.ide$ID,sep="_") wscc.gblup.CrossValSet4_5.ide <- wscc.gblup.CrossValSet4_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet4_5.total <- wscc.gblup.CrossValSet4_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet4_5.total) <- c("IEXPT","ID","4_5.total.pres","4_5.total.blup","4_5.total.regblup") wscc.gblup.CrossValSet4_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet4_5.total$IEXPT, wscc.gblup.CrossValSet4_5.total$ID,sep="_") wscc.gblup.CrossValSet4_5.total <- wscc.gblup.CrossValSet4_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet4_5.total,by="IEXPT_ID",all=TRUE) # output CrossValSet5_1 wscc.gblup.CrossValSet5_1.giv <- wscc.gblup.CrossValSet5_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet5_1.giv) <- c("5_1.giv.blup","IEXPT","ID","5_1.giv.regblup") wscc.gblup.CrossValSet5_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_1.giv$IEXPT, wscc.gblup.CrossValSet5_1.giv$ID,sep="_") wscc.gblup.CrossValSet5_1.giv <- wscc.gblup.CrossValSet5_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_1.ide <- wscc.gblup.CrossValSet5_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet5_1.ide) <- c("5_1.ide.blup","IEXPT","ID","5_1.ide.regblup") wscc.gblup.CrossValSet5_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_1.ide$IEXPT, wscc.gblup.CrossValSet5_1.ide$ID,sep="_") wscc.gblup.CrossValSet5_1.ide <- wscc.gblup.CrossValSet5_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_1.total <- wscc.gblup.CrossValSet5_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet5_1.total) <- c("IEXPT","ID","5_1.total.pres","5_1.total.blup","5_1.total.regblup") wscc.gblup.CrossValSet5_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_1.total$IEXPT, wscc.gblup.CrossValSet5_1.total$ID,sep="_") wscc.gblup.CrossValSet5_1.total <- wscc.gblup.CrossValSet5_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_1.total,by="IEXPT_ID",all=TRUE) # output CrossValSet5_2 wscc.gblup.CrossValSet5_2.giv <- wscc.gblup.CrossValSet5_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet5_2.giv) <- c("5_2.giv.blup","IEXPT","ID","5_2.giv.regblup") wscc.gblup.CrossValSet5_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_2.giv$IEXPT, wscc.gblup.CrossValSet5_2.giv$ID,sep="_") wscc.gblup.CrossValSet5_2.giv <- wscc.gblup.CrossValSet5_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_2.ide <- wscc.gblup.CrossValSet5_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet5_2.ide) <- c("5_2.ide.blup","IEXPT","ID","5_2.ide.regblup") wscc.gblup.CrossValSet5_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_2.ide$IEXPT, wscc.gblup.CrossValSet5_2.ide$ID,sep="_") wscc.gblup.CrossValSet5_2.ide <- wscc.gblup.CrossValSet5_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_2.total <- wscc.gblup.CrossValSet5_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet5_2.total) <- c("IEXPT","ID","5_2.total.pres","5_2.total.blup","5_2.total.regblup") wscc.gblup.CrossValSet5_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_2.total$IEXPT, wscc.gblup.CrossValSet5_2.total$ID,sep="_") wscc.gblup.CrossValSet5_2.total <- wscc.gblup.CrossValSet5_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet5_3 wscc.gblup.CrossValSet5_3.giv <- wscc.gblup.CrossValSet5_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet5_3.giv) <- c("5_3.giv.blup","IEXPT","ID","5_3.giv.regblup") wscc.gblup.CrossValSet5_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_3.giv$IEXPT, wscc.gblup.CrossValSet5_3.giv$ID,sep="_") wscc.gblup.CrossValSet5_3.giv <- wscc.gblup.CrossValSet5_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_3.ide <- wscc.gblup.CrossValSet5_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet5_3.ide) <- c("5_3.ide.blup","IEXPT","ID","5_3.ide.regblup") wscc.gblup.CrossValSet5_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_3.ide$IEXPT, wscc.gblup.CrossValSet5_3.ide$ID,sep="_") wscc.gblup.CrossValSet5_3.ide <- wscc.gblup.CrossValSet5_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_3.total <- wscc.gblup.CrossValSet5_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet5_3.total) <- c("IEXPT","ID","5_3.total.pres","5_3.total.blup","5_3.total.regblup") wscc.gblup.CrossValSet5_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_3.total$IEXPT, wscc.gblup.CrossValSet5_3.total$ID,sep="_") wscc.gblup.CrossValSet5_3.total <- wscc.gblup.CrossValSet5_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet5_4 wscc.gblup.CrossValSet5_4.giv <- wscc.gblup.CrossValSet5_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet5_4.giv) <- c("5_4.giv.blup","IEXPT","ID","5_4.giv.regblup") wscc.gblup.CrossValSet5_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_4.giv$IEXPT, wscc.gblup.CrossValSet5_4.giv$ID,sep="_") wscc.gblup.CrossValSet5_4.giv <- wscc.gblup.CrossValSet5_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_4.ide <- wscc.gblup.CrossValSet5_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet5_4.ide) <- c("5_4.ide.blup","IEXPT","ID","5_4.ide.regblup") wscc.gblup.CrossValSet5_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_4.ide$IEXPT, wscc.gblup.CrossValSet5_4.ide$ID,sep="_") wscc.gblup.CrossValSet5_4.ide <- wscc.gblup.CrossValSet5_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_4.total <- wscc.gblup.CrossValSet5_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet5_4.total) <- c("IEXPT","ID","5_4.total.pres","5_4.total.blup","5_4.total.regblup") wscc.gblup.CrossValSet5_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_4.total$IEXPT, wscc.gblup.CrossValSet5_4.total$ID,sep="_") wscc.gblup.CrossValSet5_4.total <- wscc.gblup.CrossValSet5_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet5_5 wscc.gblup.CrossValSet5_5.giv <- wscc.gblup.CrossValSet5_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet5_5.giv) <- c("5_5.giv.blup","IEXPT","ID","5_5.giv.regblup") wscc.gblup.CrossValSet5_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_5.giv$IEXPT, wscc.gblup.CrossValSet5_5.giv$ID,sep="_") wscc.gblup.CrossValSet5_5.giv <- wscc.gblup.CrossValSet5_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_5.ide <- wscc.gblup.CrossValSet5_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet5_5.ide) <- c("5_5.ide.blup","IEXPT","ID","5_5.ide.regblup") wscc.gblup.CrossValSet5_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_5.ide$IEXPT, wscc.gblup.CrossValSet5_5.ide$ID,sep="_") wscc.gblup.CrossValSet5_5.ide <- wscc.gblup.CrossValSet5_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet5_5.total <- wscc.gblup.CrossValSet5_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet5_5.total) <- c("IEXPT","ID","5_5.total.pres","5_5.total.blup","5_5.total.regblup") wscc.gblup.CrossValSet5_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet5_5.total$IEXPT, wscc.gblup.CrossValSet5_5.total$ID,sep="_") wscc.gblup.CrossValSet5_5.total <- wscc.gblup.CrossValSet5_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet5_5.total,by="IEXPT_ID",all=TRUE) # output CrossValSet6_1 wscc.gblup.CrossValSet6_1.giv <- wscc.gblup.CrossValSet6_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet6_1.giv) <- c("6_1.giv.blup","IEXPT","ID","6_1.giv.regblup") wscc.gblup.CrossValSet6_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_1.giv$IEXPT, wscc.gblup.CrossValSet6_1.giv$ID,sep="_") wscc.gblup.CrossValSet6_1.giv <- wscc.gblup.CrossValSet6_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_1.ide <- wscc.gblup.CrossValSet6_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet6_1.ide) <- c("6_1.ide.blup","IEXPT","ID","6_1.ide.regblup") wscc.gblup.CrossValSet6_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_1.ide$IEXPT, wscc.gblup.CrossValSet6_1.ide$ID,sep="_") wscc.gblup.CrossValSet6_1.ide <- wscc.gblup.CrossValSet6_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_1.total <- wscc.gblup.CrossValSet6_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet6_1.total) <- c("IEXPT","ID","6_1.total.pres","6_1.total.blup","6_1.total.regblup") wscc.gblup.CrossValSet6_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_1.total$IEXPT, wscc.gblup.CrossValSet6_1.total$ID,sep="_") wscc.gblup.CrossValSet6_1.total <- wscc.gblup.CrossValSet6_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_1.total,by="IEXPT_ID",all=TRUE) # output CrossValSet6_2 wscc.gblup.CrossValSet6_2.giv <- wscc.gblup.CrossValSet6_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet6_2.giv) <- c("6_2.giv.blup","IEXPT","ID","6_2.giv.regblup") wscc.gblup.CrossValSet6_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_2.giv$IEXPT, wscc.gblup.CrossValSet6_2.giv$ID,sep="_") wscc.gblup.CrossValSet6_2.giv <- wscc.gblup.CrossValSet6_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_2.ide <- wscc.gblup.CrossValSet6_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet6_2.ide) <- c("6_2.ide.blup","IEXPT","ID","6_2.ide.regblup") wscc.gblup.CrossValSet6_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_2.ide$IEXPT, wscc.gblup.CrossValSet6_2.ide$ID,sep="_") wscc.gblup.CrossValSet6_2.ide <- wscc.gblup.CrossValSet6_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_2.total <- wscc.gblup.CrossValSet6_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet6_2.total) <- c("IEXPT","ID","6_2.total.pres","6_2.total.blup","6_2.total.regblup") wscc.gblup.CrossValSet6_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_2.total$IEXPT, wscc.gblup.CrossValSet6_2.total$ID,sep="_") wscc.gblup.CrossValSet6_2.total <- wscc.gblup.CrossValSet6_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet6_3 wscc.gblup.CrossValSet6_3.giv <- wscc.gblup.CrossValSet6_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet6_3.giv) <- c("6_3.giv.blup","IEXPT","ID","6_3.giv.regblup") wscc.gblup.CrossValSet6_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_3.giv$IEXPT, wscc.gblup.CrossValSet6_3.giv$ID,sep="_") wscc.gblup.CrossValSet6_3.giv <- wscc.gblup.CrossValSet6_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_3.ide <- wscc.gblup.CrossValSet6_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet6_3.ide) <- c("6_3.ide.blup","IEXPT","ID","6_3.ide.regblup") wscc.gblup.CrossValSet6_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_3.ide$IEXPT, wscc.gblup.CrossValSet6_3.ide$ID,sep="_") wscc.gblup.CrossValSet6_3.ide <- wscc.gblup.CrossValSet6_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_3.total <- wscc.gblup.CrossValSet6_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet6_3.total) <- c("IEXPT","ID","6_3.total.pres","6_3.total.blup","6_3.total.regblup") wscc.gblup.CrossValSet6_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_3.total$IEXPT, wscc.gblup.CrossValSet6_3.total$ID,sep="_") wscc.gblup.CrossValSet6_3.total <- wscc.gblup.CrossValSet6_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet6_4 wscc.gblup.CrossValSet6_4.giv <- wscc.gblup.CrossValSet6_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet6_4.giv) <- c("6_4.giv.blup","IEXPT","ID","6_4.giv.regblup") wscc.gblup.CrossValSet6_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_4.giv$IEXPT, wscc.gblup.CrossValSet6_4.giv$ID,sep="_") wscc.gblup.CrossValSet6_4.giv <- wscc.gblup.CrossValSet6_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_4.ide <- wscc.gblup.CrossValSet6_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet6_4.ide) <- c("6_4.ide.blup","IEXPT","ID","6_4.ide.regblup") wscc.gblup.CrossValSet6_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_4.ide$IEXPT, wscc.gblup.CrossValSet6_4.ide$ID,sep="_") wscc.gblup.CrossValSet6_4.ide <- wscc.gblup.CrossValSet6_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_4.total <- wscc.gblup.CrossValSet6_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet6_4.total) <- c("IEXPT","ID","6_4.total.pres","6_4.total.blup","6_4.total.regblup") wscc.gblup.CrossValSet6_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_4.total$IEXPT, wscc.gblup.CrossValSet6_4.total$ID,sep="_") wscc.gblup.CrossValSet6_4.total <- wscc.gblup.CrossValSet6_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet6_5 wscc.gblup.CrossValSet6_5.giv <- wscc.gblup.CrossValSet6_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet6_5.giv) <- c("6_5.giv.blup","IEXPT","ID","6_5.giv.regblup") wscc.gblup.CrossValSet6_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_5.giv$IEXPT, wscc.gblup.CrossValSet6_5.giv$ID,sep="_") wscc.gblup.CrossValSet6_5.giv <- wscc.gblup.CrossValSet6_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_5.ide <- wscc.gblup.CrossValSet6_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet6_5.ide) <- c("6_5.ide.blup","IEXPT","ID","6_5.ide.regblup") wscc.gblup.CrossValSet6_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_5.ide$IEXPT, wscc.gblup.CrossValSet6_5.ide$ID,sep="_") wscc.gblup.CrossValSet6_5.ide <- wscc.gblup.CrossValSet6_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet6_5.total <- wscc.gblup.CrossValSet6_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet6_5.total) <- c("IEXPT","ID","6_5.total.pres","6_5.total.blup","6_5.total.regblup") wscc.gblup.CrossValSet6_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet6_5.total$IEXPT, wscc.gblup.CrossValSet6_5.total$ID,sep="_") wscc.gblup.CrossValSet6_5.total <- wscc.gblup.CrossValSet6_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet6_5.total,by="IEXPT_ID",all=TRUE) # output CrossValSet7_1 wscc.gblup.CrossValSet7_1.giv <- wscc.gblup.CrossValSet7_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet7_1.giv) <- c("7_1.giv.blup","IEXPT","ID","7_1.giv.regblup") wscc.gblup.CrossValSet7_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_1.giv$IEXPT, wscc.gblup.CrossValSet7_1.giv$ID,sep="_") wscc.gblup.CrossValSet7_1.giv <- wscc.gblup.CrossValSet7_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_1.ide <- wscc.gblup.CrossValSet7_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet7_1.ide) <- c("7_1.ide.blup","IEXPT","ID","7_1.ide.regblup") wscc.gblup.CrossValSet7_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_1.ide$IEXPT, wscc.gblup.CrossValSet7_1.ide$ID,sep="_") wscc.gblup.CrossValSet7_1.ide <- wscc.gblup.CrossValSet7_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_1.total <- wscc.gblup.CrossValSet7_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet7_1.total) <- c("IEXPT","ID","7_1.total.pres","7_1.total.blup","7_1.total.regblup") wscc.gblup.CrossValSet7_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_1.total$IEXPT, wscc.gblup.CrossValSet7_1.total$ID,sep="_") wscc.gblup.CrossValSet7_1.total <- wscc.gblup.CrossValSet7_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_1.total,by="IEXPT_ID",all=TRUE) # output CrossValSet7_2 wscc.gblup.CrossValSet7_2.giv <- wscc.gblup.CrossValSet7_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet7_2.giv) <- c("7_2.giv.blup","IEXPT","ID","7_2.giv.regblup") wscc.gblup.CrossValSet7_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_2.giv$IEXPT, wscc.gblup.CrossValSet7_2.giv$ID,sep="_") wscc.gblup.CrossValSet7_2.giv <- wscc.gblup.CrossValSet7_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_2.ide <- wscc.gblup.CrossValSet7_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet7_2.ide) <- c("7_2.ide.blup","IEXPT","ID","7_2.ide.regblup") wscc.gblup.CrossValSet7_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_2.ide$IEXPT, wscc.gblup.CrossValSet7_2.ide$ID,sep="_") wscc.gblup.CrossValSet7_2.ide <- wscc.gblup.CrossValSet7_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_2.total <- wscc.gblup.CrossValSet7_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet7_2.total) <- c("IEXPT","ID","7_2.total.pres","7_2.total.blup","7_2.total.regblup") wscc.gblup.CrossValSet7_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_2.total$IEXPT, wscc.gblup.CrossValSet7_2.total$ID,sep="_") wscc.gblup.CrossValSet7_2.total <- wscc.gblup.CrossValSet7_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet7_3 wscc.gblup.CrossValSet7_3.giv <- wscc.gblup.CrossValSet7_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet7_3.giv) <- c("7_3.giv.blup","IEXPT","ID","7_3.giv.regblup") wscc.gblup.CrossValSet7_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_3.giv$IEXPT, wscc.gblup.CrossValSet7_3.giv$ID,sep="_") wscc.gblup.CrossValSet7_3.giv <- wscc.gblup.CrossValSet7_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_3.ide <- wscc.gblup.CrossValSet7_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet7_3.ide) <- c("7_3.ide.blup","IEXPT","ID","7_3.ide.regblup") wscc.gblup.CrossValSet7_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_3.ide$IEXPT, wscc.gblup.CrossValSet7_3.ide$ID,sep="_") wscc.gblup.CrossValSet7_3.ide <- wscc.gblup.CrossValSet7_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_3.total <- wscc.gblup.CrossValSet7_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet7_3.total) <- c("IEXPT","ID","7_3.total.pres","7_3.total.blup","7_3.total.regblup") wscc.gblup.CrossValSet7_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_3.total$IEXPT, wscc.gblup.CrossValSet7_3.total$ID,sep="_") wscc.gblup.CrossValSet7_3.total <- wscc.gblup.CrossValSet7_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet7_4 wscc.gblup.CrossValSet7_4.giv <- wscc.gblup.CrossValSet7_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet7_4.giv) <- c("7_4.giv.blup","IEXPT","ID","7_4.giv.regblup") wscc.gblup.CrossValSet7_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_4.giv$IEXPT, wscc.gblup.CrossValSet7_4.giv$ID,sep="_") wscc.gblup.CrossValSet7_4.giv <- wscc.gblup.CrossValSet7_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_4.ide <- wscc.gblup.CrossValSet7_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet7_4.ide) <- c("7_4.ide.blup","IEXPT","ID","7_4.ide.regblup") wscc.gblup.CrossValSet7_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_4.ide$IEXPT, wscc.gblup.CrossValSet7_4.ide$ID,sep="_") wscc.gblup.CrossValSet7_4.ide <- wscc.gblup.CrossValSet7_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_4.total <- wscc.gblup.CrossValSet7_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet7_4.total) <- c("IEXPT","ID","7_4.total.pres","7_4.total.blup","7_4.total.regblup") wscc.gblup.CrossValSet7_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_4.total$IEXPT, wscc.gblup.CrossValSet7_4.total$ID,sep="_") wscc.gblup.CrossValSet7_4.total <- wscc.gblup.CrossValSet7_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet7_5 wscc.gblup.CrossValSet7_5.giv <- wscc.gblup.CrossValSet7_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet7_5.giv) <- c("7_5.giv.blup","IEXPT","ID","7_5.giv.regblup") wscc.gblup.CrossValSet7_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_5.giv$IEXPT, wscc.gblup.CrossValSet7_5.giv$ID,sep="_") wscc.gblup.CrossValSet7_5.giv <- wscc.gblup.CrossValSet7_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_5.ide <- wscc.gblup.CrossValSet7_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet7_5.ide) <- c("7_5.ide.blup","IEXPT","ID","7_5.ide.regblup") wscc.gblup.CrossValSet7_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_5.ide$IEXPT, wscc.gblup.CrossValSet7_5.ide$ID,sep="_") wscc.gblup.CrossValSet7_5.ide <- wscc.gblup.CrossValSet7_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet7_5.total <- wscc.gblup.CrossValSet7_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet7_5.total) <- c("IEXPT","ID","7_5.total.pres","7_5.total.blup","7_5.total.regblup") wscc.gblup.CrossValSet7_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet7_5.total$IEXPT, wscc.gblup.CrossValSet7_5.total$ID,sep="_") wscc.gblup.CrossValSet7_5.total <- wscc.gblup.CrossValSet7_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet7_5.total,by="IEXPT_ID",all=TRUE) # output CrossValSet8_1 wscc.gblup.CrossValSet8_1.giv <- wscc.gblup.CrossValSet8_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet8_1.giv) <- c("8_1.giv.blup","IEXPT","ID","8_1.giv.regblup") wscc.gblup.CrossValSet8_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_1.giv$IEXPT, wscc.gblup.CrossValSet8_1.giv$ID,sep="_") wscc.gblup.CrossValSet8_1.giv <- wscc.gblup.CrossValSet8_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_1.ide <- wscc.gblup.CrossValSet8_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet8_1.ide) <- c("8_1.ide.blup","IEXPT","ID","8_1.ide.regblup") wscc.gblup.CrossValSet8_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_1.ide$IEXPT, wscc.gblup.CrossValSet8_1.ide$ID,sep="_") wscc.gblup.CrossValSet8_1.ide <- wscc.gblup.CrossValSet8_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_1.total <- wscc.gblup.CrossValSet8_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet8_1.total) <- c("IEXPT","ID","8_1.total.pres","8_1.total.blup","8_1.total.regblup") wscc.gblup.CrossValSet8_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_1.total$IEXPT, wscc.gblup.CrossValSet8_1.total$ID,sep="_") wscc.gblup.CrossValSet8_1.total <- wscc.gblup.CrossValSet8_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_1.total,by="IEXPT_ID",all=TRUE) # output CrossValSet8_2 wscc.gblup.CrossValSet8_2.giv <- wscc.gblup.CrossValSet8_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet8_2.giv) <- c("8_2.giv.blup","IEXPT","ID","8_2.giv.regblup") wscc.gblup.CrossValSet8_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_2.giv$IEXPT, wscc.gblup.CrossValSet8_2.giv$ID,sep="_") wscc.gblup.CrossValSet8_2.giv <- wscc.gblup.CrossValSet8_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_2.ide <- wscc.gblup.CrossValSet8_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet8_2.ide) <- c("8_2.ide.blup","IEXPT","ID","8_2.ide.regblup") wscc.gblup.CrossValSet8_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_2.ide$IEXPT, wscc.gblup.CrossValSet8_2.ide$ID,sep="_") wscc.gblup.CrossValSet8_2.ide <- wscc.gblup.CrossValSet8_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_2.total <- wscc.gblup.CrossValSet8_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet8_2.total) <- c("IEXPT","ID","8_2.total.pres","8_2.total.blup","8_2.total.regblup") wscc.gblup.CrossValSet8_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_2.total$IEXPT, wscc.gblup.CrossValSet8_2.total$ID,sep="_") wscc.gblup.CrossValSet8_2.total <- wscc.gblup.CrossValSet8_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet8_3 wscc.gblup.CrossValSet8_3.giv <- wscc.gblup.CrossValSet8_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet8_3.giv) <- c("8_3.giv.blup","IEXPT","ID","8_3.giv.regblup") wscc.gblup.CrossValSet8_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_3.giv$IEXPT, wscc.gblup.CrossValSet8_3.giv$ID,sep="_") wscc.gblup.CrossValSet8_3.giv <- wscc.gblup.CrossValSet8_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_3.ide <- wscc.gblup.CrossValSet8_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet8_3.ide) <- c("8_3.ide.blup","IEXPT","ID","8_3.ide.regblup") wscc.gblup.CrossValSet8_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_3.ide$IEXPT, wscc.gblup.CrossValSet8_3.ide$ID,sep="_") wscc.gblup.CrossValSet8_3.ide <- wscc.gblup.CrossValSet8_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_3.total <- wscc.gblup.CrossValSet8_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet8_3.total) <- c("IEXPT","ID","8_3.total.pres","8_3.total.blup","8_3.total.regblup") wscc.gblup.CrossValSet8_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_3.total$IEXPT, wscc.gblup.CrossValSet8_3.total$ID,sep="_") wscc.gblup.CrossValSet8_3.total <- wscc.gblup.CrossValSet8_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet8_4 wscc.gblup.CrossValSet8_4.giv <- wscc.gblup.CrossValSet8_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet8_4.giv) <- c("8_4.giv.blup","IEXPT","ID","8_4.giv.regblup") wscc.gblup.CrossValSet8_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_4.giv$IEXPT, wscc.gblup.CrossValSet8_4.giv$ID,sep="_") wscc.gblup.CrossValSet8_4.giv <- wscc.gblup.CrossValSet8_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_4.ide <- wscc.gblup.CrossValSet8_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet8_4.ide) <- c("8_4.ide.blup","IEXPT","ID","8_4.ide.regblup") wscc.gblup.CrossValSet8_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_4.ide$IEXPT, wscc.gblup.CrossValSet8_4.ide$ID,sep="_") wscc.gblup.CrossValSet8_4.ide <- wscc.gblup.CrossValSet8_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_4.total <- wscc.gblup.CrossValSet8_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet8_4.total) <- c("IEXPT","ID","8_4.total.pres","8_4.total.blup","8_4.total.regblup") wscc.gblup.CrossValSet8_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_4.total$IEXPT, wscc.gblup.CrossValSet8_4.total$ID,sep="_") wscc.gblup.CrossValSet8_4.total <- wscc.gblup.CrossValSet8_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet8_5 wscc.gblup.CrossValSet8_5.giv <- wscc.gblup.CrossValSet8_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet8_5.giv) <- c("8_5.giv.blup","IEXPT","ID","8_5.giv.regblup") wscc.gblup.CrossValSet8_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_5.giv$IEXPT, wscc.gblup.CrossValSet8_5.giv$ID,sep="_") wscc.gblup.CrossValSet8_5.giv <- wscc.gblup.CrossValSet8_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_5.ide <- wscc.gblup.CrossValSet8_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet8_5.ide) <- c("8_5.ide.blup","IEXPT","ID","8_5.ide.regblup") wscc.gblup.CrossValSet8_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_5.ide$IEXPT, wscc.gblup.CrossValSet8_5.ide$ID,sep="_") wscc.gblup.CrossValSet8_5.ide <- wscc.gblup.CrossValSet8_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet8_5.total <- wscc.gblup.CrossValSet8_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet8_5.total) <- c("IEXPT","ID","8_5.total.pres","8_5.total.blup","8_5.total.regblup") wscc.gblup.CrossValSet8_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet8_5.total$IEXPT, wscc.gblup.CrossValSet8_5.total$ID,sep="_") wscc.gblup.CrossValSet8_5.total <- wscc.gblup.CrossValSet8_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet8_5.total,by="IEXPT_ID",all=TRUE) # output CrossValSet9_1 wscc.gblup.CrossValSet9_1.giv <- wscc.gblup.CrossValSet9_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet9_1.giv) <- c("9_1.giv.blup","IEXPT","ID","9_1.giv.regblup") wscc.gblup.CrossValSet9_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_1.giv$IEXPT, wscc.gblup.CrossValSet9_1.giv$ID,sep="_") wscc.gblup.CrossValSet9_1.giv <- wscc.gblup.CrossValSet9_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_1.ide <- wscc.gblup.CrossValSet9_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet9_1.ide) <- c("9_1.ide.blup","IEXPT","ID","9_1.ide.regblup") wscc.gblup.CrossValSet9_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_1.ide$IEXPT, wscc.gblup.CrossValSet9_1.ide$ID,sep="_") wscc.gblup.CrossValSet9_1.ide <- wscc.gblup.CrossValSet9_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_1.total <- wscc.gblup.CrossValSet9_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet9_1.total) <- c("IEXPT","ID","9_1.total.pres","9_1.total.blup","9_1.total.regblup") wscc.gblup.CrossValSet9_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_1.total$IEXPT, wscc.gblup.CrossValSet9_1.total$ID,sep="_") wscc.gblup.CrossValSet9_1.total <- wscc.gblup.CrossValSet9_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_1.total,by="IEXPT_ID",all=TRUE) # output CrossValSet9_2 wscc.gblup.CrossValSet9_2.giv <- wscc.gblup.CrossValSet9_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet9_2.giv) <- c("9_2.giv.blup","IEXPT","ID","9_2.giv.regblup") wscc.gblup.CrossValSet9_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_2.giv$IEXPT, wscc.gblup.CrossValSet9_2.giv$ID,sep="_") wscc.gblup.CrossValSet9_2.giv <- wscc.gblup.CrossValSet9_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_2.ide <- wscc.gblup.CrossValSet9_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet9_2.ide) <- c("9_2.ide.blup","IEXPT","ID","9_2.ide.regblup") wscc.gblup.CrossValSet9_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_2.ide$IEXPT, wscc.gblup.CrossValSet9_2.ide$ID,sep="_") wscc.gblup.CrossValSet9_2.ide <- wscc.gblup.CrossValSet9_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_2.total <- wscc.gblup.CrossValSet9_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet9_2.total) <- c("IEXPT","ID","9_2.total.pres","9_2.total.blup","9_2.total.regblup") wscc.gblup.CrossValSet9_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_2.total$IEXPT, wscc.gblup.CrossValSet9_2.total$ID,sep="_") wscc.gblup.CrossValSet9_2.total <- wscc.gblup.CrossValSet9_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet9_3 wscc.gblup.CrossValSet9_3.giv <- wscc.gblup.CrossValSet9_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet9_3.giv) <- c("9_3.giv.blup","IEXPT","ID","9_3.giv.regblup") wscc.gblup.CrossValSet9_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_3.giv$IEXPT, wscc.gblup.CrossValSet9_3.giv$ID,sep="_") wscc.gblup.CrossValSet9_3.giv <- wscc.gblup.CrossValSet9_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_3.ide <- wscc.gblup.CrossValSet9_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet9_3.ide) <- c("9_3.ide.blup","IEXPT","ID","9_3.ide.regblup") wscc.gblup.CrossValSet9_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_3.ide$IEXPT, wscc.gblup.CrossValSet9_3.ide$ID,sep="_") wscc.gblup.CrossValSet9_3.ide <- wscc.gblup.CrossValSet9_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_3.total <- wscc.gblup.CrossValSet9_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet9_3.total) <- c("IEXPT","ID","9_3.total.pres","9_3.total.blup","9_3.total.regblup") wscc.gblup.CrossValSet9_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_3.total$IEXPT, wscc.gblup.CrossValSet9_3.total$ID,sep="_") wscc.gblup.CrossValSet9_3.total <- wscc.gblup.CrossValSet9_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet9_4 wscc.gblup.CrossValSet9_4.giv <- wscc.gblup.CrossValSet9_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet9_4.giv) <- c("9_4.giv.blup","IEXPT","ID","9_4.giv.regblup") wscc.gblup.CrossValSet9_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_4.giv$IEXPT, wscc.gblup.CrossValSet9_4.giv$ID,sep="_") wscc.gblup.CrossValSet9_4.giv <- wscc.gblup.CrossValSet9_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_4.ide <- wscc.gblup.CrossValSet9_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet9_4.ide) <- c("9_4.ide.blup","IEXPT","ID","9_4.ide.regblup") wscc.gblup.CrossValSet9_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_4.ide$IEXPT, wscc.gblup.CrossValSet9_4.ide$ID,sep="_") wscc.gblup.CrossValSet9_4.ide <- wscc.gblup.CrossValSet9_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_4.total <- wscc.gblup.CrossValSet9_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet9_4.total) <- c("IEXPT","ID","9_4.total.pres","9_4.total.blup","9_4.total.regblup") wscc.gblup.CrossValSet9_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_4.total$IEXPT, wscc.gblup.CrossValSet9_4.total$ID,sep="_") wscc.gblup.CrossValSet9_4.total <- wscc.gblup.CrossValSet9_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet9_5 wscc.gblup.CrossValSet9_5.giv <- wscc.gblup.CrossValSet9_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet9_5.giv) <- c("9_5.giv.blup","IEXPT","ID","9_5.giv.regblup") wscc.gblup.CrossValSet9_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_5.giv$IEXPT, wscc.gblup.CrossValSet9_5.giv$ID,sep="_") wscc.gblup.CrossValSet9_5.giv <- wscc.gblup.CrossValSet9_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_5.ide <- wscc.gblup.CrossValSet9_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet9_5.ide) <- c("9_5.ide.blup","IEXPT","ID","9_5.ide.regblup") wscc.gblup.CrossValSet9_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_5.ide$IEXPT, wscc.gblup.CrossValSet9_5.ide$ID,sep="_") wscc.gblup.CrossValSet9_5.ide <- wscc.gblup.CrossValSet9_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet9_5.total <- wscc.gblup.CrossValSet9_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet9_5.total) <- c("IEXPT","ID","9_5.total.pres","9_5.total.blup","9_5.total.regblup") wscc.gblup.CrossValSet9_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet9_5.total$IEXPT, wscc.gblup.CrossValSet9_5.total$ID,sep="_") wscc.gblup.CrossValSet9_5.total <- wscc.gblup.CrossValSet9_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet9_5.total,by="IEXPT_ID",all=TRUE) # output CrossValSet10_1 wscc.gblup.CrossValSet10_1.giv <- wscc.gblup.CrossValSet10_1.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet10_1.giv) <- c("10_1.giv.blup","IEXPT","ID","10_1.giv.regblup") wscc.gblup.CrossValSet10_1.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_1.giv$IEXPT, wscc.gblup.CrossValSet10_1.giv$ID,sep="_") wscc.gblup.CrossValSet10_1.giv <- wscc.gblup.CrossValSet10_1.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_1.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_1.ide <- wscc.gblup.CrossValSet10_1.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet10_1.ide) <- c("10_1.ide.blup","IEXPT","ID","10_1.ide.regblup") wscc.gblup.CrossValSet10_1.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_1.ide$IEXPT, wscc.gblup.CrossValSet10_1.ide$ID,sep="_") wscc.gblup.CrossValSet10_1.ide <- wscc.gblup.CrossValSet10_1.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_1.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_1.total <- wscc.gblup.CrossValSet10_1.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet10_1.total) <- c("IEXPT","ID","10_1.total.pres","10_1.total.blup","10_1.total.regblup") wscc.gblup.CrossValSet10_1.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_1.total$IEXPT, wscc.gblup.CrossValSet10_1.total$ID,sep="_") wscc.gblup.CrossValSet10_1.total <- wscc.gblup.CrossValSet10_1.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_1.total,by="IEXPT_ID",all=TRUE) # output CrossValSet10_2 wscc.gblup.CrossValSet10_2.giv <- wscc.gblup.CrossValSet10_2.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet10_2.giv) <- c("10_2.giv.blup","IEXPT","ID","10_2.giv.regblup") wscc.gblup.CrossValSet10_2.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_2.giv$IEXPT, wscc.gblup.CrossValSet10_2.giv$ID,sep="_") wscc.gblup.CrossValSet10_2.giv <- wscc.gblup.CrossValSet10_2.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_2.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_2.ide <- wscc.gblup.CrossValSet10_2.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet10_2.ide) <- c("10_2.ide.blup","IEXPT","ID","10_2.ide.regblup") wscc.gblup.CrossValSet10_2.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_2.ide$IEXPT, wscc.gblup.CrossValSet10_2.ide$ID,sep="_") wscc.gblup.CrossValSet10_2.ide <- wscc.gblup.CrossValSet10_2.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_2.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_2.total <- wscc.gblup.CrossValSet10_2.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet10_2.total) <- c("IEXPT","ID","10_2.total.pres","10_2.total.blup","10_2.total.regblup") wscc.gblup.CrossValSet10_2.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_2.total$IEXPT, wscc.gblup.CrossValSet10_2.total$ID,sep="_") wscc.gblup.CrossValSet10_2.total <- wscc.gblup.CrossValSet10_2.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_2.total,by="IEXPT_ID",all=TRUE) # output CrossValSet10_3 wscc.gblup.CrossValSet10_3.giv <- wscc.gblup.CrossValSet10_3.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet10_3.giv) <- c("10_3.giv.blup","IEXPT","ID","10_3.giv.regblup") wscc.gblup.CrossValSet10_3.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_3.giv$IEXPT, wscc.gblup.CrossValSet10_3.giv$ID,sep="_") wscc.gblup.CrossValSet10_3.giv <- wscc.gblup.CrossValSet10_3.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_3.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_3.ide <- wscc.gblup.CrossValSet10_3.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet10_3.ide) <- c("10_3.ide.blup","IEXPT","ID","10_3.ide.regblup") wscc.gblup.CrossValSet10_3.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_3.ide$IEXPT, wscc.gblup.CrossValSet10_3.ide$ID,sep="_") wscc.gblup.CrossValSet10_3.ide <- wscc.gblup.CrossValSet10_3.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_3.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_3.total <- wscc.gblup.CrossValSet10_3.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet10_3.total) <- c("IEXPT","ID","10_3.total.pres","10_3.total.blup","10_3.total.regblup") wscc.gblup.CrossValSet10_3.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_3.total$IEXPT, wscc.gblup.CrossValSet10_3.total$ID,sep="_") wscc.gblup.CrossValSet10_3.total <- wscc.gblup.CrossValSet10_3.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_3.total,by="IEXPT_ID",all=TRUE) # output CrossValSet10_4 wscc.gblup.CrossValSet10_4.giv <- wscc.gblup.CrossValSet10_4.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet10_4.giv) <- c("10_4.giv.blup","IEXPT","ID","10_4.giv.regblup") wscc.gblup.CrossValSet10_4.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_4.giv$IEXPT, wscc.gblup.CrossValSet10_4.giv$ID,sep="_") wscc.gblup.CrossValSet10_4.giv <- wscc.gblup.CrossValSet10_4.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_4.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_4.ide <- wscc.gblup.CrossValSet10_4.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet10_4.ide) <- c("10_4.ide.blup","IEXPT","ID","10_4.ide.regblup") wscc.gblup.CrossValSet10_4.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_4.ide$IEXPT, wscc.gblup.CrossValSet10_4.ide$ID,sep="_") wscc.gblup.CrossValSet10_4.ide <- wscc.gblup.CrossValSet10_4.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_4.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_4.total <- wscc.gblup.CrossValSet10_4.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet10_4.total) <- c("IEXPT","ID","10_4.total.pres","10_4.total.blup","10_4.total.regblup") wscc.gblup.CrossValSet10_4.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_4.total$IEXPT, wscc.gblup.CrossValSet10_4.total$ID,sep="_") wscc.gblup.CrossValSet10_4.total <- wscc.gblup.CrossValSet10_4.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_4.total,by="IEXPT_ID",all=TRUE) # output CrossValSet10_5 wscc.gblup.CrossValSet10_5.giv <- wscc.gblup.CrossValSet10_5.sum$blups$"fa(IEXPT, 2):giv(ID)"$blups colnames(wscc.gblup.CrossValSet10_5.giv) <- c("10_5.giv.blup","IEXPT","ID","10_5.giv.regblup") wscc.gblup.CrossValSet10_5.giv$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_5.giv$IEXPT, wscc.gblup.CrossValSet10_5.giv$ID,sep="_") wscc.gblup.CrossValSet10_5.giv <- wscc.gblup.CrossValSet10_5.giv[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_5.giv,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_5.ide <- wscc.gblup.CrossValSet10_5.sum$blups$"fa(IEXPT, 2):ide(ID)"$blups colnames(wscc.gblup.CrossValSet10_5.ide) <- c("10_5.ide.blup","IEXPT","ID","10_5.ide.regblup") wscc.gblup.CrossValSet10_5.ide$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_5.ide$IEXPT, wscc.gblup.CrossValSet10_5.ide$ID,sep="_") wscc.gblup.CrossValSet10_5.ide <- wscc.gblup.CrossValSet10_5.ide[,-c(2,3)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_5.ide,by="IEXPT_ID",all=TRUE) # wscc.gblup.CrossValSet10_5.total <- wscc.gblup.CrossValSet10_5.sum$blups$"IEXPT:ID-total"$blups.inmet colnames(wscc.gblup.CrossValSet10_5.total) <- c("IEXPT","ID","10_5.total.pres","10_5.total.blup","10_5.total.regblup") wscc.gblup.CrossValSet10_5.total$IEXPT_ID <- paste(wscc.gblup.CrossValSet10_5.total$IEXPT, wscc.gblup.CrossValSet10_5.total$ID,sep="_") wscc.gblup.CrossValSet10_5.total <- wscc.gblup.CrossValSet10_5.total[,-c(1,2)] IEXPT_ID <- merge(IEXPT_ID,wscc.gblup.CrossValSet10_5.total,by="IEXPT_ID",all=TRUE) ######################################################### # write IEXPT_ID to file as that has all the cross val data in it: head(IEXPT_ID) dim(IEXPT_ID) write.csv(IEXPT_ID,"wscc.am.gblup.cross.val.blups.combined.csv") #########################################################