##
## demo file for asreml.batch().
##
library(asreml)
library(AAfun)
##### example I for dataset without pedigree
data(PrSpa)
df<-PrSpa
# exmaple 1.1 for sigle trait model
df1=subset(df,Spacing==3)
asreml.batch(data=df1,factorN=1:5,traitN=c(9:13),
FMod=y~1+Rep+Plot,RMod=~Fam,
pformula=h2 ~ 4 * V1/(V1+V2))
# exmaple 1.2 for us model
asreml.batch(data=df1,factorN=1:5,traitN=c(10:13),
FMod=cbind(y1,y2)~trait+trait:Rep,
RMod=~us(trait):Fam,
EMod=~units:us(trait),
mulT=TRUE,mulN=2,mulR=TRUE,corMout=T,
pformula=r.g ~ V2/sqrt(V1*V3),
pformula1=h2.A ~ 4*V1/(V1+V5),
pformula2=h2.B ~ 4*V3/sqrt(V3+V7))
# exmaple 1.3 for corr model
asreml.batch(data=df1,factorN=1:5,traitN=c(10:13),
FMod=cbind(y1,y2,y3)~trait+trait:Rep,
RMod=~corgh(trait):Fam,
EMod=~units:us(trait), maxit=30,
mulT=TRUE,mulN=3,mulR=TRUE,corM=TRUE)
##### example II for dataset with pedigree
data(dfm2);df=dfm2
ped<-df[,1:3]
pedinv<-asreml.Ainverse(ped)$ginv
df1=subset(df,Spacing==3)
# example 2.1 sigle trait model
asreml.batch(data=df1,factorN=1:6,traitN=c(7:14),
FMod=y~1+Rep,RMod=~ped(TreeID),
ped=T,pedinv=pedinv,
ginverse=list(TreeID=pedinv),
pformula=h2 ~ V1/(V1+V2))
# exmaple 2.2 us model
asreml.batch(data=df1,factorN=1:6,traitN=c(10:14),
FMod=cbind(y1,y2)~trait+trait:Rep,
RMod=~us(trait):ped(TreeID),
EMod=~units:us(trait),maxit=40,
mulT=TRUE,mulN=2,mulR=TRUE,corMout=F,
ped=T,pedinv=pedinv,
ginverse=list(TreeID=pedinv),
pformula=r.g ~ V2/sqrt(V1*V3),
pformula1=h2.A ~ V1/(V1+V5),
pformula2=h2.B ~ V3/(V3+V7))
# exmaple 2.3 corr model
asreml.batch(data=df1,factorN=1:6,traitN=c(10:14),
FMod=cbind(y1,y2)~trait+trait:Rep,
RMod=~corgh(trait):ped(TreeID),
EMod=~units:us(trait),maxit=40,
mulT=TRUE,mulN=2,corM=TRUE,
ped=T,pedinv=pedinv,
ginverse=list(TreeID=pedinv))
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