Description Usage Arguments References Examples
This function carries out batch analysis for mult-trait with same model and also output heritability etc. in ASReml-R package.
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data |
The data in use. |
factorN |
A vector with sites of all factors. |
traitN |
A vector with sites of all traits. |
FMod |
Fixed mode. |
RMod |
Randomed variance structure. |
EMod |
Error variance structure for multi-trait model. |
mulT |
Value "T" or "TRUE" for multi-trait model, "F"(default). |
mulN |
Number of trait for one model in multi-trait analysis,2(default). |
mulR |
Value "T" or "TRUE" to count corr/error matrix, only works for bitrait, "F"(default). |
corM |
Value "T" or "TRUE" for corr model, "F"(default). |
corMout |
Value "T" or "TRUE" to output corr matrix, "F"(default). |
pformula |
Formula for h2 or corr. |
pformula1 |
Formula for h2 or corr. |
maxit |
Maximum number of iterations. |
ped |
Value "T" or "TRUE" for animal model with pedigree, "F"(default). |
pedinv |
A G-inverse matrix for pedigree from ASReml.Ainverse(). |
ginverse |
a named list with each component identifying a G-inverse matrix. |
Yuanzhen Lin, Xiaoyang Chen. R & ASReml-R Statistical Analysis Tutorial. China Forestry Publishing House. 2014
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | library(asreml)
library(vsnc)
data(fm)
head(fm)
# Single trait, no pedigree, batch analysis
asreml.batch(data=fm, factorN=1:5, traitN=6:13,
FMod = y ~ Rep + Plot, RMod =~ Fam,
pformula = h2 ~ 4*V1/(V1+V2))
# Two trait, no pedigree, batch analysis
asreml.batch(data=fm,factorN=1:5,traitN=c(10:12),
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/(V3+V7))
# Single trait, pedigree, batch analysis
data("BTdata")
data("BTped")
head(BTdata)
head(BTped)
ainv <- asreml.Ainverse(BTped)$ginv
asreml.batch(data=BTdata,factorN=c(3:5,7),traitN=c(1:2),
FMod=y~1+sex,RMod=~ped(animal),
ped=T,pedinv=ainv,ginverse=list(animal=ainv),
pformula=h2 ~ V1/(V1+V2))
# Bivariate, pedigree, batch analysis
asreml.batch(data=BTdata,factorN=c(3:5,7),traitN=c(1:2),
FMod=cbind(y1,y2)~trait+trait:sex,RMod=~us(trait):ped(animal),
EMod=~units:us(trait),mulT=TRUE,mulN=2,
ped=T,pedinv=ainv,ginverse=list(animal=ainv),
pformula = hy1 ~ V1/(V1+V5),
pformula1 = hy2 ~ V3/(V3+V7),
pformula2 = hgr ~ V2/sqrt((V1*V3)))
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