asreml.batch: ASReml-R batch analysis

In dengfei2013/learnasreml: The package is to help learn the asreml

ASReml-R batch analysis

Description

This function carries out batch analysis for mult-trait with same model and also output heritability etc. in ASReml-R package.

Usage

asreml.batch(data, factorN, traitN, FMod = NULL, RMod = NULL, EMod = NULL,
  mulT = NULL, mulN = NULL, mulR = NULL, corM = NULL, corMout = FALSE,
  pformula = NULL, pformula1 = NULL, pformula2 = NULL, pformula3 = NULL,
  pformula4 = NULL, maxit = NULL, ped = NULL, pedinv = NULL,
  ginverse = NULL)

Arguments

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.

References

Yuanzhen Lin, Xiaoyang Chen. R & ASReml-R Statistical Analysis Tutorial. China Forestry Publishing House. 2014

Examples

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)))
        

dengfei2013/learnasreml documentation built on Oct. 25, 2024, 7 a.m.