batch1: Run batch analysis for single trait in breedR

In yzhlinscau/breedRPlus: Augments the Use of 'breedR' in Fitting Mixed Models

Description

batch1 This function carries out batch analysis for mult-trait with same model and also output heritability etc. in breedR package.

Usage

batch1(data, FMod, RMod = NULL, geneticM = NULL, SpM = NULL,
  pformula = NULL)

Arguments

data	aim dataset
FMod	Fixed mode,should be 'y~1+fixed.factors'.
RMod	Randomed mode, should be '~random.factors'.
geneticM	Randomed terms for tree model, details see example.
SpM	Spatial error terms. details see example.
pformula	formula for h2 (or corr).

Details

breedR batch analysis

Value

the result is returned directly.

Author(s)

Yuanzhen Lin <[e-mail]>

References

breedRPlus website:https://github.com/yzhlinscau/

Examples

library(breedR)
library(breedRPlus)
library(tidyr)

data(douglas)
S3<-subset(douglas,site=='s3')
#summary(S3);str(S3)

S3a<-filter(S3,is.na(dad)) # hs
S3a<-transform(S3a,Mum=factor(mum))
S3a<-droplevels(S3a)
names(S3a)[7:8]<-c('x1','y1')

df<-tidyr::gather(S3a,key=Trait,y,c(-1:-8,-12,-14:-16))
#str(df)


# for parent model
fixed = y ~ 1+orig
random1=~Mum+block
pformula1=h2~4*V1/(V1+V3)

mm<-plyr::ddply(df,'Trait',
    function(dat) batch1(dat,FMod=fixed,
                             RMod=random1,
                             pformula=pformula1)
                             )
#result                             
mm                      

# for tree model
random2=~block
genetic=list(model = 'add_animal',
             pedigree = S3a[,1:3],
             id = 'self')
pformula2=h2~V2/(V2+V3)

mm1<-plyr::ddply(df,'Trait',
    function(dat) batch1(dat,FMod=fixed,
                             RMod=random2,
                             geneticM=genetic,
                             pformula=pformula2)
                             )

#result                             
mm1

  

yzhlinscau/breedRPlus documentation built on May 10, 2019, 1:54 a.m.