引子：

 本人于2019年主译出版的《动植物育种遗传数据分析》，原书主要使用ASReml进行分析。本博客将陆续演示使用AFEchidna包达到类似ASReml的结果。

第一章的代码如下：

// chapter one

library(AFEchidna)

get.es0.file(dat.file='pine_provenance.csv') # .es file

get.es0.file(es.file='pine_provenance.es',pedS=1) # .es0 file

# file.edit('pine_provenance.es0')

HT <- echidna(height ~ 1+Prov, 

             random = ~ Female*Block,

             residual=~units,

             es0.file = 'pine_provenance.es0' ) 

names(HT)

HT$Version

Var(HT)

# wald(HT)

waldT(HT)

HT$Converge

HT$LogLikelihood

# gets AIC and BIC for a model

IC(HT)

# fixed effects

coef(HT)$fixed

# random effects

bv<-coef(HT)$random

nrow(bv)

bv[1:10,]

tail(bv)

# Block bv

library(dplyr)

bv %>% filter(Term=='Block')

# Female bv

bv %>% filter(Term=='Female') %>% head

# Female:Block bv

bv %>% filter(Term=='Female:Block') %>% head

plot(HT)

## variance component and heritability

Var(HT)

## Linear Combinations of Variance Components

pin(HT)

pin(HT,mulp=c(Va~4*V3,

              VP~V1+V3+V4,

              H2i~4*V3/(V1+V3+V4)))

### TABULATE

library(dplyr)

pine_prov %>% group_by(Prov) %>% dplyr::select(height) %>%

  summarise(Mean=mean(height,na.rm=T),

            SD=sd(height,na.rm=T),

            Min=min(height,na.rm=T),

            Max=max(height,na.rm=T),

            Count=n()

  )

### prediction

#predict prov levels

HT1<-update(HT,predict="Prov")

HTprov_pred <- predict(HT1) 

predict.prov <- HTprov_pred$pred

predict.prov

HTprov_pred$ased

# Not adjusted for prov effect

HT2<-update(HT,predict="Female")

HTprov_female <- predict(HT2) 

predict.female <- HTprov_female$pred 

head(predict.female$pred1)

HTprov_female$ased

# adjusted for prov effect

HT3<-update(HT,predict="Prov Female !present Prov Female")

HTprov_fem.prov <- predict(HT3)

#includes non-estimable combinations

all_fem.prov<-HTprov_fem.prov$pred$pred1

head(all_fem.prov[,1:5])

#tail(all_fem.prov[,1:5])

## batch analysis, similar to !cycle for win Version

tba<-update(HT,trait=~height+diameter+volume,

            batch=TRUE)

Var(tba)

参考文献

1 . Zhang WH, Wei RY, Liu Y, Lin YZ. AFEchidna is a R package for genetic evaluation of plant and animal breeding datasets. BioRxiv. DOI: 10.1101/2021.06.24.449740.

2. 林元震 丁昌俊 主译，动植物育种遗传数据分析, 科学出版社，2019.9

博文首发链接：https://blog.csdn.net/yzhlinscau/article/details/124202572