Description Usage Arguments Details Value Author(s) References Examples
pin
This function counts standard error(se) for heritability(h2) and
corr value and also outputs significent level for corr value in asreml and breedR package.
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object |
asreml or breedR results. |
formula |
formula for h2 or corr. |
asrV |
Index for asreml version, 3(default),or 4(new version). |
signif |
Index to output signif levels, F(default) for non-signif. |
corN |
Number of corr, 1(default). |
Rdf |
Index to output results to vector, F(default) for non-vector output. |
digit |
Index for decimal number, 3(default). |
vres |
Index(T) to return results in vectors, F(default) for direct results. |
Count error for h2 and corr value, also outputs significent level.
the result is returned directly.
Yuanzhen Lin <yzhlinscau@163.com>
Yuanzhen Lin. R & ASReml-R Statistics. China Forestry Publishing House. 2016 AAFMM website:https://github.com/yzhlinscau/AAFMM
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## working for breedR package
library(breedR)
library(AAFMM)
data(globulus)
res.animal <- remlf90(fixed = phe_X ~ 1,
random = ~ gg,
genetic = list(model = 'add_animal',
pedigree = globulus[, 1:3],
id = 'self'),
data = globulus)
pin(res.animal,h2~V2/(V1+V2+V3))
## End(Not run)
## Not run:
## working for asreml or asreml4 package
library(AAFMM)
data(PrSpa)
df<-PrSpa
## when works for ASReml-R V3.0
library(asreml) # V3.0
# exmaple 1.1 single trait model
fm1<-asreml(h5~1+Rep, random=~Fam,
subset=Spacing=='3',data=df)
summary(fm)$varcomp[,1:3]
pin(fm1, h2 ~4*V1/(V1+V2))
pin(fm1, h2 ~4*V1/(V1+V2),Rdf=TRUE)
# exmaple 1.2 us model
fm2<-asreml(cbind(dj,h5)~ trait+trait:Rep,
random=~ us(trait):Fam,
rcov=~units:us(trait),
subset=Spacing=='3',data=df,maxit=40)
summary(fm2)$varcomp[,1:3]
pin(fm2, h2_A ~ 4 * V1/(V1+V5)) # heritability for trait A
pin(fm2, h2_B ~ 4 * V3/(V3+V7)) # heritability for trait B
# genetic corr
pin(fm2, gCORR ~ V2/sqrt(V1*V3),signif=TRUE)
# phenotype corr
pin(fm2, pCORR ~ (V2+V6)/sqrt((V1+V5)*(V3+V7)),signif=TRUE)
# exmaple 1.3 corr model
fm3<-asreml(cbind(dj,h3,h5)~ trait+trait:Rep,
random=~ corgh(trait):Fam,
rcov=~units:us(trait),
subset=Spacing=='3',data=df,maxit=40)
summary(fm3)$varcomp[,1:3]
pin(fm3,corN=3)
## when works for ASReml-R V4.0
library(asreml4)
# exmaple 2.1 single trait model, default gamma parameterization.
fm1b<-asreml(h5~1+Rep, random=~Fam, subset=Spacing=='3',data=df)
summary(fm)$varcomp[,1:3]
pin(fm1b, h2 ~4*V1/(V1+V2),asrV=4)
pin4(fm1b, h2 ~4*V1/(V1+V2)) # same results, but with pin4()
# The same model with fm1b, but with sigma parameterization.
fm1c<-asreml(h5~1+Rep, random=~Fam,
residual=~idv(units),
subset=Spacing=='3',data=df)
summary(fm1c)$varcomp[,1:3]
pin(fm1c, h2 ~4*V1/(V1+V3),asrV=4)
pin4(fm1c, h2 ~4*V1/(V1+V3))
# exmaple 2.2 us model
fm2b<-asreml(cbind(h3,h5)~ trait+trait:Rep,
random=~ us(trait):Fam,
residual=~units:us(trait),
subset=Spacing=='3',data=df,maxit=40)
summary(fm2b)$varcomp[,1:3]
# heritability for trait A
pin(fm2b, h2_A ~ 4 * V1/(V1+V5),asrV=4)
pin4(fm2b, h2_A ~ 4 * V1/(V1+V5))
# heritability for trait B
pin(fm2b, h2_B ~ 4 * V3/(V3+V7),asrV=4)
pin4(fm2b, h2_B ~ 4 * V3/(V3+V7))
# genetic corr
pin(fm2b, gCORR ~ V2/sqrt(V1*V3),signif=TRUE,asrV=4)
pin4(fm2b, gCORR ~ V2/sqrt(V1*V3),signif=TRUE)
# phenotype corr
pin(fm2b, pCORR ~ (V2+V6)/sqrt((V1+V5)*(V3+V7)),signif=TRUE,asrV=4)
pin4(fm2b, pCORR ~ (V2+V6)/sqrt((V1+V5)*(V3+V7)),signif=TRUE)
# exmaple 2.3 corr model
fm3b<-asreml(cbind(h3,h4,h5)~ trait+trait:Rep,
random=~ corgh(trait):Fam,
residual=~units:us(trait),
subset=Spacing=='3',data=df,maxit=40)
summary(fm3b)$varcomp[,1:3]
pin(fm3b,corN=3,asrV=4)
pin4(fm3b,corN=3)
## End(Not run)
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