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AFEchidna包可以运行1个或多个非正态分布变量的多性状模型,简单示例如下:
- 仅1个非正态分布变量
单性状:
res11<-echidna(es0.file="dfm2.es0",
fixed=dis~1+Rep,
random=~Mum,
family=esr_binomial())
运行结果:
> res11<-echidna(es0.file="dfm2.es0",
+ fixed=dis~1+Rep,
+ random=~Mum,
+ family=esr_binomial())
Running Echidna for analysis: dis !binomial !probit
Wed Aug 11 21:51:04 2021
Iteration LogL eSigma NEDF
1 1 -424.14 0.9763 554
2 2 -421.41 0.9800 554
3 3 -418.93 0.9858 554
4 4 -418.98 0.9855 554
5 5 -418.99 0.9855 554
6 6 -418.99 0.9855 554
Wed Aug 11 21:51:04 2021 LogL Converged
> Var(res11)
Term Sigma SE Z.ratio
1 Residual 0.985460 0.062299 15.818231
2 Mum 0.048413 0.040492 1.195619
双性状:
res12<-echidna(es0.file="dfm2.es0",
fixed=cbind(h5,lt)~Trait+Trait:Rep,
random=~us(Trait):Mum,
residual= ~units:us(Trait),
mulT=T,
family=c(esr_gaussian(),esr_binomial()))
运行结果:
> res12<-echidna(es0.file="dfm2.es0",
+ fixed=cbind(h5,lt)~Trait+Trait:Rep,
+ random=~us(Trait):Mum,
+ residual= ~units:us(Trait),
+ mulT=T,
+ family=c(esr_gaussian(),esr_binomial()))
Running Echidna for analysis: h5 lt !binomial !probit
Wed Aug 11 21:54:00 2021
Iteration LogL NEDF
1 1 -2520.08 1105
2 2 -2269.22 1105
3 3 -2100.84 1105
4 4 -2077.23 1105
5 5 -2082.81 1105
6 6 -2084.85 1105
7 7 -2084.81 1105
8 8 -2084.81 1105
Wed Aug 11 21:54:01 2021 LogL Converged
> Var(res12)
Term Sigma SE Z.ratio
1 Residual 1.00000 0.000000 Inf
2 us(Trait):Mum;us(Trait) 4.38440 1.862800 2.3536612
3 us(Trait):Mum;us(Trait) -0.23360 0.198340 -1.1777755
4 us(Trait):Mum;us(Trait) 0.05461 0.040974 1.3327964
5 units:us(Trait);us(Trait) 53.35500 3.373600 15.8154494
6 units:us(Trait);us(Trait) -0.29465 0.313050 -0.9412234
7 units:us(Trait);us(Trait) 1.00380 0.063915 15.7052335
- 2个非正态分布变量
示例代码:
res13<-echidna(es0.file="dfm2.es0",
fixed=cbind(dis,lt)~Trait+Trait:Rep,
random=~us(Trait):Mum,
residual= ~units:us(Trait),
mulT=T,
family=c(esr_binomial(),esr_binomial()))
运行结果:
> res13<-echidna(es0.file="dfm2.es0",
+ fixed=cbind(dis,lt)~Trait+Trait:Rep,
+ random=~us(Trait):Mum,
+ residual = ~units:us(Trait),
+ mulT=T,
+ family=c(esr_binomial(),esr_binomial()))
Running Echidna for analysis: dis !binomial !probit lt !binomial !probit
Wed Aug 11 21:52:56 2021
Iteration LogL NEDF
1 1 -1518.66 1108
2 2 -1181.84 1108
3 3 -891.98 1108
4 4 -824.48 1108
5 5 -833.78 1108
6 6 -838.83 1108
7 7 -838.75 1108
8 8 -838.73 1108
9 9 -838.73 1108
Wed Aug 11 21:52:57 2021 LogL Converged
> Var(res13)
Term Sigma SE Z.ratio
1 Residual 1.0000000 0.000000 Inf
2 us(Trait):Mum;us(Trait) 0.0456910 0.040544 1.1269485
3 us(Trait):Mum;us(Trait) 0.0044974 0.028819 0.1560568
4 us(Trait):Mum;us(Trait) 0.0559140 0.041292 1.3541122
5 units:us(Trait);us(Trait) 1.0044000 0.064116 15.6653565
6 units:us(Trait);us(Trait) -0.0328440 0.045304 -0.7249691
7 units:us(Trait);us(Trait) 1.0030000 0.063919 15.6917349
AFEchidna包免费对外开放,仅用于学术研究,不可用于商业研究,否则造成的后果自负。。
感兴趣者,可发邮件到yzhlinscau@163.com免费索取程序包。
参考文献:
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.
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