[R] r question

[Rui Barradas]

Hello,

There's a paenthesis missing in

 > relativerisk<- matrix(log(c(1,1,2,2),ncol=4,byrow = TRUE)
+ beta_true<-relativerisk
Error: unexpected symbol in:
"relativerisk<- matrix(log(c(1,1,2,2),ncol=4,byrow = TRUE)
beta_true"

The correct instruction would be

relativerisk<- matrix(log(c(1,1,2,2)),ncol=4,byrow = TRUE)

And there's an error in your matrix multiply.

 > Ti=exp(x_true%*%beta_true)*ei
Error in x_true %*% beta_true : non-conformable arguments

It can be corrected if you transpose beta_true.

Ti=exp(x_true %*% t(beta_true))*ei

At this point I've stoped running your code, I believe you must revise 
it and try to see what's wrong instruction by instruction. Do that and 
post again.
ALso, get rid of the <<-, use <-
If you do this, I'll explain the difference in the next answer to your 
doubts.

Hope this helps,

Rui Barradas


Em 22-03-2017 08:11, 謝孟珂 escreveu:
> Hi ,I have some question about simulate, I don't know how to paste question
> to this website,so I paste below.
> I use genoud to find the maximum likelihood value, but when I use numcut=3
> ,it will get error message,like this " coxph.wtest(fit$var[nabeta, nabeta],
> temp, control$toler.chol) : NA/NaN/Inf"
> and this is my code
> library(rgenoud)
> library(survival)
> N=500
> ei=rexp(N)
> censor=rep(1,N)
> x1=runif(N)
> x2=runif(N)
> x3=runif(N)
> truecut=c(0.3,0.6)
> dum1=1*(x1>truecut[1] & x1<truecut[2])
> dum2=1*(x1>truecut[2])
> x_true=cbind(dum1,dum2,x2,x3)
> relativerisk<- matrix(log(c(1,1,2,2),ncol=4,byrow = TRUE)
> beta_true<-relativerisk
> Ti=exp(x_true%*%beta_true)*ei
> confound=cbind(x2,x3)
> initial2<-c(0.09,0.299,0.597,-0.17,-1.3,-3.1,-1.4,-1.12)
> numcut=2
>   domain2<<-matrix(c(rep(c(0.05,0.95),numcut),rep(c(0,5),numcut+dim(confound)[2])),ncol=2,byrow
> = TRUE)
>
> loglikfun <- function(beta, formula) {
>    beta1 <- coxph(formula, init = beta,
> control=list('iter.max'=0))#iteration is zero
>    return(beta1$loglik[2])
> }
> obj <- function(xx){
>    cutoff <- xx[1:numcut_global] #cutpoint
>    cut_design <-
> cut(target_global,breaks=c(0,sort(cutoff)+seq(0,gap_global*(length(cutoff)-1),by=gap_global),target_max),quantile=FALSE,labels=c(0:numcut_global))
>    beta <- -xx[(numcut+1):nvars]  #coefficients of parameters
>    logliks <-
> loglikfun(beta,Surv(time_global,censor_global)~cut_design+confound_global)
>    return(logliks)
> }
> maxloglik<-function(target,numcut,time,censor,confound,domain2,initial2,gap){
>    time_global<<-time
>    censor_global<<-censor
>    target_global<<-target
>    nvars<<-2*numcut+dim(confound)[2]
>    confound_global<<-confound
>    numcut_global<<-numcut
>    target_max<<-max(target)
>    gap_global<<-gap
>    ccc<-genoud(obj, nvars, max=TRUE, pop.size=100, max.generations=6,
> wait.generations=10,
>                hard.generation.limit=TRUE, starting.values=initial2,
> MemoryMatrix=TRUE,
>                Domains=domain2, solution.tolerance=0.001,
>                gr=NULL, boundary.enforcement=2, lexical=FALSE,
> gradient.check=TRUE)
>    ccc$par_corr<-ccc$par #the coefficients of genoud
>
> ccc$par_corr[1:numcut]<-sort(ccc$par[1:numcut])+seq(0,gap_global*(numcut-1),by=gap_global)
> #sort cutpoint
>    return(ccc)
> }
>
>
> maxloglik(x1,3,Ti,censor,confound,domain2,initial2,0.02)$par_corr
>
> I have no idea about the error ,maybe is my initial is wrong.
> thank you
>   From Meng-Ke
>
> 	[[alternative HTML version deleted]]
>
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