Your code is still not runnable.
It gives the error message
Error in fitglm(0.05, 1) : could not find function "prediction"
Berend
On 25-10-2012, at 21:55, Adel Powell wrote:
> I think I have corrected it. Can you tell me are my spec and sens values
> correct
> n <- 1000; # Sample size
>
> fitglm <- function(sigma,tau){
> x <- rnorm(n,0,sigma)
> intercept <- 0
> beta <- 0
> ystar <- intercept+beta*x
> z <- rbinom(n,1,plogis(ystar))
> xerr <- x + rnorm(n,0,tau)
> model<-glm(z ~ xerr, family=binomial(logit))
> int<-coef(model)[1]
> slope<-coef(model)[2]
> pred<-predict(model)
>
> result<-ifelse(pred>.5,1,0)
>
> accuracy<-length(which(result==z))/length(z)
> accuracy
>
> rocpreds<-prediction(result,z)
> auc<-performance(rocpreds,"auc")@y.values
> fp<-performance(rocpreds,"sens")
> sentiv<-slot(fp,"y.values")[[1]]
> sentiv<-sentiv[2]
> sentiv
> fp2<-performance(rocpreds,"spec")
> specs<-slot(fp2,"y.values")[[1]]
> specs<-specs[2]
> specs
> output<-c(int,slope,.5,accuracy,auc,sentiv,specs)
>
> names(output)<-c("Intercept","Slope","CutPoint","Accuracy","AUC","Sentivity","Specificity")
> return(output)
>
> }
>
> y<-fitglm(.05,1)
> y
>
>
> On Thu, Oct 25, 2012 at 3:43 PM, Berend Hasselman <b...@xs4all.nl> wrote:
>
> On 25-10-2012, at 21:28, Adel Powell wrote:
>
> > I am running my code in a loop and it does not work but when I run it
> > outside the loop I get the values I want.
> >
> > n <- 1000; # Sample size
> >
> > fitglm <- function(sigma,tau){
> > x <- rnorm(n,0,sigma)
> > intercept <- 0
> > beta <- 0
> > ystar <- intercept+beta*x
> > z <- rbinom(n,1,plogis(ystar))
> > xerr <- x + rnorm(n,0,tau)
> > model<-glm(z ~ xerr, family=binomial(logit))
> > int<-coef(model)[1]
> > slope<-coef(model)[2]
> > pred<-predict(model)
> >
> > result<-ifelse(pred>.5,1,0)
> >
> > accuracy<-length(which(result==z))/length(z)
> > accuracy
> >
> > rocpreds<-prediction(result,z)
> > auc<-performance(rocpreds,"auc")@y.values
> > sentiv<-performance(rocpreds,"sens")@y.values
> > sentiv<-slot(fp,"y.values")[[1]]
> > sentiv<-sentiv[2]
> > sentiv
> > specs<-performance(rocpreds,"spec")@y.values
> > specs<-slot(fp2,"y.values")[[1]]
> > specs<-specs[2]
> > specs
> > output<-c(int,slope,.5,accuracy,auc,sentiv,specs)
> >
> > names(output)<-c("Intercept","Slope","CutPoint","Accuracy","AUC","Sentivity",Specificity")
>
> A missing " before Specificity?
>
> > return(output)
> >
> > }
> >
> > y<-fitglm(.05,1)
> > y
> >
>
> Running this after correction of the missing " one gets en error
>
> Error in fitglm(0.05, 1) : could not find function "prediction"
>
> How are you using a loop?
> Your example is not reproducible.
>
> Berend
>
>
> >
> > The code runs without the sentiv and specs but when I remove the loop i can
> > get the sensitivity and spec. values ???
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>
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