> > Hi All: > > I am using R to calculate exact 95% confidence interval using Clopper > Pearson method. I am using the following code but it seems to get into a > loop and not get out of it, it goes on forever although I am looping it > only 10 times across 63 sites with 10 observations per site. I was hoping > to get some help. > > Thanks >Anamika> set.seed(111) #so that you can regenerate the same values > # another time if you need to > k<-63 > n<-10 > x<-NULL > eta<-rnorm(63,-0.085,.990) # generating data using Binomial Logit Normal > p<-exp(eta)/(1+exp(eta)) > for(i in 1:k) > x<-cbind(x,rbinom(10,n,p[i])) > > rate<-t(t(x)/n) > > # Exact Confidence Interval > > for (i in 1:10){ > > for (j in 1:63) > { > > if (x==0) > { > l_cl_exact<-0 > u_cl_exact<-qbeta(.975,x+1,n-x) > } > else if (x==n) > { > l_cl_exact<-qbeta(.025,x,n-x+1) > u_cl_exact<-1 > } > else > l_cl_exact<-qbeta(.025,x,n-x+1) > u_cl_exact<-qbeta(.975,x+1,n-x) > > } > }_____________________________________________ > 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<http://www.r-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
On Mar 7, 2012, at 3:35 PM, Anamika Chaudhuri wrote:>> >> Hi All: >> >> I am using R to calculate exact 95% confidence interval using Clopper >> Pearson method. I am using the following code but it seems to get >> into a >> loop and not get out of it, it goes on forever although I am >> looping it >> only 10 times across 63 sites with 10 observations per site. I was >> hoping >> to get some help.?binom.test # returns Clopper-Pearson intervals Laura A. Thompson's excellent "S-PLUS (and R) Manual to Accompany Agresti?s Categorical Data Analysis (2002) , 2nd edition" 2007? cites several other methods. It's easy to access this resource with a web search since Agresti cites it and Google searches generaly bring it up as the first hit. -- David.>> >> Thanks >> > Anamika > >> set.seed(111) #so that you can regenerate the same values >> # another time if you need to >> k<-63 >> n<-10 >> x<-NULL >> eta<-rnorm(63,-0.085,.990) # generating data using Binomial Logit >> Normal >> p<-exp(eta)/(1+exp(eta)) >> for(i in 1:k) >> x<-cbind(x,rbinom(10,n,p[i])) >> >> rate<-t(t(x)/n) >> >> # Exact Confidence Interval >> >> for (i in 1:10){ >> >> for (j in 1:63) >> { >> >> if (x==0) >> { >> l_cl_exact<-0 >> u_cl_exact<-qbeta(.975,x+1,n-x) >> } >> else if (x==n) >> { >> l_cl_exact<-qbeta(.025,x,n-x+1) >> u_cl_exact<-1 >> } >> else >> l_cl_exact<-qbeta(.025,x,n-x+1) >> u_cl_exact<-qbeta(.975,x+1,n-x) >> >> } >> }_____________________________________________ >> R-help at 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<http://www.r-project.org/posting-guide.html >> > >> and provide commented, minimal, self-contained, reproducible code. >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.David Winsemius, MD West Hartford, CT
Hello, Anamika Chaudhuri-2 wrote> >> >> Hi All: >> >> I am using R to calculate exact 95% confidence interval using Clopper >> Pearson method. I am using the following code but it seems to get into a >> loop and not get out of it, it goes on forever although I am looping it >> only 10 times across 63 sites with 10 observations per site. I was hoping >> to get some help. >> >> Thanks >> > Anamika > >> set.seed(111) #so that you can regenerate the same values >> # another time if you need to >> k<-63 >> n<-10 >> x<-NULL >> eta<-rnorm(63,-0.085,.990) # generating data using Binomial Logit Normal >> p<-exp(eta)/(1+exp(eta)) >> for(i in 1:k) >> x<-cbind(x,rbinom(10,n,p[i])) >> >> rate<-t(t(x)/n) >> >> # Exact Confidence Interval >> >> for (i in 1:10){ >> >> for (j in 1:63) >> { >> >> if (x==0) >> { >> l_cl_exact<-0 >> u_cl_exact<-qbeta(.975,x+1,n-x) >> } >> else if (x==n) >> { >> l_cl_exact<-qbeta(.025,x,n-x+1) >> u_cl_exact<-1 >> } >> else >> l_cl_exact<-qbeta(.025,x,n-x+1) >> u_cl_exact<-qbeta(.975,x+1,n-x) >> >> } >> }_____________________________________________ >> R-help@ mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html> >> and provide commented, minimal, self-contained, reproducible code. >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@ 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. >See package 'binom'. Function 'binom.confint' gives a choice of 8 different methods, Clopper-Pearson is the 'exact', and function 'binom.test' also uses it. Hope this helps, Rui Barradas -- View this message in context: http://r.789695.n4.nabble.com/Exact-Confidence-Interval-tp4454603p4455178.html Sent from the R help mailing list archive at Nabble.com.