Thanks for the response, I should have clarified that the NOEL is the smallest dose above which there is a statistically significant effect.
On Tue, Apr 3, 2012 at 12:44 PM, Drew Tyre <aty...@unl.edu> wrote: > Is this the smallest observed dose that has an effect? If so, then you > don't need the glm to find it. Here is a simulated example: > > set.seed(101) > X = rep(1:10,each=10) > lp = -5 + 0.5*X > Y = rbinom(length(X),size=1,p=1/(1+exp(-lp))) > # is this the NOEL? > min(X[Y==1]) # picks out observations with adverse effects, chooses the > smallest value > glmfit = glm(Y~X,family=binomial) > plot(1:10, predict(glmfit,newdata=data.frame(X=1:10),type="response"), > type="l",ylim=c(0,1),xlab="X",ylab="Y") > rug(jitter(X[Y==0]),side=1) > rug(jitter(X[Y==1]),side=3) > > On Tue, Apr 3, 2012 at 3:19 PM, Danielle Duncan <dldunc...@alaska.edu>wrote: > >> Thanks, that is interesting, but what I'm really after is an easy "no >> observed effect level", using a binomial logistic model ie glm. Have a >> great day! >> >> On Mon, Apr 2, 2012 at 3:38 PM, vito.muggeo <vito.mug...@unipa.it> wrote: >> >> > dear Danielle, >> > >> > The NOEL is a threshold value or breakpoint in the range of dose. Have a >> > look to the >> > package segmented to estimate a GLM with unknown breakpoints. The code >> > (untested) should >> > be something like >> > >> > library(segmented) >> > o<-glm(y~1, family=binomial) >> > os<-segmented(o, ~dose, psi=starting_psi) >> > >> > Also the package segmented includes the dataset down that can be useful >> as >> > an example.. >> > >> > data(down) >> > with(down, plot(age, cases/births)) >> > >> > There is a paper of mine on R news 2008 discussing the package.. >> > >> > hope this helps you, >> > vito >> > >> > >> > >> > On Mon, 2 Apr 2012 14:45:06 -0800, Danielle Duncan wrote >> > > Hello, I used the glm function in R to fit a dose-response >> relationship >> > and >> > > then have been using dose.p to calculate the LC50, however I would >> like >> > to >> > > calculate the NOEL (no observed effect level), ie the lowest dose >> above >> > > which responses start occurring. Does anyone know how to do this? >> > > >> > > [[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. >> > >> > >> > -- >> > Open WebMail Project (http://openwebmail.org) >> > >> > >> >> [[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. >> > > > > -- > Drew Tyre > > School of Natural Resources > University of Nebraska-Lincoln > 416 Hardin Hall, East Campus > 3310 Holdrege Street > Lincoln, NE 68583-0974 > > phone: +1 402 472 4054 > fax: +1 402 472 2946 > email: aty...@unl.edu > http://snr.unl.edu/tyre > http://aminpractice.blogspot.com > http://www.flickr.com/photos/atiretoo > [[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.
