OK, a bit of reading on Google / Wikipedia etc seems to indicate that there isn't a good definition of a NOEL, which makes advising a statistical approach dodgy at best. Your clarification raises all sorts of wrinkles, like how significant is significant, what's the background rate of adverse events etc etc. I believe, but could not test because of issues with loading R packages on my laptop, that packages drc and bmd together might make good headway. Without a better definition, I think the answer to "Can I calculate a NOEL with glm(...)" is no.
Good luck! On Tue, Apr 3, 2012 at 3:47 PM, Danielle Duncan <dldunc...@alaska.edu>wrote: > 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 >> > > -- 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.
