Re: [R] Calculating NOEL using R and logistic regression - Toxicology
I suppose I'll just report a LC10 using the dose.p function in the package MASS using my glm fitted logistic regression on binomial data. Thanks everyone for ideas & input! The LOEC seems to be a flawed calculation...I'll research it. Again, thanks all! On Mon, Apr 2, 2012 at 2:45 PM, 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? -- "Wilderness isnt the wide open spaces. Its the wild things in it [[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.
Re: [R] Calculating NOEL using R and logistic regression - Toxicology
Thanks everyone for the advice, you raise interesting points. Maybe the best thing for me to do is do an ANOVA in R with binomial data (if possible) and find the lowest dose that gives a significant difference from the controls. On Mon, Apr 2, 2012 at 2:45 PM, 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? -- "Wilderness isnt the wide open spaces. Its the wild things in it [[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.
[R] Calculating NOEL using R and logistic regression - Toxicology
Make that bmd(fit, 0.01) in my previous post. Jarno __ 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.
[R] Calculating NOEL using R and logistic regression - Toxicology
Dear Danielle, At least in industrial toxicology (my original background) the recent tendency has been to use benchmark dose (BSD) approach instead of NOEL or NOAEL approach due to various problems with the definition and estimation of NO(A)EL. In R this can be achieved using the packages drc and bmd as already mentioned by Drew Tyre. Here's a short code example that gives you the BMD at 1% level: library(drc) library(bmd) data(daphnids) d24<-daphnids[daphnids$time=="24h",] fit <- drm(no/total~dose, weights = total, data = d24, fct = LL.2(), type = "binomial") ED(fit, 1) bmd(FIT, 0.01) See the following documents for more information, if you're interested in using BSD instead of NO(A)EL: http://www.cdpr.ca.gov/docs/risk/bmdquant.pdf http://www.efsa.europa.eu/en/efsajournal/doc/1150.pdf Jarno __ 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.
Re: [R] Calculating NOEL using R and logistic regression - Toxicology
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 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 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 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 >>> 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.
Re: [R] Calculating NOEL using R and logistic regression - Toxicology
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 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 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.
Re: [R] Calculating NOEL using R and logistic regression - Toxicology
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 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 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 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.
Re: [R] Calculating NOEL using R and logistic regression - Toxicology
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 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.
Re: [R] Calculating NOEL using R and logistic regression - Toxicology
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) __ 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.
[R] Calculating NOEL using R and logistic regression - Toxicology
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.
