[R] Calculating NOEL using R and logistic regression - Toxicology

Drew Tyre
Tue, 03 Apr 2012 20:44:21 -0000

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
<dlduncan2@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.muggeo@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]]
> > >
> > > ______________________________________________
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> > > 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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> >
> >
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide
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>



--
Drew Tyre

School of Natural Resources
University of Nebraska-Lincoln
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3310 Holdrege Street
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