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
Make that
bmd(fit, 0.01)
in my previous post.
Jarno
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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
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
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
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
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
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
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?
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)
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