[R-sig-ME] deriv example for nlmer

Helen Sofaer helen at lamar.colostate.edu
Tue Oct 19 19:43:12 CEST 2010


Thanks!!

With your deriv code I got the error: Function '`{`' is not in the
derivatives table
Googling the error led me to a suggestion that I add [[2]] to the deriv
function like this:

logisSiteDeriv = deriv(body(logisKsite)[[2]], namevec = c("Asym", "xmid",
"K", "Kdiff", "middiff"), function.arg=logisKsite)

And that function runs in nlmer! So, I've very happy, except I am curious
as to what the [[2]] does...

Thanks again for your quick response.
Helen

On Tue, 19 Oct 2010 13:11:47 -0400, Manuel Morales
<Manuel.A.Morales at williams.edu> wrote:
> How about:
> 
> grModel <- function(Age, site, Asym, xmid, K, Kdiff, middiff) {
>   Asym/(1 + exp((xmid+middiff*site - Age)*(K+Kdiff*site)))
> }
> 
> grModg <- deriv(body(grModel),
>                 namevec = c("Asym", "xmid", "K", "Kdiff", "middiff"),
>                 function.arg=grModel)
> 
> startsite <- c(Asym=9, xmid=3, K=.5, Kdiff=0, middiff=0)
> 
> 
> nlmer(weight ~ grModg(Age,site,Asym,xmid,K,Kdiff,middiff) ~ (K|Nest_ID),
>                       data=growth, start=startsite, verbose = TRUE)
> 
> On Tue, 2010-10-19 at 08:25 -0600, Helen Sofaer wrote:
>> Hi Thierry,
>> My main goal is to test for a difference between populations, which I
>> can't do with SSlogis.
>> Check out the code for my function to see the model I'm trying to run.
>> 
>> Thanks,
>> Helen
>> 
>> 
>> On Tue, 19 Oct 2010 10:09:33 +0200, "ONKELINX, Thierry"
>> <Thierry.ONKELINX at inbo.be> wrote:
>> > Dear Helen,
>> > 
>> > Won't it be easier to stick with Sslogis to run the model and then
>> > convert scal to K for your report?
>> > 
>> > HTH,
>> > 
>> > Thierry
>> > 
>> >
------------------------------------------------------------------------
>> > ----
>> > ir. Thierry Onkelinx
>> > Instituut voor natuur- en bosonderzoek
>> > team Biometrie & Kwaliteitszorg
>> > Gaverstraat 4
>> > 9500 Geraardsbergen
>> > Belgium
>> > 
>> > Research Institute for Nature and Forest
>> > team Biometrics & Quality Assurance
>> > Gaverstraat 4
>> > 9500 Geraardsbergen
>> > Belgium
>> > 
>> > tel. + 32 54/436 185
>> > Thierry.Onkelinx at inbo.be
>> > www.inbo.be
>> > 
>> > To call in the statistician after the experiment is done may be no
more
>> > than asking him to perform a post-mortem examination: he may be able
to
>> > say what the experiment died of.
>> > ~ Sir Ronald Aylmer Fisher
>> > 
>> > The plural of anecdote is not data.
>> > ~ Roger Brinner
>> > 
>> > The combination of some data and an aching desire for an answer does
>> > not
>> > ensure that a reasonable answer can be extracted from a given body of
>> > data.
>> > ~ John Tukey
>> >   
>> > 
>> >> -----Oorspronkelijk bericht-----
>> >> Van: r-sig-mixed-models-bounces at r-project.org 
>> >> [mailto:r-sig-mixed-models-bounces at r-project.org] Namens Helen
Sofaer
>> >> Verzonden: dinsdag 19 oktober 2010 4:07
>> >> Aan: r-sig-mixed-models at r-project.org
>> >> Onderwerp: [R-sig-ME] deriv example for nlmer
>> >> 
>> >> 
>> >> Hello modelers,
>> >> I am working on a growth rate analysis in lme4, where my goal 
>> >> is to test for differences in growth rates between two 
>> >> populations of birds while incorporating random effects for 
>> >> nests (to deal with the lack of independence between 
>> >> siblings) and for each nestling (to deal with repeated 
>> >> measures of individuals). 
>> >> 
>> >> I'd like to build a model that is parameterized slightly 
>> >> differently than the SSlogis self-starting model, where K = 
>> >> 1/scal (this is simply due to convention in the bird world). 
>> >> I can tweak the SSlogis code (given in the help file for 
>> >> selfStart) and the model runs, but cannot test for 
>> >> differences between populations. Since determining reasonable 
>> >> starting values is not a problem, and I'd like to be able to 
>> >> easily adjust the formula to incorporate additional 
>> >> covariates, I would like to avoid using a self-starting function.
>> >> 
>> >> It is my understanding that nlmer requires a function, but 
>> >> not necessarily a self-starting one. However, I can't find an 
>> >> example of any code that does this. 
>> >> 
>> >> I can build a very simple function that allows for 
>> >> differences between populations (referred to as site, which 
>> >> is a 0 1 dummy variable) in both the inflection point (xmid) 
>> >> and the growth rate (K). I'm trying to start with the 
>> >> simplest reasonable model, so I didn't allow for differences 
>> >> in the asymptote. This function works in nls:
>> >> 
>> >> logisKsite = function(Age, site, Asym, xmid, K, Kdiff, middiff){
>> >> 	Asym/(1 + exp((xmid+middiff*site - Age)*(K+Kdiff*site)))
>> >> 	}
>> >> 
>> >> startsite = c(Asym = 9, xmid = 3, K = .5, Kdiff=0, middiff=0) 
>> >> nls_logisKsite = nls(weight ~ logisKsite(Age, site, Asym, 
>> >> xmid, K, Kdiff, middiff), growth, start = startsite)
>> >> 
>> >> The nlmer model I am trying to run is (for simplicity, this 
>> >> model includes only a random effect of nest, only on the K
parameter):
>> >> nlmer_logisKsite = nlmer(weight ~ logisKsite(Age, site, Asym, 
>> >> xmid, K, Kdiff, middiff) ~ (K | Nest_ID), growth, start = 
>> >> startsite, verbose = TRUE)
>> >> 
>> >> Running this model in nlmer produces the error: gradient 
>> >> attribute of evaluated model must be a numeric matrix Dr. 
>> >> Bates' posted lectures note that the model must provide 
>> >> derivatives, via the deriv function. I haven't been 
>> >> successful getting this to work, even in the model without 
>> >> site effects.
>> >> 
>> >> If there is an example of how to run nlmer without a 
>> >> self-start function, could someone please point me to it? 
>> >> Advise on how to implement the deriv function would also be 
>> >> very helpful. 
>> >> 
>> >> Thank you very much,
>> >> 
>> >> Helen
>> >> 
>> >> Helen Sofaer, PhD Candidate in Ecology, Colorado State University
>> >> 
>> >> _______________________________________________
>> >> R-sig-mixed-models at r-project.org mailing list 
>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> >>
>>

-- 
Helen Sofaer
PhD Candidate
Colorado State University
Graduate Degree Program in Ecology
Biology Department
Program for Interdisciplinary Mathematics, Ecology, and Statistics Fellow
(970) 491-2782




More information about the R-sig-mixed-models mailing list