[R-sig-ME] deriv example for nlmer

[Helen Sofaer]

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