[R-sig-ME] deriv example for nlmer

Manuel Morales Manuel.A.Morales at williams.edu
Tue Oct 19 20:49:24 CEST 2010 

Oops - I should have checked the code before posting! Note that the
issue is with what is returned by body(logisKsite) ... you wouldn't need
the [[2]] if the function logisKsite didn't have brackets.

Compare:

fn1 <- function(x) x
fn2 <- function(x) {
  x
}

body(fn1)
body(fn2)
body(fn2)[[2]]               



On Tue, 2010-10-19 at 11:43 -0600, Helen Sofaer wrote:
> 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
> >> >>
> >>
> 

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