[R] Incidence Function Model in R help

[David Winsemius]

On Jul 5, 2009, at 5:15 PM, sjkimble wrote:

>
> R Help:
>
>>
>> When I look at the object S, I see about half of them are
>> zeroes.
>
> I've address the object S being zero so often by changing the value of
> alpha, which I'm allowed to do according to the author. All values  
> of S are
> non zero and should not give Inf.
>
>> The "expectation" of a binomial model is for the LHS of the
>> formulat to be either a 1/0 vector or something of the form
>> cbind(events, non_events). You have satisfied that expectation with p
>> but there are only 2 such cases. It seems unreasonable to my thinking
>> to expect that a logistic regression model can deliver sensible  
>> output
>> from only 2 events. And that holds doubly (or perhaps infinitely?)
>> true when you are starting out with half of your covariates equal to
>> log(0) = -Inf.
>
> Object p is presence (1) or absence (0) of a species on the 12  
> islands, and
> some of them are rare so they are mostly zeros. Nevertheless I tried  
> with a
> more common species whose data are:
>
>    x.crd   y.crd           A p
> 1  361763 1034071      94.169 1
> 2  370325 1027277     127.642 1
> 3  370416 1027166     127.961 1
> 4  370471 1027148    1804.846 1
> 5  369050 1031312    1790.493 1
> 6  370908 1026354     199.103 1
> 7  361562 1034311    2047.637 1
> 8  365437 1022188 1622678.961 1
> 9  347047 1025334      21.169 1
> 10 349186 1024441  408556.801 1
> 11 361762 1034052       3.414 0
> 12 370799 1026557     103.994 0
>
> The code, plus error message:
>
>> haliclona_reniera_manglaris<-read.table(file.choose(),header=T)
>> attach(haliclona_reniera_manglaris)
>> alphascan<-function(alpha,d,A,p){
> + edis<-as.matrix(exp(-alpha*d))
> + edis<-sweep(edis,2,A,"*")
> + S<-rowSums(edis[,p>0])
> + mod<-glm(p~offset(2*log(S))+log(A),family=binomial)
> + deviance(mod)
> + }
>> (sol<-optimize(alphascan,c(0.001,10),d=d,A=A,p=p))
                                         ^^^^
Looking at the code at that point I am wondering what "d" is?

> Error: NA/NaN/Inf in foreign function call (arg 4)
>
>
> Details:
> Reference: Incidence Function Model in R, J Oksanen, 2004, available
> at:
> cc.oulu.fi/~jarioksa/opetus/openmeta/metafit.pdf
> OS: Mac OS 10.5.7
> R version: 2.9.0
> GUI: 1.28 Tiger build 32-bit
>
> Thanks,
> Steve Kimble
> Department of Forestry and Natural Resources
> Purdue UniversityWest Lafayette, IN 47907
>
> -- 
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>
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT