[R] Incidence Function Model in R help

[sjkimble]

R Help:

Another question:

My data are:

    x.crd   y.crd           A p
1  361762 1034052       3.414 0
2  361763 1034071      94.169 0
3  370325 1027277     127.642 1
4  370416 1027166     127.961 0
5  370471 1027148    1804.846 1
6  369050 1031312    1790.493 0
7  370799 1026557     103.994 0
8  370908 1026354     199.103 0
9  361562 1034311    2047.637 0
10 365437 1022188 1622678.961 0
11 347047 1025334      21.169 0
12 349186 1024441  408556.801 0

and the code, complete with error message, is:

> amphimedon_compressa<-read.table(file.choose(),header=T)
> attach(amphimedon_compressa)
> d<-dist(cbind(x.crd,y.crd))
> alpha<-1
> 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)
Error: NA/NaN/Inf in foreign function call (arg 4)
>

R Help tells me that argument 4 for glm is "weights	 an optional vector of
‘prior weights’ to be used in the fitting process. Should be NULL or a
numeric vector." I am unsure why this optional vector needs to employed and
how to correct the NA/NaN/Inf error if in fact it is necessary.

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
seesionInfo output:
Error in system.file(package = pkg, lib.loc = lib.loc) : 
  'package' must be of length 1
In addition: Warning messages:
1: In if (pkg == "base") pkgpath <- file.path(.Library, "base") else if
((envname <- paste("package:",  :
  the condition has length > 1 and only the first element will be used
2: In if ((envname <- paste("package:", pkg, sep = "")) %in% search()) { :
  the condition has length > 1 and only the first element will be used
3: In if (file.access(file.path(lib, pkg), 5) == 0L) { :
  the condition has length > 1 and only the first element will be used

Thanks,
Steve Kimble
Department of Forestry and Natural Resources
Purdue University
West Lafayette, IN 47907

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