[R-sig-ME] Help with glmmPQL using Scottish Lip Cancer data

[Corey Sparks]

Dear list,
Please forgive the double posting ( i sent this to the geo sig as well)
>
> Dear List,
> I'm trying to replicate results from several sources that analyze the
> Clayton and Kaldor (1987) Scottish Lip Cancer data using a Poisson  
> GLMM with
> spatial correlation structure using a simple exponential variogram  
> model.
> The only way (I think) that my data are different from the published  
> data
> are that i'm using the Lat/Long instead of the OSGB projection.
>
> Here is what I've tried:
> scot<-read.csv("scotland.csv")
> names(scot)
> scot$aff<-scot$AFF/10
> scot$x<-scot$Longitude
> scot$y<-scot$Latitude
> scot$smr<-scot$Observed/scot$Expected
> scot$logsmr<-log(scot$smr+1)
> coordinates(scot)=~x+y
>
> library(MASS)
> library(nlme)
>
> #This is the first try, using the corEXP() directly in glmmPQL
>
> fit<-glmmPQL(Observed~offset(log(Expected))+aff,family=poisson,  
> data=scot,
> random=~1|District, correlation=corExp(form=~x+y), niter=200)
>
> #it fails with:
> iteration 1
> Error in corFactor.corSpatial(object) :
>  NA/NaN/Inf in foreign function call (arg 1)
> In addition: Warning messages:
> 1: In min(unlist(attr(object, "covariate"))) :
>  no non-missing arguments to min; returning Inf
> 2: In min(unlist(attr(object, "covariate"))) :
>  no non-missing arguments to min; returning Inf
>
>
> #Then I try to initialize the spatial correlation as in ASDAR
> sp2<-corSpatial( form=~x+y, type="exponential")
> spcor<-Initialize(sp2, as(scot, "data.frame")[,c("x","y")])
>
> glmmPQL(Observed~offset(log(Expected))+aff,family=poisson, data=scot,
> random=~1|District, correlation=spcor, niter=200, na.action="na.omit")
>
> #This fails with:
> iteration 1
> iteration 2
> iteration 3
> iteration 4
> iteration 5
> Error in lme.formula(fixed = zz ~ offset(log(Expected)) + aff,  
> random = ~1 |
> :
>  nlminb problem, convergence error code = 1
>  message = function evaluation limit reached without convergence (9)
>
> Basically, i'm wondering if  anyone can get this to work, because  
> i'm at my
> wits end.
>
>
> My system info is:
> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] nlme_3.1-96  MASS_7.3-6   gstat_0.9-69 sp_0.9-64
>
> loaded via a namespace (and not attached):
> [1] grid_2.11.1    lattice_0.18-8 tools_2.11.1
>
>
> Best,
> Corey
>
> I'm pasting in the data, in case anyone wants to have a look:
>
> District,Observed,Expected,AFF,Latitude,Longitude
> 1,9,1.4,16,57.29,5.5
> 2,39,8.7,16,57.56,2.36
> 3,11,3,10,58.44,3.9
> 4,9,2.5,24,55.76,2.4
> 5,15,4.3,10,57.71,5.09
> 6,8,2.4,24,59.13,3.25
> 7,26,8.1,10,57.47,3.3
> 8,7,2.3,7,60.24,1.43
> 9,6,2,7,56.9,5.42
> 10,20,6.6,16,57.24,2.6
> 11,13,4.4,7,58.12,6.8
> 12,5,1.8,16,58.06,4.64
> 13,3,1.1,10,57.47,3.98
> 14,8,3.3,24,54.94,5
> 15,17,7.8,7,56.3,3.1
> 16,9,4.6,16,57,3
> 17,2,1.1,10,57.06,4.09
> 18,7,4.2,7,55.65,2.88
> 19,9,5.5,7,57.24,4.73
> 20,7,4.4,10,55.35,2.9
> 21,16,10.5,7,56.75,2.98
> 22,31,22.7,16,57.12,2.2
> 23,11,8.8,10,56.4,5.27
> 24,7,5.6,7,55.63,3.96
> 25,19,15.5,1,56.2,3.3
> 26,15,12.5,1,56.1,3.6
> 27,7,6,7,55.24,4.09
> 28,10,9,7,55.95,2.8
> 29,16,14.4,10,56.6,4.09
> 30,11,10.2,10,55.9,3.8
> 31,5,4.8,7,55.47,4.55
> 32,3,2.9,24,55,4.36
> 33,7,7,10,55.83,3.2
> 34,8,8.5,7,56.3,4.73
> 35,11,12.3,7,55.29,4.98
> 36,9,10.1,0,55.94,4.95
> 37,11,12.7,10,55.76,5.02
> 38,8,9.4,1,55.91,4.18
> 39,6,7.2,16,56.15,4.99
> 40,4,5.3,0,56.05,4.91
> 41,10,18.8,1,55.88,4.82
> 42,8,15.8,16,56.03,4
> 43,2,4.3,16,56.15,3.96
> 44,6,14.6,0,55.82,4.09
> 45,19,50.7,1,55.93,3.4
> 46,3,8.2,7,55.65,4.75
> 47,2,5.6,1,55.71,4.45
> 48,3,9.3,1,55.79,4.27
> 49,28,88.7,0,55.9,4.55
> 50,6,19.6,1,56.45,3.2
> 51,1,3.4,1,56,4.27
> 52,1,3.6,0,56.15,4.64
> 53,1,5.7,1,55.79,4.7
> 54,1,7,1,55.99,4.45
> 55,0,4.2,16,55.68,3.38
> 56,0,1.8,10,55.18,3.4
>
>
> -- 
> Corey Sparks
> Assistant Professor
> Department of Demography and Organization Studies
> University of Texas at San Antonio
> 501 West Durango Blvd
> Monterey Building 2.270C
> San Antonio, TX 78207
> 210-458-3166
> corey.sparks 'at' utsa.edu
> https://rowdyspace.utsa.edu/users/ozd504/www/index.htm
>