Hi all, I'm wondering if I can get a little advice on using DCluster. I have produced a map of areal incidence rates and I'd like to try and detect clusters. I have also implemented Bayesian smoothing and have therefore pre and post smoothing maps.
I have some code as follow for detecting clusters using the Kuldorff-Nagarwalla analysis (code based on Fig11.18 in the ASDAR book and this useful question and answer: http://r-sig-geo.2731867.n2.nabble.com/Strange-results-in-DCluster-package-td7326832.html ) # get centroids of polygons Areas$x<-coordinates(Areas)[,1] Areas$y<-coordinates(Areas)[,2] #Create the data frame demanded by DCluster sa<-data.frame(Observed=Areas$obs) sa<-cbind(sa, Expected=mean(Areas$exp)) sa<-cbind(sa, x=Areas$x, y=Areas$y) sa$Observed<-as.numeric(sa$Observed) #Kuldorff-Nagarwalla analysis mle<-calculate.mle(sa, model="poisson") knres<-opgam(data=sa, thegrid=sa[,c("x", "y")], alpha=.1, R=20, iscluster=kn.iscluster, fractpop=.10, model="poisson", mle=mle, log.v=TRUE) This seems to work ok however there are a few things I'm confused on: 1) Should I be using this algorithm on my incidence rates pre or post Bayesian smoothing ? I'm thinking that the mle expression above includes a smooth (do I understand that correctly ?) - but I' prefer to utilise my hard-won Bayesian smooth if possible. 2) Will opgam/kn.iscluster only detect "hotspots" or will they also detect "coldspots" i.e. areas of statistically unlikely lower incidence rates ? 3) I'm not familiar with bootstrapping - how many bootstraps should I be running and why (i.e. - what should I set R to) ? 4) How do I decide what the correct value for fractpop is ? I initially had it set to .25 and I was getting cluster of 50% of my cases which made no sense. 5) Is there any correction for multiple testing in the opgam() command ? I have over 3000 areas - do I need to set a very low alpha ? I would be grateful for any enlightenment anyone may have to pass on :) Many thanks, James _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo