For completeness of the archives, this problem seems to have been solved via a private conversation.
From my perspective the problem was trying to complicate a situation that was essentially solved. Instead of trying to comprehend how to conform the present situation to someone's implementation of a permutation test, it is much easier to just do the computation. Something like: permvec <- numeric(1000) for(i in 1:1000) permvec[i] <- statistic.from.permuted.data p.value <- mean(permvec <= original.statistic) I think the same is true of bootstrapping. This is more controversial since there are some techniques -- such as bias correction -- with bootstrapping that can improve the results. However, virtually always in the work that I do a naive bootstrap is good enough. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and "A Guide for the Unwilling S User") Jean-Francois Savard wrote: >Dear R users, > >I am trying to perform a hypothesis test on a marked point pattern. I >would like to calculate the mean of the absolute value of the >difference of marks between nearest neigbours, randomize the marks >among points, then calculate this mean again. Ideally, I would test >whether random mean values smaller than the observed mean value occur >less than 5% of the time. I suppose 1000 permutations would be a >reasonable starting point (the ppp object has 27 points). > >so far, I've figured out how to: > >-create a marked ppp object: ms.ppp > >-calculate my test statistic: >teststat <- mean(abs(markstat(ms.ppp, diff, N=2))) > >-randomly allocate marks to a point pattern: >Y <- rlabel (ms.ppp, labels=ms.ppp$marks, permute=TRUE) > >I have looked at perm.test{exactRankTests} and perused the R help >archive but haven't been able to find how to work the permutation test >with a marked ppp object. > >I thank you in advance for any help, > > >J-F Savard >Doctoral Candidate >University of Maryland > >______________________________________________ >[email protected] mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > > > ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
