[R-sig-Geo] SaTScan in R

Michael Höhle Michael.Hoehle at stat.uni-muenchen.de
Tue Dec 14 13:27:37 CET 2010

> I'm wondering is there a package in R that has similar functions as SaTscan? In particular, I'm looking for space-time cluster detection. The D-cluster package doesn't appear to have a function for space-time detection (please correct me if I'm wrong).

As already mentioned by Barry Rowlingson the R package "surveillance" contains some functionality 
to perform space-time outbreak detection.

The appropriate method depends a bit on your data structure: if you have point referenced data then the 
function stcd by Assuncao & Correa could apply (see lit ref in the package). There is no specific SatScan functionality for area data,
but you might add some cluster detection on the algo.hhh function for multivariate time series of counts
or follow the approach by Raubertas (1989, Stats in Med, 8(3), 267-271) by monitoring several CUSUM aggregations
of spatial units using, e.g., function algo.glrnb/glrnb

As presented on the IBC2010 last week, we are also working on some further ideas on doing model based spatio-temporal cluster detection,
but unfortunately there is no schedule on how/when something like this is going to appear in the package.

As an aside: Should anyone have some available R code for such spatio-temporal cluster detection I'd be 
happy to integrate it in the surveillance package as I think there is definitely some need for open-source code
on this matter. Maybe this issue would be fun to discuss at the spacetime workshop in March...
I'll certainly be looking forward to the newest spatstat developments.

Best regards,


More information about the R-sig-Geo mailing list