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). Any ideas would be highly appreciated! K.
SaTScan in R
6 messages · Kitty Lee, Barry Rowlingson, Renaud Lancelot +2 more
On Fri, Dec 3, 2010 at 8:25 AM, Kitty Lee <lee.kitty at yahoo.com> wrote:
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). Any ideas would be highly appreciated!
SaTScan (TM) seems to be a Java GUI on a whole bunch of scan
statistics devised by Kulldorff. Running RSiteSearch("kulldorff")
doesn't find any implementations of space-time scan statistics in R.
So I'm thinking not.
But it would be a heck of a great project to start. SaTScan (TM) is
closed source, but has a fairly permissive license (it allows
redistribution). I thought it would be able to produce pretty maps
like on its web page, but that appears to be misleading - one would
have to load the output data into a GIS (or R) for mapping.
Also, don't forget that SaTScan(TM) is trademarked to Kulldorff so
you have to say (TM) every time you mention it. All the methods are
published, so reimplementations of them should not be covered by
trademark, patent, copyright problems (oh, I'm not a lawyer...).
So basically, the answer is no, but if Kulldorff reads this, how
about opening the source?
Barry
Le 03/12/2010 18:57, Barry Rowlingson a ?crit :
On Fri, Dec 3, 2010 at 8:25 AM, Kitty Lee<lee.kitty at yahoo.com> wrote:
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). Any ideas would be highly appreciated!
SaTScan (TM) seems to be a Java GUI on a whole bunch of scan
statistics devised by Kulldorff. Running RSiteSearch("kulldorff")
doesn't find any implementations of space-time scan statistics in R.
So I'm thinking not.
But it would be a heck of a great project to start. SaTScan (TM) is
closed source, but has a fairly permissive license (it allows
redistribution). I thought it would be able to produce pretty maps
like on its web page, but that appears to be misleading - one would
have to load the output data into a GIS (or R) for mapping.
Also, don't forget that SaTScan(TM) is trademarked to Kulldorff so
you have to say (TM) every time you mention it. All the methods are
published, so reimplementations of them should not be covered by
trademark, patent, copyright problems (oh, I'm not a lawyer...).
So basically, the answer is no, but if Kulldorff reads this, how
about opening the source?
That would be great! I feel we miss these methods in the current implementation of R packages for spatial epidemiology. All the best, Renaud
Barry
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Renaud Lancelot EDEN Project, coordinator http://www.eden-fp6project.net/ UMR CIRAD-INRA "Contr?le des maladies animales exotiques et ?mergentes" Joint research unit "Control of emerging and exotic animal diseases" CIRAD, Campus International de Baillarguet TA A-DIR / B F34398 Montpellier http://umr-cmaee.cirad.fr/ Tel. +33 4 67 59 37 17 - Fax +33 4 67 59 37 95 Secr. +33 4 67 59 37 37 - Cell. +33 6 77 52 08 69
1 day later
Although there's no specific scan statistic functions in it, the 'surveillance' package has lots of functions for doing space-time outbreak detection: http://surveillance.r-forge.r-project.org/ Barry
9 days later
You may find R codes for space-time cluster detection in Tango's "Statistical Methods for Disease Clustering" (http://www.amazon.com/dp/1441915710/). I do not write here the downloadable url of these R functions written in the book because I am not sure it can be disclosed to public. So, what I can advise to you is that you may read the book. I hope it can help you. -- Susumu On Fri, 3 Dec 2010 00:25:40 -0800 (PST)
Kitty Lee <lee.kitty at yahoo.com> wrote:
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). Any ideas would be highly appreciated! K.
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Kitty, You might want to try SpatialEpi (although I think it only has Spatial, not Spatio-Temporal detection) cheers Ben
On 03/12/2010, at 7:25 PM, Kitty Lee wrote:
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). Any ideas would be highly appreciated! K.
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