[R-sig-Geo] Prepping data for FlexScan

[Simone Mordue (PGR)]

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Simone Mordue MSc.
Ph.D. student

BCES Modelling Group, Newcastle University
Telephone: 07840524435 l Email: s.m.mordue at ncl.ac.uk<mailto:s.m.mordue at ncl.ac.uk>
Research: http://www.researchgate.net/profile/Simone Mordue l Twitter: @SimoneMordue
Address: School of Biology, Ridley Building 2, Newcastle Upon Tyne. NE1 7RU

On 29 Dec 2015, at 11:42, Paul Lantos <paul.lantos at duke.edu<mailto:paul.lantos at duke.edu>> wrote:

Here is the link to the user manual; there is an image of the matrix definition file on page 9.

https://sites.google.com/site/flexscansoftware/download_e/FleXScan%20User%20Guide_e31.pdf?attredirects=0&d=1

Martin Kulldorff is on at least one of the publications with the Japanese group that designed FlexScan, which is a sign in its favor. He's never incorporated it into SatScan, however.

Paul


-----Original Message-----
From: b.rowlingson at gmail.com<mailto:b.rowlingson at gmail.com> [mailto:b.rowlingson at gmail.com] On Behalf Of Barry Rowlingson
Sent: Tuesday, December 29, 2015 6:06 AM
To: Roger Bivand <Roger.Bivand at nhh.no<mailto:Roger.Bivand at nhh.no>>
Cc: Paul Lantos <paul.lantos at dm.duke.edu<mailto:paul.lantos at dm.duke.edu>>; r-sig-geo at r-project.org<mailto:r-sig-geo at r-project.org>
Subject: Re: [R-sig-Geo] Prepping data for FlexScan

FlexScan seems to be distributed as a closed-source Windows-binary only piece of software:

https://sites.google.com/site/flexscansoftware/home

which raises lots of "avoid at all costs" red flags for me.

The methodology is published and could be re-implemented as an R package by a smart enough programmer... Are we too late for a Google SoC project?

Barry


On Mon, Dec 28, 2015 at 10:23 PM, Roger Bivand <Roger.Bivand at nhh.no<mailto:Roger.Bivand at nhh.no>> wrote:
Please provide a link to the documentation of what FlexScan expects to
read and possibly your script, output file, and a sample correctly
formatted file; it appears it is not actively used here (at this time of year anyway).
Is this a case where the OS line feed/carriage return may make a difference?

Roger

On Wed, 23 Dec 2015, Paul Lantos wrote:

Hi,

I'm trying to prepare data for FlexScan to use the flexible cluster
scan statistic, and I'm having difficulty getting data in the right format.


The problem seems to be in the creation of a neighbor matrix file.
I've been using a point data source, creating thiessen polygons (in
ArcGIS), then exporting as a shapefile to R where in spdep I create
an nb object using poly2nb. I've then exported it using the nb2inla function.


But FlexScan does not seem to like the neighbor matrix file I've
created, it gives me a generic error.




Thanks,

Paul


______________________________________
Paul M. Lantos, M.D., FIDSA, FAAP, FACP
  Pediatric Infectious Diseases
  Hospital Medicine
Depts of Internal Medicine and Pediatrics Duke University Medical
Center

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Roger Bivand
Department of Economics, Norwegian School of Economics, Helleveien 30,
N-5045 Bergen, Norway.
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