SUNY Albany School of Public Health GIS and Public Health, Spring 2008
Cluster Detection Lab 1, Thomas Talbot
Questions: tot01@health.state.ny.us
Determine the approximate locations of the most likely clusters of cancer in New York State
using a new beta version of the spatial scan statistic software (SatScan). The Windows
version and Mac Version of the software are available on Tom Talbot’s course website
http://www.albany.edu/faculty/ttalbot/. It may be best to download and install the software
using your home computer and then use that version from your Flash drive both at home and
in the SPH Computer Lab. More information on SaTScan may be found at http://satscan.org/
We will be using publicly available cancer incidence data which provided on the NYSDOH
WebSite.
The numbers of Observed and Expected cases of cancer by census block group we obtained
from. https://apps.nyhealth.gov/METRIX/main.action.
There is also metadata available.
The files you will be using in the lab are available on the SPH server the instructor will
provide the name and location of the files you will be using. We added centroids to the
Metrix data file so you can run it in SaTScan.
To protect confidentaility some of the block groups were merged together using NYSDOH’s’
Geographic Aggregation Tool. The crosswalk file provides inforamtion on which
blockgroups were merged into larger areas in order to provide the cancer counts to the public.
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Maps of the most likely cluster for each cancer site NY are available at:
https://apps.nyhealth.gov/statistics/cancer/environmental_facilities/mapping/map/
The maps may look different from the ones you create since the SaTScan parameters you use
are different.
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Homework Assignment Cluster Lab 1
Each student will run SatScan on two different types of cancer. The cancer each student
will use are listed below. You will need to create a pop and cas for each cancer site you use.
You can use the same geo file for both cancers. Make sure that after you run SatScan for
each cancer you rename input files for example the lung case file you might want to name
lung.cas.
Use the same parameters for each run as described previously in the lab exercise.
Name
Cancer 1
Cancer 2
Ya Li Meng
Ginger Jin
Temilayo Adeyeye
Chris Hensel
Casey O'Brien
Stephen Goins
Dut Lwal
Eva Tanner
Wendy Strollo
Fida Khatib
Nazia Saiyed
Isaac Michaels
Mina Tehrani
Breast
Stomach
Liver
Prostate
Lung
Brain
Thyroid
Mesothelioma
Breast
Stomach
Liver
Prostate
Liver
Mesothelioma
Thyroid
Brain
Lung
Breast
Stomach
Liver
Prostate
Thyroid
Mesothelioma
Lung
Brain
Breast
1. Save the parameter files for each type of cancer you use and add it to your homework
label it with the type of cancer.
From the SaTScan Output files provide the following information
2. Cancer 1
a. Type of cancer?
b. What is the latitude, longitude and radius of the most likely cluster?
c. Of all the clusters listed, what is the relative risk, latitude, longitude and radius of
the cluster with the highest relative risk?
c. What are the observed and expected numbers of the most likely cluster?
d. How many high clusters are listed in your output?
e. How many high clusters are statistically significant p<0.05?
f. How many low clusters are listed in your output?
g. How many low clusters are statistically significant p<0.05?
3. Cancer 2
Provide the same information for cancer 2 as you did in cancer 1.
4. Cancer 1: Open the KML file in Google Earth. Take a screenshot of the map and
include in your homework. The extent of the map should include the locations of all the
clusters.
5. Cancer 2 Provide a similar Google Earth screen shot as you did in for Cancer 1
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