National Cancer Institute
National Cancer Institute
Extensions useful for examining geographic patterns of health data Paper #: 1073
Authors: James Cucinelli (IMS), David Stinchcomb (NCI), Jeremy Lyman (IMS), Michael Barrett (IMS), Linda Pickle (NCI)
National Cancer Institute
Agenda • Overview • SEER*Stat Bridge • ColorTool • Smoothing Tools • Head-Bang • Empirical Bayes • Other tools (JoinTool, SaTScan, Disease Rate Calculator, Areal Interpolator)
National Cancer Institute
Overview • Why did we create these tools? • Reduce repetitive tasks/save time • Using other tools effectively and easily from ArcMap
National Cancer Institute
SEER*Stat • What is it? SEER*Stat is a powerful PC tool to view individual cancer records and to produce statistics for studying the impact of cancer on a population
• Where can I get it? http://seer.cancer.gov/seerstat/
National Cancer Institute
What data is available? • SEER Incidence • U.S. Mortality by state/county • U.S. Populations • Census County Attributes
National Cancer Institute
What statistics are available? • Crude and age-adjusted rates • Counts and pops • Survival and prevalence statistics • Multiple Primary Standardized Incidence Ratios
National Cancer Institute
SEER*Stat Bridge • What is it? A tool that facilitates access to SEER*Stat data • How does it work? From within ArcMap, the tool reformats SEER*Stat output so that it can be easily joined to shapefiles • Where can I get it? Email: [email protected]
National Cancer Institute
SEER*Stat Output
National Cancer Institute
Exported Output
National Cancer Institute
Adding a toolbar
National Cancer Institute
Creating a new toolbar
National Cancer Institute
Create NCI GIS Tools
National Cancer Institute
New toolbar has been added
National Cancer Institute
Adding SEER*Stat Bridge
National Cancer Institute
Button added to the toolbar
National Cancer Institute
SEER*Stat Bridge Interface
National Cancer Institute
SEER*Stat Bridge Result
National Cancer Institute
SEER*Stat Bridge • Requirements • Microsoft .NET framework • ArcMap 9.0 or 9.1 • Contact Us: Email: [email protected]
National Cancer Institute
ColorTool • What is it? A tool designed to help people select good color schemes for maps
• How did we create it? We used the color ramps from Cindy Brewer’s work which can be found on http://colorbrewer.org
• Where can I get the tool? Email: [email protected]
National Cancer Institute
Poor color choices can affect your audiences’ interpretation of your message
National Cancer Institute
What’s the geographic pattern? (poor color choice)
National Cancer Institute
Red (high) – Green (low) (better color choice)
National Cancer Institute
What’s the pattern to a colorblind user?
(can’t distinguish reds and greens)
National Cancer Institute
Red (high) – Blue (low) (best for color printers and monitors)
National Cancer Institute
Color Ramp Comparison
National Cancer Institute
Sequential Color Ramp
National Cancer Institute
Qualitative Color Ramp
National Cancer Institute
Screenshot of the tool • Layer • Field • Classification • Ramp Type • Color Scheme • Legend • Groups • Outlines • Exclusion
National Cancer Institute
ColorTool Conclusion • Requirements • Microsoft .NET framework • ArcMap 9.0 or 9.1 • Contact Us: Email: [email protected]
National Cancer Institute
Smoothing Health Data • Purpose: Remove background noise to clarify the underlying spatial pattern • The variance of both rates and counts is proportional to 1/population, so rates are more or less reliable depending on population size. Therefore, the smoother needs to use weights. • Most smoothers in the past did not allow weights, several new ones do • Very stable rates are smoothed less • More unstable rates (due to small populations) are smoothed more
National Cancer Institute
Head-Bang • What is it? A tool to smooth rates using an algorithm that is a median-based moving average of a specified # of nearest neighbors for each point • Who created it? Proposed by Tukey & Tukey, 1981, implemented by Hansen Simonson in 1991 Weights added by Mungiole, Pickle, Hansen Simonson in 1999 • Where can I get it? http://srab.cancer.gov/headbang
National Cancer Institute
Head-Bang for ArcMap™ • What is it? A tool from within ArcMap that calls Head-Bang • How did you create it? We used VB.NET to create a tool that calls Head-Bang and imports the results into ArcMap • Where can I get it? Email: [email protected]
National Cancer Institute
Lung cancer mortality rates (before smoothing)
National Cancer Institute
Lung cancer mortality rates (after smoothing)
National Cancer Institute Observed Data Smoothed Data
National Cancer Institute
Screenshot of the Tool
National Cancer Institute
Empirical Bayes Tool • What is it? A method to smooth disease rates in which the data for small numbers is pooled across areas to provide a more stable estimate of the rate.
• Who created it? Created for the NCI in connection with the Geographic Information System for the Breast Cancer Studies on Long Island
• Where can I get it? http://arcscripts.esri.com/details.asp?dbid=13905
National Cancer Institute
Screenshot of the tool (step 1)
National Cancer Institute
Screenshot of the tool (step 2)
National Cancer Institute
Screenshot of the tool (step 3)
National Cancer Institute
Raw Data
National Cancer Institute
Local Smoothing
National Cancer Institute
Global Smoothing
National Cancer Institute
Empirical Bayes Tool Raw Local
Global
National Cancer Institute
Other Tools • SaTScan for ArcMap: Performs geographical surveillance of disease, detects spatial or space-time disease clusters and checks if they are statistically significant. • Disease Rate Calculator: Can calculate disease rates with adjustments for age, race, or sex (indirectly and directly) • Areal Interpolator: Uses simple areal interpolation to calculate a variable for a given area • JoinTool: compares data to shapefiles
National Cancer Institute
Recommendations for Mapping Disease Rates • Design for particular audience and purpose: quantile-categorized choropleth maps work well • Use standard legend design • Colors should be chosen for visually impaired and consistent with conventions • Identify unreliable rates, don’t blank out • Multiple maps are often needed •
To address different questions
•
To focus attention on different scales
•
To compare modeled (smoothed) to observed…
National Cancer Institute
Questions/Contact Information
• Check out the National Cancer Institute’s GIS web site at:
http://gis.cancer.gov • Contact us: [email protected]
Extensions useful for examining geographic patterns of health data Paper #: 1073
Authors: James Cucinelli (IMS), David Stinchcomb (NCI), Jeremy Lyman (IMS), Michael Barrett (IMS), Linda Pickle (NCI)
National Cancer Institute
Agenda • Overview • SEER*Stat Bridge • ColorTool • Smoothing Tools • Head-Bang • Empirical Bayes • Other tools (JoinTool, SaTScan, Disease Rate Calculator, Areal Interpolator)
National Cancer Institute
Overview • Why did we create these tools? • Reduce repetitive tasks/save time • Using other tools effectively and easily from ArcMap
National Cancer Institute
SEER*Stat • What is it? SEER*Stat is a powerful PC tool to view individual cancer records and to produce statistics for studying the impact of cancer on a population
• Where can I get it? http://seer.cancer.gov/seerstat/
National Cancer Institute
What data is available? • SEER Incidence • U.S. Mortality by state/county • U.S. Populations • Census County Attributes
National Cancer Institute
What statistics are available? • Crude and age-adjusted rates • Counts and pops • Survival and prevalence statistics • Multiple Primary Standardized Incidence Ratios
National Cancer Institute
SEER*Stat Bridge • What is it? A tool that facilitates access to SEER*Stat data • How does it work? From within ArcMap, the tool reformats SEER*Stat output so that it can be easily joined to shapefiles • Where can I get it? Email: [email protected]
National Cancer Institute
SEER*Stat Output
National Cancer Institute
Exported Output
National Cancer Institute
Adding a toolbar
National Cancer Institute
Creating a new toolbar
National Cancer Institute
Create NCI GIS Tools
National Cancer Institute
New toolbar has been added
National Cancer Institute
Adding SEER*Stat Bridge
National Cancer Institute
Button added to the toolbar
National Cancer Institute
SEER*Stat Bridge Interface
National Cancer Institute
SEER*Stat Bridge Result
National Cancer Institute
SEER*Stat Bridge • Requirements • Microsoft .NET framework • ArcMap 9.0 or 9.1 • Contact Us: Email: [email protected]
National Cancer Institute
ColorTool • What is it? A tool designed to help people select good color schemes for maps
• How did we create it? We used the color ramps from Cindy Brewer’s work which can be found on http://colorbrewer.org
• Where can I get the tool? Email: [email protected]
National Cancer Institute
Poor color choices can affect your audiences’ interpretation of your message
National Cancer Institute
What’s the geographic pattern? (poor color choice)
National Cancer Institute
Red (high) – Green (low) (better color choice)
National Cancer Institute
What’s the pattern to a colorblind user?
(can’t distinguish reds and greens)
National Cancer Institute
Red (high) – Blue (low) (best for color printers and monitors)
National Cancer Institute
Color Ramp Comparison
National Cancer Institute
Sequential Color Ramp
National Cancer Institute
Qualitative Color Ramp
National Cancer Institute
Screenshot of the tool • Layer • Field • Classification • Ramp Type • Color Scheme • Legend • Groups • Outlines • Exclusion
National Cancer Institute
ColorTool Conclusion • Requirements • Microsoft .NET framework • ArcMap 9.0 or 9.1 • Contact Us: Email: [email protected]
National Cancer Institute
Smoothing Health Data • Purpose: Remove background noise to clarify the underlying spatial pattern • The variance of both rates and counts is proportional to 1/population, so rates are more or less reliable depending on population size. Therefore, the smoother needs to use weights. • Most smoothers in the past did not allow weights, several new ones do • Very stable rates are smoothed less • More unstable rates (due to small populations) are smoothed more
National Cancer Institute
Head-Bang • What is it? A tool to smooth rates using an algorithm that is a median-based moving average of a specified # of nearest neighbors for each point • Who created it? Proposed by Tukey & Tukey, 1981, implemented by Hansen Simonson in 1991 Weights added by Mungiole, Pickle, Hansen Simonson in 1999 • Where can I get it? http://srab.cancer.gov/headbang
National Cancer Institute
Head-Bang for ArcMap™ • What is it? A tool from within ArcMap that calls Head-Bang • How did you create it? We used VB.NET to create a tool that calls Head-Bang and imports the results into ArcMap • Where can I get it? Email: [email protected]
National Cancer Institute
Lung cancer mortality rates (before smoothing)
National Cancer Institute
Lung cancer mortality rates (after smoothing)
National Cancer Institute Observed Data Smoothed Data
National Cancer Institute
Screenshot of the Tool
National Cancer Institute
Empirical Bayes Tool • What is it? A method to smooth disease rates in which the data for small numbers is pooled across areas to provide a more stable estimate of the rate.
• Who created it? Created for the NCI in connection with the Geographic Information System for the Breast Cancer Studies on Long Island
• Where can I get it? http://arcscripts.esri.com/details.asp?dbid=13905
National Cancer Institute
Screenshot of the tool (step 1)
National Cancer Institute
Screenshot of the tool (step 2)
National Cancer Institute
Screenshot of the tool (step 3)
National Cancer Institute
Raw Data
National Cancer Institute
Local Smoothing
National Cancer Institute
Global Smoothing
National Cancer Institute
Empirical Bayes Tool Raw Local
Global
National Cancer Institute
Other Tools • SaTScan for ArcMap: Performs geographical surveillance of disease, detects spatial or space-time disease clusters and checks if they are statistically significant. • Disease Rate Calculator: Can calculate disease rates with adjustments for age, race, or sex (indirectly and directly) • Areal Interpolator: Uses simple areal interpolation to calculate a variable for a given area • JoinTool: compares data to shapefiles
National Cancer Institute
Recommendations for Mapping Disease Rates • Design for particular audience and purpose: quantile-categorized choropleth maps work well • Use standard legend design • Colors should be chosen for visually impaired and consistent with conventions • Identify unreliable rates, don’t blank out • Multiple maps are often needed •
To address different questions
•
To focus attention on different scales
•
To compare modeled (smoothed) to observed…
National Cancer Institute
Questions/Contact Information
• Check out the National Cancer Institute’s GIS web site at:
http://gis.cancer.gov • Contact us: [email protected]
