Using Open Source GISto Analyze Public Health Data

Geog 596aCapstone Proposal Peer Review

Advisor: Frank HardistyPenn State MGIS

July 2008

Considering presenting at

URISA’s GIS in Public Health ConferencePutting Health in Place with GIS

June 5-8, 2009 - Providence, Rhode Island

Outline Presentation

• Introduce Capstone

• Introduce Open Source

• Describe Datasets

• Describe Analyzes

• Open Source Applications Re-visited

Capstone Objective• Employ open source applications to evaluate the spatial relationship of

persons with asthma that are within 200% of the federal poverty level*

• Secondary Objective– Create an open source GIS model for other organizations to follow

– Create a web based GIS with little or no capital investment

* Defined by the Department of Health and Human Services

Open Source

• Better quality, higher reliability, more flexibility, lower cost, and an end to predatory vendor lock-in

• Must comply with 10 criteriafor example

• Free redistribution

• Open access to the source code

• License must be technology-neutral

Source: Open Source Initiative

Significance of Open Source

• Leading edge of technology– Always has been

– Becoming part of mainstream computing

– Where propriety software often gets its ideas and base code

• Runs on older and newer computers

• Large learning curve

• Community Supported– Ask the right question Get help

• ie: show that you tried to fix the problem, not just ask for help

• The “tweak factor”– A lot of times it does not work out of the box

– Once configured, it just works, and works, and…

Open Source

ProprietaryIntegration

CommunityDeveloped

“Ease of Use”

$$$

FuturePresentPast

ProprietaryIntegration

CommunityDeveloped

$$$

CommunitySupported

CommunityDeveloped

Ease of Use&

“just works”

Supportedby a largercommunity

Supportedby a select

group

ProprietaryIntegration

“Ease of Use”

Mainstreamintegration the

Black Hole

Open Source Applications

• Linux (Ubuntu) - operating system

• GRASS GIS - spatial analysis, desktop display; plug-in for R-Spatial

• R-Spatial - statistical package

• PostGIS – spatially enabled database

• QGIS – desktop display; plug-in for GRASS

• OpenLayers - web map interface

• MapServer – GIS server; web map interface

Asthma Dataset• From the UNMCare program at the

University of New Mexico Hospital.

• UNMCare is a healthcare coverage program for low-income families in Bernalillo County, NM.

• Data provided by the New Mexico Department of Health and the UNM Health Sciences Center.

Attributes of UNMCare Dataset

• Medical Record Number (Unique ID)• Street level address (de-identified down to

a census block to satisfy HIPPA)• Primary, secondary, and tertiary

diagnostics (ICD-9 Codes)• Visit type (inpatient, outpatient)• Race, gender, and age• Visit start and end date• Cost to health care system

US Census Data• Tract

– Housing type• cost, own/rent

• Block Group– Age– Race– Gender– Employment– Income

• Block– Population

GIS data clearinghouse for New Mexicohttp://rgis.unm.edu/data_entry.cfm

Emission Data

• Sources:

– City of Albuquerque

– EPA

• Constituents:– Particulate Matter <10 µm (PM10)

– Particulate Matter <2.5 µm (PM2.5)

– Sulfur Dioxide– Carbon Monoxide– Ozone

Albuquerque Ambient Air Monitoring

Stations

Work Flow

ObtainHospital, Census,and Environmental

Data

Load DataInto PostGIS

Install OpenSource

Applications

Display dataIn GIS

for QA/QC(GRASS, QGIS)

PerformNon-Spatial

Analysis(R-spatial)

Perform SpatialAnalysis

(PostGIS, Grasswith R-spatial

Add-on)

Display inWeb GIS

(OpenLayers)

De-identify UNMData

(PostGIS)

Analysis of Asthma Admissions

1. Demographic Correlations

2. Air Quality Correlations

Analysis - demographics

• Identify census blocks with higher percentages of asthma admissions

• Look for spatial clustering and correlations between persons with asthma and:– Race, age, and gender– Housing type (own/rent, # of units, cost)

• bias that low-income households have sub-standard living conditions

Analysis – air quality• Identify census blocks with higher

percentages of asthma admissions

• Does a correlation exist between asthma admissions and proximity to an air quality monitoring station that exhibits poor air quality?– If correlation exists, compare the ratios of

PM10, PM2.5, sulfur dioxide, and ozone. Is

one constituent present more often than another?

Analysis – air qualitycontinued

• Does a correlation exist between asthma admissions and proximity to a major traffic corridor?

• Do low-income households cluster near air monitoring stations?

EU

BA

NK

2

5

1

4

3I40

I40

I25

I25

WHERE DO LOW-INCOME ADULTS LIVE IN BERNALILLO COUNTY?

Most low-income adults live in the southern half of the city and along the north-south corridor.

121,173 adults in Bernalillo County earn less than 200% of the federal poverty level. This number represents 30% of the population 18 years of age or older.

COUNTY COMMISSION DISTRICT

% LOW-INCOME ADULTS (<200% FPL)< 13.7%13.7 to 22.1%22.1 to 32.8%32.8 to 46.8%46.8 to 69.8%

Source: Tom Scharmen, NMDOH

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EU

BA

NK

2

5

1

4

3

ALBUQUERQUE, NM

WHAT PERCENT OF LOW-INCOME ADULTS ARE ON UNM CARE? 11.2% of Low-

Income Adults were Enrolled in UNMCare on July 2003.

An estimated 13,513 low-income adults were enrolled in UNMCare in July 2003 of the 121,173 adults in the County earning less than 200% of the federal poverty level.

The census tracts with the best UNMCare enrollment rates are not in the poorest sections of the county.

COUNTY COMMISSION DISTRICT

% LOW-INCOME ENROLLED IN UNMCARE0 to 6.3%6.3 to 10.0%10.0 to 13.1%13.1 to 17.2%17.2 to 22.5%

Source: Tom Scharmen, NMDOH

Open Source Applicationsre-visited

Briefly discuss features and uses– GRASS GIS– R-spatial– PostGIS– QGIS– OpenLayers– MapServer

Grass GIS• Used for Desktop GIS

– Map generation – Data visualization (2D, 2.5D and 3D) – Spatial analysis– Modeling

• Data formats supported– Raster (2D and 3D) – Vector (2D and 3D) – Vector Point

• DBMS Support– PostgreSQL/PostGIS, mySQL, SQLite, ODBC, ...

• Supported platforms– Linux, Windows, Mac, and Handhelds

GRASS GUI (http://grass.itc.it/screenshots/platforms.php

R-spatial

• R is a language and environment for statistical computing and graphics

• Provides a variety of statistical and graphical techniques – linear and nonlinear modeling, classical statistical

tests, time-series analysis, classification, clustering

• Runs on Linux, Windows and Mac. • Provides classes and methods for spatial data

– points, lines, polygons, grids

• Add-in package for GRASS GIS

R-spatial ExampleSource: http://www.r-project.org/

PostGIS

• PostGIS "spatially enables" the PostgreSQL database.

• It is a database server used as a backend spatial database for geographic information systems (GIS)

• Functions like ESRI's SDE or Oracle's Spatial extension.

• Supports Linux, Windows and Mac

PostGIScontinued

The following is an example of a PostGIS script. The script can be called within a GIS, command line, web page, etc.

The below example is a script that locates features within a distance of 5km.

Source: http://postgis.refractions.net/support/wiki/index.php?ExamplesFindNearby

QGIS

• Quantum GIS (QGIS) runs on Linux, Windows, and Mac

• Supports many vector, raster, and database formats

• Supports many common spatial data formats (e.g. ESRI ShapeFile, geotiff)

• Supports many plug-ins – display tracks from a GPS

– Perform spatial analysis and model via GRASS GIS

QGIS GUI

Source: http://qgis.org/images/screenshots/qgis4.png

OpenLayers

• Web map application that displays geographic data from a variety of sources and data types– Geographic data in DBMS and text files– MapServer– Aerial Photography (Virtual Earth, Google Maps,

Yahoo Maps, TerraServer)– WMS, WFS – USGS Topographic Maps and DEMs– TIGER data

• Client-sided (javascript and AJAX); browser independent

Op

en

La

yers

Exa

mp

leh

ttp://

ma

ps.

ho

stgi

s.co

m/r

thic

ks/in

de

x.h

tml

MapServer

• Server-sided GIS for building spatially-enabled internet applications.

• Best for rendering spatial data for the web. • Cross-platform support

– Linux, Windows, and Mac

• Support many raster and vector data formats– TIFF/GeoTIFF, EPPL7, etc– ESRI shapfiles, PostGIS, ESRI ArcSDE, Oracle Spatial, MySQL,

etc

• Is a WMS and WFS client/server• Offers map projection support• On-the-fly map projection

MapServer ExampleSource:

http://maps.hostgis.com/mww-lib/?template=template2&map=/maps/rthicks/mapfile.map

Links to Data and Applications

GRASS GIS http://grass.itc.it/

MapServer http://mapserver.gis.umn.edu/

New Mexico State Air Quality Bureau

http://air.state.nm.us/

OpenLayers http://www.openlayers.org/

Open Source Initiative http://www.opensource.org/

PostGIS http://postgis.refractions.net/

QGIS http://www.qgis.org/

R-spatial http://www.r-project.org/index.html

Ubuntu http://www.ubuntu.com/

US Census Data (RGIS) http://rgis.unm.edu/data_entry.cfm