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SaTScan
TM
User Guide
for version 10.1
By Martin Kulldorff
July 2022
http://www.satscan.org/
SaTScan User Guide v10.1
Table of Contents
INTRODUCTION .................................................................................................................................. 1
THE SATSCAN SOFTWARE .......................................................................................................................... 1
DOWNLOAD AND INSTALLATION ................................................................................................................ 2
TEST RUN ................................................................................................................................................... 2
HELP SYSTEM ............................................................................................................................................. 3
SAMPLE DATA SETS .................................................................................................................................... 3
STATISTICAL METHODOLOGY ....................................................................................................... 6
SPATIAL, TEMPORAL AND SPACE-TIME SCAN STATISTICS .......................................................................... 6
BERNOULLI MODEL .................................................................................................................................... 8
DISCRETE POISSON MODEL ........................................................................................................................ 9
SPACE-TIME PERMUTATION MODEL ........................................................................................................... 9
MULTINOMIAL MODEL ............................................................................................................................. 10
ORDINAL MODEL ...................................................................................................................................... 10
EXPONENTIAL MODEL .............................................................................................................................. 12
NORMAL MODEL ...................................................................................................................................... 12
CONTINUOUS POISSON MODEL ................................................................................................................. 13
PROBABILITY MODEL COMPARISON ......................................................................................................... 14
LIKELIHOOD RATIO TEST .......................................................................................................................... 16
SECONDARY CLUSTERS ............................................................................................................................ 17
ADJUSTING FOR MORE LIKELY CLUSTERS ................................................................................................ 17
DRILLDOWN .............................................................................................................................................. 18
COVARIATE ADJUSTMENTS ....................................................................................................................... 18
SPATIAL AND TEMPORAL ADJUSTMENTS .................................................................................................. 21
MISSING DATA ......................................................................................................................................... 22
MULTIVARIATE SCAN WITH MULTIPLE DATA SETS .................................................................................. 24
COMPARISON WITH OTHER METHODS...................................................................................... 25
SCAN STATISTICS ...................................................................................................................................... 25
SPATIAL AND SPACE-TIME CLUSTERING .................................................................................................. 25
INPUT DATA ....................................................................................................................................... 27
DATA REQUIREMENTS .............................................................................................................................. 27
CASE FILE ................................................................................................................................................. 28
CONTROL FILE .......................................................................................................................................... 30
POPULATION FILE ..................................................................................................................................... 30
COORDINATES FILE ................................................................................................................................... 31
GRID FILE ................................................................................................................................................. 32
NETWORK FILE ......................................................................................................................................... 32
NON-EUCLIDEAN NEIGHBORS FILE........................................................................................................... 33
META LOCATION FILE .............................................................................................................................. 33
MAX CIRCLE SIZE FILE ............................................................................................................................. 34
ADJUSTMENTS FILE .................................................................................................................................. 34
ALTERNATIVE HYPOTHESIS FILE .............................................................................................................. 35
SATSCAN IMPORT WIZARD ...................................................................................................................... 35
SATSCAN ASCII FILE FORMAT ................................................................................................................ 37
BASIC SATSCAN FEATURES ........................................................................................................... 40
INPUT TAB ................................................................................................................................................ 40
ANALYSIS TAB.......................................................................................................................................... 43
OUTPUT TAB ............................................................................................................................................. 46
SaTScan User Guide v10.1
ADVANCED FEATURES .................................................................................................................... 49
MULTIPLE DATA SETS TAB ....................................................................................................................... 49
DATA CHECKING TAB ............................................................................................................................... 50
SPATIAL NEIGHBORS TAB ......................................................................................................................... 51
NETWORK TAB ......................................................................................................................................... 52
LINE LIST TAB .......................................................................................................................................... 53
SPATIAL WINDOW TAB ............................................................................................................................. 55
TEMPORAL WINDOW TAB ......................................................................................................................... 58
CLUSTER RESTRICTIONS TAB ................................................................................................................... 60
SPACE AND TIME ADJUSTMENTS TAB ....................................................................................................... 61
INFERENCE TAB ........................................................................................................................................ 64
POWER EVALUATION TAB ........................................................................................................................ 67
DRILLDOWN TAB ...................................................................................................................................... 68
MISCELLANEOUS TAB ............................................................................................................................... 69
SPATIAL OUTPUT TAB .............................................................................................................................. 71
TEMPORAL OUTPUT TAB .......................................................................................................................... 74
OTHER OUTPUT TAB ................................................................................................................................. 75
ALERTS TAB ............................................................................................................................................. 77
RUNNING SATSCAN .......................................................................................................................... 79
SPECIFYING ANALYSIS AND DATA OPTIONS ............................................................................................. 79
LAUNCHING THE ANALYSIS ...................................................................................................................... 79
STATUS MESSAGES ................................................................................................................................... 80
WARNINGS AND ERRORS .......................................................................................................................... 80
SAVING ANALYSIS PARAMETERS .............................................................................................................. 81
PARALLEL PROCESSORS ............................................................................................................................ 81
BATCH MODE ........................................................................................................................................... 82
MULTIPLE ANALYSES ............................................................................................................................... 82
COMPUTING TIME ..................................................................................................................................... 85
MEMORY REQUIREMENTS ......................................................................................................................... 86
RESULTS OF ANALYSIS ................................................................................................................... 89
STANDARD TEXT-BASED RESULTS FILE (*.OUT.*) ................................................................................... 89
KML GEOGRAPHICAL OUTPUT FILE (*.KML) ........................................................................................... 91
SHAPEFILE GEOGRAPHICAL OUTPUT (*.SHP AND *.SHX) .......................................................................... 91
TEMPORAL GRAPHS HTML FILE (*.TEMPORAL.HTML) ............................................................................ 91
CLUSTER INFORMATION FILE (*.COL.*) .................................................................................................... 92
STRATIFIED CLUSTER INFORMATION FILE (*.SCI.*) .................................................................................. 94
LOCATION INFORMATION FILE (*.GIS.*) ................................................................................................... 94
RISK ESTIMATES FOR EACH LOCATION FILE (*.RR.*) ............................................................................... 95
SIMULATED LOG LIKELIHOOD RATIOS FILE (*.LLR.*) .............................................................................. 95
MISCELLANEOUS ............................................................................................................................. 96
NEW VERSIONS ......................................................................................................................................... 96
ANALYSIS HISTORY FILE .......................................................................................................................... 96
RANDOM NUMBER GENERATOR ............................................................................................................... 96
CONTACT US ............................................................................................................................................ 97
ACKNOWLEDGEMENTS ............................................................................................................................. 97
FREQUENTLY ASKED QUESTIONS ............................................................................................... 99
INPUT DATA .............................................................................................................................................. 99
ANALYSIS ............................................................................................................................................... 100
RESULTS ................................................................................................................................................. 100
SaTScan User Guide v10.1
INTERPRETATION .................................................................................................................................... 101
OPERATING SYSTEMS ............................................................................................................................. 103
SATSCAN BIBLIOGRAPHY ............................................................................................................ 104
SUGGESTED CITATIONS .......................................................................................................................... 104
SATSCAN METHODOLOGY PAPERS......................................................................................................... 105
SELECTED SATSCAN APPLICATIONS BY FIELD OF STUDY ...................................................................... 108
OTHER REFERENCES MENTIONED IN THE USER GUIDE ........................................................................... 129
SaTScan User Guide v10.1 1
Introduction
The SaTScan Software
Purpose
SaTScan is a free software that analyzes spatial, temporal and space-time data using the spatial, temporal,
or space-time scan statistics. It is designed for any of the following interrelated purposes:
• Perform geographical surveillance of disease, to detect spatial or space-time disease clusters, and
to see if they are statistically significant.
• Test whether a disease is randomly distributed over space, over time or over space and time.
• Evaluate the statistical significance of disease cluster alarms.
• Perform prospective real-time or time-periodic disease surveillance for the early detection of
disease outbreaks.
The software may also be used for similar problems in other fields such as archaeology, astronomy, botany,
criminology, ecology, economics, engineering, forestry, genetics, geography, geology, history, neurology
or zoology.
Data Types and Methods
SaTScan can be used for discrete as well as continuous scan statistics. For discrete scan statistics the
geographical locations where data are observed are non-random and fixed by the user. These locations may
be the actual locations of the observations, such as houses, schools or ant nests, or it could be a central
location representing a larger area, such as the geographical or population weighted centroids of postal
areas, counties or provinces. For continuous scan statistics, the locations of the observations are random
and can occur anywhere within a predefined study area defined by the user, such as a rectangle.
For discrete scan statistics, SaTScan uses either a discrete Poisson-based model, where the number of events
in a geographical location is Poisson-distributed, according to a known underlying population at risk; a
Bernoulli model, with 0/1 event data such as cases and controls; a space-time permutation model, using
only case data; a multinomial model for categorical data; an ordinal model, for ordered categorical data; an
exponential model for survival time data with or without censored variables; a normal model for other types
of continuous data; or a spatial variation in temporal trends model, looking for geographical areas with
unusually high or low temporal trends. A common feature of all these discrete scan statistics is that the
geographical locations where data can be observed are non-random and fixed by the user.
For the discrete scan statistics, the data may be either aggregated at the census tract, zip code, county or
other geographical level, or there may be unique coordinates for each observation. SaTScan adjusts for the
underlying spatial inhomogeneity of a background population. It can also adjust for any number of
categorical covariates provided by the user, as well as for temporal trends, known space-time clusters and
missing data. It is possible to scan multiple data sets simultaneously to look for clusters that occur in one
or more of them.
For continuous scan statistics, SaTScan uses a continuous Poisson model.
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