In Kenkleinman/rsatscan: Tools, Classes, and Methods for Interfacing with SaTScan Stand-Alone Software

knitr::opts_chunk$set(
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rsatscan is a set of tools that function as wrappers for SaTScan, a stand-alone engine for Spatial and Temporal Scan statistics. It has no functions useful outside this context. In order to use the package, you probably need a fairly sophisticated understanding of what SaTScan does.

Included functions useful for most users include

• write.???()
• ss.options()
• satscan()

The write.???() functions take data from data.frame objects and write them to the OS in SaTScan-readable formats.

The ss.options() function is used to set the parameters the SaTScan engine will use. It functions similarly to options() and par() in that there is a set of default parameter settings, and the user can change any or all of them, and reset the options as needed, or recover the defaults. Key parameters include the names of the input data files and the type of analysis and model to be used.

The satscan() function calls into the operating system to run SaTScan. An object is returned with all the output files that SaTScan made. By default, this is all possible outputs, but this can be controlled by changing the default parameter settings.

Three data sets distributed with SaTScan are also included with the package. An example of using the package, replicated from the vignettes, follows. See the vignette for additional explanatory text.

Begin by resetting the paremeter file:

library("rsatscan")
invisible(ss.options(reset=TRUE))

Then, change the parameters. The parameters used in the SaTScan manual are replicated:

ss.options(list(CaseFile="NYCfever.cas", PrecisionCaseTimes=3))
ss.options(c("StartDate=2001/11/1","EndDate=2001/11/24"))
ss.options(list(CoordinatesFile="NYCfever.geo", AnalysisType=4, ModelType=2, TimeAggregationUnits=3))
ss.options(list(UseDistanceFromCenterOption="y", MaxSpatialSizeInDistanceFromCenter=3, NonCompactnessPenalty=0))
ss.options(list(MaxTemporalSizeInterpretation=1, MaxTemporalSize=7))
ss.options(list(ProspectiveStartDate="2001/11/24", ReportGiniClusters="n", LogRunToHistoryFile="n"))

Then, write the parameter file, the case file, and the geometry file to the OS.

td = tempdir()

write.ss.prm(td,"NYCfever")
write.cas(NYCfevercas,td,"NYCfever")
write.geo(NYCfevergeo,td,"NYCfever")

Then run SaTScan.

# This step omitted in compliance with CRAN policies
# Please install SaTScan and run the vignette with this and following code uncommented
# SaTScan can be downloaded from www.satscan.org, free of charge

# NYCfever = satscan(td,"NYCfever", sslocation="C:/Program Files (x86)/SaTScan")

The rsatscan package provides a summary method for satscan objects.

# summary(NYCfever)

SaTScan is available for free from www.satscan.org.

Kenkleinman/rsatscan documentation built on May 27, 2019, 4:06 a.m.