Additional File 5

Abstract

SAS code for parameters macro. This section contains the SAS code for the parameters macro described in this paper.

Full text

%macro parameters(datastreams=, cases_text=, control_text=,
population_text=, coordinates_text=, usegridfile=, gridfile=,
timeprecision=, coordinatestype=, startdate=, enddate=, analysistype=,
modeltype=, scanareas=, timeaggunits=, timeagglength=, mcreps=,
results_text=, llr_ascii=, llr_dbase=, rr_ascii=, rr_dbase=,
gis_dbase=, cluster_dbase=, mdspurpose=, casefile2=, controlfile2=,
popfile2=, maxgeosize=, includepurelytemp=, maxspatialinterp=,
maxcirclepopfile=, maxtempsize=, includepurelyspatial=,
maxtemporalinterp=, includeclusters=, intervalstartrange=,
intervalendrange=, timetrendadjtype=, timetrendpercent=,
adjustmentsbyrrfile=, useadjustmentbyrrfile=, spatialadjtype=,
prospectivestartdate=, earlytermination=, adjustearly=,
secondarycriteria=, reportmaxgeosize=, usereportmaxgeosize=,);
data prms;
length value $135.;
* Input;
value='[Input]'; output;
value="CaseFile=&cases_text..txt"; output; * Case file;
%if &modeltype=1 %then %do;
value="ControlFile=&control_text..txt"; output; * Control file -
only needed when using Bernoulli model;
%end;
%else %if &modeltype=0 %then %do;
value="PopulationFile=&population_text..txt"; output; *
Population file - only needed when using Poisson model;
%end;
value="CoordinatesFile=&coordinates_text..txt"; output; * File
containing coordinates of zip code centroids;
value="UseGridFile=&usegridfile"; output;
value="GridFile=&gridfile"; output;
value="PrecisionCaseTimes=&timeprecision"; output; * 0=None, 1=Year,
2=Month, 3=Day;
value="CoordinatesType=&coordinatestype"; output; * 0=Cartesian,
1=Lat/Long;
value="StartDate=&startdate"; output;
value="EndDate=&enddate"; output;
value=" "; output;
* Analysis;
value='[Analysis]'; output;
value="AnalysisType=&analysistype"; output; * 1=Purely Spatial,
2=Purely Temporal, 3=Retrospective Space-Time, 4=Prospective Space-
Time, 5=N/A, 6=Prospective Purely Temporal;
value="ModelType=&modeltype"; output; * 0=Poisson, 1=Bernoulli,
2=Space-Time Permutation;
value="ScanAreas=&scanareas"; output; * Scan for areas with: 1=High
Rates, 2=Low Rates, 3=High or Low Rates;
value="TimeAggregationUnits=&timeaggunits"; output; * 0=None,
1=Year, 2=Month, 3=Day;
value="TimeAggregationLength=&timeagglength"; output; * positive
integer;
value="MonteCarloReps=&mcreps"; output;
value=" "; output;
* Output;

value='[Output]'; output;
value="ResultsFile=&results_text..txt"; output;
value="SaveSimLLRsASCII=&llr_ascii"; output;
value="SaveSimLLRsDBase=&llr_dbase"; output;
value="IncludeRelativeRisksCensusAreasASCII=&rr_ascii"; output;
value="IncludeRelativeRisksCensusAreasDBase=&rr_dbase"; output;
value="CensusAreasReportedClustersASCII=y"; output;
value="CensusAreasReportedClustersDBase=&gis_dbase"; output;
value="MostLikelyClusterEachCentroidASCII=y"; output;
value="MostLikelyClusterEachCentroidDBase=&cluster_dbase"; output;
value=" "; output;
%if "&datastreams" gt 1 %then %do; * Multiple Data Sets;
value='[Multiple Data Sets]'; output;
value="MultipleDataSetsPurposeType=&mdspurpose"; output; *
0=multivariate, 1=adjustment;
value="CaseFile2=&casefile2..txt"; output; * case data set 2;
%if &modeltype=1 %then %do;
value="ControlFile2=&controlfile2..txt"; output; * control
data 2;
%end;
%else %if &modeltype=1 %then %do;
value="PopulationFile2=&popfile2..txt"; output; * population data
2;
%end;
value=" "; output;
%end;
* Spatial Window;
value='[Spatial Window]'; output;
value="MaxGeographicSize=&maxgeosize"; output; * <=50%;
value="IncludePurelyTemporal=&includepurelytemp"; output;
value="MaxSpatialSizeInterpretation=&maxspatialinterp"; output;
* 0=Percentage, 1=Distance, 2=Percentage of max circle population
file;
value="MaxCirclePopulationFile=&maxcirclepopfile"; output; *
maximum circle size filename;
value=" "; output;
* Temporal Window;
value='[Temporal Window]'; output;
value="MaxTemporalSize=&maxtempsize"; output; * <=90%;
value="IncludePurelySpatial=&includepurelyspatial"; output;
value="MaxTemporalSizeInterpretation=&maxtemporalinterp"; output;
* 0=Percentage, 1=Time;
value="IncludeClusters=&includeclusters"; output; * clusters to
include: 0=All, 1=Alive, 2=Flexible Window;
value=" "; output;
* Space and Time Adjustments;
value='[Space and Time Adjustments]'; output;
value="IntervalStartRange=&intervalstartrange"; output; * flexible
temporal window start range (YYYY/MM/DD,YYYY/MM/DD);
value="IntervalEndRange=&intervalendrange"; output; * flexible
temporal window end range (YYYY/MM/DD,YYYY/MM/DD);

value="TimeTrendAdjustmentType=&timetrendadjtype"; output;
* 0=None, 1=Nonparametric, 2=LogLinearPercentage,
3=CalculatedLogLinearPercentage, 4=TimeStratifiedRandomization;
value="TimeTrendPercentage=&timetrendpercent"; output; * time
trend adjustment percentage (>-100);
value="AdjustmentsByKnownRelativeRisksFilename=&adjustmentsbyrrfile"
; output; * adjustments by known relative risks file name (with HA
Randomization=1 or ...);
value="UseAdjustmentsByRRFile=&useadjustmentbyrrfile"; output; * use
adjustments by known relative risks file? (y/n);
value="SpatialAdjustmentType=&spatialadjtype"; output; * 0=no
spatial adjustment, 1=spatially stratified randomization;
value=" "; output;
* Inference;
value='[Inference]'; output;
if "&adjustearly"='n' then do;
value="ProspectiveStartDate=&enddate"; output;
end; * prospective surveillance start date (YYYY/MM/DD);
else if "&adjustearly"='y' then do;
value="ProspectiveStartDate=&prospectivestartdate"; output;
end; * prospective surveillance start date (YYYY/MM/DD);
value="EarlySimulationTermination=&earlytermination"; output;
value="AdjustForEarlierAnalyses=&adjustearly"; output; *
Prospective only (y/n);
value=" "; output;
* Clusters Reported;
value='[Clusters Reported]'; output;
value="CriteriaForReportingSecondaryClusters=&secondarycriteria";
output; * 0=NoGeoOverlap, 1=NoCentersInOther,
2=NoCentersInMostLikely, 3=NoCentersInLessLikely,
4=NoPairsCentersEachOther, 5=NoRestrictions;
value="MaxReportedGeoClusterSize=&reportmaxgeosize"; output; * < max
geographical cluster size %;
value="UseReportOnlySmallerClusters=&usereportmaxgeosize"; output;
value=" "; output;
* Batch Mode Features;
value='[BatchMode Features]'; output;
value='ValidateParameters=y'; output;
value=" "; output;
* System Features;
value='[System]'; output;
value='; system setting - do not modify'; output;
value='Version=5.1.0'; output;
value=' '; output;
run;
data _null_;
set prms;
file "&satscandir.\parameterfile.prm"; * Save the parameter file in
the SaTScan directory;
put value;
run;

/* Check for the existence of the parameter file. If it does not
exist, write an error message in the log */
%if %sysfunc(fileexist(&satscandir.\parameterfile.prm))=0 %then %do;
%put ERROR: The file "&satscandir.\parameterfile.prm", which should
contain the parameter file for SaTScan, does not exist.;
%end;
data _null_;
set prms;
file "&results_text..prm"; * Save the parameter file in the SaTScan
directory;
put value;
run;
/* Check for the existence of the parameter file. If it does not
exist, write an error message in the log */
%if %sysfunc(fileexist(&results_text..prm))=0 %then %do;
%put WARNING: The file "&results_text..prm", which should contain
the parameter file for SaTScan, does not exist.;
%end;
%exit: %mend parameters;