R/zzz.R

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

.onAttach <- function(libname, pkgname) { 
  packageStartupMessage("rsatscan only does anything useful if you have SaTScan")
  packageStartupMessage("See http://www.satscan.org/ for free access")

  #These resemble defaults in satscan, but save all the dbase files
  
  ssenv <<- new.env(parent=emptyenv())
  x = c("[Input]",";case data filename","CaseFile=",";control data filename","ControlFile=",";time precision (0=None, 1=Year, 2=Month, 3=Day, 4=Generic)","PrecisionCaseTimes=1",";study period start date (YYYY/MM/DD)","StartDate=2000/1/1",";study period end date (YYYY/MM/DD)","EndDate=2000/12/31",";population data filename","PopulationFile=",";coordinate data filename","CoordinatesFile=",";use grid file? (y/n)","UseGridFile=n",";grid data filename","GridFile=",";coordinate type (0=Cartesian, 1=latitude/longitude)","CoordinatesType=1","","[Analysis]",";analysis type (1=Purely Spatial, 2=Purely Temporal, 3=Retrospective Space-Time, 4=Prospective Space-Time, 5=Spatial Variation in Temporal Trends, 6=Prospective Purely Temporal)","AnalysisType=1",";model type (0=Discrete Poisson, 1=Bernoulli, 2=Space-Time Permutation, 3=Ordinal, 4=Exponential, 5=Normal, 6=Continuous Poisson, 7=Multinomial)","ModelType=0",
        ";scan areas (1=High Rates(Poison,Bernoulli,STP); High Values(Ordinal,Normal); Short Survival(Exponential), 2=Low Rates(Poison,Bernoulli,STP); Low Values(Ordinal,Normal); Long Survival(Exponential), 3=Both Areas)","ScanAreas=1",";time aggregation units (0=None, 1=Year, 2=Month, 3=Day, 4=Generic)","TimeAggregationUnits=1",";time aggregation length (Positive Integer)","TimeAggregationLength=1","","[Output]",";analysis results output filename","ResultsFile=",";output Google Earth KML file (y/n)","OutputGoogleEarthKML=n",";output shapefiles (y/n)","OutputShapefiles=y",";output cluster information in ASCII format? (y/n)","MostLikelyClusterEachCentroidASCII=n",";output cluster information in dBase format? (y/n)","MostLikelyClusterEachCentroidDBase=y",";output cluster case information in ASCII format? (y/n)","MostLikelyClusterCaseInfoEachCentroidASCII=n",";output cluster case information in dBase format? (y/n)",
        "MostLikelyClusterCaseInfoEachCentroidDBase=y",";output location information in ASCII format? (y/n)","CensusAreasReportedClustersASCII=n",";output location information in dBase format? (y/n)","CensusAreasReportedClustersDBase=y",";output relative risks in ASCII format? (y/n)","IncludeRelativeRisksCensusAreasASCII=n",";output relative risks in dBase format? (y/n)","IncludeRelativeRisksCensusAreasDBase=y",";output simulated log likelihoods ratios in ASCII format? (y/n)","SaveSimLLRsASCII=n",";output simulated log likelihoods ratios in dBase format? (y/n)","SaveSimLLRsDBase=y","","[Multiple Data Sets]","; multiple data sets purpose type (0=Multivariate, 1=Adjustment)","MultipleDataSetsPurposeType=0","","[Data Checking]",";study period data check (0=Strict Bounds, 1=Relaxed Bounds)","StudyPeriodCheckType=0",";geographical coordinates data check (0=Strict Coordinates, 1=Relaxed Coordinates)",
        "GeographicalCoordinatesCheckType=0","","[Spatial Neighbors]",";use neighbors file (y/n)","UseNeighborsFile=n",";neighbors file","NeighborsFilename=",";use meta locations file (y/n)","UseMetaLocationsFile=n",";meta locations file","MetaLocationsFilename=",";multiple coordinates type (0=OnePerLocation, 1=AtLeastOneLocation, 2=AllLocations)","MultipleCoordinatesType=0","","[Spatial Window]",";maximum spatial size in population at risk (<=50%)","MaxSpatialSizeInPopulationAtRisk=50",";restrict maximum spatial size - max circle file? (y/n)","UseMaxCirclePopulationFileOption=n",";maximum spatial size in max circle population file (<=50%)","MaxSpatialSizeInMaxCirclePopulationFile=50",";maximum circle size filename","MaxCirclePopulationFile=",";restrict maximum spatial size - distance? (y/n)","UseDistanceFromCenterOption=n",";maximum spatial size in distance from center (positive integer)",
        "MaxSpatialSizeInDistanceFromCenter=1",";include purely temporal clusters? (y/n)","IncludePurelyTemporal=n",";window shape (0=Circular, 1=Elliptic)","SpatialWindowShapeType=0",";elliptic non-compactness penalty (0=NoPenalty, 1=MediumPenalty, 2=StrongPenalty)","NonCompactnessPenalty=1",";isotonic scan (0=Standard, 1=Monotone)","IsotonicScan=0","","[Temporal Window]",";how max temporal size should be interpretted (0=Percentage, 1=Time)","MaxTemporalSizeInterpretation=0",";maximum temporal cluster size (<=90%)","MaxTemporalSize=50",";include purely spatial clusters? (y/n)","IncludePurelySpatial=n",";temporal clusters evaluated (0=All, 1=Alive, 2=Flexible Window)","IncludeClusters=0",";flexible temporal window start range (YYYY/MM/DD,YYYY/MM/DD)","IntervalStartRange=2000/1/1,2000/12/31",";flexible temporal window end range (YYYY/MM/DD,YYYY/MM/DD)","IntervalEndRange=2000/1/1,2000/12/31","",
        "[Space and Time Adjustments]",";time trend adjustment type (0=None, 1=Nonparametric, 2=LogLinearPercentage, 3=CalculatedLogLinearPercentage, 4=TimeStratifiedRandomization, 5=CalculatedQuadraticPercentage)","TimeTrendAdjustmentType=0",";time trend adjustment percentage (>-100)","TimeTrendPercentage=0",";time trend type - SVTT only (Linear=0, Quadratic=1)","TimeTrendType=0",";adjust for weekly trends, nonparametric","AdjustForWeeklyTrends=n",";spatial adjustments type (0=No Spatial Adjustment, 1=Spatially Stratified Randomization)","SpatialAdjustmentType=0",";use adjustments by known relative risks file? (y/n)","UseAdjustmentsByRRFile=n",";adjustments by known relative risks file name (with HA Randomization=1)","AdjustmentsByKnownRelativeRisksFilename=","","[Inference]",";p-value reporting type (Default p-value=0, Standard Monte Carlo=1, Early Termination=2, Gumbel p-value=3) ",
        "PValueReportType=0",";early termination threshold","EarlyTerminationThreshold=50",";report Gumbel p-values (y/n)","ReportGumbel=n",";Monte Carlo replications (0, 9, 999, n999)","MonteCarloReps=999",";adjust for earlier analyses(prospective analyses only)? (y/n)","AdjustForEarlierAnalyses=n",";prospective surveillance start date (YYYY/MM/DD)","ProspectiveStartDate=2000/12/31",";perform iterative scans? (y/n)","IterativeScan=n",";maximum iterations for iterative scan (0-32000)","IterativeScanMaxIterations=10",";max p-value for iterative scan before cutoff (0.000-1.000)","IterativeScanMaxPValue=0.05","","[Power Evaluation]",";perform power evaluation - Poisson only (y/n)","PerformPowerEvaluation=n",";power evaluation method (0=Analysis And Power Evaluation Together, 1=Only Power Evaluation With Case File, 2=Only Power Evaluation With Defined Total Cases)","PowerEvaluationsMethod=0",
        ";total cases in power evaluation","PowerEvaluationTotalCases=600",";critical value type (0=Monte Carlo, 1=Gumbel, 2=User Specified Values)","CriticalValueType=0",";power evaluation critical value .05 (> 0)","CriticalValue05=0",";power evaluation critical value .001 (> 0)","CriticalValue01=0",";power evaluation critical value .001 (> 0)","CriticalValue001=0",";power estimation type (0=Monte Carlo, 1=Gumbel)","PowerEstimationType=0",";number of replications in power step","NumberPowerReplications=1000",";power evaluation alternative hypothesis filename","AlternativeHypothesisFilename=",";power evaluation simulation method for power step (0=Null Randomization, 1=N/A, 2=File Import)","PowerEvaluationsSimulationMethod=0",";power evaluation simulation data source filename","PowerEvaluationsSimulationSourceFilename=",";report power evaluation randomization data from power step (y/n)",
        "ReportPowerEvaluationSimulationData=n",";power evaluation simulation data output filename","PowerEvaluationsSimulationOutputFilename=","","[Spatial Output]",";automatically launch Google Earth - gui only (y/n)","LaunchKMLViewer=y",";create compressed KMZ file instead of KML file (y/n)","CompressKMLtoKMZ=n",";whether to include cluster locations kml output (y/n)","IncludeClusterLocationsKML=y",";threshold for generating separate kml files for cluster locations (positive integer)","ThresholdLocationsSeparateKML=1000",";report hierarchical clusters (y/n)","ReportHierarchicalClusters=y",";criteria for reporting secondary clusters(0=NoGeoOverlap, 1=NoCentersInOther, 2=NoCentersInMostLikely,  3=NoCentersInLessLikely, 4=NoPairsCentersEachOther, 5=NoRestrictions)","CriteriaForReportingSecondaryClusters=0",";report gini clusters (y/n)","ReportGiniClusters=y",";gini index cluster reporting type (0=optimal index only, 1=all values)",
        "GiniIndexClusterReportingType=0",";spatial window maxima stops (comma separated decimal values[<=50%] )","SpatialMaxima=1,2,3,4,5,6,8,10,12,15,20,25,30,40,50",";max p-value for clusters used in calculation of index based coefficients (0.000-1.000)","GiniIndexClustersPValueCutOff=0.05",";report gini index coefficents to results file (y/n)","ReportGiniIndexCoefficents=n",";restrict reported clusters to maximum geographical cluster size? (y/n)","UseReportOnlySmallerClusters=n",";maximum reported spatial size in population at risk (<=50%)","MaxSpatialSizeInPopulationAtRisk_Reported=50",";restrict maximum reported spatial size - max circle file? (y/n)","UseMaxCirclePopulationFileOption_Reported=n",";maximum reported spatial size in max circle population file (<=50%)","MaxSizeInMaxCirclePopulationFile_Reported=50",";restrict maximum reported spatial size - distance? (y/n)","UseDistanceFromCenterOption_Reported=n",
        ";maximum reported spatial size in distance from center (positive integer)","MaxSpatialSizeInDistanceFromCenter_Reported=1","","[Temporal Output]",";output temporal graph HTML file (y/n)","OutputTemporalGraphHTML=n","","[Other Output]",";report critical values for .01 and .05? (y/n)","CriticalValue=n",";report cluster rank (y/n)","ReportClusterRank=n",";print ascii headers in output files (y/n)","PrintAsciiColumnHeaders=n","","[Elliptic Scan]",";elliptic shapes - one value for each ellipse (comma separated decimal values)","EllipseShapes=1.5,2,3,4,5",";elliptic angles - one value for each ellipse (comma separated integer values)","EllipseAngles=4,6,9,12,15","","[Power Simulations]",";simulation methods (0=Null Randomization, 1=N/A, 2=File Import)","SimulatedDataMethodType=0",";simulation data input file name (with File Import=2)","SimulatedDataInputFilename=",
        ";print simulation data to file? (y/n)","PrintSimulatedDataToFile=n",";simulation data output filename","SimulatedDataOutputFilename=","","[Run Options]",";number of parallel processes to execute (0=All Processors, x=At Most X Processors)","NumberParallelProcesses=0",";suppressing warnings? (y/n)","SuppressWarnings=n",";log analysis run to history file? (y/n)","LogRunToHistoryFile=y",";analysis execution method  (0=Automatic, 1=Successively, 2=Centrically)","ExecutionType=0","","[System]",";system setting - do not modify","Version=9.2.0","")
  
  ssenv$.ss.params.defaults = x
  ssenv$.ss.params = x
  
}