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Settings

DynaFit Settings

Listing of initialization file ./system/DynaFit/settings.txt

{DynaFit}
   RandomizationSeed                = 4357 ; | 0 for system time
   DefaultFittingAlgorithm          = trust-region ; | marquardt

{ODESolver}
   Iterations                       = 1000
   AbsoluteError                    = 1.e-14
   RelativeError                    = 1.e-8

{TrustRegion}
   ConstrainedFit                   = y
   RobustFit                        = n
   EqualizeDatasets                 = n
   AutomaticScaling                 = n
   FixedScaleValue                  = 1

{Marquardt}
   IterationsPerParameter           = 100
   RestartPerturbation              = 0.1
   Restarts                         = 2
   RestartsConfidence               = 1
   RobustFit                        = n
   EqualizeDatasets                 = n
   FixRedundantParameters           = y

{ConfidenceIntervals}
   LevelPercent                     = 95
   OnlyConstants                    = n
   JointProbability                 = n
   MaxSteps                         = 30
   SquaresIncreasePercent           = 0 ; | 10 for continuous assays

{DifferentialEvolution}
   PopulationSizeFixed              = 0
   PopulationSizeMinimal            = 1000
   PopulationSizePerParameter       = 5
   PopulationSizePerOrderOfMag      = 3
   MinimumGenerationsPerParameter   = 5
   MaximumGenerationsPerParameter   = 100
   MaximumEvolutions                = 6
   MinimumEvolutions                = 6
   RandomSeed                       = 1234
   RootMeanSquareMin                = 0
   RootMeanSquareMax                = 0
   OutputTextFileType               = csv ; | txt

{Constraints}
   Constants                        = 1000000
   Responses                        = 1000000
   Concentrations                   = 1000
   AllParametersConstrained         = y
   AllParametersRelativeBound       = 1000000

{Filter}
   XMin                             = 0
   XMax                             = 0
   XShift                           = 0
   XFirstMesh                       = 0
   PointsPerDataset                 = 0
   ExponentialSpacing               = n
   ReadEveryNthPoint                = 0
   SkipFirstNPoints                 = 0
   TimeInitialRate                  = 1
   PrintInitialRate                 = y
   SmoothData                       = n
   SmoothingMethod                  = savitzky-golay ; | average
   SavitzkyGolayWindow              = 10
   SavitzkyGolayDegree              = 4
   ExtrapolationMethod              = quadratic ; | linear
   SmoothingPasses                  = 4
   AverageReplicates                = n
   ZeroBaselineSignal               = n

{PieceWiseLinearFit}
   Points                           = 0
   Segments                         = 4
   Time                             = 0
   Overlap                          = n

{Output}
   UseDefaultDirectory              = y
   Autocorrelations                 = n
   ConfidenceBands                  = n
   PredictionBands                  = n
   WriteTXT                         = n
   WriteEPS                         = y
   ColorEPS                         = y
   ResidualsEPS                     = y
   WriteTeX                         = n
   XAxisUnit                        =
   XAxisLabel                       =
   YAxisLabel                       =
   BlackBackground                  = y
   IncludeXZero                     = n
   IncludeYZero                     = n
   InitialRateDigits                = 4
   StartDefaultBrowser              = n
   PlotRatesLogarithmic             = n
   PlotStateLogarithmic             = n
   SignificantDigits                = 2
   ResidualRange                    = 0   

{MonteCarlo}
   PerformInitialFit                = y
   Runs                             = 1000
   RandomizationMethod              = simulate  ;  | shuffle | shift
   Distribution                     = normal    ;  | cauchy | logistic | uniform
   StandardDeviationSource          = fit       ;  | data | explicit
   StandardDeviation                = 1.2
   SignificantDigits                = 4
   HistogramBuckets                 = 20
   TruncateMeanPercent              = 5
   ColorOutput                      = y
   RandomizationSeed                = 1267
   ConcentrationErrorPercent        = 0
   OriginalEstimates                = n
   ConfidenceLevel                  = 100

{EstimateScan}
   ReportSizeMax                    = 1000
   RefineMarquardt                  = 10

{ExponentialFit}
   Degree                           = 4
   Automatic                        = y
   AllowOscillations                = n
   TinyAmplitudes                   = 0 ; or 0.000001
   RefineMarquardt                  = n

{OptimalDesign}
   Algorithm                        = AS ; | DE | BFGS
   Function                         = D  ; | T  | E  | V  ; see manual

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Program DynaFit ver. 4.07.115 Copyright © 1996-2016 by BioKin Ltd.
Wed Oct 05 08:33:47 2016
Licensed to: DynaFit Demo (BioKin Ltd.) <dynafit@biokin.com>
Computer ID: n/a