ROOT 6.12/07 Reference Guide |
BayesianCalculator is a concrete implementation of IntervalCalculator, providing the computation of a credible interval using a Bayesian method.
The class works only for one single parameter of interest and it integrates the likelihood function with the given prior probability density function to compute the posterior probability. The result of the class is a one dimensional interval (class SimpleInterval ), which is obtained from inverting the cumulative posterior distribution. This calculator works then only for model with a single parameter of interest. The model can instead have several nuisance parameters which are integrated (marginalized) in the computation of the posterior function. The integration and normalization of the posterior is computed using numerical integration methods provided by ROOT. See the MCMCCalculator for model with multiple parameters of interest.
The interface allows one to construct the class by passing the data set, probability density function for the model, the prior functions and then the parameter of interest to scan. The nuisance parameters can also be passed to be marginalized when computing the posterior. Alternatively, the class can be constructed by passing the data and the ModelConfig containing all the needed information (model pdf, prior pdf, parameter of interest, nuisance parameters, etc..)
After configuring the calculator, one only needs to ask GetInterval(), which will return an SimpleInterval object. By default the extrem of the integral are obtained by inverting directly the cumulative posterior distribution. By using the method SetScanOfPosterior(nbins) the interval is then obtained by scanning the posterior function in the given number of points. The first method is in general faster but it requires an integration one extra dimension ( in the poi in addition to the nuisance parameters), therefore in some case it can be less robust.
The class can also return the posterior function (method GetPosteriorFunction) or if needed the normalized posterior function (the posterior pdf) (method GetPosteriorPdf). A posterior plot is also obtained using the GetPosteriorPlot method.
The class allows to use different integration methods for integrating in (marginalizing) the nuisances and in the poi. All the numerical integration methods of ROOT can be used via the method SetIntegrationType (see more in the documentation of this method).
Calculator estimating a credible interval using the Bayesian procedure. The calculator computes given the model the posterior distribution and estimates the credible interval from the given function.
Definition at line 36 of file BayesianCalculator.h.
Public Member Functions | |
BayesianCalculator () | |
default constructor More... | |
BayesianCalculator (RooAbsData &data, RooAbsPdf &pdf, const RooArgSet &POI, RooAbsPdf &priorPdf, const RooArgSet *nuisanceParameters=0) | |
Constructor from data set, model pdf, parameter of interests and prior pdf If nuisance parameters are given they will be integrated according either to the prior or their constraint term included in the model. More... | |
BayesianCalculator (RooAbsData &data, ModelConfig &model) | |
Constructor from a data set and a ModelConfig model pdf, poi and nuisances will be taken from the ModelConfig. More... | |
virtual | ~BayesianCalculator () |
virtual Double_t | ConfidenceLevel () const |
Get the Confidence level for the test. More... | |
void | ForceNuisancePdf (RooAbsPdf &pdf) |
virtual SimpleInterval * | GetInterval () const |
Compute the interval. More... | |
double | GetMode () const |
Returns the value of the parameter for the point in parameter-space that is the most likely. More... | |
RooAbsReal * | GetPosteriorFunction () const |
Build and return the posterior function (not normalized) as a RooAbsReal the posterior is obtained from the product of the likelihood function and the prior pdf which is then integrated in the nuisance parameters (if existing). More... | |
RooAbsPdf * | GetPosteriorPdf () const |
Build and return the posterior pdf (i.e posterior function normalized to all range of poi) Note that an extra integration in the POI is required for the normalization NOTE: user must delete the returned object. More... | |
RooPlot * | GetPosteriorPlot (bool norm=false, double precision=0.01) const |
return a RooPlot with the posterior and the credibility region NOTE: User takes ownership of the returned object More... | |
void | SetBrfPrecision (double precision) |
virtual void | SetConditionalObservables (const RooArgSet &set) |
virtual void | SetConfidenceLevel (Double_t cl) |
set the confidence level for the interval (e.g. 0.95 for a 95% Confidence Interval) More... | |
virtual void | SetData (RooAbsData &data) |
Set the DataSet ( add to the the workspace if not already there ?) More... | |
virtual void | SetGlobalObservables (const RooArgSet &set) |
void | SetIntegrationType (const char *type) |
set the integration type (possible type are) : More... | |
void | SetLeftSideTailFraction (Double_t leftSideFraction) |
virtual void | SetModel (const ModelConfig &model) |
set the model to use The model pdf, prior pdf, parameter of interest and nuisances will be taken according to the model More... | |
virtual void | SetNuisanceParameters (const RooArgSet &set) |
virtual void | SetNumIters (Int_t numIters) |
virtual void | SetParameters (const RooArgSet &set) |
virtual void | SetPriorPdf (RooAbsPdf &pdf) |
void | SetScanOfPosterior (int nbin=100) |
void | SetShortestInterval () |
virtual void | SetTestSize (Double_t size) |
set the size of the test (rate of Type I error) ( e.g. 0.05 for a 95% Confidence Interval) More... | |
virtual Double_t | Size () const |
Get the size of the test (eg. rate of Type I error) More... | |
Public Member Functions inherited from RooStats::IntervalCalculator | |
virtual | ~IntervalCalculator () |
Public Member Functions inherited from TNamed | |
TNamed () | |
TNamed (const char *name, const char *title) | |
TNamed (const TString &name, const TString &title) | |
TNamed (const TNamed &named) | |
TNamed copy ctor. More... | |
virtual | ~TNamed () |
TNamed destructor. More... | |
virtual void | Clear (Option_t *option="") |
Set name and title to empty strings (""). More... | |
virtual TObject * | Clone (const char *newname="") const |
Make a clone of an object using the Streamer facility. More... | |
virtual Int_t | Compare (const TObject *obj) const |
Compare two TNamed objects. More... | |
virtual void | Copy (TObject &named) const |
Copy this to obj. More... | |
virtual void | FillBuffer (char *&buffer) |
Encode TNamed into output buffer. More... | |
virtual const char * | GetName () const |
Returns name of object. More... | |
virtual const char * | GetTitle () const |
Returns title of object. More... | |
virtual ULong_t | Hash () const |
Return hash value for this object. More... | |
virtual Bool_t | IsSortable () const |
virtual void | ls (Option_t *option="") const |
List TNamed name and title. More... | |
TNamed & | operator= (const TNamed &rhs) |
TNamed assignment operator. More... | |
virtual void | Print (Option_t *option="") const |
Print TNamed name and title. More... | |
virtual void | SetName (const char *name) |
Set the name of the TNamed. More... | |
virtual void | SetNameTitle (const char *name, const char *title) |
Set all the TNamed parameters (name and title). More... | |
virtual void | SetTitle (const char *title="") |
Set the title of the TNamed. More... | |
virtual Int_t | Sizeof () const |
Return size of the TNamed part of the TObject. More... | |
Public Member Functions inherited from TObject | |
TObject () | |
TObject constructor. More... | |
TObject (const TObject &object) | |
TObject copy ctor. More... | |
virtual | ~TObject () |
TObject destructor. More... | |
void | AbstractMethod (const char *method) const |
Use this method to implement an "abstract" method that you don't want to leave purely abstract. More... | |
virtual void | AppendPad (Option_t *option="") |
Append graphics object to current pad. More... | |
virtual void | Browse (TBrowser *b) |
Browse object. May be overridden for another default action. More... | |
ULong_t | CheckedHash () |
Checked and record whether for this class has a consistent Hash/RecursiveRemove setup (*) and then return the regular Hash value for this object. More... | |
virtual const char * | ClassName () const |
Returns name of class to which the object belongs. More... | |
virtual void | Delete (Option_t *option="") |
Delete this object. More... | |
virtual Int_t | DistancetoPrimitive (Int_t px, Int_t py) |
Computes distance from point (px,py) to the object. More... | |
virtual void | Draw (Option_t *option="") |
Default Draw method for all objects. More... | |
virtual void | DrawClass () const |
Draw class inheritance tree of the class to which this object belongs. More... | |
virtual TObject * | DrawClone (Option_t *option="") const |
Draw a clone of this object in the current selected pad for instance with: gROOT->SetSelectedPad(gPad) . More... | |
virtual void | Dump () const |
Dump contents of object on stdout. More... | |
virtual void | Error (const char *method, const char *msgfmt,...) const |
Issue error message. More... | |
virtual void | Execute (const char *method, const char *params, Int_t *error=0) |
Execute method on this object with the given parameter string, e.g. More... | |
virtual void | Execute (TMethod *method, TObjArray *params, Int_t *error=0) |
Execute method on this object with parameters stored in the TObjArray. More... | |
virtual void | ExecuteEvent (Int_t event, Int_t px, Int_t py) |
Execute action corresponding to an event at (px,py). More... | |
virtual void | Fatal (const char *method, const char *msgfmt,...) const |
Issue fatal error message. More... | |
virtual TObject * | FindObject (const char *name) const |
Must be redefined in derived classes. More... | |
virtual TObject * | FindObject (const TObject *obj) const |
Must be redefined in derived classes. More... | |
virtual Option_t * | GetDrawOption () const |
Get option used by the graphics system to draw this object. More... | |
virtual const char * | GetIconName () const |
Returns mime type name of object. More... | |
virtual char * | GetObjectInfo (Int_t px, Int_t py) const |
Returns string containing info about the object at position (px,py). More... | |
virtual Option_t * | GetOption () const |
virtual UInt_t | GetUniqueID () const |
Return the unique object id. More... | |
virtual Bool_t | HandleTimer (TTimer *timer) |
Execute action in response of a timer timing out. More... | |
Bool_t | HasInconsistentHash () const |
Return true is the type of this object is known to have an inconsistent setup for Hash and RecursiveRemove (i.e. More... | |
virtual void | Info (const char *method, const char *msgfmt,...) const |
Issue info message. More... | |
virtual Bool_t | InheritsFrom (const char *classname) const |
Returns kTRUE if object inherits from class "classname". More... | |
virtual Bool_t | InheritsFrom (const TClass *cl) const |
Returns kTRUE if object inherits from TClass cl. More... | |
virtual void | Inspect () const |
Dump contents of this object in a graphics canvas. More... | |
void | InvertBit (UInt_t f) |
virtual Bool_t | IsEqual (const TObject *obj) const |
Default equal comparison (objects are equal if they have the same address in memory). More... | |
virtual Bool_t | IsFolder () const |
Returns kTRUE in case object contains browsable objects (like containers or lists of other objects). More... | |
R__ALWAYS_INLINE Bool_t | IsOnHeap () const |
R__ALWAYS_INLINE Bool_t | IsZombie () const |
void | MayNotUse (const char *method) const |
Use this method to signal that a method (defined in a base class) may not be called in a derived class (in principle against good design since a child class should not provide less functionality than its parent, however, sometimes it is necessary). More... | |
virtual Bool_t | Notify () |
This method must be overridden to handle object notification. More... | |
void | Obsolete (const char *method, const char *asOfVers, const char *removedFromVers) const |
Use this method to declare a method obsolete. More... | |
void | operator delete (void *ptr) |
Operator delete. More... | |
void | operator delete[] (void *ptr) |
Operator delete []. More... | |
void * | operator new (size_t sz) |
void * | operator new (size_t sz, void *vp) |
void * | operator new[] (size_t sz) |
void * | operator new[] (size_t sz, void *vp) |
TObject & | operator= (const TObject &rhs) |
TObject assignment operator. More... | |
virtual void | Paint (Option_t *option="") |
This method must be overridden if a class wants to paint itself. More... | |
virtual void | Pop () |
Pop on object drawn in a pad to the top of the display list. More... | |
virtual Int_t | Read (const char *name) |
Read contents of object with specified name from the current directory. More... | |
virtual void | RecursiveRemove (TObject *obj) |
Recursively remove this object from a list. More... | |
void | ResetBit (UInt_t f) |
virtual void | SaveAs (const char *filename="", Option_t *option="") const |
Save this object in the file specified by filename. More... | |
virtual void | SavePrimitive (std::ostream &out, Option_t *option="") |
Save a primitive as a C++ statement(s) on output stream "out". More... | |
void | SetBit (UInt_t f, Bool_t set) |
Set or unset the user status bits as specified in f. More... | |
void | SetBit (UInt_t f) |
virtual void | SetDrawOption (Option_t *option="") |
Set drawing option for object. More... | |
virtual void | SetUniqueID (UInt_t uid) |
Set the unique object id. More... | |
virtual void | SysError (const char *method, const char *msgfmt,...) const |
Issue system error message. More... | |
R__ALWAYS_INLINE Bool_t | TestBit (UInt_t f) const |
Int_t | TestBits (UInt_t f) const |
virtual void | UseCurrentStyle () |
Set current style settings in this object This function is called when either TCanvas::UseCurrentStyle or TROOT::ForceStyle have been invoked. More... | |
virtual void | Warning (const char *method, const char *msgfmt,...) const |
Issue warning message. More... | |
virtual Int_t | Write (const char *name=0, Int_t option=0, Int_t bufsize=0) |
Write this object to the current directory. More... | |
virtual Int_t | Write (const char *name=0, Int_t option=0, Int_t bufsize=0) const |
Write this object to the current directory. More... | |
Protected Member Functions | |
void | ApproximatePosterior () const |
approximate posterior in nbins using a TF1 scan the poi values and evaluate the posterior at each point and save the result in a cloned TF1 For each point the posterior is evaluated by integrating the nuisance parameters More... | |
void | ClearAll () const |
clear all cached pdf objects More... | |
void | ComputeIntervalFromApproxPosterior (double c1, double c2) const |
compute the interval using the approximate posterior function More... | |
void | ComputeIntervalFromCdf (double c1, double c2) const |
internal function compute the interval using Cdf integration More... | |
void | ComputeIntervalUsingRooFit (double c1, double c2) const |
internal function compute the interval using RooFit More... | |
void | ComputeShortestInterval () const |
compute the shortest interval More... | |
Protected Member Functions inherited from TObject | |
virtual void | DoError (int level, const char *location, const char *fmt, va_list va) const |
Interface to ErrorHandler (protected). More... | |
void | MakeZombie () |
Additional Inherited Members | |
Public Types inherited from TObject | |
enum | { kIsOnHeap = 0x01000000, kNotDeleted = 0x02000000, kZombie = 0x04000000, kInconsistent = 0x08000000, kBitMask = 0x00ffffff } |
enum | { kSingleKey = BIT(0), kOverwrite = BIT(1), kWriteDelete = BIT(2) } |
enum | EDeprecatedStatusBits { kObjInCanvas = BIT(3) } |
enum | EStatusBits { kCanDelete = BIT(0), kMustCleanup = BIT(3), kIsReferenced = BIT(4), kHasUUID = BIT(5), kCannotPick = BIT(6), kNoContextMenu = BIT(8), kInvalidObject = BIT(13) } |
Static Public Member Functions inherited from TObject | |
static Long_t | GetDtorOnly () |
Return destructor only flag. More... | |
static Bool_t | GetObjectStat () |
Get status of object stat flag. More... | |
static void | SetDtorOnly (void *obj) |
Set destructor only flag. More... | |
static void | SetObjectStat (Bool_t stat) |
Turn on/off tracking of objects in the TObjectTable. More... | |
Protected Attributes inherited from TNamed | |
TString | fName |
TString | fTitle |
#include <RooStats/BayesianCalculator.h>
RooStats::BayesianCalculator::BayesianCalculator | ( | ) |
default constructor
Definition at line 645 of file BayesianCalculator.cxx.
RooStats::BayesianCalculator::BayesianCalculator | ( | RooAbsData & | data, |
RooAbsPdf & | pdf, | ||
const RooArgSet & | POI, | ||
RooAbsPdf & | priorPdf, | ||
const RooArgSet * | nuisanceParameters = 0 |
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) |
Constructor from data set, model pdf, parameter of interests and prior pdf If nuisance parameters are given they will be integrated according either to the prior or their constraint term included in the model.
Definition at line 667 of file BayesianCalculator.cxx.
RooStats::BayesianCalculator::BayesianCalculator | ( | RooAbsData & | data, |
ModelConfig & | model | ||
) |
Constructor from a data set and a ModelConfig model pdf, poi and nuisances will be taken from the ModelConfig.
Definition at line 698 of file BayesianCalculator.cxx.
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Definition at line 718 of file BayesianCalculator.cxx.
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approximate posterior in nbins using a TF1 scan the poi values and evaluate the posterior at each point and save the result in a cloned TF1 For each point the posterior is evaluated by integrating the nuisance parameters
Definition at line 1322 of file BayesianCalculator.cxx.
clear all cached pdf objects
Definition at line 727 of file BayesianCalculator.cxx.
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compute the interval using the approximate posterior function
Definition at line 1367 of file BayesianCalculator.cxx.
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internal function compute the interval using Cdf integration
Definition at line 1246 of file BayesianCalculator.cxx.
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internal function compute the interval using RooFit
Definition at line 1194 of file BayesianCalculator.cxx.
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compute the shortest interval
Definition at line 1387 of file BayesianCalculator.cxx.
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Get the Confidence level for the test.
Implements RooStats::IntervalCalculator.
Definition at line 104 of file BayesianCalculator.h.
Definition at line 138 of file BayesianCalculator.h.
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Compute the interval.
By Default a central interval is computed and the result is a SimpleInterval object.
Using the method (to be called before SetInterval) SetLeftSideTailFraction the user can choose the type of interval. By default the returned interval is a central interval with the confidence level specified previously in the constructor ( LeftSideTailFraction = 0.5).
NOTE: The BayesianCalculator covers only the case with one single parameter of interest
NOTE: User takes ownership of the returned object
Implements RooStats::IntervalCalculator.
Definition at line 1096 of file BayesianCalculator.cxx.
double RooStats::BayesianCalculator::GetMode | ( | ) | const |
Returns the value of the parameter for the point in parameter-space that is the most likely.
How do we do if there are points that are equi-probable? use approximate posterior t.b.d use real function to find the mode
Definition at line 1183 of file BayesianCalculator.cxx.
RooAbsReal * RooStats::BayesianCalculator::GetPosteriorFunction | ( | ) | const |
Build and return the posterior function (not normalized) as a RooAbsReal the posterior is obtained from the product of the likelihood function and the prior pdf which is then integrated in the nuisance parameters (if existing).
A prior function for the nuisance can be specified either in the prior pdf object or in the model itself. If no prior nuisance is specified, but prior parameters are then the integration is performed assuming a flat prior for the nuisance parameters.
NOTE: the return object is managed by the class, users do not need to delete it
Definition at line 782 of file BayesianCalculator.cxx.
RooAbsPdf * RooStats::BayesianCalculator::GetPosteriorPdf | ( | ) | const |
Build and return the posterior pdf (i.e posterior function normalized to all range of poi) Note that an extra integration in the POI is required for the normalization NOTE: user must delete the returned object.
Definition at line 983 of file BayesianCalculator.cxx.
RooPlot * RooStats::BayesianCalculator::GetPosteriorPlot | ( | bool | norm = false , |
double | precision = 0.01 |
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) | const |
return a RooPlot with the posterior and the credibility region NOTE: User takes ownership of the returned object
Definition at line 1002 of file BayesianCalculator.cxx.
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Definition at line 117 of file BayesianCalculator.h.
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Definition at line 88 of file BayesianCalculator.h.
set the confidence level for the interval (e.g. 0.95 for a 95% Confidence Interval)
Implements RooStats::IntervalCalculator.
Definition at line 100 of file BayesianCalculator.h.
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Set the DataSet ( add to the the workspace if not already there ?)
Implements RooStats::IntervalCalculator.
Definition at line 68 of file BayesianCalculator.h.
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Definition at line 92 of file BayesianCalculator.h.
void RooStats::BayesianCalculator::SetIntegrationType | ( | const char * | type | ) |
set the integration type (possible type are) :
Extra integration types are:
Definition at line 1074 of file BayesianCalculator.cxx.
Definition at line 110 of file BayesianCalculator.h.
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set the model to use The model pdf, prior pdf, parameter of interest and nuisances will be taken according to the model
Implements RooStats::IntervalCalculator.
Definition at line 752 of file BayesianCalculator.cxx.
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Definition at line 81 of file BayesianCalculator.h.
Definition at line 129 of file BayesianCalculator.h.
Definition at line 78 of file BayesianCalculator.h.
Definition at line 84 of file BayesianCalculator.h.
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Definition at line 122 of file BayesianCalculator.h.
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Definition at line 114 of file BayesianCalculator.h.
set the size of the test (rate of Type I error) ( e.g. 0.05 for a 95% Confidence Interval)
Implements RooStats::IntervalCalculator.
Definition at line 95 of file BayesianCalculator.h.
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Get the size of the test (eg. rate of Type I error)
Implements RooStats::IntervalCalculator.
Definition at line 102 of file BayesianCalculator.h.
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Definition at line 175 of file BayesianCalculator.h.
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Definition at line 181 of file BayesianCalculator.h.
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Definition at line 166 of file BayesianCalculator.h.
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Definition at line 160 of file BayesianCalculator.h.
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Definition at line 167 of file BayesianCalculator.h.
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Definition at line 172 of file BayesianCalculator.h.
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Definition at line 186 of file BayesianCalculator.h.
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Definition at line 180 of file BayesianCalculator.h.
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Definition at line 171 of file BayesianCalculator.h.
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Definition at line 170 of file BayesianCalculator.h.
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Definition at line 176 of file BayesianCalculator.h.
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Definition at line 178 of file BayesianCalculator.h.
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Definition at line 182 of file BayesianCalculator.h.
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Definition at line 165 of file BayesianCalculator.h.
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Definition at line 164 of file BayesianCalculator.h.
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Definition at line 183 of file BayesianCalculator.h.
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Definition at line 162 of file BayesianCalculator.h.
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Definition at line 174 of file BayesianCalculator.h.
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Definition at line 173 of file BayesianCalculator.h.
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Definition at line 163 of file BayesianCalculator.h.
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Definition at line 179 of file BayesianCalculator.h.
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Definition at line 184 of file BayesianCalculator.h.