Changeset 693 for library/bdm

Timestamp:

11/02/09 17:27:29 (15 years ago)

Author:

mido

Message:

mpdf renamed to pdf in the whole library

Location:

library/bdm

Files:

• CMakeLists.txt (modified) (1 diff)
• base/bdmbase.cpp (modified) (4 diffs)
• base/bdmbase.h (modified) (16 diffs)
• base/datasources.cpp (modified) (1 diff)
• base/datasources.h (modified) (10 diffs)
• estim/particles.h (modified) (9 diffs)
• stat/emix.cpp (modified) (3 diffs)
• stat/emix.h (modified) (9 diffs)
• stat/exp_family.h (modified) (27 diffs)
• stat/merger.cpp (modified) (5 diffs)
• stat/merger.h (modified) (7 diffs)

library/bdm/CMakeLists.txt

@@ -18 +18 @@
 IF(WIN32)
    SET(bdm_support ${bdm_support} dirent.c dirent.h)
-   ADD_DEFINITIONS(-DLIBCONFIG_STATIC -DLIBCONFIGXX_STATIC)
 ENDIF()
 

library/bdm/base/bdmbase.cpp

@@ -146 +146 @@
 }
 
-shared_ptr<mpdf> epdf::condition ( const RV &rv ) const {
+shared_ptr<pdf> epdf::condition ( const RV &rv ) const {
         bdm_warning ( "Not implemented" );
-        return shared_ptr<mpdf>();
+        return shared_ptr<pdf>();
 }
 
@@ -180 +180 @@
 }
 
-mat mpdf::samplecond_m ( const vec &cond, int N ) {
+mat pdf::samplecond_m ( const vec &cond, int N ) {
         mat M ( dimension(), N );
         for ( int i = 0; i < N; i++ ) {
@@ -189 +189 @@
 }
 
-void mpdf::from_setting ( const Setting &set ) {
+void pdf::from_setting ( const Setting &set ) {
         shared_ptr<RV> r = UI::build<RV> ( set, "rv", UI::optional );
         if ( r ) {
@@ -373 +373 @@
 }
 
-RV get_composite_rv ( const Array<shared_ptr<mpdf> > &mpdfs,
+RV get_composite_rv ( const Array<shared_ptr<pdf> > &pdfs,
                       bool checkoverlap ) {
         RV rv; //empty rv
         bool rvaddok;
-        for ( int i = 0; i < mpdfs.length(); i++ ) {
-                rvaddok = rv.add ( mpdfs ( i )->_rv() ); //add rv to common rvs.
-                // If rvaddok==false, mpdfs overlap => assert error.
-                bdm_assert_debug ( rvaddok || !checkoverlap, "mprod::mprod() input mpdfs overlap in rv!" );
+        for ( int i = 0; i < pdfs.length(); i++ ) {
+                rvaddok = rv.add ( pdfs ( i )->_rv() ); //add rv to common rvs.
+                // If rvaddok==false, pdfs overlap => assert error.
+                bdm_assert_debug ( rvaddok || !checkoverlap, "mprod::mprod() input pdfs overlap in rv!" );
         }
 

library/bdm/base/bdmbase.h

@@ -386 +386 @@
 
 //! Conditional probability density, e.g. modeling \f$ f( x | y) \f$, where \f$ x \f$ is random variable, \c rv, and \f$ y \f$ is conditioning variable, \c rvc.
-class mpdf : public root {
+class pdf : public root {
 protected:
         //!dimension of the condition
@@ -403 +403 @@
         //! @{
 
-        mpdf() : dimc ( 0 ), rvc(), dim(0), rv() { }
-
-        mpdf ( const mpdf &m ) : dimc ( m.dimc ), rvc ( m.rvc ), dim( m.dim), rv( m.rv ) { }
+        pdf() : dimc ( 0 ), rvc(), dim(0), rv() { }
+
+        pdf ( const pdf &m ) : dimc ( m.dimc ), rvc ( m.rvc ), dim( m.dim), rv( m.rv ) { }
         
         //! copy of the current object - make sure to implement
-        virtual mpdf* _copy_() const {return new mpdf(*this);}
+        virtual pdf* _copy_() const {return new pdf(*this);}
         //!@}
 
@@ -467 +467 @@
         //! Load from structure with elements:
         //!  \code
-        //! { class = "mpdf_offspring",
+        //! { class = "pdf_offspring",
         //!   rv = {class="RV", names=(...),}; // RV describing meaning of random variable
         //!   rvc= {class="RV", names=(...),}; // RV describing meaning of random variable in condition
@@ -491 +491 @@
         //!@}
 };
-SHAREDPTR ( mpdf );
+SHAREDPTR ( pdf );
 
 //! Probability density function with numerical statistics, e.g. posterior density.
-class epdf : public mpdf {
+class epdf : public pdf {
 
 public:
@@ -509 +509 @@
         @{*/
         epdf() {};
-        epdf ( const epdf &e ) : mpdf(e) {};
+        epdf ( const epdf &e ) : pdf(e) {};
         void set_parameters ( int dim0 ) {
                 dim = dim0;
@@ -542 +542 @@
 
         //! Return conditional density on the given RV, the remaining rvs will be in conditioning
-        virtual shared_ptr<mpdf> condition ( const RV &rv ) const;
+        virtual shared_ptr<pdf> condition ( const RV &rv ) const;
 
         //! Return marginal density on the given RV, the remainig rvs are intergrated out
@@ -633 +633 @@
 SHAREDPTR ( epdf );
 
-//! Mpdf with internal epdf that is modified by function \c condition
+//! pdf with internal epdf that is modified by function \c condition
 template <class EPDF>
-class mpdf_internal: public mpdf {
+class pdf_internal: public pdf {
 protected :
         //! Internal epdf used for sampling
@@ -641 +641 @@
 public:
         //! constructor
-        mpdf_internal() : mpdf(), iepdf() {
+        pdf_internal() : pdf(), iepdf() {
 //              set_ep ( iepdf ); TODO!
         }
 
-        //! Update \c iepdf so that it represents this mpdf conditioned on \c rvc = cond
+        //! Update \c iepdf so that it represents this pdf conditioned on \c rvc = cond
         //! This function provides convenient reimplementation in offsprings
         virtual void condition ( const vec &cond ) {
@@ -896 +896 @@
 };
 
-//!DataLink is a connection between mpdf and its superordinate (Up)
+//!DataLink is a connection between pdf and its superordinate (Up)
 //! This class links
 class datalink_m2m: public datalink_m2e {
@@ -928 +928 @@
 
 
-//! \brief Combines RVs from a list of mpdfs to a single one.
-RV get_composite_rv ( const Array<shared_ptr<mpdf> > &mpdfs, bool checkoverlap = false );
+//! \brief Combines RVs from a list of pdfs to a single one.
+RV get_composite_rv ( const Array<shared_ptr<pdf> > &pdfs, bool checkoverlap = false );
 
 /*! \brief Abstract class for discrete-time sources of data.
@@ -1118 +1118 @@
         };
         //!Constructs conditional density of 1-step ahead predictor \f$ f(d_{t+1} |d_{t+h-1}, \ldots d_{t}) \f$
-        virtual mpdf* predictor() const {
+        virtual pdf* predictor() const {
                 bdm_error ( "Not implemented" );
                 return NULL;
@@ -1229 +1229 @@
 //! array of pointers to epdf
 typedef Array<shared_ptr<epdf> > epdf_array;
-//! array of pointers to mpdf
-typedef Array<shared_ptr<mpdf> > mpdf_array;
+//! array of pointers to pdf
+typedef Array<shared_ptr<pdf> > pdf_array;
 
 template<class EPDF>
-vec mpdf_internal<EPDF>::samplecond ( const vec &cond ) {
+vec pdf_internal<EPDF>::samplecond ( const vec &cond ) {
         condition ( cond );
         vec temp = iepdf.sample();
@@ -1240 +1240 @@
 
 template<class EPDF>
-mat mpdf_internal<EPDF>::samplecond_m ( const vec &cond, int N ) {
+mat pdf_internal<EPDF>::samplecond_m ( const vec &cond, int N ) {
         condition ( cond );
         mat temp ( dimension(), N );
@@ -1253 +1253 @@
 
 template<class EPDF>
-double mpdf_internal<EPDF>::evallogcond ( const vec &yt, const vec &cond ) {
+double pdf_internal<EPDF>::evallogcond ( const vec &yt, const vec &cond ) {
         double tmp;
         condition ( cond );
@@ -1261 +1261 @@
 
 template<class EPDF>
-vec mpdf_internal<EPDF>::evallogcond_m ( const mat &Yt, const vec &cond ) {
+vec pdf_internal<EPDF>::evallogcond_m ( const mat &Yt, const vec &cond ) {
         condition ( cond );
         return iepdf.evallog_m ( Yt );
@@ -1267 +1267 @@
 
 template<class EPDF>
-vec mpdf_internal<EPDF>::evallogcond_m ( const Array<vec> &Yt, const vec &cond ) {
+vec pdf_internal<EPDF>::evallogcond_m ( const Array<vec> &Yt, const vec &cond ) {
         condition ( cond );
         return iepdf.evallog_m ( Yt );

library/bdm/base/datasources.cpp

@@ -123 +123 @@
 
 void stateDS::from_setting ( const Setting &set ) {
-        IM = UI::build<mpdf> ( set, "IM", UI::compulsory );
-        OM = UI::build<mpdf> ( set, "OM", UI::compulsory );
+        IM = UI::build<pdf> ( set, "IM", UI::compulsory );
+        OM = UI::build<pdf> ( set, "OM", UI::compulsory );
 
         dt.set_length ( OM->dimension() );

library/bdm/base/datasources.h

@@ -145 +145 @@
 Still having only one density but allowing conditioning on either input or delayed values.
 */
-class MpdfDS :public DS {
+class PdfDS :public DS {
         protected:
                 //! internal pointer to epdf from which we samplecond
-                shared_ptr<mpdf> impdf;
+                shared_ptr<pdf> ipdf;
                 //! internal storage of data sample
                 vec yt;
@@ -165 +165 @@
                         ut2rgr.filldown ( ut,rgr );
                         yt2rgr.filldown ( yt,rgr );
-                        yt=impdf->samplecond ( rgr );
+                        yt=ipdf->samplecond ( rgr );
                         ut2rgr.step(ut); //u is now history
                 }
@@ -177 +177 @@
                 /*!
                 \code
-                class = "MpdfDS";
-                mpdf = {class="mpdf_offspring", ...};  // mpdf to simulate
+                class = "PdfDS";
+                pdf = {class="pdf_offspring", ...};  // pdf to simulate
                 --- optional ---
                 init_rv = {class="RV",names=...};      // define what rv to initialize - typically delayed values!
@@ -187 +187 @@
                 */
                 void from_setting ( const Setting &set ) {
-                        impdf=UI::build<mpdf> ( set,"mpdf",UI::compulsory );
+                        ipdf=UI::build<pdf> ( set,"pdf",UI::compulsory );
                         
-                        Yrv = impdf->_rv();
+                        Yrv = ipdf->_rv();
                         // get unique rvs form rvc
-                        RV rgrv0=impdf->_rvc().remove_time();
+                        RV rgrv0=ipdf->_rvc().remove_time();
                         // input is what in not in Yrv
                         Urv=rgrv0.subt(Yrv); 
                         set_drv(Yrv, Urv);
                         // connect input and output to rvc
-                        ut2rgr.set_connection(impdf->_rvc(), Urv); 
-                        yt2rgr.set_connection(impdf->_rvc(), Yrv); 
+                        ut2rgr.set_connection(ipdf->_rvc(), Urv); 
+                        yt2rgr.set_connection(ipdf->_rvc(), Yrv); 
                         
                         //set history - if given
@@ -212 +212 @@
                         }
 
-                        yt = zeros ( impdf->dimension() );
-                        rgr = zeros ( impdf->dimensionc() );
+                        yt = zeros ( ipdf->dimension() );
+                        rgr = zeros ( ipdf->dimensionc() );
                         ut = zeros(Urv._dsize());
 
@@ -225 +225 @@
                         ut2rgr.filldown ( ut,rgr );
                         yt2rgr.filldown ( yt,rgr );
-                        yt=impdf->samplecond ( rgr );
-                }
-};
-UIREGISTER ( MpdfDS );
+                        yt=ipdf->samplecond ( rgr );
+                }
+};
+UIREGISTER ( PdfDS );
 
 /*! Pseudovirtual class for reading data from files
@@ -307 +307 @@
         private:
                 //!conditional pdf of the state evolution \f$ f(x_t|x_{t-1}) \f$
-                shared_ptr<mpdf> IM;
+                shared_ptr<pdf> IM;
 
                 //!conditional pdf of the observations \f$ f(d_t|x_t) \f$
-                shared_ptr<mpdf> OM;
+                shared_ptr<pdf> OM;
 
         protected:
@@ -331 +331 @@
                 }
                 //! convenience constructor
-                stateDS ( const shared_ptr<mpdf> &IM0, const shared_ptr<mpdf> &OM0, int usize ) : IM ( IM0 ), OM ( OM0 ),
+                stateDS ( const shared_ptr<pdf> &IM0, const shared_ptr<pdf> &OM0, int usize ) : IM ( IM0 ), OM ( OM0 ),
                                 dt ( OM0->dimension() ), xt ( IM0->dimension() ),
                                 ut ( usize ), L_xt ( 0 ) { }
@@ -360 +360 @@
                         type = "stateDS";
                         //Internal model
-                        IM = { type = "mpdf"; //<-- valid offspring! e.g. "mlnorm"
+                        IM = { type = "pdf"; //<-- valid offspring! e.g. "mlnorm"
                                 rv = { //description of x_t
                                         names=["name1",...];
@@ -373 +373 @@
                                 };
                         //Observation model
-                        OM = { type = "mpdf-offspring";
+                        OM = { type = "pdf-offspring";
                                 rv = {}; //description of d_t
                                 rvu = {type="internal", path="system.IM.rvu"}; //description of u_t

library/bdm/estim/particles.h

@@ -36 +36 @@
         Array<vec> &_samples;
         //! Parameter evolution model
-        shared_ptr<mpdf> par;
+        shared_ptr<pdf> par;
         //! Observation model
-        shared_ptr<mpdf> obs;
+        shared_ptr<pdf> obs;
         //! internal structure storing loglikelihood of predictions
         vec lls;
@@ -63 +63 @@
                 resmethod = rm;
         };
-        void set_model ( shared_ptr<mpdf> par0, shared_ptr<mpdf> obs0) {
+        void set_model ( shared_ptr<pdf> par0, shared_ptr<pdf> obs0) {
                 par = par0;
                 obs = obs0;
@@ -105 +105 @@
         /*! configuration structure for basic PF
         \code
-        parameter_pdf   = mpdf_class;         // parameter evolution pdf
-        observation_pdf = mpdf_class;         // observation pdf
+        parameter_pdf   = pdf_class;         // parameter evolution pdf
+        observation_pdf = pdf_class;         // observation pdf
         prior           = epdf_class;         // prior probability density
         --- optional ---
@@ -117 +117 @@
         void from_setting(const Setting &set){
                 BM::from_setting(set);
-                par = UI::build<mpdf>(set,"parameter_pdf",UI::compulsory);
-                obs = UI::build<mpdf>(set,"observation_pdf",UI::compulsory);
+                par = UI::build<pdf>(set,"parameter_pdf",UI::compulsory);
+                obs = UI::build<pdf>(set,"observation_pdf",UI::compulsory);
                 
                 prior_from_set(set);
@@ -196 +196 @@
 
 A composition of particle filter with exact (or almost exact) bayesian models (BMs).
-The Bayesian models provide marginalized predictive density. Internaly this is achieved by virtual class MPFmpdf.
+The Bayesian models provide marginalized predictive density. Internaly this is achieved by virtual class MPFpdf.
 */
 
@@ -206 +206 @@
         Array<BM*> BMs;
 
-        //! internal class for MPDF providing composition of eEmp with external components
+        //! internal class for pdf providing composition of eEmp with external components
 
         class mpfepdf : public epdf  {
@@ -306 +306 @@
         MPF () :  jest (pf,BMs) {};
         //! set all parameters at once
-        void set_parameters ( shared_ptr<mpdf> par0, shared_ptr<mpdf> obs0, int n0, RESAMPLING_METHOD rm = SYSTEMATIC ) {
+        void set_parameters ( shared_ptr<pdf> par0, shared_ptr<pdf> obs0, int n0, RESAMPLING_METHOD rm = SYSTEMATIC ) {
                 pf->set_model ( par0, obs0); 
                 pf->set_parameters(n0, rm );
@@ -341 +341 @@
         \code
         BM              = BM_class;           // Bayesian filtr for analytical part of the model
-        parameter_pdf   = mpdf_class;         // transitional pdf for non-parametric part of the model
+        parameter_pdf   = pdf_class;         // transitional pdf for non-parametric part of the model
         prior           = epdf_class;         // prior probability density
         --- optional ---
@@ -350 +350 @@
         */      
         void from_setting(const Setting &set){
-                shared_ptr<mpdf> par = UI::build<mpdf>(set,"parameter_pdf",UI::compulsory);
-                shared_ptr<mpdf> obs= new mpdf(); // not used!!
+                shared_ptr<pdf> par = UI::build<pdf>(set,"parameter_pdf",UI::compulsory);
+                shared_ptr<pdf> obs= new pdf(); // not used!!
 
                 pf = new PF;

library/bdm/stat/emix.cpp

@@ -54 +54 @@
 }
 
-shared_ptr<mpdf> emix::condition ( const RV &rv ) const {
+shared_ptr<pdf> emix::condition ( const RV &rv ) const {
         bdm_assert ( isnamed(), "rvs are not assigned" );
         mratio *tmp = new mratio ( this, rv );
-        return shared_ptr<mpdf>(tmp);
+        return shared_ptr<pdf>(tmp);
 }
 
@@ -203 +203 @@
 };
 
-void mprod::set_elements (const Array<shared_ptr<mpdf> > &mFacs ) {
-        mpdfs = mFacs;
+void mprod::set_elements (const Array<shared_ptr<pdf> > &mFacs ) {
+        pdfs = mFacs;
         dls.set_size ( mFacs.length() );
 
-        rv = get_composite_rv ( mpdfs, true );
+        rv = get_composite_rv ( pdfs, true );
         dim = rv._dsize();
 
-        for ( int i = 0; i < mpdfs.length(); i++ ) {
-                RV rvx = mpdfs ( i )->_rvc().subt ( rv );
+        for ( int i = 0; i < pdfs.length(); i++ ) {
+                RV rvx = pdfs ( i )->_rvc().subt ( rv );
                 rvc.add ( rvx ); // add rv to common rvc
         }
         dimc=rvc._dsize();
 
-        // rv and rvc established = > we can link them with mpdfs
-        for ( int i = 0; i < mpdfs.length(); i++ ) {
+        // rv and rvc established = > we can link them with pdfs
+        for ( int i = 0; i < pdfs.length(); i++ ) {
                 dls ( i ) = new datalink_m2m;
-                dls ( i )->set_connection ( mpdfs ( i )->_rv(), mpdfs ( i )->_rvc(), _rv(), _rvc() );
+                dls ( i )->set_connection ( pdfs ( i )->_rv(), pdfs ( i )->_rvc(), _rv(), _rvc() );
         }
 }
@@ -239 +239 @@
 
 }
-// mprod::mprod ( Array<mpdf*> mFacs, bool overlap) : mpdf ( RV(), RV() ), n ( mFacs.length() ), epdfs ( n ), mpdfs ( mFacs ), rvinds ( n ), rvcinrv ( n ), irvcs_rvc ( n ) {
+// mprod::mprod ( Array<pdf*> mFacs, bool overlap) : pdf ( RV(), RV() ), n ( mFacs.length() ), epdfs ( n ), pdfs ( mFacs ), rvinds ( n ), rvcinrv ( n ), irvcs_rvc ( n ) {
 //              int i;
 //              bool rvaddok;
 //              // Create rv
 //              for ( i = 0;i < n;i++ ) {
-//                      rvaddok=rv.add ( mpdfs ( i )->_rv() ); //add rv to common rvs.
-//                      // If rvaddok==false, mpdfs overlap => assert error.
-//                      epdfs ( i ) = & ( mpdfs ( i )->posterior() ); // add pointer to epdf
+//                      rvaddok=rv.add ( pdfs ( i )->_rv() ); //add rv to common rvs.
+//                      // If rvaddok==false, pdfs overlap => assert error.
+//                      epdfs ( i ) = & ( pdfs ( i )->posterior() ); // add pointer to epdf
 //              };
 //              // Create rvc
 //              for ( i = 0;i < n;i++ ) {
-//                      rvc.add ( mpdfs ( i )->_rvc().subt ( rv ) ); //add rv to common rvs.
+//                      rvc.add ( pdfs ( i )->_rvc().subt ( rv ) ); //add rv to common rvs.
 //              };
 //
 // //           independent = true;
-//              //test rvc of mpdfs and fill rvinds
+//              //test rvc of pdfs and fill rvinds
 //              for ( i = 0;i < n;i++ ) {
 //                      // find ith rv in common rv
-//                      rvsinrv ( i ) = mpdfs ( i )->_rv().dataind ( rv );
+//                      rvsinrv ( i ) = pdfs ( i )->_rv().dataind ( rv );
 //                      // find ith rvc in common rv
-//                      rvcinrv ( i ) = mpdfs ( i )->_rvc().dataind ( rv );
+//                      rvcinrv ( i ) = pdfs ( i )->_rvc().dataind ( rv );
 //                      // find ith rvc in common rv
-//                      irvcs_rvc ( i ) = mpdfs ( i )->_rvc().dataind ( rvc );
+//                      irvcs_rvc ( i ) = pdfs ( i )->_rvc().dataind ( rvc );
 //                      //
 // /*                   if ( rvcinrv ( i ).length() >0 ) {independent = false;}

library/bdm/stat/emix.h

@@ -35 +35 @@
 At present the only supported operation is evallogcond().
  */
-class mratio: public mpdf {
+class mratio: public pdf {
 protected:
-        //! Nominator in the form of mpdf
+        //! Nominator in the form of pdf
         const epdf* nom;
 
@@ -50 +50 @@
         //!Default constructor. By default, the given epdf is not copied!
         //! It is assumed that this function will be used only temporarily.
-        mratio ( const epdf* nom0, const RV &rv, bool copy = false ) : mpdf ( ), dl ( ) {
+        mratio ( const epdf* nom0, const RV &rv, bool copy = false ) : pdf ( ), dl ( ) {
                 // adjust rv and rvc
 
@@ -178 +178 @@
         //! Update already existing marginal density  \c target
         void marginal ( const RV &rv, emix &target ) const;
-        shared_ptr<mpdf> condition ( const RV &rv ) const;
+        shared_ptr<pdf> condition ( const RV &rv ) const;
 
 //Access methods
@@ -283 +283 @@
 Note that
 */
-class mprod: public mpdf {
+class mprod: public pdf {
 private:
-        Array<shared_ptr<mpdf> > mpdfs;
-
-        //! Data link for each mpdfs
+        Array<shared_ptr<pdf> > pdfs;
+
+        //! Data link for each pdfs
         Array<shared_ptr<datalink_m2m> > dls;
 
@@ -300 +300 @@
         /*!\brief Constructor from list of mFacs
         */
-        mprod ( const Array<shared_ptr<mpdf> > &mFacs ) {
+        mprod ( const Array<shared_ptr<pdf> > &mFacs ) {
                 set_elements ( mFacs );
         }
-        //! Set internal \c mpdfs from given values
-        void set_elements (const Array<shared_ptr<mpdf> > &mFacs );
+        //! Set internal \c pdfs from given values
+        void set_elements (const Array<shared_ptr<pdf> > &mFacs );
 
         double evallogcond ( const vec &val, const vec &cond ) {
                 int i;
                 double res = 0.0;
-                for ( i = mpdfs.length() - 1; i >= 0; i-- ) {
-                        /*                      if ( mpdfs(i)->_rvc().count() >0) {
-                                                        mpdfs ( i )->condition ( dls ( i )->get_cond ( val,cond ) );
+                for ( i = pdfs.length() - 1; i >= 0; i-- ) {
+                        /*                      if ( pdfs(i)->_rvc().count() >0) {
+                                                        pdfs ( i )->condition ( dls ( i )->get_cond ( val,cond ) );
                                                 }
                                                 // add logarithms
                                                 res += epdfs ( i )->evallog ( dls ( i )->pushdown ( val ) );*/
-                        res += mpdfs ( i )->evallogcond (
+                        res += pdfs ( i )->evallogcond (
                                    dls ( i )->pushdown ( val ),
                                    dls ( i )->get_cond ( val, cond )
@@ -344 +344 @@
                 vec smpi;
                 // Hard assumption here!!! We are going backwards, to assure that samples that are needed from smp are already generated!
-                for ( int i = ( mpdfs.length() - 1 ); i >= 0; i-- ) {
-                        // generate contribution of this mpdf
-                        smpi = mpdfs(i)->samplecond(dls ( i )->get_cond ( smp , cond ));                        
+                for ( int i = ( pdfs.length() - 1 ); i >= 0; i-- ) {
+                        // generate contribution of this pdf
+                        smpi = pdfs(i)->samplecond(dls ( i )->get_cond ( smp , cond ));                 
                         // copy contribution of this pdf into smp
                         dls ( i )->pushup ( smp, smpi );
@@ -356 +356 @@
         //!  \code
         //! { class='mprod';
-        //!   mpdfs = (..., ...);     // list of mpdfs in the order of chain rule
+        //!   pdfs = (..., ...);     // list of pdfs in the order of chain rule
         //! }
         //! \endcode
         //!@}
         void from_setting ( const Setting &set ) {
-                Array<shared_ptr<mpdf> > atmp; //temporary Array
-                UI::get ( atmp, set, "mpdfs", UI::compulsory );
+                Array<shared_ptr<pdf> > atmp; //temporary Array
+                UI::get ( atmp, set, "pdfs", UI::compulsory );
                 set_elements ( atmp );
         }
@@ -460 +460 @@
 
 
-/*! \brief Mixture of mpdfs with constant weights, all mpdfs are of equal RV and RVC
+/*! \brief Mixture of pdfs with constant weights, all pdfs are of equal RV and RVC
 
 */
-class mmix : public mpdf {
+class mmix : public pdf {
 protected:
-        //! Component (mpdfs)
-        Array<shared_ptr<mpdf> > Coms;
+        //! Component (pdfs)
+        Array<shared_ptr<pdf> > Coms;
         //!weights of the components
         vec w;
@@ -474 +474 @@
 
         //! Set weights \c w and components \c R
-        void set_parameters ( const vec &w0, const Array<shared_ptr<mpdf> > &Coms0 ) {
+        void set_parameters ( const vec &w0, const Array<shared_ptr<pdf> > &Coms0 ) {
                 //!\todo check if all components are OK
                 Coms = Coms0;

library/bdm/stat/exp_family.h

@@ -163 +163 @@
                 vec variance() const {return diag (R.to_mat());}
 //      mlnorm<sq_T>* condition ( const RV &rvn ) const ; <=========== fails to cmpile. Why?
-                shared_ptr<mpdf> condition ( const RV &rvn ) const;
+                shared_ptr<pdf> condition ( const RV &rvn ) const;
 
                 // target not typed to mlnorm<sq_T, enorm<sq_T> > &
@@ -169 +169 @@
                 // haven't finished defining enorm yet), but the type
                 // is required
-                void condition ( const RV &rvn, mpdf &target ) const;
+                void condition ( const RV &rvn, pdf &target ) const;
 
                 shared_ptr<epdf> marginal (const RV &rvn ) const;
@@ -367 +367 @@
 */
 
-class mDirich: public mpdf_internal<eDirich> {
+class mDirich: public pdf_internal<eDirich> {
         protected:
                 //! constant \f$ k \f$ of the random walk
@@ -376 +376 @@
                 vec betac;
         public:
-                mDirich(): mpdf_internal<eDirich>(), _beta(iepdf._beta()){};
+                mDirich(): pdf_internal<eDirich>(), _beta(iepdf._beta()){};
                 void condition (const vec &val) {_beta =  val/k+betac; };
                 /*! Create Dirichlet random walk 
@@ -391 +391 @@
                 */
                 void from_setting (const Setting &set) {
-                        mpdf::from_setting (set); // reads rv and rvc
+                        pdf::from_setting (set); // reads rv and rvc
                         if (_rv()._dsize()>0){
                                 rvc = _rv().copy_t(-1);
@@ -408 +408 @@
                 }
                 void validate() { 
-                        mpdf_internal<eDirich>::validate();
+                        pdf_internal<eDirich>::validate();
                         bdm_assert(_beta.length()==betac.length(),"beta0 and betac are not compatible");
                         if (_rv()._dsize()>0){
@@ -644 +644 @@
 
 //! Uniform density with conditional mean value
-class mguni : public mpdf_internal<euni>{
+class mguni : public pdf_internal<euni>{
         //! function of the mean value
         shared_ptr<fnc> mean;
@@ -656 +656 @@
                 //! load from
                 void from_setting(const Setting &set){
-                        mpdf::from_setting(set); //reads rv and rvc
+                        pdf::from_setting(set); //reads rv and rvc
                         UI::get(delta,set,"delta",UI::compulsory);
                         mean = UI::build<fnc>(set,"mean",UI::compulsory);
@@ -672 +672 @@
 */
 template < class sq_T, template <typename> class TEpdf = enorm >
-class mlnorm : public mpdf_internal< TEpdf<sq_T> >
+class mlnorm : public pdf_internal< TEpdf<sq_T> >
 {
         protected:
@@ -683 +683 @@
                 //! \name Constructors
                 //!@{
-                mlnorm() : mpdf_internal< TEpdf<sq_T> >() {};
-                mlnorm (const mat &A, const vec &mu0, const sq_T &R) : mpdf_internal< TEpdf<sq_T> >() {
+                mlnorm() : pdf_internal< TEpdf<sq_T> >() {};
+                mlnorm (const mat &A, const vec &mu0, const sq_T &R) : pdf_internal< TEpdf<sq_T> >() {
                         set_parameters (A, mu0, R);
                 }
@@ -724 +724 @@
                 */
                 void from_setting (const Setting &set) {
-                        mpdf::from_setting (set);
+                        pdf::from_setting (set);
 
                         UI::get (A, set, "A", UI::compulsory);
@@ -734 +734 @@
                 };
                 void validate() {
-                        mpdf_internal<TEpdf<sq_T> >::validate();
+                        pdf_internal<TEpdf<sq_T> >::validate();
                         bdm_assert (A.rows() == mu_const.length(), "mlnorm: A vs. mu mismatch");
                         bdm_assert (A.rows() == _R().rows(), "mlnorm: A vs. R mismatch");
@@ -747 +747 @@
 SHAREDPTR2 ( mlnorm, chmat );
 
-//! Mpdf with general function for mean value
+//! pdf with general function for mean value
 template<class sq_T>
-class mgnorm : public mpdf_internal< enorm< sq_T > >
+class mgnorm : public pdf_internal< enorm< sq_T > >
 {
         private:
@@ -757 +757 @@
         public:
                 //!default constructor
-                mgnorm() : mpdf_internal<enorm<sq_T> >() { }
+                mgnorm() : pdf_internal<enorm<sq_T> >() { }
                 //!set mean function
                 inline void set_parameters (const shared_ptr<fnc> &g0, const sq_T &R0);
@@ -782 +782 @@
 
                 void from_setting (const Setting &set) {
-                        mpdf::from_setting(set);
+                        pdf::from_setting(set);
                         shared_ptr<fnc> g = UI::build<fnc> (set, "g", UI::compulsory);
 
@@ -863 +863 @@
 The standard deviation of the walk is then: \f$\mu/\sqrt(k)\f$.
 */
-class mgamma : public mpdf_internal<egamma>
+class mgamma : public pdf_internal<egamma>
 {
         protected:
@@ -875 +875 @@
         public:
                 //! Constructor
-                mgamma() : mpdf_internal<egamma>(), k (0),
+                mgamma() : pdf_internal<egamma>(), k (0),
                                 _beta (iepdf._beta()) {
                 }
@@ -895 +895 @@
                 */
                 void from_setting (const Setting &set) {
-                        mpdf::from_setting (set); // reads rv and rvc
+                        pdf::from_setting (set); // reads rv and rvc
                         vec betatmp; // ugly but necessary
                         UI::get (betatmp, set, "beta", UI::compulsory);
@@ -903 +903 @@
                 }
                 void validate() {
-                        mpdf_internal<egamma>::validate();
+                        pdf_internal<egamma>::validate();
                         
                         dim = _beta.length();
@@ -921 +921 @@
 The standard deviation of the walk is then: \f$ \mu/\sqrt(k)\f$.
  */
-class migamma : public mpdf_internal<eigamma>
+class migamma : public pdf_internal<eigamma>
 {
         protected:
@@ -936 +936 @@
                 //! \name Constructors
                 //!@{
-                migamma() : mpdf_internal<eigamma>(),
+                migamma() : pdf_internal<eigamma>(),
                                 k (0),
                                 _alpha (iepdf._alpha()),
@@ -942 +942 @@
                 }
 
-                migamma (const migamma &m) : mpdf_internal<eigamma>(),
+                migamma (const migamma &m) : pdf_internal<eigamma>(),
                                 k (0),
                                 _alpha (iepdf._alpha()),
@@ -1074 +1074 @@
 
  */
-class mlognorm : public mpdf_internal<elognorm>
+class mlognorm : public pdf_internal<elognorm>
 {
         protected:
@@ -1084 +1084 @@
         public:
                 //! Constructor
-                mlognorm() : mpdf_internal<elognorm>(),
+                mlognorm() : pdf_internal<elognorm>(),
                                 sig2 (0),
                                 mu (iepdf._mu()) {
@@ -1221 +1221 @@
 
 //! Random Walk on inverse Wishart
-class rwiWishartCh : public mpdf_internal<eiWishartCh>
+class rwiWishartCh : public pdf_internal<eiWishartCh>
 {
         protected:
@@ -1474 +1474 @@
 
 template<class sq_T>
-shared_ptr<mpdf> enorm<sq_T>::condition ( const RV &rvn ) const
+shared_ptr<pdf> enorm<sq_T>::condition ( const RV &rvn ) const
 {
         mlnorm<sq_T> *tmp = new mlnorm<sq_T> ();
-        shared_ptr<mpdf> narrow(tmp);
+        shared_ptr<pdf> narrow(tmp);
         condition ( rvn, *tmp );
         return narrow;
@@ -1483 +1483 @@
 
 template<class sq_T>
-void enorm<sq_T>::condition ( const RV &rvn, mpdf &target ) const
+void enorm<sq_T>::condition ( const RV &rvn, pdf &target ) const
 {
         typedef mlnorm<sq_T> TMlnorm;

library/bdm/stat/merger.cpp

@@ -5 +5 @@
 namespace bdm {
 
-merger_base::merger_base ( const Array<shared_ptr<mpdf> > &S ):
+merger_base::merger_base ( const Array<shared_ptr<pdf> > &S ):
         Npoints(0), DBG(false), dbg_file(0) {
         set_sources ( S );
@@ -134 +134 @@
 
 
-                        sprintf ( dbg_str, "Mpdf%d", niter );
+                        sprintf ( dbg_str, "pdf%d", niter );
                         for ( int i = 0; i < Npoints; i++ ) {
                                 Mix_pdf ( i ) = Mix.logpred ( Smp_ex.get_col ( i ) );
@@ -145 +145 @@
                 }
                 //Importace weighting
-                for ( int i = 0; i < mpdfs.length(); i++ ) {
+                for ( int i = 0; i < pdfs.length(); i++ ) {
                         lw_src = 0.0;
                         //======== Same RVs ===========
                         //Split according to dependency in rvs
-                        if ( mpdfs ( i )->dimension() == dim ) {
+                        if ( pdfs ( i )->dimension() == dim ) {
                                 // no need for conditioning or marginalization
-                                lw_src = mpdfs ( i )->evallogcond_m ( Smp , vec(0));
+                                lw_src = pdfs ( i )->evallogcond_m ( Smp , vec(0));
                         } else {
                                 // compute likelihood of marginal on the conditional variable
-                                if ( mpdfs ( i )->dimensionc() > 0 ) {
+                                if ( pdfs ( i )->dimensionc() > 0 ) {
                                         // Make marginal on rvc_i
-                                        shared_ptr<epdf> tmp_marg = Mpred->marginal ( mpdfs ( i )->_rvc() );
+                                        shared_ptr<epdf> tmp_marg = Mpred->marginal ( pdfs ( i )->_rvc() );
                                         //compute vector of lw_src
                                         for ( int k = 0; k < Npoints; k++ ) {
-                                                // Here val of tmp_marg = cond of mpdfs(i) ==> calling dls->get_cond
+                                                // Here val of tmp_marg = cond of pdfs(i) ==> calling dls->get_cond
                                                 lw_src ( k ) += tmp_marg->evallog ( dls ( i )->get_cond ( Smp ( k ) ) );
                                         }
@@ -168 +168 @@
                                 }
                                 // Compute likelihood of the missing variable
-                                if ( dim > ( mpdfs ( i )->dimension() + mpdfs ( i )->dimensionc() ) ) {
+                                if ( dim > ( pdfs ( i )->dimension() + pdfs ( i )->dimensionc() ) ) {
                                         ///////////////
-                                        // There are variales unknown to mpdfs(i) : rvzs
-                                        shared_ptr<mpdf> tmp_cond = Mpred->condition ( rvzs ( i ) );
+                                        // There are variales unknown to pdfs(i) : rvzs
+                                        shared_ptr<pdf> tmp_cond = Mpred->condition ( rvzs ( i ) );
                                         // Compute likelihood
                                         vec lw_dbg = lw_src;
@@ -187 +187 @@
                                 // Compute likelihood of the partial source
                                 for ( int k = 0; k < Npoints; k++ ) {
-                                        lw_src ( k ) += mpdfs ( i )->evallogcond ( dls ( i )->pushdown ( Smp ( k ) ),  
+                                        lw_src ( k ) += pdfs ( i )->evallogcond ( dls ( i )->pushdown ( Smp ( k ) ),  
                                                          dls ( i )->get_cond ( Smp ( k ) ));
                                 }

library/bdm/stat/merger.h

@@ -46 +46 @@
 protected:
         //! Elements of composition
-        Array<shared_ptr<mpdf> > mpdfs;
-
-        //! Data link for each mpdf in mpdfs
+        Array<shared_ptr<pdf> > pdfs;
+
+        //! Data link for each pdf in pdfs
         Array<datalink_m2e*> dls;
 
-        //! Array of rvs that are not modelled by mpdfs at all, \f$ z_i \f$
+        //! Array of rvs that are not modelled by pdfs at all, \f$ z_i \f$
         Array<RV> rvzs;
 
@@ -90 +90 @@
 
         //!Constructor from sources
-        merger_base ( const Array<shared_ptr<mpdf> > &S );
+        merger_base ( const Array<shared_ptr<pdf> > &S );
 
         //! Function setting the main internal structures
-        void set_sources ( const Array<shared_ptr<mpdf> > &Sources ) {
-                mpdfs = Sources;
-                Nsources = mpdfs.length();
+        void set_sources ( const Array<shared_ptr<pdf> > &Sources ) {
+                pdfs = Sources;
+                Nsources = pdfs.length();
                 //set sizes
                 dls.set_size ( Sources.length() );
@@ -101 +101 @@
                 zdls.set_size ( Sources.length() );
 
-                rv = get_composite_rv ( mpdfs, /* checkoverlap = */ false );
+                rv = get_composite_rv ( pdfs, /* checkoverlap = */ false );
 
                 RV rvc;
                 // Extend rv by rvc!
-                for ( int i = 0; i < mpdfs.length(); i++ ) {
-                        RV rvx = mpdfs ( i )->_rvc().subt ( rv );
+                for ( int i = 0; i < pdfs.length(); i++ ) {
+                        RV rvx = pdfs ( i )->_rvc().subt ( rv );
                         rvc.add ( rvx ); // add rv to common rvc
                 }
@@ -117 +117 @@
                 // create links between sources and common rv
                 RV xytmp;
-                for ( int i = 0; i < mpdfs.length(); i++ ) {
-                        //Establich connection between mpdfs and merger
+                for ( int i = 0; i < pdfs.length(); i++ ) {
+                        //Establich connection between pdfs and merger
                         dls ( i ) = new datalink_m2e;
-                        dls ( i )->set_connection ( mpdfs ( i )->_rv(), mpdfs ( i )->_rvc(), rv );
-
-                        // find out what is missing in each mpdf
-                        xytmp = mpdfs ( i )->_rv();
-                        xytmp.add ( mpdfs ( i )->_rvc() );
+                        dls ( i )->set_connection ( pdfs ( i )->_rv(), pdfs ( i )->_rvc(), rv );
+
+                        // find out what is missing in each pdf
+                        xytmp = pdfs ( i )->_rv();
+                        xytmp.add ( pdfs ( i )->_rvc() );
                         // z_i = common_rv-xy
                         rvzs ( i ) = rv.subt ( xytmp );
@@ -185 +185 @@
                 //check if sources overlap:
                 bool OK = true;
-                for ( int i = 0; i < mpdfs.length(); i++ ) {
+                for ( int i = 0; i < pdfs.length(); i++ ) {
                         OK &= ( rvzs ( i )._dsize() == 0 ); // z_i is empty
-                        OK &= ( mpdfs ( i )->_rvc()._dsize() == 0 ); // y_i is empty
+                        OK &= ( pdfs ( i )->_rvc()._dsize() == 0 ); // y_i is empty
                 }
 
                 if ( OK ) {
-                        mat lW = zeros ( mpdfs.length(), eSmp._w().length() );
+                        mat lW = zeros ( pdfs.length(), eSmp._w().length() );
 
                         vec emptyvec ( 0 );
-                        for ( int i = 0; i < mpdfs.length(); i++ ) {
+                        for ( int i = 0; i < pdfs.length(); i++ ) {
                                 for ( int j = 0; j < eSmp._w().length(); j++ ) {
-                                        lW ( i, j ) = mpdfs ( i )->evallogcond ( eSmp._samples() ( j ), emptyvec );
+                                        lW ( i, j ) = pdfs ( i )->evallogcond ( eSmp._samples() ( j ), emptyvec );
                                 }
                         }
@@ -313 +313 @@
         merger_mix ():Ncoms(0), effss_coef(0), stop_niter(0) { }
 
-        merger_mix ( const Array<shared_ptr<mpdf> > &S ):
+        merger_mix ( const Array<shared_ptr<pdf> > &S ):
                 Ncoms(0), effss_coef(0), stop_niter(0) {
                 set_sources ( S );
@@ -319 +319 @@
 
         //! Set sources and prepare all internal structures
-        void set_sources ( const Array<shared_ptr<mpdf> > &S ) {
+        void set_sources ( const Array<shared_ptr<pdf> > &S ) {
                 merger_base::set_sources ( S );
                 Nsources = S.length();