Renamed NegativeBinomialFactory into PolyaFactory

ChangeLog

@@ -24,6 +24,7 @@
  * Deprecated BayesDistribution in favor of JointByConditioningDistribution
  * Deprecated ConditionalDistribution in favor of DeconditionedDistribution
  * Deprecated NegativeBinomial in favor of Polya
+ * Deprecated NegativeBinomialFactory in favor of PolyaFactory
 
 === Documentation ===
  * Copy button for code blocks

lib/etc/openturns.conf.in

@@ -626,11 +626,11 @@
   <Multinomial-eta    value_float="1.0e-9" />
   <Multinomial-smallA value_float="10.0"   />
 
-  <!-- OT::NegativeBinomialFactory parameters -->
-  <NegativeBinomialFactory-AbsolutePrecision value_float="1e-12"        />
-  <NegativeBinomialFactory-RelativePrecision value_float="1e-12"        />
-  <NegativeBinomialFactory-ResidualPrecision value_float="1e-12"        />
-  <NegativeBinomialFactory-MaximumIteration  value_int="50" />
+  <!-- OT::PolyaFactory parameters -->
+  <PolyaFactory-AbsolutePrecision value_float="1e-12"        />
+  <PolyaFactory-RelativePrecision value_float="1e-12"        />
+  <PolyaFactory-ResidualPrecision value_float="1e-12"        />
+  <PolyaFactory-MaximumIteration  value_int="50" />
 
   <!-- OT::Normal parameters -->
   <Normal-MaximumCDFEpsilon              value_float="5.0e-6"             />

lib/src/Base/Common/ResourceMap.cxx

@@ -1252,11 +1252,11 @@ void ResourceMap::loadDefaultConfiguration()
   addAsScalar("Multinomial-eta", 1.0e-9);
   addAsScalar("Multinomial-smallA", 10.0);
 
-  // NegativeBinomialFactory parameters //
-  addAsScalar("NegativeBinomialFactory-AbsolutePrecision", 1.0e-12);
-  addAsScalar("NegativeBinomialFactory-RelativePrecision", 1.0e-12);
-  addAsScalar("NegativeBinomialFactory-ResidualPrecision", 1.0e-12);
-  addAsUnsignedInteger("NegativeBinomialFactory-MaximumIteration", 50);
+  // PolyaFactory parameters //
+  addAsScalar("PolyaFactory-AbsolutePrecision", 1.0e-12);
+  addAsScalar("PolyaFactory-RelativePrecision", 1.0e-12);
+  addAsScalar("PolyaFactory-ResidualPrecision", 1.0e-12);
+  addAsUnsignedInteger("PolyaFactory-MaximumIteration", 50);
 
   // Normal parameters //
   addAsScalar("Normal-MaximumCDFEpsilon", 5.0e-6);

lib/src/Uncertainty/Distribution/CMakeLists.txt

@@ -119,7 +119,7 @@ ot_add_source_file (Mixture.cxx)
 ot_add_source_file (Multinomial.cxx)
 ot_add_source_file (MultinomialFactory.cxx)
 ot_add_source_file (Polya.cxx)
-ot_add_source_file (NegativeBinomialFactory.cxx)
+ot_add_source_file (PolyaFactory.cxx)
 ot_add_source_file (NonCentralChiSquare.cxx)
 ot_add_source_file (NonCentralStudent.cxx)
 ot_add_source_file (Normal2DCDF.cxx)
@@ -294,7 +294,7 @@ ot_install_header_file (Mixture.hxx)
 ot_install_header_file (MultinomialFactory.hxx)
 ot_install_header_file (Multinomial.hxx)
 ot_install_header_file (Polya.hxx)
-ot_install_header_file (NegativeBinomialFactory.hxx)
+ot_install_header_file (PolyaFactory.hxx)
 ot_install_header_file (NonCentralChiSquare.hxx)
 ot_install_header_file (NonCentralStudent.hxx)
 ot_install_header_file (Normal2DCDF.hxx)

lib/src/Uncertainty/Distribution/NegativeBinomialFactory.cxx → lib/src/Uncertainty/Distribution/PolyaFactory.cxx

@@ -18,7 +18,7 @@
  *  along with this library.  If not, see <http://www.gnu.org/licenses/>.
  *
  */
-#include "openturns/NegativeBinomialFactory.hxx"
+#include "openturns/PolyaFactory.hxx"
 #include "openturns/SpecFunc.hxx"
 #include "openturns/MethodBoundEvaluation.hxx"
 #include "openturns/Brent.hxx"
@@ -27,21 +27,21 @@
 
 BEGIN_NAMESPACE_OPENTURNS
 
-CLASSNAMEINIT(NegativeBinomialFactory)
+CLASSNAMEINIT(PolyaFactory)
 
-static const Factory<NegativeBinomialFactory> Factory_NegativeBinomialFactory;
+static const Factory<PolyaFactory> Factory_PolyaFactory;
 
 /* Default constructor */
-NegativeBinomialFactory::NegativeBinomialFactory()
+PolyaFactory::PolyaFactory()
   : DistributionFactoryImplementation()
 {
   // Nothing to do
 }
 
 /* Virtual constructor */
-NegativeBinomialFactory * NegativeBinomialFactory::clone() const
+PolyaFactory * PolyaFactory::clone() const
 {
-  return new NegativeBinomialFactory(*this);
+  return new PolyaFactory(*this);
 }
 
 
@@ -76,22 +76,22 @@ struct NegativeBinomialFactoryParameterConstraint
   Scalar mean_;
 };
 
-Distribution NegativeBinomialFactory::build(const Sample & sample) const
+Distribution PolyaFactory::build(const Sample & sample) const
 {
   return buildAsNegativeBinomial(sample).clone();
 }
 
-Distribution NegativeBinomialFactory::build(const Point & parameters) const
+Distribution PolyaFactory::build(const Point & parameters) const
 {
   return buildAsNegativeBinomial(parameters).clone();
 }
 
-Distribution NegativeBinomialFactory::build() const
+Distribution PolyaFactory::build() const
 {
   return buildAsNegativeBinomial().clone();
 }
 
-Polya NegativeBinomialFactory::buildAsNegativeBinomial(const Sample & sample) const
+Polya PolyaFactory::buildAsNegativeBinomial(const Sample & sample) const
 {
   const UnsignedInteger size = sample.getSize();
   if (size < 2) throw InvalidArgumentException(HERE) << "Error: cannot build a Polya distribution from a sample of size < 2";
@@ -134,7 +134,7 @@ Polya NegativeBinomialFactory::buildAsNegativeBinomial(const Sample & sample) co
     fB = f(Point(1, b))[0];
   }
   // Solve the constraint equation
-  Brent solver(ResourceMap::GetAsScalar("NegativeBinomialFactory-AbsolutePrecision"), ResourceMap::GetAsScalar("NegativeBinomialFactory-RelativePrecision"), ResourceMap::GetAsScalar("NegativeBinomialFactory-ResidualPrecision"), ResourceMap::GetAsUnsignedInteger("NegativeBinomialFactory-MaximumIteration"));
+  Brent solver(ResourceMap::GetAsScalar("PolyaFactory-AbsolutePrecision"), ResourceMap::GetAsScalar("PolyaFactory-RelativePrecision"), ResourceMap::GetAsScalar("PolyaFactory-ResidualPrecision"), ResourceMap::GetAsUnsignedInteger("PolyaFactory-MaximumIteration"));
   // R estimate
   const Scalar r = solver.solve(f, 0.0, a, b, fA, fB);
   // Corresponding p estimate
@@ -144,7 +144,7 @@ Polya NegativeBinomialFactory::buildAsNegativeBinomial(const Sample & sample) co
   return result;
 }
 
-Polya NegativeBinomialFactory::buildAsNegativeBinomial(const Point & parameters) const
+Polya PolyaFactory::buildAsNegativeBinomial(const Point & parameters) const
 {
   try
   {
@@ -158,7 +158,7 @@ Polya NegativeBinomialFactory::buildAsNegativeBinomial(const Point & parameters)
   }
 }
 
-Polya NegativeBinomialFactory::buildAsNegativeBinomial() const
+Polya PolyaFactory::buildAsNegativeBinomial() const
 {
   return Polya();
 }

lib/src/Uncertainty/Distribution/openturns/OTDistribution.hxx

@@ -128,7 +128,7 @@
 #include "openturns/Multinomial.hxx"
 #include "openturns/MultinomialFactory.hxx"
 #include "openturns/Polya.hxx"
-#include "openturns/NegativeBinomialFactory.hxx"
+#include "openturns/PolyaFactory.hxx"
 #include "openturns/NonCentralChiSquare.hxx"
 #include "openturns/NonCentralStudent.hxx"
 #include "openturns/Normal2DCDF.hxx"

lib/src/Uncertainty/Distribution/openturns/NegativeBinomialFactory.hxx → lib/src/Uncertainty/Distribution/openturns/PolyaFactory.hxx

@@ -18,8 +18,8 @@
  *  along with this library.  If not, see <http://www.gnu.org/licenses/>.
  *
  */
-#ifndef OPENTURNS_NEGATIVEBINOMIALFACTORY_HXX
-#define OPENTURNS_NEGATIVEBINOMIALFACTORY_HXX
+#ifndef OPENTURNS_POLYAFACTORY_HXX
+#define OPENTURNS_POLYAFACTORY_HXX
 
 #include "openturns/OTprivate.hxx"
 #include "openturns/DistributionFactoryImplementation.hxx"
@@ -28,19 +28,19 @@
 BEGIN_NAMESPACE_OPENTURNS
 
 /**
- * @class NegativeBinomialFactory
+ * @class PolyaFactory
  */
-class OT_API NegativeBinomialFactory
+class OT_API PolyaFactory
   : public DistributionFactoryImplementation
 {
   CLASSNAME
 public:
 
   /** Default constructor */
-  NegativeBinomialFactory();
+  PolyaFactory();
 
   /** Virtual constructor */
-  NegativeBinomialFactory * clone() const override;
+  PolyaFactory * clone() const override;
 
   /* Here is the interface that all derived class must implement */
   using DistributionFactoryImplementation::build;
@@ -52,9 +52,9 @@ public:
   Polya buildAsNegativeBinomial(const Point & parameters) const;
   Polya buildAsNegativeBinomial() const;
 
-}; /* class NegativeBinomialFactory */
+}; /* class PolyaFactory */
 
 
 END_NAMESPACE_OPENTURNS
 
-#endif /* OPENTURNS_NEGATIVEBINOMIALFACTORY_HXX */
+#endif /* OPENTURNS_POLYAFACTORY_HXX */

lib/src/Uncertainty/Model/DistributionFactory.cxx

@@ -53,7 +53,7 @@
 #include "openturns/LogUniformFactory.hxx"
 #include "openturns/MeixnerDistributionFactory.hxx"
 #include "openturns/MultinomialFactory.hxx"
-#include "openturns/NegativeBinomialFactory.hxx"
+#include "openturns/PolyaFactory.hxx"
 #include "openturns/NormalCopulaFactory.hxx"
 #include "openturns/NormalFactory.hxx"
 #include "openturns/ParetoFactory.hxx"
@@ -141,7 +141,7 @@ DistributionFactory::DistributionFactoryCollection DistributionFactory::GetDiscr
   collection.add(DiracFactory());
   collection.add(GeometricFactory());
   collection.add(MultinomialFactory());
-  collection.add(NegativeBinomialFactory());
+  collection.add(PolyaFactory());
   collection.add(PoissonFactory());
   collection.add(UserDefinedFactory());
   collection.add(SkellamFactory());

lib/test/CMakeLists.txt

@@ -413,7 +413,7 @@ ot_check_test (Mixture_std)
 ot_check_test (Multinomial_std)
 ot_check_test (MultinomialFactory_std)
 ot_check_test (Polya_std)
-ot_check_test (NegativeBinomialFactory_std)
+ot_check_test (PolyaFactory_std)
 ot_check_test (NonCentralChiSquare_std)
 if (Boost_FOUND)
 ot_check_test (NonCentralStudent_std)

lib/test/t_DistributionFactory_std.expout

@@ -1,6 +1,6 @@
 Continuous univariate factories=[ArcsineFactory,BetaFactory,BurrFactory,ChiFactory,ChiSquareFactory,DirichletFactory,ExponentialFactory,FisherSnedecorFactory,FrechetFactory,GammaFactory,GeneralizedParetoFactory,GumbelFactory,HistogramFactory,InverseNormalFactory,LaplaceFactory,LogisticFactory,LogNormalFactory,LogUniformFactory,MeixnerDistributionFactory,NormalFactory,ParetoFactory,RayleighFactory,RiceFactory,SmoothedUniformFactory,StudentFactory,TrapezoidalFactory,TriangularFactory,TruncatedNormalFactory,UniformFactory,VonMisesFactory,WeibullMaxFactory,WeibullMinFactory]#32
 Continuous multivariate factories=[AliMikhailHaqCopulaFactory,BernsteinCopulaFactory,ClaytonCopulaFactory,DirichletFactory,FarlieGumbelMorgensternCopulaFactory,FrankCopulaFactory,GumbelCopulaFactory,NormalCopulaFactory,NormalFactory,PlackettCopulaFactory,StudentFactory]#11
-Discrete univariate factories=[BernoulliFactory,BinomialFactory,DiracFactory,GeometricFactory,MultinomialFactory,NegativeBinomialFactory,PoissonFactory,UserDefinedFactory,SkellamFactory]
+Discrete univariate factories=[BernoulliFactory,BinomialFactory,DiracFactory,GeometricFactory,MultinomialFactory,PolyaFactory,PoissonFactory,UserDefinedFactory,SkellamFactory]
 Discrete multivariate factories=[DiracFactory,MultinomialFactory,UserDefinedFactory]
-Univariate factories=[ArcsineFactory,BetaFactory,BurrFactory,ChiFactory,ChiSquareFactory,DirichletFactory,ExponentialFactory,FisherSnedecorFactory,FrechetFactory,GammaFactory,GeneralizedParetoFactory,GumbelFactory,HistogramFactory,InverseNormalFactory,LaplaceFactory,LogisticFactory,LogNormalFactory,LogUniformFactory,MeixnerDistributionFactory,NormalFactory,ParetoFactory,RayleighFactory,RiceFactory,SmoothedUniformFactory,StudentFactory,TrapezoidalFactory,TriangularFactory,TruncatedNormalFactory,UniformFactory,VonMisesFactory,WeibullMaxFactory,WeibullMinFactory,BernoulliFactory,BinomialFactory,DiracFactory,GeometricFactory,MultinomialFactory,NegativeBinomialFactory,PoissonFactory,UserDefinedFactory,SkellamFactory]#41
+Univariate factories=[ArcsineFactory,BetaFactory,BurrFactory,ChiFactory,ChiSquareFactory,DirichletFactory,ExponentialFactory,FisherSnedecorFactory,FrechetFactory,GammaFactory,GeneralizedParetoFactory,GumbelFactory,HistogramFactory,InverseNormalFactory,LaplaceFactory,LogisticFactory,LogNormalFactory,LogUniformFactory,MeixnerDistributionFactory,NormalFactory,ParetoFactory,RayleighFactory,RiceFactory,SmoothedUniformFactory,StudentFactory,TrapezoidalFactory,TriangularFactory,TruncatedNormalFactory,UniformFactory,VonMisesFactory,WeibullMaxFactory,WeibullMinFactory,BernoulliFactory,BinomialFactory,DiracFactory,GeometricFactory,MultinomialFactory,PolyaFactory,PoissonFactory,UserDefinedFactory,SkellamFactory]#41
 Multivariate factories=[AliMikhailHaqCopulaFactory,BernsteinCopulaFactory,ClaytonCopulaFactory,DirichletFactory,FarlieGumbelMorgensternCopulaFactory,FrankCopulaFactory,GumbelCopulaFactory,NormalCopulaFactory,NormalFactory,PlackettCopulaFactory,StudentFactory,DiracFactory,MultinomialFactory,UserDefinedFactory]#14

lib/test/t_NegativeBinomialFactory_std.cxx → lib/test/t_PolyaFactory_std.cxx

@@ -35,7 +35,7 @@ int main(int, char *[])
     Polya distribution(15, 0.7);
     UnsignedInteger size = 10000;
     Sample sample(distribution.getSample(size));
-    NegativeBinomialFactory factory;
+    PolyaFactory factory;
     Distribution estimatedDistribution(factory.build(sample));
     fullprint << "Distribution          =" << distribution << std::endl;
     fullprint << "Estimated distribution=" << estimatedDistribution << std::endl;

python/doc/user_manual/statistics_on_sample.rst

@@ -85,7 +85,7 @@ Building distributions from samples
     :template: DistributionFactory.rst_t
 
     MultinomialFactory
-    NegativeBinomialFactory
+    PolyaFactory
     NormalFactory
     ParetoFactory
     PoissonFactory

python/src/CMakeLists.txt

@@ -710,7 +710,7 @@ ot_add_python_module(dist_bundle2 dist_bundle2_module.i
                       Multinomial.i Multinomial_doc.i.in
                       MultinomialFactory.i MultinomialFactory_doc.i.in
                       Polya.i Polya_doc.i.in
-                      NegativeBinomialFactory.i NegativeBinomialFactory_doc.i.in
+                      PolyaFactory.i PolyaFactory_doc.i.in
                       NonCentralChiSquare.i NonCentralChiSquare_doc.i.in
                       NonCentralStudent.i NonCentralStudent_doc.i.in
                       Normal.i Normal_doc.i.in

python/src/PolyaFactory.i

@@ -0,0 +1,11 @@
+// SWIG file PolyaFactory.i
+
+%{
+#include "openturns/PolyaFactory.hxx"
+%}
+
+%include PolyaFactory_doc.i
+
+%copyctor OT::PolyaFactory;
+
+%include openturns/PolyaFactory.hxx

python/src/NegativeBinomialFactory_doc.i.in → python/src/PolyaFactory_doc.i.in

@@ -1,4 +1,4 @@
-%feature("docstring") OT::NegativeBinomialFactory
+%feature("docstring") OT::PolyaFactory
 "Negative Binomial factory.
 
 Notes
@@ -22,7 +22,7 @@ DistributionFactory, Polya"
 
 // ---------------------------------------------------------------------
 
-%feature("docstring") OT::NegativeBinomialFactory::buildAsNegativeBinomial
+%feature("docstring") OT::PolyaFactory::buildAsNegativeBinomial
 "Estimate the distribution as native distribution.
 
 **Available usages**:

python/src/dist_bundle2_module.i

@@ -62,7 +62,7 @@
 %include Multinomial.i
 %include MultinomialFactory.i
 %include Polya.i
-%include NegativeBinomialFactory.i
+%include PolyaFactory.i
 %include NonCentralChiSquare.i
 %include NonCentralStudent.i
 %include Normal.i

python/test/CMakeLists.txt

@@ -521,7 +521,7 @@ ot_pyinstallcheck_test (Mixture_std)
 ot_pyinstallcheck_test (Multinomial_std)
 ot_pyinstallcheck_test (MultinomialFactory_std)
 ot_pyinstallcheck_test (Polya_std)
-ot_pyinstallcheck_test (NegativeBinomialFactory_std)
+ot_pyinstallcheck_test (PolyaFactory_std)
 ot_pyinstallcheck_test (NonCentralChiSquare_std)
 if (Boost_FOUND)
 ot_pyinstallcheck_test (NonCentralStudent_std)

python/test/t_NegativeBinomialFactory_std.py → python/test/t_PolyaFactory_std.py

@@ -7,7 +7,7 @@
 distribution = ot.Polya(15, 0.7)
 size = 10000
 sample = distribution.getSample(size)
-factory = ot.NegativeBinomialFactory()
+factory = ot.PolyaFactory()
 estimatedDistribution = factory.build(sample)
 print("distribution=", repr(distribution))
 print("Estimated distribution=", repr(estimatedDistribution))