bpp-phyl3 3.0.0
bpp::MultinomialFromTransitionModel Member List

This is the complete list of members for bpp::MultinomialFromTransitionModel, including all inherited members.

AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
AbstractWrappedModel(const std::string &prefix)bpp::AbstractWrappedModelinline
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
addRateParameter() overridebpp::MultinomialFromTransitionModelinlinevirtual
aliasListenersRegister_bpp::AbstractParameterAliasableprivate
aliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)bpp::AbstractParameterAliasablevirtual
alphabet() const overridebpp::AbstractWrappedModelinlinevirtual
BranchModelInterface()bpp::BranchModelInterfaceinline
clone() const overridebpp::MultinomialFromTransitionModelinlinevirtual
compute_d2Multinomial_dt2_(const Eigen::VectorXd &counts) constbpp::MultinomialFromTransitionModelprivate
compute_dMultinomial_dt_(const Eigen::VectorXd &counts) constbpp::MultinomialFromTransitionModelprivate
compute_Multinomial_(const Eigen::VectorXd &counts) constbpp::MultinomialFromTransitionModelprivate
d2Lik_dt2(const Eigen::VectorXd &from, double t) const overridebpp::MultinomialFromTransitionModelvirtual
d2Pi_bpp::MultinomialFromTransitionModelprivate
d2Pij_dt2bpp::MultinomialFromTransitionModelprivate
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParameterAliasableprotectedvirtual
dLik_dt(const Eigen::VectorXd &from, double t) const overridebpp::MultinomialFromTransitionModelvirtual
dPi_bpp::MultinomialFromTransitionModelprivate
dPij_dtbpp::MultinomialFromTransitionModelprivate
factorial(uint n)bpp::MultinomialFromTransitionModelinlineprivatestatic
fireParameterChanged(const ParameterList &parameters) overridebpp::MultinomialFromTransitionModelinlinevirtual
frequencySet() const overridebpp::AbstractWrappedModelinlinevirtual
getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getAliases() constbpp::AbstractParameterAliasablevirtual
getAlphabet() const overridebpp::AbstractWrappedModelinlinevirtual
getAlphabetStateAsChar(size_t i) const overridebpp::AbstractWrappedModelinlinevirtual
getAlphabetStateAsInt(size_t i) const overridebpp::AbstractWrappedModelinlinevirtual
getAlphabetStates() const overridebpp::AbstractWrappedModelinlinevirtual
getFact_(const Eigen::VectorXd &counts) constbpp::MultinomialFromTransitionModelinlineprivate
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getInitValue(size_t i, int state) const overridebpp::MultinomialFromTransitionModelinlinevirtual
getModelStates(int code) const overridebpp::AbstractWrappedModelinlinevirtual
getModelStates(const std::string &code) const overridebpp::AbstractWrappedModelinlinevirtual
getName() const overridebpp::MultinomialFromTransitionModelinlinevirtual
getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfStates() const overridebpp::AbstractWrappedModelinlinevirtual
getParameter(const std::string &name) constbpp::AbstractParameterAliasable
getParameter(size_t i) constbpp::AbstractParameterAliasableprotected
getParameter(size_t i)bpp::AbstractParameterAliasableprotected
getParameter_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index) constbpp::AbstractParameterAliasableprotected
getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameters() const overridebpp::AbstractParameterAliasablevirtual
getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
getParameterValue(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParameterAliasableprotected
getRate() const overridebpp::MultinomialFromTransitionModelinlinevirtual
getStateMap() const overridebpp::AbstractWrappedModelinlinevirtual
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
lessEigen(Eigen::VectorXd const &a, Eigen::VectorXd const &b)bpp::MultinomialFromTransitionModelinlineprivatestatic
lessEigenType typedefbpp::MultinomialFromTransitionModelprivate
Lik_t(const Eigen::VectorXd &from, double t) const overridebpp::MultinomialFromTransitionModelvirtual
mapFact_bpp::MultinomialFromTransitionModelmutableprivate
matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
model()bpp::MultinomialFromTransitionModelinlineprotected
model() const overridebpp::MultinomialFromTransitionModelinlinevirtual
MultinomialFromTransitionModel(std::shared_ptr< TransitionModelInterface > originalModel)bpp::MultinomialFromTransitionModelinline
MultinomialFromTransitionModel(const MultinomialFromTransitionModel &fmsm)bpp::MultinomialFromTransitionModelinline
operator=(const MultinomialFromTransitionModel &fmsm)bpp::MultinomialFromTransitionModelinline
bpp::AbstractWrappedModel::operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
parameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
ParameterAliasable()bpp::ParameterAliasable
parameters_bpp::AbstractParameterAliasableprivate
Parametrizable()bpp::Parametrizable
Pi_bpp::MultinomialFromTransitionModelmutableprivate
Pij_tbpp::MultinomialFromTransitionModelmutableprivate
prefix_bpp::AbstractParameterAliasableprivate
removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
setFreq(std::map< int, double > &m)bpp::MultinomialFromTransitionModelinlinevirtual
setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0)bpp::MultinomialFromTransitionModelinline
setNamespace(const std::string &prefix)bpp::AbstractParameterAliasablevirtual
setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
setRate(double rate) overridebpp::MultinomialFromTransitionModelinlinevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
size_bpp::MultinomialFromTransitionModelprivate
stateMap() const overridebpp::AbstractWrappedModelinlinevirtual
subModel_bpp::MultinomialFromTransitionModelprivate
transitionModel()bpp::MultinomialFromTransitionModelinlineprotected
transitionModel() constbpp::MultinomialFromTransitionModelinline
tref_bpp::MultinomialFromTransitionModelmutableprivate
unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
WrappedModelInterface()bpp::WrappedModelInterfaceinline
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractWrappedModel()bpp::AbstractWrappedModelinlinevirtual
~BranchModelInterface()bpp::BranchModelInterfaceinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~MultinomialFromTransitionModel()bpp::MultinomialFromTransitionModelinlinevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual
~WrappedModelInterface()bpp::WrappedModelInterfaceinlinevirtual