/** Return member rules (no members) */
const MemberRules& Move_SynchronizedVectorFixedSingleElementSlide::getParameterRules(void) const
{
static MemberRules move_member_rules;
static bool rules_set = false;
if ( !rules_set )
{
move_member_rules.push_back( new ArgumentRule( "x" , ModelVector<ModelVector<Real> >::getClassTypeSpec(), "The variable (a deterministic variable holding the vector of stochastic variable) on which this move operates.", ArgumentRule::BY_REFERENCE, ArgumentRule::DETERMINISTIC ) );
std::vector<TypeSpec> index_types;
index_types.push_back( Natural::getClassTypeSpec() );
index_types.push_back( ModelVector<Natural>::getClassTypeSpec() );
move_member_rules.push_back( new ArgumentRule( "element", index_types, "The index or indices of the element to scale.", ArgumentRule::BY_VALUE, ArgumentRule::ANY ) );
move_member_rules.push_back( new ArgumentRule( "lambda" , RealPos::getClassTypeSpec() , "The scaling factor (strength) of this move.", ArgumentRule::BY_VALUE , ArgumentRule::ANY, new Real(1.0) ) );
move_member_rules.push_back( new ArgumentRule( "tune" , RlBoolean::getClassTypeSpec() , "Should we tune the scaling factor during burnin?", ArgumentRule::BY_VALUE , ArgumentRule::ANY, new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
move_member_rules.insert( move_member_rules.end(), inheritedRules.begin(), inheritedRules.end() );
rules_set = true;
}
return move_member_rules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the diversity-dependent pure-birth process are:
* (1) the initial speciation rate lambda which must be a positive real.
* (2) the carrying capacity that must be a natural number.
* (3) all member rules specified by BirthDeathProcess.
*
* \return The member rules.
*/
const MemberRules& Dist_divDepYuleProcess::getMemberRules(void) const
{
static MemberRules distcBirthDeathMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
distcBirthDeathMemberRules.push_back( new ArgumentRule( "lambda" , true, RealPos::getClassTypeSpec() ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "capacity", true, Natural::getClassTypeSpec() ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "origin", true, RealPos::getClassTypeSpec() ) );
std::vector<RlString> optionsCondition;
optionsCondition.push_back( RlString("time") );
optionsCondition.push_back( RlString("survival") );
optionsCondition.push_back( RlString("nTaxa") );
distcBirthDeathMemberRules.push_back( new OptionRule( "condition", new RlString("survival"), optionsCondition ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "nTaxa" , true, Natural::getClassTypeSpec() ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "names" , true, ModelVector<RlString>::getClassTypeSpec() ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "constraints" , true, ModelVector<Clade>::getClassTypeSpec(), new ModelVector<Clade>() ) );
// add the rules from the base class
const MemberRules &parentRules = TypedDistribution<TimeTree>::getMemberRules();
distcBirthDeathMemberRules.insert(distcBirthDeathMemberRules.end(), parentRules.begin(), parentRules.end());
rulesSet = true;
}
return distcBirthDeathMemberRules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the diversity-dependent pure-birth process are:
* (1) the initial speciation rate lambda which must be a positive real.
* (2) the carrying capacity that must be a natural number.
* (3) all member rules specified by BirthDeathProcess.
*
* \return The member rules.
*/
const MemberRules& Dist_serialBDP::getParameterRules(void) const
{
static MemberRules distcBirthDeathMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
distcBirthDeathMemberRules.push_back( new ArgumentRule( "origin" , RealPos::getClassTypeSpec(), ArgumentRule::BY_CONSTANT_REFERENCE, ArgumentRule::ANY, NULL ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "rootAge", RealPos::getClassTypeSpec(), ArgumentRule::BY_CONSTANT_REFERENCE, ArgumentRule::ANY, NULL ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "lambda" , RealPos::getClassTypeSpec(), ArgumentRule::BY_CONSTANT_REFERENCE ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "mu" , RealPos::getClassTypeSpec(), ArgumentRule::BY_CONSTANT_REFERENCE, ArgumentRule::ANY, new RealPos(0.0) ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "psi" , RealPos::getClassTypeSpec(), ArgumentRule::BY_CONSTANT_REFERENCE, ArgumentRule::ANY, new RealPos(0.0) ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "rho" , Probability::getClassTypeSpec(), ArgumentRule::BY_CONSTANT_REFERENCE, ArgumentRule::ANY, new Probability(1.0) ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "timeSinceLastSample", RealPos::getClassTypeSpec(), ArgumentRule::BY_CONSTANT_REFERENCE, ArgumentRule::ANY, new RealPos(0.0) ) );
std::vector<std::string> optionsCondition;
optionsCondition.push_back( "time" );
optionsCondition.push_back( "survival" );
optionsCondition.push_back( "nTaxa" );
distcBirthDeathMemberRules.push_back( new OptionRule( "condition", new RlString("survival"), optionsCondition ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "names" , ModelVector<RlString>::getClassTypeSpec(), ArgumentRule::BY_VALUE ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "constraints", ModelVector<Clade>::getClassTypeSpec(), ArgumentRule::BY_VALUE, ArgumentRule::ANY, new ModelVector<Clade>() ) );
// add the rules from the base class
const MemberRules &parentRules = TypedDistribution<TimeTree>::getParameterRules();
distcBirthDeathMemberRules.insert(distcBirthDeathMemberRules.end(), parentRules.begin(), parentRules.end());
rulesSet = true;
}
return distcBirthDeathMemberRules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the scale move are:
* (1) the variable which must be a positive real.
* (2) the tuning parameter lambda that defines the size of the proposal (positive real)
* (3) a flag whether auto-tuning should be used.
*
* \return The member rules.
*/
const MemberRules& Move_NodeCharacterHistoryRejectionSample::getMemberRules(void) const
{
static MemberRules nodeChrsMoveMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
nodeChrsMoveMemberRules.push_back( new ArgumentRule( "ctmc", false, AbstractDiscreteCharacterData::getClassTypeSpec() ) );
nodeChrsMoveMemberRules.push_back( new ArgumentRule( "qmap", false, RateMap::getClassTypeSpec() ) );
nodeChrsMoveMemberRules.push_back( new ArgumentRule( "tree", false, TimeTree::getClassTypeSpec() ) );
nodeChrsMoveMemberRules.push_back( new ArgumentRule( "lambda", true, Probability::getClassTypeSpec() , new Probability(1.0) ) );
// nodeChrsMoveMemberRules.push_back( new ArgumentRule( "type", true, RlString::getClassTypeSpec(), new RlString("std") ) );
std::vector<RlString> options;
options.push_back( RlString("std") );
options.push_back( RlString("biogeo") );
nodeChrsMoveMemberRules.push_back( new OptionRule( "type", new RlString("std"), options ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getMemberRules();
nodeChrsMoveMemberRules.insert( nodeChrsMoveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return nodeChrsMoveMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_SubtreeScale::getMemberRules(void) const {
static MemberRules nniMemberRules;
static bool rulesSet = false;
if ( !rulesSet ) {
nniMemberRules.push_back( new ArgumentRule( "tree", false, TimeTree::getClassTypeSpec() ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getMemberRules();
nniMemberRules.insert( nniMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return nniMemberRules;
}
/** Return member rules (no members) */
const MemberRules& HillClimber::getParameterRules(void) const
{
static MemberRules memberRules;
static bool rules_set = false;
if ( !rules_set )
{
// add the rules from the base class
const MemberRules &parentRules = MaximumLikelihoodAnalysis::getParameterRules();
memberRules.insert(memberRules.end(), parentRules.begin(), parentRules.end());
rules_set = true;
}
return memberRules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the scale move are:
* (1) the variable which must be a positive real.
* (2) the tuning parameter lambda that defines the size of the proposal (positive real)
* (3) a flag whether auto-tuning should be used.
*
* \return The member rules.
*/
const MemberRules& RevLanguage::Move_CharacterHistory::getParameterRules(void) const
{
static MemberRules nodeChrsmove_member_rules;
static bool rules_set = false;
if ( !rules_set )
{
nodeChrsmove_member_rules.push_back( new ArgumentRule( "ctmc", AbstractHomologousDiscreteCharacterData::getClassTypeSpec(), "The PhyloCTMC variable.", ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
nodeChrsmove_member_rules.push_back( new ArgumentRule( "qmap", RateMap::getClassTypeSpec() , "Some rate-map.", ArgumentRule::BY_REFERENCE, ArgumentRule::ANY ) );
nodeChrsmove_member_rules.push_back( new ArgumentRule( "tree", Tree::getClassTypeSpec() , "The tree.", ArgumentRule::BY_REFERENCE, ArgumentRule::ANY ) );
nodeChrsmove_member_rules.push_back( new ArgumentRule( "lambda", Probability::getClassTypeSpec() , "", ArgumentRule::BY_VALUE , ArgumentRule::ANY, new Probability(1.0) ) );
std::vector<std::string> optionsType;
optionsType.push_back( "Biogeo" );
optionsType.push_back( "DNA" );
optionsType.push_back( "RNA" );
optionsType.push_back( "AA" );
optionsType.push_back( "Protein" );
optionsType.push_back( "Standard" );
nodeChrsmove_member_rules.push_back( new OptionRule( "type", new RlString("Standard"), optionsType, "The data type." ) );
std::vector<std::string> optionsGraph;
optionsGraph.push_back( "node" );
optionsGraph.push_back( "branch" );
nodeChrsmove_member_rules.push_back( new OptionRule( "graph", new RlString("node"), optionsGraph, "" ) );
std::vector<std::string> optionsProposal;
optionsProposal.push_back( "rejection" );
optionsProposal.push_back( "uniformization" );
nodeChrsmove_member_rules.push_back( new OptionRule( "proposal", new RlString("rejection"), optionsProposal, "" ) );
/* Inherit weight from Move, put it after variable */
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
nodeChrsmove_member_rules.insert( nodeChrsmove_member_rules.end(), inheritedRules.begin(), inheritedRules.end() );
rules_set = true;
}
return nodeChrsmove_member_rules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the scale move are:
* (1) the variable which must be a time-tree.
*
* \return The member rules.
*/
const MemberRules& Move_SubtreeScale::getParameterRules(void) const
{
static MemberRules memberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
memberRules.push_back( new ArgumentRule( "tree", TimeTree::getClassTypeSpec(), ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
memberRules.insert( memberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return memberRules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the scale move are:
* (1) the variable which must be an integer.
*
* \return The member rules.
*/
const MemberRules& Move_BinarySwitch::getParameterRules(void) const
{
static MemberRules moveMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
moveMemberRules.push_back( new ArgumentRule( "x", Natural::getClassTypeSpec(), "The variable on which this move operates.", ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
moveMemberRules.insert( moveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return moveMemberRules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the scale move are:
* (1) the variable which must be a vector of positive reals.
* (2) the weight how often the move is used.
*
* \return The member rules.
*/
const MemberRules& Move_SwitchRateJump::getParameterRules(void) const
{
static MemberRules moveMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
moveMemberRules.push_back( new ArgumentRule( "x", ModelVector<RealPos>::getClassTypeSpec(), ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
moveMemberRules.insert( moveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return moveMemberRules;
}
/** Return member rules */
const MemberRules& Move::getParameterRules(void) const
{
static MemberRules moveMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
moveMemberRules.push_back( new ArgumentRule( "weight", RealPos::getClassTypeSpec(), ArgumentRule::BY_VALUE, ArgumentRule::ANY, new RealPos( 1.0 ) ) );
/* Inherit variables from WorkspaceObject, put them last */
const MemberRules& inheritedRules = WorkspaceObject::getParameterRules();
moveMemberRules.insert( moveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return moveMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_VectorSingleElementSlide::getMemberRules(void) const {
static MemberRules scalingMoveMemberRules;
static bool rulesSet = false;
if ( !rulesSet ) {
scalingMoveMemberRules.push_back( new ArgumentRule( "x", false, ModelVector<Real>::getClassTypeSpec() ) );
scalingMoveMemberRules.push_back( new ArgumentRule( "lambda", true, RealPos::getClassTypeSpec() , new Real(1.0) ) );
scalingMoveMemberRules.push_back( new ArgumentRule( "tune" , true, RlBoolean::getClassTypeSpec(), new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getMemberRules();
scalingMoveMemberRules.insert( scalingMoveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return scalingMoveMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_RootTimeSlide::getMemberRules(void) const {
static MemberRules nniMemberRules;
static bool rulesSet = false;
if ( !rulesSet ) {
nniMemberRules.push_back( new ArgumentRule( "tree", false, TimeTree::getClassTypeSpec() ) );
nniMemberRules.push_back( new ArgumentRule( "delta", true, RealPos::getClassTypeSpec() , new Real(1.0) ) );
nniMemberRules.push_back( new ArgumentRule( "tune" , true, RlBoolean::getClassTypeSpec(), new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getMemberRules();
nniMemberRules.insert( nniMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return nniMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_MultivariatePhyloProcessTranslation::getMemberRules(void) const {
static MemberRules nniMemberRules;
static bool rulesSet = false;
if ( !rulesSet ) {
nniMemberRules.push_back( new ArgumentRule( "process", false, MultivariatePhyloProcess::getClassTypeSpec() ) );
nniMemberRules.push_back( new ArgumentRule( "lambda", true, RealPos::getClassTypeSpec(), new RealPos( 1.0 ) ) );
nniMemberRules.push_back( new ArgumentRule( "tune", true, RlBoolean::getClassTypeSpec(), new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getMemberRules();
nniMemberRules.insert( nniMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return nniMemberRules;
}
/** Return member rules */
const MemberRules& StationarityStoppingRule::getParameterRules(void) const
{
static MemberRules memberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
memberRules.push_back( new ArgumentRule( "prob", Probability::getClassTypeSpec() , ArgumentRule::BY_VALUE ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = AbstractConvergenceStoppingRule::getParameterRules();
memberRules.insert( memberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return memberRules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the constant-rate birth-death process are:
* (1) the speciation rate lambda which must be a positive real.
* (2) the extinction rate mu that must be a positive real.
* (3) all member rules specified by BirthDeathProcess.
*
* \return The member rules.
*/
const MemberRules& Dist_bdp::getMemberRules(void) const
{
static MemberRules distcBirthDeathMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
distcBirthDeathMemberRules.push_back( new ArgumentRule( "lambda", true, RealPos::getClassTypeSpec() ) );
distcBirthDeathMemberRules.push_back( new ArgumentRule( "mu" , true, RealPos::getClassTypeSpec(), new RealPos(0.0) ) );
// add the rules from the base class
const MemberRules &parentRules = BirthDeathProcess::getMemberRules();
distcBirthDeathMemberRules.insert(distcBirthDeathMemberRules.end(), parentRules.begin(), parentRules.end());
rulesSet = true;
}
return distcBirthDeathMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_NNIClock::getParameterRules(void) const
{
static MemberRules nniMemberRules;
static bool rules_set = false;
if ( !rules_set )
{
nniMemberRules.push_back( new ArgumentRule( "tree", TimeTree::getClassTypeSpec(), "The tree on which this move operates.", ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
nniMemberRules.insert( nniMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rules_set = true;
}
return nniMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_SliderUpDown::getParameterRules(void) const {
static MemberRules mixingStepMemberRules;
static bool rulesSet = false;
if ( !rulesSet ) {
mixingStepMemberRules.push_back( new ArgumentRule( "value_1", Real::getClassTypeSpec() , ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
mixingStepMemberRules.push_back( new ArgumentRule( "value_2", Real::getClassTypeSpec() , ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
mixingStepMemberRules.push_back( new ArgumentRule( "slide" , RealPos::getClassTypeSpec() , ArgumentRule::BY_VALUE, ArgumentRule::ANY, new Real(1.0) ) );
mixingStepMemberRules.push_back( new ArgumentRule( "tune" , RlBoolean::getClassTypeSpec(), ArgumentRule::BY_VALUE, ArgumentRule::ANY, new RlBoolean( false ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
mixingStepMemberRules.insert( mixingStepMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return mixingStepMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_DPPScaleCatValsMove::getParameterRules(void) const {
static MemberRules dppMove;
static bool rulesSet = false;
if ( !rulesSet )
{
dppMove.push_back( new ArgumentRule( "x" , ModelVector<RealPos>::getClassTypeSpec(), ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
dppMove.push_back( new ArgumentRule( "lambda", RealPos::getClassTypeSpec() , ArgumentRule::BY_VALUE , ArgumentRule::ANY , new Real(1.0) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
dppMove.insert( dppMove.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return dppMove;
}
/** Return member rules */
const MemberRules& GelmanRubinStoppingRule::getParameterRules(void) const
{
static MemberRules memberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
memberRules.push_back( new ArgumentRule( "R", RealPos::getClassTypeSpec(), "The maximum allowed potential scale reduction factor.", ArgumentRule::BY_VALUE, ArgumentRule::ANY ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = AbstractConvergenceStoppingRule::getParameterRules();
memberRules.insert( memberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return memberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_SimplexSingleElementScale::getMemberRules(void) const {
static MemberRules moveMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
moveMemberRules.push_back( new ArgumentRule( "x" , Simplex::getClassTypeSpec() , ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
moveMemberRules.push_back( new ArgumentRule( "alpha", RealPos::getClassTypeSpec() , ArgumentRule::BY_VALUE, ArgumentRule::ANY, new Real(1.0) ) );
moveMemberRules.push_back( new ArgumentRule( "tune" , RlBoolean::getClassTypeSpec(), ArgumentRule::BY_VALUE, ArgumentRule::ANY, new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getMemberRules();
moveMemberRules.insert( moveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return moveMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_ElementSlide::getParameterRules(void) const {
static MemberRules moveMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
moveMemberRules.push_back( new ArgumentRule( "x" , ModelVector<Real>::getClassTypeSpec(), ArgumentRule::BY_REFERENCE, ArgumentRule::DETERMINISTIC ) );
moveMemberRules.push_back( new ArgumentRule( "delta", RealPos::getClassTypeSpec() , ArgumentRule::BY_VALUE , ArgumentRule::ANY, new RealPos(1.0) ) );
moveMemberRules.push_back( new ArgumentRule( "tune" , RlBoolean::getClassTypeSpec() , ArgumentRule::BY_VALUE , ArgumentRule::ANY, new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
moveMemberRules.insert( moveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return moveMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_WeightedNodeTimeSlide::getParameterRules(void) const
{
static MemberRules memberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
memberRules.push_back( new ArgumentRule( "tree" , TimeTree::getClassTypeSpec(), "The tree on which this move operates.", ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
memberRules.push_back( new ArgumentRule( "blocks", Natural::getClassTypeSpec() , "The number of bocks into which the branch will be broken.", ArgumentRule::BY_VALUE , ArgumentRule::ANY , new Natural(8) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
memberRules.insert( memberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return memberRules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the scale move are:
* (1) the variable which must be a positive real.
* (2) the tuning parameter window that defines the size of the proposal (positive real)
* (3) a flag whether auto-tuning should be used.
*
* \return The member rules.
*/
const MemberRules& Move_SliceSampling::getParameterRules(void) const
{
static MemberRules moveMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
moveMemberRules.push_back( new ArgumentRule( "x" , Real::getClassTypeSpec() , "The variable on which this move operates", ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
moveMemberRules.push_back( new ArgumentRule( "window", RealPos::getClassTypeSpec() , "The window (steps-size) of proposals.", ArgumentRule::BY_VALUE , ArgumentRule::ANY, new RealPos(1.0) ) );
moveMemberRules.push_back( new ArgumentRule( "tune" , RlBoolean::getClassTypeSpec(), "Should we tune the move during burnin?", ArgumentRule::BY_VALUE , ArgumentRule::ANY, new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
moveMemberRules.insert( moveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return moveMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_ScaleSingleACLNRates::getMemberRules(void) const {
static MemberRules scalingMoveMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
scalingMoveMemberRules.push_back( new ArgumentRule( "x" , ModelVector<RealPos>::getClassTypeSpec(), ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
scalingMoveMemberRules.push_back( new ArgumentRule( "lambda", RealPos::getClassTypeSpec() , ArgumentRule::BY_VALUE , ArgumentRule::ANY, new Real(1.0) ) );
scalingMoveMemberRules.push_back( new ArgumentRule( "tune" , RlBoolean::getClassTypeSpec() , ArgumentRule::BY_VALUE , ArgumentRule::ANY, new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getMemberRules();
scalingMoveMemberRules.insert( scalingMoveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return scalingMoveMemberRules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the constant-rate birth-death process are:
* (1) the speciation rate lambda which must be a positive real.
* (2) the extinction rate mu that must be a positive real.
* (3) all member rules specified by BirthDeathProcess.
*
* \return The member rules.
*/
const MemberRules& Dist_bdpTopology::getParameterRules(void) const
{
static MemberRules memberRules;
static bool rules_set = false;
if ( !rules_set )
{
memberRules.push_back( new ArgumentRule( "lambda", RealPos::getClassTypeSpec(), "The constant speciation rate.", ArgumentRule::BY_CONSTANT_REFERENCE, ArgumentRule::ANY ) );
memberRules.push_back( new ArgumentRule( "mu" , RealPos::getClassTypeSpec(), "The constant extinction rate.", ArgumentRule::BY_CONSTANT_REFERENCE, ArgumentRule::ANY, new RealPos(0.0) ) );
// add the rules from the base class
const MemberRules &parentRules = BirthDeathProcess::getParameterRules();
memberRules.insert( memberRules.end(), parentRules.begin(), parentRules.end());
rules_set = true;
}
return memberRules;
}
/**
* Get the member rules used to create the constructor of this object.
*
* The member rules of the slide move are:
* (1) the variable which must be a real.
* (2) the tuning parameter lambda that defines the size of the proposal (positive real)
* (3) a flag whether auto-tuning should be used.
*
* \return The member rules.
*/
const MemberRules& Move_Slide::getParameterRules(void) const
{
static MemberRules slidingmove_member_rules;
static bool rules_set = false;
if ( !rules_set )
{
slidingmove_member_rules.push_back( new ArgumentRule( "x" , Real::getClassTypeSpec() , "The variable on which this move operates.", ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
slidingmove_member_rules.push_back( new ArgumentRule( "delta" , RealPos::getClassTypeSpec() , "The window size parameter.", ArgumentRule::BY_VALUE , ArgumentRule::ANY , new RealPos(1.0) ) );
slidingmove_member_rules.push_back( new ArgumentRule( "tune" , RlBoolean::getClassTypeSpec(), "Should we tune the window size during burnin?", ArgumentRule::BY_VALUE , ArgumentRule::ANY , new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
slidingmove_member_rules.insert( slidingmove_member_rules.end(), inheritedRules.begin(), inheritedRules.end() );
rules_set = true;
}
return slidingmove_member_rules;
}
/** Return member rules (no members) */
const MemberRules& Move_RealNodeValTreeSliding::getMemberRules(void) const
{
static MemberRules memberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
memberRules.push_back( new ArgumentRule( "process", RealNodeValTree::getClassTypeSpec(), ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
memberRules.push_back( new ArgumentRule( "lambda" , RealPos::getClassTypeSpec() , ArgumentRule::BY_VALUE , ArgumentRule::ANY , new RealPos( 1.0 ) ) );
memberRules.push_back( new ArgumentRule( "tune" , RlBoolean::getClassTypeSpec() , ArgumentRule::BY_VALUE , ArgumentRule::ANY, new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getMemberRules();
memberRules.insert( memberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return memberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_VectorSingleElementSlide::getParameterRules(void) const
{
static MemberRules moveMemberRules;
static bool rulesSet = false;
if ( !rulesSet )
{
moveMemberRules.push_back( new ArgumentRule( "x" , ModelVector<Real>::getClassTypeSpec(), "The variable on which this move operates.", ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
moveMemberRules.push_back( new ArgumentRule( "lambda", RealPos::getClassTypeSpec() , "The scaling factor (strength) of the move.", ArgumentRule::BY_VALUE , ArgumentRule::ANY, new Real(1.0) ) );
moveMemberRules.push_back( new ArgumentRule( "tune" , RlBoolean::getClassTypeSpec() , "Should we tune the scaling factor during burnin?", ArgumentRule::BY_VALUE , ArgumentRule::ANY, new RlBoolean( true ) ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
moveMemberRules.insert( moveMemberRules.end(), inheritedRules.begin(), inheritedRules.end() );
rulesSet = true;
}
return moveMemberRules;
}
/** Return member rules (no members) */
const MemberRules& Move_ConjugateInverseWishartBrownian::getParameterRules(void) const
{
static MemberRules move_member_rules;
static bool rules_set = false;
if ( !rules_set )
{
move_member_rules.push_back( new ArgumentRule( "x" , MatrixRealSymmetric::getClassTypeSpec(), "The variable on which this move operates.", ArgumentRule::BY_REFERENCE, ArgumentRule::STOCHASTIC ) );
move_member_rules.push_back( new ArgumentRule( "kappa" , Real::getClassTypeSpec() , "The scaling parameter of the distribution.", ArgumentRule::BY_REFERENCE, ArgumentRule::ANY ) );
move_member_rules.push_back( new ArgumentRule( "df" , Natural::getClassTypeSpec() , "The degrees of freedom of the distribution.", ArgumentRule::BY_REFERENCE, ArgumentRule::ANY ) );
/* Inherit weight from Move, put it after variable */
const MemberRules& inheritedRules = Move::getParameterRules();
move_member_rules.insert( move_member_rules.end(), inheritedRules.begin(), inheritedRules.end() );
rules_set = true;
}
return move_member_rules;
}