Empirical
emp::Systematics< ORG, ORG_INFO, DATA_STRUCT > Member List

This is the complete list of members for emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >, including all inherited members.

AddDataNode(const std::string &name)emp::SystematicsBase< ORG >inline
AddDataNode(std::function< emp::vector< double >()> pull_set_fun, const std::string &name)emp::SystematicsBase< ORG >inline
AddDataNode(std::function< double()> pull_fun, const std::string &name)emp::SystematicsBase< ORG >inline
AddDeleteriousStepDataNode(const std::string &name="deleterious_steps")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
AddDeleteriousStepDataNodeImpl(bool decoy, const std::string &name="deleterious_steps")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
AddDeleteriousStepDataNodeImpl(typename std::enable_if< DATA_STRUCT::has_fitness_t::value, T >::type decoy, const std::string &name="deleterious_steps")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
AddEvolutionaryDistinctivenessDataNode(const std::string &name="evolutionary_distinctiveness")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
AddMutationCountDataNode(const std::string &name="mutation_count", const std::string &mutation="substitution")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
AddMutationCountDataNodeImpl(bool decoy, const std::string &name="mutation_count", const std::string &mutation="substitution")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
AddMutationCountDataNodeImpl(typename std::enable_if< DATA_STRUCT::has_mutations_t::value, T >::type decoy, const std::string &name="mutation_count", const std::string &mutation="substitution")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
AddOrg(ORG &&org, int pos, int update=-1, bool next=false)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >virtual
AddOrg(ORG &&org, int pos, Ptr< taxon_t > parent=nullptr, int update=-1, bool next=false)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
AddOrg(ORG &&org, Ptr< taxon_t > parent=nullptr, int update=-1, bool next=false)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
AddOrg(ORG &org, int pos, int update=-1, bool next=false)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >virtual
AddOrg(ORG &org, int pos, Ptr< taxon_t > parent=nullptr, int update=-1, bool next=false)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
AddOrg(ORG &org, Ptr< taxon_t > parent=nullptr, int update=-1, bool next=false)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
AddPairwiseDistanceDataNode(const std::string &name="pairwise_distances")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
AddPhylogeneticDiversityDataNode(const std::string &name="phylogenetic_diversity")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
AddUniqueTaxaDataNode(const std::string &name="unique_taxa")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
AddUniqueTaxaDataNodeImpl(bool decoy, const std::string &name="unique_taxa")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
AddUniqueTaxaDataNodeImpl(typename std::enable_if< DATA_STRUCT::has_phen_t::value, T >::type decoy, const std::string &name="unique_taxa")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
AddVolatilityDataNode(const std::string &name="volatility")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
AddVolatilityDataNodeImpl(bool decoy, const std::string &name="volatility")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
AddVolatilityDataNodeImpl(typename std::enable_if< DATA_STRUCT::has_phen_t::value, T >::type decoy, const std::string &name="volatility")emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
archiveemp::SystematicsBase< ORG >protected
CalcDiversity() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >virtual
curr_updateemp::SystematicsBase< ORG >protected
data_node_t typedefemp::SystematicsBase< ORG >
data_nodesemp::SystematicsBase< ORG >protected
GetActive() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
GetActivePtr()emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
GetAncestors() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
GetArchive() const emp::SystematicsBase< ORG >inline
GetAveDepth() const emp::SystematicsBase< ORG >inline
GetBranchesToRoot(Ptr< taxon_t > tax) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
GetDataNode(const std::string &name)emp::SystematicsBase< ORG >inline
GetDistanceToRoot(Ptr< taxon_t > tax) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
GetEvolutionaryDistinctiveness(Ptr< taxon_t > tax, double time) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
GetMeanPairwiseDistance(bool branch_only=false) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
GetMRCA() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
GetMRCADepth() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >virtual
GetNextTaxonAt(int id)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
GetNumActive() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
GetNumAncestors() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
GetNumOutside() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
GetNumRoots() const emp::SystematicsBase< ORG >inline
GetNumTaxa() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
GetPairwiseDistances(bool branch_only=false) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
GetPhylogeneticDiversity() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
GetStoreActive() const emp::SystematicsBase< ORG >inline
GetStoreAncestors() const emp::SystematicsBase< ORG >inline
GetStoreOutside() const emp::SystematicsBase< ORG >inline
GetStorePosition() const emp::SystematicsBase< ORG >inline
GetSumPairwiseDistance(bool branch_only=false) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
GetTaxonAt(int id)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
GetTaxonDistinctiveness(Ptr< taxon_t > tax) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
GetTotalOrgs() const emp::SystematicsBase< ORG >inline
GetTrackSynchronous() const emp::SystematicsBase< ORG >inline
GetTreeSize() const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
GetVariancePairwiseDistance(bool branch_only=false) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
next_idemp::SystematicsBase< ORG >protected
num_rootsemp::SystematicsBase< ORG >protected
OnNew(std::function< void(Ptr< taxon_t >)> &fun)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
OnPrune(std::function< void(Ptr< taxon_t >)> &fun)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
org_countemp::SystematicsBase< ORG >protected
Parent(Ptr< taxon_t > taxon) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
PrintLineage(Ptr< taxon_t > taxon, std::ostream &os=std::cout) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
PrintStatus(std::ostream &os=std::cout) const emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >virtual
RemoveNextOrg(int pos)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >virtual
RemoveNextOrg(Ptr< taxon_t > taxon)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
RemoveOrg(int pos)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >virtual
RemoveOrg(Ptr< taxon_t > taxon)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
SetArchive(bool new_val)emp::SystematicsBase< ORG >inline
SetCalcInfoFun(fun_calc_info_t f)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
SetNextParent(int pos)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
SetNextParent(Ptr< taxon_t > p)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
SetStoreActive(bool new_val)emp::SystematicsBase< ORG >inline
SetStoreAncestors(bool new_val)emp::SystematicsBase< ORG >inline
SetStoreOutside(bool new_val)emp::SystematicsBase< ORG >inline
SetStorePosition(bool new_val)emp::SystematicsBase< ORG >inline
SetTrackSynchronous(bool new_val)emp::SystematicsBase< ORG >inline
store_activeemp::SystematicsBase< ORG >protected
store_ancestorsemp::SystematicsBase< ORG >protected
store_outsideemp::SystematicsBase< ORG >protected
store_positionemp::SystematicsBase< ORG >protected
Systematics(fun_calc_info_t calc_taxon, bool _active=true, bool _anc=true, bool _all=false, bool _pos=true)emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
Systematics(const Systematics &)=deleteemp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
Systematics(Systematics &&)=defaultemp::Systematics< ORG, ORG_INFO, DATA_STRUCT >
SystematicsBase(bool _active=true, bool _anc=true, bool _all=false, bool _pos=true)emp::SystematicsBase< ORG >inline
total_depthemp::SystematicsBase< ORG >protected
track_synchronousemp::SystematicsBase< ORG >protected
Update()emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inlinevirtual
~Systematics()emp::Systematics< ORG, ORG_INFO, DATA_STRUCT >inline
~SystematicsBase()emp::SystematicsBase< ORG >inlinevirtual