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 |
archive | emp::SystematicsBase< ORG > | protected |
CalcDiversity() const | emp::Systematics< ORG, ORG_INFO, DATA_STRUCT > | virtual |
curr_update | emp::SystematicsBase< ORG > | protected |
data_node_t typedef | emp::SystematicsBase< ORG > | |
data_nodes | emp::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_id | emp::SystematicsBase< ORG > | protected |
num_roots | emp::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_count | emp::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_active | emp::SystematicsBase< ORG > | protected |
store_ancestors | emp::SystematicsBase< ORG > | protected |
store_outside | emp::SystematicsBase< ORG > | protected |
store_position | emp::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 &)=delete | emp::Systematics< ORG, ORG_INFO, DATA_STRUCT > | |
Systematics(Systematics &&)=default | emp::Systematics< ORG, ORG_INFO, DATA_STRUCT > | |
SystematicsBase(bool _active=true, bool _anc=true, bool _all=false, bool _pos=true) | emp::SystematicsBase< ORG > | inline |
total_depth | emp::SystematicsBase< ORG > | protected |
track_synchronous | emp::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 |