Full API

Namespaces

• Namespace eastl
  • Functions

• Namespace necsim
  • Classes
  • Enums
  • Functions
  • Variables

• Namespace neutral_analytical
  • Functions

• Namespace random_numbers
  • Classes
  • Functions
  • Variables

• Namespace std

Classes and Structs

• Struct module_state
  • Struct Documentation

• Struct CommunitiesArray
  • Struct Documentation

• Struct CommunityParameters
  • Struct Documentation

• Struct ConfigException
  • Inheritance Relationships
    • Base Type
  • Struct Documentation

• Struct FatalException
  • Inheritance Relationships
    • Base Type
    • Derived Type
  • Struct Documentation

• Struct Fragment
  • Struct Documentation

• Struct HistoricalMapParameters
  • Struct Documentation

• Struct MapLocation
  • Inheritance Relationships
    • Derived Types
  • Struct Documentation

• Struct MetacommunitiesArray
  • Struct Documentation

• Struct MetacommunityParameters
  • Struct Documentation

• Struct ProtractedSpeciationParameters
  • Struct Documentation

• Struct SectionOption
  • Struct Documentation

• Struct SimParameters
  • Struct Documentation

• Struct SQLStatement
  • Struct Documentation

• Class LandscapeMetricsCalculator
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class ActivityMap
  • Class Documentation

• Class AnalyticalSpeciesAbundancesHandler
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class Cell
  • Class Documentation

• Class Community
  • Inheritance Relationships
    • Derived Type
  • Class Documentation

• Class ConfigParser
  • Class Documentation

• Class DataMask
  • Inheritance Relationships
    • Derived Type
  • Class Documentation

• Class DataPoint
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class DispersalCoordinator
  • Class Documentation

• Class GillespieHeapNode
  • Class Documentation

• Class GillespieProbability
  • Class Documentation

• Class Landscape
  • Class Documentation

• Class LogFile
  • Class Documentation

• Class Logger
  • Inheritance Relationships
    • Derived Type
  • Class Documentation

• Template Class Map
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Template Class Matrix
  • Inheritance Relationships
    • Derived Type
  • Class Documentation

• Class Metacommunity
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class ProtractedSpatialTree
  • Inheritance Relationships
    • Base Types
  • Class Documentation

• Class ProtractedTree
  • Inheritance Relationships
    • Base Type
    • Derived Type
  • Class Documentation

• Class PyLogger
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class Samplematrix
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class SimulateDispersal
  • Class Documentation

• Class SimulatedSpeciesAbundancesHandler
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class SpatialTree
  • Inheritance Relationships
    • Base Type
    • Derived Type
  • Class Documentation

• Class SpeciationCommands
  • Class Documentation

• Class SpeciesAbundancesHandler
  • Inheritance Relationships
    • Derived Types
  • Class Documentation

• Class SpeciesList
  • Class Documentation

• Class SpecSimParameters
  • Class Documentation

• Class SQLiteHandler
  • Class Documentation

• Class Step
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class Tree
  • Inheritance Relationships
    • Derived Types
  • Class Documentation

• Class TreeNode
  • Class Documentation

• Class ProtractedTree
  • Class Documentation

• Template Class PyCommunityTemplate
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class PyLMC
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class PySimulateDispersal
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Template Class PyTemplate
  • Inheritance Relationships
    • Derived Type
  • Class Documentation

• Class RNGController
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class SplitMix64
  • Class Documentation

• Class Xoroshiro256plus
  • Inheritance Relationships
    • Derived Type
  • Class Documentation

Enums

• Enum CellEventType
  • Enum Documentation

• Enum EventType
  • Enum Documentation

Functions

• Template Function addGillespie
  • Function Documentation

• Template Function addProtractedParameters
  • Function Documentation

• Template Function addTime
  • Function Documentation

• Template Function apply
  • Function Documentation

• Template Function applySpeciationRates
  • Function Documentation

• Function calculateCLUMPY
  • Function Documentation

• Function calculateMNN
  • Function Documentation

• Template Function eastl::adjust_heap(RandomAccessIterator, Distance, Distance, Distance, const T&)
  • Function Documentation

• Template Function eastl::adjust_heap(RandomAccessIterator, Distance, Distance, Distance, T&&)
  • Function Documentation

• Template Function eastl::adjust_heap(RandomAccessIterator, Distance, Distance, Distance, const T&, Compare)
  • Function Documentation

• Template Function eastl::adjust_heap(RandomAccessIterator, Distance, Distance, Distance, T&&, Compare)
  • Function Documentation

• Template Function eastl::adjust_heap_impl(RandomAccessIterator, Distance, Distance, Distance, T)
  • Function Documentation

• Template Function eastl::adjust_heap_impl(RandomAccessIterator, Distance, Distance, Distance, T, Compare)
  • Function Documentation

• Template Function eastl::change_heap(RandomAccessIterator, Distance, Distance)
  • Function Documentation

• Template Function eastl::change_heap(RandomAccessIterator, Distance, Distance, Compare)
  • Function Documentation

• Template Function eastl::is_heap(RandomAccessIterator, RandomAccessIterator)
  • Function Documentation

• Template Function eastl::is_heap(RandomAccessIterator, RandomAccessIterator, Compare)
  • Function Documentation

• Template Function eastl::is_heap_until(RandomAccessIterator, RandomAccessIterator)
  • Function Documentation

• Template Function eastl::is_heap_until(RandomAccessIterator, RandomAccessIterator, Compare)
  • Function Documentation

• Template Function eastl::make_heap(RandomAccessIterator, RandomAccessIterator)
  • Function Documentation

• Template Function eastl::make_heap(RandomAccessIterator, RandomAccessIterator, Compare)
  • Function Documentation

• Template Function eastl::pop_heap(RandomAccessIterator, RandomAccessIterator)
  • Function Documentation

• Template Function eastl::pop_heap(RandomAccessIterator, RandomAccessIterator, Compare)
  • Function Documentation

• Template Function eastl::promote_heap(RandomAccessIterator, Distance, Distance, const T&)
  • Function Documentation

• Template Function eastl::promote_heap(RandomAccessIterator, Distance, Distance, T&&)
  • Function Documentation

• Template Function eastl::promote_heap(RandomAccessIterator, Distance, Distance, const T&, Compare)
  • Function Documentation

• Template Function eastl::promote_heap(RandomAccessIterator, Distance, Distance, T&&, Compare)
  • Function Documentation

• Template Function eastl::promote_heap_impl(RandomAccessIterator, Distance, Distance, T)
  • Function Documentation

• Template Function eastl::promote_heap_impl(RandomAccessIterator, Distance, Distance, T, Compare)
  • Function Documentation

• Template Function eastl::push_heap(RandomAccessIterator, RandomAccessIterator)
  • Function Documentation

• Template Function eastl::push_heap(RandomAccessIterator, RandomAccessIterator, Compare)
  • Function Documentation

• Template Function eastl::remove_heap(RandomAccessIterator, Distance, Distance)
  • Function Documentation

• Template Function eastl::remove_heap(RandomAccessIterator, Distance, Distance, Compare)
  • Function Documentation

• Template Function eastl::sort_heap(RandomAccessIterator, RandomAccessIterator)
  • Function Documentation

• Template Function eastl::sort_heap(RandomAccessIterator, RandomAccessIterator, Compare)
  • Function Documentation

• Template Function genCommunityMethods
  • Function Documentation

• Template Function genCommunityType(char *, char *)
  • Function Documentation

• Template Function genCommunityType(string, string)
  • Function Documentation

• Function genLMCType
  • Function Documentation

• Template Function genPySimulationMethods
  • Function Documentation

• Function genSimulateDispersalType
  • Function Documentation

• Template Function genSimulationType
  • Function Documentation

• Template Function importConfig
  • Function Documentation

• Template Function importConfigFromString
  • Function Documentation

• Function importPyListsToVectorCell(PyObject *, PyObject *, vector<Cell>&, const string&)
  • Function Documentation

• Function importPyListsToVectorCell(PyObject *, PyObject *, vector<Cell>&, const string&)
  • Function Documentation

• Function importPyListToVectorDouble(PyObject *, vector<double>&, const string&)
  • Function Documentation

• Function importPyListToVectorDouble(PyObject *, vector<double>&, const string&)
  • Function Documentation

• Function importPyListToVectorString(PyObject *, vector<string>&, const string&)
  • Function Documentation

• Function importPyListToVectorString(PyObject *, vector<string>&, const string&)
  • Function Documentation

• Function importPyListToVectorULong(PyObject *, vector<unsigned long>&, const string&)
  • Function Documentation

• Function importPyListToVectorULong(PyObject *, vector<unsigned long>&, const string&)
  • Function Documentation

• Template Function initialise_logger
  • Function Documentation

• Function initlibnecsim(void)
  • Function Documentation

• Function initlibnecsim(void)
  • Function Documentation

• Function necsim::archimedesSpiralX
  • Function Documentation

• Function necsim::archimedesSpiralY
  • Function Documentation

• Function necsim::calculateDistance
  • Function Documentation

• Function necsim::cantorPairing
  • Function Documentation

• Function necsim::checkSpeciation
  • Function Documentation

• Function necsim::cplNecsimCustomErrorHandler
  • Function Documentation

• Function necsim::createParent
  • Function Documentation

• Function necsim::distanceBetweenCells
  • Function Documentation

• Function necsim::doesExist
  • Function Documentation

• Function necsim::doesExistNull
  • Function Documentation

• Function necsim::doubleCompare(double, double, double)
  • Function Documentation

• Function necsim::doubleCompare(long double, long double, long double)
  • Function Documentation

• Function necsim::doubleCompare(long double, long double, double)
  • Function Documentation

• Function necsim::elegantPairing
  • Function Documentation

• Template Function necsim::findMinCols
  • Function Documentation

• Template Function necsim::findMinRows
  • Function Documentation

• Function necsim::getConfigFileFromCmdArgs
  • Function Documentation

• Function necsim::getCsvLineAndSplitIntoTokens
  • Function Documentation

• Function necsim::getDefaultLogFile
  • Function Documentation

• Function necsim::getGlobalLogger
  • Function Documentation

• Function necsim::getTime
  • Function Documentation

• Function necsim::getUniqueFileName
  • Function Documentation

• Function necsim::importArgs
  • Function Documentation

• Function necsim::importToMapAndRound
  • Function Documentation

• Function necsim::inverseSpeciation
  • Function Documentation

• Function necsim::loggerIsSetup
  • Function Documentation

• Function necsim::main
  • Function Documentation

• Function necsim::openSQLiteDatabase
  • Function Documentation

• Function necsim::operator<<(ostream&, ActivityMap&)
  • Function Documentation

• Function necsim::operator<<(ostream&, const SectionOption&)
  • Function Documentation

• Function necsim::operator<<(ostream&, const ConfigParser&)
  • Function Documentation

• Function necsim::operator<<(ostream&, const DataPoint&)
  • Function Documentation

• Template Function necsim::operator<<(ostream&, const vector<T>&)
  • Function Documentation

• Function necsim::operator<<(ostream&, const GillespieProbability&)
  • Function Documentation

• Function necsim::operator<<(std::ostream&, const MapLocation&)
  • Function Documentation

• Function necsim::operator<<(ostream&, const SpeciesList&)
  • Function Documentation

• Function necsim::operator<<(ostream&, const TreeNode&)
  • Function Documentation

• Function necsim::operator>>(istream&, ActivityMap&)
  • Function Documentation

• Function necsim::operator>>(istream&, SectionOption&)
  • Function Documentation

• Function necsim::operator>>(istream&, ConfigParser&)
  • Function Documentation

• Function necsim::operator>>(istream&, DataPoint&)
  • Function Documentation

• Template Function necsim::operator>>(istream&, vector<T>&)
  • Function Documentation

• Function necsim::operator>>(std::istream&, GillespieProbability&)
  • Function Documentation

• Function necsim::operator>>(std::istream&, MapLocation&)
  • Function Documentation

• Function necsim::operator>>(istream&, SpeciesList&)
  • Function Documentation

• Function necsim::operator>>(istream&, TreeNode&)
  • Function Documentation

• Function necsim::removeComOption
  • Function Documentation

• Function necsim::removeGlobalLogger
  • Function Documentation

• Function necsim::runAsDefault
  • Function Documentation

• Function necsim::runLarge
  • Function Documentation

• Template Function necsim::runMain
  • Function Documentation

• Function necsim::runXL
  • Function Documentation

• Function necsim::writeCritical
  • Function Documentation

• Function necsim::writeError
  • Function Documentation

• Function necsim::writeInfo
  • Function Documentation

• Function necsim::writeWarning
  • Function Documentation

• Function neutral_analytical::calcFundamentalBiodiversityNumber
  • Function Documentation

• Function neutral_analytical::calcSpeciationRate
  • Function Documentation

• Function neutral_analytical::siMetacommunitySpeciesWithAbundance
  • Function Documentation

• Function neutral_analytical::siSpeciesAbundanceCumulativeDistribution
  • Function Documentation

• Function neutral_analytical::siSpeciesRichness
  • Function Documentation

• Function neutral_analytical::siSpeciesRichnessDeprecated
  • Function Documentation

• Template Function output
  • Function Documentation

• Template Function pyAddMetacommunityParameters
  • Function Documentation

• Template Function PyCommunity_dealloc
  • Function Documentation

• Template Function PyCommunity_init
  • Function Documentation

• Function PyLMC_dealloc
  • Function Documentation

• Function PyLMC_init
  • Function Documentation

• Function PySimulateDispersal_dealloc
  • Function Documentation

• Function PySimulateDispersal_init
  • Function Documentation

• Function PySimulateDispersal_new
  • Function Documentation

• Template Function pySpeciateRemainingLineages
  • Function Documentation

• Template Function PyTemplate_clear
  • Function Documentation

• Template Function PyTemplate_dealloc
  • Function Documentation

• Template Function PyTemplate_gen_getsetters
  • Function Documentation

• Template Function PyTemplate_getCallLogger
  • Function Documentation

• Template Function PyTemplate_getLogging
  • Function Documentation

• Template Function PyTemplate_init
  • Function Documentation

• Template Function PyTemplate_new
  • Function Documentation

• Template Function PyTemplate_setCallLogger
  • Function Documentation

• Template Function PyTemplate_setLogging
  • Function Documentation

• Template Function PyTemplate_traverse
  • Function Documentation

• Function random_numbers::intToDouble
  • Function Documentation

• Function random_numbers::rotl
  • Function Documentation

• Function readyPyTypeObject
  • Function Documentation

• Template Function reset
  • Function Documentation

• Template Function run
  • Function Documentation

• Function runADT
  • Function Documentation

• Function runMDT
  • Function Documentation

• Function runMeanDispersal
  • Function Documentation

• Function runSRW
  • Function Documentation

• Function set_all_map_parameters
  • Function Documentation

• Function set_dispersal_parameters
  • Function Documentation

• Function set_historical_map_parameters
  • Function Documentation

• Function set_map
  • Function Documentation

• Function set_maps
  • Function Documentation

• Function set_output_database
  • Function Documentation

• Template Function setup
  • Function Documentation

• Template Function setupApplySpeciation
  • Function Documentation

• Template Function setupResume
  • Function Documentation

• Template Function wipeProtractedParameters
  • Function Documentation

Variables

• Variable _state
  • Variable Documentation

• Variable C_CommunityType
  • Variable Documentation

• Variable C_LMCType
  • Variable Documentation

• Variable C_MetacommunityType
  • Variable Documentation

• Variable C_NSESimulationType
  • Variable Documentation

• Variable C_ProtractedNSESimulationType
  • Variable Documentation

• Variable C_ProtractedSpatialSimulationType
  • Variable Documentation

• Variable C_SimulateDispersalType
  • Variable Documentation

• Variable C_SpatialSimulationType
  • Variable Documentation

• Variable necsim::gdal_data_sizes
  • Variable Documentation

• Variable necsim::log_name
  • Variable Documentation

• Variable necsim::logger
  • Variable Documentation

• Variable necsim::pyLogger
  • Variable Documentation

• Variable necsim::saved_stdout
  • Variable Documentation

• Variable necsimError
  • Variable Documentation

• Variable NecsimMethods
  • Variable Documentation

• Variable PyLMCMethods
  • Variable Documentation

• Variable random_numbers::ktab
  • Variable Documentation

• Variable random_numbers::wtab
  • Variable Documentation

• Variable random_numbers::ytab
  • Variable Documentation

• Variable saved_stdout
  • Variable Documentation

• Variable SimulateDispersalMethods
  • Variable Documentation

Defines

• Define _USE_MATH_DEFINES
  • Define Documentation

• Define _USE_MATH_DEFINES
  • Define Documentation

• Define _USE_MATH_DEFINES
  • Define Documentation

• Define GETSTATE
  • Define Documentation

• Define INITERROR
  • Define Documentation

• Define INITERROR
  • Define Documentation

• Define LOGNAME_FORMAT
  • Define Documentation

• Define null
  • Define Documentation

• Define PARAM_R
  • Define Documentation

• Define PYTHON_COMPILE
  • Define Documentation

• Define PYTHON_COMPILE
  • Define Documentation

• Define PYTHON_COMPILE
  • Define Documentation

• Define PYTHON_COMPILE
  • Define Documentation

• Define SPECIATIONCOUNTER_FILESYSTEM_H
  • Define Documentation

• Define SPECIATIONCOUNTER_PROTRACTEDSPATIALTREE_H
  • Define Documentation