necsim packageΒΆ
The full documentation for the c++ code which performs the actual simulations is provided below. An API is provided in Python which should be sufficient for most users (see here).
- Full API
- Namespaces
- Classes and Structs
- Struct module_state
- Struct CommunitiesArray
- Struct CommunityParameters
- Struct ConfigException
- Struct FatalException
- Struct Fragment
- Struct HistoricalMapParameters
- Struct MapLocation
- Struct MetacommunitiesArray
- Struct MetacommunityParameters
- Struct ProtractedSpeciationParameters
- Struct SectionOption
- Struct SimParameters
- Struct SQLStatement
- Class LandscapeMetricsCalculator
- Class ActivityMap
- Class AnalyticalSpeciesAbundancesHandler
- Class Cell
- Class Community
- Class ConfigParser
- Class DataMask
- Class DataPoint
- Class DispersalCoordinator
- Class GillespieHeapNode
- Class GillespieProbability
- Class Landscape
- Class LogFile
- Class Logger
- Template Class Map
- Template Class Matrix
- Class Metacommunity
- Class ProtractedSpatialTree
- Class ProtractedTree
- Class PyLogger
- Class Samplematrix
- Class SimulateDispersal
- Class SimulatedSpeciesAbundancesHandler
- Class SpatialTree
- Class SpeciationCommands
- Class SpeciesAbundancesHandler
- Class SpeciesList
- Class SpecSimParameters
- Class SQLiteHandler
- Class Step
- Class Tree
- Class TreeNode
- Class ProtractedTree
- Template Class PyCommunityTemplate
- Class PyLMC
- Class PySimulateDispersal
- Template Class PyTemplate
- Class RNGController
- Class SplitMix64
- Class Xoroshiro256plus
- Enums
- Functions
- Template Function addGillespie
- Template Function addProtractedParameters
- Template Function addTime
- Template Function apply
- Template Function applySpeciationRates
- Function calculateCLUMPY
- Function calculateMNN
- Template Function eastl::adjust_heap(RandomAccessIterator, Distance, Distance, Distance, const T&)
- Template Function eastl::adjust_heap(RandomAccessIterator, Distance, Distance, Distance, T&&)
- Template Function eastl::adjust_heap(RandomAccessIterator, Distance, Distance, Distance, const T&, Compare)
- Template Function eastl::adjust_heap(RandomAccessIterator, Distance, Distance, Distance, T&&, Compare)
- Template Function eastl::adjust_heap_impl(RandomAccessIterator, Distance, Distance, Distance, T)
- Template Function eastl::adjust_heap_impl(RandomAccessIterator, Distance, Distance, Distance, T, Compare)
- Template Function eastl::change_heap(RandomAccessIterator, Distance, Distance)
- Template Function eastl::change_heap(RandomAccessIterator, Distance, Distance, Compare)
- Template Function eastl::is_heap(RandomAccessIterator, RandomAccessIterator)
- Template Function eastl::is_heap(RandomAccessIterator, RandomAccessIterator, Compare)
- Template Function eastl::is_heap_until(RandomAccessIterator, RandomAccessIterator)
- Template Function eastl::is_heap_until(RandomAccessIterator, RandomAccessIterator, Compare)
- Template Function eastl::make_heap(RandomAccessIterator, RandomAccessIterator)
- Template Function eastl::make_heap(RandomAccessIterator, RandomAccessIterator, Compare)
- Template Function eastl::pop_heap(RandomAccessIterator, RandomAccessIterator)
- Template Function eastl::pop_heap(RandomAccessIterator, RandomAccessIterator, Compare)
- Template Function eastl::promote_heap(RandomAccessIterator, Distance, Distance, const T&)
- Template Function eastl::promote_heap(RandomAccessIterator, Distance, Distance, T&&)
- Template Function eastl::promote_heap(RandomAccessIterator, Distance, Distance, const T&, Compare)
- Template Function eastl::promote_heap(RandomAccessIterator, Distance, Distance, T&&, Compare)
- Template Function eastl::promote_heap_impl(RandomAccessIterator, Distance, Distance, T)
- Template Function eastl::promote_heap_impl(RandomAccessIterator, Distance, Distance, T, Compare)
- Template Function eastl::push_heap(RandomAccessIterator, RandomAccessIterator)
- Template Function eastl::push_heap(RandomAccessIterator, RandomAccessIterator, Compare)
- Template Function eastl::remove_heap(RandomAccessIterator, Distance, Distance)
- Template Function eastl::remove_heap(RandomAccessIterator, Distance, Distance, Compare)
- Template Function eastl::sort_heap(RandomAccessIterator, RandomAccessIterator)
- Template Function eastl::sort_heap(RandomAccessIterator, RandomAccessIterator, Compare)
- Template Function genCommunityMethods
- Template Function genCommunityType(char *, char *)
- Template Function genCommunityType(string, string)
- Function genLMCType
- Template Function genPySimulationMethods
- Function genSimulateDispersalType
- Template Function genSimulationType
- Template Function importConfig
- Template Function importConfigFromString
- Function importPyListsToVectorCell(PyObject *, PyObject *, vector<Cell>&, const string&)
- Function importPyListsToVectorCell(PyObject *, PyObject *, vector<Cell>&, const string&)
- Function importPyListToVectorDouble(PyObject *, vector<double>&, const string&)
- Function importPyListToVectorDouble(PyObject *, vector<double>&, const string&)
- Function importPyListToVectorString(PyObject *, vector<string>&, const string&)
- Function importPyListToVectorString(PyObject *, vector<string>&, const string&)
- Function importPyListToVectorULong(PyObject *, vector<unsigned long>&, const string&)
- Function importPyListToVectorULong(PyObject *, vector<unsigned long>&, const string&)
- Template Function initialise_logger
- Function initlibnecsim(void)
- Function initlibnecsim(void)
- Function necsim::archimedesSpiralX
- Function necsim::archimedesSpiralY
- Function necsim::calculateDistance
- Function necsim::cantorPairing
- Function necsim::checkSpeciation
- Function necsim::cplNecsimCustomErrorHandler
- Function necsim::createParent
- Function necsim::distanceBetweenCells
- Function necsim::doesExist
- Function necsim::doesExistNull
- Function necsim::doubleCompare(double, double, double)
- Function necsim::doubleCompare(long double, long double, long double)
- Function necsim::doubleCompare(long double, long double, double)
- Function necsim::elegantPairing
- Template Function necsim::findMinCols
- Template Function necsim::findMinRows
- Function necsim::getConfigFileFromCmdArgs
- Function necsim::getCsvLineAndSplitIntoTokens
- Function necsim::getDefaultLogFile
- Function necsim::getGlobalLogger
- Function necsim::getTime
- Function necsim::getUniqueFileName
- Function necsim::importArgs
- Function necsim::importToMapAndRound
- Function necsim::inverseSpeciation
- Function necsim::loggerIsSetup
- Function necsim::main
- Function necsim::openSQLiteDatabase
- Function necsim::operator<<(ostream&, ActivityMap&)
- Function necsim::operator<<(ostream&, const SectionOption&)
- Function necsim::operator<<(ostream&, const ConfigParser&)
- Function necsim::operator<<(ostream&, const DataPoint&)
- Template Function necsim::operator<<(ostream&, const vector<T>&)
- Function necsim::operator<<(ostream&, const GillespieProbability&)
- Function necsim::operator<<(std::ostream&, const MapLocation&)
- Function necsim::operator<<(ostream&, const SpeciesList&)
- Function necsim::operator<<(ostream&, const TreeNode&)
- Function necsim::operator>>(istream&, ActivityMap&)
- Function necsim::operator>>(istream&, SectionOption&)
- Function necsim::operator>>(istream&, ConfigParser&)
- Function necsim::operator>>(istream&, DataPoint&)
- Template Function necsim::operator>>(istream&, vector<T>&)
- Function necsim::operator>>(std::istream&, GillespieProbability&)
- Function necsim::operator>>(std::istream&, MapLocation&)
- Function necsim::operator>>(istream&, SpeciesList&)
- Function necsim::operator>>(istream&, TreeNode&)
- Function necsim::removeComOption
- Function necsim::removeGlobalLogger
- Function necsim::runAsDefault
- Function necsim::runLarge
- Template Function necsim::runMain
- Function necsim::runXL
- Function necsim::writeCritical
- Function necsim::writeError
- Function necsim::writeInfo
- Function necsim::writeWarning
- Function neutral_analytical::calcFundamentalBiodiversityNumber
- Function neutral_analytical::calcSpeciationRate
- Function neutral_analytical::siMetacommunitySpeciesWithAbundance
- Function neutral_analytical::siSpeciesAbundanceCumulativeDistribution
- Function neutral_analytical::siSpeciesRichness
- Function neutral_analytical::siSpeciesRichnessDeprecated
- Template Function output
- Template Function pyAddMetacommunityParameters
- Template Function PyCommunity_dealloc
- Template Function PyCommunity_init
- Function PyLMC_dealloc
- Function PyLMC_init
- Function PySimulateDispersal_dealloc
- Function PySimulateDispersal_init
- Function PySimulateDispersal_new
- Template Function pySpeciateRemainingLineages
- Template Function PyTemplate_clear
- Template Function PyTemplate_dealloc
- Template Function PyTemplate_gen_getsetters
- Template Function PyTemplate_getCallLogger
- Template Function PyTemplate_getLogging
- Template Function PyTemplate_init
- Template Function PyTemplate_new
- Template Function PyTemplate_setCallLogger
- Template Function PyTemplate_setLogging
- Template Function PyTemplate_traverse
- Function random_numbers::intToDouble
- Function random_numbers::rotl
- Function readyPyTypeObject
- Template Function reset
- Template Function run
- Function runADT
- Function runMDT
- Function runMeanDispersal
- Function runSRW
- Function set_all_map_parameters
- Function set_dispersal_parameters
- Function set_historical_map_parameters
- Function set_map
- Function set_maps
- Function set_output_database
- Template Function setup
- Template Function setupApplySpeciation
- Template Function setupResume
- Template Function wipeProtractedParameters
- Variables
- Variable _state
- Variable C_CommunityType
- Variable C_LMCType
- Variable C_MetacommunityType
- Variable C_NSESimulationType
- Variable C_ProtractedNSESimulationType
- Variable C_ProtractedSpatialSimulationType
- Variable C_SimulateDispersalType
- Variable C_SpatialSimulationType
- Variable necsim::gdal_data_sizes
- Variable necsim::log_name
- Variable necsim::logger
- Variable necsim::pyLogger
- Variable necsim::saved_stdout
- Variable necsimError
- Variable NecsimMethods
- Variable PyLMCMethods
- Variable random_numbers::ktab
- Variable random_numbers::wtab
- Variable random_numbers::ytab
- Variable saved_stdout
- Variable SimulateDispersalMethods
- Defines
- Define _USE_MATH_DEFINES
- Define _USE_MATH_DEFINES
- Define _USE_MATH_DEFINES
- Define GETSTATE
- Define INITERROR
- Define INITERROR
- Define LOGNAME_FORMAT
- Define null
- Define PARAM_R
- Define PYTHON_COMPILE
- Define PYTHON_COMPILE
- Define PYTHON_COMPILE
- Define PYTHON_COMPILE
- Define SPECIATIONCOUNTER_FILESYSTEM_H
- Define SPECIATIONCOUNTER_PROTRACTEDSPATIALTREE_H