pycoalescence
stable
pycoalescence
necsim
Simulating and generating landscapes
Merging simulation outputs
Example simulations and analysis using pycoalescence
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pycoalescence package
necsim package
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Namespaces
Classes and Structs
Enums
Functions
Variables
Defines
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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
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