- necsim::ActivityMap (C++ class)
- necsim::ActivityMap::actionOccurs (C++ function)
- necsim::ActivityMap::activity_map (C++ member)
- necsim::ActivityMap::activity_map_checker_fptr (C++ member)
- necsim::ActivityMap::ActivityMap (C++ function)
- necsim::ActivityMap::get (C++ function)
- necsim::ActivityMap::getMean (C++ function)
- necsim::ActivityMap::getVal (C++ function)
- necsim::ActivityMap::import (C++ function)
- necsim::ActivityMap::isNull (C++ function)
- necsim::ActivityMap::map_file (C++ member)
- necsim::ActivityMap::max_val (C++ member)
- necsim::ActivityMap::null_map (C++ member)
- necsim::ActivityMap::offset_x (C++ member)
- necsim::ActivityMap::offset_y (C++ member)
- necsim::ActivityMap::operator= (C++ function)
- necsim::ActivityMap::random (C++ member)
- necsim::ActivityMap::rejectionSample (C++ function)
- necsim::ActivityMap::rejectionSampleNull (C++ function)
- necsim::ActivityMap::rep_ptr (C++ type)
- necsim::ActivityMap::setActivityFunction (C++ function)
- necsim::ActivityMap::setOffsets (C++ function)
- necsim::ActivityMap::standardiseValues (C++ function)
- necsim::ActivityMap::x_dim (C++ member)
- necsim::ActivityMap::y_dim (C++ member)
- necsim::AnalyticalSpeciesAbundancesHandler (C++ class)
- necsim::AnalyticalSpeciesAbundancesHandler::addNewSpecies (C++ function)
- necsim::AnalyticalSpeciesAbundancesHandler::AnalyticalSpeciesAbundancesHandler (C++ function)
- necsim::AnalyticalSpeciesAbundancesHandler::generateSpeciesAbundances (C++ function)
- necsim::AnalyticalSpeciesAbundancesHandler::getRandomAbundanceOfSpecies (C++ function)
- necsim::AnalyticalSpeciesAbundancesHandler::getRandomSpeciesID (C++ function)
- necsim::AnalyticalSpeciesAbundancesHandler::ind_to_species (C++ member)
- necsim::AnalyticalSpeciesAbundancesHandler::pickPreviousIndividual (C++ function)
- necsim::AnalyticalSpeciesAbundancesHandler::seen_no_individuals (C++ member)
- necsim::AnalyticalSpeciesAbundancesHandler::setup (C++ function)
- necsim::AnalyticalSpeciesAbundancesHandler::~AnalyticalSpeciesAbundancesHandler (C++ function)
- necsim::archimedesSpiralX (C++ function)
- necsim::archimedesSpiralY (C++ function)
- necsim::calculateDistance (C++ function)
- necsim::cantorPairing (C++ function)
- necsim::Cell (C++ class)
- necsim::Cell::Cell (C++ function), [1]
- necsim::Cell::operator!= (C++ function)
- necsim::Cell::operator= (C++ function)
- necsim::Cell::operator== (C++ function)
- necsim::Cell::x (C++ member)
- necsim::Cell::y (C++ member)
- necsim::cell_event (C++ enumerator)
- necsim::CellEventType (C++ enum)
- necsim::checkSpeciation (C++ function)
- necsim::coalescence_event (C++ enumerator)
- necsim::CommunitiesArray (C++ class)
- necsim::CommunitiesArray::addNew (C++ function)
- necsim::CommunitiesArray::comm_parameters (C++ member)
- necsim::CommunitiesArray::CommunitiesArray (C++ function)
- necsim::CommunitiesArray::hasPair (C++ function)
- necsim::CommunitiesArray::pushBack (C++ function), [1]
- necsim::CommunitiesArray::~CommunitiesArray (C++ function)
- necsim::Community (C++ class)
- necsim::Community::addCalculationPerformed (C++ function), [1]
- necsim::Community::addSpecies (C++ function)
- necsim::Community::applied_protracted_parameters (C++ member), [1]
- necsim::Community::apply (C++ function), [1]
- necsim::Community::applyFragments (C++ function), [1]
- necsim::Community::applyNoOutput (C++ function), [1], [2]
- necsim::Community::bSqlConnection (C++ member), [1]
- necsim::Community::calcFragments (C++ function), [1]
- necsim::Community::calcSpeciesAbundance (C++ function), [1]
- necsim::Community::calculateCoalescenceTree (C++ function), [1]
- necsim::Community::calculateTree (C++ function), [1]
- necsim::Community::checkCalculationsPerformed (C++ function), [1]
- necsim::Community::checkSpeciesAbundancesReference (C++ function), [1]
- necsim::Community::checkSpeciesLocationsReference (C++ function), [1]
- necsim::Community::closeSqlConnection (C++ function), [1]
- necsim::Community::Community (C++ function), [1]
- necsim::Community::countSpecies (C++ function), [1]
- necsim::Community::createDatabase (C++ function), [1]
- necsim::Community::createFragmentDatabase (C++ function), [1]
- necsim::Community::createSpeciesList (C++ function), [1]
- necsim::Community::current_community_parameters (C++ member), [1]
- necsim::Community::current_metacommunity_parameters (C++ member), [1]
- necsim::Community::database (C++ member), [1]
- necsim::Community::database_set (C++ member), [1]
- necsim::Community::deleteSpeciesList (C++ function), [1]
- necsim::Community::doApplication (C++ function), [1], [2], [3]
- necsim::Community::doApplicationInternal (C++ function), [1]
- necsim::Community::exportDatabase (C++ function), [1]
- necsim::Community::forceSimCompleteParameter (C++ function), [1]
- necsim::Community::fragments (C++ member), [1]
- necsim::Community::generateBiodiversity (C++ function), [1]
- necsim::Community::getCumulativeAbundances (C++ function), [1]
- necsim::Community::getMaxFragmentAbundancesID (C++ function), [1]
- necsim::Community::getMaxSpeciesAbundancesID (C++ function), [1]
- necsim::Community::getMaxSpeciesLocationsID (C++ function), [1]
- necsim::Community::getMinimumSpeciation (C++ function), [1]
- necsim::Community::getPreviousCalcs (C++ function), [1]
- necsim::Community::getRowOut (C++ function), [1]
- necsim::Community::getSpeciesAbundances (C++ function), [1], [2], [3]
- necsim::Community::getSpeciesNumber (C++ function), [1]
- necsim::Community::getSpeciesRichness (C++ function), [1]
- necsim::Community::getUniqueCommunityRefs (C++ function), [1]
- necsim::Community::getUniqueMetacommunityRefs (C++ function), [1]
- necsim::Community::grid_x_size (C++ member), [1]
- necsim::Community::grid_y_size (C++ member), [1]
- necsim::Community::has_imported_data (C++ member), [1]
- necsim::Community::has_imported_samplemask (C++ member), [1]
- necsim::Community::hasImportedData (C++ function), [1]
- necsim::Community::importData (C++ function), [1]
- necsim::Community::importSamplemask (C++ function), [1]
- necsim::Community::importSimParameters (C++ function), [1]
- necsim::Community::in_mem (C++ member), [1]
- necsim::Community::internalOption (C++ function), [1]
- necsim::Community::isDatabaseNullPtr (C++ function), [1]
- necsim::Community::iSpecies (C++ member), [1]
- necsim::Community::isSetDatabase (C++ function), [1]
- necsim::Community::max_fragment_id (C++ member), [1]
- necsim::Community::max_locations_id (C++ member), [1]
- necsim::Community::max_species_id (C++ member), [1]
- necsim::Community::min_spec_rate (C++ member), [1]
- necsim::Community::minimum_protracted_parameters (C++ member), [1]
- necsim::Community::nodes (C++ member), [1]
- necsim::Community::openSqlConnection (C++ function), [1]
- necsim::Community::output (C++ function), [1]
- necsim::Community::outputSpeciesAbundances (C++ function), [1]
- necsim::Community::overrideProtractedParameters (C++ function), [1]
- necsim::Community::past_communities (C++ member), [1]
- necsim::Community::past_metacommunities (C++ member), [1]
- necsim::Community::printEndTimes (C++ function), [1]
- necsim::Community::protracted (C++ member), [1]
- necsim::Community::recordSpatial (C++ function), [1]
- necsim::Community::resetTree (C++ function), [1]
- necsim::Community::samplemask (C++ member), [1]
- necsim::Community::samplemask_x_offset (C++ member), [1]
- necsim::Community::samplemask_x_size (C++ member), [1]
- necsim::Community::samplemask_y_offset (C++ member), [1]
- necsim::Community::samplemask_y_size (C++ member), [1]
- necsim::Community::setDatabase (C++ function), [1]
- necsim::Community::setInternalDatabase (C++ function), [1]
- necsim::Community::setList (C++ function), [1]
- necsim::Community::setProtracted (C++ function), [1]
- necsim::Community::setProtractedParameters (C++ function), [1]
- necsim::Community::setSimParameters (C++ function), [1]
- necsim::Community::setSpecSimParameters (C++ function), [1]
- necsim::Community::setupApplication (C++ function), [1]
- necsim::Community::setupInternal (C++ function), [1]
- necsim::Community::spec_sim_parameters (C++ member), [1]
- necsim::Community::speciateRemainingLineages (C++ function), [1]
- necsim::Community::species_abundances (C++ member), [1]
- necsim::Community::updateCommunityParameters (C++ function), [1]
- necsim::Community::writeNewCommunityParameters (C++ function), [1]
- necsim::Community::writeNewMetacommunityParameters (C++ function), [1]
- necsim::Community::writeSpeciationRates (C++ function), [1]
- necsim::Community::writeSpeciesList (C++ function), [1]
- necsim::Community::~Community (C++ function)
- necsim::CommunityParameters (C++ class)
- necsim::CommunityParameters::CommunityParameters (C++ function), [1]
- necsim::CommunityParameters::compare (C++ function), [1], [2]
- necsim::CommunityParameters::fragment (C++ member)
- necsim::CommunityParameters::metacommunity_reference (C++ member)
- necsim::CommunityParameters::protracted_parameters (C++ member)
- necsim::CommunityParameters::reference (C++ member)
- necsim::CommunityParameters::setup (C++ function)
- necsim::CommunityParameters::speciation_rate (C++ member)
- necsim::CommunityParameters::time (C++ member)
- necsim::CommunityParameters::updated (C++ member)
- necsim::CommunityParameters::~CommunityParameters (C++ function)
- necsim::ConfigException (C++ class)
- necsim::ConfigException::ConfigException (C++ function), [1]
- necsim::ConfigParser (C++ class)
- necsim::ConfigParser::ConfigParser (C++ function)
- necsim::ConfigParser::getSectionOptions (C++ function), [1], [2]
- necsim::ConfigParser::getSectionOptionsSize (C++ function)
- necsim::ConfigParser::getSections (C++ function)
- necsim::ConfigParser::getSectionValues (C++ function)
- necsim::ConfigParser::hasSection (C++ function)
- necsim::ConfigParser::importConfig (C++ function)
- necsim::ConfigParser::operator[] (C++ function)
- necsim::ConfigParser::parseConfig (C++ function), [1]
- necsim::ConfigParser::setConfig (C++ function)
- necsim::ConfigParser::setSectionOption (C++ function)
- necsim::cplNecsimCustomErrorHandler (C++ function)
- necsim::createParent (C++ function)
- necsim::DataMask (C++ class)
- necsim::DataMask::checkCanUseDefault (C++ function), [1]
- necsim::DataMask::clearSpatialMask (C++ function), [1]
- necsim::DataMask::completeBoolImport (C++ function), [1]
- necsim::DataMask::convertBoolean (C++ function), [1]
- necsim::DataMask::DataMask (C++ function)
- necsim::DataMask::doImport (C++ function), [1]
- necsim::DataMask::fptr (C++ type), [1]
- necsim::DataMask::getBoolProportion (C++ function), [1]
- necsim::DataMask::getExactValue (C++ function), [1]
- necsim::DataMask::getNullProportion (C++ function), [1]
- necsim::DataMask::getProportionfptr (C++ member), [1]
- necsim::DataMask::getSampleProportion (C++ function), [1]
- necsim::DataMask::getVal (C++ function), [1]
- necsim::DataMask::importBooleanMask (C++ function), [1]
- necsim::DataMask::importSampleMask (C++ function), [1]
- necsim::DataMask::inputfile (C++ member), [1]
- necsim::DataMask::isGridOffset (C++ member), [1]
- necsim::DataMask::isNull (C++ function), [1]
- necsim::DataMask::isNullSample (C++ member), [1]
- necsim::DataMask::mask_x_dim (C++ member), [1]
- necsim::DataMask::mask_y_dim (C++ member), [1]
- necsim::DataMask::recalculateCoordinates (C++ function), [1]
- necsim::DataMask::sample_mask (C++ member), [1]
- necsim::DataMask::sample_mask_exact (C++ member), [1]
- necsim::DataMask::setup (C++ function), [1]
- necsim::DataMask::setupNull (C++ function), [1]
- necsim::DataMask::x_dim (C++ member), [1]
- necsim::DataMask::x_offset (C++ member), [1]
- necsim::DataMask::y_dim (C++ member), [1]
- necsim::DataMask::y_offset (C++ member), [1]
- necsim::DataMask::~DataMask (C++ function)
- necsim::DataPoint (C++ class)
- necsim::DataPoint::DataPoint (C++ function)
- necsim::DataPoint::decreaseNwrap (C++ function)
- necsim::DataPoint::getListpos (C++ function)
- necsim::DataPoint::getMinmax (C++ function)
- necsim::DataPoint::getNext (C++ function)
- necsim::DataPoint::getNwrap (C++ function)
- necsim::DataPoint::getReference (C++ function)
- necsim::DataPoint::getXpos (C++ function)
- necsim::DataPoint::getXwrap (C++ function)
- necsim::DataPoint::getYpos (C++ function)
- necsim::DataPoint::getYwrap (C++ function)
- necsim::DataPoint::setEndpoint (C++ function)
- necsim::DataPoint::setListPosition (C++ function)
- necsim::DataPoint::setMinmax (C++ function)
- necsim::DataPoint::setNext (C++ function)
- necsim::DataPoint::setNwrap (C++ function)
- necsim::DataPoint::setReference (C++ function)
- necsim::DataPoint::setup (C++ function), [1], [2]
- necsim::DataPoint::~DataPoint (C++ function)
- necsim::dispersal_event (C++ enumerator)
- necsim::DispersalCoordinator (C++ class)
- necsim::DispersalCoordinator::addDensity (C++ function)
- necsim::DispersalCoordinator::addReproduction (C++ function)
- necsim::DispersalCoordinator::calculateCellCoordinates (C++ function)
- necsim::DispersalCoordinator::calculateCellIndex (C++ function)
- necsim::DispersalCoordinator::calculateCellReference (C++ function)
- necsim::DispersalCoordinator::checkDispersalRow (C++ function)
- necsim::DispersalCoordinator::checkEndPoint (C++ function)
- necsim::DispersalCoordinator::checkEndPointDensity (C++ function)
- necsim::DispersalCoordinator::checkEndPointDensityReproduction (C++ function)
- necsim::DispersalCoordinator::checkEndPointDensityRestrictedReproduction (C++ function)
- necsim::DispersalCoordinator::checkEndPointFptr (C++ member)
- necsim::DispersalCoordinator::checkEndPointRestricted (C++ function)
- necsim::DispersalCoordinator::dispersal_fptr (C++ type)
- necsim::DispersalCoordinator::dispersal_prob_map (C++ member)
- necsim::DispersalCoordinator::DispersalCoordinator (C++ function)
- necsim::DispersalCoordinator::disperse (C++ function)
- necsim::DispersalCoordinator::disperseDensityMap (C++ function)
- necsim::DispersalCoordinator::disperseDispersalMap (C++ function)
- necsim::DispersalCoordinator::disperseNearestHabitat (C++ function)
- necsim::DispersalCoordinator::disperseNullDispersalMap (C++ function)
- necsim::DispersalCoordinator::doDispersal (C++ member)
- necsim::DispersalCoordinator::end_fptr (C++ type)
- necsim::DispersalCoordinator::fixDispersal (C++ function)
- necsim::DispersalCoordinator::fixDispersalRow (C++ function)
- necsim::DispersalCoordinator::full_dispersal_map (C++ member)
- necsim::DispersalCoordinator::generation (C++ member)
- necsim::DispersalCoordinator::getSelfDispersalValue (C++ function)
- necsim::DispersalCoordinator::importDispersal (C++ function)
- necsim::DispersalCoordinator::isFullDispersalMap (C++ function)
- necsim::DispersalCoordinator::landscape (C++ member)
- necsim::DispersalCoordinator::NR (C++ member)
- necsim::DispersalCoordinator::raw_dispersal_prob_map (C++ member)
- necsim::DispersalCoordinator::reimportRawDispersalMap (C++ function)
- necsim::DispersalCoordinator::removeSelfDispersal (C++ function)
- necsim::DispersalCoordinator::reproduction_map (C++ member)
- necsim::DispersalCoordinator::setDispersal (C++ function), [1]
- necsim::DispersalCoordinator::setEndPointFptr (C++ function)
- necsim::DispersalCoordinator::setGenerationPtr (C++ function)
- necsim::DispersalCoordinator::setMaps (C++ function), [1]
- necsim::DispersalCoordinator::setRandomNumber (C++ function)
- necsim::DispersalCoordinator::setRawDispersalMap (C++ function)
- necsim::DispersalCoordinator::sumDispersalValues (C++ function)
- necsim::DispersalCoordinator::updateDispersalMap (C++ function)
- necsim::DispersalCoordinator::verifyDispersalMapDensity (C++ function)
- necsim::DispersalCoordinator::verifyDispersalMapSetup (C++ function)
- necsim::DispersalCoordinator::xdim (C++ member)
- necsim::DispersalCoordinator::ydim (C++ member)
- necsim::DispersalCoordinator::~DispersalCoordinator (C++ function)
- necsim::distanceBetweenCells (C++ function)
- necsim::doesExist (C++ function)
- necsim::doesExistNull (C++ function)
- necsim::doubleCompare (C++ function), [1], [2]
- necsim::elegantPairing (C++ function)
- necsim::EventType (C++ enum)
- necsim::FatalException (C++ class)
- necsim::FatalException::FatalException (C++ function), [1]
- necsim::findMinCols (C++ function)
- necsim::findMinRows (C++ function)
- necsim::Fragment (C++ class)
- necsim::Fragment::area (C++ member)
- necsim::Fragment::name (C++ member)
- necsim::Fragment::num (C++ member)
- necsim::Fragment::x_east (C++ member)
- necsim::Fragment::x_west (C++ member)
- necsim::Fragment::y_north (C++ member)
- necsim::Fragment::y_south (C++ member)
- necsim::gdal_data_sizes (C++ member)
- necsim::getConfigFileFromCmdArgs (C++ function)
- necsim::getCsvLineAndSplitIntoTokens (C++ function)
- necsim::getDefaultLogFile (C++ function)
- necsim::getGlobalLogger (C++ function)
- necsim::getTime (C++ function)
- necsim::getUniqueFileName (C++ function)
- necsim::GillespieHeapNode (C++ class)
- necsim::GillespieHeapNode::cell (C++ member)
- necsim::GillespieHeapNode::event_type (C++ member)
- necsim::GillespieHeapNode::GillespieHeapNode (C++ function), [1], [2], [3], [4]
- necsim::GillespieHeapNode::heap (C++ member)
- necsim::GillespieHeapNode::locator (C++ member)
- necsim::GillespieHeapNode::operator< (C++ function)
- necsim::GillespieHeapNode::operator= (C++ function), [1]
- necsim::GillespieHeapNode::time_of_event (C++ member)
- necsim::GillespieProbability (C++ class)
- necsim::GillespieProbability::calcTimeToNextEvent (C++ function)
- necsim::GillespieProbability::coalescence_probability (C++ member)
- necsim::GillespieProbability::dispersal_outside_cell_probability (C++ member)
- necsim::GillespieProbability::generateRandomEvent (C++ function)
- necsim::GillespieProbability::getInCellProbability (C++ function)
- necsim::GillespieProbability::getLambda (C++ function)
- necsim::GillespieProbability::getMapLocation (C++ function), [1]
- necsim::GillespieProbability::GillespieProbability (C++ function), [1]
- necsim::GillespieProbability::location (C++ member)
- necsim::GillespieProbability::random_number (C++ member)
- necsim::GillespieProbability::reset (C++ function)
- necsim::GillespieProbability::setCoalescenceProbability (C++ function)
- necsim::GillespieProbability::setDispersalOutsideCellProbability (C++ function)
- necsim::GillespieProbability::setRandomNumber (C++ function)
- necsim::GillespieProbability::setSpeciationProbability (C++ function)
- necsim::GillespieProbability::speciation_probability (C++ member)
- necsim::HistoricalMapParameters (C++ class)
- necsim::HistoricalMapParameters::coarse_map_file (C++ member)
- necsim::HistoricalMapParameters::fine_map_file (C++ member)
- necsim::HistoricalMapParameters::generation (C++ member)
- necsim::HistoricalMapParameters::habitat_change_rate (C++ member)
- necsim::HistoricalMapParameters::HistoricalMapParameters (C++ function), [1]
- necsim::HistoricalMapParameters::operator< (C++ function)
- necsim::HistoricalMapParameters::operator> (C++ function)
- necsim::importArgs (C++ function)
- necsim::importToMapAndRound (C++ function)
- necsim::inverseSpeciation (C++ function)
- necsim::Landscape (C++ class)
- necsim::Landscape::calcCoarseMap (C++ function)
- necsim::Landscape::calcFineMap (C++ function)
- necsim::Landscape::calcHistoricalCoarseMap (C++ function)
- necsim::Landscape::calcHistoricalFineMap (C++ function)
- necsim::Landscape::calcOffset (C++ function)
- necsim::Landscape::calculateOffsetsFromMaps (C++ function)
- necsim::Landscape::calculateOffsetsFromParameters (C++ function)
- necsim::Landscape::check_set_dim (C++ member)
- necsim::Landscape::checkAllDimensionsZero (C++ function)
- necsim::Landscape::checkHistorical (C++ function)
- necsim::Landscape::checkMap (C++ function)
- necsim::Landscape::checkMapExists (C++ function)
- necsim::Landscape::clearMap (C++ function)
- necsim::Landscape::coarse_map (C++ member)
- necsim::Landscape::coarse_max (C++ member)
- necsim::Landscape::coarse_x_max (C++ member)
- necsim::Landscape::coarse_x_min (C++ member)
- necsim::Landscape::coarse_x_offset (C++ member)
- necsim::Landscape::coarse_y_max (C++ member)
- necsim::Landscape::coarse_y_min (C++ member)
- necsim::Landscape::coarse_y_offset (C++ member)
- necsim::Landscape::convertFineToSample (C++ function)
- necsim::Landscape::convertSampleXToFineX (C++ function)
- necsim::Landscape::convertSampleYToFineY (C++ function)
- necsim::Landscape::current_map_time (C++ member)
- necsim::Landscape::deme (C++ member)
- necsim::Landscape::dispersal_relative_cost (C++ member)
- necsim::Landscape::distanceToNearestHabitat (C++ function)
- necsim::Landscape::doUpdate (C++ function)
- necsim::Landscape::findAnyHabitatCell (C++ function)
- necsim::Landscape::findNearestHabitatCell (C++ function)
- necsim::Landscape::fine_map (C++ member)
- necsim::Landscape::fine_max (C++ member)
- necsim::Landscape::fine_x_max (C++ member)
- necsim::Landscape::fine_x_min (C++ member)
- necsim::Landscape::fine_x_offset (C++ member)
- necsim::Landscape::fine_y_max (C++ member)
- necsim::Landscape::fine_y_min (C++ member)
- necsim::Landscape::fine_y_offset (C++ member)
- necsim::Landscape::fixGridCoordinates (C++ function)
- necsim::Landscape::fptr (C++ type)
- necsim::Landscape::gen_since_historical (C++ member)
- necsim::Landscape::getCoarseMap (C++ function), [1]
- necsim::Landscape::getFineMap (C++ function), [1]
- necsim::Landscape::getHabitatMax (C++ function)
- necsim::Landscape::getHistorical (C++ function)
- necsim::Landscape::getInitialCount (C++ function)
- necsim::Landscape::getLandscapeType (C++ function)
- necsim::Landscape::getSimParameters (C++ function)
- necsim::Landscape::getVal (C++ function)
- necsim::Landscape::getValCoarse (C++ function)
- necsim::Landscape::getValCoarseClamped (C++ function)
- necsim::Landscape::getValCoarseTiled (C++ function)
- necsim::Landscape::getValFine (C++ function)
- necsim::Landscape::getValFineClamped (C++ function)
- necsim::Landscape::getValFineTiled (C++ function)
- necsim::Landscape::getValFinite (C++ function)
- necsim::Landscape::getValFunc (C++ member)
- necsim::Landscape::getValInfinite (C++ function)
- necsim::Landscape::habitat_change_rate (C++ member)
- necsim::Landscape::habitat_max (C++ member)
- necsim::Landscape::has_coarse (C++ member)
- necsim::Landscape::has_historical (C++ member)
- necsim::Landscape::hasHistorical (C++ function)
- necsim::Landscape::historical_coarse_map (C++ member)
- necsim::Landscape::historical_coarse_max (C++ member)
- necsim::Landscape::historical_fine_map (C++ member)
- necsim::Landscape::historical_fine_max (C++ member)
- necsim::Landscape::infinite_boundaries (C++ member)
- necsim::Landscape::is_historical (C++ member)
- necsim::Landscape::isHistorical (C++ function)
- necsim::Landscape::isOnCoarse (C++ function)
- necsim::Landscape::isOnFine (C++ function)
- necsim::Landscape::isOnMap (C++ function)
- necsim::Landscape::Landscape (C++ function)
- necsim::Landscape::landscape_type (C++ member)
- necsim::Landscape::mapvars (C++ member)
- necsim::Landscape::NextMap (C++ member)
- necsim::Landscape::printVars (C++ function)
- necsim::Landscape::recalculateHabitatMax (C++ function)
- necsim::Landscape::requiresUpdate (C++ function)
- necsim::Landscape::resetHistorical (C++ function)
- necsim::Landscape::runDispersal (C++ function)
- necsim::Landscape::scale (C++ member)
- necsim::Landscape::setDims (C++ function)
- necsim::Landscape::setHistorical (C++ function)
- necsim::Landscape::setLandscape (C++ function)
- necsim::Landscape::setTimeVars (C++ function)
- necsim::Landscape::update_time (C++ member)
- necsim::Landscape::updateMap (C++ function)
- necsim::Landscape::validateMaps (C++ function)
- necsim::Landscape::x_dim (C++ member)
- necsim::Landscape::y_dim (C++ member)
- necsim::log_name (C++ member)
- necsim::LogFile (C++ class)
- necsim::LogFile::file_name (C++ member)
- necsim::LogFile::init (C++ function)
- necsim::LogFile::levels_map (C++ member)
- necsim::LogFile::LogFile (C++ function), [1], [2]
- necsim::LogFile::operator= (C++ function)
- necsim::LogFile::output_stream (C++ member)
- necsim::LogFile::write (C++ function), [1]
- necsim::LogFile::~LogFile (C++ function)
- necsim::Logger (C++ class)
- necsim::logger (C++ member)
- necsim::Logger::Logger (C++ function)
- necsim::Logger::writeCritical (C++ function), [1]
- necsim::Logger::writeError (C++ function), [1]
- necsim::Logger::writeInfo (C++ function), [1]
- necsim::Logger::writeWarning (C++ function), [1]
- necsim::Logger::~Logger (C++ function)
- necsim::loggerIsSetup (C++ function)
- necsim::main (C++ function)
- necsim::Map (C++ class)
- necsim::Map::block_x_size (C++ member), [1]
- necsim::Map::block_y_size (C++ member), [1]
- necsim::Map::calculateOffset (C++ function), [1]
- necsim::Map::checkTifImportFailure (C++ function), [1]
- necsim::Map::close (C++ function), [1]
- necsim::Map::closeOffsetMap (C++ function), [1]
- necsim::Map::cpl_error (C++ member), [1]
- necsim::Map::cpl_error_set (C++ member), [1]
- necsim::Map::defaultImport (C++ function), [1]
- necsim::Map::file_name (C++ member), [1]
- necsim::Map::gdal_data_type (C++ member), [1]
- necsim::Map::getBlockSizes (C++ function), [1]
- necsim::Map::getFileName (C++ function), [1]
- necsim::Map::getMetaData (C++ function), [1]
- necsim::Map::getRasterBand (C++ function), [1]
- necsim::Map::getUpperLeftX (C++ function), [1]
- necsim::Map::getUpperLeftY (C++ function), [1]
- necsim::Map::import (C++ function), [1]
- necsim::Map::importFromDoubleAndMakeBool (C++ function), [1]
- necsim::Map::importTif (C++ function), [1]
- necsim::Map::importUsingBuffer (C++ function), [1]
- necsim::Map::internalImport (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19]
- necsim::Map::isOpen (C++ function), [1]
- necsim::Map::Map (C++ function)
- necsim::Map::no_data_value (C++ member), [1]
- necsim::Map::open (C++ function), [1], [2], [3]
- necsim::Map::openOffsetMap (C++ function), [1]
- necsim::Map::operator= (C++ function)
- necsim::Map::po_band (C++ member), [1]
- necsim::Map::po_dataset (C++ member), [1]
- necsim::Map::printNumberComplete (C++ function), [1]
- necsim::Map::removeCPLErrorHandler (C++ function), [1]
- necsim::Map::roundedScale (C++ function), [1]
- necsim::Map::setCPLErrorHandler (C++ function), [1]
- necsim::Map::upper_left_x (C++ member), [1]
- necsim::Map::upper_left_y (C++ member), [1]
- necsim::Map::x_res (C++ member), [1]
- necsim::Map::y_res (C++ member), [1]
- necsim::Map::~Map (C++ function)
- necsim::map_event (C++ enumerator)
- necsim::MapLocation (C++ class)
- necsim::MapLocation::isOnGrid (C++ function), [1], [2]
- necsim::MapLocation::MapLocation (C++ function), [1]
- necsim::MapLocation::operator!= (C++ function), [1], [2]
- necsim::MapLocation::operator== (C++ function), [1], [2]
- necsim::MapLocation::x (C++ member), [1], [2]
- necsim::MapLocation::xwrap (C++ member), [1], [2]
- necsim::MapLocation::y (C++ member), [1], [2]
- necsim::MapLocation::ywrap (C++ member), [1], [2]
- necsim::Matrix (C++ class)
- necsim::Matrix::begin (C++ function), [1], [2], [3], [4], [5]
- necsim::Matrix::end (C++ function), [1], [2], [3], [4], [5]
- necsim::Matrix::fill (C++ function), [1], [2]
- necsim::Matrix::get (C++ function), [1], [2], [3], [4], [5]
- necsim::Matrix::getCols (C++ function), [1], [2]
- necsim::Matrix::getCopy (C++ function), [1], [2]
- necsim::Matrix::getMean (C++ function), [1], [2]
- necsim::Matrix::getRows (C++ function), [1], [2]
- necsim::Matrix::import (C++ function)
- necsim::Matrix::importCsv (C++ function), [1], [2]
- necsim::Matrix::index (C++ function), [1], [2]
- necsim::Matrix::Matrix (C++ function), [1]
- necsim::Matrix::matrix (C++ member), [1], [2]
- necsim::Matrix::num_cols (C++ member), [1], [2]
- necsim::Matrix::num_rows (C++ member), [1], [2]
- necsim::Matrix::operator* (C++ function), [1], [2], [3], [4], [5]
- necsim::Matrix::operator*= (C++ function), [1], [2], [3], [4], [5]
- necsim::Matrix::operator+ (C++ function), [1], [2]
- necsim::Matrix::operator+= (C++ function), [1], [2]
- necsim::Matrix::operator- (C++ function), [1], [2]
- necsim::Matrix::operator-= (C++ function), [1], [2]
- necsim::Matrix::operator/ (C++ function), [1], [2]
- necsim::Matrix::operator/= (C++ function), [1], [2], [3], [4], [5]
- necsim::Matrix::operator= (C++ function)
- necsim::Matrix::setSize (C++ function), [1], [2]
- necsim::Matrix::setValue (C++ function), [1], [2], [3], [4], [5]
- necsim::Matrix::sum (C++ function), [1], [2]
- necsim::Matrix::~Matrix (C++ function)
- necsim::MetacommunitiesArray (C++ class)
- necsim::MetacommunitiesArray::addNew (C++ function), [1]
- necsim::MetacommunitiesArray::addNull (C++ function)
- necsim::MetacommunitiesArray::begin (C++ function), [1]
- necsim::MetacommunitiesArray::clear (C++ function)
- necsim::MetacommunitiesArray::empty (C++ function)
- necsim::MetacommunitiesArray::end (C++ function), [1]
- necsim::MetacommunitiesArray::getReference (C++ function), [1]
- necsim::MetacommunitiesArray::hasMetacommunityOption (C++ function)
- necsim::MetacommunitiesArray::hasOption (C++ function), [1], [2]
- necsim::MetacommunitiesArray::metacomm_parameters (C++ member)
- necsim::MetacommunitiesArray::MetacommunitiesArray (C++ function)
- necsim::MetacommunitiesArray::pushBack (C++ function), [1]
- necsim::MetacommunitiesArray::size (C++ function)
- necsim::MetacommunitiesArray::~MetacommunitiesArray (C++ function)
- necsim::Metacommunity (C++ class)
- necsim::Metacommunity::addSpecies (C++ function)
- necsim::Metacommunity::applyNoOutput (C++ function)
- necsim::Metacommunity::approximateSAD (C++ function)
|
- necsim::Metacommunity::checkSimulationParameters (C++ function)
- necsim::Metacommunity::createMetacommunityNSENeutralModel (C++ function)
- necsim::Metacommunity::job_type (C++ member)
- necsim::Metacommunity::Metacommunity (C++ function)
- necsim::Metacommunity::metacommunity_tree (C++ member)
- necsim::Metacommunity::parameters_checked (C++ member)
- necsim::Metacommunity::printMetacommunityParameters (C++ function)
- necsim::Metacommunity::random (C++ member)
- necsim::Metacommunity::readSAD (C++ function)
- necsim::Metacommunity::seed (C++ member)
- necsim::Metacommunity::setCommunityParameters (C++ function)
- necsim::Metacommunity::species_abundances_handler (C++ member)
- necsim::Metacommunity::~Metacommunity (C++ function)
- necsim::MetacommunityParameters (C++ class)
- necsim::MetacommunityParameters::clear (C++ function)
- necsim::MetacommunityParameters::compare (C++ function), [1], [2]
- necsim::MetacommunityParameters::external_reference (C++ member)
- necsim::MetacommunityParameters::isMetacommunityOption (C++ function)
- necsim::MetacommunityParameters::metacommunity_size (C++ member)
- necsim::MetacommunityParameters::MetacommunityParameters (C++ function), [1]
- necsim::MetacommunityParameters::operator!= (C++ function)
- necsim::MetacommunityParameters::operator= (C++ function)
- necsim::MetacommunityParameters::operator== (C++ function)
- necsim::MetacommunityParameters::option (C++ member)
- necsim::MetacommunityParameters::reference (C++ member)
- necsim::MetacommunityParameters::speciation_rate (C++ member)
- necsim::MetacommunityParameters::~MetacommunityParameters (C++ function)
- necsim::openSQLiteDatabase (C++ function)
- necsim::operator<< (C++ function), [1], [2], [3], [4], [5], [6], [7], [8]
- necsim::operator>> (C++ function), [1], [2], [3], [4], [5], [6], [7], [8]
- necsim::ProtractedSpatialTree (C++ class)
- necsim::ProtractedSpeciationParameters (C++ class)
- necsim::ProtractedSpeciationParameters::max_speciation_gen (C++ member)
- necsim::ProtractedSpeciationParameters::min_speciation_gen (C++ member)
- necsim::ProtractedSpeciationParameters::operator== (C++ function)
- necsim::ProtractedSpeciationParameters::ProtractedSpeciationParameters (C++ function)
- necsim::ProtractedTree (C++ class)
- necsim::ProtractedTree::applySpecRate (C++ function), [1]
- necsim::ProtractedTree::ProtractedTree (C++ function)
- necsim::PyLogger (C++ class)
- necsim::pyLogger (C++ member)
- necsim::PyLogger::isSetup (C++ function)
- necsim::PyLogger::PyLogger (C++ function)
- necsim::PyLogger::setLogFunction (C++ function)
- necsim::PyLogger::setLogger (C++ function)
- necsim::PyLogger::write (C++ function), [1]
- necsim::PyLogger::writeCritical (C++ function)
- necsim::PyLogger::writeError (C++ function)
- necsim::PyLogger::writeInfo (C++ function)
- necsim::PyLogger::writeWarning (C++ function)
- necsim::PyLogger::~PyLogger (C++ function)
- necsim::removeComOption (C++ function)
- necsim::removeGlobalLogger (C++ function)
- necsim::runAsDefault (C++ function)
- necsim::runLarge (C++ function)
- necsim::runMain (C++ function)
- necsim::runXL (C++ function)
- necsim::sample_event (C++ enumerator)
- necsim::Samplematrix (C++ class)
- necsim::Samplematrix::getMaskVal (C++ function)
- necsim::Samplematrix::getTestVal (C++ function)
- necsim::Samplematrix::removeFragment (C++ function)
- necsim::Samplematrix::Samplematrix (C++ function)
- necsim::Samplematrix::setFragment (C++ function)
- necsim::saved_stdout (C++ member), [1]
- necsim::SectionOption (C++ class)
- necsim::SectionOption::getOption (C++ function)
- necsim::SectionOption::refs (C++ member)
- necsim::SectionOption::section (C++ member)
- necsim::SectionOption::SectionOption (C++ function)
- necsim::SectionOption::val (C++ member)
- necsim::SimParameters (C++ class)
- necsim::SimParameters::all_historical_map_parameters (C++ member)
- necsim::SimParameters::checkNeedsUpdate (C++ function)
- necsim::SimParameters::coarse_map_file (C++ member)
- necsim::SimParameters::coarse_map_scale (C++ member)
- necsim::SimParameters::coarse_map_x_offset (C++ member)
- necsim::SimParameters::coarse_map_x_size (C++ member)
- necsim::SimParameters::coarse_map_y_offset (C++ member)
- necsim::SimParameters::coarse_map_y_size (C++ member)
- necsim::SimParameters::configs (C++ member)
- necsim::SimParameters::cutoff (C++ member)
- necsim::SimParameters::death_file (C++ member)
- necsim::SimParameters::deme (C++ member)
- necsim::SimParameters::deme_sample (C++ member)
- necsim::SimParameters::desired_specnum (C++ member)
- necsim::SimParameters::dispersal_file (C++ member)
- necsim::SimParameters::dispersal_method (C++ member)
- necsim::SimParameters::dispersal_relative_cost (C++ member)
- necsim::SimParameters::fine_map_file (C++ member)
- necsim::SimParameters::fine_map_x_offset (C++ member)
- necsim::SimParameters::fine_map_x_size (C++ member)
- necsim::SimParameters::fine_map_y_offset (C++ member)
- necsim::SimParameters::fine_map_y_size (C++ member)
- necsim::SimParameters::gen_since_historical (C++ member)
- necsim::SimParameters::grid_x_size (C++ member)
- necsim::SimParameters::grid_y_size (C++ member)
- necsim::SimParameters::habitat_change_rate (C++ member)
- necsim::SimParameters::has_parsed_historical (C++ member)
- necsim::SimParameters::hasAnotherUpdate (C++ function)
- necsim::SimParameters::historical_coarse_map_file (C++ member)
- necsim::SimParameters::historical_fine_map_file (C++ member)
- necsim::SimParameters::importParameters (C++ function), [1], [2]
- necsim::SimParameters::is_historical (C++ member)
- necsim::SimParameters::is_protracted (C++ member)
- necsim::SimParameters::job_type (C++ member)
- necsim::SimParameters::landscape_type (C++ member)
- necsim::SimParameters::m_prob (C++ member)
- necsim::SimParameters::max_speciation_gen (C++ member)
- necsim::SimParameters::max_time (C++ member)
- necsim::SimParameters::min_speciation_gen (C++ member)
- necsim::SimParameters::operator= (C++ function)
- necsim::SimParameters::output_directory (C++ member)
- necsim::SimParameters::parseHistorical (C++ function)
- necsim::SimParameters::printSpatialVars (C++ function)
- necsim::SimParameters::printVars (C++ function)
- necsim::SimParameters::reproduction_file (C++ member)
- necsim::SimParameters::restrict_self (C++ member)
- necsim::SimParameters::sample_mask_file (C++ member)
- necsim::SimParameters::sample_x_offset (C++ member)
- necsim::SimParameters::sample_x_size (C++ member)
- necsim::SimParameters::sample_y_offset (C++ member)
- necsim::SimParameters::sample_y_size (C++ member)
- necsim::SimParameters::seed (C++ member)
- necsim::SimParameters::setDispersalParameters (C++ function)
- necsim::SimParameters::setHistorical (C++ function)
- necsim::SimParameters::setHistoricalMapParameters (C++ function), [1]
- necsim::SimParameters::setInitialHistoricalParameters (C++ function)
- necsim::SimParameters::setKeyParameters (C++ function)
- necsim::SimParameters::setMapParameters (C++ function)
- necsim::SimParameters::setMetacommunityParameters (C++ function)
- necsim::SimParameters::setSpeciationParameters (C++ function)
- necsim::SimParameters::sigma (C++ member)
- necsim::SimParameters::SimParameters (C++ function)
- necsim::SimParameters::spec (C++ member)
- necsim::SimParameters::tau (C++ member)
- necsim::SimParameters::times (C++ member)
- necsim::SimParameters::times_file (C++ member)
- necsim::SimParameters::uses_spatial_sampling (C++ member)
- necsim::SimulateDispersal (C++ class)
- necsim::SimulateDispersal::cells (C++ member)
- necsim::SimulateDispersal::checkMaxIdNumber (C++ function)
- necsim::SimulateDispersal::checkMaxParameterReference (C++ function)
- necsim::SimulateDispersal::clearParameters (C++ function)
- necsim::SimulateDispersal::data_mask (C++ member)
- necsim::SimulateDispersal::database (C++ member)
- necsim::SimulateDispersal::density_landscape (C++ member)
- necsim::SimulateDispersal::dispersal_coordinator (C++ member)
- necsim::SimulateDispersal::distances (C++ member)
- necsim::SimulateDispersal::generation (C++ member)
- necsim::SimulateDispersal::getEndPoint (C++ function), [1]
- necsim::SimulateDispersal::getMaxNumberSteps (C++ function)
- necsim::SimulateDispersal::getRandomCell (C++ function)
- necsim::SimulateDispersal::importMaps (C++ function)
- necsim::SimulateDispersal::is_sequential (C++ member)
- necsim::SimulateDispersal::max_parameter_reference (C++ member)
- necsim::SimulateDispersal::num_repeats (C++ member)
- necsim::SimulateDispersal::num_steps (C++ member)
- necsim::SimulateDispersal::num_workers (C++ member)
- necsim::SimulateDispersal::parameter_references (C++ member)
- necsim::SimulateDispersal::random (C++ member)
- necsim::SimulateDispersal::runAllDistanceTravelled (C++ function)
- necsim::SimulateDispersal::runDistanceLoop (C++ function)
- necsim::SimulateDispersal::runDistanceWorker (C++ function)
- necsim::SimulateDispersal::runMeanDispersalDistance (C++ function)
- necsim::SimulateDispersal::runMeanDistanceTravelled (C++ function)
- necsim::SimulateDispersal::runSampleDistanceTravelled (C++ function)
- necsim::SimulateDispersal::seed (C++ member)
- necsim::SimulateDispersal::setDispersalParameters (C++ function)
- necsim::SimulateDispersal::setNumberRepeats (C++ function)
- necsim::SimulateDispersal::setNumberSteps (C++ function)
- necsim::SimulateDispersal::setNumberWorkers (C++ function)
- necsim::SimulateDispersal::setOutputDatabase (C++ function)
- necsim::SimulateDispersal::setSeed (C++ function)
- necsim::SimulateDispersal::setSequential (C++ function)
- necsim::SimulateDispersal::setSimulationParameters (C++ function)
- necsim::SimulateDispersal::setSizes (C++ function)
- necsim::SimulateDispersal::simParameters (C++ member)
- necsim::SimulateDispersal::SimulateDispersal (C++ function)
- necsim::SimulateDispersal::storeCellList (C++ function)
- necsim::SimulateDispersal::writeDatabase (C++ function)
- necsim::SimulateDispersal::writeParameters (C++ function)
- necsim::SimulateDispersal::writeRepeatInfo (C++ function)
- necsim::SimulatedSpeciesAbundancesHandler (C++ class)
- necsim::SimulatedSpeciesAbundancesHandler::cumulative_abundance_map (C++ member)
- necsim::SimulatedSpeciesAbundancesHandler::generateAbundanceTable (C++ function)
- necsim::SimulatedSpeciesAbundancesHandler::generateCumulativeAbundances (C++ function)
- necsim::SimulatedSpeciesAbundancesHandler::getRandomAbundanceOfIndividual (C++ function)
- necsim::SimulatedSpeciesAbundancesHandler::getRandomSpeciesID (C++ function)
- necsim::SimulatedSpeciesAbundancesHandler::number_of_individuals (C++ member)
- necsim::SimulatedSpeciesAbundancesHandler::setAbundanceList (C++ function), [1]
- necsim::SimulatedSpeciesAbundancesHandler::SimulatedSpeciesAbundancesHandler (C++ function)
- necsim::SimulatedSpeciesAbundancesHandler::species_abundances (C++ member)
- necsim::SimulatedSpeciesAbundancesHandler::species_richness_per_abundance (C++ member)
- necsim::SimulatedSpeciesAbundancesHandler::total_species_number (C++ member)
- necsim::SimulatedSpeciesAbundancesHandler::~SimulatedSpeciesAbundancesHandler (C++ function)
- necsim::SpatialTree (C++ class)
- necsim::SpatialTree::addGillespie (C++ function), [1]
- necsim::SpatialTree::addLineages (C++ function), [1]
- necsim::SpatialTree::addLocation (C++ function), [1]
- necsim::SpatialTree::addNewEvent (C++ function), [1]
- necsim::SpatialTree::addWrappedLineage (C++ function), [1]
- necsim::SpatialTree::assignNonSpeciationProbability (C++ function), [1]
- necsim::SpatialTree::calcMinMax (C++ function), [1]
- necsim::SpatialTree::calcMove (C++ function), [1]
- necsim::SpatialTree::calcNewPos (C++ function), [1]
- necsim::SpatialTree::calcNextStep (C++ function), [1]
- necsim::SpatialTree::calculateCoalescenceProbability (C++ function), [1]
- necsim::SpatialTree::calcWrappedCoalescence (C++ function), [1]
- necsim::SpatialTree::cellToHeapPositions (C++ member), [1]
- necsim::SpatialTree::checkFolders (C++ function), [1]
- necsim::SpatialTree::checkMapEvents (C++ function), [1]
- necsim::SpatialTree::checkSampleEvents (C++ function), [1]
- necsim::SpatialTree::clearGillespieObjects (C++ function), [1]
- necsim::SpatialTree::coarse_map_input (C++ member), [1]
- necsim::SpatialTree::convertGlobalGenerationsToLocalGenerations (C++ function), [1]
- necsim::SpatialTree::convertMapLocationToCell (C++ function), [1]
- necsim::SpatialTree::countCellExpansion (C++ function), [1]
- necsim::SpatialTree::createEventList (C++ function), [1]
- necsim::SpatialTree::death_map (C++ member), [1]
- necsim::SpatialTree::desired_specnum (C++ member), [1]
- necsim::SpatialTree::detectLineages (C++ function), [1]
- necsim::SpatialTree::dispersal_coordinator (C++ member), [1]
- necsim::SpatialTree::dumpGrid (C++ function), [1]
- necsim::SpatialTree::dumpMap (C++ function), [1]
- necsim::SpatialTree::estSpecnum (C++ function), [1]
- necsim::SpatialTree::expandCell (C++ function), [1]
- necsim::SpatialTree::fillObjects (C++ function), [1]
- necsim::SpatialTree::findLocations (C++ function), [1]
- necsim::SpatialTree::fine_map_input (C++ member), [1]
- necsim::SpatialTree::fullSetupGillespieProbability (C++ function), [1]
- necsim::SpatialTree::getCellOfMapLocation (C++ function), [1]
- necsim::SpatialTree::getIndividualsSampled (C++ function), [1]
- necsim::SpatialTree::getInitialCount (C++ function), [1]
- necsim::SpatialTree::getLocalDeathRate (C++ function), [1]
- necsim::SpatialTree::getLocalSelfDispersalRate (C++ function), [1]
- necsim::SpatialTree::getNumberIndividualsAtLocation (C++ function), [1]
- necsim::SpatialTree::getNumberLineagesAtLocation (C++ function), [1]
- necsim::SpatialTree::gillespie_threshold (C++ member), [1]
- necsim::SpatialTree::gillespieCellEvent (C++ function), [1]
- necsim::SpatialTree::gillespieCoalescenceEvent (C++ function), [1]
- necsim::SpatialTree::gillespieDispersalEvent (C++ function), [1]
- necsim::SpatialTree::gillespieLocationRemainingCheck (C++ function), [1]
- necsim::SpatialTree::gillespieSampleIndividuals (C++ function), [1]
- necsim::SpatialTree::gillespieSpeciationEvent (C++ function), [1]
- necsim::SpatialTree::gillespieUpdateGeneration (C++ function), [1]
- necsim::SpatialTree::gillespieUpdateMap (C++ function), [1]
- necsim::SpatialTree::global_individuals (C++ member), [1]
- necsim::SpatialTree::grid (C++ member), [1]
- necsim::SpatialTree::heap (C++ member), [1]
- necsim::SpatialTree::historical_coarse_map_input (C++ member), [1]
- necsim::SpatialTree::historical_fine_map_input (C++ member), [1]
- necsim::SpatialTree::importActivityMaps (C++ function), [1]
- necsim::SpatialTree::importMaps (C++ function), [1]
- necsim::SpatialTree::incrementGeneration (C++ function), [1]
- necsim::SpatialTree::landscape (C++ member), [1]
- necsim::SpatialTree::loadGridSave (C++ function), [1]
- necsim::SpatialTree::loadMapSave (C++ function), [1]
- necsim::SpatialTree::probabilities (C++ member), [1]
- necsim::SpatialTree::recordLineagePosition (C++ function), [1]
- necsim::SpatialTree::removeHeapTop (C++ function), [1]
- necsim::SpatialTree::removeOldPosition (C++ function), [1]
- necsim::SpatialTree::reproduction_map (C++ member), [1]
- necsim::SpatialTree::runFileChecks (C++ function), [1]
- necsim::SpatialTree::runGillespieLoop (C++ function), [1]
- necsim::SpatialTree::runSimulationGillespie (C++ function), [1]
- necsim::SpatialTree::samplegrid (C++ member), [1]
- necsim::SpatialTree::selectRandomLineage (C++ function), [1]
- necsim::SpatialTree::selectTwoRandomLineages (C++ function), [1]
- necsim::SpatialTree::self_dispersal_probabilities (C++ member), [1]
- necsim::SpatialTree::setParameters (C++ function), [1]
- necsim::SpatialTree::setStepVariable (C++ function), [1]
- necsim::SpatialTree::setup (C++ function), [1]
- necsim::SpatialTree::setupDispersalCoordinator (C++ function), [1]
- necsim::SpatialTree::setupGillespie (C++ function), [1]
- necsim::SpatialTree::setupGillespieLineages (C++ function), [1]
- necsim::SpatialTree::setupGillespieMaps (C++ function), [1]
- necsim::SpatialTree::setupGillespieProbability (C++ function), [1]
- necsim::SpatialTree::simPause (C++ function), [1]
- necsim::SpatialTree::simResume (C++ function), [1]
- necsim::SpatialTree::simulationParametersSqlInsertion (C++ function), [1]
- necsim::SpatialTree::sortEvents (C++ function), [1]
- necsim::SpatialTree::SpatialTree (C++ function)
- necsim::SpatialTree::summed_death_rate (C++ member), [1]
- necsim::SpatialTree::switchPositions (C++ function), [1]
- necsim::SpatialTree::UNUSED (C++ member), [1]
- necsim::SpatialTree::updateAllProbabilities (C++ function), [1]
- necsim::SpatialTree::updateCellCoalescenceProbability (C++ function), [1]
- necsim::SpatialTree::updateInhabitedCellOnHeap (C++ function), [1]
- necsim::SpatialTree::updateStepCoalescenceVariables (C++ function), [1]
- necsim::SpatialTree::verifyActivityMaps (C++ function), [1]
- necsim::SpatialTree::~SpatialTree (C++ function)
- necsim::speciation_event (C++ enumerator)
- necsim::SpeciationCommands (C++ class)
- necsim::SpeciationCommands::applyFromComargs (C++ function)
- necsim::SpeciationCommands::parseArgs (C++ function)
- necsim::SpeciationCommands::SpeciationCommands (C++ function)
- necsim::SpeciesAbundancesHandler (C++ class)
- necsim::SpeciesAbundancesHandler::getRandomSpeciesID (C++ function)
- necsim::SpeciesAbundancesHandler::local_community_size (C++ member), [1], [2]
- necsim::SpeciesAbundancesHandler::max_species_id (C++ member), [1], [2]
- necsim::SpeciesAbundancesHandler::metacommunity_size (C++ member), [1], [2]
- necsim::SpeciesAbundancesHandler::random (C++ member), [1], [2]
- necsim::SpeciesAbundancesHandler::setAbundanceList (C++ function), [1], [2], [3]
- necsim::SpeciesAbundancesHandler::setup (C++ function), [1]
- necsim::SpeciesAbundancesHandler::speciation_rate (C++ member), [1], [2]
- necsim::SpeciesAbundancesHandler::SpeciesAbundancesHandler (C++ function)
- necsim::SpeciesAbundancesHandler::~SpeciesAbundancesHandler (C++ function)
- necsim::SpeciesList (C++ class)
- necsim::SpeciesList::addSpecies (C++ function)
- necsim::SpeciesList::changePercentCover (C++ function)
- necsim::SpeciesList::decreaseNwrap (C++ function)
- necsim::SpeciesList::deleteSpecies (C++ function)
- necsim::SpeciesList::getCoalescenceProbability (C++ function)
- necsim::SpeciesList::getLineageIndex (C++ function)
- necsim::SpeciesList::getListLength (C++ function)
- necsim::SpeciesList::getListSize (C++ function)
- necsim::SpeciesList::getMaxSize (C++ function)
- necsim::SpeciesList::getNext (C++ function)
- necsim::SpeciesList::getNwrap (C++ function)
- necsim::SpeciesList::getRandLineage (C++ function)
- necsim::SpeciesList::increaseListSize (C++ function)
- necsim::SpeciesList::increaseNwrap (C++ function)
- necsim::SpeciesList::initialise (C++ function)
- necsim::SpeciesList::setMaxsize (C++ function)
- necsim::SpeciesList::setNext (C++ function)
- necsim::SpeciesList::setNwrap (C++ function)
- necsim::SpeciesList::setSpecies (C++ function)
- necsim::SpeciesList::setSpeciesEmpty (C++ function)
- necsim::SpeciesList::SpeciesList (C++ function)
- necsim::SpeciesList::wipeList (C++ function)
- necsim::SpeciesList::~SpeciesList (C++ function)
- necsim::SpecSimParameters (C++ class)
- necsim::SpecSimParameters::addMetacommunityParameters (C++ function)
- necsim::SpecSimParameters::addProtractedParameters (C++ function)
- necsim::SpecSimParameters::addSpeciationRate (C++ function)
- necsim::SpecSimParameters::addTime (C++ function)
- necsim::SpecSimParameters::all_speciation_rates (C++ member)
- necsim::SpecSimParameters::all_times (C++ member)
- necsim::SpecSimParameters::bMultiRun (C++ member)
- necsim::SpecSimParameters::filename (C++ member)
- necsim::SpecSimParameters::fragment_config_file (C++ member)
- necsim::SpecSimParameters::importTimeConfig (C++ function)
- necsim::SpecSimParameters::metacommunity_parameters (C++ member)
- necsim::SpecSimParameters::protracted_parameters (C++ member)
- necsim::SpecSimParameters::samplemask (C++ member)
- necsim::SpecSimParameters::setup (C++ function), [1], [2]
- necsim::SpecSimParameters::SpecSimParameters (C++ function), [1]
- necsim::SpecSimParameters::times_file (C++ member)
- necsim::SpecSimParameters::use_fragments (C++ member)
- necsim::SpecSimParameters::use_spatial (C++ member)
- necsim::SpecSimParameters::wipe (C++ function)
- necsim::SQLiteHandler (C++ class)
- necsim::SQLiteHandler::backupFrom (C++ function)
- necsim::SQLiteHandler::beginTransaction (C++ function)
- necsim::SQLiteHandler::close (C++ function)
- necsim::SQLiteHandler::createStatement (C++ function)
- necsim::SQLiteHandler::database (C++ member)
- necsim::SQLiteHandler::endTransaction (C++ function)
- necsim::SQLiteHandler::execute (C++ function)
- necsim::SQLiteHandler::file_name (C++ member)
- necsim::SQLiteHandler::finalise (C++ function)
- necsim::SQLiteHandler::getErrorMsg (C++ function), [1]
- necsim::SQLiteHandler::hasTable (C++ function)
- necsim::SQLiteHandler::isOpen (C++ function)
- necsim::SQLiteHandler::open (C++ function)
- necsim::SQLiteHandler::prepare (C++ function)
- necsim::SQLiteHandler::SQLiteHandler (C++ function)
- necsim::SQLiteHandler::step (C++ function)
- necsim::SQLiteHandler::stmt (C++ member)
- necsim::SQLiteHandler::useStatement (C++ function)
- necsim::SQLiteHandler::~SQLiteHandler (C++ function)
- necsim::SQLStatement (C++ class)
- necsim::SQLStatement::clearAndReset (C++ function)
- necsim::SQLStatement::last_command (C++ member)
- necsim::SQLStatement::SQLStatement (C++ function)
- necsim::SQLStatement::step (C++ function)
- necsim::SQLStatement::stmt (C++ member)
- necsim::Step (C++ class)
- necsim::Step::bContinueSim (C++ member)
- necsim::Step::chosen (C++ member)
- necsim::Step::coal (C++ member)
- necsim::Step::coalchosen (C++ member)
- necsim::Step::Step (C++ function), [1]
- necsim::Step::time_reference (C++ member)
- necsim::Step::wipeData (C++ function)
- necsim::Tree (C++ class)
- necsim::Tree::active (C++ member), [1], [2], [3]
- necsim::Tree::addGillespie (C++ function), [1]
- necsim::Tree::addLineages (C++ function), [1]
- necsim::Tree::addSpeciationRates (C++ function), [1], [2], [3]
- necsim::Tree::applyMultipleRates (C++ function), [1], [2], [3]
- necsim::Tree::applySpecRate (C++ function), [1], [2], [3], [4], [5], [6], [7]
- necsim::Tree::applySpecRateInternal (C++ function), [1], [2], [3]
- necsim::Tree::bConfig (C++ member), [1], [2], [3]
- necsim::Tree::bFullMode (C++ member), [1], [2], [3]
- necsim::Tree::bIsProtracted (C++ member), [1], [2], [3]
- necsim::Tree::bResume (C++ member), [1], [2], [3]
- necsim::Tree::calcNextStep (C++ function), [1]
- necsim::Tree::calcSpeciation (C++ function), [1], [2]
- necsim::Tree::checkOutputDirectory (C++ function), [1], [2], [3]
- necsim::Tree::checkProportionAdded (C++ function), [1], [2], [3]
- necsim::Tree::checkSims (C++ function), [1], [2], [3], [4], [5], [6], [7]
- necsim::Tree::checkSimSize (C++ function), [1], [2], [3]
- necsim::Tree::checkTimeUpdate (C++ function), [1], [2], [3]
- necsim::Tree::chooseRandomLineage (C++ function), [1], [2], [3]
- necsim::Tree::coalescenceEvent (C++ function), [1], [2], [3]
- necsim::Tree::community (C++ member), [1], [2], [3]
- necsim::Tree::completePause (C++ function), [1], [2], [3]
- necsim::Tree::convertTip (C++ function), [1], [2], [3]
- necsim::Tree::createAndOutputData (C++ function), [1], [2], [3]
- necsim::Tree::data (C++ member), [1], [2], [3]
- necsim::Tree::database (C++ member), [1], [2], [3]
- necsim::Tree::deme (C++ member), [1], [2], [3]
- necsim::Tree::deme_sample (C++ member), [1], [2], [3]
- necsim::Tree::determineSpeciationRates (C++ function), [1], [2], [3]
- necsim::Tree::dumpActive (C++ function), [1], [2], [3]
- necsim::Tree::dumpData (C++ function), [1], [2], [3]
- necsim::Tree::dumpMain (C++ function), [1], [2], [3]
- necsim::Tree::endactive (C++ member), [1], [2], [3]
- necsim::Tree::enddata (C++ member), [1], [2], [3]
- necsim::Tree::fillObjects (C++ function), [1]
- necsim::Tree::generateObjects (C++ function), [1], [2], [3]
- necsim::Tree::generation (C++ member), [1], [2], [3]
- necsim::Tree::getCumulativeAbundances (C++ function), [1], [2], [3]
- necsim::Tree::getGeneration (C++ function), [1], [2], [3]
- necsim::Tree::getInitialCount (C++ function), [1]
- necsim::Tree::getJobType (C++ function), [1], [2], [3]
- necsim::Tree::getProtracted (C++ function), [1], [2]
- necsim::Tree::getProtractedGenerationMax (C++ function), [1], [2]
- necsim::Tree::getProtractedGenerationMin (C++ function), [1], [2]
- necsim::Tree::getProtractedVariables (C++ function), [1], [2]
- necsim::Tree::getSeed (C++ function), [1], [2], [3]
- necsim::Tree::getSpeciesAbundances (C++ function), [1], [2], [3], [4], [5], [6], [7]
- necsim::Tree::getTemporalSampling (C++ function), [1], [2], [3]
- necsim::Tree::has_imported_pause (C++ member), [1], [2], [3]
- necsim::Tree::has_imported_vars (C++ member), [1], [2], [3]
- necsim::Tree::has_paused (C++ member), [1], [2], [3]
- necsim::Tree::hasPaused (C++ function), [1], [2], [3]
- necsim::Tree::importSimulationVariables (C++ function), [1], [2], [3], [4], [5], [6], [7]
- necsim::Tree::incrementGeneration (C++ function), [1]
- necsim::Tree::initiatePause (C++ function), [1], [2], [3]
- necsim::Tree::initiateResume (C++ function), [1], [2], [3]
- necsim::Tree::internalSetup (C++ function), [1], [2], [3]
- necsim::Tree::job_type (C++ member), [1], [2], [3]
- necsim::Tree::loadActiveSave (C++ function), [1], [2], [3]
- necsim::Tree::loadDataSave (C++ function), [1], [2], [3]
- necsim::Tree::loadMainSave (C++ function), [1], [2], [3]
- necsim::Tree::makeTip (C++ function), [1], [2], [3]
- necsim::Tree::maxsimsize (C++ member), [1], [2], [3]
- necsim::Tree::maxtime (C++ member), [1], [2], [3]
- necsim::Tree::now (C++ member), [1], [2], [3]
- necsim::Tree::NR (C++ member), [1], [2], [3]
- necsim::Tree::openSaveFile (C++ function), [1], [2], [3]
- necsim::Tree::openSQLDatabase (C++ function), [1], [2], [3]
- necsim::Tree::out_directory (C++ member), [1], [2], [3]
- necsim::Tree::out_finish (C++ member), [1], [2], [3]
- necsim::Tree::outputData (C++ function), [1], [2], [3]
- necsim::Tree::pause_sim_directory (C++ member), [1], [2], [3]
- necsim::Tree::printSetup (C++ function), [1], [2], [3]
- necsim::Tree::protractedVarsToString (C++ function), [1], [2]
- necsim::Tree::reference_times (C++ member), [1], [2], [3]
- necsim::Tree::removeOldPosition (C++ function), [1]
- necsim::Tree::runFileChecks (C++ function), [1]
- necsim::Tree::runSimulation (C++ function), [1], [2], [3]
- necsim::Tree::runSimulationGillespie (C++ function), [1]
- necsim::Tree::runSimulationNoGillespie (C++ function), [1], [2], [3]
- necsim::Tree::runSingleLoop (C++ function), [1], [2], [3]
- necsim::Tree::seed (C++ member), [1], [2], [3]
- necsim::Tree::seeded (C++ member), [1], [2], [3]
- necsim::Tree::setInitialValues (C++ function), [1], [2], [3]
- necsim::Tree::setObjectSizes (C++ function), [1], [2], [3]
- necsim::Tree::setParameters (C++ function), [1]
- necsim::Tree::setProtractedVariables (C++ function), [1], [2]
- necsim::Tree::setResumeParameters (C++ function), [1], [2], [3], [4], [5], [6], [7]
- necsim::Tree::setSeed (C++ function), [1], [2], [3]
- necsim::Tree::setSimStartVariables (C++ function), [1], [2], [3]
- necsim::Tree::setTimes (C++ function), [1], [2], [3]
- necsim::Tree::setup (C++ function), [1]
- necsim::Tree::setupCommunity (C++ function), [1], [2], [3]
- necsim::Tree::setupCommunityCalculation (C++ function), [1], [2], [3]
- necsim::Tree::setupOutputDirectory (C++ function), [1], [2], [3]
- necsim::Tree::sim_complete (C++ member), [1], [2], [3]
- necsim::Tree::sim_end (C++ member), [1], [2], [3]
- necsim::Tree::sim_finish (C++ member), [1], [2], [3]
- necsim::Tree::sim_parameters (C++ member), [1], [2], [3]
- necsim::Tree::sim_start (C++ member), [1], [2], [3]
- necsim::Tree::simPause (C++ function), [1]
- necsim::Tree::simResume (C++ function), [1]
- necsim::Tree::simulationParametersSqlInsertion (C++ function), [1]
- necsim::Tree::sortData (C++ function), [1], [2], [3]
- necsim::Tree::spec (C++ member), [1], [2], [3]
- necsim::Tree::speciateLineage (C++ function), [1], [2]
- necsim::Tree::speciation (C++ function), [1], [2], [3]
- necsim::Tree::speciation_rates (C++ member), [1], [2], [3]
- necsim::Tree::sql_output_database (C++ member), [1], [2], [3]
- necsim::Tree::sqlCreate (C++ function), [1], [2], [3]
- necsim::Tree::sqlCreateSimulationParameters (C++ function), [1], [2], [3]
- necsim::Tree::sqlOutput (C++ function), [1], [2], [3]
- necsim::Tree::start (C++ member), [1], [2], [3]
- necsim::Tree::startendactive (C++ member), [1], [2], [3]
- necsim::Tree::steps (C++ member), [1], [2], [3]
- necsim::Tree::stopSimulation (C++ function), [1], [2], [3]
- necsim::Tree::switchPositions (C++ function), [1]
- necsim::Tree::this_step (C++ member), [1], [2], [3]
- necsim::Tree::time_taken (C++ member), [1], [2], [3]
- necsim::Tree::times_file (C++ member), [1], [2], [3]
- necsim::Tree::Tree (C++ function)
- necsim::Tree::updateStepCoalescenceVariables (C++ function), [1]
- necsim::Tree::uses_temporal_sampling (C++ member), [1], [2], [3]
- necsim::Tree::using_gillespie (C++ member), [1], [2], [3]
- necsim::Tree::wipeSimulationVariables (C++ function), [1], [2], [3]
- necsim::Tree::writeSimStartToConsole (C++ function), [1], [2], [3]
- necsim::Tree::writeStepToConsole (C++ function), [1], [2], [3]
- necsim::Tree::writeTimes (C++ function), [1], [2], [3]
- necsim::Tree::~Tree (C++ function)
- necsim::TreeNode (C++ class)
- necsim::TreeNode::burnSpecies (C++ function)
- necsim::TreeNode::exists (C++ function)
- necsim::TreeNode::getGeneration (C++ function)
- necsim::TreeNode::getGenerationRate (C++ function)
- necsim::TreeNode::getParent (C++ function)
- necsim::TreeNode::getSpeciesID (C++ function)
- necsim::TreeNode::getSpecRate (C++ function)
- necsim::TreeNode::getXpos (C++ function)
- necsim::TreeNode::getXwrap (C++ function)
- necsim::TreeNode::getYpos (C++ function)
- necsim::TreeNode::getYwrap (C++ function)
- necsim::TreeNode::hasSpeciated (C++ function)
- necsim::TreeNode::increaseGen (C++ function)
- necsim::TreeNode::isTip (C++ function)
- necsim::TreeNode::operator= (C++ function)
- necsim::TreeNode::qReset (C++ function)
- necsim::TreeNode::resetSpecies (C++ function)
- necsim::TreeNode::setExistence (C++ function)
- necsim::TreeNode::setGeneration (C++ function)
- necsim::TreeNode::setGenerationRate (C++ function)
- necsim::TreeNode::setParent (C++ function)
- necsim::TreeNode::setPosition (C++ function)
- necsim::TreeNode::setSpec (C++ function)
- necsim::TreeNode::setSpeciation (C++ function)
- necsim::TreeNode::setTip (C++ function)
- necsim::TreeNode::setup (C++ function), [1], [2]
- necsim::TreeNode::speciate (C++ function)
- necsim::TreeNode::TreeNode (C++ function)
- necsim::TreeNode::~TreeNode (C++ function)
- necsim::undefined (C++ enumerator), [1]
- necsim::writeCritical (C++ function)
- necsim::writeError (C++ function)
- necsim::writeInfo (C++ function)
- necsim::writeWarning (C++ function)
- necsimError (C++ member)
- neutral_analytical::calcFundamentalBiodiversityNumber (C++ function)
- neutral_analytical::calcSpeciationRate (C++ function)
- neutral_analytical::siMetacommunitySpeciesWithAbundance (C++ function)
- neutral_analytical::siSpeciesAbundanceCumulativeDistribution (C++ function)
- neutral_analytical::siSpeciesRichness (C++ function)
- neutral_analytical::siSpeciesRichnessDeprecated (C++ function)
- null (C macro)
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