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Nemo
2.4.0b
Simulate forward-in-time genetic evolution in a spatially explicit, individual-based stochastic simulator
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| CBinaryDataLoader | A class to load a whole population from a binary data file |
| CBinaryStorageBuffer | A class to store any kind of data in a char buffer before unloading it in a binary data file |
| Cbitstring | Non-template and faster implementation of std::bitset |
| ▼CComponentManager | Class to manage the simulation components and prototypes |
| ▼CParamManager | Class to manage the sets of parameters of the simulation components |
| ►CSimBuilder | Provides methods to build the user's selected set of life cycle events and traits from the parameters |
| CDataTable< T > | A class to aggregate structured data in an array |
| CDataTable< double > | |
| CDataTable< unsigned int > | |
| CGeneticMap | GeneticMap |
| ▼CHandler | Service handler (an observer) |
| ▼CFileHandler | Interface to handle file input/output for any SimComponent |
| ►CEventFileHandler< LCE_Breed_Wolbachia > | |
| ►CEventFileHandler< LCE_Cross > | |
| ►CEventFileHandler< LCE_Selection_base > | |
| ►CEventFileHandler< LCE_FileServicesNotifier > | |
| ►CTraitFileHandler< TProtoDeletMutations_bitstring > | |
| ►CTraitFileHandler< TProtoQuanti > | |
| ►CTraitFileHandler< TProtoNeutralGenes > | |
| ►CTraitFileHandler< TProtoBDMI > | |
| CBinaryDataSaver | A class to handle simulation data saving in binary format |
| CEventFileHandler< LCE > | Template class for the LCEs StatHandler classes |
| CFHLogWriter | File Handler used to save the simulation parameters to a log file |
| CLCE_StatFH | FileHandler of the LCE_StatServiceNotifier class, writes the recorded stats to txt files |
| CMPFileHandler | |
| CTraitFileHandler< TP > | Template class for the trait's FileHandler |
| ▼CParamUpdaterBase | Base class of the ParamUpdater class used to handle the temporal parameter argument values |
| CParamUpdater< SC > | Implementation of the ParamUpdaterBase interface |
| ▼CStatHandlerBase | Base class of the StatHandler class, implements the Handler interface |
| ►CStatHandler< MPStatHandler > | |
| ►CStatHandler< TTDispersalSH > | |
| ►CStatHandler< SH > | A class to compute and store the summary statistics associated with a SimComponent |
| ▼CIndFactory | Factory of Individual, stores the individual prototype and the trait prototypes, manages the individual garbage collector |
| CMetapop | Top class of the metapopulation structure, contains the patches |
| CIndividual | This class contains traits along with other individual information (sex, pedigree, etc. ) |
| CMacroCaller | |
| CMPIenv | MPI environment setup |
| CMPImanager | |
| CParam | This structure stores one parameter, its definition and its string argument |
| CParamSet | Parameters container, implemented in each SimComponent |
| ▼CParamsParser | Provides interface to read input parameters from various sources and parses them |
| ▼CStreamParser | Read parameters from a text buffer |
| CBinaryFileParser | Retrieves simulation parameters from a binary data file |
| CFileParser | Text input parameter file parser |
| CPatch | Second class in the metapopulation design structure, between the Metapop and Individual classes |
| CRAND | Random number generation class, uses various types of random generators depending on the implementation |
| Cbitstring::reference | |
| ▼CService | Interface for the simulation services (files and stats) |
| CFileServices | A class to manage the files associated with each components of the simulation |
| CStatServices | The Service class used to manage the StatHandler objects |
| CUpdaterServices | Class to update the simulation components' state during a simulation |
| ▼CSimComponent | Interface to all basic components of a simulation (traits, life cycle events, pop, etc. ) |
| ▼CLifeCycleEvent | Base class of the Life Cycle Events, declares the LCE interface |
| CBinaryDataSaver | A class to handle simulation data saving in binary format |
| CLCE_Aging | Removes all adults from the patches and randomly moves the offspring to the adults age class |
| ►CLCE_Breed_base | Base class for the breeding (and mating) life cycle events |
| CLCE_Cross | A class to perform crosses within patches, implements the NC1 mating design |
| ►CLCE_Disperse_base | The base class of the dispersal LCEs, all events move offspring to the post-dispersal patch containers |
| CLCE_FileServicesNotifier | Event used to notify all file handlers to update their state through the FileServices::notify() interface |
| CLCE_Init_BDMI | Allelic frequency initialiser for the DBMI trait |
| CLCE_NtrlInit | Set patch-specifiec initial genotypes values |
| CLCE_ParamUpdaterNotifier | Calls the UpdaterServices to notify its components of a generation change |
| CLCE_Patch_Extinction | Randomly removes individuals from the patches according to the extinction rate parameter |
| CLCE_PhenotypeExpression | |
| CLCE_QuantiInit | Set patch-specifiec initial genotypes values |
| CLCE_QuantiModifier | Set patch-specifiec initial genotypes values |
| CLCE_Regulation | Regulates the patches to their carrying capacity, acts on each age class separately |
| CLCE_Resize | A class to change the size of the population/patches during a simulation |
| ►CLCE_Selection_base | Base class performing (viability) selection on an arbitrary trait |
| CLCE_StatServiceNotifier | Initiates the StatServices' parameters (log time) when registering, calls StatServices::notify() when executing |
| CMetapop | Top class of the metapopulation structure, contains the patches |
| ▼CTraitPrototype | TTrait setter |
| CTProtoDispersal | Prototype of the evolving dispersal trait, defines the sex-specific trait type |
| CTProtoWolbachia | Prototype of the Wolbachia trait |
| ►CTTProtoWithMap | TTProtoWithMap |
| CSIMenv | Global class exposing the current SimRunner throughout the code |
| ▼CStatRecBase | Base class for the StatRecorder's, declares the interface to record stat values |
| CStatRecorder< SH > | |
| CStatRecorder< S > | Stores the pointers to the StatHandler's stat functions |
| ▼CStorableComponent | Provides an interface to binary data saving and uploading |
| CMetapop | Top class of the metapopulation structure, contains the patches |
| ▼CTTrait | Interface for all trait types, declares all basic trait operations |
| CTTDeletMutations_bitstring | Bitstring implementation of TTDeletMutations with recombination |
| CTTDispersal | Evolving dispersal trait, codes for female (_type = FDISP) or male (_type = MDISP) sex-specific dispersal rates |
| CTTNeutralGenes | Microsatellites genome |
| ►CTTQuanti | TTQuanti |
| CTTWolbachia | Trait used to study the dynamics of spread of Wolbachia, an endosymbiotic parasite causing cytoplasmic incompatibility |
| CTT_BDMI | |
| CTTraitWithMap | TTraitWithMap |
| CTraitPrototype | TTrait setter |
| CTMatrix | A class to handle matrix in params, coerces matrix into a vector of same total size |
| Ctstring | A global class to handle string conversions and operations |
1.9.1 -- Nemo is hosted on 
