| BinaryDataLoader | A class to load a whole population from a binary data file |
| BinaryDataSaver | A class to handle simulation data saving in binary format |
| BinaryFileParser | Retrieves simulation parameters from a binary data file |
| BinaryStorageBuffer | A class to store any kind of data in a char buffer before unloading it in a binary data file |
| bitstring | Non-template and faster implementation of std::bitset |
| ComponentManager | Class to manage the simulation components and prototypes |
| DataTable< T > | A class to aggregate structured data in an array |
| EventFileHandler< LCE > | Template class for the LCEs StatHandler classes |
| EventStatHandler< LCE, SH > | Template class for the LCEs StatHandler classes |
| FHLogWriter | File Handler used to save the simulation parameters to a log file |
| FileHandler | Interface to handle file input/output for any SimComponent |
| FileParser | Text input parameter file parser |
| FileServices | A class to manage the files associated with each components of the simulation |
| Handler | Service handler (an observer) |
| IndFactory | Factory of Individual, stores the individual prototype and the trait prototypes, manages the individual garbage collector |
| Individual | This class contains traits along with other individual information (sex, pedigree, etc. ) |
| LCE_Aging | Removes all adults from the patches and randomly moves the offspring to the adults age class |
| LCE_Breed | Implementation of the basic breeding and mating procedures, does not link to any trait |
| LCE_Breed_base | Base class for the breeding (and mating) life cycle events |
| LCE_Breed_Disperse | Performs breeding and migration in one, migration rates are backward rates |
| LCE_Breed_Selection | Composite LCE implementing breeding and viability selection on a given trait type |
| LCE_Breed_Selection_Disperse | Composite LCE performing breeding, migration and viability selection all in one |
| LCE_Breed_Wolbachia | Breeding LCE when individuals carry the Wolbachia endosymbiotic parasite |
| LCE_Cross | A class to perform crosses within patches, implements the NC1 mating design |
| LCE_Disperse_base | The base class of the dispersal LCEs, all events move offspring to the post-dispersal patch containers |
| LCE_Disperse_ConstDisp | Dispersal event with constant dispersal rates |
| LCE_Disperse_EvolDisp | Dispersal event with an evolving dispersal rate given by the "disp" trait |
| LCE_FileServicesNotifier | Event used to notify all file handlers to update their state through the FileServices::notify() interface |
| LCE_ParamUpdaterNotifier | Calls the UpdaterServices to notify its components of a generation change |
| LCE_Patch_Extinction | Randomly removes individuals from the patches according to the extinction rate parameter |
| LCE_QuantiInit | Set patch-specifiec initial genotypes values |
| LCE_Regulation | Regulates the patches to their carrying capacity, acts on each age class separately |
| LCE_Resize | A class to change the size of the population/patches during a simulation |
| LCE_Selection_base | Base class performing (viability) selection |
| LCE_SelectionSH | StatHandler class for the LCE_Selection class |
| LCE_StatFH | FileHandler of the LCE_StatServiceNotifier class, writes the recorded stats to txt files |
| LCE_StatServiceNotifier | Initiates the StatServices' parameters (log time) when registering, calls StatServices::notify() when executing |
| LCE_StatSH | StatHandler of the LCE_StatServiceNotifier class, adds a default StatRecorder to the recorders list (alive.rpl) |
| LifeCycleEvent | Base class of the Life Cycle Events, declares the LCE interface |
| Metapop | Top class of the metapopulation structure, contains the patches |
| MPIenv | MPI environment setup |
| MPImanager | The abstract manager class |
| MPStatHandler | A StatHandler for the Metapop SimComponent |
| Param | This structure stores one parameter, its definition and its string argument |
| ParamManager | Class to manage the sets of parameters of the simulation components |
| ParamSet | Parameters container, implemented in each SimComponent |
| ParamsParser | Provides interface to read input parameters from various sources and parses them |
| ParamUpdater< SC > | Implementation of the ParamUpdaterBase interface |
| ParamUpdaterBase | Base class of the ParamUpdater class used to handle the temporal parameter argument values |
| Patch | Second class in the metapopulation design structure, between the Metapop and Individual classes |
| RAND | Random number generation class, uses various types of random generators depending on the implementation |
| bitstring::reference | |
| Service | Interface for the simulation services (files and stats) |
| SimBuilder | Provides methods to build the user's selected set of life cycle events and traits from the parameters |
| SimComponent | Interface to all basic components of a simulation (traits, life cycle events, pop, etc. ) |
| SIMenv | Global class exposing the current SimRunner throughout the code |
| SimRunner | Performs the setup of the Metapop and SimComponents and runs the simulation |
| StatHandler< SH > | A class to compute and store the summary statistics associated with a SimComponent |
| StatHandlerBase | Base class of the StatHandler class, implements the Handler interface |
| StatRecBase | Base class for the StatRecorder's, stores the stat values in a matrix |
| StatRecorder< S > | Stores the pointers to the StatHandler's stat functions |
| StatServices | The Service class used to manage the StatHandler objects |
| StorableComponent | Provides an interface to binary data saving and uploading |
| StreamParser | Read parameters from a text buffer |
| TMatrix | A class to handle matrix in params, coerces matrix into a vector of same total size |
| TProtoDeletMutations_bitstring | Prototype class of the bitstring-deleterious mutations trait class |
| TProtoDispersal | Prototype of the evolving dispersal trait, defines the sex-specific trait type |
| TProtoNeutralGenes | Prototype class for the TTNeutralGenes trait class |
| TProtoQuanti | |
| TProtoWolbachia | Prototype of the Wolbachia trait |
| TraitFileHandler< TP > | Template class for the trait's FileHandler |
| TraitPrototype | TTrait setter |
| TraitStatHandler< TP, SH > | Template class for the trait's StatHandler |
| tstring | A global class to handle string conversions and operations |
| TTDeletMutations_bitstring | Bitstring implementation of TTDeletMutations with recombination |
| TTDeletMutBitstrFH | The FileHandler associated with the TTDeletMutations_bitstring trait |
| TTDeletMutBitstrSH | The StatHandler for TTDeletMutations_bitstring |
| TTDispersal | Evolving dispersal trait, codes for female (_type = FDISP) or male (_type = MDISP) sex-specific dispersal rates |
| TTDispersalSH | The StatHandler for the evolving dispersal traits |
| TTNeutralGenes | Microsatellites genome |
| TTNeutralGenesFH | A file handler to save the neutral markers genotypes in the FSTAT format (extended) |
| TTNeutralGenesSH | The stat handler for neutral markers |
| TTQuanti | |
| TTQuantiFH | |
| TTQuantiSH | |
| TTrait | Interface for all trait types, declares all basic trait operations |
| TTWolbachia | Trait used to study the dynamics of spread of Wolbachia, an endosymbiotic parasite causing cytoplasmic incompatibility |
| TTWolbachiaFH | FileHandler of the Wolbachia trait |
| TTWolbachiaSH | StatHandler of the Wolbachia trait |
| UpdaterServices | Class to update the simulation components' state during a simulation |
