A Framework for Data-Driven Stochastic Disease Spread Simulations

boxplot-SimInf_model-method | Box plot of number of individuals in each compartment |

C_code | Extract the C code from a 'SimInf_model' object |

compile_model | Function to compile custom 'SimInf_model'. |

distance_matrix | Create a distance matrix between nodes for spatial models |

events | Extract the events from a 'SimInf_model' object |

events_SEIR | Example data to initialize events for the 'SEIR' model |

events_SIR | Example data to initialize events for the 'SIR' model |

events_SISe | Example data to initialize events for the 'SISe' model |

events_SISe3 | Example data to initialize events for the 'SISe3' model |

gdata | Extract global data from a 'SimInf_model' object |

gdata-set | Set a global data parameter for a 'SimInf_model' object |

indegree | Determine in-degree for each node in a model |

ldata | Extract local data from a node |

mparse | Model parser to define new models to run in 'SimInf' |

Nn | Extract number of nodes in a model |

nodes | Example data with spatial distribution of nodes |

outdegree | Determine out-degree for each node in a model |

package_skeleton | Create a package skeleton from a 'SimInf_model' |

pairs-SimInf_model-method | Scatterplot of number of individuals in each compartment |

plot | Display the outcome from a simulated trajectory |

plot-SimInf_events-method | Display the distribution of scheduled events over time |

prevalence | Calculate prevalence from a model object with trajectory data |

run | Run the SimInf stochastic simulation algorithm |

run_outer | Run 'SimInf_model' on scaled parameters |

SEIR | Create an SEIR model |

SEIR-class | Definition of the 'SEIR' model |

select_matrix | Extract the select matrix from a 'SimInf_model' object |

select_matrix-set | Set the select matrix for a 'SimInf_model' object |

shift_matrix | Extract the shift matrix from a 'SimInf_model' object |

shift_matrix-set | Set the shift matrix for a 'SimInf_model' object |

show-SimInf_events-method | Brief summary of 'SimInf_events' |

show-SimInf_model-method | Brief summary of 'SimInf_model' |

SimInf | A Framework for Data-Driven Stochastic Disease Spread... |

SimInf_events | Create a 'SimInf_events' object |

SimInf_events-class | Class '"SimInf_events"' |

SimInf_model | Create a 'SimInf_model' |

SimInf_model-class | Class '"SimInf_model"' |

SimInf_model_dll-class | Class to handle a compiled custom 'SimInf_model' |

SIR | Create an SIR model |

SIR-class | Definition of the SIR model |

SISe | Create a SISe model |

SISe3 | Create a 'SISe3' model |

SISe3-class | Definition of the 'SISe3' model |

SISe3_sp | Create a SISe3_sp model |

SISe3_sp-class | Definition of the 'SISe3_sp' model |

SISe-class | Definition of the 'SISe' model |

SISe_sp | Create a 'SISe_sp' model |

SISe_sp-class | Definition of the 'SISe_sp' model |

summary-SimInf_events-method | Detailed summary of a 'SimInf_events' object |

summary-SimInf_model-method | Detailed summary of a 'SimInf_model' object |

trajectory | Extract data from a simulated trajectory |

u0_SEIR | Example data to initialize the 'SEIR' model |

u0_SIR | Example data to initialize the 'SIR' model |

u0_SISe | Example data to initialize the 'SISe' model |

u0_SISe3 | Example data to initialize the 'SISe3' model |

U-set | Set a template for where to write the U result matrix |

V-set | Set a template for where to write the V result matrix |

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