Man pages for SimInf
A Framework for Data-Driven Stochastic Disease Spread Simulations
| abc | Approximate Bayesian computation |
| as.data.frame.SimInf_abc | Coerce to data frame |
| as.data.frame.SimInf_events | Coerce events to a data frame |
| as.data.frame.SimInf_indiv_events | Coerce to data frame |
| boxplot-SimInf_model-method | Box plot of number of individuals in each compartment |
| C_code | Extract the C code from a 'SimInf_model' object |
| continue | Run more generations of ABC SMC |
| distance_matrix | Create a distance matrix between nodes for spatial models |
| edge_properties_to_matrix | Convert an edge list with properties to a matrix |
| 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_SIS | Example data to initialize events for the 'SIS' 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 |
| get_individuals | Extract individuals from 'SimInf_indiv_events' |
| indegree | Determine in-degree for each node in a model |
| individual_events | Individual events |
| ldata | Extract local data from a node |
| logLik-SimInf_pfilter-method | Log likelihood |
| mparse | Model parser to define new models to run in 'SimInf' |
| n_generations | Determine the number of generations |
| n_nodes | Determine the number of nodes in a model |
| node_events | Transform individual events to node events for 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 |
| pfilter | Bootstrap particle filter |
| plot | Display the outcome from a simulated trajectory |
| plot-SimInf_abc-method | Display the ABC posterior distribution |
| plot-SimInf_events-method | Display the distribution of scheduled events over time |
| plot-SimInf_indiv_events-method | Display the distribution of individual events over time |
| plot-SimInf_pfilter-method | Diagnostic plot of a particle filter object |
| prevalence | Generic function to calculate prevalence from trajectory data |
| prevalence-SimInf_model-method | Calculate prevalence from a model object with trajectory data |
| prevalence-SimInf_pfilter-method | Extract prevalence from running a particle filter |
| punchcard-set | Set a template for where to record result during a simulation |
| run | Run the SimInf stochastic simulation algorithm |
| 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 |
| set_num_threads | Specify the number of threads that SimInf should use |
| 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_abc-method | Print summary of a 'SimInf_abc' object |
| show-SimInf_events-method | Brief summary of 'SimInf_events' |
| show-SimInf_indiv_events-method | Print summary of a 'SimInf_indiv_events' object |
| show-SimInf_model-method | Brief summary of 'SimInf_model' |
| show-SimInf_pfilter-method | Brief summary of a 'SimInf_pfilter' object |
| SimInf | A Framework for Data-Driven Stochastic Disease Spread... |
| SimInf_abc-class | Class '"SimInf_abc"' |
| SimInf_events | Create a 'SimInf_events' object |
| SimInf_events-class | Class '"SimInf_events"' |
| SimInf_indiv_events-class | Class '"SimInf_indiv_events"' |
| SimInf_model | Create a 'SimInf_model' |
| SimInf_model-class | Class '"SimInf_model"' |
| SimInf_pfilter-class | Class '"SimInf_pfilter"' |
| SIR | Create an SIR model |
| SIR-class | Definition of the SIR model |
| SIS | Create an SIS model |
| SIS-class | Definition of the SIS model |
| SISe | Create a SISe model |
| SISe3 | Create a 'SISe3' model |
| SISe3-class | Definition of the 'SISe3' model |
| SISe3_sp | Create an '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_abc-method | Detailed summary of a 'SimInf_abc' object |
| summary-SimInf_events-method | Detailed summary of a 'SimInf_events' object |
| summary-SimInf_indiv_events-method | Detailed summary of a 'SimInf_indiv_events' object |
| summary-SimInf_model-method | Detailed summary of a 'SimInf_model' object |
| summary-SimInf_pfilter-method | Detailed summary of a 'SimInf_pfilter' object |
| trajectory | Generic function to extract data from a simulated trajectory |
| trajectory-SimInf_model-method | Extract data from a simulated trajectory |
| trajectory-SimInf_pfilter-method | Extract filtered trajectory from running a particle filter |
| u0 | Get the initial compartment state |
| u0_SEIR | Example data to initialize the 'SEIR' model |
| u0-set | Update the initial compartment state u0 in each node |
| u0_SIR | Example data to initialize the 'SIR' model |
| u0_SIS | Example data to initialize the 'SIS' model |
| u0_SISe | Example data to initialize the 'SISe' model |
| u0_SISe3 | Example data to initialize the 'SISe3' model |
| v0-set | Update the initial continuous state v0 in each node |
