| Approximate Bayesian computation | abc abc,SimInf_model-method |
| Add information about spatial coupling between nodes to 'ldata' | add_spatial_coupling_to_ldata |
| Coerce to data frame | as.data.frame.SimInf_abc |
| Coerce events to a data frame | as.data.frame.SimInf_events |
| Coerce to data frame | as.data.frame.SimInf_individual_events |
| Coerce to data frame | as.data.frame.SimInf_pmcmc |
| Box plot of number of individuals in each compartment | boxplot,SimInf_model-method |
| Extract the C code from a 'SimInf_model' object | C_code |
| Run more generations of ABC SMC | continue_abc continue_abc,SimInf_abc-method |
| Run more iterations of PMCMC | continue_pmcmc continue_pmcmc,SimInf_pmcmc-method |
| Create a distance matrix between nodes for spatial models | distance_matrix |
| Convert an edge list with properties to a matrix | edge_properties_to_matrix |
| Extract the events from a 'SimInf_model' object | events events,SimInf_model-method |
| Example data to initialize events for the 'SEIR' model | events_SEIR |
| Example data to initialize events for the 'SIR' model | events_SIR |
| Example data to initialize events for the 'SIS' model | events_SIS |
| Example data to initialize events for the 'SISe' model | events_SISe |
| Example data to initialize events for the 'SISe3' model | events_SISe3 |
| Extract global data from a 'SimInf_model' object | gdata gdata,SimInf_model-method |
| Set a global data parameter for a 'SimInf_model' object | gdata<- gdata<-,SimInf_model-method |
| Extract individuals from 'SimInf_individual_events' | get_individuals get_individuals,SimInf_individual_events-method |
| Determine in-degree for each node in a model | indegree |
| Individual events | individual_events |
| Lambert W0 function | lambertW0 |
| Extract local data from a node | ldata ldata,SimInf_model-method |
| Length of the MCMC chain | length,SimInf_pmcmc-method |
| Log likelihood | logLik,SimInf_pfilter-method |
| Model parser to define new models to run in 'SimInf' | mparse |
| Determine the number of compartments in a model | n_compartments n_compartments,SimInf_model-method |
| Determine the number of generations | n_generations n_generations,SimInf_abc-method |
| Determine the number of nodes in a model | n_nodes n_nodes,SimInf_model-method n_nodes,SimInf_pfilter-method n_nodes,SimInf_pmcmc-method |
| Determine the number of replicates in a model | n_replicates n_replicates,SimInf_model-method |
| Transform individual events to node events for a model | node_events node_events,SimInf_individual_events-method |
| Example data with spatial distribution of nodes | nodes |
| Determine out-degree for each node in a model | outdegree |
| Create a package skeleton from a 'SimInf_model' | package_skeleton |
| Scatterplot of number of individuals in each compartment | pairs,SimInf_model-method |
| Bootstrap particle filter | pfilter pfilter,SimInf_model-method |
| Display the ABC posterior distribution | plot,SimInf_abc-method |
| Display the distribution of scheduled events over time | plot,SimInf_events-method |
| Display the distribution of individual events over time | plot,SimInf_individual_events-method |
| Display the outcome from a simulated trajectory | plot,SimInf_model-method |
| Diagnostic plot of a particle filter object | plot,SimInf_pfilter-method |
| Display the PMCMC posterior distribution | plot,SimInf_pmcmc-method |
| Particle Markov chain Monte Carlo (PMCMC) algorithm | pmcmc pmcmc,SimInf_model-method |
| Generic function to calculate prevalence from trajectory data | prevalence |
| Calculate prevalence from a model object with trajectory data | prevalence,SimInf_model-method |
| Extract prevalence from running a particle filter | prevalence,SimInf_pfilter-method |
| Extract prevalence from fitting a PMCMC algorithm | prevalence,SimInf_pmcmc-method |
| Set a template for where to record result during a simulation | punchcard<- punchcard<-,SimInf_model-method |
| Run the SimInf stochastic simulation algorithm | run run,SEIR-method run,SimInf_abc-method run,SimInf_model-method run,SIR-method run,SIS-method run,SISe-method run,SISe3-method run,SISe3_sp-method run,SISe_sp-method |
| Create an SEIR model | SEIR |
| Definition of the 'SEIR' model | SEIR-class |
| Extract the select matrix from a 'SimInf_model' object | select_matrix select_matrix,SimInf_model-method |
| Set the select matrix for a 'SimInf_model' object | select_matrix<- select_matrix<-,SimInf_model-method |
| Specify the number of threads that SimInf should use | set_num_threads |
| Extract the shift matrix from a 'SimInf_model' object | shift_matrix shift_matrix,SimInf_model-method |
| Set the shift matrix for a 'SimInf_model' object | shift_matrix<- shift_matrix<-,SimInf_model-method |
| Print summary of a 'SimInf_abc' object | show,SimInf_abc-method |
| Brief summary of 'SimInf_events' | show,SimInf_events-method |
| Print summary of a 'SimInf_individual_events' object | show,SimInf_individual_events-method |
| Brief summary of 'SimInf_model' | show,SimInf_model-method |
| Brief summary of a 'SimInf_pfilter' object | show,SimInf_pfilter-method |
| Brief summary of a 'SimInf_pmcmc' object | show,SimInf_pmcmc-method |
| A Framework for Data-Driven Stochastic Disease Spread Simulations | SimInf-package SimInf |
| Class '"SimInf_abc"' | SimInf_abc-class |
| Create a 'SimInf_events' object | SimInf_events |
| Class '"SimInf_events"' | SimInf_events-class |
| Class '"SimInf_individual_events"' | SimInf_individual_events-class |
| Create a 'SimInf_model' | SimInf_model |
| Class '"SimInf_model"' | SimInf_model-class |
| Class '"SimInf_pfilter"' | SimInf_pfilter-class |
| Class '"SimInf_pmcmc"' | SimInf_pmcmc-class |
| Create an SIR model | SIR |
| Definition of the SIR model | SIR-class |
| Create an SIS model | SIS |
| Definition of the SIS model | SIS-class |
| Create a SISe model | SISe |
| Create a 'SISe_sp' model | SISe_sp |
| Definition of the 'SISe_sp' model | SISe_sp-class |
| Definition of the 'SISe' model | SISe-class |
| Create a 'SISe3' model | SISe3 |
| Create an 'SISe3_sp' model | SISe3_sp |
| Definition of the 'SISe3_sp' model | SISe3_sp-class |
| Definition of the 'SISe3' model | SISe3-class |
| Detailed summary of a 'SimInf_abc' object | summary,SimInf_abc-method |
| Detailed summary of a 'SimInf_events' object | summary,SimInf_events-method |
| Detailed summary of a 'SimInf_individual_events' object | summary,SimInf_individual_events-method |
| Detailed summary of a 'SimInf_model' object | summary,SimInf_model-method |
| Detailed summary of a 'SimInf_pfilter' object | summary,SimInf_pfilter-method |
| Detailed summary of a 'SimInf_pmcmc' object | summary,SimInf_pmcmc-method |
| Generic function to extract data from a simulated trajectory | trajectory |
| Extract data from a simulated trajectory | trajectory,SimInf_model-method |
| Extract filtered trajectory from running a particle filter | trajectory,SimInf_pfilter-method |
| Extract filtered trajectories from fitting a PMCMC algorithm | trajectory,SimInf_pmcmc-method |
| Get the initial compartment state | u0 u0,SimInf_individual_events-method u0,SimInf_model-method |
| Example data to initialize the 'SEIR' model | u0_SEIR |
| Example data to initialize the 'SIR' model | u0_SIR |
| Example data to initialize the 'SIS' model | u0_SIS |
| Example data to initialize the 'SISe' model | u0_SISe |
| Example data to initialize the 'SISe3' model | u0_SISe3 |
| Update the initial compartment state u0 in each node | u0<- u0<-,SimInf_model-method |
| Update the initial continuous state v0 in each node | v0<- v0<-,SimInf_model-method |
