C_code                  Extract the C code from a 'SimInf_model' object
SEIR                    Create an SEIR model
SEIR-class              Definition of the 'SEIR' model
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
SISe-class              Definition of the '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_sp                 Create a 'SISe_sp' model
SISe_sp-class           Definition of the 'SISe_sp' model
SimInf                  A Framework for Data-Driven Stochastic Disease
                        Spread Simulations
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"'
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
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 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,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_model-method
                        Display the outcome from a simulated trajectory
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 a template for where to record result
                        during a simulation
run                     Run the SimInf stochastic simulation algorithm
select_matrix           Extract the select matrix from a 'SimInf_model'
                        object
select_matrix<-         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 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
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<-                    Update the initial compartment state u0 in each
                        node
u0_SEIR                 Example data to initialize the 'SEIR' model
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<-                    Update the initial continuous state v0 in each
                        node
