C_code                  Extract the C code from a 'SimInf_model' object
SEIR                    Create an SEIR model
SEIR-class              Class SEIR
SIR                     Create an SIR model
SIR-class               Class SIR
SIS                     Create an SIS model
SIS-class               Class SIS
SISe                    Create an SISe model
SISe-class              Class SISe
SISe3                   Create a 'SISe3' model
SISe3-class             Class SISe3
SISe3_sp                Create an SISe3_sp model
SISe3_sp-class          Class SISe3_sp
SISe_sp                 Create an SISe_sp model
SISe_sp-class           Class SISe_sp
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_individual_events-class
                        Class 'SimInf_individual_events'
SimInf_model            Create a 'SimInf_model' object
SimInf_model-class      Class 'SimInf_model'
SimInf_pfilter-class    Class 'SimInf_pfilter'
SimInf_pmcmc-class      Class 'SimInf_pmcmc'
abc                     Approximate Bayesian computation
add_spatial_coupling_to_ldata
                        Add spatial coupling information to local data
as.data.frame.SimInf_abc
                        Coerce a 'SimInf_abc' object to a 'data.frame'
as.data.frame.SimInf_events
                        Coerce a 'SimInf_events' object to a
                        'data.frame'
as.data.frame.SimInf_individual_events
                        Coerce a 'SimInf_individual_events' object to a
                        'data.frame'
as.data.frame.SimInf_pmcmc
                        Coerce a 'SimInf_pmcmc' object to a
                        'data.frame'
boxplot,SimInf_model-method
                        Box plot of number of individuals in each
                        compartment
continue_abc            Run more generations of ABC SMC
continue_pmcmc          Continue PMCMC from an Existing Chain
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 scheduled events from a
                        'SimInf_model' object
events_SEIR             Example event data for the SEIR model with
                        cattle herds
events_SIR              Example event data for the SIR model with
                        cattle herds
events_SIS              Example event data for the SIS model with
                        cattle herds
events_SISe3            Example event data for the SISe3 model with
                        cattle herds
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_individual_events'
indegree                Determine in-degree for each node in a model
individual_events       Individual events
lambertW0               Lambert W0 function
ldata                   Extract local data from a node
length,SimInf_pmcmc-method
                        Length of the MCMC chain
logLik,SimInf_pfilter-method
                        Extract Log-Likelihood
mparse                  Model parser to define new models for 'SimInf'
n_compartments          Determine the number of compartments in a model
n_generations           Determine the number of generations in an ABC
                        analysis
n_nodes                 Determine the number of nodes in a model
n_replicates            Determine the number of replicates 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 matrix 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_individual_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
plot,SimInf_pmcmc-method
                        Display the PMCMC posterior distribution
pmcmc                   Particle Markov chain Monte Carlo (PMCMC)
                        algorithm
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
prevalence,SimInf_pmcmc-method
                        Extract prevalence from fitting a PMCMC
                        algorithm
punchcard<-             Set a sparse recording template for simulation
                        results
run                     Run a SimInf model simulation
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
                        Brief summary of a 'SimInf_abc' object
show,SimInf_events-method
                        Brief summary of a 'SimInf_events' object
show,SimInf_individual_events-method
                        Brief summary of a 'SimInf_individual_events'
                        object
show,SimInf_model-method
                        Brief summary of a 'SimInf_model' object
show,SimInf_pfilter-method
                        Brief summary of a 'SimInf_pfilter' object
show,SimInf_pmcmc-method
                        Brief summary of a 'SimInf_pmcmc' 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_individual_events-method
                        Detailed summary of a
                        'SimInf_individual_events' object
summary,SimInf_model-method
                        Detailed summary of a 'SimInf_model' object
summary,SimInf_pfilter-method
                        Detailed summary of a 'SimInf_pfilter' object
summary,SimInf_pmcmc-method
                        Detailed summary of a 'SimInf_pmcmc' 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') in
                        each node
u0<-                    Update the initial compartment state ('u0') in
                        each node
u0_SEIR                 Example initial population data for the SEIR
                        model
u0_SIR                  Example initial population data for the SIR
                        model
u0_SIS                  Example initial population data for the SIS
                        model
u0_SISe3                Example initial population data for the SISe3
                        model
u0_from_individual_events
                        Derive the initial compartment state from
                        individual events
v0<-                    Update the initial continuous state ('v0') in
                        each node
