C_code                  Extract the C code from a 'SimInf_model' object
Nn                      Extract number of nodes in a model
SEIR                    Create an SEIR model
SEIR-class              Definition of the 'SEIR' model
SIR                     Create an SIR model
SIR-class               Definition of the SIR 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 a 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_events           Create a 'SimInf_events' object
SimInf_events-class     Class '"SimInf_events"'
SimInf_model            Create a 'SimInf_model'
SimInf_model-class      Class '"SimInf_model"'
U<-                     Set a template for where to write the U result
                        matrix
V<-                     Set a template for where to write the V result
                        matrix
boxplot,SimInf_model-method
                        Box plot of number of individuals in each
                        compartment
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 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'
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,SimInf_events-method
                        Display the distribution of scheduled events
                        over time
plot,SimInf_model-method
                        Display the outcome from a simulated trajectory
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
select_matrix           Extract the select matrix from a 'SimInf_model'
                        object
select_matrix<-         Set the select matrix for a 'SimInf_model'
                        object
shift_matrix            Extract the shift matrix from a 'SimInf_model'
                        object
shift_matrix<-          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'
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
