# A Framework for Data-Driven Stochastic Disease Spread Simulations

## Documentation for package ‘SimInf’ version 9.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

abc | Approximate Bayesian computation
abc-method | Approximate Bayesian computation
as.data.frame.SimInf_abc | Coerce to data frame
as.data.frame.SimInf_events | Coerce events to a data frame
boxplot-method | Box plot of number of individuals in each compartment
continue | Run more generations of ABC SMC
continue-method | Run more generations of ABC SMC
C_code | Extract the C code from a 'SimInf_model' object
distance_matrix | Create a distance matrix between nodes for spatial models
events | Extract the events from a 'SimInf_model' object
events-method | 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-method | Extract global data from a 'SimInf_model' object
gdata<- | Set a global data parameter for a 'SimInf_model' object
gdata<--method | 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
ldata-method | Extract local data from a node
logLik-method | Log likelihood
mparse | Model parser to define new models to run in 'SimInf'
nodes | Example data with spatial distribution of nodes
n_generations | Determine the number of generations
n_generations-method | Determine the number of generations
n_nodes | Determine the number of nodes in a model
n_nodes-method | Determine the number of nodes in a model
outdegree | Determine out-degree for each node in a model
package_skeleton | Create a package skeleton from a 'SimInf_model'
pairs-method | Scatterplot of number of individuals in each compartment
pfilter | Bootstrap particle filter
pfilter-method | Bootstrap particle filter
plot-method | Display the ABC posterior distribution
plot-method | Display the distribution of scheduled events over time
plot-method | Diagnostic plot of a particle filter object
plot-method | Display the outcome from a simulated trajectory
prevalence | Generic function to calculate prevalence from trajectory data
prevalence-method | Calculate prevalence from a model object with trajectory data
punchcard<- | Set a template for where to record result during a simulation
punchcard<--method | Set a template for where to record result during a simulation
run | Run the SimInf stochastic simulation algorithm
run-method | 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-method | Extract the select matrix from a 'SimInf_model' object
select_matrix<- | Set the select matrix for a 'SimInf_model' object
select_matrix<--method | 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-method | Extract the shift matrix from a 'SimInf_model' object
shift_matrix<- | Set the shift matrix for a 'SimInf_model' object
shift_matrix<--method | Set the shift matrix for a 'SimInf_model' object
show-method | Print summary of a 'SimInf_abc' object
show-method | Brief summary of 'SimInf_events'
show-method | Brief summary of 'SimInf_model'
show-method | Brief summary of a 'SimInf_pfilter' object
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_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
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
summary-method | Detailed summary of a 'SimInf_abc' object
summary-method | Detailed summary of a 'SimInf_events' object
summary-method | Detailed summary of a 'SimInf_model' object
summary-method | Detailed summary of a 'SimInf_pfilter' object
trajectory | Generic function to extract data from a simulated trajectory
trajectory-method | Extract data from a simulated trajectory
trajectory-method | Extract filtered trajectory from running a particle filter
u0 | Get the initial compartment state
u0-method | Get the initial compartment state
u0<- | Update the initial compartment state u0 in each node
u0<--method | 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
v0<--method | Update the initial continuous state v0 in each node