A Framework for Data-Driven Stochastic Disease Spread Simulations


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Documentation for package ‘SimInf’ version 8.4.0

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abc Approximate Bayesian computation
abc-method Approximate Bayesian computation
abc_accept Return result for ABC whether the particles match the data
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_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
mparse Model parser to define new models to run in 'SimInf'
nodes Example data with spatial distribution of nodes
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
plot-method Display the ABC posterior distribution
plot-method Display the distribution of scheduled events over time
plot-method Display the outcome from a simulated trajectory
prevalence Calculate prevalence from a model object with 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'
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"'
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 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
trajectory Extract data from a simulated trajectory
trajectory-method 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