A Framework for Data-Driven Stochastic Disease Spread Simulations

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Documentation for package ‘SimInf’ version 4.0.0

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SimInf-package A Framework for Stochastic Disease Spread Simulations
demo_model Generate a model for demonstration
distance_matrix Create distance matrix
events_SEIR Scheduled events example data for the 'SEIR' model
events_SIR Scheduled events example data for the 'SIR' model
events_SISe3 Scheduled events example data
infected Infected
infected-method Infected
init Init a 'SimInf_mparse' object
init-method Init a 'SimInf_mparse' object
mparse Model parser
plot Plot 'scheduled_events'
plot-method Plot 'scheduled_events'
plot-methods Plot 'scheduled_events'
prevalence Prevalence
prevalence-method Prevalence
recovered Recovered
recovered-method Recovered
run Run the SimInf stochastic simulation algorithm
run-method Run the SimInf stochastic simulation algorithm
run_outer Run 'SimInf_model' on scaled parameters
run_outer-method Run 'SimInf_model' on scaled parameters
scheduled_events Create a '"scheduled_events"' object
scheduled_events-class Class '"scheduled_events"'
SEIR Create a SEIR model
SEIR-class Class '"SEIR"'
show,scheduled_events-methods Brief summary of 'scheduled_events'
show,SimInf_model-methods Brief summary of 'SimInf_model'
show-method Brief summary of 'SimInf_model'
show-method Brief summary of 'scheduled_events'
SimInf A Framework for Stochastic Disease Spread Simulations
SimInf_model Create a 'SimInf_model'
SimInf_model-class Class '"SimInf_model"'
SimInf_mparse-class Class '"SimInf_mparse"'
SIR Create a SIR model
SIR-class Class '"SIR"'
SISe Create a SISe model
SISe-class Class '"SISe"'
SISe3 Create a SISe3 model
SISe3-class Class '"SISe3"'
SISe3_sp Create a SISe3_sp model
SISe3_sp-class Class '"SISe3_sp"'
SISe_sp Create a 'SISe_sp' model
SISe_sp-class Class '"SISe_sp"'
summary,scheduled_events-methods Summary of 'scheduled_events'
summary,SimInf_model-methods Summary of 'SimInf_model'
summary-method Summary of 'SimInf_model'
summary-method Summary of 'scheduled_events'
susceptible Susceptible
susceptible-method Susceptible
U Extract the number of individuals in each compartment
U-method Extract the number of individuals in each compartment
u0_SEIR Example data to initialize the 'SEIR' model
u0_SIR Example data to initialize the 'SIR' model
u0_SISe3 Example data to initialize a model
U<- Set a template for where to write the U result matrix
U<--method Set a template for where to write the U result matrix
V Extract the continuous state variables
V-method Extract the continuous state variables
V<- Set a template for where to write the V result matrix
V<--method Set a template for where to write the V result matrix