A Framework for Data-Driven Stochastic Disease Spread Simulations

Documentation for package ‘SimInf’ version 9.7.0

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A Framework for Data-Driven Stochastic Disease Spread Simulations

-- A --

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
as.data.frame.SimInf_indiv_events	Coerce to data frame

-- B --

boxplot-method

Box plot of number of individuals in each compartment

-- C --

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

-- D --

distance_matrix

Create a distance matrix between nodes for spatial models

-- E --

edge_properties_to_matrix	Convert an edge list with properties to a matrix
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

-- G --

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
get_individuals	Extract individuals from 'SimInf_indiv_events'
get_individuals-method	Extract individuals from 'SimInf_indiv_events'

-- I --

indegree	Determine in-degree for each node in a model
individual_events	Individual events

-- L --

ldata	Extract local data from a node
ldata-method	Extract local data from a node
logLik-method	Log likelihood

-- M --

mparse

Model parser to define new models to run in 'SimInf'

-- N --

nodes	Example data with spatial distribution of nodes
node_events	Transform individual events to node events for a model
node_events-method	Transform individual events to node events for a model
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

-- O --

outdegree

Determine out-degree for each node in a model

-- P --

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	Display the distribution of individual 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
prevalence-method	Extract prevalence from running a particle filter
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

-- R --

run	Run the SimInf stochastic simulation algorithm
run-method	Run the SimInf stochastic simulation algorithm

-- S --

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	Print summary of a 'SimInf_indiv_events' object
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_indiv_events-class	Class '"SimInf_indiv_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_indiv_events' object
summary-method	Detailed summary of a 'SimInf_model' object
summary-method	Detailed summary of a 'SimInf_pfilter' object

-- T --

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

-- U --

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

-- V --

v0<-	Update the initial continuous state v0 in each node
v0<--method	Update the initial continuous state v0 in each node