A Framework for Data-Driven Stochastic Disease Spread Simulations

Documentation for package ‘SimInf’ version 11.1.0

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A Framework for Data-Driven Stochastic Disease Spread Simulations

-- A --

abc	Approximate Bayesian computation
abc-method	Approximate Bayesian computation
add_spatial_coupling_to_ldata	Add spatial coupling information to local data
as.data.frame.SimInf_abc	Coerce a 'SimInf_abc' object to a 'data.frame'
as.data.frame.SimInf_events	Coerce a 'SimInf_events' object to a 'data.frame'
as.data.frame.SimInf_individual_events	Coerce a 'SimInf_individual_events' object to a 'data.frame'
as.data.frame.SimInf_pmcmc	Coerce a 'SimInf_pmcmc' object to a 'data.frame'

-- B --

boxplot-method

Box plot of number of individuals in each compartment

-- C --

continue_abc	Run more generations of ABC SMC
continue_abc-method	Run more generations of ABC SMC
continue_pmcmc	Continue PMCMC from an Existing Chain
continue_pmcmc-method	Continue PMCMC from an Existing Chain
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 scheduled events from a 'SimInf_model' object
events-method	Extract the scheduled events from a 'SimInf_model' object
events_SEIR	Example event data for the SEIR model with cattle herds
events_SIR	Example event data for the SIR model with cattle herds
events_SIS	Example event data for the SIS model with cattle herds
events_SISe3	Example event data for the SISe3 model with cattle herds

-- 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_individual_events'
get_individuals-method	Extract individuals from 'SimInf_individual_events'

-- I --

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

-- L --

lambertW0	Lambert W0 function
ldata	Extract local data from a node
ldata-method	Extract local data from a node
length-method	Length of the MCMC chain
logLik-method	Extract Log-Likelihood

-- M --

mparse

Model parser to define new models for '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_compartments	Determine the number of compartments in a model
n_compartments-method	Determine the number of compartments in a model
n_generations	Determine the number of generations in an ABC analysis
n_generations-method	Determine the number of generations in an ABC analysis
n_nodes	Determine the number of nodes in a model
n_nodes-method	Determine the number of nodes in a model
n_replicates	Determine the number of replicates in a model
n_replicates-method	Determine the number of replicates 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 matrix 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 PMCMC posterior distribution
plot-method	Display the outcome from a simulated trajectory
pmcmc	Particle Markov chain Monte Carlo (PMCMC) algorithm
pmcmc-method	Particle Markov chain Monte Carlo (PMCMC) algorithm
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
prevalence-method	Extract prevalence from fitting a PMCMC algorithm
punchcard<-	Set a sparse recording template for simulation results
punchcard<--method	Set a sparse recording template for simulation results

-- R --

run	Run a SimInf model simulation
run-method	Run a SimInf model simulation

-- S --

SEIR	Create an SEIR model
SEIR-class	Class SEIR
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	Brief summary of a 'SimInf_abc' object
show-method	Brief summary of a 'SimInf_events' object
show-method	Brief summary of a 'SimInf_individual_events' object
show-method	Brief summary of a 'SimInf_model' object
show-method	Brief summary of a 'SimInf_pfilter' object
show-method	Brief summary of a 'SimInf_pmcmc' 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_individual_events-class	Class 'SimInf_individual_events'
SimInf_model	Create a 'SimInf_model' object
SimInf_model-class	Class 'SimInf_model'
SimInf_pfilter-class	Class 'SimInf_pfilter'
SimInf_pmcmc-class	Class 'SimInf_pmcmc'
SIR	Create an SIR model
SIR-class	Class SIR
SIS	Create an SIS model
SIS-class	Class SIS
SISe	Create an SISe model
SISe-class	Class SISe
SISe3	Create a 'SISe3' model
SISe3-class	Class SISe3
SISe3_sp	Create an SISe3_sp model
SISe3_sp-class	Class SISe3_sp
SISe_sp	Create an SISe_sp model
SISe_sp-class	Class SISe_sp
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_individual_events' object
summary-method	Detailed summary of a 'SimInf_model' object
summary-method	Detailed summary of a 'SimInf_pfilter' object
summary-method	Detailed summary of a 'SimInf_pmcmc' 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') in each node
u0-method	Get the initial compartment state ('u0') in each node
u0<-	Update the initial compartment state ('u0') in each node
u0<--method	Update the initial compartment state ('u0') in each node
u0_from_individual_events	Derive the initial compartment state from individual events
u0_from_individual_events-method	Derive the initial compartment state from individual events
u0_SEIR	Example initial population data for the SEIR model
u0_SIR	Example initial population data for the SIR model
u0_SIS	Example initial population data for the SIS model
u0_SISe3	Example initial population data for 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