SimInf: A Framework for Data-Driven Stochastic Disease Spread Simulations
Version 4.0.0

Livestock movements are important for the spread of many infectious diseases between herds. The package provides an efficient and flexible framework for stochastic disease spread modelling that integrates within-herd disease dynamics as continuous-time Markov chains and livestock movements between herds as scheduled events. The core simulation solver is implemented in C and uses 'OpenMP' (if available) to divide work over multiple processors. The package contains template models and can be extended with user defined models.

Browse man pages Browse package API and functions Browse package files

AuthorStefan Widgren (National Veterinary Institute, Sweden), Pavol Bauer (Uppsala University, Sweden), Stefan Engblom (Uppsala University, Sweden)
Date of publication2017-03-21 06:50:24 UTC
MaintainerStefan Widgren <stefan.widgren@gmail.com>
LicenseGPL-3
Version4.0.0
URL https://github.com/stewid/SimInf
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SimInf")

Man pages

check_end_t_arg: Check arguments for interval endpoints
check_gdata_arg: Check arguments for 'gdata'
check_infectious_pressure_arg: Check integer arguments
check_integer_arg: Check integer arguments
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
have_openmp: Is OpenMP available
infected-methods: Infected
init-methods: Init a 'SimInf_mparse' object
is_wholenumber: Check if wholenumbers
mparse: Model parser
plot-methods: Plot 'scheduled_events'
plot_scheduled_events: Plot scheduled events
prevalence-methods: Prevalence
recovered-methods: Recovered
run-methods: Run the SimInf stochastic simulation algorithm
run_outer-methods: 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-method: Brief summary of 'scheduled_events'
show-SimInf_model-method: Brief summary of 'SimInf_model'
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
SISe3: Create a SISe3 model
SISe3-class: Class '"SISe3"'
SISe3_sp: Create a SISe3_sp model
SISe3_sp-class: Class '"SISe3_sp"'
SISe-class: Class '"SISe"'
SISe_sp: Create a 'SISe_sp' model
SISe_sp-class: Class '"SISe_sp"'
summary-scheduled_events-method: Summary of 'scheduled_events'
summary-SimInf_model-method: Summary of 'SimInf_model'
susceptible-methods: Susceptible
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-methods: Extract the number of individuals in each compartment
U_set-methods: Set a template for where to write the U result matrix
V-methods: Extract the continuous state variables
V_set-methods: Set a template for where to write the V result matrix

Functions

C_code_mparse Source code
C_compartments Source code
C_heading Source code
C_include Source code
C_ptsFun Source code
C_rate_constants Source code
C_run Source code
C_trFun Source code
Nc Source code
Nd Source code
Nn Source code
Nt Source code
SEIR Man page Source code
SEIR-class Man page
SIR Man page Source code
SIR-class Man page
SISe Man page Source code
SISe-class Man page
SISe3 Man page Source code
SISe3-class Man page
SISe3_sp Man page Source code
SISe3_sp-class Man page
SISe_sp Man page Source code
SISe_sp-class Man page
SimInf Man page
SimInf-package Man page
SimInf_model Man page Source code
SimInf_model-class Man page
SimInf_mparse-class Man page
U Man page
U,SimInf_model-method Man page
U<- Man page
U<-,SimInf_model-method Man page
V Man page
V,SimInf_model-method Man page
V<- Man page
V<-,SimInf_model-method Man page
check_end_t_arg Man page Source code
check_gdata_arg Man page Source code
check_infectious_pressure_arg Man page Source code
check_integer_arg Man page Source code
demo_model Man page Source code
distance_matrix Man page Source code
events_SEIR Man page Source code
events_SIR Man page Source code
events_SISe3 Man page
have_openmp Man page Source code
infected Man page
infected,SEIR-method Man page
infected,SIR-method Man page
infected,SISe-method Man page
infected,SISe3-method Man page
infected,SISe3_sp-method Man page
infected,SISe_sp-method Man page
init Man page
init,SimInf_mparse-method Man page
is_wholenumber Man page Source code
mparse Man page Source code
onUnload Source code
plot Man page Man page Man page Man page Man page Man page Man page Man page
plot,SEIR-method Man page
plot,SIR-method Man page
plot,SISe-method Man page
plot,SISe3-method Man page
plot,SISe3_sp-method Man page
plot,SISe_sp-method Man page
plot,SimInf_model-method Man page
plot,scheduled_events-method Man page
plot-methods Man page Man page Man page Man page Man page Man page Man page Man page
plot_scheduled_events Man page Source code
prevalence Man page
prevalence,SISe-method Man page
prevalence,SISe3-method Man page
prevalence,SISe3_sp-method Man page
prevalence,SISe_sp-method Man page
recovered Man page
recovered,SEIR-method Man page
recovered,SIR-method Man page
rewriteprop Source code
run Man page
run,SimInf_model-method Man page
run_outer Man page
run_outer,numeric,numeric,SimInf_model-method Man page
scheduled_events Man page Source code
scheduled_events-class Man page
show,SimInf_model-method Man page
show,SimInf_model-methods Man page
show,scheduled_events-method Man page
show,scheduled_events-methods Man page
show_U Source code
show_V Source code
summary,SimInf_model-method Man page
summary,SimInf_model-methods Man page
summary,scheduled_events-method Man page
summary,scheduled_events-methods Man page
susceptible Man page
susceptible,SEIR-method Man page
susceptible,SIR-method Man page
susceptible,SISe-method Man page
susceptible,SISe3-method Man page
susceptible,SISe3_sp-method Man page
susceptible,SISe_sp-method Man page
u0_SEIR Man page Source code
u0_SIR Man page Source code
u0_SISe3 Man page

Files

inst
inst/CITATION
inst/include
inst/include/SimInf.h
configure.ac
tests
tests/siminf_model.R
tests/SISe.R
tests/phi.R
tests/SIR.R
tests/demo_model.R
tests/SISe3.R
tests/SISe3_sp.R
tests/sample_select.R
tests/sparse.R
tests/SISe_sp.R
tests/SEIR.R
tests/ldata_sp.R
tests/scheduled_events.R
tests/measures.R
tests/run_outer.R
tests/siminf.R
src
src/core
src/core/siminf_solver.h
src/core/siminf_solver.c
src/misc
src/misc/siminf_local_spread.c
src/misc/siminf_forward_euler_linear_decay.h
src/misc/siminf_ldata.h
src/misc/siminf_arg.h
src/misc/siminf_arg.c
src/misc/siminf_local_spread.h
src/misc/siminf_ldata.c
src/misc/siminf_forward_euler_linear_decay.c
src/models
src/models/SIR.c
src/models/SISe3.c
src/models/SISe.c
src/models/SISe3_sp.c
src/models/SISe_sp.c
src/models/SEIR.c
src/SimInf.c
src/Makevars.in
src/SimInf.h
src/Makevars.win
src/init.c
NAMESPACE
NEWS
data
data/u0_SISe3.rda
data/events_SISe3.rda
data/datalist
R
R/AllGenerics.R
R/SISe.R
R/SIR.R
R/demo_model.R
R/SISe3.R
R/SISe3_sp.R
R/check_arguments.R
R/SimInf_model.R
R/SISe_sp.R
R/SimInf.R
R/SEIR.R
R/model_builder.R
R/scheduled_events.R
R/run_outer.R
R/distance.R
MD5
DESCRIPTION
configure
man
man/check_end_t_arg.Rd
man/demo_model.Rd
man/SISe_sp-class.Rd
man/U-methods.Rd
man/prevalence-methods.Rd
man/events_SIR.Rd
man/u0_SIR.Rd
man/plot-methods.Rd
man/V_set-methods.Rd
man/u0_SEIR.Rd
man/infected-methods.Rd
man/SISe3_sp.Rd
man/plot_scheduled_events.Rd
man/u0_SISe3.Rd
man/SISe3.Rd
man/SimInf_mparse-class.Rd
man/check_gdata_arg.Rd
man/events_SISe3.Rd
man/mparse.Rd
man/events_SEIR.Rd
man/SimInf_model-class.Rd
man/run-methods.Rd
man/is_wholenumber.Rd
man/U_set-methods.Rd
man/SimInf_model.Rd
man/SISe3-class.Rd
man/SEIR-class.Rd
man/scheduled_events.Rd
man/V-methods.Rd
man/SEIR.Rd
man/SIR.Rd
man/SimInf.Rd
man/summary-SimInf_model-method.Rd
man/SISe_sp.Rd
man/have_openmp.Rd
man/SISe.Rd
man/scheduled_events-class.Rd
man/recovered-methods.Rd
man/SISe-class.Rd
man/init-methods.Rd
man/show-scheduled_events-method.Rd
man/run_outer-methods.Rd
man/show-SimInf_model-method.Rd
man/distance_matrix.Rd
man/check_integer_arg.Rd
man/SIR-class.Rd
man/SISe3_sp-class.Rd
man/susceptible-methods.Rd
man/summary-scheduled_events-method.Rd
man/check_infectious_pressure_arg.Rd
configure.win
cleanup
cleanup.win
SimInf documentation built on May 19, 2017, 8:39 p.m.