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

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.

AuthorStefan Widgren (National Veterinary Institute, Sweden), Pavol Bauer (Uppsala University, Sweden), Stefan Engblom (Uppsala University, Sweden)
Date of publication2017-01-29 18:59:07
MaintainerStefan Widgren <stefan.widgren@gmail.com>
LicenseGPL-3
Version3.0.0
https://github.com/stewid/SimInf

View on CRAN

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

is_wholenumber: Check if wholenumbers

plot-methods: Plot 'siminf_model'

plot_scheduled_events: Plot scheduled events

prevalence-methods: Prevalence

recovered-methods: Recovered

run-methods: Run 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"'

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

Functions

check_end_t_arg Man page
check_gdata_arg Man page
check_infectious_pressure_arg Man page
check_integer_arg Man page
demo_model Man page
distance_matrix Man page
events_SEIR Man page
events_SIR Man page
events_SISe3 Man page
have_openmp Man page
infected Man page
infected,SEIR-method Man page
infected,SIR-method Man page
infected,SISe3-method Man page
infected,SISe3_sp-method Man page
infected,SISe-method Man page
infected,SISe_sp-method Man page
is_wholenumber Man page
plot Man page
plot-methods Man page
plot_scheduled_events Man page
plot,scheduled_events-method Man page
plot,SEIR-method Man page
plot,siminf_model-method Man page
plot,SIR-method Man page
plot,SISe3-method Man page
plot,SISe3_sp-method Man page
plot,SISe-method Man page
plot,SISe_sp-method Man page
prevalence Man page
prevalence,SISe3-method Man page
prevalence,SISe3_sp-method Man page
prevalence,SISe-method Man page
prevalence,SISe_sp-method Man page
recovered Man page
recovered,SEIR-method Man page
recovered,SIR-method Man page
run Man page
run_outer Man page
run_outer,numeric,numeric,siminf_model-method Man page
run,siminf_model-method Man page
scheduled_events Man page
scheduled_events-class Man page
SEIR Man page
SEIR-class Man page
show,scheduled_events-method Man page
show,scheduled_events-methods Man page
show,siminf_model-method Man page
show,siminf_model-methods Man page
SimInf Man page
siminf_model Man page
siminf_model-class Man page
SimInf-package Man page
SIR Man page
SIR-class Man page
SISe Man page
SISe3 Man page
SISe3-class Man page
SISe3_sp Man page
SISe3_sp-class Man page
SISe-class Man page
SISe_sp Man page
SISe_sp-class Man page
summary,scheduled_events-method Man page
summary,scheduled_events-methods Man page
summary,siminf_model-method Man page
summary,siminf_model-methods Man page
susceptible Man page
susceptible,SEIR-method Man page
susceptible,SIR-method Man page
susceptible,SISe3-method Man page
susceptible,SISe3_sp-method Man page
susceptible,SISe-method Man page
susceptible,SISe_sp-method Man page
u0_SEIR Man page
u0_SIR Man page
u0_SISe3 Man page

Files

SimInf
SimInf/inst
SimInf/inst/CITATION
SimInf/configure.ac
SimInf/tests
SimInf/tests/siminf_model.R
SimInf/tests/SISe.R
SimInf/tests/phi.R
SimInf/tests/SIR.R
SimInf/tests/demo_model.R
SimInf/tests/SISe3.R
SimInf/tests/SISe3_sp.R
SimInf/tests/sample_select.R
SimInf/tests/SISe_sp.R
SimInf/tests/SEIR.R
SimInf/tests/ldata_sp.R
SimInf/tests/scheduled_events.R
SimInf/tests/measures.R
SimInf/tests/run_outer.R
SimInf/tests/siminf.R
SimInf/src
SimInf/src/core
SimInf/src/core/siminf_solver.h
SimInf/src/core/siminf_solver.c
SimInf/src/misc
SimInf/src/misc/siminf_local_spread.c
SimInf/src/misc/siminf_forward_euler_linear_decay.h
SimInf/src/misc/siminf_ldata.h
SimInf/src/misc/siminf_arg.h
SimInf/src/misc/siminf_arg.c
SimInf/src/misc/siminf_local_spread.h
SimInf/src/misc/siminf_ldata.c
SimInf/src/misc/siminf_forward_euler_linear_decay.c
SimInf/src/models
SimInf/src/models/SIR.c
SimInf/src/models/SISe3.c
SimInf/src/models/SISe.c
SimInf/src/models/SISe3_sp.c
SimInf/src/models/SISe_sp.c
SimInf/src/models/SEIR.c
SimInf/src/Makevars.in
SimInf/src/Makevars.win
SimInf/src/siminf.h
SimInf/src/siminf.c
SimInf/NAMESPACE
SimInf/NEWS
SimInf/data
SimInf/data/u0_SISe3.rda
SimInf/data/events_SISe3.rda
SimInf/data/datalist
SimInf/R
SimInf/R/siminf_model.R SimInf/R/AllGenerics.R SimInf/R/SISe.R SimInf/R/SIR.R SimInf/R/demo_model.R SimInf/R/SISe3.R SimInf/R/SISe3_sp.R SimInf/R/check_arguments.R SimInf/R/dependencies.R SimInf/R/SISe_sp.R SimInf/R/SimInf.R SimInf/R/SEIR.R
SimInf/R/dependencies.R.in
SimInf/R/scheduled_events.R SimInf/R/run_outer.R SimInf/R/distance.R
SimInf/MD5
SimInf/DESCRIPTION
SimInf/configure
SimInf/man
SimInf/man/check_end_t_arg.Rd SimInf/man/demo_model.Rd SimInf/man/SISe_sp-class.Rd SimInf/man/prevalence-methods.Rd SimInf/man/events_SIR.Rd SimInf/man/u0_SIR.Rd SimInf/man/plot-methods.Rd SimInf/man/u0_SEIR.Rd SimInf/man/infected-methods.Rd SimInf/man/SISe3_sp.Rd SimInf/man/summary-siminf_model-method.Rd SimInf/man/siminf_model-class.Rd SimInf/man/plot_scheduled_events.Rd SimInf/man/u0_SISe3.Rd SimInf/man/SISe3.Rd SimInf/man/check_gdata_arg.Rd SimInf/man/events_SISe3.Rd SimInf/man/events_SEIR.Rd SimInf/man/run-methods.Rd SimInf/man/is_wholenumber.Rd SimInf/man/SISe3-class.Rd SimInf/man/SEIR-class.Rd SimInf/man/scheduled_events.Rd SimInf/man/SEIR.Rd SimInf/man/SIR.Rd SimInf/man/SimInf.Rd SimInf/man/SISe_sp.Rd SimInf/man/have_openmp.Rd SimInf/man/SISe.Rd SimInf/man/scheduled_events-class.Rd SimInf/man/show-siminf_model-method.Rd SimInf/man/siminf_model.Rd SimInf/man/recovered-methods.Rd SimInf/man/SISe-class.Rd SimInf/man/show-scheduled_events-method.Rd SimInf/man/run_outer-methods.Rd SimInf/man/distance_matrix.Rd SimInf/man/check_integer_arg.Rd SimInf/man/SIR-class.Rd SimInf/man/SISe3_sp-class.Rd SimInf/man/susceptible-methods.Rd SimInf/man/summary-scheduled_events-method.Rd SimInf/man/check_infectious_pressure_arg.Rd
SimInf/configure.win
SimInf/cleanup
SimInf/cleanup.win

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.