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

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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.

Author
Stefan Widgren (National Veterinary Institute, Sweden), Pavol Bauer (Uppsala University, Sweden), Stefan Engblom (Uppsala University, Sweden)
Date of publication
2016-05-04 07:56:46
Maintainer
Stefan Widgren <stefan.widgren@gmail.com>
License
GPL-3
Version
2.0.0
URLs

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_SISe3
Scheduled events example data
have_openmp
Is OpenMP available
infected-methods
Infected
is_wholenumber
Check if wholenumbers
plot-methods
Plot 'siminf_model'
prevalence-methods
Prevalence
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"'
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"'
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_SISe3
Example data to initialize a model

Files in this package

SimInf
SimInf/configure.ac
SimInf/tests
SimInf/tests/siminf_model.R
SimInf/tests/SISe.R
SimInf/tests/phi.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/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_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_ldata.c
SimInf/src/misc/siminf_forward_euler_linear_decay.c
SimInf/src/models
SimInf/src/models/SISe3.c
SimInf/src/models/SISe.c
SimInf/src/models/SISe3_sp.c
SimInf/src/models/SISe_sp.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/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/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/plot-methods.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/u0_SISe3.Rd
SimInf/man/SISe3.Rd
SimInf/man/check_gdata_arg.Rd
SimInf/man/events_SISe3.Rd
SimInf/man/run-methods.Rd
SimInf/man/is_wholenumber.Rd
SimInf/man/SISe3-class.Rd
SimInf/man/scheduled_events.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/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/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