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 publication2016-05-04 07:56:46
MaintainerStefan Widgren <stefan.widgren@gmail.com>
LicenseGPL-3
Version2.0.0
https://github.com/stewid/SimInf

View on CRAN

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

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

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