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SimInf  

A Framework for Data-Driven Stochastic Disease Spread Simulations
View on CRAN: Click here


Download and install SimInf package within the R console
Install from CRAN:
install.packages("SimInf")

Install from Github:
library("remotes")
install_github("cran/SimInf")

Install by package version:
library("remotes")
install_version("SimInf", "9.7.0")



Attach the package and use:
library("SimInf")
Maintained by
Stefan Widgren
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-01-08
Latest Update: 2023-12-20
Description:
Provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and 'OpenMP' (if available) to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make the package extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. The package contains template models and can be extended with user-defined models. For more details see the paper by Widgren, Bauer, Eriksson and Engblom (2019) <doi:10.18637/jss.v091.i12>. The package also provides functionality to fit models to time series data using the Approximate Bayesian Computation Sequential Monte Carlo ('ABC-SMC') algorithm of Toni and others (2009) <doi:10.1098/rsif.2008.0172>.
How to cite:
Stefan Widgren (2016). SimInf: A Framework for Data-Driven Stochastic Disease Spread Simulations. R package version 9.7.0, https://cran.r-project.org/web/packages/SimInf
Previous versions and publish date:
1.0.0 (2016-01-08 18:36), 2.0.0 (2016-05-04 07:56), 3.0.0 (2017-01-29 18:59), 4.0.0 (2017-03-21 07:50), 5.0.0 (2017-06-13 16:41), 5.1.0 (2017-10-18 13:02), 6.0.0 (2018-04-21 00:44), 6.1.0 (2018-08-13 14:10), 6.2.0 (2018-11-20 10:30), 6.3.0 (2019-05-26 17:10), 6.4.0 (2019-11-12 00:50), 6.5.0 (2020-03-29 15:00), 6.5.1 (2020-04-01 19:50), 7.0.0 (2020-05-23 18:40), 7.0.1 (2020-06-18 19:20), 8.0.0 (2020-09-13 10:10), 8.1.0 (2020-10-18 12:30), 8.2.0 (2020-12-06 16:40), 8.3.0 (2021-06-25 13:30), 8.3.2 (2021-06-30 10:00), 8.4.0 (2021-09-19 16:40), 9.0.0 (2022-04-20 10:42), 9.1.0 (2022-06-08 09:00), 9.2.0 (2022-09-03 19:40), 9.3.1 (2022-10-07 09:10), 9.4.0 (2023-01-06 12:10), 9.5.0 (2023-01-23 09:50), 9.6.0 (2023-12-20 14:50)
Other packages that cited SimInf R package
View SimInf citation profile
Other R packages that SimInf depends, imports, suggests or enhances
Functions, R codes and Examples using the SimInf R package
Some associated functions: C_code . SEIR-class . SEIR . SIR-class . SIR . SIS-class . SIS . SISe-class . SISe . SISe3-class . SISe3 . SISe3_sp-class . SISe3_sp . SISe_sp-class . SISe_sp . SimInf . SimInf_abc-class . SimInf_events-class . SimInf_events . SimInf_model-class . SimInf_model . SimInf_pfilter-class . abc . as.data.frame.SimInf_abc . as.data.frame.SimInf_events . boxplot-SimInf_model-method . continue . distance_matrix . events . events_SEIR . events_SIR . events_SIS . events_SISe . events_SISe3 . gdata-set . gdata . indegree . ldata . logLik-SimInf_pfilter-method . mparse . n_generations . n_nodes . nodes . outdegree . package_skeleton . pairs-SimInf_model-method . pfilter . plot-SimInf_abc-method . plot-SimInf_events-method . plot-SimInf_pfilter-method . plot . prevalence-SimInf_model-method . prevalence . punchcard-set . run . select_matrix-set . select_matrix . set_num_threads . shift_matrix-set . shift_matrix . show-SimInf_abc-method . show-SimInf_events-method . show-SimInf_model-method . show-SimInf_pfilter-method . summary-SimInf_abc-method . summary-SimInf_events-method . summary-SimInf_model-method . summary-SimInf_pfilter-method . trajectory-SimInf_model-method . trajectory-SimInf_pfilter-method . trajectory . u0-set . u0 . u0_SEIR . u0_SIR . u0_SIS . u0_SISe . u0_SISe3 . v0-set . 
Some associated R codes: C-generator.R . SEIR.R . SIR.R . SIS.R . SISe.R . SISe3.R . SISe3_sp.R . SISe_sp.R . SimInf.R . SimInf_events.R . SimInf_model.R . abc.R . check_arguments.R . classes.R . degree.R . density_ratio.R . distance.R . distributions.R . init.R . match_compartments.R . mparse.R . n.R . openmp.R . package_skeleton.R . pfilter.R . plot.R . prevalence.R . print.R . punchcard.R . run.R . trajectory.R . u0.R . v0.R . valid.R .  Full SimInf package functions and examples
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