A Framework for Data-Driven Stochastic Disease Spread Simulations

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) .


News

SimInf 6.2.0

IMPROVEMENTS

  • The 'mparse' model builder functionality has been improved to be able to generate models that contain node specific local data and continuous state variables. It is also possible to pass the C code of the post time step function to 'mparse'. See documentation.

  • The package skeleton method has been updated to handle the the improved functionlity of 'mparse'.

  • Print summary of the local data when the 'ldata' matrix in the model has row names.

  • It's now possible to pass 'gdata', 'ldata' and 'v0' as data.frames to the 'SimInf_model' function.

  • Better error message when an invalid rate or a negative state is detected during a simulation.

SimInf 6.1.0

IMPROVEMENTS

  • Print better error message when processing scheduleed events to facilitate debugging.

  • Some fixes to the vignette.

  • Updated CITATION file.

BUG FIXES

  • Fixed broken mparse example.

SimInf 6.0.0

IMPROVEMENTS

  • The 'print' and 'summary' methods have been improved to include a summary of the data in the model and the number of individuals in each compartment.

  • Added the 'trajectory' method to facilitate post-processing of simulation data. See documentation.

  • The event type, when specifying the scheduled events from a data.frame, can now be coded either as a numerical value or as a character string, see the documentataion for the 'SimInf_events' method.

  • Now SimInf also includes the All Events Method (AEM) solver (Bauer P., Engblom S. (2015) Sensitivity Estimation and Inverse Problems in Spatial Stochastic Models of Chemical Kinetics. In: Abdulle A., Deparis S., Kressner D., Nobile F., Picasso M. (eds) Numerical Mathematics and Advanced Applications - ENUMATH 2013. Lecture Notes in Computational Science and Engineering, vol 103. Springer, Cham. Doi: 10.1007/978-3-319-10705-9_51). A core feature of the AEM solver is that reaction events are carried out in channels which access private streams of random numbers, in contrast to the Gillespie direct method where one use only one stream for all events. We have added a new 'solver' argument to the 'run' method.

  • The 'package_skeleton' method have been updated to handle the new 'solver' argument.

  • The event type, when specifying the scheduled events from a data.frame, can now be coded either as a numerical value or as a character string, see the documentataion for the 'SimInf_events' method.

  • Added the utility function 'select_matrix' to get/set the E matrix of the events slot of a SimInf_model object.

  • Added the utility function 'shift_matrix' to get/set the N matrix of the events slot of a SimInf_model object.

  • Added the utility function 'gdata' to get/set parameters in the global data vector that is common to all nodes in a SimInf_model object.

  • Added the utility function 'ldata' to get the local data vector of a node in a SimInf_model object.

BREAKING CHANGES

  • We have changed 'mparse' method to make it even easier to specify a new model for the Siminf framework, see the documentation.

  • Removed the following methods: 'U', 'V', 'recovered', 'susceptible', and 'infected'. Use the new 'trajectory' method instead, see the documentation.

  • Renamed the type option 'bnp' to 'nop' in the 'prevalence' method to calculate the proportion of nodes with at least one case.

  • Removed the 'seed' argument from the 'run' method. Use 'set.seed' instead.

SimInf 5.1.0

BUG FIXES

  • Added missing calls to 'PROTECT' to protect newly created R objects in C code from the garbage collector.

  • Protect against invalid transition index in direct SSA.

SimInf 5.0.1

IMPROVEMENTS

  • Improvements in the vignette.

SimInf 5.0.0

NEW FEATURES

  • Added a vignette that provide a technical description of the framework, how to use a predefined model in SimInf, demonstrate a case study, and finally show how to extend the framework with a user defined model.

  • Added the 'pairs' and 'boxplot' methods to visualise the number of individuals in each compartment.

  • Added 'spaghetti' argument to the plot method to draw one line for each node.

  • Added the method 'package_skeleton' to create a package skeleton for a model depending on SimInf.

CHANGES

  • Renamed 'plot' argument 'which' to 'N'.

IMPROVEMENTS

  • The core solver now checks the return value from the transition rate functions and raise an error if the return value is non-finite or less than zero.

  • Added example data ('nodes') with a population of 1600 nodes within a 50 square kilometer region to facilitate illustration of various models.

BUG FIXES

  • Added missing call to 'PROTECT' to protect newly created matrices (R objects) from the garbage collector.

SimInf 4.0.0

NEW FEATURES

  • Added the 'V' and 'U' getter/setter methods to the 'SimInf_model'.

  • The header file 'SimInf.h' was added to the folder 'inst/include' to enable 'LinkingTo: SimInf'. A call to 'R_RegisterCCallable' was added to make the 'SimInf_run' C routine available to other packages.

  • The slots 'U_sparse' and 'V_sparse' was added to the 'SimInf_model'. The slots 'U_sparse' and 'V_sparse' holds the result if the model was initialized to write the solution to a sparse matrix.

  • The slot 'C_code' was added to the 'SimInf_model'. Character vector with optional model C code. If non-empty, the C code is written to a temporary C-file when the 'run' method is called. The temporary C-file is compiled and the resulting DLL is dynamically loaded. The DLL is unloaded and the temporary files are removed after running the model.

  • The 'mparse' model parser was added. The parser generates the model matrices 'G' and 'S' and C code from a text string specification of the model, for example, c("S -> k1SI -> I", "I -> k2*I -> R") expresses a SIR model. The S4 class 'SimInf_mparse' was added to support this feature.

IMPROVEMENTS

  • Added the model compartment names to the model 'u0' and 'U' matrices to facilitate inspection of data.

  • Removed the max node size constraint when sampling individuals for scheduled events from more than two compartments (fixes issue #3).

  • The 'tspan' vector argument to the 'siminf_model' method can now be either an 'integer' or a 'Date' vector. A 'Date' vector is internally coerced to a numeric vector as days, where 'tspan[1]' becomes the day of the year of the first year of the tspan argument. The dates are added as names to the numeric vector.

  • Improved plot methods by adding colors and increase line widths.

  • Improved build configuration to register native routines.

CHANGES

  • The S4 class 'siminf_model' was renamed to 'SimInf_model'.

  • Copy 'u0' and 'v0' to the first column in 'U' and 'V', respectively. Prior to this change, the state was copied after the first time step.

SimInf 3.0.0

NEW FEATURES

  • Two new built-in models: 'SIR' and 'SEIR'.

CHANGES

  • Removed the sub-domain argument. Instead use the local data vector 'ldata' to pass node specific data.

  • Removed the unused parameter 'epsilon' from the 'SISe_sp' and 'SISe3_sp' models.

  • Refactoring of local spread in the 'SISe_sp' and 'SISe3_sp' models.

  • Added a parameter with a pointer to a random number generator to the post time step function.

SimInf 2.0.0

NEW FEATURES

  • Two new built-in models: 'SISe_sp' and 'SISe3_sp' with spatial coupling.

  • Added the 'run_outer' method to run a model on scaled 'gdata' parameters.

IMPROVEMENTS

  • Added two synthetic datasets 'u0_SISe3' and 'events_SISe3' to demonstrate how to use SimInf.

  • Several improvements to the documentation.

  • Added summary method to the siminf_model class and the scheduled_events class.

CHANGES

  • The slot N in scheduled_events is changed from dgCMatrix to matrix.

  • Refactoring of the 'show' method for the siminf_model class and the scheduled_events class.

  • Renamed function prototype 'PostTimeStepFun' to 'PTSFun' and 'PropensityFun' to 'TRFun'.

  • Renamed 'init' argument to 'u0' in the 'SISe' and 'SISe3' methods.

  • Changed 'node', 'dest', 'select' and 'shift' to one-based indices in 'scheduled_events'.

BUG FIXES

  • Changed to use 'gsl_rng_uniform_pos' instead of 'gsl_rng_uniform' to avoid 0 in the direct SSA. If zero was randomly selected and the first compartment empty, the simulator could enter a negative state.

SimInf 1.0.0

  • First release.

Reference manual

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install.packages("SimInf")

7.0.0 by Stefan Widgren, 10 days ago


https://github.com/stewid/SimInf


Report a bug at https://github.com/stewid/SimInf/issues


Browse source code at https://github.com/cran/SimInf


Authors: Stefan Widgren [aut, cre] , Robin Eriksson [aut] , Stefan Engblom [aut] , Pavol Bauer [aut] , Thomas Rosendal [ctb] , Attractive Chaos [cph] (Author of 'kvec.h'.)


Documentation:   PDF Manual  


GPL-3 license


Imports digest, graphics, grDevices, methods, stats, utils, Matrix

System requirements: GNU Scientific Library (GSL)


See at CRAN