- Added package anchors in the documentation for all Rd \link{} targets not in the package itself and the base packages.
- Fix model parser (mparse) to resolve dependencies between variables in the transitions when multiple variables have zero dependencies.
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Two new features have been added to the model parser. First, it is now possible to define variables in the transitions, which can then be used in calculations of propensities or in calculations of other variables. Secondly, enumeration constants can now be generated for the indices to each parameter in the
u,v,ldata, andgdatavectors in the generated C code. See themparse()documentation. -
Added a utility function
node_events()to facilitate cleaning raw individual event data and prepare it for usage in SimInf. -
Added a new vignette about how to post-process data from a simulated trajectory.
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Added a new section about varying probability of picking individuals to the scheduled events vignette.
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Added a missing PROTECT in the C function SimInf_distance_matrix. This was uncovered by rchk on CRAN.
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Fixed CRAN check warnings for print format specifiers.
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Added a utility function 'individual_events' to facilitate cleaning raw individual event data and prepare it for usage in SimInf.
- Fixed the configuration script to use R to find the compiler to use.
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Fix the 'package_skeleton' function to generate internal C code with valid C entry names if the package name contains '.', for example, for a package named 'pkg.name'.
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Changed the usage of 'any(is.na(x))' to 'anyNA(x)' in the R code.
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Internal refactoring of the 'distance_matrix' function to reduce memory usage.
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Ensure to check for a valid model object after updating model data.
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Moved the enumeration of event types to the header file 'inst/SimInf.h'
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Fixed problems identified with static analysis of the C code using the cppcheck and scan-build tools.
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Added the getter function 'u0' to get the initial compartment state of a model.
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Cast the return value from R_GetCCallable("SimInf", "SimInf_run"); to the correct function pointer type.
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Fix strict-prototype warnings.
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Renamed the set/get funtions
update_u0andupdate_v0tou0andv0, respectively. -
Some internal refactoring of the C code to set number of threads when using OpenMP.
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Changed to coerce to a sparse matrix via virtual classes in order to work with the upcoming Matrix package update.
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Added a new built-in Susceptible-Infected-Susceptible model:
SIS. -
Added the functions
update_u0andupdate_v0to update the initial state in a model. -
Added the
pfilterfunction to run a bootstrap particle algorithm on a model. See the documentation for an example.
- Fixed the unnamed non-character argument 'usr' in par() when ploting the density of the ABC posterior distribution.
This release of SimInf focuses primarily on improving the functionality for performing Approximate Bayesian computation.
Backwards incompatible changes that are the reason why the major version has been incremented.
- Redesigned the S4 class SimInf_abc and the interface to using the Approximate Bayesian Computation Sequential Monte Carlo ('ABC-SMC') algorithm, see the documentation for the 'abc' function. Moreover, added functionality to adaptively select a sequence of tolerances using the algorithm 'Adaptive Approximate Bayesian Computation Tolerance Selection' of Simola and others (2021), Bayesian Analysis.
- Added the function 'n_generations' to determine the number of generations in a 'SimInf_abc' object.
- The
plotfunction for the SimInf_abc class now passes the additional arguments in '...' to the underlying plot functions.
- The 'events', 'gdata', 'gdata<-', 'ldata', 'punchcard<-', 'select_matrix', 'select_matrix<-' 'shift_matrix', and 'shift_matrix<-' functions were changed to S4 methods.
- Protect against an integer overflow that could occur in the 'punchcard' method for a model with many nodes, compartments and time-points.
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Updated the build configuration script ('src/Makevars.ucrt') for Windows UCRT to fix the installation failure on CRAN introduced in version 8.3.0. Thanks to Tomas Kalibera for providing the patch.
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Improved the test logic for checks using multiple threads to also check that the number of available threads is greater than one before running a test using two threads. Thanks to Tomas Kalibera for reporting a test failure on CRAN r-devel-windows-x86_64-gcc10-UCRT on a machine using one thread.
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Changed the R dependency to R(>= 4.0).
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Refactoring of the build configuration script on Windows.
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Added 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.
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Added a vignette about scheduled events. This vignette is work-in-progress and not yet complete.
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Prevalence function: better handling of condition in prevalence formula.
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Use 'Date' on the x-axis when plotting events if time was specified in a Date format.
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Return event 'time' as Date and 'event' type as character when coercing events to a 'data.frame' if they were specified as Date and character.
This release of SimInf focuses primarily on improving the plotting of trajectory data.
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The plotting functionality has been improved to allow visualisation of the prevalence using the same formula notation as the 'prevalence' function, see the documentation. In addition, the box around the plot has been removed and the legend has been moved to the top.
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The prevalence function has been updated to always return a matrix when format='matrix'. Before it returned a vector instead of a '1 x length(tspan)' matrix when the level argument was equal to 1 or 2, or when level = 3 and the prevalence included one node only.
This release of SimInf includes improvements and changes to facilitate post-processing of trajectory data and future development of the package.
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Added the 'compartments' and 'index' arguments to the 'boxplot' and 'pairs' plotting methods to facilitate analysis of a simulated trajectory, see the documentation.
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The build configuration script has been improved to identify if OpenMP can be used. It is also possible to skip the check for OpenMP if --disable-openmp is specified when installing the package.
Backwards incompatible changes that are the reason why the major version has been incremented.
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The 'prevalence' function was changed to an S4 method. Moreover, the 'type' character argument was renamed to 'level' and changed to an integer argument. The reason for renaming the 'type' argument was to prepare for improvements in the plot function in the future to display the prevalence but where there is already an argument called 'type'. Additionally, the 'as.is' argument was renamed to 'format' for clarity. Finally, the unused '...' argument was removed. See the documentation for examples.
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The 'trajectory' function was changed to an S4 method. Furthermore, the node index argument was renamed from 'node' to 'index' to facilitate future development where indices can also represent other structures in a model. Additionally, the 'as.is' argument was renamed to 'format' for clarity. Finally, the unused '...' argument was removed. See the documentation for examples.
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The 'Nn' function to determine the number of nodes in a model has been replaced with the S4 method 'n_nodes'.
- Removed the timestamp from the first line of the C code generated by 'mparse' in order to keep the hash of the C-code constant, even if the code is regenerated at a later time with an identical model. This avoids re-compiling the C-code for the model, if the source code has already been compiled.
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Fixed a problem that prevented re-compiling the model C-code even though it had changed.
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Changed to use the 'R_FINITE' instead of 'isfinite' in the internal C function 'SimInf_print_status'
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The beta and gamma parameters in the built-in SIR model have been moved internally from 'gdata' to 'ldata' to allow node specific parameter values.
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The beta, gamma and epsilon parameters in the built-in SEIR model have been moved internally from 'gdata' to 'ldata' to allow node specific parameter values.
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In order to reduce the compilation-time when running multiple simulations of a model that contains C code, the MD5 hash of the C code is used to determine if a model has already been compiled and the DLL loaded, and thus the compilation step can be skipped before running a trajectory.
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The C functions 'SimInf_forward_euler_linear_decay' and 'SimInf_local_spread' are now available to be called by C code in another package.
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The values in the 'E' matrix are now used as weights when sampling individuals for the exit, internal transfer and external transfer events. The individuals are sampled, one by one, without replacement from the compartments specified by 'E[, select]' in such a way that the probability that a particular individual is sampled at a given draw is proportional to the weight in 'E[, select]'.
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The values in the 'E' matrix are now used as weights for enter events. If the column 'E[, select]' contains several non-zero entries, the compartment to add an individual to is sampled in such a way that the probability is proportional to the weight in 'E[, select]'.
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The scheduled enter events can now use 'proportion' when 'n = 0', see description of breaking changes below. Additionally, the 'shift' feature can also be used to further control in which compartments individuals are added.
Backwards incompatible changes that are the reason why the major version has been incremented.
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Removed the 'run_outer' function.
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Removed the unused 'threads' argument from the 'SimInf_run' function (use 'set_num_threads' to specify the number of threads). The 'SimInf_run' function is the C function that a model calls to simulate a trajectory. Because of this change, model packages created with a previous version of SimInf must be modified/recreated to work with this version of SimInf.
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Events with n = 0 utilize the proportion instead to calculate the number of individuals affected by the event. The number was previously calculated by multiplying the number of individuals in a node by the proportion in the event. This made it tricky to use proportion for a scheduled event when the proportion was very small or very large and the number of individuals in a node was small, since the result was that it always rounded to 0 individuals with a small proportion and all individuals with a large proportion. This has been replaced with a sampling from a binomial distribution to determine the number of individuals affected by the event. Thanks to Thomas Rosendal in PR #28.
- Fixed a memory access error in the internal C code that was introduced in the recently released 6.5.0 version. Detected by the CRAN gcc-UBSAN tests (Undefined Behavior Sanitizer).
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It's now possible to have a 'tspan' vector of length one to simulate over one time-unit only i.e. [t, t+1).
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The
trajectoryfunction has been ported to C and parallelized to efficiently transform simulated data from a model to adata.frame. -
Static code analysis of the codebase has been performed using the
lintrpackage in order to improve code style, consistency and readability. -
It's now possible to specify what type of plot should be drawn from the simulated data, see the documentation.
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Better documentation of the SISe, SISe3, SISe_sp, and SISe3_sp models.
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The way to specify the number of threads to use in parallelized functions has been changed to fix that specifying the number of threads should only affect SimInf and not other packages using OpenMP. Use
set_num_threadsto specify the number of threads, see documentation. It still works to pass the number of threads to therun()function, however, thethreadsargument will be removed fromrun()in a future release. -
Updated the vignette to use the 'set_num_threads' function.
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To avoid cluttering the error message, the name of the internal function that generated the error has been removed from the error message (use
tracebackto print the call stack of the last uncaught error). Additionally, all error messages now ends with a.(full stop). -
Removed the row and column names from the internal matrices U and V because they were not used anywhere in the code.
- Fix storing solution of the state vectors of the first time point until after simulated time has passed the the first time point in tspan.
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Updated the vignette, the CITATION file and added the DOI for the JSS publication to DESCRIPTION/Description.
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Renamed the NEWS file to NEWS.md and changed to use markdown format style.
- Removed a timestamp from a test to avoid a possible test failure.
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The
prevalencefunction now supports an additional condition in the formula specification to further control the population to include in the calculation, see the documentation. -
It is now possible to write the C code snippet of the
pts_funargument tomparseas a text string with line breaks instead of as a vector of character lines. -
The summary function of a model generated with the
mparsefunctionality now includes the propensity of each transition.
- Removed the
U<-andV<-methods. Use the newpunchcard<-method instead, see the documentation.
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Fix storing solution of the continuous state vector v up to time t, but not including t, when t has passed the next time in tspan.
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Fix a link-type optimization type mismatch in the internal C function
SimInf_ldata_sp(detected by the CRAN checks).
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The
mparsemodel 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 tomparse. 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
ldatamatrix in the model has row names. -
It's now possible to pass
gdata,ldataandv0as data.frames to theSimInf_modelfunction. -
Better error message when an invalid rate or a negative state is detected during a simulation.
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Print better error message when processing scheduleed events to facilitate debugging.
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Some fixes to the vignette.
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Updated CITATION file.
- Fixed broken mparse example.
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The
printandsummarymethods have been improved to include a summary of the data in the model and the number of individuals in each compartment. -
Added the
trajectorymethod 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_eventsmethod. -
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
solverargument to therunmethod. -
The
package_skeletonmethod have been updated to handle the newsolverargument. -
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_eventsmethod. -
Added the utility function
select_matrixto get/set the E matrix of the events slot of a SimInf_model object. -
Added the utility function
shift_matrixto get/set the N matrix of the events slot of a SimInf_model object. -
Added the utility function
gdatato get/set parameters in the global data vector that is common to all nodes in a SimInf_model object. -
Added the utility function
ldatato get the local data vector of a node in a SimInf_model object.
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We have changed
mparsemethod 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, andinfected. Use the newtrajectorymethod instead, see the documentation. -
Renamed the type option
bnptonopin theprevalencemethod to calculate the proportion of nodes with at least one case. -
Removed the
seedargument from therunmethod. Useset.seedinstead.
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Added missing calls to
PROTECTto protect newly created R objects in C code from the garbage collector. -
Protect against invalid transition index in direct SSA.
- Improvements in the vignette.
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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.
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Added the
pairsandboxplotmethods to visualise the number of individuals in each compartment. -
Added
spaghettiargument to the plot method to draw one line for each node. -
Added the method
package_skeletonto create a package skeleton for a model depending on SimInf.
- Renamed
plotargumentwhichtoN.
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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.
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Added example data (
nodes) with a population of 1600 nodes within a 50 square kilometer region to facilitate illustration of various models.
- Added missing call to
PROTECTto protect newly created matrices (R objects) from the garbage collector.
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Added the
VandUgetter/setter methods to theSimInf_model. -
The header file
SimInf.hwas added to the folderinst/includeto enableLinkingTo: SimInf. A call toR_RegisterCCallablewas added to make theSimInf_runC routine available to other packages. -
The slots
U_sparseandV_sparsewas added to theSimInf_model. The slotsU_sparseandV_sparseholds the result if the model was initialized to write the solution to a sparse matrix. -
The slot
C_codewas added to theSimInf_model. Character vector with optional model C code. If non-empty, the C code is written to a temporary C-file when therunmethod 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
mparsemodel parser was added. The parser generates the model matricesGandSand 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 classSimInf_mparsewas added to support this feature.
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Added the model compartment names to the model
u0andUmatrices 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).
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The
tspanvector argument to thesiminf_modelmethod can now be either anintegeror aDatevector. ADatevector is internally coerced to a numeric vector as days, wheretspan[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.
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Improved build configuration to register native routines.
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The S4 class
siminf_modelwas renamed toSimInf_model. -
Copy
u0andv0to the first column inUandV, respectively. Prior to this change, the state was copied after the first time step.
- Two new built-in models:
SIRandSEIR.
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Removed the sub-domain argument. Instead use the local data vector
ldatato pass node specific data. -
Removed the unused parameter
epsilonfrom theSISe_spandSISe3_spmodels. -
Refactoring of local spread in the
SISe_spandSISe3_spmodels. -
Added a parameter with a pointer to a random number generator to the post time step function.
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Two new built-in models:
SISe_spandSISe3_spwith spatial coupling. -
Added the
run_outermethod to run a model on scaledgdataparameters.
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Added two synthetic datasets
u0_SISe3andevents_SISe3to demonstrate how to use SimInf. -
Several improvements to the documentation.
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Added summary method to the siminf_model class and the scheduled_events class.
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The slot N in scheduled_events is changed from dgCMatrix to matrix.
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Refactoring of the
showmethod for the siminf_model class and the scheduled_events class. -
Renamed function prototype
PostTimeStepFuntoPTSFunandPropensityFuntoTRFun. -
Renamed
initargument tou0in theSISeandSISe3methods. -
Changed
node,dest,selectandshiftto one-based indices inscheduled_events.
- Changed to use
gsl_rng_uniform_posinstead ofgsl_rng_uniformto avoid 0 in the direct SSA. If zero was randomly selected and the first compartment empty, the simulator could enter a negative state.
- First release.