CRAN release v8.3.2

BUG FIXES

• 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.

• 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.

CRAN release v8.3.0

CHANGES OR IMPROVEMENTS

• Changed the R dependency to R(>= 4.0).

• Refactoring of the build configuration script on Windows.

• 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.

• Added a vignette about scheduled events. This vignette is work-in-progress and not yet complete.

CRAN release v8.2.0

IMPROVEMENTS

• Prevalence function: better handling of condition in prevalence
  formula.

• Use 'Date' on the x-axis when plotting events if time was specified
  in a Date format.

• 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.

CRAN release v8.1.0

This release of SimInf focuses primarily on improving the plotting of
trajectory data.

CHANGES OR IMPROVEMENTS

• 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.

• 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.

CRAN release v8.0.0

This release of SimInf includes improvements and changes to facilitate
post-processing of trajectory data and future development of the
package.

IMPROVEMENTS

• Added the 'compartments' and 'index' arguments to the 'boxplot' and
  'pairs' plotting methods to facilitate analysis of a simulated
  trajectory, see the documentation.

• 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.

BREAKING CHANGES

Backwards incompatible changes that are the reason why the major
version has been incremented.

• 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.

• 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.

• The 'Nn' function to determine the number of nodes in a model has
  been replaced with the S4 method 'n_nodes'.

CRAN release v7.0.1

CHANGES

• 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.

BUG FIXES

• Fixed a problem that prevented re-compiling the model C-code even
  though it had changed.

• Changed to use the 'R_FINITE' instead of 'isfinite' in the internal
  C function 'SimInf_print_status'

CRAN release v7.0.0

CHANGES OR IMPROVEMENTS

• 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.

• 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.

• 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.

• The C functions 'SimInf_forward_euler_linear_decay' and
  'SimInf_local_spread' are now available to be called by C code in
  another package.

• 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]'.

• 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]'.

• 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.

BREAKING CHANGES

Backwards incompatible changes that are the reason why the major
version has been incremented.

• Removed the 'run_outer' function.

• 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.

• 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.

CRAN release v6.5.1

BUG FIXES

• 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).

CRAN release v6.5.0

IMPROVEMENTS

• It's now possible to have a 'tspan' vector of length one to simulate
  over one time-unit only i.e. [t, t+1).

• The trajectory function has been ported to C and parallelized to
  efficiently transform simulated data from a model to a data.frame.

• Static code analysis of the codebase has been performed using the
  lintr package 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.

• Better documentation of the SISe, SISe3, SISe_sp, and SISe3_sp
  models.

CHANGES

• 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_threads to specify the number of threads, see
  documentation. It still works to pass the number of threads to the
  run() function, however, the threads argument will be removed
  from run() in a future release.

• Updated the vignette to use the 'set_num_threads' function.

• To avoid cluttering the error message, the name of the internal
  function that generated the error has been removed from the error
  message (use traceback to 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.

BUG FIXES

• 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.

CRAN release v6.4.0

CHANGES

• Updated the vignette, the CITATION file and added the DOI for the
  JSS publication to DESCRIPTION/Description.

• Renamed the NEWS file to NEWS.md and changed to use markdown
  format style.

BUG FIX

• Removed a timestamp from a test to avoid a possible test failure.