CRAN release v9.8.1

CHANGES OR IMPROVEMENTS

• Added package anchors in the documentation for all Rd \link{}
  targets not in the package itself and the base packages.

BUG FIXES

• Fix model parser (mparse) to resolve dependencies between variables
  in the transitions when multiple variables have zero dependencies.

CRAN release v9.7.0

CHANGES OR IMPROVEMENTS

• 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, and gdata
  vectors in the generated C code. See the mparse() 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.

• Added a new section about varying probability of picking individuals
  to the scheduled events vignette.

• Added a missing PROTECT in the C function SimInf_distance_matrix.
  This was uncovered by rchk on CRAN.

CRAN release v9.6.0

CHANGES OR IMPROVEMENTS

• Fixed CRAN check warnings for print format specifiers.

• Added a utility function 'individual_events' to facilitate cleaning
  raw individual event data and prepare it for usage in SimInf.

CRAN release v9.5.0

CHANGES OR IMPROVEMENTS

• Fixed the configuration script to use R to find the compiler to use.

CRAN release v9.4.0

CHANGES OR IMPROVEMENTS

• 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'.

• Changed the usage of 'any(is.na(x))' to 'anyNA(x)' in the R code.

• Internal refactoring of the 'distance_matrix' function to reduce
  memory usage.

• Ensure to check for a valid model object after updating model data.

• Moved the enumeration of event types to the header file
  'inst/SimInf.h'

• Fixed problems identified with static analysis of the C code using
  the cppcheck and scan-build tools.

• Added the getter function 'u0' to get the initial compartment state
  of a model.

CRAN release v9.3.1

CHANGES OR IMPROVEMENTS

• Cast the return value from R_GetCCallable("SimInf", "SimInf_run");
  to the correct function pointer type.

• Fix strict-prototype warnings.

CRAN release v9.2.0

CHANGES OR IMPROVEMENTS

• Renamed the set/get funtions update_u0 and update_v0 to u0and
  v0, respectively.

• Some internal refactoring of the C code to set number of threads
  when using OpenMP.

• Changed to coerce to a sparse matrix via virtual classes in order to
  work with the upcoming Matrix package update.

CRAN release v9.1.0

CHANGES OR IMPROVEMENTS

• Added a new built-in Susceptible-Infected-Susceptible model: SIS.

• Added the functions update_u0 and update_v0 to update the
  initial state in a model.

• Added the pfilter function to run a bootstrap particle algorithm
  on a model. See the documentation for an example.

BUG FIXES

• Fixed the unnamed non-character argument 'usr' in par() when ploting
  the density of the ABC posterior distribution.

CRAN release v9.0.0

This release of SimInf focuses primarily on improving the functionality for performing Approximate Bayesian computation.

BREAKING CHANGES

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.

CHANGES OR IMPROVEMENTS

• Added the function 'n_generations' to determine the number of generations in a 'SimInf_abc' object.

BUG FIXES

• The plot function for the SimInf_abc class now passes the additional arguments in '...' to the underlying plot functions.

CRAN release v8.4.0

CHANGES OR IMPROVEMENTS

• The 'events', 'gdata', 'gdata<-', 'ldata', 'punchcard<-',
  'select_matrix', 'select_matrix<-' 'shift_matrix', and
  'shift_matrix<-' functions were changed to S4 methods.

BUG FIXES

• Protect against an integer overflow that could occur in the
  'punchcard' method for a model with many nodes, compartments and
  time-points.