CRAN release v10.1.0

CHANGES OR IMPROVEMENTS

• Internal change to avoid using memcpy on zero-length continuous
  state vector, i.e., access elements of a 0-length R vector. This was
  uncovered by checks on M1mac system on CRAN.

CRAN release v10.0.0

BREAKING CHANGES

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

• Redesigned the S4 class SimInf_pfilter and the interface to using
  the bootstrap filtering algorithm, see the documentation for the
  pfilter function. Moreover, a variant of the split-step solver
  (ssm) was added to efficiently simulate multiple particles in one
  trajectory (mssm).

• The slot replicates was added to the SimInf_model. The slot
  replicates holds the number of replicates of each node in a
  model. This new functionality is used by the bootstrap filtering
  algorithm.

CHANGES OR IMPROVEMENTS

• Added functionality to fit models to time series data using the
  Particle Markov Chain Monte Carlo ('PMCMC') algorithm of Andrieu and
  others (2010)
  doi:10.1111/j.1467-9868.2009.00736.x.

• The model parser (mparse) now allows the global data vector
  gdata to have parameters without a name.

• On Windows, use gsl from the system, via pkg-config when available.

• Renamed the abc function argument ninit to n_init.

• Renamed the abc function argument npart to n_particles.

• When using use_enum=TRUE in mparse, the enumeration constants
  N_COMPARTMENTS_U and N_COMPARTMENTS_V will be automatically
  added to facilitate indexing 'u' and 'v' in the C code.
  Additionally, enumeration values are added to all enumeration
  constants.

• The plot function of a SimInf_model object now accepts a log
  argument, see the documentation. Thanks to Alfredo Acosta in PR #56.

• Static code analysis of the C codebase has been performed using the
  clang-tidy and cppcheck tools in order to improve code.

• The GNU Indent program has been used to style the C code for
  consistency and readability.

• Add a function to calculate the Lambert W0 function using the GNU
  Scientific Library (GSL).

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.