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CRAN release v10.0.0

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@stewid stewid released this 13 Nov 19:33
· 347 commits to main since this release

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).