_N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p'

_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _1._7:

        • Improvement of the test suite and of error messages.

        • Improve the ‘show’ and ‘print’ methods for ‘pomp’ objects.

        • Some internal refactoring.

        • Improve error messages for missing basic components.

        • Fix typos in one of the help-page examples.

        • Several obscure bug-fixes.

        • Add some references.

_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _1._6:

        • Major revisions to the package help pages and manual.  The
          separate documentation on C snippets and process-model
          plugins has been merged into the main ‘pomp’ help page, which
          now has comprehensive instructions on building a ‘pomp’
          object.

        • Update to the package help page.

        • New methods for the Ensemble Kalman Filter (‘enkf’) and
          Ensemble Adjustment Kalman Filter (‘eakf’) have been added to
          the package.

        • There is a new plugin for ‘rprocess’ called ‘kleap.sim’.
          This implements the so-called “K-leap method” of Cai & Xu
          (2007).

        • Major overhaul of error handling system and to error and
          warning messages.  Many more errors are now trapped and
          reported with more informative messages.

        • The matrix and numeric vector options for the ‘data’ argument
          to ‘pomp’ are now deprecated and will be removed in a future
          release.  In calls to ‘pomp’, ‘data’ should be either a data
          frame or a ‘pomp’-class object.

        • In ‘mif2’, it is now required that ‘Nmif>0’.

        • Redundant ‘bootstrap’ argument to ‘nlf’ has been removed.

        • Many improvements to the test suite to obtain better code
          coverage.

        • Fixed bugs that might arise in rare circumstances in
          ‘simulate’ and ‘eulermultinom’ functions.

        • Fixed a bug in ‘pompExample’.

        • Fixed several small, rare bugs found as a result of improved
          testing.

        • Fixed bug in specification of skeleton in pompExamples.

        • ‘pomp’ is no longer an S4 method.  Its new status as an
          ordinary function abbreviates and consolidates the code and
          simplifies the documentation.

        • A bug restricting access in C code to ‘userdata’ has been
          fixed.

        • Fixed bug in ‘pompExample(...,show=TRUE)’.

_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _1._5:

        • A better interface for specifying a model's deterministic
          skeleton is provided.  One specifies
          ‘skeleton=map(f,delta.t)’ for a discrete-time skeleton (a
          map) and ‘skeleton=vectorfield(f)’ for a continuous-time
          skeleton (a vectorfield).  The old arguments ‘skeleton.type’
          and ‘skelmap.delta.t’ are deprecated and will be removed in a
          future release.

        • The ‘pfilter’ help page has been improved.  Specifically, the
          discussion of filtering failures is better.

        • Miscellaneous improvements to the help pages.

        • ‘mif2’ no longer computes filter means.

        • The new argument ‘show’ of ‘pompExamples’ allows one to
          display the example code instead of executing it.

        • The minimum version of R supported is now 3.1.2.

        • ‘init.state’ now has the optional argument ‘nsim’.  Using
          this, one can request multiple initial state vectors per
          parameter vector.

        • ‘pfilter’ now uses less memory when it is asked to run at a
          single point in parameter space.

        • A bug associated with the ‘rw.sd’ argument to ‘mif2’ on
          Windows platforms has been fixed.

        • The ‘method="mif2"’ option to ‘mif’ has been removed.  Use
          ‘mif2’ instead.

        • The ‘particles’ method (rarely if ever used), has been
          removed to streamline the ‘mif’ codes.

        • The ‘method="mif2"’ option to ‘mif’ is now deprecated.  It
          will be removed in a future release.  Use ‘mif2’ instead.

_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _1._4:

        • Following the publication of the Journal of Statistical
          Software announcement paper, the ‘CITATION’ has been modified
          to include the appropriate citation.  Please use
          ‘citation("pomp")’ to learn about how to cite ‘pomp’
          correctly.

        • ‘conv.rec’ on the results of a ‘mif2’ computation now play
          nicely with ‘reshape2::melt’.

        • It is now possible to direct ‘pomp’ to place ‘Csnippet’ codes
          in a specified location.  This is accomplished via the new
          ‘cdir’ and ‘cfile’ arguments to ‘pomp’.

        • When several concurrent R processes attempt to simultaneously
          compile ‘Csnipet’ code from copies of a ‘pomp’ object on the
          same machine, a race condition exists.  This release fixes
          this by ensuring that ‘Csnippet’ codes are written and
          compiled in a process-specific directory.

_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _1._3:

     This release removes several long-deprecated features.

        • The ‘seed’ argument to ‘pfilter’ has been removed.  Use
          ‘freeze’ to obtain similar functionality.

        • The redundant ‘pars’ argument to ‘mif’ has been removed.
          Names of parameters to be estimated are taken from the
          nonzero entries of ‘rw.sd’.  Initial-value parameters are
          designated using the ‘ivps’ argument.

        • The old ‘parameter.transform’ and ‘parameter.inv.transform’
          arguments to ‘pomp’ have been removed.  They were superseded
          by the arguments ‘fromEstimationScale’ and
          ‘toEstimationScale’ in version 0.65-1.

        • Some internal changes to ‘mif2’ by C. Breto, in support of
          panel methods under development.

_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _1._2:

        • Bug fix: for POMPs with a scalar state variable, the
          ‘filter.mean’, ‘pred.mean’, and ‘pred.var’ methods dropped
          the singleton dimension of the respective arrays, in conflict
          with the assumptions of certain ‘plot’ methods.  This
          resolves issue #3.

        • Documentation improvements.  Specifically, the details of how
          step-sizes are chosen in the ‘euler.sim’,
          ‘discrete.time.sim’, and ‘onestep.sim’ plugins has been
          spelled out explicitly.  Also, incompleteness in the
          ‘sannbox’ documentation has been corrected.

        • Provide ‘filter.traj’ method for ‘pmcmcList’ objects.

        • Fixed a bug in ‘mif’ and ‘mif2’ when
          ‘cooling.type="hyperbolic"’ and ‘cooling.fraction.50=1’.

