changes             package:HiddenMarkov             R Documentation

_C_h_a_n_g_e_s _M_a_d_e _t_o _t_h_e _P_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     This page contains a listing of recent changes made to the
     package.

_D_e_t_a_i_l_s:

        1.  Since we have included different classes of HMMs (see
           'dthmm', 'mmglm' and 'mmpp'), it is much tidier to use an
           object orientated approach. This ensures that the functions
           across all models follow a more consistent naming
           convention, and also the argument list for the different
           model functions are more simple and consistent (see
           'Overview'). (14 Sep 2007)

        2.  The main tasks (model fitting, residuals, simulation,
           Viterbi, etc) can now be called by generic functions (see
           topic 'Overview'). The package documentation has been
           rearranged so that these generic functions contain the
           documentation for all model types (e.g. see 'BaumWelch').
           (14 Sep 2007)

        3.  There are a number of functions, still contained in the
           package, that are obsolete. This is either because they do
           not easily fit into the current naming convention used to
           implement the more object orientated approach, or their
           argument list is slightly complicated. These functions have
           been grouped in the topics 'dthmm.obsolete' and
           'mmpp.obsolete'. (14 Sep 2007)

        4.  There are various _second level_ functions. For example,
           the model fitting is achieved by the generic 'BaumWelch'
           function. However, this will call functions to do the
           E-step, M-step, forward and backward probabilities, and so
           on. At the moment, these _second level_ functions have not
           been modified into an object orientated approach. It is not
           clear at this point whether this would be advantageous. If
           one went down this route, then one would probably group all
           of the E-step functions (for all models) under the same
           topic. If not, then it may be best to group all second level
           functions for each model under the same topic (e.g.
           'forwardback', 'probhmm' and 'Estep' would be grouped
           together, being the second level functions for the 'dthmm'
           model). (14 Sep 2007)

        5.  The original function called 'Viterbi' has been renamed to
           'Viterbihmm', and 'Viterbi' is now a generic function. (14
           Sep 2007)

        6.  Programming code that uses old versions of the functions
           should still work with this revised version of the package.
           However, you will get warning messages stating that certain
           functions are deprecated, and suggesting a possible
           alternative. To get a quick overview of the programming
           style, have a look at the examples in topic 'dthmm'. (09 Nov
           2007)

_F_u_t_u_r_e _D_e_v_e_l_o_p_m_e_n_t:

        1.  The functions 'residuals' and 'Viterbi' need methods for
           objects with class 'mmpp'.

        2.  A number of the original functions have names that are too
           general. For example 'forwardback' calculates the
           forward-backward probabilities, but only for the model
           'dthmm'. The corresponding function for the 'mmpp' model is
           'forwardback.mmpp'. It would be more consistent to attach to
           these original functions a 'dthmm' suffix.

        3.  The 'for' loops in the evaluation of the forward and
           backward equations are too slow. These should be implemented
           in C.

        4.  The demonstration examples are all for 'dthmm'. Also need
           some for 'mmglm' and 'mmpp'.

