MmgraphR: Graphing for Markov, Hidden Markov, and 
Mixture Transition Distribution Models

 SUMMARY OF MAIN FUNCTION
 
 The work horse function of MmgraphR is 'trmatplot()'.
 
 'trmatplot()' produces a coordinate plot which maps each element 
  in the probability transition matrix as a line, where each line
  is weighted by probability. 
  
  Input is either an object of class ‘matrix’, ‘array’, 
  ‘depmix.fitted’, or a ‘list’ of class ‘msm’, ‘hmm’ or ‘dthmm’.
  
  Users can apply filters to emphasize the most (or
  least) probable state sequences overall, or by initial state.
  
  Various color palettes using the Hue-Chroma-Luminance color scheme
  can be easily selected by the user. 

  Details below.


  PROBABILITY TRANSITION MATRIX TO BE PLOTTED
  
  The object ‘d’ to be plotted, is a probability matrix which, when
  of class ‘matrix’ or ‘array’, can be user defined, or extracted
  directly from the output of another package (see below).
  Objects of class ‘depmix.fitted’, ‘dthmm’, ‘hmm’, ‘msm’
  are also accepted as input.

  Probability transition matrix is the output of packages
  implemented using ‘S3’ methods and classes: 

  - Package ‘HMM’, function ‘initHMM()’ returns a ‘list’
    containing the element ‘transProbs’ with the probability
    transition matrix. 

  - Package ‘HiddenMarkov’, function ‘dthmm()’ returns a ‘list’ 
    of class ‘dthmm’ with the element ‘Pi’ which is a probability
    transition matrix. 

  - Package ‘seqHMM’, functions ‘build_mm()’ and ‘build_hmm()’ return 
    a ‘list’ of class ‘hmm’ containing the element ‘transition_probs’
    with the estimated probability transition matrix. 

  - Package ‘msm’, function ‘msm()’ returns a ‘list’ of class ‘msm’.
    Functions ‘pmatrix.msm()’ and ‘pmatrix.piecewise.msm()’ then 
    extract the probability transition matrix. 

  In the case of ‘S4’ classes:

  - Package ‘depmixS4’, functions ‘depmix()’ followed by ‘fit()’ 
    will return an object of class ‘depmix.fitted’. Display the
    probability transtion matrix using ‘summary()’ on a 
    ‘depmix.fitted’ object. Not all ‘depmix.fitted’ objects contain
    a probability transition matrix.

  KEY FEATURES OF 'trmatplot()'

  - 'pfilter' argument can easily be applied to emphasize the most
     (or least) probable state sequences overall, or by initial state. 

  - 'filter' argument can be used to highlight any specific 
     element(s) of the probability transition matrix. 
  
  - 'cspal' argument can be used to select various built-in 
     color palettes using  the Hue-Chroma-Luminance color scheme.

  - 'cpal' argument can be used to insert an external color palette.

