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+## Copyright (C) 2006, 2007 Arno Onken <asnelt@asnelt.org>
+##
+## This program is free software; you can redistribute it and/or modify it under
+## the terms of the GNU General Public License as published by the Free Software
+## Foundation; either version 3 of the License, or (at your option) any later
+## version.
+##
+## This program is distributed in the hope that it will be useful, but WITHOUT
+## ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+## FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+## details.
+##
+## You should have received a copy of the GNU General Public License along with
+## this program; if not, see <http://www.gnu.org/licenses/>.
+
+## -*- texinfo -*-
+## @deftypefn {Function File} {[@var{sequence}, @var{states}] =} hmmgenerate (@var{len}, @var{transprob}, @var{outprob})
+## @deftypefnx {Function File} {} hmmgenerate (@dots{}, 'symbols', @var{symbols})
+## @deftypefnx {Function File} {} hmmgenerate (@dots{}, 'statenames', @var{statenames})
+## Generate an output sequence and hidden states of a hidden Markov model.
+## The model starts in state @code{1} at step @code{0} but will not include
+## step @code{0} in the generated states and sequence.
+##
+## @subheading Arguments
+##
+## @itemize @bullet
+## @item
+## @var{len} is the number of steps to generate. @var{sequence} and
+## @var{states} will have @var{len} entries each.
+##
+## @item
+## @var{transprob} is the matrix of transition probabilities of the states.
+## @code{transprob(i, j)} is the probability of a transition to state
+## @code{j} given state @code{i}.
+##
+## @item
+## @var{outprob} is the matrix of output probabilities.
+## @code{outprob(i, j)} is the probability of generating output @code{j}
+## given state @code{i}.
+## @end itemize
+##
+## @subheading Return values
+##
+## @itemize @bullet
+## @item
+## @var{sequence} is a vector of length @var{len} of the generated
+## outputs. The outputs are integers ranging from @code{1} to
+## @code{columns (outprob)}.
+##
+## @item
+## @var{states} is a vector of length @var{len} of the generated hidden
+## states. The states are integers ranging from @code{1} to
+## @code{columns (transprob)}.
+## @end itemize
+##
+## If @code{'symbols'} is specified, then the elements of @var{symbols} are
+## used for the output sequence instead of integers ranging from @code{1} to
+## @code{columns (outprob)}. @var{symbols} can be a cell array.
+##
+## If @code{'statenames'} is specified, then the elements of
+## @var{statenames} are used for the states instead of integers ranging from
+## @code{1} to @code{columns (transprob)}. @var{statenames} can be a cell
+## array.
+##
+## @subheading Examples
+##
+## @example
+## @group
+## transprob = [0.8, 0.2; 0.4, 0.6];
+## outprob = [0.2, 0.4, 0.4; 0.7, 0.2, 0.1];
+## [sequence, states] = hmmgenerate (25, transprob, outprob)
+## @end group
+##
+## @group
+## symbols = @{'A', 'B', 'C'@};
+## statenames = @{'One', 'Two'@};
+## [sequence, states] = hmmgenerate (25, transprob, outprob,
+##                      'symbols', symbols, 'statenames', statenames)
+## @end group
+## @end example
+##
+## @subheading References
+##
+## @enumerate
+## @item
+## Wendy L. Martinez and Angel R. Martinez. @cite{Computational Statistics
+## Handbook with MATLAB}. Appendix E, pages 547-557, Chapman & Hall/CRC,
+## 2001.
+##
+## @item
+## Lawrence R. Rabiner. A Tutorial on Hidden Markov Models and Selected
+## Applications in Speech Recognition. @cite{Proceedings of the IEEE},
+## 77(2), pages 257-286, February 1989.
+## @end enumerate
+## @end deftypefn
+
+## Author: Arno Onken <asnelt@asnelt.org>
+## Description: Output sequence and hidden states of a hidden Markov model
+
+function [sequence, states] = hmmgenerate (len, transprob, outprob, varargin)
+
+  # Check arguments
+  if (nargin < 3 || mod (length (varargin), 2) != 0)
+    print_usage ();
+  endif
+
+  if (! isscalar (len) || len < 0 || round (len) != len)
+    error ("hmmgenerate: len must be a non-negative scalar integer")
+  endif
+
+  if (! ismatrix (transprob))
+    error ("hmmgenerate: transprob must be a non-empty numeric matrix");
+  endif
+  if (! ismatrix (outprob))
+    error ("hmmgenerate: outprob must be a non-empty numeric matrix");
+  endif
+
+  # nstate is the number of states of the hidden Markov model
+  nstate = rows (transprob);
+  # noutput is the number of different outputs that the hidden Markov model
+  # can generate
+  noutput = columns (outprob);
+
+  # Check whether transprob and outprob are feasible for a hidden Markov
+  # model
+  if (columns (transprob) != nstate)
+    error ("hmmgenerate: transprob must be a square matrix");
+  endif
+  if (rows (outprob) != nstate)
+    error ("hmmgenerate: outprob must have the same number of rows as transprob");
+  endif
+
+  # Flag for symbols
+  usesym = false;
+  # Flag for statenames
+  usesn = false;
+
+  # Process varargin
+  for i = 1:2:length (varargin)
+    # There must be an identifier: 'symbols' or 'statenames'
+    if (! ischar (varargin{i}))
+      print_usage ();
+    endif
+    # Upper case is also fine
+    lowerarg = lower (varargin{i});
+    if (strcmp (lowerarg, 'symbols'))
+      if (length (varargin{i + 1}) != noutput)
+        error ("hmmgenerate: number of symbols does not match number of possible outputs");
+      endif
+      usesym = true;
+      # Use the following argument as symbols
+      symbols = varargin{i + 1};
+    # The same for statenames
+    elseif (strcmp (lowerarg, 'statenames'))
+      if (length (varargin{i + 1}) != nstate)
+        error ("hmmgenerate: number of statenames does not match number of states");
+      endif
+      usesn = true;
+      # Use the following argument as statenames
+      statenames = varargin{i + 1};
+    else
+      error ("hmmgenerate: expected 'symbols' or 'statenames' but found '%s'", varargin{i});
+    endif
+  endfor
+
+  # Each row in transprob and outprob should contain probabilities
+  # => scale so that the sum is 1
+  # A zero row remains zero
+  # - for transprob
+  s = sum (transprob, 2);
+  s(s == 0) = 1;
+  transprob = transprob ./ repmat (s, 1, nstate);
+  # - for outprob
+  s = sum (outprob, 2);
+  s(s == 0) = 1;
+  outprob = outprob ./ repmat (s, 1, noutput);
+
+  # Generate sequences of uniformly distributed random numbers between 0 and
+  # 1
+  # - for the state transitions
+  transdraw = rand (1, len);
+  # - for the outputs
+  outdraw = rand (1, len);
+
+  # Generate the return vectors
+  # They remain unchanged if the according probability row of transprob
+  # and outprob contain, respectively, only zeros
+  sequence = ones (1, len);
+  states = ones (1, len);
+
+  if (len > 0)
+    # Calculate cumulated probabilities backwards for easy comparison with
+    # the generated random numbers
+    # Cumulated probability in first column must always be 1
+    # We might have a zero row
+    # - for transprob
+    transprob(:, end:-1:1) = cumsum (transprob(:, end:-1:1), 2);
+    transprob(:, 1) = 1;
+    # - for outprob
+    outprob(:, end:-1:1) = cumsum (outprob(:, end:-1:1), 2);
+    outprob(:, 1) = 1;
+
+    # cstate is the current state
+    # Start in state 1 but do not include it in the states vector
+    cstate = 1;
+    for i = 1:len
+      # Compare the randon number i of transdraw to the cumulated
+      # probability of the state transition and set the transition
+      # accordingly
+      states(i) = sum (transdraw(i) <= transprob(cstate, :));
+      cstate = states(i);
+    endfor
+
+    # Compare the random numbers of outdraw to the cumulated probabilities
+    # of the outputs and set the sequence vector accordingly
+    sequence = sum (repmat (outdraw, noutput, 1) <= outprob(states, :)', 1);
+
+    # Transform default matrices into symbols/statenames if requested
+    if (usesym)
+      sequence = reshape (symbols(sequence), 1, len);
+    endif
+    if (usesn)
+      states = reshape (statenames(states), 1, len);
+    endif
+  endif
+
+endfunction
+
+%!test
+%! len = 25;
+%! transprob = [0.8, 0.2; 0.4, 0.6];
+%! outprob = [0.2, 0.4, 0.4; 0.7, 0.2, 0.1];
+%! [sequence, states] = hmmgenerate (len, transprob, outprob);
+%! assert (length (sequence), len);
+%! assert (length (states), len);
+%! assert (min (sequence) >= 1);
+%! assert (max (sequence) <= columns (outprob));
+%! assert (min (states) >= 1);
+%! assert (max (states) <= rows (transprob));
+
+%!test
+%! len = 25;
+%! transprob = [0.8, 0.2; 0.4, 0.6];
+%! outprob = [0.2, 0.4, 0.4; 0.7, 0.2, 0.1];
+%! symbols = {'A', 'B', 'C'};
+%! statenames = {'One', 'Two'};
+%! [sequence, states] = hmmgenerate (len, transprob, outprob, 'symbols', symbols, 'statenames', statenames);
+%! assert (length (sequence), len);
+%! assert (length (states), len);
+%! assert (strcmp (sequence, 'A') + strcmp (sequence, 'B') + strcmp (sequence, 'C') == ones (1, len));
+%! assert (strcmp (states, 'One') + strcmp (states, 'Two') == ones (1, len));