--- a/main/statistics/inst/hmmestimate.m	Sun Oct 15 08:55:05 2006 +0000
+++ b/main/statistics/inst/hmmestimate.m	Sun Oct 15 19:50:42 2006 +0000
@@ -16,97 +16,116 @@
 
 ## -*- texinfo -*-
 ## @deftypefn {Function File} {[@var{transprobest}, @var{outprobest}] =} hmmestimate (@var{sequence}, @var{states})
-## @deftypefnx {Function File} hmmestimate (@dots{}, 'statenames', @var{statenames})
-## @deftypefnx {Function File} hmmestimate (@dots{}, 'symbols', @var{symbols})
-## @deftypefnx {Function File} hmmestimate (@dots{}, 'pseudotransitions', @var{pseudotransitions})
-## @deftypefnx {Function File} hmmestimate (@dots{}, 'pseudoemissions', @var{pseudoemissions})
-## Estimates the matrix with the transition probabilities and the matrix
-## with the output probabilities for a given sequence with outputs and
-## states produced by a Hidden Markov Model. The model assumes that the
-## generation begins with state @code{1} in step @code{0} but does not
-## include step @code{0} in the generated states and sequence
+## @deftypefnx {Function File} {} hmmestimate (@dots{}, 'statenames', @var{statenames})
+## @deftypefnx {Function File} {} hmmestimate (@dots{}, 'symbols', @var{symbols})
+## @deftypefnx {Function File} {} hmmestimate (@dots{}, 'pseudotransitions', @var{pseudotransitions})
+## @deftypefnx {Function File} {} hmmestimate (@dots{}, 'pseudoemissions', @var{pseudoemissions})
+## Estimates the matrix of transition probabilities and the matrix of output
+## probabilities for a given sequence of outputs and states generated by a
+## Hidden Markov Model. The model assumes that the generation starts in
+## state @code{1} at step @code{0} but does not include step @code{0} in the
+## generated states and sequence.
 ##
 ## Arguments are
 ##
-## @itemize
+## @itemize @bullet
 ## @item
-## @var{sequence} is a vector with a sequence of given outputs. The
-## outputs must be integers ranging from @code{1} to the number of outputs
-## of the Hidden Markov Model
+## @var{sequence} is a vector of a sequence of given outputs. The outputs
+## must be integers ranging from @code{1} to the number of outputs of the
+## Hidden Markov Model.
+##
 ## @item
-## @var{states} is a vector of the same length as @var{sequence} with given
+## @var{states} is a vector of the same length as @var{sequence} of given
 ## states. The states must be integers ranging from @code{1} to the number
-## of states of the Hidden Markov Model
+## of states of the Hidden Markov Model.
 ## @end itemize
 ##
 ## Return values are
 ##
-## @itemize
+## @itemize @bullet
 ## @item
-## @var{transprobest} is the matrix with the estimated transition
+## @var{transprobest} is the matrix of the estimated transition
 ## probabilities for the states. @code{transprobest (i, j)} is the estimated
-## probability for a transition to state @code{j} given state @code{i}
+## probability for a transition to state @code{j} given state @code{i}.
+##
 ## @item
-## @var{outprobest} is the matrix with the estimated output probabilities.
+## @var{outprobest} is the matrix of the estimated output probabilities.
 ## @code{outprobest (i, j)} is the estimated probability for generating
-## output @code{j} given state @code{i}
+## output @code{j} given state @code{i}.
 ## @end itemize
 ##
-## If 'symbols' is specified, then @var{sequence} is expected to be a
+## If @code{'symbols'} is specified, then @var{sequence} is expected to be a
 ## sequence of the elements of @var{symbols} instead of integers.
-## @var{symbols} can be a cell array
+## @var{symbols} can be a cell array.
 ##
-## If 'statenames' is specified, then @var{states} is expected to be a
-## sequence of the elements of @var{statenames} instead of integers.
-## @var{statenames} can be a cell array
+## If @code{'statenames'} is specified, then @var{states} is expected to be
+## a sequence of the elements of @var{statenames} instead of integers.
+## @var{statenames} can be a cell array.
 ##
-## If 'pseudotransitions' is specified then the integer matrix
+## If @code{'pseudotransitions'} is specified then the integer matrix
 ## @var{pseudotransitions} is used as an initial number of counted
 ## transitions. @code{pseudotransitions (i, j)} is the initial number of
 ## counted transitions from state @code{i} to state @code{j}.
 ## @var{transprobest} will have the same size as @var{pseudotransitions}.
-## Use this if you have transitions that are very unlikely to occur
+## Use this if you have transitions that are very unlikely to occur.
 ##
-## If 'pseudoemissions' is specified then the integer matrix
+## If @code{'pseudoemissions'} is specified then the integer matrix
 ## @var{pseudoemissions} is used as an initial number of counted outputs.
 ## @code{pseudoemissions (i, j)} is the initial number of counted outputs
-## @code{j} given state @code{i}. If 'pseudoemissions' is also specified
-## then the number of rows of @var{pseudoemissions} must be the same as the
-## number of rows of @var{pseudotransitions}. @var{outprobest} will have the
-## same size as @var{pseudoemissions}. Use this if you have outputs or
-## states that are very unlikely to occur
+## @code{j} given state @code{i}. If @code{'pseudoemissions'} is also
+## specified then the number of rows of @var{pseudoemissions} must be the
+## same as the number of rows of @var{pseudotransitions}. @var{outprobest}
+## will have the same size as @var{pseudoemissions}. Use this if you have
+## outputs or states that are very unlikely to occur.
 ##
 ## 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);
 ## [transprobest, outprobest] = hmmestimate (sequence, states)
+## @end group
 ##
+## @group
 ## symbols = @{'A', 'B', 'C'@};
 ## statenames = @{'One', 'Two'@};
 ## [sequence, states] = hmmgenerate (25, transprob, outprob, 'symbols', symbols, 'statenames', statenames);
 ## [transprobest, outprobest] = hmmestimate (sequence, states, 'symbols', symbols, 'statenames', statenames)
+## @end group
 ##
+## @group
 ## pseudotransitions = [8, 2; 4, 6];
 ## pseudoemissions = [2, 4, 4; 7, 2, 1];
 ## [sequence, states] = hmmgenerate (25, transprob, outprob);
 ## [transprobest, outprobest] = hmmestimate (sequence, states, 'pseudotransitions', pseudotransitions, 'pseudoemissions', pseudoemissions)
+## @end group
 ## @end example
 ##
 ## References:
 ##
-## @itemize
+## @enumerate
 ## @item
-## @cite{Matlab 7.0 documentation (pdf)}
+## W. L. Martinez and A. R. Martinez. @cite{Computational Statistics
+## Handbook with MATLAB.} Chapman & Hall/CRC, pages 547-557, 2001.
+##
 ## @item
-## @uref{http://en.wikipedia.org/wiki/Maximum_likelihood}
-## @end itemize
+## Wikipedia contributors. Hidden Markov model. @cite{Wikipedia, The Free
+## Encyclopedia.}
+## @uref{http://en.wikipedia.org/w/index.php?title=Hidden_Markov_model&oldid=81100294},
+## October 2006.
 ##
+## @item
+## Wikipedia contributors. Maximum likelihood. @cite{Wikipedia, The Free
+## Encyclopedia.}
+## @uref{http://en.wikipedia.org/w/index.php?title=Maximum_likelihood&oldid=80805216},
+## October 2006.
+## @end enumerate
 ## @end deftypefn
 
 ## Author: Arno Onken <whyly@gmx.net>
+## Description: Hidden Markov Model estimation for a given sequence
 
 function [transprobest, outprobest] = hmmestimate (sequence, states, varargin)
 

--- a/main/statistics/inst/hmmgenerate.m	Sun Oct 15 08:55:05 2006 +0000
+++ b/main/statistics/inst/hmmgenerate.m	Sun Oct 15 19:50:42 2006 +0000
@@ -19,70 +19,83 @@
 ## @deftypefnx {Function File} {} hmmgenerate (@dots{}, 'symbols', @var{symbols})
 ## @deftypefnx {Function File} {} hmmgenerate (@dots{}, 'statenames', @var{statenames})
 ## Generates an output sequence and hidden states for a Hidden Markov Model.
-## The model starts with state @code{1} at step @code{0} but will not
-## include step @code{0} in the generated states and sequence
+## The model starts in state @code{1} at step @code{0} but will not include
+## step @code{0} in the generated states and sequence.
 ##
 ## Arguments are
 ##
-## @itemize
+## @itemize @bullet
 ## @item
 ## @var{len} is the number of steps to generate. @var{sequence} and
-## @var{states} will have @var{len} entries each
+## @var{states} will have @var{len} entries each.
+##
 ## @item
-## @var{transprob} is the matrix with the transition probabilities for the
-## states. @code{transprob (i, j)} is the probability for a transition to
-## state @code{j} given state @code{i}
+## @var{transprob} is the matrix of transition probabilities for the states.
+## @code{transprob (i, j)} is the probability for a transition to state
+## @code{j} given state @code{i}.
+##
 ## @item
-## @var{outprob} is the matrix with the output probabilities.
+## @var{outprob} is the matrix of output probabilities.
 ## @code{outprob (i, j)} is the probability for generating output @code{j}
-## given state @code{i}
+## given state @code{i}.
 ## @end itemize
 ##
 ## Return values are
 ##
-## @itemize
+## @itemize @bullet
 ## @item
-## @var{sequence} is a vector of length @var{len} with the generated
+## @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)}
+## @code{columns (outprob)}.
+##
 ## @item
-## @var{states} is a vector of length @var{len} with the generated hidden
+## @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)}
+## @code{columns (transprob)}.
 ## @end itemize
 ##
-## If '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{'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 '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
+## 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.
 ##
 ## 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
 ##
 ## References:
 ##
-## @itemize
+## @enumerate
 ## @item
-## @cite{Matlab 7.0 documentation (pdf)}
+## W. L. Martinez and A. R. Martinez. @cite{Computational Statistics
+## Handbook with MATLAB.} Chapman & Hall/CRC, pages 547-557, 2001.
+##
 ## @item
-## @uref{http://en.wikipedia.org/wiki/Hidden_Markov_Model}
-## @end itemize
-##
+## Wikipedia contributors. Hidden Markov model. @cite{Wikipedia, The Free
+## Encyclopedia.}
+## @uref{http://en.wikipedia.org/w/index.php?title=Hidden_Markov_model&oldid=81100294},
+## October 2006.
+## @end enumerate
 ## @end deftypefn
 
 ## Author: Arno Onken <whyly@gmx.net>
+## Description: Output sequence and hidden states for a Hidden Markov Model
 
 function [sequence, states] = hmmgenerate (len, transprob, outprob, varargin)
 

--- a/main/statistics/inst/hmmviterbi.m	Sun Oct 15 08:55:05 2006 +0000
+++ b/main/statistics/inst/hmmviterbi.m	Sun Oct 15 19:50:42 2006 +0000
@@ -20,68 +20,87 @@
 ## @deftypefnx {Function File} {} hmmviterbi (@dots{}, 'statenames', @var{statenames})
 ## Uses the Viterbi algorithm to find the Viterbi path for a Hidden Markov
 ## Model given a sequence of outputs. The model assumes that the generation
-## begins with state @code{1} in step @code{0} but does not include step
-## @code{0} in the generated states and sequence
+## starts in state @code{1} at step @code{0} but does not include step
+## @code{0} in the generated states and sequence.
 ##
 ## Arguments are
 ##
-## @itemize
+## @itemize @bullet
 ## @item
-## @var{sequence} is the vector of length @var{len} with given outputs. The
-## outputs must be integers ranging from @code{1} to @code{columns (outprob)}
+## @var{sequence} is the vector of length @var{len} of given outputs. The
+## outputs must be integers ranging from @code{1} to
+## @code{columns (outprob)}.
+##
 ## @item
-## @var{transprob} is the matrix with the transition probabilities for the
-## states. @code{transprob (i, j)} is the probability for a transition to
-## state @code{j} given state @code{i}
+## @var{transprob} is the matrix of transition probabilities for the states.
+## @code{transprob (i, j)} is the probability for a transition to state
+## @code{j} given state @code{i}.
+##
 ## @item
-## @var{outprob} is the matrix with the output probabilities.
+## @var{outprob} is the matrix of output probabilities.
 ## @code{outprob (i, j)} is the probability for generating output @code{j}
-## given state @code{i}
+## given state @code{i}.
 ## @end itemize
 ##
 ## Return values are
 ##
-## @itemize
+## @itemize @bullet
 ## @item
-## @var{vpath} is the vector of the same length as @var{sequence} with the
+## @var{vpath} is the vector of the same length as @var{sequence} of the
 ## estimated hidden states. The states are integers ranging from @code{1} to
-## @code{columns (transprob)}
+## @code{columns (transprob)}.
 ## @end itemize
 ##
-## If 'symbols' is specified, then @var{sequence} is expected to be a
+## If @code{'symbols'} is specified, then @var{sequence} is expected to be a
 ## sequence of the elements of @var{symbols} instead of integers ranging
-## from @code{1} to @code{columns (outprob)}. @var{symbols} can be a cell array
+## from @code{1} to @code{columns (outprob)}. @var{symbols} can be a cell array.
 ##
-## If 'statenames' is specified, then the elements of @var{statenames} are
-## used for the states in @var{vpath} instead of integers ranging from
-## @code{1} to @code{columns (transprob)}. @var{statenames} can be a cell array
+## If @code{'statenames'} is specified, then the elements of
+## @var{statenames} are used for the states in @var{vpath} instead of
+## integers ranging from @code{1} to @code{columns (transprob)}.
+## @var{statenames} can be a cell array.
 ##
 ## 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)
 ## vpath = hmmviterbi (sequence, transprob, outprob)
+## @end group
 ##
+## @group
 ## symbols = @{'A', 'B', 'C'@};
 ## statenames = @{'One', 'Two'@};
 ## [sequence, states] = hmmgenerate (25, transprob, outprob, 'symbols', symbols, 'statenames', statenames)
 ## vpath = hmmviterbi (sequence, transprob, outprob, 'symbols', symbols, 'statenames', statenames)
+## @end group
 ## @end example
 ##
 ## References:
 ##
-## @itemize
+## @enumerate
 ## @item
-## @cite{Matlab 7.0 documentation (pdf)}
+## W. L. Martinez and A. R. Martinez. @cite{Computational Statistics
+## Handbook with MATLAB.} Chapman & Hall/CRC, pages 547-557, 2001.
+##
 ## @item
-## @uref{http://en.wikipedia.org/wiki/Viterbi_algorithm}
-## @end itemize
+## Wikipedia contributors. Hidden Markov model. @cite{Wikipedia, The Free
+## Encyclopedia.}
+## @uref{http://en.wikipedia.org/w/index.php?title=Hidden_Markov_model&oldid=81100294},
+## October 2006.
 ##
+## @item
+## Wikipedia contributors. Viterbi algorithm. @cite{Wikipedia, The Free
+## Encyclopedia.}
+## @uref{http://en.wikipedia.org/w/index.php?title=Viterbi_algorithm&oldid=73517908},
+## September 2006.
+## @end enumerate
 ## @end deftypefn
 
 ## Author: Arno Onken <whyly@gmx.net>
+## Description: Viterbi path for a Hidden Markov Model
 
 function vpath = hmmviterbi (sequence, transprob, outprob, varargin)