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[Octave-cvsupdate] SF.net SVN: octave:[11049] trunk/octave-forge/main/statistics
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From: <jpi...@us...> - 2012-09-18 21:35:48
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Revision: 11049
http://octave.svn.sourceforge.net/octave/?rev=11049&view=rev
Author: jpicarbajal
Date: 2012-09-18 21:35:42 +0000 (Tue, 18 Sep 2012)
Log Message:
-----------
statistics:adding dendogram function. Working but not finshed.
Modified Paths:
--------------
trunk/octave-forge/main/statistics/INDEX
trunk/octave-forge/main/statistics/NEWS
trunk/octave-forge/main/statistics/inst/linkage.m
Added Paths:
-----------
trunk/octave-forge/main/statistics/inst/dendogram.m
Modified: trunk/octave-forge/main/statistics/INDEX
===================================================================
--- trunk/octave-forge/main/statistics/INDEX 2012-09-18 18:43:56 UTC (rev 11048)
+++ trunk/octave-forge/main/statistics/INDEX 2012-09-18 21:35:42 UTC (rev 11049)
@@ -57,6 +57,7 @@
normplot
histfit
repanova
+ dendogram
Models
hmmestimate hmmgenerate hmmviterbi
Hypothesis testing
Modified: trunk/octave-forge/main/statistics/NEWS
===================================================================
--- trunk/octave-forge/main/statistics/NEWS 2012-09-18 18:43:56 UTC (rev 11048)
+++ trunk/octave-forge/main/statistics/NEWS 2012-09-18 21:35:42 UTC (rev 11049)
@@ -3,7 +3,7 @@
** The following functions are new:
- regress_gp
+ regress_gp dendogram
** The interface of the following functions has been modified:
Added: trunk/octave-forge/main/statistics/inst/dendogram.m
===================================================================
--- trunk/octave-forge/main/statistics/inst/dendogram.m (rev 0)
+++ trunk/octave-forge/main/statistics/inst/dendogram.m 2012-09-18 21:35:42 UTC (rev 11049)
@@ -0,0 +1,114 @@
+%% Copyright (c) 2012 Juan Pablo Carbajal <car...@if...>
+%%
+%% 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
+%% 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{h} = } dendogram (@var{tree})
+%% Plots a dendogram using the output of function @command{linkage}.
+%%
+%% TODO: This function needs your help to be finished! Leafs must be ordered to
+%% prevent corssing of edges.
+%% @seealso{linkage}
+%% @end deftypefn
+
+## TODO
+# Order leafs nodes to avoid edge crossing.
+
+function h = dendogram (tree)
+
+ [m d] = size (tree);
+ if d != 3
+ error ("Input data must be a tree as returned by function linkage.")
+ end
+ n = m + 1;
+
+ nc = max(tree(:,1:2)(:));
+
+ % Vector with the horizontal and vertical position of each cluster
+ p = zeros (nc,2);
+
+##### This is an ugly hack and is a partial solution. If you know how to oder
+##### the leafs do it. Please do not copy from dendogram.m of Mathworks!
+
+ %% Order the leafs
+ % find which clusters contain th eleafs
+ tf = ismember (tree(:,1:2),1:n);
+ [idx_i,idx_j] = find (tf);
+ ind0 = find(tf(:));
+
+ % Assign a position between 1:n to the leafs according to clustering
+ % I am trying to avoid crossings. Better way? sure!.
+ i = 1;
+ j = 0;
+ while j < n
+
+ % If the current leaf hasn't a position assigned, assign one.
+ if p(tree(idx_i(i),idx_j(i)),1) == 0
+ j+=1;
+ p(tree(idx_i(i),idx_j(i)),1) = j;
+ end
+
+ % Check if the current cluster has another leaf. If it has and the leaf
+ % doesn't have a position, assign one.
+ next = tree(idx_i(i),setdiff(1:2,idx_j(i)));
+ if next <= n && p(next,1) == 0
+ j+=1;
+ p(next,1) = j;
+ end
+
+ % Find the id of the current cluster and check if any other cluster
+ % that will be merged with this one has a leaf.
+ c_id = idx_i(i) + n;
+ [idx,~] = find (tree(:,1:2)==c_id);
+ idx2 = find (tree(idx,1:2)<=n);
+ if ~isempty (idx2) && p(tree(idx,idx2),1) == 0
+ j+=1;
+ p(tree(idx,idx2),1) = j;
+ end
+ i+=1;
+ end
+
+##### End of the hack
+
+ % Compute the horizontal position, begin-end
+ % and vertical position of all clusters.
+ for i = 1:m
+ p(n+i,1) = mean (p(tree(i,1:2),1));
+ p(n+i,2) = tree(i,3);
+ x(i,1:2) = p(tree(i,1:2),1);
+ end
+
+
+
+ clf
+ % plot horizontal lines
+ tmp = line (x', tree(:,[3 3])');
+
+ % plot vertical lines
+ for i=1:nc
+ [ind,~] = find (tree(:,1:2)==i);
+ tmp = line (p([i; i],1),[p(i,2); tree(ind,3)]);
+ end
+
+ xticks = 1:n;
+ xl_txt = arrayfun (@num2str, tree(:,1:2)(ind0),"uniformoutput",false);
+ set (gca,"xticklabel",xl_txt,"xtick",xticks);
+ axis ([0.5 n+0.5 0 max(tree(:,3))+0.1*min(tree(:,3))]);
+
+endfunction
+
+%!demo
+%! y = [4 5; 2 6; 3 7; 8 9; 1 10];
+%! y(:,3) = 1:5;
+%! dendogram(y);
Modified: trunk/octave-forge/main/statistics/inst/linkage.m
===================================================================
--- trunk/octave-forge/main/statistics/inst/linkage.m 2012-09-18 18:43:56 UTC (rev 11048)
+++ trunk/octave-forge/main/statistics/inst/linkage.m 2012-09-18 21:35:42 UTC (rev 11049)
@@ -34,8 +34,8 @@
## cluster and numbering those from 1 to n. Then it merges two
## clusters, chosen according to @var{method}, to create a new cluster
## numbered n+1, and so on until all observations are grouped into
-## a single cluster numbered 2*n-1. Row m of the
-## (m-1)x3 output matrix relates to cluster n+m: the first
+## a single cluster numbered 2(n-1). Row k of the
+## (m-1)x3 output matrix relates to cluster n+k: the first
## two columns are the numbers of the two component clusters and column
## 3 contains their distance.
##
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