Author: bugman
Date: Fri Oct 9 18:41:08 2009
New Revision: 9704
URL: http://svn.gna.org/viewcvs/relax?rev=9704&view=rev
Log:
Merged revisions 9696,9700 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r9696 | semor | 2009-10-09 14:44:40 +0200 (Fri, 09 Oct 2009) | 10 lines
Improved the error handling for AICc model selection.
The code now tells users with too small datasets (n<=k) why AICc model
selection does not work in
their situation.
This follows a discussion started at:
https://mail.gna.org/public/relax-devel/2009-10/msg00015.html
(# Message-id: <4ACD6F60.7060102@xxxxxxxxx>)
........
r9700 | bugman | 2009-10-09 18:00:30 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a copyright notice and a function for returning the SVN revision
number to the version module.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/generic_fns/model_selection.py
branches/bmrb/version.py
Propchange: branches/bmrb/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Oct 9 18:41:08 2009
@@ -1,1 +1,1 @@
-/1.3:1-9658
+/1.3:1-9703
Modified: branches/bmrb/generic_fns/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/model_selection.py?rev=9704&r1=9703&r2=9704&view=diff
==============================================================================
--- branches/bmrb/generic_fns/model_selection.py (original)
+++ branches/bmrb/generic_fns/model_selection.py Fri Oct 9 18:41:08 2009
@@ -73,7 +73,12 @@
@rtype: float
"""
- return chi2 + 2.0*k + 2.0*k*(k + 1.0) / (n - k - 1.0)
+ if n > (k+1):
+ return chi2 + 2.0*k + 2.0*k*(k + 1.0) / (n - k - 1.0)
+ elif n == (k+1):
+ raise RelaxError("The size of the dataset, n=%s, is too small for
this model of size k=%s. This situation causes a fatal division by zero
as:\n AICc = chi2 + 2k + 2k*(k + 1) / (n - k - 1).\n\nPlease use AIC model
selection instead." % (n, k))
+ elif n < (k+1):
+ raise RelaxError("The size of the dataset, n=%s, is too small for
this model of size k=%s. This situation produces a negative, and hence
nonsense, AICc score as:\n AICc = chi2 + 2k + 2k*(k + 1) / (n - k -
1).\n\nPlease use AIC model selection instead." % (n, k))
def bic(chi2, k, n):
Modified: branches/bmrb/version.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/version.py?rev=9704&r1=9703&r2=9704&view=diff
==============================================================================
--- branches/bmrb/version.py (original)
+++ branches/bmrb/version.py Fri Oct 9 18:41:08 2009
@@ -1,1 +1,60 @@
+###############################################################################
+#
#
+# Copyright (C) 2009 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax 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 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax 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 relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""Module for relax version information."""
+
+# Python module imports.
+from os import F_OK, access
+from string import split
+from subprocess import PIPE, Popen
+
+
version = "repository checkout"
+
+
+def get_revision():
+ """Attempt to retrieve the SVN revision number, if this is a checked out
copy.
+
+ @return: The SVN revision number, or None if unsuccessful.
+ @rtype: None or str
+ """
+
+ # Does the base directory exist (i.e. is this a checked out copy).
+ if not access('.svn', F_OK):
+ return
+
+ # Try to run 'svn info'.
+ pipe = Popen('svn info', shell=True, stdin=PIPE, stdout=PIPE,
stderr=PIPE, close_fds=True)
+
+ # Errors.
+ if pipe.stderr.readlines():
+ return
+
+ # Loop over the output lines.
+ for line in pipe.stdout.readlines():
+ # Split up the line.
+ row = split(line)
+
+ # The revision.
+ if row[0] == 'Revision:':
+ return row[1]
r9704 - in /branches/bmrb: ./ generic_fns/model_selection.py version.py