Randomisations - add tree perturbation option

[GoogleCodeExporter]

The randomisations currently work only on the basedata (although see recent 
work on group properties - issue #388).  

A useful addition would be to randomly perturb the positions of nodes on any 
trees used as analysis arguments.  

In the first instance this would work only on the terminals, randomly 
reassigning terminal nodes across the tree while maintaining the topology and 
branch structure.  

Further variants could randomly re-assign any named nodes (for cases where 
internals are named).  Later work can also randomly reassign branch lengths.  

Note:  Need to add references for this sort of work. as it has been implemented 
in other systems.

Original issue reported on code.google.com by shawnlaffan on 13 Jul 2013 at 3:56

[GoogleCodeExporter]

This issue was updated by revision r1638.

Add branch for issue related changes

Original comment by shawnlaffan on 13 Jul 2013 at 4:10

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[GoogleCodeExporter]

This issue was updated by revision r1639.

Implement terminal node shuffle.  Includes initial test.

Original comment by shawnlaffan on 13 Jul 2013 at 5:12

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[GoogleCodeExporter]

This issue was updated by revision r1640.

Add tests for shuffling (in progress).

Original comment by shawnlaffan on 13 Jul 2013 at 9:07

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[GoogleCodeExporter]

This issue was updated by revision r1641.

More work on the test for shuffling terminals.  Still too much hard coding, but 
works for now.  

Original comment by shawnlaffan on 13 Jul 2013 at 10:06

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[GoogleCodeExporter]

This issue was updated by revision r1642.

Start caching the shuffled trees.  Make the methods more generic - more needed 
on that front. 
Add tests to check we use the cached objects, and also that we don't corrupt 
the original args. 

Original comment by shawnlaffan on 14 Jul 2013 at 3:31

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[GoogleCodeExporter]

This issue was updated by revision r1643.

Test that the shuffled trees are different between randomisation iterations.  

Original comment by shawnlaffan on 14 Jul 2013 at 3:55

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[GoogleCodeExporter]

This issue was updated by revision r1644.

Fix incorrect search for arguments hash.

Original comment by shawnlaffan on 14 Jul 2013 at 4:09

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[GoogleCodeExporter]

This issue was updated by revision r1645.

Add a no change shuffle option.  Modify tests to handle new shuffles as they 
are developed.  

Original comment by shawnlaffan on 14 Jul 2013 at 6:54

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[GoogleCodeExporter]

This issue was updated by revision r1646.

Now testing a second tree used as an analysis argument.  

Original comment by shawnlaffan on 14 Jul 2013 at 11:18

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[GoogleCodeExporter]

This issue was updated by revision r1647.

Add infrastructure to the GUI.  

Original comment by shawnlaffan on 14 Jul 2013 at 1:30

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[GoogleCodeExporter]

Original comment by shawnlaffan on 14 Jul 2013 at 11:55

• Changed state: Started
• Added labels: Milestone-Release0.18
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[GoogleCodeExporter]

This issue was updated by revision r1649.

Merge changes into the trunk.

Original comment by shawnlaffan on 15 Jul 2013 at 12:25

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[GoogleCodeExporter]

This issue was updated by revision r1650.

Allow abbreviated forms for the shuffling (i.e. we can skip the leading 
"shuffle_").

Original comment by shawnlaffan on 15 Jul 2013 at 1:50

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[GoogleCodeExporter]

This issue was updated by revision r1651.

Merge latest changes into the trunk.

Original comment by shawnlaffan on 15 Jul 2013 at 1:51

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[GoogleCodeExporter]

Default value is coming across as text instead of an array index.  

Argument "no_change" isn't numeric in subroutine entry at 
Biodiverse/GUI/ParametersTable.pm line 177.
Argument "no_change" isn't numeric in subroutine entry at 
Biodiverse/GUI/ParametersTable.pm line 177.

Original comment by shawnlaffan on 15 Jul 2013 at 3:16

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[GoogleCodeExporter]

This issue was updated by revision r1655.

Avoid an undef warning.  

Original comment by shawnlaffan on 15 Jul 2013 at 4:27

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[GoogleCodeExporter]

This issue was updated by revision r1656.

Fix default parameter handling for choice types.

Original comment by shawnlaffan on 15 Jul 2013 at 4:46

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[GoogleCodeExporter]

This issue was updated by revision r1657.

Merge changes to trunk

Original comment by shawnlaffan on 15 Jul 2013 at 5:02

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[GoogleCodeExporter]

Original comment by shawnlaffan on 16 Jul 2013 at 11:05

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• Now blocked on: Randomisations - cache args at the run_analysis level #391

[GoogleCodeExporter]

Mark as fixed
Blocker issue #391 is now fixed.  

Original comment by shawnlaffan on 18 Aug 2013 at 11:09

• Changed state: Fixed
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[GoogleCodeExporter]

This issue was updated by revision r1768.

Delete branch associated with this issue.  

Original comment by shawnlaffan on 19 Aug 2013 at 10:27

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