-------- Original Message --------
Subject: MorphoJ update
Date: Wed, 29 Feb 2012 06:47:00 -0500
From: Chris Klingenberg <[email protected]>
Reply-To: [email protected]
Organization: University of Manchester
To: [email protected]
Dear morphometricians
I have just uploaded a new version 1.04b of MorphoJ to the web site:
http://www.flywings.org.uk/MorphoJ_page.htm
This version contains a number of minor bug fixes, including problems
with the user interface when switching outlines or wireframes in graphs
of shape changes, and several changes to the user interface and to the
computations of phylogenetically independent contrasts.
The most important change is that analyses involving independent
contrasts are now done without mean-centering (variances and covariances
are computed using deviations from the origin, not the sample mean).
This means, for instance, that regressions are forced through the origin
and covariance matrices are computed from the deviations of independent
contrasts around the origin. This ensures that the order of taxa in the
tree does not matter (i.e., whether contrasts are computed as Left –
Right sister node or Right – Left sister node). In practice, the change
from the previous versions that did not make this distinction is usually
small, because means of independent contrasts are often close to zero
(but this depends on the ordering of taxa, and it is easy to set up a
data set so that there is a big difference!).
For this reason, some minor adjustments were made to principal component
analysis, partial least squares (both PLS between separate blocks and
PLS within a single configuration), and regression analysis for handling
independent contrasts.
The new version also contains a new feature that is likely to be helpful
to users. Graphical output from MorphoJ is more flexible from this
version on, because a new interface has been added, where a variety of
options for the output of shape changes can be set (Set Options for
Shape Graphs in the Preliminaries menu). The options include the color
scheme, whether starting shapes and the numbers of landmarks are to be
displayed, etc. These options are stored with the project and will
therefore be retrieved if the project is saved and opened again later.
http://www.flywings.org.uk/MorphoJ_guide/frameset.htm?preliminaries/setGraphOptions.htm
In addition, changes of the size of the points for landmarks in warped
outline drawings and wireframe graphs (with "Resize Landmark Points" in
the pop-up menu of the respective graph) are now stored with the outline
or wireframe and will apply to all graphs generated with that outline or
wireframe later (i.e., until it is changed again by the user). (For
applying the change to the graphs already displayed in the Graphics tab,
the user needs to generate a fresh copy using "Display Graphs" in the
pop-up menu in the Project Tree window, or change the graph type at
least once.) The changes will apply permanently to the respective
wireframe or outline, that is, until point size is changed again, and
are stored in the project file with the wireframe or outline.
Finally, if the user invokes the "Display Results" command in the pop-up
menu of the Project Tree window for a dataset that has object symmetry,
the pairing of landmarks is now included as part of the information that
is displayed in the results window (previously, this was only in the
output from a Procrustes fit).
I hope these changes and new features will be useful.
Best wishes,
Chris
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Christian Peter Klingenberg
Faculty of Life Sciences
The University of Manchester
Michael Smith Building
Oxford Road
Manchester M13 9PT
United Kingdom
Telephone: +44 161 275 3899
Fax: +44 161 275 5082
E-mail: [email protected]
Web: http://www.flywings.org.uk
Skype: chris_klingenberg
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