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Constraints on tree (Read 2168 times)

ofedrigo

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Constraints on tree
Feb 8^th, 2006 at 7:22am

Hi,

If you try to contrain differently one branch and the rest of the tree. I was wondering if there is a required order to specify the constraints. When you apply a contraint, does it automatically clear previously specified constraints?

In other words, is it equivalent to do:

ExecuteCommands ("tree1."+branch+".t:=omega1*tree2."+branch+".t;");
ReplicateConstraint ("this1.?.t:=omega2*this2.?.t",tree1,tree2);
or
ReplicateConstraint ("this1.?.t:=omega2*this2.?.t",tree1,tree2);
ExecuteCommands ("tree1."+branch+".t:=omega1*tree2."+branch+".t;");
?

thanks,

Olivier

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Sergei

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Re: Constraints on tree
Reply #1 - Feb 10^th, 2006 at 9:55am

Dear Olivier,

Quote:

If you try to contrain differently one branch and the rest of the tree. I was wondering if there is a required order to specify the constraints. When you apply a contraint, does it automatically clear previously specified constraints?

In other words, is it equivalent to do:

ExecuteCommands ("tree1."+branch+".t:=omega1*tree2."+branch+".t;");
ReplicateConstraint ("this1.?.t:=omega2*this2.?.t",tree1,tree2);
or
ReplicateConstraint ("this1.?.t:=omega2*this2.?.t",tree1,tree2);
ExecuteCommands ("tree1."+branch+".t:=omega1*tree2."+branch+".t;");
?

The order is not important in this case. ReplicateConstraint will scan all the branches, and apply constraints (when appropriate) only if the parameters have niot been previously constained. If you choose order 1 (branch/rest), ReplicateConstraint will not be applied to the branch (you need to use ClearConstraints before calling ReplicateConstraint if you want to override this behavior). In order 2, ReplicateConstraint will apply to all branches of the tree not previously constrained, but ExecuteCommand will override the assignment for the branch you want. messages.log will contain the constraints generated by ReplicateConstraint if you wanted to double-check.

It also is probably a good idea to call ClearConstraints (givenTree) before you impose any new constraints to make sure nothing unwanted carries over from the previous commands.

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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