small update, and question

[cecileane]

I changed the order of the 2 root models to have "OUfixedRoot" come first, to make it the default model. That's because the covariance of the random root model can become near singular sometimes.

Also, the documentation for the estimation function says this: "The row names of the data must be in the same order as the tip labels." It that still true? It looks like you changed the code to avoid this constraint. Would the constraint still apply to the plotting function though? The order is changed, if needed, inside the estimating function, but this re-ordering would not affect the data outside that function. So the constraint may persist for the plotting function. I wished I had time right now to check this, but I don't...

[khabbazian]

Thanks for the corrections. I do reordering of the tree but the shift configuration is the index of the edges in postorder. I should convert it into the original order of the tree. The same thing about the plot_l1ou. There are couple of other things that you suggested that I havn't implement them yet. I will try to fix all over weekend. Thanks-Mohammad