he nodes of the DAG
are permuted according to the topological order. If <code>FALSE</code> the nodes are
in the order they first appear in the model formulae (from left to right).
For use in the <code>phylopath</code> package, this should always be kept to <code>TRUE</code>,
but the argument is available to avoid potential problems with masking the
function from other packages.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>An object of classes <code>matrix</code> and <code>DAG</code