treetime/clock_tree.py
def date_uncertainty_due_to_rate(self, node, interval=(0.05, 0.095)):
        """use previously calculated variation of the rate to estimate
        the uncertainty in a particular numdate due to rate variation.

        Parameters
        ----------
        node : PhyloTree.Clade
            node for which the confidence interval is to be calculated
        interval : tuple, optional
            Array of length two, or tuple, defining the bounds of the confidence interval

        """
        if hasattr(node, "numdate_rate_variation"):
            from scipy.special import erfinv
            nsig = [np.sqrt(2.0)*erfinv(-1.0 + 2.0*x) if x*(1.0-x) else 0
                    for x in interval]
            l,c,u = [x[1] for x in node.numdate_rate_variation]
            return np.array([c + x*np.abs(y-c) for x,y in zip(nsig, (l,u))])

        else:
            return None
def date_uncertainty_due_to_rate(self, node, interval=(0.05, 0.095)):
        if hasattr(node, "numdate_rate_variation"):
            from scipy.special import erfinv
            nsig = [np.sqrt(2.0)*erfinv(-1.0 + 2.0*x) if x*(1.0-x) else 0
                    for x in interval]
            l,c,u = [x[1] for x in node.numdate_rate_variation]
            return np.array([c + x*np.abs(y-c) for x,y in zip(nsig, (l,u))])

        else:
            return None
def date_uncertainty_due_to_rate ( self , node , interval = ( 0.05 , 0.095 ) ) : if hasattr ( node , "numdate_rate_variation" ) : from scipy . special import erfinv nsig = [ np . sqrt ( 2.0 ) * erfinv ( - 1.0 + 2.0 * x ) if x * ( 1.0 - x ) else 0 for x in interval ] l , c , u = [ x [ 1 ] for x in node . numdate_rate_variation ] return np . array ( [ c + x * np . abs ( y - c ) for x , y in zip ( nsig , ( l , u ) ) ] ) else : return None
use previously calculated variation of the rate to estimate
        the uncertainty in a particular numdate due to rate variation.

        Parameters
        ----------
        node : PhyloTree.Clade
            node for which the confidence interval is to be calculated
        interval : tuple, optional
            Array of length two, or tuple, defining the bounds of the confidence interval
use previously calculated variation of the rate to estimate the uncertainty in a particular numdate due to rate variation .