treetime/treetime.py
def print_lh(self, joint=True):
        """
        Print the total likelihood of the tree given the constrained leaves

        Parameters
        ----------

         joint : bool
            If true, print joint LH, else print marginal LH

        """
        try:
            u_lh = self.tree.unconstrained_sequence_LH
            if joint:
                s_lh = self.tree.sequence_joint_LH
                t_lh = self.tree.positional_joint_LH
                c_lh = self.tree.coalescent_joint_LH
            else:
                s_lh = self.tree.sequence_marginal_LH
                t_lh = self.tree.positional_marginal_LH
                c_lh = 0

            print ("###  Tree Log-Likelihood  ###\n"
                " Sequence log-LH without constraints: \t%1.3f\n"
                " Sequence log-LH with constraints:    \t%1.3f\n"
                " TreeTime sequence log-LH:            \t%1.3f\n"
                " Coalescent log-LH:                   \t%1.3f\n"
               "#########################"%(u_lh, s_lh,t_lh, c_lh))
        except:
            print("ERROR. Did you run the corresponding inference (joint/marginal)?")
def print_lh(self, joint=True):
        """
        Print the total likelihood of the tree given the constrained leaves

        Parameters
        ----------

         joint : bool
            If true, print joint LH, else print marginal LH

        """
        try:
            u_lh = self.tree.unconstrained_sequence_LH
            if joint:
                s_lh = self.tree.sequence_joint_LH
                t_lh = self.tree.positional_joint_LH
                c_lh = self.tree.coalescent_joint_LH
            else:
                s_lh = self.tree.sequence_marginal_LH
                t_lh = self.tree.positional_marginal_LH
                c_lh = 0

            print ("###  Tree Log-Likelihood  ###\n"
                " Sequence log-LH without constraints: \t%1.3f\n"
                " Sequence log-LH with constraints:    \t%1.3f\n"
                " TreeTime sequence log-LH:            \t%1.3f\n"
                " Coalescent log-LH:                   \t%1.3f\n"
               "#########################"%(u_lh, s_lh,t_lh, c_lh))
        except:
            print("ERROR. Did you run the corresponding inference (joint/marginal)?")
Print the total likelihood of the tree given the constrained leaves

        Parameters
        ----------

         joint : bool
            If true, print joint LH, else print marginal LH