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):
        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 ) : 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
Print the total likelihood of the tree given the constrained leaves