treetime/clock_tree.py
def make_time_tree(self, time_marginal=False, clock_rate=None, **kwargs):
        '''
        Use the date constraints to calculate the most likely positions of
        unconstrained nodes.

        Parameters
        ----------

         time_marginal : bool
            If true, use marginal reconstruction for node positions

         **kwargs
            Key word arguments to initialize dates constraints

        '''
        self.logger("ClockTree: Maximum likelihood tree optimization with temporal constraints",1)

        self.init_date_constraints(clock_rate=clock_rate, **kwargs)

        if time_marginal:
            self._ml_t_marginal(assign_dates = time_marginal=="assign")
        else:
            self._ml_t_joint()

        self.convert_dates()
def make_time_tree(self, time_marginal=False, clock_rate=None, **kwargs):
        '''
        Use the date constraints to calculate the most likely positions of
        unconstrained nodes.

        Parameters
        ----------

         time_marginal : bool
            If true, use marginal reconstruction for node positions

         **kwargs
            Key word arguments to initialize dates constraints

        '''
        self.logger("ClockTree: Maximum likelihood tree optimization with temporal constraints",1)

        self.init_date_constraints(clock_rate=clock_rate, **kwargs)

        if time_marginal:
            self._ml_t_marginal(assign_dates = time_marginal=="assign")
        else:
            self._ml_t_joint()

        self.convert_dates()
def make_time_tree ( self , time_marginal = False , clock_rate = None , * * kwargs ) : self . logger ( "ClockTree: Maximum likelihood tree optimization with temporal constraints" , 1 ) self . init_date_constraints ( clock_rate = clock_rate , * * kwargs ) if time_marginal : self . _ml_t_marginal ( assign_dates = time_marginal == "assign" ) else : self . _ml_t_joint ( ) self . convert_dates ( )
Use the date constraints to calculate the most likely positions of
        unconstrained nodes.

        Parameters
        ----------

         time_marginal : bool
            If true, use marginal reconstruction for node positions

         **kwargs
            Key word arguments to initialize dates constraints
Use the date constraints to calculate the most likely positions of unconstrained nodes .