treetime/clock_tree.py
def _ml_t_marginal(self, assign_dates=False):
        """
        Compute the marginal probability distribution of the internal nodes positions by
        propagating from the tree leaves towards the root. The result of
        this operation are the probability distributions of each internal node,
        conditional on the constraints on all leaves of the tree, which have sampling dates.
        The probability distributions are set as marginal_pos_LH attributes to the nodes.

        Parameters
        ----------

         assign_dates : bool, default False
            If True, the inferred dates will be assigned to the nodes as
            :code:`time_before_present' attributes, and their branch lengths
            will be corrected accordingly.
            .. Note::
                Normally, the dates are assigned by running joint reconstruction.

        Returns
        -------

         None
            Every internal node is assigned the probability distribution in form
            of an interpolation object and sends this distribution further towards the
            root.

        """

        def _cleanup():
            for node in self.tree.find_clades():
                try:
                    del node.marginal_pos_Lx
                    del node.subtree_distribution
                    del node.msg_from_parent
                    #del node.marginal_pos_LH
                except:
                    pass


        self.logger("ClockTree - Marginal reconstruction:  Propagating leaves -> root...", 2)
        # go through the nodes from leaves towards the root:
        for node in self.tree.find_clades(order='postorder'):  # children first, msg to parents
            if node.bad_branch:
                # no information
                node.marginal_pos_Lx = None
            else: # all other nodes
                if node.date_constraint is not None and node.date_constraint.is_delta: # there is a time constraint
                    # initialize the Lx for nodes with precise date constraint:
                    # subtree probability given the position of the parent node
                    # position of the parent node is given by the branch length
                    # distribution attached to the child node position
                    node.subtree_distribution = node.date_constraint
                    bl = node.branch_length_interpolator.x
                    x = bl + node.date_constraint.peak_pos
                    node.marginal_pos_Lx = Distribution(x, node.branch_length_interpolator(bl),
                                                        min_width=self.min_width, is_log=True)

                else: # all nodes without precise constraint but positional information
                      # subtree likelihood given the node's constraint and child msg:
                    msgs_to_multiply = [node.date_constraint] if node.date_constraint is not None else []
                    msgs_to_multiply.extend([child.marginal_pos_Lx for child in node.clades
                                             if child.marginal_pos_Lx is not None])

                    # combine the different msgs and constraints
                    if len(msgs_to_multiply)==0:
                        # no information
                        node.marginal_pos_Lx = None
                        continue
                    elif len(msgs_to_multiply)==1:
                        node.subtree_distribution = msgs_to_multiply[0]
                    else: # combine the different msgs and constraints
                        node.subtree_distribution = Distribution.multiply(msgs_to_multiply)

                    if node.up is None: # this is the root, set dates
                        node.subtree_distribution._adjust_grid(rel_tol=self.rel_tol_prune)
                        node.marginal_pos_Lx = node.subtree_distribution
                        node.marginal_pos_LH = node.subtree_distribution
                        self.tree.positional_marginal_LH = -node.subtree_distribution.peak_val
                    else: # otherwise propagate to parent
                        res, res_t = NodeInterpolator.convolve(node.subtree_distribution,
                                        node.branch_length_interpolator,
                                        max_or_integral='integral',
                                        n_grid_points = self.node_grid_points,
                                        n_integral=self.n_integral,
                                        rel_tol=self.rel_tol_refine)
                        res._adjust_grid(rel_tol=self.rel_tol_prune)
                        node.marginal_pos_Lx = res

        self.logger("ClockTree - Marginal reconstruction:  Propagating root -> leaves...", 2)
        from scipy.interpolate import interp1d
        for node in self.tree.find_clades(order='preorder'):

            ## The root node
            if node.up is None:
                node.msg_from_parent = None # nothing beyond the root
            # all other cases (All internal nodes + unconstrained terminals)
            else:
                parent = node.up
                # messages from the complementary subtree (iterate over all sister nodes)
                complementary_msgs = [sister.marginal_pos_Lx for sister in parent.clades
                                            if (sister != node) and (sister.marginal_pos_Lx is not None)]

                # if parent itself got smth from the root node, include it
                if parent.msg_from_parent is not None:
                    complementary_msgs.append(parent.msg_from_parent)
                elif parent.marginal_pos_Lx is not None:
                    complementary_msgs.append(parent.marginal_pos_LH)

                if len(complementary_msgs):
                    msg_parent_to_node = NodeInterpolator.multiply(complementary_msgs)
                    msg_parent_to_node._adjust_grid(rel_tol=self.rel_tol_prune)
                else:
                    x = [parent.numdate, numeric_date()]
                    msg_parent_to_node = NodeInterpolator(x, [1.0, 1.0],min_width=self.min_width)

                # integral message, which delivers to the node the positional information
                # from the complementary subtree
                res, res_t = NodeInterpolator.convolve(msg_parent_to_node, node.branch_length_interpolator,
                                                    max_or_integral='integral',
                                                    inverse_time=False,
                                                    n_grid_points = self.node_grid_points,
                                                    n_integral=self.n_integral,
                                                    rel_tol=self.rel_tol_refine)

                node.msg_from_parent = res
                if node.marginal_pos_Lx is None:
                    node.marginal_pos_LH = node.msg_from_parent
                else:
                    node.marginal_pos_LH = NodeInterpolator.multiply((node.msg_from_parent, node.subtree_distribution))

                self.logger('ClockTree._ml_t_root_to_leaves: computed convolution'
                                ' with %d points at node %s'%(len(res.x),node.name),4)

                if self.debug:
                    tmp = np.diff(res.y-res.peak_val)
                    nsign_changed = np.sum((tmp[1:]*tmp[:-1]<0)&(res.y[1:-1]-res.peak_val<500))
                    if nsign_changed>1:
                        import matplotlib.pyplot as plt
                        plt.ion()
                        plt.plot(res.x, res.y-res.peak_val, '-o')
                        plt.plot(res.peak_pos - node.branch_length_interpolator.x,
                                 node.branch_length_interpolator(node.branch_length_interpolator.x)-node.branch_length_interpolator.peak_val, '-o')
                        plt.plot(msg_parent_to_node.x,msg_parent_to_node.y-msg_parent_to_node.peak_val, '-o')
                        plt.ylim(0,100)
                        plt.xlim(-0.05, 0.05)
                        import ipdb; ipdb.set_trace()

            # assign positions of nodes and branch length only when desired
            # since marginal reconstruction can result in negative branch length
            if assign_dates:
                node.time_before_present = node.marginal_pos_LH.peak_pos
                if node.up:
                    node.clock_length = node.up.time_before_present - node.time_before_present
                    node.branch_length = node.clock_length

            # construct the inverse cumulant distribution to evaluate confidence intervals
            if node.marginal_pos_LH.is_delta:
                node.marginal_inverse_cdf=interp1d([0,1], node.marginal_pos_LH.peak_pos*np.ones(2), kind="linear")
            else:
                dt = np.diff(node.marginal_pos_LH.x)
                y = node.marginal_pos_LH.prob_relative(node.marginal_pos_LH.x)
                int_y = np.concatenate(([0], np.cumsum(dt*(y[1:]+y[:-1])/2.0)))
                int_y/=int_y[-1]
                node.marginal_inverse_cdf = interp1d(int_y, node.marginal_pos_LH.x, kind="linear")
                node.marginal_cdf = interp1d(node.marginal_pos_LH.x, int_y, kind="linear")

        if not self.debug:
            _cleanup()

        return
def _ml_t_marginal(self, assign_dates=False):
        """
        Compute the marginal probability distribution of the internal nodes positions by
        propagating from the tree leaves towards the root. The result of
        this operation are the probability distributions of each internal node,
        conditional on the constraints on all leaves of the tree, which have sampling dates.
        The probability distributions are set as marginal_pos_LH attributes to the nodes.

        Parameters
        ----------

         assign_dates : bool, default False
            If True, the inferred dates will be assigned to the nodes as
            :code:`time_before_present' attributes, and their branch lengths
            will be corrected accordingly.
            .. Note::
                Normally, the dates are assigned by running joint reconstruction.

        Returns
        -------

         None
            Every internal node is assigned the probability distribution in form
            of an interpolation object and sends this distribution further towards the
            root.

        """

        def _cleanup():
            for node in self.tree.find_clades():
                try:
                    del node.marginal_pos_Lx
                    del node.subtree_distribution
                    del node.msg_from_parent
                    #del node.marginal_pos_LH
                except:
                    pass


        self.logger("ClockTree - Marginal reconstruction:  Propagating leaves -> root...", 2)
        # go through the nodes from leaves towards the root:
        for node in self.tree.find_clades(order='postorder'):  # children first, msg to parents
            if node.bad_branch:
                # no information
                node.marginal_pos_Lx = None
            else: # all other nodes
                if node.date_constraint is not None and node.date_constraint.is_delta: # there is a time constraint
                    # initialize the Lx for nodes with precise date constraint:
                    # subtree probability given the position of the parent node
                    # position of the parent node is given by the branch length
                    # distribution attached to the child node position
                    node.subtree_distribution = node.date_constraint
                    bl = node.branch_length_interpolator.x
                    x = bl + node.date_constraint.peak_pos
                    node.marginal_pos_Lx = Distribution(x, node.branch_length_interpolator(bl),
                                                        min_width=self.min_width, is_log=True)

                else: # all nodes without precise constraint but positional information
                      # subtree likelihood given the node's constraint and child msg:
                    msgs_to_multiply = [node.date_constraint] if node.date_constraint is not None else []
                    msgs_to_multiply.extend([child.marginal_pos_Lx for child in node.clades
                                             if child.marginal_pos_Lx is not None])

                    # combine the different msgs and constraints
                    if len(msgs_to_multiply)==0:
                        # no information
                        node.marginal_pos_Lx = None
                        continue
                    elif len(msgs_to_multiply)==1:
                        node.subtree_distribution = msgs_to_multiply[0]
                    else: # combine the different msgs and constraints
                        node.subtree_distribution = Distribution.multiply(msgs_to_multiply)

                    if node.up is None: # this is the root, set dates
                        node.subtree_distribution._adjust_grid(rel_tol=self.rel_tol_prune)
                        node.marginal_pos_Lx = node.subtree_distribution
                        node.marginal_pos_LH = node.subtree_distribution
                        self.tree.positional_marginal_LH = -node.subtree_distribution.peak_val
                    else: # otherwise propagate to parent
                        res, res_t = NodeInterpolator.convolve(node.subtree_distribution,
                                        node.branch_length_interpolator,
                                        max_or_integral='integral',
                                        n_grid_points = self.node_grid_points,
                                        n_integral=self.n_integral,
                                        rel_tol=self.rel_tol_refine)
                        res._adjust_grid(rel_tol=self.rel_tol_prune)
                        node.marginal_pos_Lx = res

        self.logger("ClockTree - Marginal reconstruction:  Propagating root -> leaves...", 2)
        from scipy.interpolate import interp1d
        for node in self.tree.find_clades(order='preorder'):

            ## The root node
            if node.up is None:
                node.msg_from_parent = None # nothing beyond the root
            # all other cases (All internal nodes + unconstrained terminals)
            else:
                parent = node.up
                # messages from the complementary subtree (iterate over all sister nodes)
                complementary_msgs = [sister.marginal_pos_Lx for sister in parent.clades
                                            if (sister != node) and (sister.marginal_pos_Lx is not None)]

                # if parent itself got smth from the root node, include it
                if parent.msg_from_parent is not None:
                    complementary_msgs.append(parent.msg_from_parent)
                elif parent.marginal_pos_Lx is not None:
                    complementary_msgs.append(parent.marginal_pos_LH)

                if len(complementary_msgs):
                    msg_parent_to_node = NodeInterpolator.multiply(complementary_msgs)
                    msg_parent_to_node._adjust_grid(rel_tol=self.rel_tol_prune)
                else:
                    x = [parent.numdate, numeric_date()]
                    msg_parent_to_node = NodeInterpolator(x, [1.0, 1.0],min_width=self.min_width)

                # integral message, which delivers to the node the positional information
                # from the complementary subtree
                res, res_t = NodeInterpolator.convolve(msg_parent_to_node, node.branch_length_interpolator,
                                                    max_or_integral='integral',
                                                    inverse_time=False,
                                                    n_grid_points = self.node_grid_points,
                                                    n_integral=self.n_integral,
                                                    rel_tol=self.rel_tol_refine)

                node.msg_from_parent = res
                if node.marginal_pos_Lx is None:
                    node.marginal_pos_LH = node.msg_from_parent
                else:
                    node.marginal_pos_LH = NodeInterpolator.multiply((node.msg_from_parent, node.subtree_distribution))

                self.logger('ClockTree._ml_t_root_to_leaves: computed convolution'
                                ' with %d points at node %s'%(len(res.x),node.name),4)

                if self.debug:
                    tmp = np.diff(res.y-res.peak_val)
                    nsign_changed = np.sum((tmp[1:]*tmp[:-1]<0)&(res.y[1:-1]-res.peak_val<500))
                    if nsign_changed>1:
                        import matplotlib.pyplot as plt
                        plt.ion()
                        plt.plot(res.x, res.y-res.peak_val, '-o')
                        plt.plot(res.peak_pos - node.branch_length_interpolator.x,
                                 node.branch_length_interpolator(node.branch_length_interpolator.x)-node.branch_length_interpolator.peak_val, '-o')
                        plt.plot(msg_parent_to_node.x,msg_parent_to_node.y-msg_parent_to_node.peak_val, '-o')
                        plt.ylim(0,100)
                        plt.xlim(-0.05, 0.05)
                        import ipdb; ipdb.set_trace()

            # assign positions of nodes and branch length only when desired
            # since marginal reconstruction can result in negative branch length
            if assign_dates:
                node.time_before_present = node.marginal_pos_LH.peak_pos
                if node.up:
                    node.clock_length = node.up.time_before_present - node.time_before_present
                    node.branch_length = node.clock_length

            # construct the inverse cumulant distribution to evaluate confidence intervals
            if node.marginal_pos_LH.is_delta:
                node.marginal_inverse_cdf=interp1d([0,1], node.marginal_pos_LH.peak_pos*np.ones(2), kind="linear")
            else:
                dt = np.diff(node.marginal_pos_LH.x)
                y = node.marginal_pos_LH.prob_relative(node.marginal_pos_LH.x)
                int_y = np.concatenate(([0], np.cumsum(dt*(y[1:]+y[:-1])/2.0)))
                int_y/=int_y[-1]
                node.marginal_inverse_cdf = interp1d(int_y, node.marginal_pos_LH.x, kind="linear")
                node.marginal_cdf = interp1d(node.marginal_pos_LH.x, int_y, kind="linear")

        if not self.debug:
            _cleanup()

        return
def _ml_t_marginal ( self , assign_dates = False ) : def _cleanup ( ) : for node in self . tree . find_clades ( ) : try : del node . marginal_pos_Lx del node . subtree_distribution del node . msg_from_parent #del node.marginal_pos_LH except : pass self . logger ( "ClockTree - Marginal reconstruction:  Propagating leaves -> root..." , 2 ) # go through the nodes from leaves towards the root: for node in self . tree . find_clades ( order = 'postorder' ) : # children first, msg to parents if node . bad_branch : # no information node . marginal_pos_Lx = None else : # all other nodes if node . date_constraint is not None and node . date_constraint . is_delta : # there is a time constraint # initialize the Lx for nodes with precise date constraint: # subtree probability given the position of the parent node # position of the parent node is given by the branch length # distribution attached to the child node position node . subtree_distribution = node . date_constraint bl = node . branch_length_interpolator . x x = bl + node . date_constraint . peak_pos node . marginal_pos_Lx = Distribution ( x , node . branch_length_interpolator ( bl ) , min_width = self . min_width , is_log = True ) else : # all nodes without precise constraint but positional information # subtree likelihood given the node's constraint and child msg: msgs_to_multiply = [ node . date_constraint ] if node . date_constraint is not None else [ ] msgs_to_multiply . extend ( [ child . marginal_pos_Lx for child in node . clades if child . marginal_pos_Lx is not None ] ) # combine the different msgs and constraints if len ( msgs_to_multiply ) == 0 : # no information node . marginal_pos_Lx = None continue elif len ( msgs_to_multiply ) == 1 : node . subtree_distribution = msgs_to_multiply [ 0 ] else : # combine the different msgs and constraints node . subtree_distribution = Distribution . multiply ( msgs_to_multiply ) if node . up is None : # this is the root, set dates node . subtree_distribution . _adjust_grid ( rel_tol = self . rel_tol_prune ) node . marginal_pos_Lx = node . subtree_distribution node . marginal_pos_LH = node . subtree_distribution self . tree . positional_marginal_LH = - node . subtree_distribution . peak_val else : # otherwise propagate to parent res , res_t = NodeInterpolator . convolve ( node . subtree_distribution , node . branch_length_interpolator , max_or_integral = 'integral' , n_grid_points = self . node_grid_points , n_integral = self . n_integral , rel_tol = self . rel_tol_refine ) res . _adjust_grid ( rel_tol = self . rel_tol_prune ) node . marginal_pos_Lx = res self . logger ( "ClockTree - Marginal reconstruction:  Propagating root -> leaves..." , 2 ) from scipy . interpolate import interp1d for node in self . tree . find_clades ( order = 'preorder' ) : ## The root node if node . up is None : node . msg_from_parent = None # nothing beyond the root # all other cases (All internal nodes + unconstrained terminals) else : parent = node . up # messages from the complementary subtree (iterate over all sister nodes) complementary_msgs = [ sister . marginal_pos_Lx for sister in parent . clades if ( sister != node ) and ( sister . marginal_pos_Lx is not None ) ] # if parent itself got smth from the root node, include it if parent . msg_from_parent is not None : complementary_msgs . append ( parent . msg_from_parent ) elif parent . marginal_pos_Lx is not None : complementary_msgs . append ( parent . marginal_pos_LH ) if len ( complementary_msgs ) : msg_parent_to_node = NodeInterpolator . multiply ( complementary_msgs ) msg_parent_to_node . _adjust_grid ( rel_tol = self . rel_tol_prune ) else : x = [ parent . numdate , numeric_date ( ) ] msg_parent_to_node = NodeInterpolator ( x , [ 1.0 , 1.0 ] , min_width = self . min_width ) # integral message, which delivers to the node the positional information # from the complementary subtree res , res_t = NodeInterpolator . convolve ( msg_parent_to_node , node . branch_length_interpolator , max_or_integral = 'integral' , inverse_time = False , n_grid_points = self . node_grid_points , n_integral = self . n_integral , rel_tol = self . rel_tol_refine ) node . msg_from_parent = res if node . marginal_pos_Lx is None : node . marginal_pos_LH = node . msg_from_parent else : node . marginal_pos_LH = NodeInterpolator . multiply ( ( node . msg_from_parent , node . subtree_distribution ) ) self . logger ( 'ClockTree._ml_t_root_to_leaves: computed convolution' ' with %d points at node %s' % ( len ( res . x ) , node . name ) , 4 ) if self . debug : tmp = np . diff ( res . y - res . peak_val ) nsign_changed = np . sum ( ( tmp [ 1 : ] * tmp [ : - 1 ] < 0 ) & ( res . y [ 1 : - 1 ] - res . peak_val < 500 ) ) if nsign_changed > 1 : import matplotlib . pyplot as plt plt . ion ( ) plt . plot ( res . x , res . y - res . peak_val , '-o' ) plt . plot ( res . peak_pos - node . branch_length_interpolator . x , node . branch_length_interpolator ( node . branch_length_interpolator . x ) - node . branch_length_interpolator . peak_val , '-o' ) plt . plot ( msg_parent_to_node . x , msg_parent_to_node . y - msg_parent_to_node . peak_val , '-o' ) plt . ylim ( 0 , 100 ) plt . xlim ( - 0.05 , 0.05 ) import ipdb ipdb . set_trace ( ) # assign positions of nodes and branch length only when desired # since marginal reconstruction can result in negative branch length if assign_dates : node . time_before_present = node . marginal_pos_LH . peak_pos if node . up : node . clock_length = node . up . time_before_present - node . time_before_present node . branch_length = node . clock_length # construct the inverse cumulant distribution to evaluate confidence intervals if node . marginal_pos_LH . is_delta : node . marginal_inverse_cdf = interp1d ( [ 0 , 1 ] , node . marginal_pos_LH . peak_pos * np . ones ( 2 ) , kind = "linear" ) else : dt = np . diff ( node . marginal_pos_LH . x ) y = node . marginal_pos_LH . prob_relative ( node . marginal_pos_LH . x ) int_y = np . concatenate ( ( [ 0 ] , np . cumsum ( dt * ( y [ 1 : ] + y [ : - 1 ] ) / 2.0 ) ) ) int_y /= int_y [ - 1 ] node . marginal_inverse_cdf = interp1d ( int_y , node . marginal_pos_LH . x , kind = "linear" ) node . marginal_cdf = interp1d ( node . marginal_pos_LH . x , int_y , kind = "linear" ) if not self . debug : _cleanup ( ) return
Compute the marginal probability distribution of the internal nodes positions by
        propagating from the tree leaves towards the root. The result of
        this operation are the probability distributions of each internal node,
        conditional on the constraints on all leaves of the tree, which have sampling dates.
        The probability distributions are set as marginal_pos_LH attributes to the nodes.

        Parameters
        ----------

         assign_dates : bool, default False
            If True, the inferred dates will be assigned to the nodes as
            :code:`time_before_present' attributes, and their branch lengths
            will be corrected accordingly.
            .. Note::
                Normally, the dates are assigned by running joint reconstruction.

        Returns
        -------

         None
            Every internal node is assigned the probability distribution in form
            of an interpolation object and sends this distribution further towards the
            root.
Compute the marginal probability distribution of the internal nodes positions by propagating from the tree leaves towards the root . The result of this operation are the probability distributions of each internal node conditional on the constraints on all leaves of the tree which have sampling dates . The probability distributions are set as marginal_pos_LH attributes to the nodes .