treetime/gtr_site_specific.py
def assign_rates(self, mu=1.0, pi=None, W=None):
        """
        Overwrite the GTR model given the provided data

        Parameters
        ----------

         mu : float
            Substitution rate

         W : nxn matrix
            Substitution matrix

         pi : n vector
            Equilibrium frequencies

        """
        n = len(self.alphabet)
        self.mu = np.copy(mu)

        if pi is not None and pi.shape[0]==n:
            self.seq_len = pi.shape[-1]
            Pi = np.copy(pi)
        else:
            if pi is not None and len(pi)!=n:
                self.logger("length of equilibrium frequency vector does not match alphabet length", 4, warn=True)
                self.logger("Ignoring input equilibrium frequencies", 4, warn=True)
            Pi = np.ones(shape=(n,self.seq_len))

        self.Pi = Pi/np.sum(Pi, axis=0)

        if W is None or W.shape!=(n,n):
            if (W is not None) and W.shape!=(n,n):
                self.logger("Substitution matrix size does not match alphabet size", 4, warn=True)
                self.logger("Ignoring input substitution matrix", 4, warn=True)
            # flow matrix
            W = np.ones((n,n))
        else:
            W=0.5*(np.copy(W)+np.copy(W).T)

        np.fill_diagonal(W,0)
        avg_pi = self.Pi.mean(axis=-1)
        average_rate = W.dot(avg_pi).dot(avg_pi)
        self.W = W/average_rate
        self.mu *=average_rate

        self._eig()
def assign_rates(self, mu=1.0, pi=None, W=None):
        """
        Overwrite the GTR model given the provided data

        Parameters
        ----------

         mu : float
            Substitution rate

         W : nxn matrix
            Substitution matrix

         pi : n vector
            Equilibrium frequencies

        """
        n = len(self.alphabet)
        self.mu = np.copy(mu)

        if pi is not None and pi.shape[0]==n:
            self.seq_len = pi.shape[-1]
            Pi = np.copy(pi)
        else:
            if pi is not None and len(pi)!=n:
                self.logger("length of equilibrium frequency vector does not match alphabet length", 4, warn=True)
                self.logger("Ignoring input equilibrium frequencies", 4, warn=True)
            Pi = np.ones(shape=(n,self.seq_len))

        self.Pi = Pi/np.sum(Pi, axis=0)

        if W is None or W.shape!=(n,n):
            if (W is not None) and W.shape!=(n,n):
                self.logger("Substitution matrix size does not match alphabet size", 4, warn=True)
                self.logger("Ignoring input substitution matrix", 4, warn=True)
            # flow matrix
            W = np.ones((n,n))
        else:
            W=0.5*(np.copy(W)+np.copy(W).T)

        np.fill_diagonal(W,0)
        avg_pi = self.Pi.mean(axis=-1)
        average_rate = W.dot(avg_pi).dot(avg_pi)
        self.W = W/average_rate
        self.mu *=average_rate

        self._eig()
Overwrite the GTR model given the provided data

        Parameters
        ----------

         mu : float
            Substitution rate

         W : nxn matrix
            Substitution matrix

         pi : n vector
            Equilibrium frequencies