treetime/gtr.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 = mu

        if pi is not None and len(pi)==n:
            Pi = np.array(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.Pi = Pi/np.sum(Pi)

        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))
            np.fill_diagonal(W, 0.0)
            np.fill_diagonal(W, - W.sum(axis=0))
        else:
            W=np.array(W)

        self.W = 0.5*(W+W.T)
        self._check_fix_Q(fixed_mu=True)
        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 = mu

        if pi is not None and len(pi)==n:
            Pi = np.array(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.Pi = Pi/np.sum(Pi)

        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))
            np.fill_diagonal(W, 0.0)
            np.fill_diagonal(W, - W.sum(axis=0))
        else:
            W=np.array(W)

        self.W = 0.5*(W+W.T)
        self._check_fix_Q(fixed_mu=True)
        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