def _update_pi_vars(self):
with scipy.errstate(divide='<STR_LIT>', under='<STR_LIT>', over='<STR_LIT>',<EOL>invalid='<STR_LIT>'):<EOL><INDENT>for r in range(self.nsites):<EOL><INDENT>self.pi_codon[r] = self.pi[r][CODON_TO_AA]<EOL>pim = scipy.tile(self.pi_codon[r], (N_CODON, <NUM_LIT:1>)) <EOL>self.piAx_piAy[r] = pim.transpose() / pim<EOL><DEDENT>self.ln_pi_codon = scipy.log(self.pi_codon)<EOL>self.piAx_piAy_beta = self.piAx_piAy**self.beta<EOL>self.ln_piAx_piAy_beta = scipy.log(self.piAx_piAy_beta)<EOL><DEDENT>
Update variables that depend on `pi`.

        These are `pi_codon`, `ln_pi_codon`, `piAx_piAy`, `piAx_piAy_beta`,
        `ln_piAx_piAy_beta`.

        Update using current `pi` and `beta`.