logit_rules.py 文件源码

def prior_contribution_phylogeny_parameters(self, state):
        """ Evaluate prior probability of phylogeny mean/std

        Log scale.

        """
        mean_prior = scipy.stats.norm.logpdf(
            state.phylogeny_mean,
            loc = self.phylogeny_lambda_l,
            scale = np.sqrt(self.phylogeny_mean_hyperprior_variance)
        )
        if (0. <= state.phylogeny_std and
            state.phylogeny_std <= self.phylogeny_std_upper_bound):
            std_prior = -1.0*np.log(self.phylogeny_std_upper_bound)
        else:
            std_prior = -np.inf
        return mean_prior + std_prior