treetime/merger_models.py
def skyline_inferred(self, gen=1.0, confidence=False):
        '''
        return the skyline, i.e., an estimate of the inverse rate of coalesence.
        This function merely returns the merger rate self.Tc that was set or
        estimated by other means. If it was determined using self.optimize_skyline,
        the returned skyline will maximize the coalescent likelihood.
        parameters:
            gen -- number of generations per year. Unit of time is branch length,
                   hence this needs to be the inverse substitution rate per generation
            confidence -- False, or number of standard deviations of confidence intervals
        '''
        if len(self.Tc.x)<=2:
            print("no skyline has been inferred, returning constant population size")
            return gen/self.date2dist.clock_rate*self.Tc.y[-1]

        skyline = interp1d(self.date2dist.to_numdate(self.Tc.x[1:-1]), gen/self.date2dist.clock_rate*self.Tc.y[1:-1])
        if confidence and hasattr(self, 'confidence'):
            conf = [skyline.y*np.exp(-confidence*self.confidence), skyline.y*np.exp(confidence*self.confidence)]
            return skyline, conf
        else:
            return skyline
def skyline_inferred(self, gen=1.0, confidence=False):
        '''
        return the skyline, i.e., an estimate of the inverse rate of coalesence.
        This function merely returns the merger rate self.Tc that was set or
        estimated by other means. If it was determined using self.optimize_skyline,
        the returned skyline will maximize the coalescent likelihood.
        parameters:
            gen -- number of generations per year. Unit of time is branch length,
                   hence this needs to be the inverse substitution rate per generation
            confidence -- False, or number of standard deviations of confidence intervals
        '''
        if len(self.Tc.x)<=2:
            print("no skyline has been inferred, returning constant population size")
            return gen/self.date2dist.clock_rate*self.Tc.y[-1]

        skyline = interp1d(self.date2dist.to_numdate(self.Tc.x[1:-1]), gen/self.date2dist.clock_rate*self.Tc.y[1:-1])
        if confidence and hasattr(self, 'confidence'):
            conf = [skyline.y*np.exp(-confidence*self.confidence), skyline.y*np.exp(confidence*self.confidence)]
            return skyline, conf
        else:
            return skyline
return the skyline, i.e., an estimate of the inverse rate of coalesence.
        This function merely returns the merger rate self.Tc that was set or
        estimated by other means. If it was determined using self.optimize_skyline,
        the returned skyline will maximize the coalescent likelihood.
        parameters:
            gen -- number of generations per year. Unit of time is branch length,
                   hence this needs to be the inverse substitution rate per generation
            confidence -- False, or number of standard deviations of confidence intervals