cbcBayesThermoInt Namespace Reference

Functions
def	extract_temp (filename)
	Extracts the PTMCMC temperature from the header lines of the given file. More...
def	get_mean_logl (filename)
	Returns the mean value of log(L) from the given filename, excluding the first 50% of samples as burn-in. More...

Variables
string	usage
	parser = OptionParser(usage=usage)
	metavar
	default
	help
	options
	args
	betas = np.array([1.0/extract_temp(f) for f in args])
	logls = np.array([get_mean_logl(f) for f in args])
	inds = np.argsort(betas)[::-1]
	ebetas = np.concatenate((betas, [0.0]))
	elogls = np.concatenate((logls, [logls[-1]]))
	ebetas2 = np.concatenate((betas[::2], [0.0]))
	elogls2 = np.concatenate((logls[::2], [logls[::2][-1]]))
	evidence = -trapezoid(elogls, ebetas)
	evidence2 = -trapezoid(elogls2, ebetas2)
	devidence = np.abs(evidence - evidence2)

Function Documentation

extract_temp()

def cbcBayesThermoInt.extract_temp

(

filename

)

Extracts the PTMCMC temperature from the header lines of the given file.

Definition at line 20 of file cbcBayesThermoInt.py.

get_mean_logl()

def cbcBayesThermoInt.get_mean_logl

(

filename

)

Returns the mean value of log(L) from the given filename, excluding the first 50% of samples as burn-in.

Definition at line 39 of file cbcBayesThermoInt.py.

Variable Documentation

usage

string cbcBayesThermoInt.usage

(

void

)

Initial value:

=  """%s [-h] [--plotfile FILE] [--evfile FILE] OUTPUT_FILE [OUTPUT_FILE ...]
 
Thermodynamic integration on PTMCMC samples.
 
positional arguments:
  OUTPUT_FILE      PTMCMC output files""" % (os.path.basename(sys.argv[0]))

Definition at line 60 of file cbcBayesThermoInt.py.

parser

cbcBayesThermoInt.parser = OptionParser(usage=usage)

Definition at line 67 of file cbcBayesThermoInt.py.

metavar

cbcBayesThermoInt.metavar

Definition at line 68 of file cbcBayesThermoInt.py.

default

cbcBayesThermoInt.default

Definition at line 68 of file cbcBayesThermoInt.py.

help

cbcBayesThermoInt.help

Definition at line 68 of file cbcBayesThermoInt.py.

options

cbcBayesThermoInt.options

Definition at line 71 of file cbcBayesThermoInt.py.

args

cbcBayesThermoInt.args

Definition at line 71 of file cbcBayesThermoInt.py.

betas

cbcBayesThermoInt.betas = np.array([1.0/extract_temp(f) for f in args])

Definition at line 77 of file cbcBayesThermoInt.py.

logls

cbcBayesThermoInt.logls = np.array([get_mean_logl(f) for f in args])

Definition at line 78 of file cbcBayesThermoInt.py.

inds

cbcBayesThermoInt.inds = np.argsort(betas)[::-1]

Definition at line 80 of file cbcBayesThermoInt.py.

ebetas

cbcBayesThermoInt.ebetas = np.concatenate((betas, [0.0]))

Definition at line 88 of file cbcBayesThermoInt.py.

elogls

cbcBayesThermoInt.elogls = np.concatenate((logls, [logls[-1]]))

Definition at line 89 of file cbcBayesThermoInt.py.

ebetas2

cbcBayesThermoInt.ebetas2 = np.concatenate((betas[::2], [0.0]))

Definition at line 91 of file cbcBayesThermoInt.py.

elogls2

cbcBayesThermoInt.elogls2 = np.concatenate((logls[::2], [logls[::2][-1]]))

Definition at line 92 of file cbcBayesThermoInt.py.

evidence

cbcBayesThermoInt.evidence = -trapezoid(elogls, ebetas)

Definition at line 94 of file cbcBayesThermoInt.py.

evidence2

cbcBayesThermoInt.evidence2 = -trapezoid(elogls2, ebetas2)

Definition at line 95 of file cbcBayesThermoInt.py.

devidence

cbcBayesThermoInt.devidence = np.abs(evidence - evidence2)

Definition at line 97 of file cbcBayesThermoInt.py.