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rst formatting of lists
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JohannesBuchner committed May 29, 2024
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Showing 1 changed file with 31 additions and 24 deletions.
55 changes: 31 additions & 24 deletions ultranest/integrator.py
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Expand Up @@ -2383,62 +2383,69 @@ def run(
results (dict): Results dictionary, with the following entries:
- samples (ndarray): re-weighted posterior samples: distributed according
to :math:`p(\theta | d)` - these points are not sorted, and can be assumed
to have been randomly shuffled.
See :py:func:`ultranest.utils.resample_equal` for more details.
to :math:`p(\theta | d)` - these points are not sorted, and can be assumed
to have been randomly shuffled.
See :py:func:`ultranest.utils.resample_equal` for more details.
- logz (float64): natural logarithm of the evidence
:math:`\log Z = \log \int p(d|\theta) p(\theta) \text{d}\theta`
:math:`\log Z = \log \int p(d|\theta) p(\theta) \text{d}\theta`
- logzerr (float64): global estimate of the :math:`1\sigma` error on
:math:`\log Z`
(`can be safely assumed to be Gaussian <https://github.com/JohannesBuchner/UltraNest/issues/63>`_);
obtained as the quadratic sum of ``logz_bs`` and ``logz_tail``.
Users are advised to use ``logz`` :math:`\pm` ``logzerr``
as the best estimate for the evidence and its error.
:math:`\log Z`
(`can be safely assumed to be Gaussian <https://github.com/JohannesBuchner/UltraNest/issues/63>`_);
obtained as the quadratic sum of ``logz_bs`` and ``logz_tail``.
Users are advised to use ``logz`` :math:`\pm` ``logzerr``
as the best estimate for the evidence and its error.
- niter (int): number of sampler iterations
- ncall (int): total number of likelihood evaluations (accepted and not)
- logz_bs (float64): estimate of :math:`\log Z` from bootstrapping -
for details, see the
`ultranest paper <https://joss.theoj.org/papers/10.21105/joss.03001>`_
for details, see the
`ultranest paper <https://joss.theoj.org/papers/10.21105/joss.03001>`_
- logzerr_bs (float64): estimate of the error on the of :math:`\log Z`
from bootstrapping
from bootstrapping
- logz_single (float64): estimate of :math:`\log Z` from a single sampler
- logzerr_single (float64): estimate of the error :math:`\log Z` from a
single sampler, obtained as :math:`\sqrt{H / n_{\text{live}}}`
single sampler, obtained as :math:`\sqrt{H / n_{\text{live}}}`
- logzerr_tail (float64): contribution of the tail (i.e. the terminal
leaves of the tree) to the error on :math:`\log Z` (?)
leaves of the tree) to the error on :math:`\log Z` (?)
- ess (float64): effective sample size, i.e. number of samples divided by
the estimated correlation length, estimated as
:math:`N / (1 + N^{-1} \sum_i (N w_i - 1)^2)` where :math:`w_i` are
the sample weights while :math:`N` is the number of samples
the estimated correlation length, estimated as
:math:`N / (1 + N^{-1} \sum_i (N w_i - 1)^2)` where :math:`w_i` are
the sample weights while :math:`N` is the number of samples
- H (float64): `information gained <https://arxiv.org/abs/2205.00009>`_
- Herr (float64): (Gaussian) :math:`1\sigma` error on :math:`H`
- posterior (dict): summary information on the posterior marginal distributions for each parameter -
a dictionary of lists each with as many items as the fit parameters,
indexed as :math:`\theta_i` in the following:
a dictionary of lists each with as many items as the fit parameters,
indexed as :math:`\theta_i` in the following:
- mean (list): expectation value of :math:`\theta_i`
- stdev (list): standard deviation of :math:`\theta_i`
- median (list): median of :math:`\theta_i`
- errlo (list): one-sigma lower quantile of the marginal for :math:`\theta_i`, i.e. 15.8655% quantile
- errup (list): one-sigma upper quantile of the marginal for :math:`\theta_i`, i.e. 84.1345% quantile
- information_gain_bits (list): information gain from the marginal prior on :math:`\theta_i` to the posterior
- weighted_samples (dict): weighted samples from the posterior, as computed during sampling,
sorted by their log-likelihood value
sorted by their log-likelihood value
- upoints (ndarray): sample locations in the unit cube :math:`[0, 1]^{d}`,
where :math:`d` is the number of parameters - the shape is ``n_iter`` by :math:`d`
where :math:`d` is the number of parameters - the shape is ``n_iter`` by :math:`d`
- points (ndarray): sample locations in the physical, user-provided space (same shape as ``upoints``)
- weights (ndarray): sample weights - shape ``n_iter``, they sum to 1
- logw (ndarray): logs of the sample weights (?)
- bootstrapped_weights (ndarray): bootstrapped estimate of the sample weights
- logl (ndarray): log-likelihood values at the sample points
- maximum_likelihood (dict): summary information on the maximum likelihood value
:math:`\theta_{ML}` found by the posterior exploration
:math:`\theta_{ML}` found by the posterior exploration
- logl (float64): value of the log-likelihood at this point: :math:`\log p(d | \theta_{ML})`
- point (list): coordinates of :math:`\theta_{ML}` in the physical space
- point_untransformed (list): coordinates of :math:`\theta_{ML}` in the unit cube :math:`[0, 1]^{d}`
- paramnames (list): input parameter names
- insertion_order_MWW_test (dict): results for the Mann-Whitney U-test;
for more information, see the :py:class:`ultranest.netiter.MultiCounter` class
or `section 4.5.2 of Buchner 2023 <http://arxiv.org/abs/2101.09675>`_
for more information, see the :py:class:`ultranest.netiter.MultiCounter` class
or `section 4.5.2 of Buchner 2023 <http://arxiv.org/abs/2101.09675>`_
- independent_iterations (float): shortest insertion order test run length
- converged (bool): whether the run is converged according to the MWW test, at the given threshold
"""
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