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Updated docstrings in FitModel
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tomasstolker committed Jan 18, 2021
1 parent 9161273 commit c92e198
Showing 1 changed file with 12 additions and 8 deletions.
20 changes: 12 additions & 8 deletions species/analysis/fit_model.py
Original file line number Diff line number Diff line change
Expand Up @@ -444,7 +444,7 @@ def __init__(self,
- The :func:`~species.plot.plot_mcmc.plot_photometry` function can be used to
calculate synthetic photometry and error bars from the posterior distribution.
- Only supported by ``run_ultranest``.
- Only supported by ``run_ultranest`` and ``run_multinest``.
Calibration parameters:
Expand Down Expand Up @@ -486,7 +486,7 @@ def __init__(self,
``bounds`` dictionary, for example ``bounds={'ism_ext': (0., 10.),
'ism_red': (0., 20.)}``.
- Only supported by ``run_ultranest``.
- Only supported by ``run_ultranest`` and ``run_multinest``.
Log-normal size distribution:
Expand All @@ -512,7 +512,7 @@ def __init__(self,
- A uniform prior is used for ``lognorm_sigma`` and ``lognorm_ext``, and a
log-uniform prior for ``lognorm_radius``.
- Only supported by ``run_ultranest``.
- Only supported by ``run_ultranest`` and ``run_multinest``.
Power-law size distribution:
Expand All @@ -537,7 +537,7 @@ def __init__(self,
- A uniform prior is used for ``powerlaw_exp`` and ``powerlaw_ext``, and a
log-uniform prior for ``powerlaw_max``.
- Only supported by ``run_ultranest``.
- Only supported by ``run_ultranest`` and ``run_multinest``.
Blackbody disk emission:
Expand All @@ -548,7 +548,7 @@ def __init__(self,
For example, ``bounds={'teff': (2000., 3000.), 'radius': (1., 5.),
'logg': (3.5, 4.5), 'disk_teff': (100., 2000.), 'disk_radius': (1., 100.)}``.
- Only supported by ``run_ultranest``.
- Only supported by ``run_ultranest`` and ``run_multinest``.
inc_phot : bool, list(str)
Include photometric data in the fit. If a boolean, either all (``True``) or none
Expand Down Expand Up @@ -915,9 +915,11 @@ def run_mcmc(self,
"""
Function to run the MCMC sampler of ``emcee``. The functionalities of ``run_mcmc`` are
more limited than :func:`~species.analysis.fit_model.FitModel.run_ultranest` and
``run_ultranest`` provides more robust results when sampling multimodal posterior
distributions and has the additional advantage of returning the model evidence. Therefore,
it is recommended to use ``run_ultranest`` instead of ``run_mcmc``.
:func:`~species.analysis.fit_model.FitModel.run_multinest`. Furthermore, ``run_ultranest``
``run_multinest`` provide more robust results when sampling multimodal posterior
distributions and have the additional advantage of returning the marginal likelihood (i.e.
"evidence"). Therefore, it is recommended to use ``run_ultranest`` or ``run_multinest``
instead of ``run_mcmc``.
Parameters
----------
Expand Down Expand Up @@ -1413,7 +1415,9 @@ def run_multinest(self,
of ``MultiNest`` should be set to the environmental variable ``LD_LIBRARY_PATH`` on a
Linux machine and ``DYLD_LIBRARY_PATH`` on a Mac. Alternatively, the variable can be
set before importing the ``species`` package, for example:
.. code-block:: python
>>> import os
>>> os.environ['DYLD_LIBRARY_PATH'] = '/path/to/MultiNest/lib'
>>> import species
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