mcmc.rst | mcmc.rst | |||
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skipping to change at line 21 | skipping to change at line 21 | |||
- emcee_walkers: emcee v3.x multi-Walkers algorithms with M oves | - emcee_walkers: emcee v3.x multi-Walkers algorithms with M oves | |||
- dynesty: unsupported | - dynesty: unsupported | |||
- multinest: still experimental | - multinest: still experimental | |||
- pymc3: to be implemented | - pymc3: to be implemented | |||
mcmc_sampling: | mcmc_sampling: | |||
- galpak: 'Cauchy' [default] | 'Normal' | 'AdaptiveCauchy' | - galpak: 'Cauchy' [default] | 'Normal' | 'AdaptiveCauchy' | |||
- emcee_walkers: 'walkers' [default] | 'walkersCauchy' | 'D E' | 'Snooker' | 'Cauchy' | 'Normal' | - emcee_walkers: 'walkers' [default] | 'walkersCauchy' | 'D E' | 'Snooker' | 'Cauchy' | 'Normal' | |||
- multinest: None | - multinest: None | |||
- pymc3: to be implemented | - pymc3: to be implemented | |||
The proposal sampling methods | The proposal sampling methods | |||
.. figure:: images/GalPaK_MCMC.png | .. figure:: images/GalPaK_MCMC.png | |||
:scale: 60% | :scale: 60% | |||
:align: center | :align: center | |||
GalPaK3D uses an internal :class:`MCMC <galpak.MCMC>` class which extend th e galpak class. | GalPaK3D uses an internal :class:`MCMC <galpak.MCMC>` class which extend th e galpak class. | |||
This can be used to call its likelihood such as : :: | This can be used to call its likelihood such as: :: | |||
li = gk(params) | li = gk(params) | |||
using a :meth:`self.__call__() <MCMC.__call__>` method which returns the ln prob | using a :meth:`self.__call__() <MCMC.__call__>` method which returns the ln prob | |||
Here is a full example: :: | Here is a full example: :: | |||
import galpak | import galpak | |||
gk=galpak.GalPaK3D('data/input/GalPaK_cube_1101_from_paper.fits',model= galpak.DefaultModel()) | gk=galpak.GalPaK3D('data/input/GalPaK_cube_1101_from_paper.fits',model= galpak.DefaultModel()) | |||
p=gk.model.Parameters() | p=gk.model.Parameters() | |||
params=p.from_ndarray([15,15,15,1e-16,5,60,90,1,100,10]) | params=p.from_ndarray([15,15,15,1e-16,5,60,90,1,100,10]) | |||
End of changes. 2 change blocks. | ||||
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