API¶
This page details the methods and classes provided by the dynesty
module.
TopLevel Interface¶
The toplevel interface (defined natively upon initialization) that
provides access to the two main sampler “superclasses” via
NestedSampler()
and DynamicNestedSampler()
.

dynesty.dynesty.
NestedSampler
(loglikelihood, prior_transform, ndim, nlive=500, bound='multi', sample='auto', periodic=None, reflective=None, update_interval=None, first_update=None, npdim=None, rstate=None, queue_size=None, pool=None, use_pool=None, live_points=None, logl_args=None, logl_kwargs=None, ptform_args=None, ptform_kwargs=None, gradient=None, grad_args=None, grad_kwargs=None, compute_jac=False, enlarge=None, bootstrap=0, vol_dec=0.5, vol_check=2.0, walks=25, facc=0.5, slices=5, fmove=0.9, max_move=100, update_func=None, ncdim=None, save_history=False, history_filename=None, **kwargs)¶ Initializes and returns a sampler object for Static Nested Sampling.
Parameters:  loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. prior_transform : function
Function translating a unit cube to the parameter space according to the prior. The input is a 1d
numpy
array with lengthndim
, where each value is in the range [0, 1). The return value should also be a 1dnumpy
array with lengthndim
, where each value is a parameter. The return value is passed to the loglikelihood function. For example, for a 2 parameter model with flat priors in the range [0, 2), the function would be:def prior_transform(u): return 2.0 * u
 ndim : int
Number of parameters returned by
prior_transform
and accepted byloglikelihood
. nlive : int, optional
Number of “live” points. Larger numbers result in a more finely sampled posterior (more accurate evidence), but also a larger number of iterations required to converge. Default is
500
. bound : {
'none'
,'single'
,'multi'
,'balls'
,'cubes'
}, optional Method used to approximately bound the prior using the current set of live points. Conditions the sampling methods used to propose new live points. Choices are no bound (
'none'
), a single bounding ellipsoid ('single'
), multiple bounding ellipsoids ('multi'
), balls centered on each live point ('balls'
), and cubes centered on each live point ('cubes'
). Default is'multi'
. sample : {
'auto'
,'unif'
,'rwalk'
,'rstagger'
, 'slice'
,'rslice'
,'hslice'
, callable}, optionalMethod used to sample uniformly within the likelihood constraint, conditioned on the provided bounds. Unique methods available are: uniform sampling within the bounds(
'unif'
), random walks with fixed proposals ('rwalk'
), random walks with variable (“staggering”) proposals ('rstagger'
), multivariate slice sampling along preferred orientations ('slice'
), “random” slice sampling along all orientations ('rslice'
), “Hamiltonian” slices along random trajectories ('hslice'
), and any callable function which follows the pattern of the sample methods defined in dynesty.sampling.'auto'
selects the sampling method based on the dimensionality of the problem (fromndim
). Whenndim < 10
, this defaults to'unif'
. When10 <= ndim <= 20
, this defaults to'rwalk'
. Whenndim > 20
, this defaults to'hslice'
if agradient
is provided and'slice'
otherwise.'rstagger'
and'rslice'
are provided as alternatives for'rwalk'
and'slice'
, respectively. Default is'auto'
. periodic : iterable, optional
A list of indices for parameters with periodic boundary conditions. These parameters will not have their positions constrained to be within the unit cube, enabling smooth behavior for parameters that may wrap around the edge. Default is
None
(i.e. no periodic boundary conditions). reflective : iterable, optional
A list of indices for parameters with reflective boundary conditions. These parameters will not have their positions constrained to be within the unit cube, enabling smooth behavior for parameters that may reflect at the edge. Default is
None
(i.e. no reflective boundary conditions). update_interval : int or float, optional
If an integer is passed, only update the proposal distribution every
update_interval
th likelihood call. If a float is passed, update the proposal after everyround(update_interval * nlive)
th likelihood call. Larger update intervals larger can be more efficient when the likelihood function is quick to evaluate. Default behavior is to target a roughly constant change in prior volume, with1.5
for'unif'
,0.15 * walks
for'rwalk'
and'rstagger'
,0.9 * ndim * slices
for'slice'
,2.0 * slices
for'rslice'
, and25.0 * slices
for'hslice'
. first_update : dict, optional
A dictionary containing parameters governing when the sampler should first update the bounding distribution from the unit cube (
'none'
) to the one specified bysample
. Options are the minimum number of likelihood calls ('min_ncall'
) and the minimum allowed overall efficiency in percent ('min_eff'
). Defaults are2 * nlive
and10.
, respectively. npdim : int, optional
Number of parameters accepted by
prior_transform
. This might differ fromndim
in the case where a parameter of loglikelihood is dependent upon multiple independently distributed parameters, some of which may be nuisance parameters. rstate :
RandomState
, optional RandomState
instance. If not given, theglobal random state of the
random
module will be used.
 queue_size : int, optional
Carry out likelihood evaluations in parallel by queueing up new live point proposals using (at most)
queue_size
many threads. Each thread independently proposes new live points until the proposal distribution is updated. If no value is passed, this defaults topool.size
(if apool
has been provided) and1
otherwise (no parallelism). pool : userprovided pool, optional
Use this pool of workers to execute operations in parallel.
 use_pool : dict, optional
A dictionary containing flags indicating where a pool should be used to execute operations in parallel. These govern whether
prior_transform
is executed in parallel during initialization ('prior_transform'
),loglikelihood
is executed in parallel during initialization ('loglikelihood'
), live points are proposed in parallel during a run ('propose_point'
), and bounding distributions are updated in parallel during a run ('update_bound'
). Default isTrue
for all options. live_points : list of 3
ndarray
each with shape (nlive, ndim) A set of live points used to initialize the nested sampling run. Contains
live_u
, the coordinates on the unit cube,live_v
, the transformed variables, andlive_logl
, the associated loglikelihoods. By default, if these are not provided the initial set of live points will be drawn uniformly from the unitnpdim
cube. WARNING: It is crucial that the initial set of live points have been sampled from the prior. Failure to provide a set of valid live points will result in incorrect results. logl_args : iterable, optional
Additional arguments that can be passed to
loglikelihood
. logl_kwargs : dict, optional
Additional keyword arguments that can be passed to
loglikelihood
. ptform_args : iterable, optional
Additional arguments that can be passed to
prior_transform
. ptform_kwargs : dict, optional
Additional keyword arguments that can be passed to
prior_transform
. gradient : function, optional
A function which returns the gradient corresponding to the provided
loglikelihood
with respect to the unit cube. If provided, this will be used when computing reflections when sampling with'hslice'
. If not provided, gradients are approximated numerically using 2sided differencing. grad_args : iterable, optional
Additional arguments that can be passed to
gradient
. grad_kwargs : dict, optional
Additional keyword arguments that can be passed to
gradient
. compute_jac : bool, optional
Whether to compute and apply the Jacobian
dv/du
from the target spacev
to the unit cubeu
when evaluating thegradient
. IfFalse
, the gradient provided is assumed to be already defined with respect to the unit cube. IfTrue
, the gradient provided is assumed to be defined with respect to the target space so the Jacobian needs to be numerically computed and applied. Default isFalse
. enlarge : float, optional
Enlarge the volumes of the specified bounding object(s) by this fraction. The preferred method is to determine this organically using bootstrapping. If
bootstrap > 0
, this defaults to1.0
. Ifbootstrap = 0
, this instead defaults to1.25
. bootstrap : int, optional
Compute this many bootstrapped realizations of the bounding objects. Use the maximum distance found to the set of points left out during each iteration to enlarge the resulting volumes. Can lead to unstable bounding ellipsoids. Default is
0
(no bootstrap). vol_dec : float, optional
For the
'multi'
bounding option, the required fractional reduction in volume after splitting an ellipsoid in order to to accept the split. Default is0.5
. vol_check : float, optional
For the
'multi'
bounding option, the factor used when checking if the volume of the original bounding ellipsoid is large enough to warrant> 2
splits viaell.vol > vol_check * nlive * pointvol
. Default is2.0
. walks : int, optional
For the
'rwalk'
sampling option, the minimum number of steps (minimum 2) before proposing a new live point. Default is25
. facc : float, optional
The target acceptance fraction for the
'rwalk'
sampling option. Default is0.5
. Bounded to be between[1. / walks, 1.]
. slices : int, optional
For the
'slice'
,'rslice'
, and'hslice'
sampling options, the number of times to execute a “slice update” before proposing a new live point. Default is5
. Note that'slice'
cycles through all dimensions when executing a “slice update”. fmove : float, optional
The target fraction of samples that are proposed along a trajectory (i.e. not reflecting) for the
'hslice'
sampling option. Default is0.9
. max_move : int, optional
The maximum number of timesteps allowed for
'hslice'
per proposal forwards and backwards in time. Default is100
. update_func : function, optional
Any callable function which takes in a
blob
andscale
as input and returns a modification to the internalscale
as output. Must follow the pattern of the update methods defined in dynesty.nestedsamplers. If provided, this will supersede the default functions used to update proposals. In the case where a custom callable function is passed tosample
but no similar function is passed toupdate_func
, this will default to no update. ncdim: int, optional
The number of clustering dimensions. The first ncdim dimensions will be sampled using the sampling method, the remaining dimensions will just sample uniformly from the prior distribution. If this is
None
(default), this will default to npdim.
Returns:  sampler : sampler from
nestedsamplers
An initialized instance of the chosen sampler specified via
bound
.

dynesty.dynesty.
DynamicNestedSampler
(loglikelihood, prior_transform, ndim, bound='multi', sample='auto', periodic=None, reflective=None, update_interval=None, first_update=None, npdim=None, rstate=None, queue_size=None, pool=None, use_pool=None, logl_args=None, logl_kwargs=None, ptform_args=None, ptform_kwargs=None, gradient=None, grad_args=None, grad_kwargs=None, compute_jac=False, enlarge=None, bootstrap=0, vol_dec=0.5, vol_check=2.0, walks=25, facc=0.5, slices=5, fmove=0.9, max_move=100, update_func=None, ncdim=None, save_history=False, history_filename=None, **kwargs)¶ Initializes and returns a sampler object for Dynamic Nested Sampling.
Parameters:  loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. prior_transform : function
Function translating a unit cube to the parameter space according to the prior. The input is a 1d
numpy
array with lengthndim
, where each value is in the range [0, 1). The return value should also be a 1dnumpy
array with lengthndim
, where each value is a parameter. The return value is passed to the loglikelihood function. For example, for a 2 parameter model with flat priors in the range [0, 2), the function would be:def prior_transform(u): return 2.0 * u
 ndim : int
Number of parameters returned by
prior_transform
and accepted byloglikelihood
. bound : {
'none'
,'single'
,'multi'
,'balls'
,'cubes'
}, optional Method used to approximately bound the prior using the current set of live points. Conditions the sampling methods used to propose new live points. Choices are no bound (
'none'
), a single bounding ellipsoid ('single'
), multiple bounding ellipsoids ('multi'
), balls centered on each live point ('balls'
), and cubes centered on each live point ('cubes'
). Default is'multi'
. sample : {
'auto'
,'unif'
,'rwalk'
,'rstagger'
, 'slice'
,'rslice'
,'hslice'
}, optionalMethod used to sample uniformly within the likelihood constraint, conditioned on the provided bounds. Unique methods available are: uniform sampling within the bounds(
'unif'
), random walks with fixed proposals ('rwalk'
), random walks with variable (“staggering”) proposals ('rstagger'
), multivariate slice sampling along preferred orientations ('slice'
), “random” slice sampling along all orientations ('rslice'
), “Hamiltonian” slices along random trajectories ('hslice'
), and any callable function which follows the pattern of the sample methods defined in dynesty.sampling.'auto'
selects the sampling method based on the dimensionality of the problem (fromndim
). Whenndim < 10
, this defaults to'unif'
. When10 <= ndim <= 20
, this defaults to'rwalk'
. Whenndim > 20
, this defaults to'hslice'
if agradient
is provided and'slice'
otherwise.'rstagger'
and'rslice'
are provided as alternatives for'rwalk'
and'slice'
, respectively. Default is'auto'
. periodic : iterable, optional
A list of indices for parameters with periodic boundary conditions. These parameters will not have their positions constrained to be within the unit cube, enabling smooth behavior for parameters that may wrap around the edge. Default is
None
(i.e. no periodic boundary conditions). reflective : iterable, optional
A list of indices for parameters with reflective boundary conditions. These parameters will not have their positions constrained to be within the unit cube, enabling smooth behavior for parameters that may reflect at the edge. Default is
None
(i.e. no reflective boundary conditions). update_interval : int or float, optional
If an integer is passed, only update the proposal distribution every
update_interval
th likelihood call. If a float is passed, update the proposal after everyround(update_interval * nlive)
th likelihood call. Larger update intervals larger can be more efficient when the likelihood function is quick to evaluate. Default behavior is to target a roughly constant change in prior volume, with1.5
for'unif'
,0.15 * walks
for'rwalk'
and'rstagger'
,0.9 * ndim * slices
for'slice'
,2.0 * slices
for'rslice'
, and25.0 * slices
for'hslice'
. first_update : dict, optional
A dictionary containing parameters governing when the sampler should first update the bounding distribution from the unit cube (
'none'
) to the one specified bysample
. Options are the minimum number of likelihood calls ('min_ncall'
) and the minimum allowed overall efficiency in percent ('min_eff'
). Defaults are2 * nlive
and10.
, respectively. npdim : int, optional
Number of parameters accepted by
prior_transform
. This might differ fromndim
in the case where a parameter of loglikelihood is dependent upon multiple independently distributed parameters, some of which may be nuisance parameters. rstate :
RandomState
, optional RandomState
instance. If not given, theglobal random state of the
random
module will be used.
 queue_size : int, optional
Carry out likelihood evaluations in parallel by queueing up new live point proposals using (at most)
queue_size
many threads. Each thread independently proposes new live points until the proposal distribution is updated. If no value is passed, this defaults topool.size
(if apool
has been provided) and1
otherwise (no parallelism). pool : userprovided pool, optional
Use this pool of workers to execute operations in parallel.
 use_pool : dict, optional
A dictionary containing flags indicating where a pool should be used to execute operations in parallel. These govern whether
prior_transform
is executed in parallel during initialization ('prior_transform'
),loglikelihood
is executed in parallel during initialization ('loglikelihood'
), live points are proposed in parallel during a run ('propose_point'
), bounding distributions are updated in parallel during a run ('update_bound'
), and the stopping criteria is evaluated in parallel during a run ('stop_function'
). Default isTrue
for all options. logl_args : iterable, optional
Additional arguments that can be passed to
loglikelihood
. logl_kwargs : dict, optional
Additional keyword arguments that can be passed to
loglikelihood
. ptform_args : iterable, optional
Additional arguments that can be passed to
prior_transform
. ptform_kwargs : dict, optional
Additional keyword arguments that can be passed to
prior_transform
. gradient : function, optional
A function which returns the gradient corresponding to the provided
loglikelihood
with respect to the unit cube. If provided, this will be used when computing reflections when sampling with'hslice'
. If not provided, gradients are approximated numerically using 2sided differencing. grad_args : iterable, optional
Additional arguments that can be passed to
gradient
. grad_kwargs : dict, optional
Additional keyword arguments that can be passed to
gradient
. compute_jac : bool, optional
Whether to compute and apply the Jacobian
dv/du
from the target spacev
to the unit cubeu
when evaluating thegradient
. IfFalse
, the gradient provided is assumed to be already defined with respect to the unit cube. IfTrue
, the gradient provided is assumed to be defined with respect to the target space so the Jacobian needs to be numerically computed and applied. Default isFalse
. enlarge : float, optional
Enlarge the volumes of the specified bounding object(s) by this fraction. The preferred method is to determine this organically using bootstrapping. If
bootstrap > 0
, this defaults to1.0
. Ifbootstrap = 0
, this instead defaults to1.25
. bootstrap : int, optional
Compute this many bootstrapped realizations of the bounding objects. Use the maximum distance found to the set of points left out during each iteration to enlarge the resulting volumes. Can lead to unstable bounding ellipsoids. Default is
0
(no bootstrap). vol_dec : float, optional
For the
'multi'
bounding option, the required fractional reduction in volume after splitting an ellipsoid in order to to accept the split. Default is0.5
. vol_check : float, optional
For the
'multi'
bounding option, the factor used when checking if the volume of the original bounding ellipsoid is large enough to warrant> 2
splits viaell.vol > vol_check * nlive * pointvol
. Default is2.0
. walks : int, optional
For the
'rwalk'
sampling option, the minimum number of steps (minimum 2) before proposing a new live point. Default is25
. facc : float, optional
The target acceptance fraction for the
'rwalk'
sampling option. Default is0.5
. Bounded to be between[1. / walks, 1.]
. slices : int, optional
For the
'slice'
,'rslice'
, and'hslice'
sampling options, the number of times to execute a “slice update” before proposing a new live point. Default is5
. Note that'slice'
cycles through all dimensions when executing a “slice update”. fmove : float, optional
The target fraction of samples that are proposed along a trajectory (i.e. not reflecting) for the
'hslice'
sampling option. Default is0.9
. max_move : int, optional
The maximum number of timesteps allowed for
'hslice'
per proposal forwards and backwards in time. Default is100
. update_func : function, optional
Any callable function which takes in a
blob
andscale
as input and returns a modification to the internalscale
as output. Must follow the pattern of the update methods defined in dynesty.nestedsamplers. If provided, this will supersede the default functions used to update proposals. In the case where a custom callable function is passed tosample
but no similar function is passed toupdate_func
, this will default to no update. ncdim: int, optional
The number of clustering dimensions. The first ncdim dimensions will be sampled using the sampling method, the remaining dimensions will just sample uniformly from the prior distribution. If this is
None
(default), this will default to npdim.
Returns:  sampler : a
dynesty.DynamicSampler
instance An initialized instance of the dynamic nested sampler.
Bounding¶
Bounding classes used when proposing new live points, along with a number of useful helper functions. Bounding objects include:
 UnitCube:
 The unit Ncube (unconstrained draws from the prior).
 Ellipsoid:
 Bounding ellipsoid.
 MultiEllipsoid:
 A set of (possibly overlapping) bounding ellipsoids.
 RadFriends:
 A set of (possibly overlapping) balls centered on each live point.
 SupFriends:
 A set of (possibly overlapping) cubes centered on each live point.

class
dynesty.bounding.
UnitCube
(ndim)¶ Bases:
object
An Ndimensional unit cube.
Parameters:  ndim : int
The number of dimensions of the unit cube.

contains
(self, x)¶ Checks if unit cube contains the point
x
.

randoffset
(self, rstate=None)¶ Draw a random offset from the center of the unit cube.

sample
(self, rstate=None)¶ Draw a sample uniformly distributed within the unit cube.
Returns:  x :
ndarray
with shape (ndim,) A coordinate within the unit cube.
 x :

samples
(self, nsamples, rstate=None)¶ Draw
nsamples
samples randomly distributed within the unit cube.Returns:  x :
ndarray
with shape (nsamples, ndim) A collection of coordinates within the unit cube.
 x :

update
(self, points, pointvol=0.0, rstate=None, bootstrap=0, pool=None)¶ Filler function.

class
dynesty.bounding.
Ellipsoid
(ctr, cov, am=None, axes=None)¶ Bases:
object
An Ndimensional ellipsoid defined by:
(x  v)^T A (x  v) = 1
where the vector
v
is the center of the ellipsoid andA
is a symmetric, positivedefiniteN x N
matrix.Parameters: 
contains
(self, x)¶ Checks if ellipsoid contains
x
.

distance
(self, x)¶ Compute the normalized distance to
x
from the center of the ellipsoid.

distance_many
(self, x)¶ Compute the normalized distance to
x
from the center of the ellipsoid.

major_axis_endpoints
(self)¶ Return the endpoints of the major axis.

randoffset
(self, rstate=None)¶ Return a random offset from the center of the ellipsoid.

sample
(self, rstate=None)¶ Draw a sample uniformly distributed within the ellipsoid.
Returns:  x :
ndarray
with shape (ndim,) A coordinate within the ellipsoid.
 x :

samples
(self, nsamples, rstate=None)¶ Draw
nsamples
samples uniformly distributed within the ellipsoid.Returns:  x :
ndarray
with shape (nsamples, ndim) A collection of coordinates within the ellipsoid.
 x :

scale_to_logvol
(self, logvol)¶ Scale ellipoid to a target volume.

unitcube_overlap
(self, ndraws=10000, rstate=None)¶ Using
ndraws
Monte Carlo draws, estimate the fraction of overlap between the ellipsoid and the unit cube.

update
(self, points, pointvol=0.0, rstate=None, bootstrap=0, pool=None, mc_integrate=False)¶ Update the ellipsoid to bound the collection of points.
Parameters:  points :
ndarray
with shape (npoints, ndim) The set of points to bound.
 pointvol : float, optional
The minimum volume associated with each point. Default is
0.
. rstate :
RandomState
, optional RandomState
instance. bootstrap : int, optional
The number of bootstrapped realizations of the ellipsoid. The maximum distance to the set of points “left out” during each iteration is used to enlarge the resulting volumes. Default is
0
. pool : userprovided pool, optional
Use this pool of workers to execute operations in parallel.
 mc_integrate : bool, optional
Whether to use Monte Carlo methods to compute the effective overlap of the final ellipsoid with the unit cube. Default is
False
.
 points :


class
dynesty.bounding.
MultiEllipsoid
(ells=None, ctrs=None, covs=None)¶ Bases:
object
A collection of M Ndimensional ellipsoids.
Parameters:  ells : list of
Ellipsoid
objects with length M, optional A set of
Ellipsoid
objects that make up the collection of Nellipsoids. Used to initializeMultiEllipsoid
if provided. ctrs :
ndarray
with shape (M, N), optional Collection of coordinates of ellipsoid centers. Used to initialize
MultiEllipsoid
ifams
is also provided. covs :
ndarray
with shape (M, N, N), optional Collection of matrices describing the axes of the ellipsoids. Used to initialize
MultiEllipsoid
ifctrs
also provided.

_MultiEllipsoid__update_arrays
(self)¶ Update internal arrays to ensure that in sync with ells

contains
(self, x)¶ Checks if the set of ellipsoids contains
x
.

major_axis_endpoints
(self)¶ Return the endpoints of the major axis of each ellipsoid.

monte_carlo_logvol
(self, ndraws=10000, rstate=None, return_overlap=True)¶ Using
ndraws
Monte Carlo draws, estimate the log volume of the union of ellipsoids. Ifreturn_overlap=True
, also returns the estimated fractional overlap with the unit cube.

overlap
(self, x, j=None)¶ Checks how many ellipsoid(s)
x
falls within, skipping thej
th ellipsoid.

sample
(self, rstate=None, return_q=False)¶ Sample a point uniformly distributed within the union of ellipsoids.
Returns:  x :
ndarray
with shape (ndim,) A coordinate within the set of ellipsoids.
 idx : int
The index of the ellipsoid
x
was sampled from. q : int, optional
The number of ellipsoids
x
falls within.
 x :

samples
(self, nsamples, rstate=None)¶ Draw
nsamples
samples uniformly distributed within the union of ellipsoids.Returns:  xs :
ndarray
with shape (nsamples, ndim) A collection of coordinates within the set of ellipsoids.
 xs :

scale_to_logvol
(self, logvols)¶ Scale ellipoids to a corresponding set of target volumes.

update
(self, points, pointvol=0.0, vol_dec=0.5, vol_check=2.0, rstate=None, bootstrap=0, pool=None, mc_integrate=False)¶ Update the set of ellipsoids to bound the collection of points.
Parameters:  points :
ndarray
with shape (npoints, ndim) The set of points to bound.
 pointvol : float, optional
The minimum volume associated with each point. Default is
0.
. vol_dec : float, optional
The required fractional reduction in volume after splitting an ellipsoid in order to to accept the split. Default is
0.5
. vol_check : float, optional
The factor used when checking if the volume of the original bounding ellipsoid is large enough to warrant
> 2
splits viaell.vol > vol_check * nlive * pointvol
. Default is2.0
. rstate :
RandomState
, optional RandomState
instance. bootstrap : int, optional
The number of bootstrapped realizations of the ellipsoids. The maximum distance to the set of points “left out” during each iteration is used to enlarge the resulting volumes. Default is
0
. pool : userprovided pool, optional
Use this pool of workers to execute operations in parallel.
 mc_integrate : bool, optional
Whether to use Monte Carlo methods to compute the effective volume and fractional overlap of the final union of ellipsoids with the unit cube. Default is
False
.
 points :

within
(self, x, j=None)¶ Checks which ellipsoid(s)
x
falls within, skipping thej
th ellipsoid.
 ells : list of

class
dynesty.bounding.
RadFriends
(ndim, cov=None)¶ Bases:
object
A collection of Nballs of identical size centered on each live point.
Parameters:  ndim : int
The number of dimensions of each ball.
 cov :
ndarray
with shape(ndim, ndim)
, optional Covariance structure (correlation and size) of each ball.

_get_covariance_from_all_points
(self, points)¶ Compute covariance using all points.

_get_covariance_from_clusters
(self, points)¶ Compute covariance from recentered clusters.

contains
(self, x, ctrs)¶ Check if the set of balls contains
x
.

monte_carlo_logvol
(self, ctrs, ndraws=10000, rstate=None, return_overlap=True)¶ Using
ndraws
Monte Carlo draws, estimate the log volume of the union of balls. Ifreturn_overlap=True
, also returns the estimated fractional overlap with the unit cube.

overlap
(self, x, ctrs)¶ Check how many balls
x
falls within.

sample
(self, ctrs, rstate=None, return_q=False)¶ Sample a point uniformly distributed within the union of balls.
Returns:  x :
ndarray
with shape (ndim,) A coordinate within the set of balls.
 q : int, optional
The number of balls
x
falls within.
 x :

samples
(self, nsamples, ctrs, rstate=None)¶ Draw
nsamples
samples uniformly distributed within the union of balls.Returns:  xs :
ndarray
with shape (nsamples, ndim) A collection of coordinates within the set of balls.
 xs :

scale_to_logvol
(self, logvol)¶ Scale ball to encompass a target volume.

update
(self, points, pointvol=0.0, rstate=None, bootstrap=0, pool=None, mc_integrate=False, use_clustering=True)¶ Update the radii of our balls.
Parameters:  points :
ndarray
with shape (npoints, ndim) The set of points to bound.
 pointvol : float, optional
The minimum volume associated with each point. Default is
0.
. rstate :
RandomState
, optional RandomState
instance. bootstrap : int, optional
The number of bootstrapped realizations of the ellipsoids. The maximum distance to the set of points “left out” during each iteration is used to enlarge the resulting volumes. Default is
0
. pool : userprovided pool, optional
Use this pool of workers to execute operations in parallel.
 mc_integrate : bool, optional
Whether to use Monte Carlo methods to compute the effective volume and fractional overlap of the final union of balls with the unit cube. Default is
False
. use_clustering : bool, optional
Whether to use clustering to avoid issues with widelyseperated modes. Default is
True
.
 points :

within
(self, x, ctrs)¶ Check which balls
x
falls within.

class
dynesty.bounding.
SupFriends
(ndim, cov=None)¶ Bases:
object
A collection of Ncubes of identical size centered on each live point.
Parameters:  ndim : int
The number of dimensions of the cube.
 cov :
ndarray
with shape(ndim, ndim)
, optional Covariance structure (correlation and size) of each cube.

_get_covariance_from_all_points
(self, points)¶ Compute covariance using all points.

_get_covariance_from_clusters
(self, points)¶ Compute covariance from recentered clusters.

contains
(self, x, ctrs)¶ Checks if the set of cubes contains
x
.

monte_carlo_logvol
(self, ctrs, ndraws=10000, rstate=None, return_overlap=False)¶ Using
ndraws
Monte Carlo draws, estimate the log volume of the union of cubes. Ifreturn_overlap=True
, also returns the estimated fractional overlap with the unit cube.

overlap
(self, x, ctrs)¶ Checks how many cubes
x
falls within, skipping thej
th cube.

sample
(self, ctrs, rstate=None, return_q=False)¶ Sample a point uniformly distributed within the union of cubes.
Returns:  x :
ndarray
with shape (ndim,) A coordinate within the set of cubes.
 q : int, optional
The number of cubes
x
falls within.
 x :

samples
(self, nsamples, ctrs, rstate=None)¶ Draw
nsamples
samples uniformly distributed within the union of cubes.Returns:  xs :
ndarray
with shape (nsamples, ndim) A collection of coordinates within the set of cubes.
 xs :

scale_to_logvol
(self, logvol)¶ Scale cube to encompass a target volume.

update
(self, points, pointvol=0.0, rstate=None, bootstrap=0, pool=None, mc_integrate=False, use_clustering=True)¶ Update the halfsidelengths of our cubes.
Parameters:  points :
ndarray
with shape (npoints, ndim) The set of points to bound.
 pointvol : float, optional
The minimum volume associated with each point. Default is
0.
. rstate :
RandomState
, optional RandomState
instance. bootstrap : int, optional
The number of bootstrapped realizations of the ellipsoids. The maximum distance to the set of points “left out” during each iteration is used to enlarge the resulting volumes. Default is
0
. pool : userprovided pool, optional
Use this pool of workers to execute operations in parallel.
 mc_integrate : bool, optional
Whether to use Monte Carlo methods to compute the effective volume and fractional overlap of the final union of cubes with the unit cube. Default is
False
. use_clustering : bool, optional
Whether to use clustering to avoid issues with widelyseperated modes. Default is
True
.
 points :

within
(self, x, ctrs)¶ Checks which cubes
x
falls within.

dynesty.bounding.
logvol_prefactor
(n, p=2.0)¶ Returns the ln(volume constant) for an
n
dimensional sphere with an \(L^p\) norm. The constant is defined as:lnf = n * ln(2.) + n * LogGamma(1./p + 1)  LogGamma(n/p + 1.)
By default the
p=2.
norm is used (i.e. the standard Euclidean norm).

dynesty.bounding.
randsphere
(n, rstate=None)¶ Draw a point uniformly within an
n
dimensional unit sphere.

dynesty.bounding.
bounding_ellipsoid
(points, pointvol=0.0)¶ Calculate the bounding ellipsoid containing a collection of points.
Parameters:  points :
ndarray
with shape (npoints, ndim) A set of coordinates.
 pointvol : float, optional
The minimum volume occupied by a single point. When provided, used to set a minimum bound on the ellipsoid volume as
npoints * pointvol
. Default is0.
.
Returns:  points :

dynesty.bounding.
bounding_ellipsoids
(points, pointvol=0.0, vol_dec=0.5, vol_check=2.0)¶ Calculate a set of ellipsoids that bound the collection of points.
Parameters:  points :
ndarray
with shape (npoints, ndim) A set of coordinates.
 pointvol : float, optional
Volume represented by a single point. When provided, used to set a minimum bound on the ellipsoid volume as
npoints * pointvol
. Default is0.
. vol_dec : float, optional
The required fractional reduction in volume after splitting an ellipsoid in order to to accept the split. Default is
0.5
. vol_check : float, optional
The factor used to when checking whether the volume of the original bounding ellipsoid is large enough to warrant more trial splits via
ell.vol > vol_check * npoints * pointvol
. Default is2.0
.
Returns:  mell :
MultiEllipsoid
object The
MultiEllipsoid
object used to bound the collection of points.
 points :

dynesty.bounding.
_bounding_ellipsoids
(points, ell, pointvol=0.0, vol_dec=0.5, vol_check=2.0)¶ Internal method used to compute a set of bounding ellipsoids when a bounding ellipsoid for the entire set has already been calculated.
Parameters:  points :
ndarray
with shape (npoints, ndim) A set of coordinates.
 ell : Ellipsoid
The bounding ellipsoid containing
points
. pointvol : float, optional
Volume represented by a single point. When provided, used to set a minimum bound on the ellipsoid volume as
npoints * pointvol
. Default is0.
. vol_dec : float, optional
The required fractional reduction in volume after splitting an ellipsoid in order to to accept the split. Default is
0.5
. vol_check : float, optional
The factor used to when checking whether the volume of the original bounding ellipsoid is large enough to warrant more trial splits via
ell.vol > vol_check * npoints * pointvol
. Default is2.0
.
Returns:  ells : list of
Ellipsoid
objects List of
Ellipsoid
objects used to bound the collection of points. Used to initialize theMultiEllipsoid
object returned inbounding_ellipsoids()
.
 points :

dynesty.bounding.
_ellipsoid_bootstrap_expand
(args)¶ Internal method used to compute the expansion factor for a bounding ellipsoid based on bootstrapping.

dynesty.bounding.
_ellipsoids_bootstrap_expand
(args)¶ Internal method used to compute the expansion factor(s) for a collection of bounding ellipsoids using bootstrapping.

dynesty.bounding.
_friends_bootstrap_radius
(args)¶ Internal method used to compute the radius (halfsidelength) for each ball (cube) used in
RadFriends
(SupFriends
) using bootstrapping.

dynesty.bounding.
_friends_leaveoneout_radius
(points, ftype)¶ Internal method used to compute the radius (halfsidelength) for each ball (cube) used in
RadFriends
(SupFriends
) using leaveoneout (LOO) crossvalidation.
Sampling¶
Functions for proposing new live points used by
Sampler
(and its children from
nestedsamplers
) and
DynamicSampler
.

dynesty.sampling.
sample_unif
(args)¶ Evaluate a new point sampled uniformly from a bounding proposal distribution. Parameters are zipped within
args
to utilizepool.map
style functions.Parameters:  u :
ndarray
with shape (npdim,) Position of the initial sample.
 loglstar : float
Ln(likelihood) bound. Not applicable here.
 axes :
ndarray
with shape (ndim, ndim) Axes used to propose new points. Not applicable here.
 scale : float
Value used to scale the provided axes. Not applicable here.
 prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. kwargs : dict
A dictionary of additional methodspecific parameters. Not applicable here.
Returns:  u :
ndarray
with shape (npdim,) Position of the final proposed point within the unit cube. For uniform sampling this is the same as the initial input position.
 v :
ndarray
with shape (ndim,) Position of the final proposed point in the target parameter space.
 logl : float
Ln(likelihood) of the final proposed point.
 nc : int
Number of function calls used to generate the sample. For uniform sampling this is
1
by construction. blob : dict
Collection of ancillary quantities used to tune
scale
. Not applicable for uniform sampling.
 u :

dynesty.sampling.
sample_rwalk
(args)¶ Return a new live point proposed by random walking away from an existing live point.
Parameters:  u :
ndarray
with shape (npdim,) Position of the initial sample. This is a copy of an existing live point.
 loglstar : float
Ln(likelihood) bound.
 axes :
ndarray
with shape (ndim, ndim) Axes used to propose new points. For random walks new positions are proposed using the
Ellipsoid
whose shape is defined by axes. scale : float
Value used to scale the provided axes.
 prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. kwargs : dict
A dictionary of additional methodspecific parameters.
Returns:  u :
ndarray
with shape (npdim,) Position of the final proposed point within the unit cube.
 v :
ndarray
with shape (ndim,) Position of the final proposed point in the target parameter space.
 logl : float
Ln(likelihood) of the final proposed point.
 nc : int
Number of function calls used to generate the sample.
 blob : dict
Collection of ancillary quantities used to tune
scale
.
 u :

dynesty.sampling.
sample_rstagger
(args)¶ Return a new live point proposed by random “staggering” away from an existing live point. The difference between this and the random walk is the step size is exponentially adjusted to reach a target acceptance rate during each proposal (in addition to between proposals).
Parameters:  u :
ndarray
with shape (npdim,) Position of the initial sample. This is a copy of an existing live point.
 loglstar : float
Ln(likelihood) bound.
 axes :
ndarray
with shape (ndim, ndim) Axes used to propose new points. For random walks new positions are proposed using the
Ellipsoid
whose shape is defined by axes. scale : float
Value used to scale the provided axes.
 prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. kwargs : dict
A dictionary of additional methodspecific parameters.
Returns:  u :
ndarray
with shape (npdim,) Position of the final proposed point within the unit cube.
 v :
ndarray
with shape (ndim,) Position of the final proposed point in the target parameter space.
 logl : float
Ln(likelihood) of the final proposed point.
 nc : int
Number of function calls used to generate the sample.
 blob : dict
Collection of ancillary quantities used to tune
scale
.
 u :

dynesty.sampling.
sample_slice
(args)¶ Return a new live point proposed by a series of random slices away from an existing live point. Standard “Gibslike” implementation where a single multivariate “slice” is a combination of
ndim
univariate slices through each axis.Parameters:  u :
ndarray
with shape (npdim,) Position of the initial sample. This is a copy of an existing live point.
 loglstar : float
Ln(likelihood) bound.
 axes :
ndarray
with shape (ndim, ndim) Axes used to propose new points. For slices new positions are proposed along the arthogonal basis defined by
axes
. scale : float
Value used to scale the provided axes.
 prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. kwargs : dict
A dictionary of additional methodspecific parameters.
Returns:  u :
ndarray
with shape (npdim,) Position of the final proposed point within the unit cube.
 v :
ndarray
with shape (ndim,) Position of the final proposed point in the target parameter space.
 logl : float
Ln(likelihood) of the final proposed point.
 nc : int
Number of function calls used to generate the sample.
 blob : dict
Collection of ancillary quantities used to tune
scale
.
 u :

dynesty.sampling.
sample_rslice
(args)¶ Return a new live point proposed by a series of random slices away from an existing live point. Standard “random” implementation where each slice is along a random direction based on the provided axes.
Parameters:  u :
ndarray
with shape (npdim,) Position of the initial sample. This is a copy of an existing live point.
 loglstar : float
Ln(likelihood) bound.
 axes :
ndarray
with shape (ndim, ndim) Axes used to propose new slice directions.
 scale : float
Value used to scale the provided axes.
 prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. kwargs : dict
A dictionary of additional methodspecific parameters.
Returns:  u :
ndarray
with shape (npdim,) Position of the final proposed point within the unit cube.
 v :
ndarray
with shape (ndim,) Position of the final proposed point in the target parameter space.
 logl : float
Ln(likelihood) of the final proposed point.
 nc : int
Number of function calls used to generate the sample.
 blob : dict
Collection of ancillary quantities used to tune
scale
.
 u :

dynesty.sampling.
sample_hslice
(args)¶ Return a new live point proposed by “Hamiltonian” Slice Sampling using a series of random trajectories away from an existing live point. Each trajectory is based on the provided axes and samples are determined by moving forwards/backwards in time until the trajectory hits an edge and approximately reflecting off the boundaries. Once a series of reflections has been established, we propose a new live point by slice sampling across the entire path.
Parameters:  u :
ndarray
with shape (npdim,) Position of the initial sample. This is a copy of an existing live point.
 loglstar : float
Ln(likelihood) bound.
 axes :
ndarray
with shape (ndim, ndim) Axes used to propose new slice directions.
 scale : float
Value used to scale the provided axes.
 prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. kwargs : dict
A dictionary of additional methodspecific parameters.
Returns:  u :
ndarray
with shape (npdim,) Position of the final proposed point within the unit cube.
 v :
ndarray
with shape (ndim,) Position of the final proposed point in the target parameter space.
 logl : float
Ln(likelihood) of the final proposed point.
 nc : int
Number of function calls used to generate the sample.
 blob : dict
Collection of ancillary quantities used to tune
scale
.
 u :
Baseline Sampler¶
The base Sampler
class containing various helpful functions. All other
samplers inherit this class either explicitly or implicitly.

class
dynesty.sampler.
Sampler
(loglikelihood, prior_transform, npdim, live_points, update_interval, first_update, rstate, queue_size, pool, use_pool, ncdim)¶ Bases:
object
The basic sampler object that performs the actual nested sampling.
Parameters:  loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 npdim : int, optional
Number of parameters accepted by
prior_transform
. live_points : list of 3
ndarray
each with shape (nlive, ndim) Initial set of “live” points. Contains
live_u
, the coordinates on the unit cube,live_v
, the transformed variables, andlive_logl
, the associated loglikelihoods. update_interval : int
Only update the bounding distribution every
update_interval
th likelihood call. first_update : dict
A dictionary containing parameters governing when the sampler should first update the bounding distribution from the unit cube to the one specified by the user.
 rstate :
RandomState
RandomState
instance. queue_size: int
Carry out likelihood evaluations in parallel by queueing up new live point proposals using (at most) this many threads/members.
 pool: pool
Use this pool of workers to execute operations in parallel.
 use_pool : dict, optional
A dictionary containing flags indicating where the provided
pool
should be used to execute operations in parallel.

_beyond_unit_bound
(self, loglstar)¶ Check whether we should update our bound beyond the initial unit cube.

_empty_queue
(self)¶ Dump all live point proposals currently on the queue.

_fill_queue
(self, loglstar)¶ Sequentially add new live point proposals to the queue.

_get_point_value
(self, loglstar)¶ Grab the first live point proposal in the queue.

_get_print_func
(self, print_func, print_progress)¶

_new_point
(self, loglstar, logvol)¶ Propose points until a new point that satisfies the loglikelihood constraint
loglstar
is found.

_remove_live_points
(self)¶ Remove the final set of live points if they were previously added to the current set of dead points.

add_final_live
(self, print_progress=True, print_func=None)¶ A wrapper that executes the loop adding the final live points. Adds the final set of live points to the preexisting sequence of dead points from the current nested sampling run.
Parameters:  print_progress : bool, optional
Whether or not to output a simple summary of the current run that updates with each iteration. Default is
True
. print_func : function, optional
A function that prints out the current state of the sampler. If not provided, the default
results.print_fn()
is used.

add_live_points
(self)¶ Add the remaining set of live points to the current set of dead points. Instantiates a generator that will be called by the user. Returns the same outputs as
sample()
.

citations
¶ Return list of papers that should be cited given the specified configuration of the sampler.

n_effective
¶ Estimate the effective number of posterior samples using the Kish Effective Sample Size (ESS) where
ESS = sum(wts)^2 / sum(wts^2)
. Note that this islen(wts)
whenwts
are uniform and1
if there is only one nonzero element inwts
.

reset
(self)¶ Reinitialize the sampler.

results
¶ Saved results from the nested sampling run. If bounding distributions were saved, those are also returned.

run_nested
(self, maxiter=None, maxcall=None, dlogz=None, logl_max=inf, n_effective=None, add_live=True, print_progress=True, print_func=None, save_bounds=True)¶ A wrapper that executes the main nested sampling loop. Iteratively replace the worst live point with a sample drawn uniformly from the prior until the provided stopping criteria are reached.
Parameters:  maxiter : int, optional
Maximum number of iterations. Iteration may stop earlier if the termination condition is reached. Default is
sys.maxsize
(no limit). maxcall : int, optional
Maximum number of likelihood evaluations. Iteration may stop earlier if termination condition is reached. Default is
sys.maxsize
(no limit). dlogz : float, optional
Iteration will stop when the estimated contribution of the remaining prior volume to the total evidence falls below this threshold. Explicitly, the stopping criterion is
ln(z + z_est)  ln(z) < dlogz
, wherez
is the current evidence from all saved samples andz_est
is the estimated contribution from the remaining volume. Ifadd_live
isTrue
, the default is1e3 * (nlive  1) + 0.01
. Otherwise, the default is0.01
. logl_max : float, optional
Iteration will stop when the sampled ln(likelihood) exceeds the threshold set by
logl_max
. Default is no bound (np.inf
). n_effective: int, optional
Minimum number of effective posterior samples. If the estimated “effective sample size” (ESS) exceeds this number, sampling will terminate. Default is no ESS (
np.inf
). add_live : bool, optional
Whether or not to add the remaining set of live points to the list of samples at the end of each run. Default is
True
. print_progress : bool, optional
Whether or not to output a simple summary of the current run that updates with each iteration. Default is
True
. print_func : function, optional
A function that prints out the current state of the sampler. If not provided, the default
results.print_fn()
is used. save_bounds : bool, optional
Whether or not to save past bounding distributions used to bound the live points internally. Default is True.

sample
(self, maxiter=None, maxcall=None, dlogz=0.01, logl_max=inf, n_effective=inf, add_live=True, save_bounds=True, save_samples=True)¶ The main nested sampling loop. Iteratively replace the worst live point with a sample drawn uniformly from the prior until the provided stopping criteria are reached. Instantiates a generator that will be called by the user.
Parameters:  maxiter : int, optional
Maximum number of iterations. Iteration may stop earlier if the termination condition is reached. Default is
sys.maxsize
(no limit). maxcall : int, optional
Maximum number of likelihood evaluations. Iteration may stop earlier if termination condition is reached. Default is
sys.maxsize
(no limit). dlogz : float, optional
Iteration will stop when the estimated contribution of the remaining prior volume to the total evidence falls below this threshold. Explicitly, the stopping criterion is
ln(z + z_est)  ln(z) < dlogz
, wherez
is the current evidence from all saved samples andz_est
is the estimated contribution from the remaining volume. Default is0.01
. logl_max : float, optional
Iteration will stop when the sampled ln(likelihood) exceeds the threshold set by
logl_max
. Default is no bound (np.inf
). n_effective: int, optional
Minimum number of effective posterior samples. If the estimated “effective sample size” (ESS) exceeds this number, sampling will terminate. Default is no ESS (
np.inf
). add_live : bool, optional
Whether or not to add the remaining set of live points to the list of samples when calculating
n_effective
. Default isTrue
. save_bounds : bool, optional
Whether or not to save past distributions used to bound the live points internally. Default is
True
. save_samples : bool, optional
Whether or not to save past samples from the nested sampling run (along with other ancillary quantities) internally. Default is
True
.
Returns:  worst : int
Index of the live point with the worst likelihood. This is our new dead point sample.
 ustar :
ndarray
with shape (npdim,) Position of the sample.
 vstar :
ndarray
with shape (ndim,) Transformed position of the sample.
 loglstar : float
Ln(likelihood) of the sample.
 logvol : float
Ln(prior volume) within the sample.
 logwt : float
Ln(weight) of the sample.
 logz : float
Cumulative ln(evidence) up to the sample (inclusive).
 logzvar : float
Estimated cumulative variance on
logz
(inclusive). h : float
Cumulative information up to the sample (inclusive).
 nc : int
Number of likelihood calls performed before the new live point was accepted.
 worst_it : int
Iteration when the live (now dead) point was originally proposed.
 boundidx : int
Index of the bound the dead point was originally drawn from.
 bounditer : int
Index of the bound being used at the current iteration.
 eff : float
The cumulative sampling efficiency (in percent).
 delta_logz : float
The estimated remaining evidence expressed as the ln(ratio) of the current evidence.
Static Nested Samplers¶
Childen of dynesty.sampler
used to proposing new live points.
Includes:
 UnitCubeSampler:
 Uses the unit cube to bound the set of live points (i.e. no bound).
 SingleEllipsoidSampler:
 Uses a single ellipsoid to bound the set of live points.
 MultiEllipsoidSampler:
 Uses multiple ellipsoids to bound the set of live points.
 RadFriendsSampler:
 Uses an Nsphere of fixed radius centered on each live point to bound the set of live points.
 SupFriendsSampler:
 Uses an Ncube of fixed length centered on each live point to bound the set of live points.

class
dynesty.nestedsamplers.
UnitCubeSampler
(loglikelihood, prior_transform, npdim, live_points, method, update_interval, first_update, rstate, queue_size, pool, use_pool, kwargs={}, ncdim=0)¶ Bases:
dynesty.sampler.Sampler
Samples conditioned on the unit Ncube (i.e. with no bounds).
Parameters:  loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 npdim : int
Number of parameters accepted by
prior_transform
. live_points : list of 3
ndarray
each with shape (nlive, ndim) Initial set of “live” points. Contains
live_u
, the coordinates on the unit cube,live_v
, the transformed variables, andlive_logl
, the associated loglikelihoods. method : {
'unif'
,'rwalk'
,'rstagger'
, 'slice'
,'rslice'
,'hslice'
}, optionalMethod used to sample uniformly within the likelihood constraint, conditioned on the provided bounds.
 update_interval : int
Only update the bounding distribution every
update_interval
th likelihood call. first_update : dict
A dictionary containing parameters governing when the sampler should first update the bounding distribution from the unit cube to the one specified by the user.
 rstate :
RandomState
RandomState
instance. queue_size: int
Carry out likelihood evaluations in parallel by queueing up new live point proposals using (at most) this many threads/members.
 pool: pool
Use this pool of workers to execute operations in parallel.
 use_pool : dict, optional
A dictionary containing flags indicating where the provided
pool
should be used to execute operations in parallel. kwargs : dict, optional
A dictionary of additional parameters.

propose_live
(self)¶ Return a live point/axes to be used by other sampling methods.

propose_unif
(self)¶ Propose a new live point by sampling uniformly within the unit cube.

update
(self, pointvol)¶ Update the unit cube bound.

update_hslice
(self, blob)¶ Update the Hamiltonian slice proposal scale based on the relative amount of time spent moving vs reflecting.

update_rwalk
(self, blob)¶ Update the random walk proposal scale based on the current number of accepted/rejected steps.

update_slice
(self, blob)¶ Update the slice proposal scale based on the relative size of the slices compared to our initial guess.

update_unif
(self, blob)¶ Filler function.

update_user
(self, blob)¶ Update the scale based on the userdefined update function.

class
dynesty.nestedsamplers.
SingleEllipsoidSampler
(loglikelihood, prior_transform, npdim, live_points, method, update_interval, first_update, rstate, queue_size, pool, use_pool, kwargs={}, ncdim=0)¶ Bases:
dynesty.sampler.Sampler
Samples conditioned on a single ellipsoid used to bound the set of live points.
Parameters:  loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 npdim : int
Number of parameters accepted by
prior_transform
. live_points : list of 3
ndarray
each with shape (nlive, ndim) Initial set of “live” points. Contains
live_u
, the coordinates on the unit cube,live_v
, the transformed variables, andlive_logl
, the associated loglikelihoods. method : {
'unif'
,'rwalk'
,'rstagger'
, 'slice'
,'rslice'
,'hslice'
}, optionalMethod used to sample uniformly within the likelihood constraint, conditioned on the provided bounds.
 update_interval : int
Only update the bounding distribution every
update_interval
th likelihood call. first_update : dict
A dictionary containing parameters governing when the sampler should first update the bounding distribution from the unit cube to the one specified by the user.
 rstate :
RandomState
RandomState
instance. queue_size: int
Carry out likelihood evaluations in parallel by queueing up new live point proposals using (at most) this many threads/members.
 pool: pool
Use this pool of workers to execute operations in parallel.
 use_pool : dict, optional
A dictionary containing flags indicating where the provided
pool
should be used to execute operations in parallel. kwargs : dict, optional
A dictionary of additional parameters.

propose_live
(self)¶ Return a live point/axes to be used by other sampling methods.

propose_unif
(self)¶ Propose a new live point by sampling uniformly within the ellipsoid.

update
(self, pointvol)¶ Update the bounding ellipsoid using the current set of live points.

update_hslice
(self, blob)¶ Update the Hamiltonian slice proposal scale based on the relative amount of time spent moving vs reflecting.

update_rwalk
(self, blob)¶ Update the random walk proposal scale based on the current number of accepted/rejected steps.

update_slice
(self, blob)¶ Update the slice proposal scale based on the relative size of the slices compared to our initial guess.

update_unif
(self, blob)¶ Filler function.

update_user
(self, blob)¶ Update the scale based on the userdefined update function.

class
dynesty.nestedsamplers.
MultiEllipsoidSampler
(loglikelihood, prior_transform, npdim, live_points, method, update_interval, first_update, rstate, queue_size, pool, use_pool, kwargs={}, ncdim=0)¶ Bases:
dynesty.sampler.Sampler
Samples conditioned on the union of multiple (possibly overlapping) ellipsoids used to bound the set of live points.
Parameters:  loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 npdim : int
Number of parameters accepted by
prior_transform
. live_points : list of 3
ndarray
each with shape (nlive, ndim) Initial set of “live” points. Contains
live_u
, the coordinates on the unit cube,live_v
, the transformed variables, andlive_logl
, the associated loglikelihoods. method : {
'unif'
,'rwalk'
,'rstagger'
, 'slice'
,'rslice'
,'hslice'
}, optionalMethod used to sample uniformly within the likelihood constraint, conditioned on the provided bounds.
 update_interval : int
Only update the bounding distribution every
update_interval
th likelihood call. first_update : dict
A dictionary containing parameters governing when the sampler should first update the bounding distribution from the unit cube to the one specified by the user.
 rstate :
RandomState
RandomState
instance. queue_size: int
Carry out likelihood evaluations in parallel by queueing up new live point proposals using (at most) this many threads/members.
 pool: pool
Use this pool of workers to execute operations in parallel.
 use_pool : dict, optional
A dictionary containing flags indicating where the provided
pool
should be used to execute operations in parallel. kwargs : dict, optional
A dictionary of additional parameters.

propose_live
(self)¶ Return a live point/axes to be used by other sampling methods.

propose_unif
(self)¶ Propose a new live point by sampling uniformly within the union of ellipsoids.

update
(self, pointvol)¶ Update the bounding ellipsoids using the current set of live points.

update_hslice
(self, blob)¶ Update the Hamiltonian slice proposal scale based on the relative amount of time spent moving vs reflecting.

update_rwalk
(self, blob)¶ Update the random walk proposal scale based on the current number of accepted/rejected steps.

update_slice
(self, blob)¶ Update the slice proposal scale based on the relative size of the slices compared to our initial guess.

update_unif
(self, blob)¶ Filler function.

update_user
(self, blob)¶ Update the scale based on the userdefined update function.

class
dynesty.nestedsamplers.
RadFriendsSampler
(loglikelihood, prior_transform, npdim, live_points, method, update_interval, first_update, rstate, queue_size, pool, use_pool, kwargs={}, ncdim=0)¶ Bases:
dynesty.sampler.Sampler
Samples conditioned on the union of (possibly overlapping) Nspheres centered on the current set of live points.
Parameters:  loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 npdim : int
Number of parameters accepted by
prior_transform
. live_points : list of 3
ndarray
each with shape (nlive, ndim) Initial set of “live” points. Contains
live_u
, the coordinates on the unit cube,live_v
, the transformed variables, andlive_logl
, the associated loglikelihoods. method : {
'unif'
,'rwalk'
,'rstagger'
, 'slice'
,'rslice'
,'hslice'
}, optionalMethod used to sample uniformly within the likelihood constraint, conditioned on the provided bounds.
 update_interval : int
Only update the bounding distribution every
update_interval
th likelihood call. first_update : dict
A dictionary containing parameters governing when the sampler should first update the bounding distribution from the unit cube to the one specified by the user.
 rstate :
RandomState
RandomState
instance. queue_size: int
Carry out likelihood evaluations in parallel by queueing up new live point proposals using (at most) this many threads/members.
 pool: pool
Use this pool of workers to execute operations in parallel.
 use_pool : dict, optional
A dictionary containing flags indicating where the provided
pool
should be used to execute operations in parallel. kwargs : dict, optional
A dictionary of additional parameters.

propose_live
(self)¶ Propose a live point/axes to be used by other sampling methods.

propose_unif
(self)¶ Propose a new live point by sampling uniformly within the union of Nspheres defined by our live points.

update
(self, pointvol)¶ Update the Nsphere radii using the current set of live points.

update_hslice
(self, blob)¶ Update the Hamiltonian slice proposal scale based on the relative amount of time spent moving vs reflecting.

update_rwalk
(self, blob)¶ Update the random walk proposal scale based on the current number of accepted/rejected steps.

update_slice
(self, blob)¶ Update the slice proposal scale based on the relative size of the slices compared to our initial guess.

update_unif
(self, blob)¶ Filler function.

update_user
(self, blob)¶ Update the scale based on the userdefined update function.

class
dynesty.nestedsamplers.
SupFriendsSampler
(loglikelihood, prior_transform, npdim, live_points, method, update_interval, first_update, rstate, queue_size, pool, use_pool, kwargs={}, ncdim=0)¶ Bases:
dynesty.sampler.Sampler
Samples conditioned on the union of (possibly overlapping) Ncubes centered on the current set of live points.
Parameters:  loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 npdim : int
Number of parameters accepted by
prior_transform
. live_points : list of 3
ndarray
each with shape (nlive, ndim) Initial set of “live” points. Contains
live_u
, the coordinates on the unit cube,live_v
, the transformed variables, andlive_logl
, the associated loglikelihoods. method : {
'unif'
,'rwalk'
,'rstagger'
, 'slice'
,'rslice'
,'hslice'
}, optionalMethod used to sample uniformly within the likelihood constraint, conditioned on the provided bounds.
 update_interval : int
Only update the bounding distribution every
update_interval
th likelihood call. first_update : dict
A dictionary containing parameters governing when the sampler should first update the bounding distribution from the unit cube to the one specified by the user.
 rstate :
RandomState
RandomState
instance. queue_size: int
Carry out likelihood evaluations in parallel by queueing up new live point proposals using (at most) this many threads/members.
 pool: pool
Use this pool of workers to execute operations in parallel.
 use_pool : dict, optional
A dictionary containing flags indicating where the provided
pool
should be used to execute operations in parallel. kwargs : dict, optional
A dictionary of additional parameters.

propose_live
(self)¶ Return a live point/axes to be used by other sampling methods.

propose_unif
(self)¶ Propose a new live point by sampling uniformly within the collection of Ncubes defined by our live points.

update
(self, pointvol)¶ Update the Ncube sidelengths using the current set of live points.

update_hslice
(self, blob)¶ Update the Hamiltonian slice proposal scale based on the relative amount of time spent moving vs reflecting.

update_rwalk
(self, blob)¶ Update the random walk proposal scale based on the current number of accepted/rejected steps.

update_slice
(self, blob)¶ Update the slice proposal scale based on the relative size of the slices compared to our initial guess.

update_unif
(self, blob)¶ Filler function.

update_user
(self, blob)¶ Update the scale based on the userdefined update function.
Dynamic Nested Sampler¶
Contains the dynamic nested sampler class DynamicSampler
used to
dynamically allocate nested samples. Note that DynamicSampler
implicitly wraps a sampler from nestedsamplers
. Also contains
the weight function weight_function()
and stopping function
stopping_function()
. These are used by default within
DynamicSampler
if corresponding functions are not provided
by the user.

class
dynesty.dynamicsampler.
DynamicSampler
(loglikelihood, prior_transform, npdim, bound, method, update_interval, first_update, rstate, queue_size, pool, use_pool, ncdim, kwargs)¶ Bases:
object
A dynamic nested sampler that allocates live points adaptively during a single run according to a specified weight function until a specified stopping criteria is reached.
Parameters:  loglikelihood : function
Function returning ln(likelihood) given parameters as a 1d
numpy
array of lengthndim
. prior_transform : function
Function transforming a sample from the a unit cube to the parameter space of interest according to the prior.
 npdim : int, optional
Number of parameters accepted by
prior_transform
. bound : {
'none'
,'single'
,'multi'
,'balls'
,'cubes'
}, optional Method used to approximately bound the prior using the current set of live points. Conditions the sampling methods used to propose new live points.
 method : {
'unif'
,'rwalk'
,'rstagger'
, 'slice'
,'rslice'
,'hslice'
}, optionalMethod used to sample uniformly within the likelihood constraint, conditioned on the provided bounds.
 update_interval : int
Only update the bounding distribution every
update_interval
th likelihood call. first_update : dict
A dictionary containing parameters governing when the sampler should first update the bounding distribution from the unit cube to the one specified by the user.
 rstate :
RandomState
RandomState
instance. queue_size: int
Carry out likelihood evaluations in parallel by queueing up new live point proposals using (at most) this many threads/members.
 pool: pool
Use this pool of workers to execute operations in parallel.
 use_pool : dict, optional
A dictionary containing flags indicating where the provided
pool
should be used to execute operations in parallel. kwargs : dict, optional
A dictionary of additional parameters (described below).

_get_print_func
(self, print_func, print_progress)¶

add_batch
(self, nlive=500, wt_function=None, wt_kwargs=None, maxiter=None, maxcall=None, logl_bounds=None, save_bounds=True, print_progress=True, print_func=None, stop_val=None)¶ Allocate an additional batch of (nested) samples based on the combined set of previous samples using the specified weight function.
Parameters:  nlive : int, optional
The number of live points used when adding additional samples in the batch. Default is
500
. wt_function : func, optional
A cost function that takes a
Results
instance and returns a loglikelihood range over which a new batch of samples should be generated. The default function simply computes a weighted average of the posterior and evidence information content as:weight = pfrac * pweight + (1.  pfrac) * zweight
 wt_kwargs : dict, optional
Extra arguments to be passed to the weight function.
 maxiter : int, optional
Maximum number of iterations allowed. Default is
sys.maxsize
(no limit). maxcall : int, optional
Maximum number of likelihood evaluations allowed. Default is
sys.maxsize
(no limit). logl_bounds : tuple of size (2,), optional
The ln(likelihood) bounds used to bracket the run. If
None
, the providedwt_function
will be used to determine the bounds (this is the default behavior). save_bounds : bool, optional
Whether or not to save distributions used to bound the live points internally during dynamic live point allocations. Default is
True
. print_progress : bool, optional
Whether to output a simple summary of the current run that updates each iteration. Default is
True
. print_func : function, optional
A function that prints out the current state of the sampler. If not provided, the default
results.print_fn()
is used. stop_val : float, optional
The value of the stopping criteria to be passed to
print_func()
. Used internally withinrun_nested()
to keep track of progress.

citations
¶ Return list of papers that should be cited given the specified configuration of the sampler.

combine_runs
(self)¶ Merge the most recent run into the previous (combined) run by “stepping through” both runs simultaneously.

n_effective
¶ Estimate the effective number of posterior samples using the Kish Effective Sample Size (ESS) where
ESS = sum(wts)^2 / sum(wts^2)
. Note that this islen(wts)
whenwts
are uniform and1
if there is only one nonzero element inwts
.

reset
(self)¶ Reinitialize the sampler.

results
¶ Saved results from the dynamic nested sampling run. All saved bounds are also returned.

run_nested
(self, nlive_init=500, maxiter_init=None, maxcall_init=None, dlogz_init=0.01, logl_max_init=inf, n_effective_init=inf, nlive_batch=500, wt_function=None, wt_kwargs=None, maxiter_batch=None, maxcall_batch=None, maxiter=None, maxcall=None, maxbatch=None, n_effective=inf, stop_function=None, stop_kwargs=None, use_stop=True, save_bounds=True, print_progress=True, print_func=None, live_points=None)¶ The main dynamic nested sampling loop. After an initial “baseline” run using a constant number of live points, dynamically allocates additional (nested) samples to optimize a specified weight function until a specified stopping criterion is reached.
Parameters:  nlive_init : int, optional
The number of live points used during the initial (“baseline”) nested sampling run. Default is
500
. maxiter_init : int, optional
Maximum number of iterations for the initial baseline nested sampling run. Iteration may stop earlier if the termination condition is reached. Default is
sys.maxsize
(no limit). maxcall_init : int, optional
Maximum number of likelihood evaluations for the initial baseline nested sampling run. Iteration may stop earlier if the termination condition is reached. Default is
sys.maxsize
(no limit). dlogz_init : float, optional
The baseline run will stop when the estimated contribution of the remaining prior volume to the total evidence falls below this threshold. Explicitly, the stopping criterion is
ln(z + z_est)  ln(z) < dlogz
, wherez
is the current evidence from all saved samples andz_est
is the estimated contribution from the remaining volume. The default is0.01
. logl_max_init : float, optional
The baseline run will stop when the sampled ln(likelihood) exceeds this threshold. Default is no bound (
np.inf
). n_effective_init: int, optional
Minimum number of effective posterior samples needed during the baseline run. If the estimated “effective sample size” (ESS) exceeds this number, sampling will terminate. Default is no ESS (
np.inf
). nlive_batch : int, optional
The number of live points used when adding additional samples from a nested sampling run within each batch. Default is
500
. wt_function : func, optional
A cost function that takes a
Results
instance and returns a loglikelihood range over which a new batch of samples should be generated. The default function simply computes a weighted average of the posterior and evidence information content as:weight = pfrac * pweight + (1.  pfrac) * zweight
 wt_kwargs : dict, optional
Extra arguments to be passed to the weight function.
 maxiter_batch : int, optional
Maximum number of iterations for the nested sampling run within each batch. Iteration may stop earlier if the termination condition is reached. Default is
sys.maxsize
(no limit). maxcall_batch : int, optional
Maximum number of likelihood evaluations for the nested sampling run within each batch. Iteration may stop earlier if the termination condition is reached. Default is
sys.maxsize
(no limit). maxiter : int, optional
Maximum number of iterations allowed. Default is
sys.maxsize
(no limit). maxcall : int, optional
Maximum number of likelihood evaluations allowed. Default is
sys.maxsize
(no limit). maxbatch : int, optional
Maximum number of batches allowed. Default is
sys.maxsize
(no limit). n_effective: int, optional
Minimum number of effective posterior samples needed during the entire run. If the estimated “effective sample size” (ESS) exceeds this number, sampling will terminate. Default is no ESS (
np.inf
). stop_function : func, optional
A function that takes a
Results
instance and returns a boolean indicating that we should terminate the run because we’ve collected enough samples. stop_kwargs : float, optional
Extra arguments to be passed to the stopping function.
 use_stop : bool, optional
Whether to evaluate our stopping function after each batch. Disabling this can improve performance if other stopping criteria such as
maxcall
are already specified. Default isTrue
. save_bounds : bool, optional
Whether or not to save distributions used to bound the live points internally during dynamic live point allocation. Default is
True
. print_progress : bool, optional
Whether to output a simple summary of the current run that updates each iteration. Default is
True
. print_func : function, optional
A function that prints out the current state of the sampler. If not provided, the default
results.print_fn()
is used. live_points : list of 3
ndarray
each with shape (nlive, ndim) A set of live points used to initialize the nested sampling run. Contains
live_u
, the coordinates on the unit cube,live_v
, the transformed variables, andlive_logl
, the associated loglikelihoods. By default, if these are not provided the initial set of live points will be drawn from the unitnpdim
cube. WARNING: It is crucial that the initial set of live points have been sampled from the prior. Failure to provide a set of valid live points will result in biased results.

sample_batch
(self, nlive_new=500, update_interval=None, logl_bounds=None, maxiter=None, maxcall=None, save_bounds=True)¶ Generate an additional series of nested samples that will be combined with the previous set of dead points. Works by hacking the internal
sampler
object. Instantiates a generator that will be called by the user.Parameters:  nlive_new : int
Number of new live points to be added. Default is
500
. update_interval : int or float, optional
If an integer is passed, only update the bounding distribution every
update_interval
th likelihood call. If a float is passed, update the bound after everyround(update_interval * nlive)
th likelihood call. Larger update intervals can be more efficient when the likelihood function is quick to evaluate. If no value is provided, defaults to the value passed during initialization. logl_bounds : tuple of size (2,), optional
The ln(likelihood) bounds used to bracket the run. If
None
, the default bounds span the entire range covered by the original run. maxiter : int, optional
Maximum number of iterations. Iteration may stop earlier if the termination condition is reached. Default is
sys.maxsize
(no limit). maxcall : int, optional
Maximum number of likelihood evaluations. Iteration may stop earlier if termination condition is reached. Default is
sys.maxsize
(no limit). save_bounds : bool, optional
Whether or not to save past distributions used to bound the live points internally. Default is
True
.
Returns:  worst : int
Index of the live point with the worst likelihood. This is our new dead point sample. Negative values indicate the index of a new live point generated when initializing a new batch.
 ustar :
ndarray
with shape (npdim,) Position of the sample.
 vstar :
ndarray
with shape (ndim,) Transformed position of the sample.
 loglstar : float
Ln(likelihood) of the sample.
 nc : int
Number of likelihood calls performed before the new live point was accepted.
 worst_it : int
Iteration when the live (now dead) point was originally proposed.
 boundidx : int
Index of the bound the dead point was originally drawn from.
 bounditer : int
Index of the bound being used at the current iteration.
 eff : float
The cumulative sampling efficiency (in percent).

sample_initial
(self, nlive=500, update_interval=None, first_update=None, maxiter=None, maxcall=None, logl_max=inf, dlogz=0.01, n_effective=inf, live_points=None, save_samples=False, resume=False)¶ Generate a series of initial samples from a nested sampling run using a fixed number of live points using an internal sampler from
nestedsamplers
. Instantiates a generator that will be called by the user.Parameters:  nlive : int, optional
The number of live points to use for the baseline nested sampling run. Default is
500
. update_interval : int or float, optional
If an integer is passed, only update the bounding distribution every
update_interval
th likelihood call. If a float is passed, update the bound after everyround(update_interval * nlive)
th likelihood call. Larger update intervals can be more efficient when the likelihood function is quick to evaluate. If no value is provided, defaults to the value passed during initialization. first_update : dict, optional
A dictionary containing parameters governing when the sampler will first update the bounding distribution from the unit cube (
'none'
) to the one specified bysample
. maxiter : int, optional
Maximum number of iterations. Iteration may stop earlier if the termination condition is reached. Default is
sys.maxsize
(no limit). maxcall : int, optional
Maximum number of likelihood evaluations. Iteration may stop earlier if termination condition is reached. Default is
sys.maxsize
(no limit). dlogz : float, optional
Iteration will stop when the estimated contribution of the remaining prior volume to the total evidence falls below this threshold. Explicitly, the stopping criterion is
ln(z + z_est)  ln(z) < dlogz
, wherez
is the current evidence from all saved samples andz_est
is the estimated contribution from the remaining volume. The default is0.01
. logl_max : float, optional
Iteration will stop when the sampled ln(likelihood) exceeds the threshold set by
logl_max
. Default is no bound (np.inf
). n_effective: int, optional
Target number of effective posterior samples. If the estimated “effective sample size” (ESS) exceeds this number, sampling will terminate. Default is no ESS (
np.inf
). live_points : list of 3
ndarray
each with shape (nlive, ndim) A set of live points used to initialize the nested sampling run. Contains
live_u
, the coordinates on the unit cube,live_v
, the transformed variables, andlive_logl
, the associated loglikelihoods. By default, if these are not provided the initial set of live points will be drawn from the unitnpdim
cube. WARNING: It is crucial that the initial set of live points have been sampled from the prior. Failure to provide a set of valid live points will lead to incorrect results.
Returns:  worst : int
Index of the live point with the worst likelihood. This is our new dead point sample.
 ustar :
ndarray
with shape (npdim,) Position of the sample.
 vstar :
ndarray
with shape (ndim,) Transformed position of the sample.
 loglstar : float
Ln(likelihood) of the sample.
 logvol : float
Ln(prior volume) within the sample.
 logwt : float
Ln(weight) of the sample.
 logz : float
Cumulative ln(evidence) up to the sample (inclusive).
 logzvar : float
Estimated cumulative variance on
logz
(inclusive). h : float
Cumulative information up to the sample (inclusive).
 nc : int
Number of likelihood calls performed before the new live point was accepted.
 worst_it : int
Iteration when the live (now dead) point was originally proposed.
 boundidx : int
Index of the bound the dead point was originally drawn from.
 bounditer : int
Index of the bound being used at the current iteration.
 eff : float
The cumulative sampling efficiency (in percent).
 delta_logz : float
The estimated remaining evidence expressed as the ln(ratio) of the current evidence.

dynesty.dynamicsampler.
weight_function
(results, args=None, return_weights=False)¶ The default weight function utilized by
DynamicSampler
. Zipped parameters are passed to the function viaargs
. Assigns each point a weight based on a weighted average of the posterior and evidence information content:weight = pfrac * pweight + (1.  pfrac) * zweight
where
pfrac
is the fractional importance placed on the posterior, the evidence weightzweight
is based on the estimated remaining posterior mass, and the posterior weightpweight
is the sample’s importance weight.Returns a set of loglikelihood bounds set by the earliest/latest samples where
weight > maxfrac * max(weight)
, with additional left/right padding based onpad
.Parameters:  results :
Results
instance Results
instance. args : dictionary of keyword arguments, optional
Arguments used to set the loglikelihood bounds used for sampling, as described above. Default values are
pfrac = 0.8
,maxfrac = 0.8
, andpad = 1
. return_weights : bool, optional
Whether to return the individual weights (and their components) used to compute the loglikelihood bounds. Default is
False
.
Returns:  logl_bounds : tuple with shape (2,)
Loglikelihood bounds
(logl_min, logl_max)
determined by the weights. weights : tuple with shape (3,), optional
The individual weights
(pweight, zweight, weight)
used to determinelogl_bounds
.
 results :

dynesty.dynamicsampler.
stopping_function
(results, args=None, rstate=None, M=None, return_vals=False)¶ The default stopping function utilized by
DynamicSampler
. Zipped parameters are passed to the function viaargs
. Assigns the run a stopping value based on a weighted average of the stopping values for the posterior and evidence:stop = pfrac * stop_post + (1. pfrac) * stop_evid
The evidence stopping value is based on the estimated evidence error (i.e. standard deviation) relative to a given threshold:
stop_evid = evid_std / evid_thresh
The posterior stopping value is based on the fractional error (i.e. standard deviation / mean) in the KullbackLeibler (KL) divergence relative to a given threshold:
stop_post = (kld_std / kld_mean) / post_thresh
Estimates of the mean and standard deviation are computed using
n_mc
realizations of the input using a provided'error'
keyword (either'jitter'
or'simulate'
, which call related functionsjitter_run()
andsimulate_run()
indynesty.utils
, respectively, or'sim_approx'
, which boosts'jitter'
by a factor of two).Returns the boolean
stop <= 1
. IfTrue
, theDynamicSampler
will stop adding new samples to our results.Parameters:  results :
Results
instance Results
instance. args : dictionary of keyword arguments, optional
Arguments used to set the stopping values. Default values are
pfrac = 1.0
,evid_thresh = 0.1
,post_thresh = 0.02
,n_mc = 128
,error = 'sim_approx'
, andapprox = True
. rstate :
RandomState
, optional RandomState
instance. M :
map
function, optional An alias to a
map
like function. This allows users to pass functions from pools (e.g.,pool.map
) to compute realizations in parallel. By default the standardmap
function is used. return_vals : bool, optional
Whether to return the stopping value (and its components). Default is
False
.
Returns:  stop_flag : bool
Boolean flag indicating whether we have passed the desired stopping criteria.
 stop_vals : tuple of shape (3,), optional
The individual stopping values
(stop_post, stop_evid, stop)
used to determine the stopping criteria.
 results :

dynesty.dynamicsampler.
_kld_error
(args)¶ Internal
pool.map
friendly wrapper forkld_error()
used bystopping_function()
.
Sampling Results¶
Utilities for handling results.

class
dynesty.results.
Results
¶ Bases:
dict
Contains the full output of a run along with a set of helper functions for summarizing the output.

summary
(self)¶ Return a formatted string giving a quick summary of the results.


dynesty.results.
print_fn
(results, niter, ncall, add_live_it=None, dlogz=None, stop_val=None, nbatch=None, logl_min=inf, logl_max=inf, pbar=None)¶ The default function used to print out results in real time.
Parameters:  results : tuple
Collection of variables output from the current state of the sampler. Currently includes: (1) particle index, (2) unit cube position, (3) parameter position, (4) ln(likelihood), (5) ln(volume), (6) ln(weight), (7) ln(evidence), (8) Var[ln(evidence)], (9) information, (10) number of (current) function calls, (11) iteration when the point was originally proposed, (12) index of the bounding object originally proposed from, (13) index of the bounding object active at a given iteration, (14) cumulative efficiency, and (15) estimated remaining ln(evidence).
 niter : int
The current iteration of the sampler.
 ncall : int
The total number of function calls at the current iteration.
 add_live_it : int, optional
If the last set of live points are being added explicitly, this quantity tracks the sorted index of the current live point being added.
 dlogz : float, optional
The evidence stopping criterion. If not provided, the provided stopping value will be used instead.
 stop_val : float, optional
The current stopping criterion (for dynamic nested sampling). Used if the
dlogz
value is not specified. nbatch : int, optional
The current batch (for dynamic nested sampling).
 logl_min : float, optional
The minimum loglikelihood used when starting sampling. Default is
np.inf
. logl_max : float, optional
The maximum loglikelihood used when stopping sampling. Default is
np.inf
.
Useful Helper Functions¶
A collection of useful functions.

dynesty.utils.
unitcheck
(u, nonbounded=None)¶ Check whether
u
is inside the unit cube. Given a masked arraynonbounded
, also allows periodic boundaries conditions to exceed the unit cube.

dynesty.utils.
resample_equal
(samples, weights, rstate=None)¶ Resample a new set of points from the weighted set of inputs such that they all have equal weight.
Each input sample appears in the output array either
floor(weights[i] * nsamples)
orceil(weights[i] * nsamples)
times, withfloor
orceil
randomly selected (weighted by proximity).Parameters:  samples :
ndarray
with shape (nsamples,) Set of unequally weighted samples.
 weights :
ndarray
with shape (nsamples,) Corresponding weight of each sample.
 rstate :
RandomState
, optional RandomState
instance.
Returns:  equal_weight_samples :
ndarray
with shape (nsamples,) New set of samples with equal weights.
Notes
Implements the systematic resampling method described in Hol, Schon, and Gustafsson (2006).
Examples
>>> x = np.array([[1., 1.], [2., 2.], [3., 3.], [4., 4.]]) >>> w = np.array([0.6, 0.2, 0.15, 0.05]) >>> utils.resample_equal(x, w) array([[ 1., 1.], [ 1., 1.], [ 1., 1.], [ 3., 3.]])
 samples :

dynesty.utils.
mean_and_cov
(samples, weights)¶ Compute the weighted mean and covariance of the samples.
Parameters: Returns: Notes
Implements the formulae found here.

dynesty.utils.
quantile
(x, q, weights=None)¶ Compute (weighted) quantiles from an input set of samples.
Parameters: Returns:  quantiles :
ndarray
with shape (nquantiles,) The weighted sample quantiles computed at
q
.
 quantiles :

dynesty.utils.
jitter_run
(res, rstate=None, approx=False)¶ Probes statistical uncertainties on a nested sampling run by explicitly generating a realization of the prior volume associated with each sample (dead point). Companion function to
resample_run()
andsimulate_run()
.Parameters:  res :
Results
instance The
Results
instance taken from a previous nested sampling run. rstate :
RandomState
, optional RandomState
instance. approx : bool, optional
Whether to approximate all sets of uniform order statistics by their associated marginals (from the Beta distribution). Default is
False
.
Returns:  res :

dynesty.utils.
resample_run
(res, rstate=None, return_idx=False)¶ Probes sampling uncertainties on a nested sampling run using bootstrap resampling techniques to generate a realization of the (expected) prior volume(s) associated with each sample (dead point). This effectively splits a nested sampling run with
K
particles (live points) into a series ofK
“strands” (i.e. runs with a single live point) which are then bootstrapped to construct a new “resampled” run. Companion function tojitter_run()
andsimulate_run()
.Parameters:  res :
Results
instance The
Results
instance taken from a previous nested sampling run. rstate :
RandomState
, optional RandomState
instance. return_idx : bool, optional
Whether to return the list of resampled indices used to construct the new run. Default is
False
.
Returns:  res :

dynesty.utils.
simulate_run
(res, rstate=None, return_idx=False, approx=False)¶ Probes combined uncertainties (statistical and sampling) on a nested sampling run by wrapping
jitter_run()
andresample_run()
.Parameters:  res :
Results
instance The
Results
instance taken from a previous nested sampling run. rstate :
RandomState
, optional RandomState
instance. return_idx : bool, optional
Whether to return the list of resampled indices used to construct the new run. Default is
False
. approx : bool, optional
Whether to approximate all sets of uniform order statistics by their associated marginals (from the Beta distribution). Default is
False
.
Returns:  res :

dynesty.utils.
reweight_run
(res, logp_new, logp_old=None)¶ Reweight a given run based on a new target distribution.
Parameters:  res :
Results
instance The
Results
instance taken from a previous nested sampling run. logp_new :
ndarray
with shape (nsamps,) New target distribution evaluated at the location of the samples.
 logp_old :
ndarray
with shape (nsamps,) Old target distribution evaluated at the location of the samples. If not provided, the
logl
values fromres
will be used.
Returns:  res :

dynesty.utils.
unravel_run
(res, save_proposals=True, print_progress=True)¶ Unravels a run with
K
live points intoK
“strands” (a nested sampling run with only 1 live point). WARNING: the anciliary quantities provided with each unraveled “strand” are only valid if the point was initialized from the prior.Parameters:  res :
Results
instance The
Results
instance taken from a previous nested sampling run. save_proposals : bool, optional
Whether to save a reference to the proposal distributions from the original run in each unraveled strand. Default is
True
. print_progress : bool, optional
Whether to output the current progress to
stderr
. Default isTrue
.
Returns:  res :

dynesty.utils.
merge_runs
(res_list, print_progress=True)¶ Merges a set of runs with differing (possibly variable) numbers of live points into one run.
Parameters: Returns:

dynesty.utils.
kl_divergence
(res1, res2)¶ Computes the KullbackLeibler (KL) divergence from the discrete probability distribution defined by
res2
to the discrete probability distribution defined byres1
.Parameters:  res1 :
Results
instance Results
instance for the distribution we are computing the KL divergence to. Note that, by construction, the samples in `res1` *must* be a subset of the samples in `res2`. res2 :
Results
instance Results
instance for the distribution we are computing the KL divergence from. Note that, by construction, the samples in `res2` *must* be a superset of the samples in `res1`.
Returns:  kld :
ndarray
with shape (nsamps,) The cumulative KL divergence defined over
res1
.
 res1 :

dynesty.utils.
kld_error
(res, error='simulate', rstate=None, return_new=False, approx=False)¶ Computes the KullbackLeibler (KL) divergence from the discrete probability distribution defined by
res
to the discrete probability distribution defined by a realization ofres
.Parameters:  res :
Results
instance Results
instance for the distribution we are computing the KL divergence from. error : {
'jitter'
,'resample'
,'simulate'
}, optional The error method employed, corresponding to
jitter_run()
,resample_run()
, andsimulate_run()
, respectively. Default is'simulate'
. rstate :
RandomState
, optional RandomState
instance. return_new : bool, optional
Whether to return the realization of the run used to compute the KL divergence. Default is
False
. approx : bool, optional
Whether to approximate all sets of uniform order statistics by their associated marginals (from the Beta distribution). Default is
False
.
Returns:  res :

dynesty.utils.
_merge_two
(res1, res2, compute_aux=False)¶ Internal method used to merges two runs with differing (possibly variable) numbers of live points into one run.
Parameters:  res1 :
Results
instance The “base” nested sampling run.
 res2 :
Results
instance The “new” nested sampling run.
 compute_aux : bool, optional
Whether to compute auxiliary quantities (evidences, etc.) associated with a given run. WARNING: these are only valid if `res1` or `res2` was initialized from the prior *and* their sampling bounds overlap. Default is
False
.
Returns:  res1 :

dynesty.utils.
_get_nsamps_samples_n
(res)¶ Helper function for calculating the number of samples
Parameters: Returns:  nsamps: int
The total number of samples
 samples_n: array
Number of live points at a given iteration
Plotting Utilities¶
A set of builtin plotting functions to help visualize dynesty
nested
sampling Results
.

dynesty.plotting.
runplot
(results, span=None, logplot=False, kde=True, nkde=1000, color='blue', plot_kwargs=None, label_kwargs=None, lnz_error=True, lnz_truth=None, truth_color='red', truth_kwargs=None, max_x_ticks=8, max_y_ticks=3, use_math_text=True, mark_final_live=True, fig=None)¶ Plot live points, ln(likelihood), ln(weight), and ln(evidence) as a function of ln(prior volume).
Parameters:  results :
Results
instance A
Results
instance from a nested sampling run. span : iterable with shape (4,), optional
A list where each element is either a length2 tuple containing lower and upper bounds or a float from
(0., 1.]
giving the fraction below the maximum. If a fraction is provided, the bounds are chosen to be equaltailed. An example would be:span = [(0., 10.), 0.001, 0.2, (5., 6.)]
Default is
(0., 1.05 * max(data))
for each element. logplot : bool, optional
Whether to plot the evidence on a log scale. Default is
False
. kde : bool, optional
Whether to use kernel density estimation to estimate and plot the PDF of the importance weights as a function of logvolume (as opposed to the importance weights themselves). Default is
True
. nkde : int, optional
The number of grid points used when plotting the kernel density estimate. Default is
1000
. color : str or iterable with shape (4,), optional
A
matplotlib
style color (either a single color or a different value for each subplot) used when plotting the lines in each subplot. Default is'blue'
. plot_kwargs : dict, optional
Extra keyword arguments that will be passed to
plot
. label_kwargs : dict, optional
Extra keyword arguments that will be sent to the
set_xlabel
andset_ylabel
methods. lnz_error : bool, optional
Whether to plot the 1, 2, and 3sigma approximate error bars derived from the ln(evidence) error approximation over the course of the run. Default is
True
. lnz_truth : float, optional
A reference value for the evidence that will be overplotted on the evidence subplot if provided.
 truth_color : str or iterable with shape (ndim,), optional
A
matplotlib
style color used when plottinglnz_truth
. Default is'red'
. truth_kwargs : dict, optional
Extra keyword arguments that will be used for plotting
lnz_truth
. max_x_ticks : int, optional
Maximum number of ticks allowed for the x axis. Default is
8
. max_y_ticks : int, optional
Maximum number of ticks allowed for the y axis. Default is
4
. use_math_text : bool, optional
Whether the axis tick labels for very large/small exponents should be displayed as powers of 10 rather than using
e
. Default isFalse
. mark_final_live : bool, optional
Whether to indicate the final addition of recycled live points (if they were added to the resulting samples) using a dashed vertical line. Default is
True
. fig : (
Figure
,Axes
), optional If provided, overplot the run onto the provided figure. Otherwise, by default an internal figure is generated.
Returns:  results :

dynesty.plotting.
traceplot
(results, span=None, quantiles=[0.025, 0.5, 0.975], smooth=0.02, thin=1, dims=None, post_color='blue', post_kwargs=None, kde=True, nkde=1000, trace_cmap='plasma', trace_color=None, trace_kwargs=None, connect=False, connect_highlight=10, connect_color='red', connect_kwargs=None, max_n_ticks=5, use_math_text=False, labels=None, label_kwargs=None, show_titles=False, title_quantiles=[0.025, 0.5, 0.975], title_fmt='.2f', title_kwargs=None, truths=None, truth_color='red', truth_kwargs=None, verbose=False, fig=None)¶ Plot traces and marginalized posteriors for each parameter.
Parameters:  results :
Results
instance A
Results
instance from a nested sampling run. Compatible with results derived from nestle. span : iterable with shape (ndim,), optional
A list where each element is either a length2 tuple containing lower and upper bounds or a float from
(0., 1.]
giving the fraction of (weighted) samples to include. If a fraction is provided, the bounds are chosen to be equaltailed. An example would be:span = [(0., 10.), 0.95, (5., 6.)]
Default is
0.999999426697
(5sigma credible interval) for each parameter. quantiles : iterable, optional
A list of fractional quantiles to overplot on the 1D marginalized posteriors as vertical dashed lines. Default is
[0.025, 0.5, 0.975]
(the 95%/2sigma credible interval). smooth : float or iterable with shape (ndim,), optional
The standard deviation (either a single value or a different value for each subplot) for the Gaussian kernel used to smooth the 1D marginalized posteriors, expressed as a fraction of the span. Default is
0.02
(2% smoothing). If an integer is provided instead, this will instead default to a simple (weighted) histogram withbins=smooth
. thin : int, optional
Thin the samples so that only each
thin
th sample is plotted. Default is1
(no thinning). dims : iterable of shape (ndim,), optional
The subset of dimensions that should be plotted. If not provided, all dimensions will be shown.
 post_color : str or iterable with shape (ndim,), optional
A
matplotlib
style color (either a single color or a different value for each subplot) used when plotting the histograms. Default is'blue'
. post_kwargs : dict, optional
Extra keyword arguments that will be used for plotting the marginalized 1D posteriors.
 kde : bool, optional
Whether to use kernel density estimation to estimate and plot the PDF of the importance weights as a function of logvolume (as opposed to the importance weights themselves). Default is
True
. nkde : int, optional
The number of grid points used when plotting the kernel density estimate. Default is
1000
. trace_cmap : str or iterable with shape (ndim,), optional
A
matplotlib
style colormap (either a single colormap or a different colormap for each subplot) used when plotting the traces, where each point is colored according to its weight. Default is'plasma'
. trace_color : str or iterable with shape (ndim,), optional
A
matplotlib
style color (either a single color or a different color for each subplot) used when plotting the traces. This overrides thetrace_cmap
option by giving all points the same color. Default isNone
(not used). trace_kwargs : dict, optional
Extra keyword arguments that will be used for plotting the traces.
 connect : bool, optional
Whether to draw lines connecting the paths of unique particles. Default is
False
. connect_highlight : int or iterable, optional
If
connect=True
, highlights the paths of a specific set of particles. If an integer is passed,connect_highlight
random particle paths will be highlighted. If an iterable is passed, then the particle paths corresponding to the provided indices will be highlighted. connect_color : str, optional
The color of the highlighted particle paths. Default is
'red'
. connect_kwargs : dict, optional
Extra keyword arguments used for plotting particle paths.
 max_n_ticks : int, optional
Maximum number of ticks allowed. Default is
5
. use_math_text : bool, optional
Whether the axis tick labels for very large/small exponents should be displayed as powers of 10 rather than using
e
. Default isFalse
. labels : iterable with shape (ndim,), optional
A list of names for each parameter. If not provided, the default name used when plotting will follow \(x_i\) style.
 label_kwargs : dict, optional
Extra keyword arguments that will be sent to the
set_xlabel
andset_ylabel
methods. show_titles : bool, optional
Whether to display a title above each 1D marginalized posterior showing the 0.5 quantile along with the upper/lower bounds associated with the 0.025 and 0.975 (95%/2sigma credible interval) quantiles. Default is
True
. title_quantiles : iterable, optional
A list of fractional quantiles to use in the title. Default is
[0.025, 0.5, 0.975]
(median plus 95%/2sigma credible interval). title_fmt : str, optional
The format string for the quantiles provided in the title. Default is
'.2f'
. title_kwargs : dict, optional
Extra keyword arguments that will be sent to the
set_title
command. truths : iterable with shape (ndim,), optional
A list of reference values that will be overplotted on the traces and marginalized 1D posteriors as solid horizontal/vertical lines. Individual values can be exempt using
None
. Default isNone
. truth_color : str or iterable with shape (ndim,), optional
A
matplotlib
style color (either a single color or a different value for each subplot) used when plottingtruths
. Default is'red'
. truth_kwargs : dict, optional
Extra keyword arguments that will be used for plotting the vertical and horizontal lines with
truths
. verbose : bool, optional
Whether to print the values of the computed quantiles associated with each parameter. Default is
False
. fig : (
Figure
,Axes
), optional If provided, overplot the traces and marginalized 1D posteriors onto the provided figure. Otherwise, by default an internal figure is generated.
Returns:  results :

dynesty.plotting.
cornerpoints
(results, dims=None, thin=1, span=None, cmap='plasma', color=None, kde=True, nkde=1000, plot_kwargs=None, labels=None, label_kwargs=None, truths=None, truth_color='red', truth_kwargs=None, max_n_ticks=5, use_math_text=False, fig=None)¶ Generate a (sub)corner plot of (weighted) samples.
Parameters:  results :
Results
instance A
Results
instance from a nested sampling run. Compatible with results derived from nestle. dims : iterable of shape (ndim,), optional
The subset of dimensions that should be plotted. If not provided, all dimensions will be shown.
 thin : int, optional
Thin the samples so that only each
thin
th sample is plotted. Default is1
(no thinning). span : iterable with shape (ndim,), optional
A list where each element is either a length2 tuple containing lower and upper bounds or a float from
(0., 1.]
giving the fraction of (weighted) samples to include. If a fraction is provided, the bounds are chosen to be equaltailed. An example would be:span = [(0., 10.), 0.95, (5., 6.)]
Default is
1.
for all parameters (no bound). cmap : str, optional
A
matplotlib
style colormap used when plotting the points, where each point is colored according to its weight. Default is'plasma'
. color : str, optional
A
matplotlib
style color used when plotting the points. This overrides thecmap
option by giving all points the same color. Default isNone
(not used). kde : bool, optional
Whether to use kernel density estimation to estimate and plot the PDF of the importance weights as a function of logvolume (as opposed to the importance weights themselves). Default is
True
. nkde : int, optional
The number of grid points used when plotting the kernel density estimate. Default is
1000
. plot_kwargs : dict, optional
Extra keyword arguments that will be used for plotting the points.
 labels : iterable with shape (ndim,), optional
A list of names for each parameter. If not provided, the default name used when plotting will follow \(x_i\) style.
 label_kwargs : dict, optional
Extra keyword arguments that will be sent to the
set_xlabel
andset_ylabel
methods. truths : iterable with shape (ndim,), optional
A list of reference values that will be overplotted on the traces and marginalized 1D posteriors as solid horizontal/vertical lines. Individual values can be exempt using
None
. Default isNone
. truth_color : str or iterable with shape (ndim,), optional
A
matplotlib
style color (either a single color or a different value for each subplot) used when plottingtruths
. Default is'red'
. truth_kwargs : dict, optional
Extra keyword arguments that will be used for plotting the vertical and horizontal lines with
truths
. max_n_ticks : int, optional
Maximum number of ticks allowed. Default is
5
. use_math_text : bool, optional
Whether the axis tick labels for very large/small exponents should be displayed as powers of 10 rather than using
e
. Default isFalse
. fig : (
Figure
,Axes
), optional If provided, overplot the points onto the provided figure object. Otherwise, by default an internal figure is generated.
Returns:  results :

dynesty.plotting.
cornerplot
(results, dims=None, span=None, quantiles=[0.025, 0.5, 0.975], color='black', smooth=0.02, quantiles_2d=None, hist_kwargs=None, hist2d_kwargs=None, labels=None, label_kwargs=None, show_titles=False, title_quantiles=[0.025, 0.5, 0.975], title_fmt='.2f', title_kwargs=None, truths=None, truth_color='red', truth_kwargs=None, max_n_ticks=5, top_ticks=False, use_math_text=False, verbose=False, fig=None)¶ Generate a corner plot of the 1D and 2D marginalized posteriors.
Parameters:  results :
Results
instance A
Results
instance from a nested sampling run. Compatible with results derived from nestle. dims : iterable of shape (ndim,), optional
The subset of dimensions that should be plotted. If not provided, all dimensions will be shown.
 span : iterable with shape (ndim,), optional
A list where each element is either a length2 tuple containing lower and upper bounds or a float from
(0., 1.]
giving the fraction of (weighted) samples to include. If a fraction is provided, the bounds are chosen to be equaltailed. An example would be:span = [(0., 10.), 0.95, (5., 6.)]
Default is
0.999999426697
(5sigma credible interval). quantiles : iterable, optional
A list of fractional quantiles to overplot on the 1D marginalized posteriors as vertical dashed lines. Default is
[0.025, 0.5, 0.975]
(spanning the 95%/2sigma credible interval). color : str or iterable with shape (ndim,), optional
A
matplotlib
style color (either a single color or a different value for each subplot) used when plotting the histograms. Default is'black'
. smooth : float or iterable with shape (ndim,), optional
The standard deviation (either a single value or a different value for each subplot) for the Gaussian kernel used to smooth the 1D and 2D marginalized posteriors, expressed as a fraction of the span. Default is
0.02
(2% smoothing). If an integer is provided instead, this will instead default to a simple (weighted) histogram withbins=smooth
. quantiles_2d : iterable with shape (nquant,), optional
The quantiles used for plotting the smoothed 2D distributions. If not provided, these default to 0.5, 1, 1.5, and 2sigma contours roughly corresponding to quantiles of
[0.1, 0.4, 0.65, 0.85]
. hist_kwargs : dict, optional
Extra keyword arguments to send to the 1D (smoothed) histograms.
 hist2d_kwargs : dict, optional
Extra keyword arguments to send to the 2D (smoothed) histograms.
 labels : iterable with shape (ndim,), optional
A list of names for each parameter. If not provided, the default name used when plotting will follow \(x_i\) style.
 label_kwargs : dict, optional
Extra keyword arguments that will be sent to the
set_xlabel
andset_ylabel
methods. show_titles : bool, optional
Whether to display a title above each 1D marginalized posterior showing the 0.5 quantile along with the upper/lower bounds associated with the 0.025 and 0.975 (95%/2sigma credible interval) quantiles. Default is
True
. title_quantiles : iterable, optional
A list of fractional quantiles to use in the title. Default is
[0.025, 0.5, 0.975]
(median plus 95%/2sigma credible interval). title_fmt : str, optional
The format string for the quantiles provided in the title. Default is
'.2f'
. title_kwargs : dict, optional
Extra keyword arguments that will be sent to the
set_title
command. truths : iterable with shape (ndim,), optional
A list of reference values that will be overplotted on the traces and marginalized 1D posteriors as solid horizontal/vertical lines. Individual values can be exempt using
None
. Default isNone
. truth_color : str or iterable with shape (ndim,), optional
A
matplotlib
style color (either a single color or a different value for each subplot) used when plottingtruths
. Default is'red'
. truth_kwargs : dict, optional
Extra keyword arguments that will be used for plotting the vertical and horizontal lines with
truths
. max_n_ticks : int, optional
Maximum number of ticks allowed. Default is
5
. top_ticks : bool, optional
Whether to label the top (rather than bottom) ticks. Default is
False
. use_math_text : bool, optional
Whether the axis tick labels for very large/small exponents should be displayed as powers of 10 rather than using
e
. Default isFalse
. verbose : bool, optional
Whether to print the values of the computed quantiles associated with each parameter. Default is
False
. fig : (
Figure
,Axes
), optional If provided, overplot the traces and marginalized 1D posteriors onto the provided figure. Otherwise, by default an internal figure is generated.
Returns:  results :

dynesty.plotting.
boundplot
(results, dims, it=None, idx=None, prior_transform=None, periodic=None, reflective=None, ndraws=5000, color='gray', plot_kwargs=None, labels=None, label_kwargs=None, max_n_ticks=5, use_math_text=False, show_live=False, live_color='darkviolet', live_kwargs=None, span=None, fig=None)¶ Return the bounding distribution used to propose either (1) live points at a given iteration or (2) a specific dead point during the course of a run, projected onto the two dimensions specified by
dims
.Parameters:  results :
Results
instance A
Results
instance from a nested sampling run. dims : length2 tuple
The dimensions used to plot the bounding.
 it : int, optional
If provided, returns the bounding distribution at the specified iteration of the nested sampling run. Note that this option and `idx` are mutually exclusive.
 idx : int, optional
If provided, returns the bounding distribution used to propose the dead point at the specified iteration of the nested sampling run. Note that this option and `it` are mutually exclusive.
 prior_transform : func, optional
The function transforming samples within the unit cube back to samples in the native model space. If provided, the transformed bounding distribution will be plotted in the native model space.
 periodic : iterable, optional
A list of indices for parameters with periodic boundary conditions. These parameters will not have their positions constrained to be within the unit cube, enabling smooth behavior for parameters that may wrap around the edge. Default is
None
(i.e. no periodic boundary conditions). reflective : iterable, optional
A list of indices for parameters with reflective boundary conditions. These parameters will not have their positions constrained to be within the unit cube, enabling smooth behavior for parameters that may reflect at the edge. Default is
None
(i.e. no reflective boundary conditions). ndraws : int, optional
The number of random samples to draw from the bounding distribution when plotting. Default is
5000
. color : str, optional
The color of the points randomly sampled from the bounding distribution. Default is
'gray'
. plot_kwargs : dict, optional
Extra keyword arguments used when plotting the bounding draws.
 labels : iterable with shape (ndim,), optional
A list of names for each parameter. If not provided, the default name used when plotting will follow \(x_i\) style.
 label_kwargs : dict, optional
Extra keyword arguments that will be sent to the
set_xlabel
andset_ylabel
methods. max_n_ticks : int, optional
Maximum number of ticks allowed. Default is
5
. use_math_text : bool, optional
Whether the axis tick labels for very large/small exponents should be displayed as powers of 10 rather than using
e
. Default isFalse
. show_live : bool, optional
Whether the live points at a given iteration (for
it
) or associated with the bounding (foridx
) should be highlighted. Default isFalse
. In the dynamic case, only the live points associated with the batch used to construct the relevant bound are plotted. live_color : str, optional
The color of the live points. Default is
'darkviolet'
. live_kwargs : dict, optional
Extra keyword arguments used when plotting the live points.
 span : iterable with shape (2,), optional
A list where each element is a length2 tuple containing lower and upper bounds. Default is
None
(no bound). fig : (
Figure
,Axes
), optional If provided, overplot the draws onto the provided figure. Otherwise, by default an internal figure is generated.
Returns:  results :

dynesty.plotting.
cornerbound
(results, it=None, idx=None, dims=None, prior_transform=None, periodic=None, reflective=None, ndraws=5000, color='gray', plot_kwargs=None, labels=None, label_kwargs=None, max_n_ticks=5, use_math_text=False, show_live=False, live_color='darkviolet', live_kwargs=None, span=None, fig=None)¶ Return the bounding distribution used to propose either (1) live points at a given iteration or (2) a specific dead point during the course of a run, projected onto all pairs of dimensions.
Parameters:  results :
Results
instance A
Results
instance from a nested sampling run. it : int, optional
If provided, returns the bounding distribution at the specified iteration of the nested sampling run. Note that this option and `idx` are mutually exclusive.
 idx : int, optional
If provided, returns the bounding distribution used to propose the dead point at the specified iteration of the nested sampling run. Note that this option and `it` are mutually exclusive.
 dims : iterable of shape (ndim,), optional
The subset of dimensions that should be plotted. If not provided, all dimensions will be shown.
 prior_transform : func, optional
The function transforming samples within the unit cube back to samples in the native model space. If provided, the transformed bounding distribution will be plotted in the native model space.
 periodic : iterable, optional
A list of indices for parameters with periodic boundary conditions. These parameters will not have their positions constrained to be within the unit cube, enabling smooth behavior for parameters that may wrap around the edge. Default is
None
(i.e. no periodic boundary conditions). reflective : iterable, optional
A list of indices for parameters with reflective boundary conditions. These parameters will not have their positions constrained to be within the unit cube, enabling smooth behavior for parameters that may reflect at the edge. Default is
None
(i.e. no reflective boundary conditions). ndraws : int, optional
The number of random samples to draw from the bounding distribution when plotting. Default is
5000
. color : str, optional
The color of the points randomly sampled from the bounding distribution. Default is
'gray'
. plot_kwargs : dict, optional
Extra keyword arguments used when plotting the bounding draws.
 labels : iterable with shape (ndim,), optional
A list of names for each parameter. If not provided, the default name used when plotting will be in \(x_i\) style.
 label_kwargs : dict, optional
Extra keyword arguments that will be sent to the
set_xlabel
andset_ylabel
methods. max_n_ticks : int, optional
Maximum number of ticks allowed. Default is
5
. use_math_text : bool, optional
Whether the axis tick labels for very large/small exponents should be displayed as powers of 10 rather than using
e
. Default isFalse
. show_live : bool, optional
Whether the live points at a given iteration (for
it
) or associated with the bounding (foridx
) should be highlighted. Default isFalse
. In the dynamic case, only the live points associated with the batch used to construct the relevant bound are plotted. live_color : str, optional
The color of the live points. Default is
'darkviolet'
. live_kwargs : dict, optional
Extra keyword arguments used when plotting the live points.
 span : iterable with shape (2,), optional
A list where each element is a length2 tuple containing lower and upper bounds. Default is
None
(no bound). fig : (
Figure
,Axes
), optional If provided, overplot the draws onto the provided figure. Otherwise, by default an internal figure is generated.
Returns:  results :

dynesty.plotting.
_hist2d
(x, y, smooth=0.02, span=None, weights=None, levels=None, ax=None, color='gray', plot_datapoints=False, plot_density=True, plot_contours=True, no_fill_contours=False, fill_contours=True, contour_kwargs=None, contourf_kwargs=None, data_kwargs=None, **kwargs)¶ Internal function called by
cornerplot()
used to generate a a 2D histogram/contour of samples.Parameters:  x : interable with shape (nsamps,)
Sample positions in the first dimension.
 y : iterable with shape (nsamps,)
Sample positions in the second dimension.
 span : iterable with shape (ndim,), optional
A list where each element is either a length2 tuple containing lower and upper bounds or a float from
(0., 1.]
giving the fraction of (weighted) samples to include. If a fraction is provided, the bounds are chosen to be equaltailed. An example would be:span = [(0., 10.), 0.95, (5., 6.)]
Default is
0.999999426697
(5sigma credible interval). weights : iterable with shape (nsamps,)
Weights associated with the samples. Default is
None
(no weights). levels : iterable, optional
The contour levels to draw. Default are
[0.5, 1, 1.5, 2]
sigma. ax :
Axes
, optional An
axes
instance on which to add the 2D histogram. If not provided, a figure will be generated. color : str, optional
The
matplotlib
style color used to draw lines and color cells and contours. Default is'gray'
. plot_datapoints : bool, optional
Whether to plot the individual data points. Default is
False
. plot_density : bool, optional
Whether to draw the density colormap. Default is
True
. plot_contours : bool, optional
Whether to draw the contours. Default is
True
. no_fill_contours : bool, optional
Whether to add absolutely no filling to the contours. This differs from
fill_contours=False
, which still adds a white fill at the densest points. Default isFalse
. fill_contours : bool, optional
Whether to fill the contours. Default is
True
. contour_kwargs : dict
Any additional keyword arguments to pass to the
contour
method. contourf_kwargs : dict
Any additional keyword arguments to pass to the
contourf
method. data_kwargs : dict
Any additional keyword arguments to pass to the
plot
method when adding the individual data points.