Index
_
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A
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B
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C
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D
|
E
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F
|
G
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H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
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R
|
S
|
T
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U
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V
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W
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X
_
_dfdp() (pints.toy.ToyODEModel method)
_log_init() (pints.Loggable method)
_log_write() (pints.Loggable method)
_rhs() (pints.toy.ToyODEModel method)
A
a() (pints.MonomialGammaHamiltonianMCMC method)
ABCController (class in pints)
ABCSampler (class in pints)
ABCSMC (class in pints)
acceptance_rate() (pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.DramACMC method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.MALAMCMC method)
(pints.MetropolisRandomWalkMCMC method)
(pints.RaoBlackwellACMC method)
acorr() (in module pints.residuals_diagnostics)
ActionPotentialModel (class in pints.toy)
active_points() (pints.NestedController method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
Adam (class in pints)
adapt_epsilon() (pints.DualAveragingAdaption method)
AdaptiveCovarianceMC (class in pints)
AdaptiveCovarianceMCMC (class in pints)
add_counter() (pints.Logger method)
add_float() (pints.Logger method)
add_int() (pints.Logger method)
add_long_float() (pints.Logger method)
add_parameter_sample() (pints.DualAveragingAdaption method)
add_string() (pints.Logger method)
add_time() (pints.Logger method)
alpha() (pints.NestedEllipsoidSampler method)
AnnulusLogPDF (class in pints.toy)
ar1() (in module pints.noise)
ar1_unity() (in module pints.noise)
AR1LogLikelihood (class in pints)
arma11() (in module pints.noise)
arma11_unity() (in module pints.noise)
ARMA11LogLikelihood (class in pints)
ask() (pints.ABCSampler method)
(pints.ABCSMC method)
(pints.Adam method)
(pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.DifferentialEvolutionMCMC method)
(pints.DramACMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.GradientDescent method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.IRPropMin method)
(pints.MALAMCMC method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.MultiChainMCMC method)
(pints.NelderMead method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
(pints.NoUTurnMCMC method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PopulationMCMC method)
(pints.PSO method)
(pints.RaoBlackwellACMC method)
(pints.RejectionABC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
(pints.SNES method)
(pints.XNES method)
autocorrelation() (in module pints.plot)
B
b() (pints.DreamMCMC method)
b_star() (pints.DreamMCMC method)
BareCMAES (class in pints)
beta() (pints.toy.ConeLogPDF method)
BetaLogPrior (class in pints)
bisection_steps() (pints.SliceStepoutMCMC method)
Boundaries (class in pints)
C
c() (pints.MonomialGammaHamiltonianMCMC method)
calculate_residuals() (in module pints.residuals_diagnostics)
calculate_sample_variance() (pints.DualAveragingAdaption method)
CauchyLogLikelihood (class in pints)
CauchyLogPrior (class in pints)
cdf() (pints.BetaLogPrior method)
(pints.CauchyLogPrior method)
(pints.ComposedLogPrior method)
(pints.ExponentialLogPrior method)
(pints.GammaLogPrior method)
(pints.GaussianLogPrior method)
(pints.HalfCauchyLogPrior method)
(pints.InverseGammaLogPrior method)
(pints.LogNormalLogPrior method)
(pints.LogPrior method)
(pints.LogUniformLogPrior method)
(pints.MultivariateGaussianLogPrior method)
(pints.NormalLogPrior method)
(pints.StudentTLogPrior method)
CDF() (pints.toy.ConeLogPDF method)
cdf() (pints.TransformedLogPrior method)
(pints.TruncatedGaussianLogPrior method)
(pints.UniformLogPrior method)
CensoredGaussianLogLikelihood (class in pints)
chains() (pints.MCMCController method)
(pints.MCMCSampling method)
(pints.MCMCSummary method)
check() (pints.Boundaries method)
(pints.LogPDFBoundaries method)
(pints.RectangularBoundaries method)
(pints.TransformedBoundaries method)
(pints.TransformedRectangularBoundaries method)
CMAES (class in pints)
ComposedLogPrior (class in pints)
ComposedTransformation (class in pints)
ConeLogPDF (class in pints.toy)
constant_crossover() (pints.DreamMCMC method)
ConstantAndMultiplicativeGaussianLogLikelihood (class in pints)
ConstantModel (class in pints.toy)
convert_boundaries() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
convert_covariance_matrix() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
convert_error_measure() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
convert_from_unit_cube() (pints.BetaLogPrior method)
(pints.CauchyLogPrior method)
(pints.ComposedLogPrior method)
(pints.ExponentialLogPrior method)
(pints.GammaLogPrior method)
(pints.GaussianLogPrior method)
(pints.HalfCauchyLogPrior method)
(pints.InverseGammaLogPrior method)
(pints.LogNormalLogPrior method)
(pints.LogPrior method)
(pints.LogUniformLogPrior method)
(pints.MultivariateGaussianLogPrior method)
(pints.NormalLogPrior method)
(pints.StudentTLogPrior method)
(pints.TransformedLogPrior method)
(pints.TruncatedGaussianLogPrior method)
(pints.UniformLogPrior method)
convert_log_pdf() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
convert_log_prior() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
convert_standard_deviation() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
convert_to_unit_cube() (pints.BetaLogPrior method)
(pints.CauchyLogPrior method)
(pints.ComposedLogPrior method)
(pints.ExponentialLogPrior method)
(pints.GammaLogPrior method)
(pints.GaussianLogPrior method)
(pints.HalfCauchyLogPrior method)
(pints.InverseGammaLogPrior method)
(pints.LogNormalLogPrior method)
(pints.LogPrior method)
(pints.LogUniformLogPrior method)
(pints.MultivariateGaussianLogPrior method)
(pints.NormalLogPrior method)
(pints.StudentTLogPrior method)
(pints.TransformedLogPrior method)
(pints.TruncatedGaussianLogPrior method)
(pints.UniformLogPrior method)
cov() (pints.BareCMAES method)
cpu_count() (pints.ParallelEvaluator static method)
CR() (pints.DreamMCMC method)
current_log_pdfs() (pints.DifferentialEvolutionMCMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.MultiChainMCMC method)
current_slice_height() (pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
curve_fit() (in module pints)
D
data() (pints.toy.EightSchoolsLogPDF method)
(pints.toy.GermanCreditHierarchicalLogPDF method)
(pints.toy.GermanCreditLogPDF method)
DegradationModel (class in pints.toy.stochastic)
delta() (pints.NoUTurnMCMC method)
delta_max() (pints.DreamMCMC method)
DifferentialEvolutionMCMC (class in pints)
distance() (pints.toy.AnnulusLogPDF method)
(pints.toy.ConeLogPDF method)
(pints.toy.EightSchoolsLogPDF method)
(pints.toy.GaussianLogPDF method)
(pints.toy.GermanCreditHierarchicalLogPDF method)
(pints.toy.GermanCreditLogPDF method)
(pints.toy.HighDimensionalGaussianLogPDF method)
(pints.toy.MultimodalGaussianLogPDF method)
(pints.toy.NealsFunnelLogPDF method)
(pints.toy.RosenbrockLogPDF method)
(pints.toy.SimpleEggBoxLogPDF method)
(pints.toy.ToyLogPDF method)
(pints.toy.TwistedGaussianLogPDF method)
divergent_iterations() (pints.HamiltonianMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.NoUTurnMCMC method)
(pints.RelativisticMCMC method)
DramACMC (class in pints)
DreamMCMC (class in pints)
DualAveragingAdaption (class in pints)
dynamic_enlargement_factor() (pints.NestedEllipsoidSampler method)
E
effective_sample_size() (in module pints)
(pints.NestedController method)
EightSchoolsLogPDF (class in pints.toy)
elementwise() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
ellipsoid_update_gap() (pints.NestedEllipsoidSampler method)
EmceeHammerMCMC (class in pints)
enlargement_factor() (pints.NestedEllipsoidSampler method)
epsilon() (pints.HamiltonianMCMC method)
(pints.MALAMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.RelativisticMCMC method)
ErrorMeasure (class in pints)
ess() (pints.MCMCSummary method)
ess_per_second() (pints.MCMCSummary method)
eta() (pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.DramACMC method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.RaoBlackwellACMC method)
evaluate() (in module pints)
(pints.Evaluator method)
(pints.MultiOutputProblem method)
(pints.MultiSequentialEvaluator method)
(pints.ParallelEvaluator method)
(pints.SequentialEvaluator method)
(pints.SingleOutputProblem method)
evaluateS1() (pints.AR1LogLikelihood method)
(pints.ARMA11LogLikelihood method)
(pints.BetaLogPrior method)
(pints.CauchyLogLikelihood method)
(pints.CauchyLogPrior method)
(pints.CensoredGaussianLogLikelihood method)
(pints.ComposedLogPrior method)
(pints.ConstantAndMultiplicativeGaussianLogLikelihood method)
(pints.ErrorMeasure method)
(pints.ExponentialLogPrior method)
(pints.GammaLogPrior method)
(pints.GaussianIntegratedLogUniformLogLikelihood method)
(pints.GaussianIntegratedUniformLogLikelihood method)
(pints.GaussianKnownSigmaLogLikelihood method)
(pints.GaussianLogLikelihood method)
(pints.GaussianLogPrior method)
(pints.HalfCauchyLogPrior method)
(pints.InverseGammaLogPrior method)
(pints.KnownNoiseLogLikelihood method)
(pints.LogNormalLogLikelihood method)
(pints.LogNormalLogPrior method)
(pints.LogPDF method)
(pints.LogPosterior method)
(pints.LogPrior method)
(pints.LogUniformLogPrior method)
(pints.MeanSquaredError method)
(pints.MultiOutputProblem method)
(pints.MultiplicativeGaussianLogLikelihood method)
(pints.MultivariateGaussianLogPrior method)
(pints.NormalisedRootMeanSquaredError method)
(pints.NormalLogPrior method)
(pints.PooledLogPDF method)
(pints.ProbabilityBasedError method)
(pints.ProblemErrorMeasure method)
(pints.ProblemLogLikelihood method)
(pints.RootMeanSquaredError method)
(pints.ScaledLogLikelihood method)
(pints.SingleOutputProblem method)
(pints.StudentTLogLikelihood method)
(pints.StudentTLogPrior method)
(pints.SumOfErrors method)
(pints.SumOfIndependentLogPDFs method)
(pints.SumOfSquaresError method)
(pints.toy.AnnulusLogPDF method)
(pints.toy.ConeLogPDF method)
(pints.toy.EightSchoolsLogPDF method)
(pints.toy.GaussianLogPDF method)
(pints.toy.GermanCreditHierarchicalLogPDF method)
(pints.toy.GermanCreditLogPDF method)
(pints.toy.HighDimensionalGaussianLogPDF method)
(pints.toy.MultimodalGaussianLogPDF method)
(pints.toy.NealsFunnelLogPDF method)
(pints.toy.ParabolicError method)
(pints.toy.RosenbrockError method)
(pints.toy.RosenbrockLogPDF method)
(pints.toy.SimpleEggBoxLogPDF method)
(pints.toy.ToyLogPDF method)
(pints.toy.TwistedGaussianLogPDF method)
(pints.TransformedErrorMeasure method)
(pints.TransformedLogPDF method)
(pints.TransformedLogPrior method)
(pints.TruncatedGaussianLogPrior method)
(pints.UniformLogPrior method)
(pints.UnknownNoiseLogLikelihood method)
evaluations() (pints.Optimisation method)
(pints.OptimisationController method)
Evaluator (class in pints)
expansion_steps() (pints.SliceDoublingMCMC method)
(pints.SliceStepoutMCMC method)
ExponentialLogPrior (class in pints)
F
f_best() (pints.Adam method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.GradientDescent method)
(pints.IRPropMin method)
(pints.NelderMead method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
f_guessed() (pints.Adam method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.GradientDescent method)
(pints.IRPropMin method)
(pints.NelderMead method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
f_guessed_tracking() (pints.Optimisation method)
(pints.OptimisationController method)
fbest() (pints.Adam method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.GradientDescent method)
(pints.IRPropMin method)
(pints.NelderMead method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
final_epsilon() (pints.DualAveragingAdaption method)
FitzhughNagumoModel (class in pints.toy)
fixed_parameters() (pints.toy.Hes1Model method)
fmin() (in module pints)
fold() (pints.toy.HodgkinHuxleyIKModel method)
format() (pints.Timer method)
ForwardModel (class in pints)
ForwardModelS1 (class in pints)
function() (in module pints.plot)
function_between_points() (in module pints.plot)
G
gamma() (pints.DifferentialEvolutionMCMC method)
gamma_switch_rate() (pints.DifferentialEvolutionMCMC method)
GammaLogPrior (class in pints)
gaussian_error() (pints.DifferentialEvolutionMCMC method)
GaussianIntegratedLogUniformLogLikelihood (class in pints)
GaussianIntegratedUniformLogLikelihood (class in pints)
GaussianKnownSigmaLogLikelihood (class in pints)
GaussianLogLikelihood (class in pints)
GaussianLogPDF (class in pints.toy)
GaussianLogPrior (class in pints)
GermanCreditHierarchicalLogPDF (class in pints.toy)
GermanCreditLogPDF (class in pints.toy)
get_epsilon() (pints.DualAveragingAdaption method)
get_mass_matrix() (pints.DualAveragingAdaption method)
GoodwinOscillatorModel (class in pints.toy)
GradientDescent (class in pints)
H
HaarioACMC (class in pints)
HaarioBardenetACMC (class in pints)
HalfCauchyLogPrior (class in pints)
hamiltonian_threshold() (pints.HamiltonianMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.NoUTurnMCMC method)
(pints.RelativisticMCMC method)
HamiltonianMCMC (class in pints)
Hes1Model (class in pints.toy)
HighDimensionalGaussianLogPDF (class in pints.toy)
histogram() (in module pints.plot)
HodgkinHuxleyIKModel (class in pints.toy)
I
icdf() (pints.BetaLogPrior method)
(pints.CauchyLogPrior method)
(pints.ComposedLogPrior method)
(pints.ExponentialLogPrior method)
(pints.GammaLogPrior method)
(pints.GaussianLogPrior method)
(pints.HalfCauchyLogPrior method)
(pints.InverseGammaLogPrior method)
(pints.LogNormalLogPrior method)
(pints.LogPrior method)
(pints.LogUniformLogPrior method)
(pints.MultivariateGaussianLogPrior method)
(pints.NormalLogPrior method)
(pints.StudentTLogPrior method)
(pints.TransformedLogPrior method)
(pints.TruncatedGaussianLogPrior method)
(pints.UniformLogPrior method)
IdentityTransformation (class in pints)
in_initial_phase() (pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.DifferentialEvolutionMCMC method)
(pints.DramACMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.MALAMCMC method)
(pints.MCMCSampler method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.MultiChainMCMC method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
(pints.NoUTurnMCMC method)
(pints.PopulationMCMC method)
(pints.RaoBlackwellACMC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
inactive_points() (pints.NestedController method)
independent() (in module pints.noise)
init_adapt_epsilon() (pints.DualAveragingAdaption method)
init_sample_covariance() (pints.DualAveragingAdaption method)
initial_conditions() (pints.toy.ActionPotentialModel method)
(pints.toy.FitzhughNagumoModel method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.ToyODEModel method)
initial_phase_iterations() (pints.MCMCController method)
(pints.MCMCSampling method)
interpolate_mol_counts() (pints.toy.stochastic.DegradationModel method)
(pints.toy.stochastic.LogisticModel method)
(pints.toy.stochastic.MarkovJumpModel method)
(pints.toy.stochastic.MichaelisMentenModel method)
(pints.toy.stochastic.ProductionDegradationModel method)
(pints.toy.stochastic.SchloglModel method)
InverseGammaLogPrior (class in pints)
IRPropMin (class in pints)
iterations() (pints.NestedController method)
(pints.Optimisation method)
(pints.OptimisationController method)
J
jacobian() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.toy.FitzhughNagumoModel method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.ToyODEModel method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
jacobian_S1() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
K
kl_divergence() (pints.toy.GaussianLogPDF method)
(pints.toy.HighDimensionalGaussianLogPDF method)
(pints.toy.MultimodalGaussianLogPDF method)
(pints.toy.NealsFunnelLogPDF method)
(pints.toy.SimpleEggBoxLogPDF method)
(pints.toy.TwistedGaussianLogPDF method)
KnownNoiseLogLikelihood (class in pints)
L
leapfrog_step_size() (pints.HamiltonianMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.RelativisticMCMC method)
leapfrog_steps() (pints.HamiltonianMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.RelativisticMCMC method)
learning_rate() (pints.GradientDescent method)
load_samples() (in module pints.io)
load_state() (pints.NoUTurnMCMC method)
log() (pints.Logger method)
log_filename() (pints.ABCController method)
log_jacobian_det() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
log_jacobian_det_S1() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
log_likelihood() (pints.LogPosterior method)
log_likelihood_vector() (pints.NestedController method)
log_pdfs() (pints.MCMCController method)
(pints.MCMCSampling method)
log_prior() (pints.LogPosterior method)
Loggable (class in pints)
Logger (class in pints)
LogisticModel (class in pints.toy)
(class in pints.toy.stochastic)
LogitTransformation (class in pints)
LogNormalLogLikelihood (class in pints)
LogNormalLogPrior (class in pints)
LogPDF (class in pints)
LogPDFBoundaries (class in pints)
LogPosterior (class in pints)
LogPrior (class in pints)
LogTransformation (class in pints)
LogUniformLogPrior (class in pints)
LotkaVolterraModel (class in pints.toy)
lower() (pints.RectangularBoundaries method)
(pints.TransformedRectangularBoundaries method)
M
m0() (pints.toy.Hes1Model method)
MALAMCMC (class in pints)
marginal_log_likelihood() (pints.NestedController method)
marginal_log_likelihood_standard_deviation() (pints.NestedController method)
marginal_log_likelihood_threshold() (pints.NestedController method)
marginal_log_pdf() (pints.toy.NealsFunnelLogPDF method)
MarkovJumpModel (class in pints.toy.stochastic)
mass() (pints.MonomialGammaHamiltonianMCMC method)
(pints.RelativisticMCMC method)
matrix2d() (in module pints)
max_evaluations() (pints.Optimisation method)
(pints.OptimisationController method)
max_iterations() (pints.ABCController method)
(pints.MCMCController method)
(pints.MCMCSampling method)
(pints.Optimisation method)
(pints.OptimisationController method)
max_step_size() (pints.IRPropMin method)
max_tree_depth() (pints.NoUTurnMCMC method)
max_unchanged_iterations() (pints.Optimisation method)
(pints.OptimisationController method)
mcmc_sample() (in module pints)
MCMCController (class in pints)
MCMCSampler (class in pints)
MCMCSampling (class in pints)
MCMCSummary (class in pints)
mean() (pints.BareCMAES method)
(pints.BetaLogPrior method)
(pints.CauchyLogPrior method)
(pints.ComposedLogPrior method)
(pints.ExponentialLogPrior method)
(pints.GammaLogPrior method)
(pints.GaussianLogPrior method)
(pints.HalfCauchyLogPrior method)
(pints.InverseGammaLogPrior method)
(pints.LogNormalLogPrior method)
(pints.LogPrior method)
(pints.LogUniformLogPrior method)
(pints.MCMCSummary method)
(pints.MultivariateGaussianLogPrior method)
(pints.NormalLogPrior method)
(pints.StudentTLogPrior method)
(pints.toy.AnnulusLogPDF method)
(pints.toy.NealsFunnelLogPDF method)
(pints.toy.stochastic.DegradationModel method)
(pints.toy.stochastic.LogisticModel method)
(pints.TransformedLogPrior method)
(pints.TruncatedGaussianLogPrior method)
(pints.UniformLogPrior method)
mean_normed() (pints.toy.AnnulusLogPDF method)
(pints.toy.ConeLogPDF method)
MeanSquaredError (class in pints)
method_needs_initial_phase() (pints.MCMCController method)
(pints.MCMCSampling method)
MetropolisRandomWalkMCMC (class in pints)
MichaelisMentenModel (class in pints.toy.stochastic)
min_index() (pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
min_step_size() (pints.IRPropMin method)
module
pints
pints.io
pints.noise
pints.plot
pints.residuals_diagnostics
moment_normed() (pints.toy.AnnulusLogPDF method)
MonomialGammaHamiltonianMCMC (class in pints)
MultiChainMCMC (class in pints)
MultimodalGaussianLogPDF (class in pints.toy)
MultiOutputProblem (class in pints)
multiplicative_gaussian() (in module pints.noise)
MultiplicativeGaussianLogLikelihood (class in pints)
MultiSequentialEvaluator (class in pints)
MultivariateGaussianLogPrior (class in pints)
N
n_active_points() (pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
n_evaluations() (pints.MCMCController method)
(pints.MCMCSampling method)
n_hyper_parameters() (pints.ABCSampler method)
(pints.ABCSMC method)
(pints.Adam method)
(pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.DifferentialEvolutionMCMC method)
(pints.DramACMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.GradientDescent method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.IRPropMin method)
(pints.MALAMCMC method)
(pints.MCMCSampler method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.MultiChainMCMC method)
(pints.NelderMead method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
(pints.NoUTurnMCMC method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PopulationMCMC method)
(pints.PSO method)
(pints.RaoBlackwellACMC method)
(pints.RejectionABC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
(pints.SNES method)
(pints.TunableMethod method)
(pints.XNES method)
n_outputs() (pints.ForwardModel method)
(pints.ForwardModelS1 method)
(pints.MultiOutputProblem method)
(pints.SingleOutputProblem method)
(pints.toy.ActionPotentialModel method)
(pints.toy.ConstantModel method)
(pints.toy.FitzhughNagumoModel method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.HodgkinHuxleyIKModel method)
(pints.toy.LogisticModel method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.RepressilatorModel method)
(pints.toy.SimpleHarmonicOscillatorModel method)
(pints.toy.SIRModel method)
(pints.toy.stochastic.DegradationModel method)
(pints.toy.stochastic.LogisticModel method)
(pints.toy.stochastic.MarkovJumpModel method)
(pints.toy.stochastic.MichaelisMentenModel method)
(pints.toy.stochastic.ProductionDegradationModel method)
(pints.toy.stochastic.SchloglModel method)
n_parameters() (pints.AR1LogLikelihood method)
(pints.ARMA11LogLikelihood method)
(pints.BetaLogPrior method)
(pints.Boundaries method)
(pints.CauchyLogLikelihood method)
(pints.CauchyLogPrior method)
(pints.CensoredGaussianLogLikelihood method)
(pints.ComposedLogPrior method)
(pints.ComposedTransformation method)
(pints.ConstantAndMultiplicativeGaussianLogLikelihood method)
(pints.ErrorMeasure method)
(pints.ExponentialLogPrior method)
(pints.ForwardModel method)
(pints.ForwardModelS1 method)
(pints.GammaLogPrior method)
(pints.GaussianIntegratedLogUniformLogLikelihood method)
(pints.GaussianIntegratedUniformLogLikelihood method)
(pints.GaussianKnownSigmaLogLikelihood method)
(pints.GaussianLogLikelihood method)
(pints.GaussianLogPrior method)
(pints.HalfCauchyLogPrior method)
(pints.IdentityTransformation method)
(pints.InverseGammaLogPrior method)
(pints.KnownNoiseLogLikelihood method)
(pints.LogitTransformation method)
(pints.LogNormalLogLikelihood method)
(pints.LogNormalLogPrior method)
(pints.LogPDF method)
(pints.LogPDFBoundaries method)
(pints.LogPosterior method)
(pints.LogPrior method)
(pints.LogTransformation method)
(pints.LogUniformLogPrior method)
(pints.MeanSquaredError method)
(pints.MultiOutputProblem method)
(pints.MultiplicativeGaussianLogLikelihood method)
(pints.MultivariateGaussianLogPrior method)
(pints.NormalisedRootMeanSquaredError method)
(pints.NormalLogPrior method)
(pints.PooledLogPDF method)
(pints.ProbabilityBasedError method)
(pints.ProblemErrorMeasure method)
(pints.ProblemLogLikelihood method)
(pints.RectangularBoundaries method)
(pints.RectangularBoundariesTransformation method)
(pints.RootMeanSquaredError method)
(pints.ScaledLogLikelihood method)
(pints.ScalingTransformation method)
(pints.SingleOutputProblem method)
(pints.StudentTLogLikelihood method)
(pints.StudentTLogPrior method)
(pints.SumOfErrors method)
(pints.SumOfIndependentLogPDFs method)
(pints.SumOfSquaresError method)
(pints.toy.ActionPotentialModel method)
(pints.toy.AnnulusLogPDF method)
(pints.toy.ConeLogPDF method)
(pints.toy.ConstantModel method)
(pints.toy.EightSchoolsLogPDF method)
(pints.toy.FitzhughNagumoModel method)
(pints.toy.GaussianLogPDF method)
(pints.toy.GermanCreditHierarchicalLogPDF method)
(pints.toy.GermanCreditLogPDF method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.HighDimensionalGaussianLogPDF method)
(pints.toy.HodgkinHuxleyIKModel method)
(pints.toy.LogisticModel method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.MultimodalGaussianLogPDF method)
(pints.toy.NealsFunnelLogPDF method)
(pints.toy.ParabolicError method)
(pints.toy.RepressilatorModel method)
(pints.toy.RosenbrockError method)
(pints.toy.RosenbrockLogPDF method)
(pints.toy.SimpleEggBoxLogPDF method)
(pints.toy.SimpleHarmonicOscillatorModel method)
(pints.toy.SIRModel method)
(pints.toy.stochastic.DegradationModel method)
(pints.toy.stochastic.LogisticModel method)
(pints.toy.stochastic.MarkovJumpModel method)
(pints.toy.stochastic.MichaelisMentenModel method)
(pints.toy.stochastic.ProductionDegradationModel method)
(pints.toy.stochastic.SchloglModel method)
(pints.toy.ToyLogPDF method)
(pints.toy.TwistedGaussianLogPDF method)
(pints.Transformation method)
(pints.TransformedBoundaries method)
(pints.TransformedErrorMeasure method)
(pints.TransformedLogPDF method)
(pints.TransformedLogPrior method)
(pints.TransformedRectangularBoundaries method)
(pints.TruncatedGaussianLogPrior method)
(pints.UniformLogPrior method)
(pints.UnitCubeTransformation method)
(pints.UnknownNoiseLogLikelihood method)
n_posterior_samples() (pints.NestedController method)
n_rejection_samples() (pints.NestedEllipsoidSampler method)
n_samples() (pints.ABCController method)
n_states() (pints.toy.FitzhughNagumoModel method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.ToyODEModel method)
n_times() (pints.MultiOutputProblem method)
(pints.SingleOutputProblem method)
name() (pints.ABCSampler method)
(pints.ABCSMC method)
(pints.Adam method)
(pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.DifferentialEvolutionMCMC method)
(pints.DramACMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.GradientDescent method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.IRPropMin method)
(pints.MALAMCMC method)
(pints.MCMCSampler method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.MultiChainMCMC method)
(pints.NelderMead method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
(pints.NoUTurnMCMC method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PopulationMCMC method)
(pints.PSO method)
(pints.RaoBlackwellACMC method)
(pints.RejectionABC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
(pints.SNES method)
(pints.XNES method)
nCR() (pints.DreamMCMC method)
NealsFunnelLogPDF (class in pints.toy)
needs_initial_phase() (pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.DifferentialEvolutionMCMC method)
(pints.DramACMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.MALAMCMC method)
(pints.MCMCSampler method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.MultiChainMCMC method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
(pints.NoUTurnMCMC method)
(pints.PopulationMCMC method)
(pints.RaoBlackwellACMC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
needs_sensitivities() (pints.Adam method)
(pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.DifferentialEvolutionMCMC method)
(pints.DramACMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.GradientDescent method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.IRPropMin method)
(pints.MALAMCMC method)
(pints.MCMCSampler method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.MultiChainMCMC method)
(pints.NelderMead method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
(pints.NoUTurnMCMC method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PopulationMCMC method)
(pints.PSO method)
(pints.RaoBlackwellACMC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
(pints.SNES method)
(pints.XNES method)
NelderMead (class in pints)
NestedController (class in pints)
NestedEllipsoidSampler (class in pints)
NestedRejectionSampler (class in pints)
NestedSampler (class in pints)
NormalisedRootMeanSquaredError (class in pints)
NormalLogPrior (class in pints)
NoUTurnMCMC (class in pints)
number_adaption_steps() (pints.NoUTurnMCMC method)
O
Optimisation (class in pints)
OptimisationController (class in pints)
optimise() (in module pints)
Optimiser (class in pints)
optimiser() (pints.Optimisation method)
(pints.OptimisationController method)
optimum() (pints.toy.ParabolicError method)
(pints.toy.RosenbrockError method)
(pints.toy.RosenbrockLogPDF method)
P
p_g() (pints.DreamMCMC method)
pairwise() (in module pints.plot)
ParabolicError (class in pints.toy)
parallel() (pints.ABCController method)
(pints.MCMCController method)
(pints.MCMCSampling method)
(pints.NestedController method)
(pints.Optimisation method)
(pints.OptimisationController method)
ParallelEvaluator (class in pints)
pints
module
pints.io
module
pints.noise
module
pints.plot
module
pints.residuals_diagnostics
module
plot_residuals_autocorrelation() (in module pints.residuals_diagnostics)
plot_residuals_binned_autocorrelation() (in module pints.residuals_diagnostics)
plot_residuals_binned_std() (in module pints.residuals_diagnostics)
plot_residuals_distance() (in module pints.residuals_diagnostics)
plot_residuals_vs_output() (in module pints.residuals_diagnostics)
PooledLogPDF (class in pints)
population_size() (pints.BareCMAES method)
(pints.CMAES method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
PopulationBasedOptimiser (class in pints)
PopulationMCMC (class in pints)
posterior_samples() (pints.NestedController method)
prior_space() (pints.NestedController method)
prob_overrelaxed() (pints.SliceStepoutMCMC method)
ProbabilityBasedError (class in pints)
ProblemErrorMeasure (class in pints)
ProblemLogLikelihood (class in pints)
ProductionDegradationModel (class in pints.toy.stochastic)
pseudo_cdf() (pints.MultivariateGaussianLogPrior method)
pseudo_icdf() (pints.MultivariateGaussianLogPrior method)
PSO (class in pints)
Q
quantiles() (pints.MCMCSummary method)
R
r0() (pints.toy.AnnulusLogPDF method)
range() (pints.RectangularBoundaries method)
(pints.TransformedRectangularBoundaries method)
RaoBlackwellACMC (class in pints)
RectangularBoundaries (class in pints)
RectangularBoundariesTransformation (class in pints)
RejectionABC (class in pints)
relative_scaling() (pints.DifferentialEvolutionMCMC method)
RelativisticMCMC (class in pints)
replace() (pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.DramACMC method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.MALAMCMC method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.NoUTurnMCMC method)
(pints.PopulationMCMC method)
(pints.RaoBlackwellACMC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
RepressilatorModel (class in pints.toy)
reset() (pints.Timer method)
rhat() (in module pints)
(pints.MCMCSummary method)
rhat_all_params() (in module pints)
rho() (pints.toy.HighDimensionalGaussianLogPDF method)
RootMeanSquaredError (class in pints)
RosenbrockError (class in pints.toy)
RosenbrockLogPDF (class in pints.toy)
run() (pints.ABCController method)
(pints.MCMCController method)
(pints.MCMCSampling method)
(pints.NestedController method)
(pints.Optimisation method)
(pints.OptimisationController method)
running() (pints.Adam method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.GradientDescent method)
(pints.IRPropMin method)
(pints.NelderMead method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
running_log_likelihood() (pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
S
sample() (pints.BetaLogPrior method)
(pints.Boundaries method)
(pints.CauchyLogPrior method)
(pints.ComposedLogPrior method)
(pints.ExponentialLogPrior method)
(pints.GammaLogPrior method)
(pints.GaussianLogPrior method)
(pints.HalfCauchyLogPrior method)
(pints.InverseGammaLogPrior method)
(pints.LogNormalLogPrior method)
(pints.LogPDFBoundaries method)
(pints.LogPrior method)
(pints.LogUniformLogPrior method)
(pints.MultivariateGaussianLogPrior method)
(pints.NormalLogPrior method)
(pints.RectangularBoundaries method)
(pints.StudentTLogPrior method)
(pints.toy.AnnulusLogPDF method)
(pints.toy.ConeLogPDF method)
(pints.toy.EightSchoolsLogPDF method)
(pints.toy.GaussianLogPDF method)
(pints.toy.GermanCreditHierarchicalLogPDF method)
(pints.toy.GermanCreditLogPDF method)
(pints.toy.HighDimensionalGaussianLogPDF method)
(pints.toy.MultimodalGaussianLogPDF method)
(pints.toy.NealsFunnelLogPDF method)
(pints.toy.RosenbrockLogPDF method)
(pints.toy.SimpleEggBoxLogPDF method)
(pints.toy.ToyLogPDF method)
(pints.toy.TwistedGaussianLogPDF method)
(pints.TransformedBoundaries method)
(pints.TransformedLogPrior method)
(pints.TransformedRectangularBoundaries method)
(pints.TruncatedGaussianLogPrior method)
(pints.UniformLogPrior method)
sample_from_posterior() (pints.NestedController method)
sample_initial_points() (in module pints)
sampler() (pints.ABCController method)
(pints.MCMCController method)
(pints.MCMCSampling method)
samplers() (pints.MCMCController method)
(pints.MCMCSampling method)
save_samples() (in module pints.io)
save_state() (pints.NoUTurnMCMC method)
scale() (pints.EmceeHammerMCMC method)
scale_coefficient() (pints.DifferentialEvolutionMCMC method)
scaled_epsilon() (pints.HamiltonianMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.RelativisticMCMC method)
ScaledLogLikelihood (class in pints)
ScalingTransformation (class in pints)
SchloglModel (class in pints.toy.stochastic)
SequentialEvaluator (class in pints)
series() (in module pints.plot)
set_a() (pints.MonomialGammaHamiltonianMCMC method)
set_alpha() (pints.NestedEllipsoidSampler method)
set_b() (pints.DreamMCMC method)
set_b_star() (pints.DreamMCMC method)
set_bisection_steps() (pints.SliceStepoutMCMC method)
set_c() (pints.MonomialGammaHamiltonianMCMC method)
set_callback() (pints.Optimisation method)
(pints.OptimisationController method)
set_chain_filename() (pints.MCMCController method)
(pints.MCMCSampling method)
set_chain_storage() (pints.MCMCController method)
(pints.MCMCSampling method)
set_constant_crossover() (pints.DreamMCMC method)
set_CR() (pints.DreamMCMC method)
set_delta() (pints.NoUTurnMCMC method)
set_delta_max() (pints.DreamMCMC method)
set_dynamic_enlargement_factor() (pints.NestedEllipsoidSampler method)
set_ellipsoid_update_gap() (pints.NestedEllipsoidSampler method)
set_enlargement_factor() (pints.NestedEllipsoidSampler method)
set_epsilon() (pints.HamiltonianMCMC method)
(pints.MALAMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.RelativisticMCMC method)
set_eta() (pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.DramACMC method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.RaoBlackwellACMC method)
set_expansion_steps() (pints.SliceDoublingMCMC method)
(pints.SliceStepoutMCMC method)
set_f_guessed_tracking() (pints.Optimisation method)
(pints.OptimisationController method)
set_filename() (pints.Logger method)
set_fixed_parameters() (pints.toy.Hes1Model method)
set_gamma() (pints.DifferentialEvolutionMCMC method)
set_gamma_switch_rate() (pints.DifferentialEvolutionMCMC method)
set_gaussian_error() (pints.DifferentialEvolutionMCMC method)
set_hamiltonian_threshold() (pints.HamiltonianMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.NoUTurnMCMC method)
(pints.RelativisticMCMC method)
set_hyper_parameters() (pints.ABCSampler method)
(pints.ABCSMC method)
(pints.Adam method)
(pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.DifferentialEvolutionMCMC method)
(pints.DramACMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.GradientDescent method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.IRPropMin method)
(pints.MALAMCMC method)
(pints.MCMCSampler method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.MultiChainMCMC method)
(pints.NelderMead method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
(pints.NoUTurnMCMC method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PopulationMCMC method)
(pints.PSO method)
(pints.RaoBlackwellACMC method)
(pints.RejectionABC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
(pints.SNES method)
(pints.TunableMethod method)
(pints.XNES method)
set_initial_conditions() (pints.toy.ActionPotentialModel method)
(pints.toy.FitzhughNagumoModel method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.ToyODEModel method)
set_initial_phase() (pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.DifferentialEvolutionMCMC method)
(pints.DramACMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.MALAMCMC method)
(pints.MCMCSampler method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.MultiChainMCMC method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
(pints.NoUTurnMCMC method)
(pints.PopulationMCMC method)
(pints.RaoBlackwellACMC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
set_initial_phase_iterations() (pints.MCMCController method)
(pints.MCMCSampling method)
set_intermediate_size() (pints.ABCSMC method)
set_inv_mass_matrix() (pints.DualAveragingAdaption method)
set_iterations() (pints.NestedController method)
set_leapfrog_step_size() (pints.HamiltonianMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.RelativisticMCMC method)
set_leapfrog_steps() (pints.HamiltonianMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.RelativisticMCMC method)
set_learning_rate() (pints.GradientDescent method)
set_local_global_balance() (pints.PSO method)
set_log_interval() (pints.ABCController method)
(pints.MCMCController method)
(pints.MCMCSampling method)
(pints.Optimisation method)
(pints.OptimisationController method)
set_log_pdf_filename() (pints.MCMCController method)
(pints.MCMCSampling method)
set_log_pdf_storage() (pints.MCMCController method)
(pints.MCMCSampling method)
set_log_to_file() (pints.ABCController method)
(pints.MCMCController method)
(pints.MCMCSampling method)
(pints.NestedController method)
(pints.Optimisation method)
(pints.OptimisationController method)
set_log_to_screen() (pints.ABCController method)
(pints.MCMCController method)
(pints.MCMCSampling method)
(pints.NestedController method)
(pints.Optimisation method)
(pints.OptimisationController method)
set_m0() (pints.toy.Hes1Model method)
set_marginal_log_likelihood_threshold() (pints.NestedController method)
set_mass() (pints.MonomialGammaHamiltonianMCMC method)
(pints.RelativisticMCMC method)
set_max_evaluations() (pints.Optimisation method)
(pints.OptimisationController method)
set_max_iterations() (pints.ABCController method)
(pints.MCMCController method)
(pints.MCMCSampling method)
(pints.Optimisation method)
(pints.OptimisationController method)
set_max_step_size() (pints.IRPropMin method)
set_max_tree_depth() (pints.NoUTurnMCMC method)
set_max_unchanged_iterations() (pints.Optimisation method)
(pints.OptimisationController method)
set_min_step_size() (pints.IRPropMin method)
set_n_active_points() (pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
set_n_posterior_samples() (pints.NestedController method)
set_n_rejection_samples() (pints.NestedEllipsoidSampler method)
set_n_samples() (pints.ABCController method)
set_nCR() (pints.DreamMCMC method)
set_number_adaption_steps() (pints.NoUTurnMCMC method)
set_p_g() (pints.DreamMCMC method)
set_parallel() (pints.ABCController method)
(pints.MCMCController method)
(pints.MCMCSampling method)
(pints.NestedController method)
(pints.Optimisation method)
(pints.OptimisationController method)
set_perturbation_kernel() (pints.ABCSMC method)
set_population_size() (pints.BareCMAES method)
(pints.CMAES method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
set_prob_overrelaxed() (pints.SliceStepoutMCMC method)
set_relative_scaling() (pints.DifferentialEvolutionMCMC method)
set_scale() (pints.EmceeHammerMCMC method)
set_scale_coefficient() (pints.DifferentialEvolutionMCMC method)
set_sigma_c() (pints.SliceRankShrinkingMCMC method)
set_sigma_scale() (pints.DramACMC method)
set_solver_tolerances() (pints.toy.ActionPotentialModel method)
set_speed_of_light() (pints.RelativisticMCMC method)
set_stream() (pints.Logger method)
set_target_acceptance_rate() (pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.DramACMC method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.RaoBlackwellACMC method)
set_temperature_schedule() (pints.PopulationMCMC method)
set_threshold() (pints.Optimisation method)
(pints.OptimisationController method)
(pints.RejectionABC method)
set_threshold_schedule() (pints.ABCSMC method)
set_use_dense_mass_matrix() (pints.NoUTurnMCMC method)
set_width() (pints.SliceDoublingMCMC method)
(pints.SliceStepoutMCMC method)
sigma() (pints.toy.AnnulusLogPDF method)
sigma_c() (pints.SliceRankShrinkingMCMC method)
sigma_scale() (pints.DramACMC method)
SimpleEggBoxLogPDF (class in pints.toy)
SimpleHarmonicOscillatorModel (class in pints.toy)
simulate() (pints.ForwardModel method)
(pints.ForwardModelS1 method)
(pints.toy.ActionPotentialModel method)
(pints.toy.ConstantModel method)
(pints.toy.FitzhughNagumoModel method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.HodgkinHuxleyIKModel method)
(pints.toy.LogisticModel method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.RepressilatorModel method)
(pints.toy.SimpleHarmonicOscillatorModel method)
(pints.toy.SIRModel method)
(pints.toy.stochastic.DegradationModel method)
(pints.toy.stochastic.LogisticModel method)
(pints.toy.stochastic.MarkovJumpModel method)
(pints.toy.stochastic.MichaelisMentenModel method)
(pints.toy.stochastic.ProductionDegradationModel method)
(pints.toy.stochastic.SchloglModel method)
(pints.toy.ToyODEModel method)
simulate_all_states() (pints.toy.ActionPotentialModel method)
(pints.toy.Hes1Model method)
simulate_raw() (pints.toy.stochastic.DegradationModel method)
(pints.toy.stochastic.LogisticModel method)
(pints.toy.stochastic.MarkovJumpModel method)
(pints.toy.stochastic.MichaelisMentenModel method)
(pints.toy.stochastic.ProductionDegradationModel method)
(pints.toy.stochastic.SchloglModel method)
simulateS1() (pints.ForwardModelS1 method)
(pints.toy.ConstantModel method)
(pints.toy.FitzhughNagumoModel method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.LogisticModel method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.SimpleHarmonicOscillatorModel method)
(pints.toy.ToyODEModel method)
SingleChainMCMC (class in pints)
SingleOutputProblem (class in pints)
SIRModel (class in pints.toy)
SliceDoublingMCMC (class in pints)
SliceRankShrinkingMCMC (class in pints)
SliceStepoutMCMC (class in pints)
SNES (class in pints)
speed_of_light() (pints.RelativisticMCMC method)
std() (pints.MCMCSummary method)
step() (pints.DualAveragingAdaption method)
stop() (pints.Adam method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.GradientDescent method)
(pints.IRPropMin method)
(pints.NelderMead method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
strfloat() (in module pints)
StudentTLogLikelihood (class in pints)
StudentTLogPrior (class in pints)
suggested_bounds() (pints.toy.AnnulusLogPDF method)
(pints.toy.ConeLogPDF method)
(pints.toy.EightSchoolsLogPDF method)
(pints.toy.GaussianLogPDF method)
(pints.toy.GermanCreditHierarchicalLogPDF method)
(pints.toy.GermanCreditLogPDF method)
(pints.toy.HighDimensionalGaussianLogPDF method)
(pints.toy.MultimodalGaussianLogPDF method)
(pints.toy.NealsFunnelLogPDF method)
(pints.toy.RosenbrockLogPDF method)
(pints.toy.SimpleEggBoxLogPDF method)
(pints.toy.ToyLogPDF method)
(pints.toy.TwistedGaussianLogPDF method)
suggested_duration() (pints.toy.HodgkinHuxleyIKModel method)
suggested_parameters() (pints.toy.ActionPotentialModel method)
(pints.toy.FitzhughNagumoModel method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.HodgkinHuxleyIKModel method)
(pints.toy.LogisticModel method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.RepressilatorModel method)
(pints.toy.SimpleHarmonicOscillatorModel method)
(pints.toy.SIRModel method)
(pints.toy.stochastic.DegradationModel method)
(pints.toy.stochastic.LogisticModel method)
(pints.toy.stochastic.MarkovJumpModel method)
(pints.toy.stochastic.MichaelisMentenModel method)
(pints.toy.stochastic.ProductionDegradationModel method)
(pints.toy.stochastic.SchloglModel method)
(pints.toy.ToyModel method)
(pints.toy.ToyODEModel method)
suggested_population_size() (pints.BareCMAES method)
(pints.CMAES method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
suggested_times() (pints.toy.ActionPotentialModel method)
(pints.toy.FitzhughNagumoModel method)
(pints.toy.GoodwinOscillatorModel method)
(pints.toy.Hes1Model method)
(pints.toy.HodgkinHuxleyIKModel method)
(pints.toy.LogisticModel method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.RepressilatorModel method)
(pints.toy.SimpleHarmonicOscillatorModel method)
(pints.toy.SIRModel method)
(pints.toy.stochastic.DegradationModel method)
(pints.toy.stochastic.LogisticModel method)
(pints.toy.stochastic.MarkovJumpModel method)
(pints.toy.stochastic.MichaelisMentenModel method)
(pints.toy.stochastic.ProductionDegradationModel method)
(pints.toy.stochastic.SchloglModel method)
(pints.toy.ToyModel method)
(pints.toy.ToyODEModel method)
suggested_values() (pints.toy.Hes1Model method)
(pints.toy.LotkaVolterraModel method)
(pints.toy.SIRModel method)
summary() (pints.MCMCSummary method)
SumOfErrors (class in pints)
SumOfIndependentLogPDFs (class in pints)
SumOfSquaresError (class in pints)
surface() (in module pints.plot)
T
target_accept_prob() (pints.DualAveragingAdaption method)
target_acceptance_rate() (pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.DramACMC method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.RaoBlackwellACMC method)
tell() (pints.ABCSampler method)
(pints.ABCSMC method)
(pints.Adam method)
(pints.AdaptiveCovarianceMC method)
(pints.AdaptiveCovarianceMCMC method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.DifferentialEvolutionMCMC method)
(pints.DramACMC method)
(pints.DreamMCMC method)
(pints.EmceeHammerMCMC method)
(pints.GradientDescent method)
(pints.HaarioACMC method)
(pints.HaarioBardenetACMC method)
(pints.HamiltonianMCMC method)
(pints.IRPropMin method)
(pints.MALAMCMC method)
(pints.MetropolisRandomWalkMCMC method)
(pints.MonomialGammaHamiltonianMCMC method)
(pints.MultiChainMCMC method)
(pints.NelderMead method)
(pints.NestedEllipsoidSampler method)
(pints.NestedRejectionSampler method)
(pints.NestedSampler method)
(pints.NoUTurnMCMC method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PopulationMCMC method)
(pints.PSO method)
(pints.RaoBlackwellACMC method)
(pints.RejectionABC method)
(pints.RelativisticMCMC method)
(pints.SingleChainMCMC method)
(pints.SliceDoublingMCMC method)
(pints.SliceRankShrinkingMCMC method)
(pints.SliceStepoutMCMC method)
(pints.SNES method)
(pints.XNES method)
temperature_schedule() (pints.PopulationMCMC method)
threshold() (pints.Optimisation method)
(pints.OptimisationController method)
(pints.RejectionABC method)
time() (pints.MCMCController method)
(pints.MCMCSampling method)
(pints.MCMCSummary method)
(pints.NestedController method)
(pints.Optimisation method)
(pints.OptimisationController method)
(pints.Timer method)
Timer (class in pints)
times() (pints.MultiOutputProblem method)
(pints.SingleOutputProblem method)
to_model() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
to_search() (pints.ComposedTransformation method)
(pints.IdentityTransformation method)
(pints.LogitTransformation method)
(pints.LogTransformation method)
(pints.RectangularBoundariesTransformation method)
(pints.ScalingTransformation method)
(pints.Transformation method)
(pints.UnitCubeTransformation method)
ToyLogPDF (class in pints.toy)
ToyModel (class in pints.toy)
ToyODEModel (class in pints.toy)
trace() (in module pints.plot)
Transformation (class in pints)
TransformedBoundaries (class in pints)
TransformedErrorMeasure (class in pints)
TransformedLogPDF (class in pints)
TransformedLogPrior (class in pints)
TransformedRectangularBoundaries (class in pints)
TruncatedGaussianLogPrior (class in pints)
TunableMethod (class in pints)
TwistedGaussianLogPDF (class in pints.toy)
U
UniformLogPrior (class in pints)
UnitCubeTransformation (class in pints)
UnknownNoiseLogLikelihood (class in pints)
untwist() (pints.toy.TwistedGaussianLogPDF method)
upper() (pints.RectangularBoundaries method)
(pints.TransformedRectangularBoundaries method)
use_dense_mass_matrix() (pints.DualAveragingAdaption method)
(pints.NoUTurnMCMC method)
V
values() (pints.MultiOutputProblem method)
(pints.SingleOutputProblem method)
var() (pints.toy.NealsFunnelLogPDF method)
var_normed() (pints.toy.AnnulusLogPDF method)
(pints.toy.ConeLogPDF method)
variance() (pints.toy.stochastic.DegradationModel method)
vector() (in module pints)
version() (in module pints)
W
warmup_steps() (pints.DualAveragingAdaption method)
width() (pints.SliceDoublingMCMC method)
(pints.SliceStepoutMCMC method)
X
x_best() (pints.Adam method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.GradientDescent method)
(pints.IRPropMin method)
(pints.NelderMead method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
x_guessed() (pints.Adam method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.GradientDescent method)
(pints.IRPropMin method)
(pints.NelderMead method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
xbest() (pints.Adam method)
(pints.BareCMAES method)
(pints.CMAES method)
(pints.GradientDescent method)
(pints.IRPropMin method)
(pints.NelderMead method)
(pints.Optimiser method)
(pints.PopulationBasedOptimiser method)
(pints.PSO method)
(pints.SNES method)
(pints.XNES method)
XNES (class in pints)
Pints
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