Index

A

a (bumps.parameter.Constraint attribute) abs (bumps.parameter.Operators attribute) acceptance_rate() (bumps.dream.state.MCMCDraw method) accumulate() (bumps.history.History method) (bumps.history.Trace method) acos() (in module bumps.parameter) (in module bumps.pmath) acosd() (in module bumps.parameter) (in module bumps.pmath) acosh() (in module bumps.parameter) (in module bumps.pmath) ACR() (in module bumps.dream.acr) adapt() (bumps.dream.crossover.AdaptiveCrossover method) (bumps.dream.crossover.BaseAdaptiveCrossover method) (bumps.dream.crossover.Crossover method) (bumps.dream.crossover.LogAdaptiveCrossover method) AdaptiveCrossover (class in bumps.dream.crossover) add (bumps.parameter.Operators attribute) add_prior() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.SupportsPrior method) add_tag() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) Alias (class in bumps.parameter) alpha (bumps.dream.core.Dream attribute) (bumps.options.BumpsOpts attribute) apply() (bumps.dream.bounds.Bounds static method) (bumps.dream.bounds.ClipBounds static method) (bumps.dream.bounds.FoldBounds static method) (bumps.dream.bounds.IgnoreBounds static method) (bumps.dream.bounds.RandomBounds static method) (bumps.dream.bounds.ReflectBounds static method) arccos (bumps.parameter.Operators attribute) arccos() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) arccosd() (in module bumps.parameter) (in module bumps.pmath) arccosh (bumps.parameter.Operators attribute) arccosh() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) arcsin (bumps.parameter.Operators attribute) arcsin() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) arcsind() (in module bumps.parameter) (in module bumps.pmath)

arcsinh (bumps.parameter.Operators attribute) arcsinh() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) arctan (bumps.parameter.Operators attribute) arctan() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) arctan2 (bumps.parameter.Operators attribute) arctan2() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) arctan2d() (in module bumps.parameter) (in module bumps.pmath) arctand() (in module bumps.parameter) (in module bumps.pmath) arctanh (bumps.parameter.Operators attribute) arctanh() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) args (bumps.bounds.DistProtocol attribute) (bumps.parameter.Expression attribute) (bumps.parameter.Function attribute) asin() (in module bumps.parameter) (in module bumps.pmath) asind() (in module bumps.parameter) (in module bumps.pmath) asinh() (in module bumps.parameter) (in module bumps.pmath) atan() (in module bumps.parameter) (in module bumps.pmath) atan2() (in module bumps.parameter) (in module bumps.pmath) atan2d() (in module bumps.parameter) (in module bumps.pmath) atand() (in module bumps.parameter) (in module bumps.pmath) atanh() (in module bumps.parameter) (in module bumps.pmath) auto_shift() (in module bumps.plotutil)

B

b (bumps.parameter.Constraint attribute) base (bumps.bounds.BoundedAbove attribute) (bumps.bounds.BoundedBelow attribute) BaseAdaptiveCrossover (class in bumps.dream.crossover) BaseMapper (class in bumps.mapper) best() (bumps.dream.state.MCMCDraw method) best_in_bin() (in module bumps.dream.parcoord) BFGSFit (class in bumps.fitters) Bounded (class in bumps.bounds) BoundedAbove (class in bumps.bounds) BoundedBelow (class in bumps.bounds) BoundedNormal (class in bumps.bounds) bounds (bumps.dream.model.Density attribute) (bumps.dream.model.LogDensity attribute) (bumps.dream.model.MCMCModel attribute) (bumps.dream.model.Mixture attribute) (bumps.dream.model.MVNormal attribute) (bumps.dream.model.Simulation attribute) (bumps.fitters.DreamModel attribute) (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) (bumps.parameter.SupportsPrior attribute) Bounds (class in bumps.bounds) (class in bumps.dream.bounds) bounds() (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.DirectProblem method) (bumps.pymcfit.PyMCProblem method) bounds_style (bumps.dream.core.Dream attribute) bspline() (in module bumps.bspline) bumps.bounds module bumps.bspline module bumps.cheby module bumps.cli module bumps.curve module bumps.data module bumps.dream.acr module bumps.dream.bounds module bumps.dream.convergence module bumps.dream.core module bumps.dream.corrplot module bumps.dream.crossover module bumps.dream.diffev module bumps.dream.entropy module bumps.dream.exppow module bumps.dream.formatnum module bumps.dream.gelman module bumps.dream.geweke module bumps.dream.initpop module bumps.dream.ksmirnov module bumps.dream.mahal module bumps.dream.metropolis module

bumps.dream.model module bumps.dream.outliers module bumps.dream.parcoord module bumps.dream.state module bumps.dream.stats module bumps.dream.tile module bumps.dream.util module bumps.dream.varplot module bumps.dream.views module bumps.errplot module bumps.fitproblem module bumps.fitservice module bumps.fitters module bumps.formatnum module bumps.history module bumps.initpop module bumps.lsqerror module bumps.mapper module bumps.monitor module bumps.mono module bumps.names module bumps.options module bumps.parameter module bumps.partemp module bumps.pdfwrapper module bumps.plotutil module bumps.plugin module bumps.pmath module bumps.pymcfit module bumps.quasinewton module bumps.random_lines module bumps.simplex module bumps.util module bumps.wsolve module BumpsOpts (class in bumps.options) burn (bumps.dream.core.Dream attribute) burn_point() (in module bumps.dream.convergence)

C

c_interface (bumps.dream.bounds.Bounds attribute) (bumps.dream.bounds.ClipBounds attribute) (bumps.dream.bounds.FoldBounds attribute) (bumps.dream.bounds.IgnoreBounds attribute) (bumps.dream.bounds.RandomBounds attribute) (bumps.dream.bounds.ReflectBounds attribute) calc_errors() (in module bumps.errplot) (in module bumps.plugin) calc_errors_from_state() (in module bumps.errplot) Calculation (class in bumps.parameter) calculation() (bumps.parameter.Parameter static method) (bumps.parameter.Reference static method) can_pickle() (in module bumps.mapper) capitalize() (bumps.parameter.Operators method) casefold() (bumps.parameter.Operators method) cdf() (bumps.bounds.DistProtocol method) ceil (bumps.parameter.Operators attribute) ceil() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) center() (bumps.parameter.Operators method) chains() (bumps.dream.state.MCMCDraw method) cheby_approx() (in module bumps.cheby) cheby_coeff() (in module bumps.cheby) cheby_points() (in module bumps.cheby) cheby_val() (in module bumps.cheby) checkpoint (bumps.fitters.CheckpointMonitor attribute) (bumps.options.BumpsOpts attribute) CheckpointMonitor (class in bumps.fitters) chisq() (bumps.fitproblem.FitProblem method) (bumps.fitters.FitDriver method) (bumps.pdfwrapper.DirectProblem method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) (bumps.pymcfit.PyMCProblem method) chisq_str() (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.DirectProblem method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) (bumps.pymcfit.PyMCProblem method) ChoiceList (class in bumps.options) chol_cov() (in module bumps.lsqerror) chol_stderr() (in module bumps.lsqerror) ci() (bumps.wsolve.LinearModel method) (bumps.wsolve.PolynomialModel method) clear() (bumps.history.History method) clip() (bumps.fitters.FitDriver method) clip_set() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) ClipBounds (class in bumps.dream.bounds) coeff (bumps.wsolve.PolynomialModel attribute) comb() (in module bumps.lsqerror)

Comparisons (class in bumps.parameter) config_history() (bumps.fitservice.ServiceMonitor method) (bumps.fitters.CheckpointMonitor method) (bumps.fitters.ConsoleMonitor method) (bumps.fitters.StepMonitor method) (bumps.monitor.Logger method) (bumps.monitor.Monitor method) (bumps.monitor.TimedUpdate method) config_matplotlib() (in module bumps.cli) console() (in module bumps.dream.util) ConsoleMonitor (class in bumps.fitters) Constant (class in bumps.parameter) Constraint (class in bumps.parameter) constraints (bumps.fitproblem.FitProblem attribute) constraints_nllf() (bumps.fitproblem.FitProblem method) coordinated_colors() (in module bumps.plotutil) copy_linked() (in module bumps.parameter) corr() (in module bumps.lsqerror) Corr2d (class in bumps.dream.corrplot) cos (bumps.parameter.Operators attribute) cos() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) cosd() (in module bumps.parameter) (in module bumps.pmath) cosh (bumps.parameter.Operators attribute) cosh() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) count() (bumps.parameter.Operators method) count_inflections() (in module bumps.mono) cov (bumps.wsolve.LinearModel property) (bumps.wsolve.PolynomialModel property) cov() (bumps.fitters.FitDriver method) (bumps.fitters.LevenbergMarquardtFit method) cov_entropy() (in module bumps.dream.entropy) cov_init() (in module bumps.dream.initpop) (in module bumps.initpop) CR (bumps.dream.core.Dream attribute) (bumps.dream.crossover.Crossover attribute) CR_spacing (bumps.dream.core.Dream attribute) CR_weight() (bumps.dream.state.MCMCDraw method) credible_interval() (in module bumps.dream.stats) Crossover (class in bumps.dream.crossover) current() (in module bumps.parameter) Curve (class in bumps.curve)

D

data_view() (in module bumps.plugin) DE_eps (bumps.dream.core.Dream attribute) DE_noise (bumps.dream.core.Dream attribute) DE_pairs (bumps.dream.core.Dream attribute) DE_snooker_rate (bumps.dream.core.Dream attribute) de_step() (in module bumps.dream.diffev) DE_steps (bumps.dream.core.Dream attribute) default() (bumps.parameter.Parameter class method) (bumps.parameter.Reference class method) DEFit (class in bumps.fitters) degree (bumps.wsolve.PolynomialModel attribute) degrees (bumps.parameter.Operators attribute) degrees() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) demo_hessian() (in module bumps.lsqerror) demo_jacobian() (in module bumps.lsqerror) demo_stderr_hilbert() (in module bumps.lsqerror) demo_stderr_perturbed() (in module bumps.lsqerror) Density (class in bumps.dream.model) der() (bumps.wsolve.PolynomialModel method) derive_vars() (bumps.dream.state.MCMCDraw method) description (bumps.parameter.Calculation attribute) dev() (bumps.parameter.Parameter method) (bumps.parameter.Reference method)

dhsv() (in module bumps.plotutil) DirectProblem (class in bumps.pdfwrapper) discrete (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) dist (bumps.bounds.Distribution attribute) (bumps.bounds.Normal attribute) DistProtocol (class in bumps.bounds) distribution (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) (bumps.parameter.SupportsPrior attribute) Distribution (class in bumps.bounds) dof (bumps.bounds.Bounded property) (bumps.bounds.BoundedAbove property) (bumps.bounds.BoundedBelow property) (bumps.bounds.BoundedNormal property) (bumps.bounds.Bounds property) (bumps.bounds.Distribution property) (bumps.bounds.Normal property) (bumps.bounds.SoftBounded property) (bumps.bounds.Unbounded property) (bumps.fitproblem.FitProblem property) DoF (bumps.wsolve.LinearModel attribute) (bumps.wsolve.PolynomialModel attribute) DR_scale (bumps.dream.core.Dream attribute) draw() (bumps.dream.state.MCMCDraw method) (in module bumps.dream.util) draws (bumps.dream.core.Dream attribute) Dream (class in bumps.dream.core) DreamFit (class in bumps.fitters) DreamModel (class in bumps.fitters) dy (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute)

E

encode() (bumps.parameter.Operators method) endswith() (bumps.parameter.Operators method) entropy (bumps.options.BumpsOpts attribute) entropy() (bumps.dream.state.MCMCDraw method) (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) (in module bumps.dream.entropy) eps_init() (in module bumps.initpop) equals() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) error_plot() (bumps.fitters.DreamFit method) exp (bumps.parameter.Operators attribute) exp() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method)

expandtabs() (bumps.parameter.Operators method) expm1 (bumps.parameter.Operators attribute) expm1() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) exppow_pars() (in module bumps.dream.exppow) Expression (class in bumps.parameter)

F

feasible() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) FIELDS (bumps.fitters.StepMonitor attribute) final() (bumps.fitters.ConsoleMonitor method) (bumps.fitters.MonitorRunner method) find() (bumps.parameter.Operators method) fit (bumps.options.BumpsOpts property) fit() (bumps.fitters.FitDriver method) (in module bumps.fitters) fit_config (bumps.options.BumpsOpts attribute) FIT_CONFIG (in module bumps.options) FitBase (class in bumps.fitters) FitConfig (class in bumps.options) FitDriver (class in bumps.fitters) fitness (bumps.fitproblem.FitProblem property) Fitness (class in bumps.fitproblem) FitProblem (class in bumps.fitproblem) fitservice() (in module bumps.fitservice) fittable (bumps.parameter.Calculation attribute) (bumps.parameter.Constant attribute) (bumps.parameter.Expression attribute) (bumps.parameter.Function attribute) (bumps.parameter.Parameter property) (bumps.parameter.Reference property) (bumps.parameter.ValueProtocol attribute) (bumps.parameter.Variable attribute) fittable() (in module bumps.parameter) fixed (bumps.parameter.Calculation attribute) (bumps.parameter.Constant attribute) (bumps.parameter.Constraint attribute) (bumps.parameter.Expression attribute) (bumps.parameter.Function attribute) (bumps.parameter.Parameter property) (bumps.parameter.Reference property) (bumps.parameter.ValueProtocol attribute) (bumps.parameter.Variable attribute)

FLAGS (bumps.options.BumpsOpts attribute) (bumps.options.ParseOpts attribute) flatten() (in module bumps.parameter) floor (bumps.parameter.Operators attribute) floor() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) floordiv (bumps.parameter.Operators attribute) fn (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute) FoldBounds (class in bumps.dream.bounds) form_quantiles() (in module bumps.plotutil) format() (bumps.parameter.Operators method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (in module bumps.parameter) format_map() (bumps.parameter.Operators method) format_uncertainty() (in module bumps.dream.formatnum) (in module bumps.formatnum) format_uncertainty_compact() (in module bumps.dream.formatnum) (in module bumps.formatnum) format_uncertainty_pm() (in module bumps.dream.formatnum) (in module bumps.formatnum) format_value() (in module bumps.dream.formatnum) (in module bumps.formatnum) format_vars() (in module bumps.dream.stats) (in module bumps.dream.views) FreeVariables (class in bumps.parameter) freevars (bumps.fitproblem.FitProblem attribute) Function (class in bumps.parameter) function() (in module bumps.parameter)

G

ge (bumps.parameter.Comparisons attribute) gelman() (bumps.dream.state.MCMCDraw method) (in module bumps.dream.gelman) generate() (in module bumps.initpop) get01() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) get_model() (bumps.parameter.FreeVariables method) (bumps.parameter.ParameterSet method) getfull() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method)

getopts() (in module bumps.options) getp() (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.DirectProblem method) (bumps.pymcfit.PyMCProblem method) geweke() (in module bumps.dream.geweke) gmm_entropy() (in module bumps.dream.entropy) goalseek_interval (bumps.dream.core.Dream attribute) goalseek_minburn (bumps.dream.core.Dream attribute) goalseek_optimizer (bumps.dream.core.Dream attribute) gradient() (in module bumps.lsqerror) gt (bumps.parameter.Comparisons attribute)

H

h5dump() (bumps.fitters.BFGSFit static method) (bumps.fitters.DEFit static method) (bumps.fitters.DreamFit static method) (bumps.fitters.FitBase static method) (bumps.fitters.LevenbergMarquardtFit static method) (bumps.fitters.MPFit static method) (bumps.fitters.MultiStart static method) (bumps.fitters.PSFit static method) (bumps.fitters.PTFit static method) (bumps.fitters.Resampler static method) (bumps.fitters.RLFit static method) (bumps.fitters.SimplexFit static method) (bumps.fitters.SnobFit static method) h5load() (bumps.fitters.BFGSFit static method) (bumps.fitters.DEFit static method) (bumps.fitters.DreamFit static method) (bumps.fitters.FitBase static method) (bumps.fitters.LevenbergMarquardtFit static method) (bumps.fitters.MPFit static method) (bumps.fitters.MultiStart static method) (bumps.fitters.PSFit static method) (bumps.fitters.PTFit static method) (bumps.fitters.Resampler static method) (bumps.fitters.RLFit static method) (bumps.fitters.SimplexFit static method) (bumps.fitters.SnobFit static method)

has_prior() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.SupportsPrior method) has_problem (bumps.mapper.BaseMapper attribute) (bumps.mapper.MPIMapper attribute) (bumps.mapper.MPMapper attribute) (bumps.mapper.SerialMapper attribute) has_residuals (bumps.fitproblem.FitProblem property) (bumps.pdfwrapper.DirectProblem attribute) (bumps.pdfwrapper.PDF attribute) (bumps.pdfwrapper.VectorPDF attribute) hermite() (in module bumps.mono) hessian() (in module bumps.lsqerror) hessian_cov() (in module bumps.lsqerror) hi (bumps.bounds.Bounded attribute) (bumps.bounds.BoundedNormal attribute) (bumps.bounds.SoftBounded attribute) high (bumps.dream.bounds.Bounds attribute) (bumps.dream.bounds.ClipBounds attribute) (bumps.dream.bounds.FoldBounds attribute) (bumps.dream.bounds.IgnoreBounds attribute) (bumps.dream.bounds.RandomBounds attribute) (bumps.dream.bounds.ReflectBounds attribute) hilbert() (in module bumps.lsqerror) hilbertinv() (in module bumps.lsqerror) History (class in bumps.history)

I

id (bumps.fitters.BFGSFit attribute) (bumps.fitters.DEFit attribute) (bumps.fitters.DreamFit attribute) (bumps.fitters.FitBase attribute) (bumps.fitters.LevenbergMarquardtFit attribute) (bumps.fitters.MPFit attribute) (bumps.fitters.MultiStart attribute) (bumps.fitters.PSFit attribute) (bumps.fitters.PTFit attribute) (bumps.fitters.Resampler attribute) (bumps.fitters.RLFit attribute) (bumps.fitters.SimplexFit attribute) (bumps.fitters.SnobFit attribute) (bumps.parameter.Constant attribute) (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) identify_outliers() (in module bumps.dream.outliers) IgnoreBounds (class in bumps.dream.bounds) IMPLICIT_VALUES (bumps.options.BumpsOpts attribute) (bumps.options.ParseOpts attribute)

index() (bumps.parameter.Operators method) indfloat() (in module bumps.data) info() (bumps.fitters.ConsoleMonitor method) (bumps.fitters.MonitorRunner method) init_bounds() (in module bumps.bounds) install_plugin() (in module bumps.cli) isalnum() (bumps.parameter.Operators method) isalpha() (bumps.parameter.Operators method) isascii() (bumps.parameter.Operators method) isdecimal() (bumps.parameter.Operators method) isdigit() (bumps.parameter.Operators method) isidentifier() (bumps.parameter.Operators method) islower() (bumps.parameter.Operators method) isnumeric() (bumps.parameter.Operators method) isprintable() (bumps.parameter.Operators method) isspace() (bumps.parameter.Operators method) istitle() (bumps.parameter.Operators method) isupper() (bumps.parameter.Operators method)

J

jacobian() (in module bumps.lsqerror)

jacobian_cov() (in module bumps.lsqerror) join() (bumps.parameter.Operators method)

K

kbhit() (in module bumps.util) keep_best() (bumps.dream.state.MCMCDraw method) ks_converged() (in module bumps.dream.convergence)

ksmirnov() (in module bumps.dream.ksmirnov) kw (bumps.parameter.Function attribute) kwds (bumps.bounds.DistProtocol attribute)

L

labels (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute) (bumps.dream.model.Density attribute) (bumps.dream.model.LogDensity attribute) (bumps.dream.model.MCMCModel attribute) (bumps.dream.model.Mixture attribute) (bumps.dream.model.MVNormal attribute) (bumps.dream.model.Simulation attribute) (bumps.dream.state.MCMCDraw property) (bumps.fitters.DreamModel attribute) labels() (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.DirectProblem method) (bumps.pymcfit.PyMCProblem method) le (bumps.parameter.Comparisons attribute) LevenbergMarquardtFit (class in bumps.fitters) lhs_init() (in module bumps.dream.initpop) (in module bumps.initpop) limits (bumps.bounds.Bounded property) (bumps.bounds.BoundedAbove property) (bumps.bounds.BoundedBelow property) (bumps.bounds.BoundedNormal property) (bumps.bounds.Bounds property) (bumps.bounds.Distribution property) (bumps.bounds.Normal property) (bumps.bounds.SoftBounded property) (bumps.bounds.Unbounded property) (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) (bumps.parameter.SupportsPrior attribute) LinearModel (class in bumps.wsolve) ljust() (bumps.parameter.Operators method) lo (bumps.bounds.Bounded attribute) (bumps.bounds.BoundedNormal attribute) (bumps.bounds.SoftBounded attribute) load() (bumps.fitters.DEFit method) (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) load_best() (in module bumps.cli) load_model() (in module bumps.cli) (in module bumps.plugin) load_problem() (in module bumps.fitproblem) load_state() (in module bumps.dream.state) log (bumps.parameter.Operators attribute)

log() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) log10 (bumps.parameter.Operators attribute) log10() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) log1p (bumps.parameter.Operators attribute) log1p() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) LogAdaptiveCrossover (class in bumps.dream.crossover) LogDensity (class in bumps.dream.model) Logger (class in bumps.monitor) logp() (bumps.dream.state.MCMCDraw method) logp_slice() (bumps.dream.state.MCMCDraw method) low (bumps.dream.bounds.Bounds attribute) (bumps.dream.bounds.ClipBounds attribute) (bumps.dream.bounds.FoldBounds attribute) (bumps.dream.bounds.IgnoreBounds attribute) (bumps.dream.bounds.RandomBounds attribute) (bumps.dream.bounds.ReflectBounds attribute) lower() (bumps.parameter.Operators method) lstrip() (bumps.parameter.Operators method) lt (bumps.parameter.Comparisons attribute)

M

mahalanobis() (in module bumps.dream.mahal) main() (in module bumps.cli) make_bounds_handler() (in module bumps.dream.bounds) maketrans() (bumps.parameter.Operators static method) manager (bumps.mapper.MPMapper attribute) map() (bumps.dream.model.Density method) (bumps.dream.model.LogDensity method) (bumps.dream.model.MCMCModel method) (bumps.dream.model.Mixture method) (bumps.dream.model.MVNormal method) (bumps.dream.model.Simulation method) (bumps.fitters.DreamModel method) mark_outliers() (bumps.dream.state.MCMCDraw method) max (bumps.parameter.Operators attribute) max() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) (in module bumps.parameter) (in module bumps.pmath) max_correlation() (in module bumps.lsqerror) max_tile_size() (in module bumps.dream.tile) MCMCDraw (class in bumps.dream.state) MCMCModel (class in bumps.dream.model) mean (bumps.bounds.BoundedNormal attribute) (bumps.bounds.Normal attribute) (bumps.parameter.Normal attribute) meshsteps (bumps.options.BumpsOpts attribute) metropolis() (in module bumps.dream.metropolis) metropolis_dr() (in module bumps.dream.metropolis) migrate_serialized() (in module bumps.plugin) min (bumps.parameter.Operators attribute) min() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) (in module bumps.parameter) (in module bumps.pmath) min_slice() (bumps.dream.state.MCMCDraw method) MINARGS (bumps.options.BumpsOpts attribute) (bumps.options.ParseOpts attribute) Mixture (class in bumps.dream.model) model (bumps.dream.core.Dream attribute) model_nllf() (bumps.fitproblem.FitProblem method) model_parameters() (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.DirectProblem method) model_points() (bumps.fitproblem.FitProblem method) model_reset() (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.DirectProblem method) (bumps.pymcfit.PyMCProblem method) model_update() (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.DirectProblem method) model_view() (in module bumps.plugin) models (bumps.fitproblem.FitProblem property) module bumps.bounds bumps.bspline bumps.cheby bumps.cli bumps.curve bumps.data bumps.dream.acr bumps.dream.bounds bumps.dream.convergence bumps.dream.core bumps.dream.corrplot bumps.dream.crossover bumps.dream.diffev bumps.dream.entropy bumps.dream.exppow bumps.dream.formatnum bumps.dream.gelman bumps.dream.geweke bumps.dream.initpop bumps.dream.ksmirnov bumps.dream.mahal bumps.dream.metropolis bumps.dream.model bumps.dream.outliers bumps.dream.parcoord bumps.dream.state bumps.dream.stats bumps.dream.tile bumps.dream.util bumps.dream.varplot bumps.dream.views bumps.errplot bumps.fitproblem bumps.fitservice bumps.fitters bumps.formatnum bumps.history bumps.initpop bumps.lsqerror bumps.mapper bumps.monitor bumps.mono bumps.names bumps.options bumps.parameter bumps.partemp bumps.pdfwrapper bumps.plotutil bumps.plugin bumps.pmath bumps.pymcfit bumps.quasinewton bumps.random_lines bumps.simplex bumps.util bumps.wsolve

Monitor (class in bumps.monitor) MonitorRunner (class in bumps.fitters) monospline() (in module bumps.mono) MPFit (class in bumps.fitters) MPIMapper (class in bumps.mapper) MPMapper (class in bumps.mapper) mul (bumps.parameter.Operators attribute) MultiStart (class in bumps.fitters) MVNEntropy (class in bumps.dream.entropy) MVNormal (class in bumps.dream.model)

N

name (bumps.bounds.DistProtocol attribute) (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute) (bumps.fitproblem.FitProblem attribute) (bumps.fitters.BFGSFit attribute) (bumps.fitters.DEFit attribute) (bumps.fitters.DreamFit attribute) (bumps.fitters.FitBase attribute) (bumps.fitters.LevenbergMarquardtFit attribute) (bumps.fitters.MPFit attribute) (bumps.fitters.MultiStart attribute) (bumps.fitters.PSFit attribute) (bumps.fitters.PTFit attribute) (bumps.fitters.Resampler attribute) (bumps.fitters.RLFit attribute) (bumps.fitters.SimplexFit attribute) (bumps.fitters.SnobFit attribute) (bumps.parameter.Constant attribute) (bumps.parameter.Expression property) (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) (bumps.parameter.UserFunction attribute) names (bumps.parameter.FreeVariables attribute) (bumps.parameter.ParameterSet attribute) Ncr (bumps.dream.state.MCMCDraw property) neg (bumps.parameter.Operators attribute) new_model() (in module bumps.plugin) next_color() (in module bumps.plotutil) Ngen (bumps.dream.state.MCMCDraw property) nice() (in module bumps.mapper) nice_range() (in module bumps.bounds) nllf() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.dream.model.Density method) (bumps.dream.model.LogDensity method) (bumps.dream.model.MCMCModel method) (bumps.dream.model.Mixture method) (bumps.dream.model.MVNormal method) (bumps.dream.model.Simulation method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.FitProblem method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.pdfwrapper.DirectProblem method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) (bumps.pymcfit.PyMCProblem method)

nnlf() (bumps.bounds.DistProtocol method) noise (bumps.options.BumpsOpts attribute) Normal (class in bumps.bounds) (class in bumps.parameter) notify (bumps.options.BumpsOpts attribute) Npop (bumps.dream.state.MCMCDraw property) Nsamples (bumps.dream.state.MCMCDraw property) Nthin (bumps.dream.state.MCMCDraw property) numpoints() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.fitproblem.Fitness method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) Nupdate (bumps.dream.state.MCMCDraw property) Nvar (bumps.dream.state.MCMCDraw property)

O

op (bumps.parameter.Constraint attribute) (bumps.parameter.Expression attribute) (bumps.parameter.Function attribute) OperatorMixin (class in bumps.parameter)

Operators (class in bumps.parameter) origin (bumps.wsolve.PolynomialModel attribute) outlier_test (bumps.dream.core.Dream attribute) outliers() (bumps.dream.state.MCMCDraw method)

P

p (bumps.wsolve.LinearModel property) (bumps.wsolve.PolynomialModel property) parallel (bumps.options.BumpsOpts attribute) parallel_coordinates() (in module bumps.dream.parcoord) parallel_tempering() (in module bumps.partemp) Parameter (class in bumps.parameter) parameter_nllf() (bumps.fitproblem.FitProblem method) parameter_residuals() (bumps.fitproblem.FitProblem method) parameterlist (bumps.parameter.ParameterSet property) parameters (bumps.fitproblem.FitProblem property) parameters() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.fitproblem.Fitness method) (bumps.parameter.Alias method) (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.FreeVariables method) (bumps.parameter.Function method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) ParameterSet (class in bumps.parameter) parametersets (bumps.parameter.FreeVariables attribute) pars (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute) (bumps.options.BumpsOpts attribute) parse_file() (in module bumps.data) parse_int() (in module bumps.options) parse_tolerance() (in module bumps.fitters) parse_var() (in module bumps.dream.stats) ParseOpts (class in bumps.options) particle_swarm() (in module bumps.random_lines) partition() (bumps.parameter.Operators method) pbs() (in module bumps.bspline) PDF (class in bumps.pdfwrapper) pdf() (bumps.bounds.DistProtocol method) penalty() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) penalty_nllf (bumps.fitproblem.FitProblem attribute) perturbed_hessian() (in module bumps.lsqerror) pi() (bumps.wsolve.LinearModel method) (bumps.wsolve.PolynomialModel method) plot (bumps.options.BumpsOpts property) plot() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.dream.corrplot.Corr2d method) (bumps.dream.model.Density method) (bumps.dream.model.LogDensity method) (bumps.dream.model.MCMCModel method) (bumps.dream.model.Mixture method) (bumps.dream.model.MVNormal method) (bumps.dream.model.Simulation method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.FitProblem method) (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) (bumps.pdfwrapper.DirectProblem method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) (bumps.pymcfit.PyMCProblem method) (bumps.wsolve.PolynomialModel method) (in module bumps.dream.parcoord) plot_all() (in module bumps.dream.views)

plot_corr() (in module bumps.dream.views) plot_corrmatrix() (in module bumps.dream.views) plot_err() (in module bumps.curve) plot_inflections() (in module bumps.mono) plot_logp() (in module bumps.dream.views) plot_quantiles() (in module bumps.plotutil) plot_trace() (in module bumps.dream.views) plot_var() (in module bumps.dream.varplot) plot_vars() (in module bumps.dream.varplot) plot_x (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute) plotter (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute) PLOTTERS (bumps.options.BumpsOpts attribute) pm() (bumps.parameter.Parameter method) (bumps.parameter.ParameterSet method) (bumps.parameter.Reference method) (in module bumps.bounds) pm_raw() (in module bumps.bounds) pmp() (bumps.parameter.Parameter method) (bumps.parameter.ParameterSet method) (bumps.parameter.Reference method) (in module bumps.bounds) pmp_raw() (in module bumps.bounds) PoissonCurve (class in bumps.curve) PolynomialModel (class in bumps.wsolve) pool (bumps.mapper.MPMapper attribute) population (bumps.dream.core.Dream attribute) pos (bumps.parameter.Operators attribute) pow (bumps.parameter.Operators attribute) ppf() (bumps.bounds.DistProtocol method) preview() (in module bumps.cli) prior (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) (bumps.parameter.SupportsPrior attribute) priors() (in module bumps.parameter) problem (bumps.fitters.LevenbergMarquardtFit attribute) (bumps.fitters.MPFit attribute) (bumps.fitters.MultiStart attribute) (bumps.fitters.PSFit attribute) (bumps.fitters.PTFit attribute) (bumps.fitters.Resampler attribute) (bumps.fitters.RLFit attribute) (bumps.fitters.SimplexFit attribute) (bumps.fitters.SnobFit attribute) (bumps.mapper.MPMapper attribute) problem_id (bumps.mapper.MPMapper attribute) profile() (in module bumps.cheby) (in module bumps.util) provides() (bumps.history.History method) PSFit (class in bumps.fitters) PTFit (class in bumps.fitters) push_seed (class in bumps.util) pushdir (class in bumps.util) put() (bumps.history.Trace method) put01() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) putfull() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) PyMCProblem (class in bumps.pymcfit)

Q

quasinewton() (in module bumps.quasinewton)

queue (bumps.options.BumpsOpts attribute)

R

R() (bumps.dream.corrplot.Corr2d method) radians (bumps.parameter.Operators attribute) radians() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) random() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) random_init() (in module bumps.initpop) random_lines() (in module bumps.random_lines) RandomBounds (class in bumps.dream.bounds) randomize() (bumps.fitproblem.FitProblem method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.pdfwrapper.DirectProblem method) (bumps.pymcfit.PyMCProblem method) (in module bumps.parameter) range() (bumps.parameter.Parameter method) (bumps.parameter.ParameterSet method) (bumps.parameter.Reference method) redirect_console (class in bumps.util) reference (bumps.parameter.ParameterSet attribute) Reference (class in bumps.parameter) ReflectBounds (class in bumps.dream.bounds) register() (in module bumps.fitters) register_webview_plot() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) reload_errors() (in module bumps.errplot) remove_outliers() (bumps.dream.state.MCMCDraw method) remove_tag() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) removeprefix() (bumps.parameter.Operators method) removesuffix() (bumps.parameter.Operators method) replace() (bumps.parameter.Operators method) requires() (bumps.history.History method) (bumps.history.Trace method) Resampler (class in bumps.fitters) reset() (bumps.dream.crossover.AdaptiveCrossover method) (bumps.dream.crossover.BaseAdaptiveCrossover method) (bumps.dream.crossover.Crossover method) (bumps.dream.crossover.LogAdaptiveCrossover method) reset_prior() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.SupportsPrior method)

residual() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) residuals() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.VectorPDF method) resize() (bumps.dream.state.MCMCDraw method) restore() (bumps.history.History method) (bumps.history.Trace method) restore_data() (bumps.fitproblem.Fitness method) (bumps.fitproblem.FitProblem method) resume (bumps.options.BumpsOpts attribute) resynth (bumps.options.BumpsOpts attribute) resynth() (in module bumps.cli) resynth_data() (bumps.fitproblem.Fitness method) (bumps.fitproblem.FitProblem method) rfind() (bumps.parameter.Operators method) rindex() (bumps.parameter.Operators method) rint (bumps.parameter.Operators attribute) rint() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) rjust() (bumps.parameter.Operators method) RLFit (class in bumps.fitters) rnorm (bumps.wsolve.LinearModel attribute) (bumps.wsolve.PolynomialModel attribute) round (bumps.parameter.Operators attribute) round() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) rpartition() (bumps.parameter.Operators method) rsplit() (bumps.parameter.Operators method) rstrip() (bumps.parameter.Operators method) rvs() (bumps.bounds.DistProtocol method)

S

sample() (bumps.dream.core.Dream method) (bumps.dream.state.MCMCDraw method) satisfied (bumps.parameter.Constraint property) satisfied() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) save() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.dream.state.MCMCDraw method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.FitProblem method) (bumps.fitters.DEFit method) (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) save_best() (in module bumps.cli) save_state() (in module bumps.dream.state) scale() (in module bumps.dream.parcoord) seed (bumps.options.BumpsOpts attribute) selected_fitter (bumps.options.FitConfig property) selected_name (bumps.options.FitConfig property) selected_values (bumps.options.FitConfig property) SerialMapper (class in bumps.mapper) ServiceMonitor (class in bumps.fitservice) set() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) set_active_model() (bumps.fitproblem.FitProblem method) set_derived_vars() (bumps.dream.state.MCMCDraw method) set_from_cli() (bumps.options.FitConfig method) set_function() (bumps.parameter.Calculation method) set_integer_vars() (bumps.dream.state.MCMCDraw method) set_model() (bumps.parameter.FreeVariables method) (bumps.parameter.ParameterSet method) set_mplconfig() (in module bumps.cli) set_visible_vars() (bumps.dream.state.MCMCDraw method) setp() (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.DirectProblem method) (bumps.pymcfit.PyMCProblem method) setpriority() (in module bumps.mapper) settings (bumps.fitters.BFGSFit attribute) (bumps.fitters.DEFit attribute) (bumps.fitters.DreamFit attribute) (bumps.fitters.FitBase attribute) (bumps.fitters.LevenbergMarquardtFit attribute) (bumps.fitters.MPFit attribute) (bumps.fitters.MultiStart attribute) (bumps.fitters.PSFit attribute) (bumps.fitters.PTFit attribute) (bumps.fitters.Resampler attribute) (bumps.fitters.RLFit attribute) (bumps.fitters.SimplexFit attribute) (bumps.fitters.SnobFit attribute) shared_pickled_problem (bumps.mapper.MPMapper attribute) shortest_credible_interval() (in module bumps.dream.stats) show() (bumps.dream.state.MCMCDraw method) (bumps.fitproblem.FitProblem method) (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) (bumps.pdfwrapper.DirectProblem method) (bumps.pymcfit.PyMCProblem method) show_cov() (bumps.fitters.FitDriver method) show_entropy() (bumps.fitters.FitDriver method) show_err() (bumps.fitters.FitDriver method) show_errors() (in module bumps.errplot) (in module bumps.plugin) show_improvement() (bumps.fitservice.ServiceMonitor method) (bumps.fitters.CheckpointMonitor method) (bumps.fitters.ConsoleMonitor method) (bumps.monitor.TimedUpdate method) show_progress() (bumps.fitservice.ServiceMonitor method) (bumps.fitters.CheckpointMonitor method) (bumps.fitters.ConsoleMonitor method) (bumps.monitor.TimedUpdate method) simplex() (in module bumps.simplex) SimplexFit (class in bumps.fitters) simulate_data() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.fitproblem.FitProblem method) Simulation (class in bumps.dream.model) sin (bumps.parameter.Operators attribute) sin() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) sind() (in module bumps.parameter) (in module bumps.pmath) sinh (bumps.parameter.Operators attribute) sinh() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method)

slot (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) snapshot() (bumps.history.History method) (bumps.history.Trace method) SnobFit (class in bumps.fitters) soft_range() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) SoftBounded (class in bumps.bounds) solve() (bumps.fitters.BFGSFit method) (bumps.fitters.DEFit method) (bumps.fitters.DreamFit method) (bumps.fitters.FitBase method) (bumps.fitters.LevenbergMarquardtFit method) (bumps.fitters.MPFit method) (bumps.fitters.MultiStart method) (bumps.fitters.PSFit method) (bumps.fitters.PTFit method) (bumps.fitters.Resampler method) (bumps.fitters.RLFit method) (bumps.fitters.SimplexFit method) (bumps.fitters.SnobFit method) split() (bumps.parameter.Operators method) splitlines() (bumps.parameter.Operators method) sqrt (bumps.parameter.Operators attribute) sqrt() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) stable_best() (bumps.dream.state.MCMCDraw method) start_mapper() (bumps.mapper.BaseMapper static method) (bumps.mapper.MPIMapper static method) (bumps.mapper.MPMapper static method) (bumps.mapper.SerialMapper static method) start_value() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) start_worker() (bumps.mapper.BaseMapper static method) (bumps.mapper.MPIMapper static method) (bumps.mapper.MPMapper static method) (bumps.mapper.SerialMapper static method) starts (bumps.options.BumpsOpts attribute) startswith() (bumps.parameter.Operators method) state (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute) (bumps.dream.core.Dream attribute) (bumps.fitters.BFGSFit attribute) (bumps.fitters.DEFit attribute) (bumps.fitters.DreamFit attribute) (bumps.fitters.FitBase attribute) (bumps.fitters.LevenbergMarquardtFit attribute) (bumps.fitters.MPFit attribute) (bumps.fitters.MultiStart attribute) (bumps.fitters.PSFit attribute) (bumps.fitters.PTFit attribute) (bumps.fitters.Resampler attribute) (bumps.fitters.RLFit attribute) (bumps.fitters.SimplexFit attribute) (bumps.fitters.SnobFit attribute) stats() (in module bumps.dream.stats) std (bumps.bounds.BoundedNormal attribute) (bumps.bounds.Normal attribute) (bumps.bounds.SoftBounded attribute) (bumps.parameter.Normal attribute) (bumps.parameter.UniformSoftBounded attribute) (bumps.wsolve.LinearModel property) (bumps.wsolve.PolynomialModel property) stderr() (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) (in module bumps.lsqerror) stderr_from_cov() (bumps.fitters.FitDriver method) StepMonitor (class in bumps.fitters) stop_mapper() (bumps.mapper.BaseMapper static method) (bumps.mapper.MPIMapper static method) (bumps.mapper.MPMapper static method) (bumps.mapper.SerialMapper static method) stopping() (bumps.fitters.MonitorRunner method) store (bumps.options.BumpsOpts attribute) strip() (bumps.parameter.Operators method) sub (bumps.parameter.Operators attribute) substitute() (in module bumps.parameter) summarize() (bumps.fitproblem.FitProblem method) (bumps.pdfwrapper.DirectProblem method) (bumps.pymcfit.PyMCProblem method) (in module bumps.parameter) SupportsPrior (class in bumps.parameter) swapcase() (bumps.parameter.Operators method)

T

tag_all() (in module bumps.parameter) tags (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) tan (bumps.parameter.Operators attribute) tan() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) tand() (in module bumps.parameter) (in module bumps.pmath) tanh (bumps.parameter.Operators attribute) tanh() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) test_fitters() (in module bumps.fitters) test_operator() (in module bumps.parameter) theory() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) thinning (bumps.dream.core.Dream attribute) time (bumps.options.BumpsOpts attribute) TimedUpdate (class in bumps.monitor) title (bumps.dream.state.MCMCDraw attribute) title() (bumps.parameter.Operators method)

to_dict() (bumps.bounds.Bounded method) (bumps.bounds.BoundedAbove method) (bumps.bounds.BoundedBelow method) (bumps.bounds.BoundedNormal method) (bumps.bounds.Bounds method) (bumps.bounds.Distribution method) (bumps.bounds.Normal method) (bumps.bounds.SoftBounded method) (bumps.bounds.Unbounded method) (bumps.fitproblem.FitProblem method) (bumps.parameter.Alias method) (bumps.parameter.FreeVariables method) (bumps.parameter.Function method) (bumps.parameter.ParameterSet method) (in module bumps.parameter) total_generations (bumps.dream.state.MCMCDraw property) Trace (class in bumps.history) translate() (bumps.parameter.Operators method) transport (bumps.options.BumpsOpts property) TRANSPORTS (bumps.options.BumpsOpts attribute) trim (bumps.options.BumpsOpts attribute) trim_portion() (bumps.dream.state.MCMCDraw method) truediv (bumps.parameter.Operators attribute) trunc (bumps.parameter.Operators attribute) trunc() (bumps.parameter.Calculation method) (bumps.parameter.Constant method) (bumps.parameter.Expression method) (bumps.parameter.Function method) (bumps.parameter.OperatorMixin method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.parameter.ValueProtocol method) (bumps.parameter.Variable method) type (bumps.bounds.BoundedBelow attribute) (bumps.bounds.Unbounded attribute)

U

Unbounded (class in bumps.bounds) Uniform (class in bumps.parameter) UniformSoftBounded (class in bumps.parameter) unique() (in module bumps.parameter) unlink() (bumps.parameter.Parameter method) (bumps.parameter.Reference method) untag_all() (in module bumps.parameter) update() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.dream.crossover.AdaptiveCrossover method) (bumps.dream.crossover.BaseAdaptiveCrossover method) (bumps.dream.crossover.Crossover method) (bumps.dream.crossover.LogAdaptiveCrossover method) (bumps.fitproblem.Fitness method) (bumps.fitters.MonitorRunner method) (bumps.fitters.StepMonitor method) (bumps.history.History method) (bumps.parameter.Alias method)

upper() (bumps.parameter.Operators method) USAGE (bumps.options.BumpsOpts attribute) (bumps.options.ParseOpts attribute) use_delayed_rejection (bumps.dream.core.Dream attribute) UserFunction (class in bumps.parameter) using_mpi() (in module bumps.mapper)

V

valid() (bumps.fitproblem.FitProblem method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) value (bumps.parameter.Calculation property) (bumps.parameter.Constant attribute) (bumps.parameter.Expression property) (bumps.parameter.Function property) (bumps.parameter.OperatorMixin attribute) (bumps.parameter.Parameter property) (bumps.parameter.Reference property) (bumps.parameter.ValueProtocol attribute) (bumps.parameter.Variable attribute)

ValueProtocol (class in bumps.parameter) VALUES (bumps.options.BumpsOpts attribute) (bumps.options.ParseOpts attribute) values (bumps.parameter.ParameterSet property) var (bumps.wsolve.LinearModel property) (bumps.wsolve.PolynomialModel property) var_plot_size() (in module bumps.dream.varplot) var_stats() (in module bumps.dream.stats) Variable (class in bumps.parameter) VarStats (class in bumps.dream.stats) varying() (in module bumps.parameter) VectorPDF (class in bumps.pdfwrapper) view (bumps.options.BumpsOpts attribute)

W

webview_plots (bumps.curve.Curve property) (bumps.curve.PoissonCurve property) weight (bumps.dream.crossover.AdaptiveCrossover attribute) (bumps.dream.crossover.BaseAdaptiveCrossover attribute) (bumps.dream.crossover.Crossover attribute) (bumps.dream.crossover.LogAdaptiveCrossover attribute)

weights (bumps.fitproblem.FitProblem attribute) wnn_entropy() (in module bumps.dream.entropy) wpolyfit() (in module bumps.wsolve) wsolve() (in module bumps.wsolve)

X

x (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute) (bumps.wsolve.LinearModel attribute)

Y

y (bumps.curve.Curve attribute) (bumps.curve.PoissonCurve attribute)

yesno() (in module bumps.options)

Z

zfill() (bumps.parameter.Operators method)