Index

A

acceptance_rate() (bumps.dream.state.MCMCDraw method) accumulate() (bumps.history.History method) (bumps.history.Trace method) acos() (in module bumps.pmath) acosd() (in module bumps.pmath) ACR() (in module bumps.dream.acr) adapt() (bumps.dream.crossover.AdaptiveCrossover method) (bumps.dream.crossover.Crossover method) (bumps.dream.crossover.LogAdaptiveCrossover method) AdaptiveCrossover (class in bumps.dream.crossover) Alias (class in bumps.parameter) AMQPMapper (class in bumps.mapper)

apply() (bumps.dream.bounds.ClipBounds method) (bumps.dream.bounds.FoldBounds method) (bumps.dream.bounds.IgnoreBounds method) (bumps.dream.bounds.RandomBounds method) (bumps.dream.bounds.ReflectBounds method) args (bumps.parameter.Function attribute) asin() (in module bumps.pmath) asind() (in module bumps.pmath) atan() (in module bumps.pmath) atan2() (in module bumps.pmath) atan2d() (in module bumps.pmath) atand() (in module bumps.pmath) auto_shift() (in module bumps.plotutil)

B

BaseFitProblem (class in bumps.fitproblem) BaseParameter (class in bumps.parameter) best() (bumps.dream.state.MCMCDraw method) 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.MVNormal attribute) (bumps.dream.model.Mixture attribute) (bumps.dream.model.Simulation attribute) (bumps.fitters.DreamModel attribute) (bumps.parameter.BaseParameter attribute) (bumps.parameter.Constant attribute) (bumps.parameter.Function attribute) (bumps.parameter.IntegerParameter attribute) (bumps.parameter.OperatorAdd attribute) (bumps.parameter.OperatorDiv attribute) (bumps.parameter.OperatorMul attribute) (bumps.parameter.OperatorPow attribute) (bumps.parameter.OperatorSub attribute) (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) Bounds (class in bumps.bounds) bounds() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem 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.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.state (module) bumps.dream.stats (module) bumps.dream.tile (module) bumps.dream.util (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.parameter (module) bumps.partemp (module) bumps.pdfwrapper (module) bumps.plotutil (module) bumps.plugin (module) bumps.pmath (module) bumps.quasinewton (module) bumps.random_lines (module) bumps.simplex (module) bumps.util (module) bumps.wsolve (module) burn (bumps.dream.core.Dream attribute)

C

calc_errors() (in module bumps.errplot) (in module bumps.plugin) calc_errors_from_state() (in module bumps.errplot) 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) chisq() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) chisq_str() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) 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_set() (bumps.parameter.IntegerParameter method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) ClipBounds (class in bumps.dream.bounds) coeff (bumps.wsolve.PolynomialModel attribute) config_history() (bumps.fitservice.ServiceMonitor 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) ConstraintEQ (class in bumps.parameter) ConstraintGE (class in bumps.parameter) ConstraintGT (class in bumps.parameter) ConstraintLE (class in bumps.parameter) ConstraintLT (class in bumps.parameter) ConstraintNE (class in bumps.parameter) constraints_nllf() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) coordinated_colors() (in module bumps.plotutil) corr() (in module bumps.lsqerror) Corr2d (class in bumps.dream.corrplot) cos() (in module bumps.pmath) cosd() (in module bumps.pmath) cosh() (in module bumps.pmath) count_inflections() (in module bumps.mono) cov (bumps.wsolve.LinearModel attribute) (bumps.wsolve.PolynomialModel attribute) cov() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.fitters.FitDriver method) (bumps.fitters.LevenbergMarquardtFit method) (in module bumps.lsqerror) cov_init() (in module bumps.dream.initpop) (in module bumps.initpop) CR (bumps.dream.core.Dream attribute) CR_spacing (bumps.dream.core.Dream attribute) CR_weight() (bumps.dream.state.MCMCDraw method) credible_intervals() (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.IntegerParameter method) (bumps.parameter.Parameter class method) (bumps.parameter.Reference method) DEFit (class in bumps.fitters) degree (bumps.wsolve.PolynomialModel attribute) degrees() (in module bumps.pmath) demo_hessian() (in module bumps.lsqerror) demo_jacobian() (in module bumps.lsqerror) Density (class in bumps.dream.model) der() (bumps.wsolve.PolynomialModel method) derive_vars() (bumps.dream.state.MCMCDraw method) dev() (bumps.parameter.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method)

dhsv() (in module bumps.plotutil) DirectProblem (class in bumps.pdfwrapper) discrete (bumps.parameter.BaseParameter attribute) (bumps.parameter.Constant attribute) (bumps.parameter.Function attribute) (bumps.parameter.IntegerParameter attribute) (bumps.parameter.OperatorAdd attribute) (bumps.parameter.OperatorDiv attribute) (bumps.parameter.OperatorMul attribute) (bumps.parameter.OperatorPow attribute) (bumps.parameter.OperatorSub attribute) (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) Distribution (class in bumps.bounds) 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) dvalue (bumps.parameter.OperatorAdd attribute) (bumps.parameter.OperatorDiv attribute) (bumps.parameter.OperatorMul attribute) (bumps.parameter.OperatorPow attribute) (bumps.parameter.OperatorSub attribute)

E

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) error_plot() (bumps.fitters.DreamFit method) exp() (in module bumps.pmath) exppow_pars() (in module bumps.dream.exppow)

F

f (in module bumps.fitters) feasible() (bumps.parameter.IntegerParameter method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) FIELDS (bumps.fitters.StepMonitor attribute) fit() (bumps.fitters.FitDriver method) FitBase (class in bumps.fitters) FitDriver (class in bumps.fitters) Fitness (class in bumps.fitproblem) FitProblem() (in module bumps.fitproblem) fitservice() (in module bumps.fitservice) fittable (bumps.parameter.BaseParameter attribute) (bumps.parameter.Constant attribute) (bumps.parameter.Function attribute) (bumps.parameter.IntegerParameter attribute) (bumps.parameter.OperatorAdd attribute) (bumps.parameter.OperatorDiv attribute) (bumps.parameter.OperatorMul attribute) (bumps.parameter.OperatorPow attribute) (bumps.parameter.OperatorSub attribute) (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) fittable() (in module bumps.parameter) fixed (bumps.parameter.BaseParameter attribute) (bumps.parameter.Constant attribute) (bumps.parameter.Function attribute) (bumps.parameter.IntegerParameter attribute) (bumps.parameter.OperatorAdd attribute) (bumps.parameter.OperatorDiv attribute) (bumps.parameter.OperatorMul attribute) (bumps.parameter.OperatorPow attribute) (bumps.parameter.OperatorSub attribute) (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute)

flatten() (in module bumps.parameter) FoldBounds (class in bumps.dream.bounds) form_quantiles() (in module bumps.plotutil) format() (bumps.parameter.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (in module bumps.parameter) 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) Function (class in bumps.parameter) function() (in module bumps.parameter)

G

gelman() (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) 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)

getp() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem method) geweke() (in module bumps.dream.geweke) goalseek_interval (bumps.dream.core.Dream attribute) goalseek_minburn (bumps.dream.core.Dream attribute) goalseek_optimizer (bumps.dream.core.Dream attribute)

H

Hcov() (bumps.fitters.BFGSFit method) hermite() (in module bumps.mono)

hessian() (in module bumps.lsqerror) History (class in bumps.history) Hstderr() (bumps.fitters.BFGSFit method)

I

id (bumps.fitters.BFGSFit attribute) (bumps.fitters.DEFit attribute) (bumps.fitters.DreamFit attribute) (bumps.fitters.LevenbergMarquardtFit attribute) (bumps.fitters.PSFit attribute) (bumps.fitters.PTFit attribute) (bumps.fitters.RLFit attribute) (bumps.fitters.SimplexFit attribute) (bumps.fitters.SnobFit attribute)

identify_outliers() (in module bumps.dream.outliers) IgnoreBounds (class in bumps.dream.bounds) indfloat() (in module bumps.data) init_bounds() (in module bumps.bounds) install_plugin() (in module bumps.cli) integer_vars() (bumps.dream.state.MCMCDraw method) IntegerParameter (class in bumps.parameter)

J

jacobian() (in module bumps.lsqerror)

K

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

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

L

labels (bumps.dream.model.Density attribute) (bumps.dream.model.LogDensity attribute) (bumps.dream.model.MCMCModel attribute) (bumps.dream.model.MVNormal attribute) (bumps.dream.model.Mixture attribute) (bumps.dream.model.Simulation attribute) (bumps.dream.state.MCMCDraw attribute) (bumps.fitters.DreamModel attribute) labels() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem method) LevenbergMarquardtFit (class in bumps.fitters) lhs_init() (in module bumps.dream.initpop) (in module bumps.initpop) limits (bumps.bounds.Bounded attribute) (bumps.bounds.BoundedAbove attribute) (bumps.bounds.BoundedBelow attribute) (bumps.bounds.BoundedNormal attribute) (bumps.bounds.Bounds attribute) (bumps.bounds.Distribution attribute) (bumps.bounds.Normal attribute) (bumps.bounds.SoftBounded attribute) (bumps.bounds.Unbounded attribute)

LinearModel (class in bumps.wsolve) load() (bumps.fitters.DEFit method) (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) load_best() (in module bumps.cli) load_history() (in module bumps.fitters) load_model() (in module bumps.cli) (in module bumps.plugin) load_problem() (in module bumps.fitproblem) load_state() (in module bumps.dream.state) log() (in module bumps.pmath) log10() (in module bumps.pmath) log_density() (bumps.dream.model.Density method) (bumps.dream.model.LogDensity method) (bumps.dream.model.MCMCModel method) (bumps.dream.model.MVNormal method) (bumps.dream.model.Mixture method) (bumps.dream.model.Simulation method) (bumps.fitters.DreamModel method) LogAdaptiveCrossover (class in bumps.dream.crossover) LogDensity (class in bumps.dream.model) Logger (class in bumps.monitor) logp() (bumps.dream.state.MCMCDraw method)

M

mahalanobis() (in module bumps.dream.mahal) main() (in module bumps.cli) make_bounds_handler() (in module bumps.dream.bounds) map() (bumps.dream.model.Density method) (bumps.dream.model.LogDensity method) (bumps.dream.model.MCMCModel method) (bumps.dream.model.MVNormal method) (bumps.dream.model.Mixture method) (bumps.dream.model.Simulation method) (bumps.fitters.DreamModel method) mark_outliers() (bumps.dream.state.MCMCDraw method) 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) metropolis() (in module bumps.dream.metropolis) metropolis_dr() (in module bumps.dream.metropolis) Mixture (class in bumps.dream.model) model (bumps.dream.core.Dream attribute) model_nllf() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method)

model_parameters() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem method) model_points() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) model_reset() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem method) model_update() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem method) model_view() (in module bumps.plugin) models (bumps.fitproblem.MultiFitProblem attribute) Monitor (class in bumps.monitor) MonitorRunner (class in bumps.fitters) monospline() (in module bumps.mono) MPIMapper (class in bumps.mapper) MPMapper (class in bumps.mapper) MultiFitProblem (class in bumps.fitproblem) MultiStart (class in bumps.fitters) MVNormal (class in bumps.dream.model)

N

name (bumps.fitters.BFGSFit attribute) (bumps.fitters.DEFit attribute) (bumps.fitters.DreamFit attribute) (bumps.fitters.LevenbergMarquardtFit attribute) (bumps.fitters.MultiStart attribute) (bumps.fitters.PSFit attribute) (bumps.fitters.PTFit attribute) (bumps.fitters.RLFit attribute) (bumps.fitters.SimplexFit attribute) (bumps.fitters.SnobFit attribute) (bumps.parameter.BaseParameter attribute) (bumps.parameter.Constant attribute) (bumps.parameter.Function attribute) (bumps.parameter.IntegerParameter attribute) (bumps.parameter.OperatorAdd attribute) (bumps.parameter.OperatorDiv attribute) (bumps.parameter.OperatorMul attribute) (bumps.parameter.OperatorPow attribute) (bumps.parameter.OperatorSub attribute) (bumps.parameter.Parameter attribute) (bumps.parameter.Reference attribute) Ncr (bumps.dream.state.MCMCDraw attribute) new_model() (in module bumps.plugin) next_color() (in module bumps.plotutil) Ngen (bumps.dream.state.MCMCDraw attribute) 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.MVNormal method) (bumps.dream.model.Mixture method) (bumps.dream.model.Simulation method) (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.MultiFitProblem method) (bumps.fitters.DreamModel method) (bumps.parameter.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.pdfwrapper.DirectProblem method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method)

Normal (class in bumps.bounds) Npop (bumps.dream.state.MCMCDraw attribute) Nthin (bumps.dream.state.MCMCDraw attribute) 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 attribute) Nvar (bumps.dream.state.MCMCDraw attribute)

O

op (bumps.parameter.Function attribute) OperatorAdd (class in bumps.parameter) OperatorDiv (class in bumps.parameter) OperatorMul (class in bumps.parameter)

OperatorPow (class in bumps.parameter) OperatorSub (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 attribute) (bumps.wsolve.PolynomialModel attribute) parallel_tempering() (in module bumps.partemp) Parameter (class in bumps.parameter) parameter_nllf() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) parameter_residuals() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) parameters() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.fitproblem.Fitness method) (bumps.parameter.Alias method) (bumps.parameter.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.FreeVariables method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) ParameterSet (class in bumps.parameter) parse_file() (in module bumps.data) parse_tolerance() (in module bumps.fitters) parse_var() (in module bumps.dream.stats) particle_swarm() (in module bumps.random_lines) pbs() (in module bumps.bspline) PDF (class in bumps.pdfwrapper) pdf() (bumps.parameter.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) perturbed_hessian() (in module bumps.lsqerror) pi() (bumps.wsolve.LinearModel method) (bumps.wsolve.PolynomialModel method) 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.MVNormal method) (bumps.dream.model.Mixture method) (bumps.dream.model.Simulation method) (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.MultiFitProblem method) (bumps.fitters.DreamFit method) (bumps.fitters.DreamModel method) (bumps.fitters.FitDriver method) (bumps.pdfwrapper.DirectProblem method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) (bumps.wsolve.PolynomialModel method) 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_R() (in module bumps.dream.views) plot_trace() (in module bumps.dream.views) plot_var() (in module bumps.dream.views) plot_vars() (in module bumps.dream.views) pm() (bumps.parameter.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (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.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (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) preview() (in module bumps.cli) prod() (in module bumps.pmath) 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)

Q

quasinewton() (in module bumps.quasinewton)

R

R() (bumps.dream.corrplot.Corr2d method) R_stat() (bumps.dream.state.MCMCDraw method) radians() (in module bumps.pmath) 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.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.parameter.IntegerParameter method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) (bumps.pdfwrapper.DirectProblem method) (in module bumps.parameter) range() (bumps.parameter.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (bumps.parameter.Parameter method) (bumps.parameter.ParameterSet method) (bumps.parameter.Reference method) redirect_console (class in bumps.util) Reference (class in bumps.parameter) ReflectBounds (class in bumps.dream.bounds) reload_errors() (in module bumps.errplot) remove_outliers() (bumps.dream.state.MCMCDraw method) requires() (bumps.history.History method) (bumps.history.Trace method) Resampler (class in bumps.fitters) reset() (bumps.dream.crossover.AdaptiveCrossover method) (bumps.dream.crossover.Crossover method) (bumps.dream.crossover.LogAdaptiveCrossover 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.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) residuals() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.PDF method) (bumps.pdfwrapper.VectorPDF method) resize() (bumps.dream.state.MCMCDraw method) restore() (bumps.history.History method) (bumps.history.Trace method) restore_data() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.MultiFitProblem method) resynth() (in module bumps.cli) resynth_data() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.MultiFitProblem method) RLFit (class in bumps.fitters) rnorm (bumps.wsolve.LinearModel attribute) (bumps.wsolve.PolynomialModel attribute) run_dream() (in module bumps.dream.core)

S

sample() (bumps.dream.core.Dream method) (bumps.dream.state.MCMCDraw method) save() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.dream.state.MCMCDraw method) (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.Fitness method) (bumps.fitproblem.MultiFitProblem method) (bumps.fitters.DEFit method) (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) save_best() (in module bumps.cli) save_history() (in module bumps.fitters) save_state() (in module bumps.dream.state) SerialMapper (class in bumps.mapper) ServiceMonitor (class in bumps.fitservice) set() (bumps.parameter.IntegerParameter method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) set_active_model() (bumps.fitproblem.MultiFitProblem 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.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem method) setpriority() (in module bumps.mapper) settings (bumps.fitters.BFGSFit attribute) (bumps.fitters.DEFit attribute) (bumps.fitters.DreamFit attribute) (bumps.fitters.LevenbergMarquardtFit attribute) (bumps.fitters.MultiStart attribute) (bumps.fitters.PSFit attribute) (bumps.fitters.PTFit attribute) (bumps.fitters.RLFit attribute) (bumps.fitters.SimplexFit attribute) (bumps.fitters.SnobFit attribute) show() (bumps.dream.state.MCMCDraw method) (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) (bumps.pdfwrapper.DirectProblem 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.ConsoleMonitor method) (bumps.monitor.TimedUpdate method) show_progress() (bumps.fitservice.ServiceMonitor 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.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) Simulation (class in bumps.dream.model) sin() (in module bumps.pmath) sind() (in module bumps.pmath) sinh() (in module bumps.pmath)

snapshot() (bumps.history.History method) (bumps.history.Trace method) SnobFit (class in bumps.fitters) soft_range() (bumps.parameter.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (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.MultiStart method) (bumps.fitters.PSFit method) (bumps.fitters.PTFit method) (bumps.fitters.RLFit method) (bumps.fitters.Resampler method) (bumps.fitters.SimplexFit method) (bumps.fitters.SnobFit method) sqrt() (in module bumps.pmath) start_mapper() (bumps.mapper.AMQPMapper 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.AMQPMapper static method) (bumps.mapper.MPIMapper static method) (bumps.mapper.MPMapper static method) (bumps.mapper.SerialMapper static method) stats() (in module bumps.dream.stats) std (bumps.wsolve.LinearModel attribute) (bumps.wsolve.PolynomialModel attribute) stderr() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.fitters.DreamFit method) (bumps.fitters.FitDriver method) (in module bumps.lsqerror) StepMonitor (class in bumps.fitters) stop_mapper() (bumps.mapper.AMQPMapper static method) (bumps.mapper.MPIMapper static method) (bumps.mapper.MPMapper static method) (bumps.mapper.SerialMapper static method) substitute() (in module bumps.parameter) sum() (in module bumps.pmath) summarize() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.pdfwrapper.DirectProblem method) (in module bumps.parameter)

T

tan() (in module bumps.pmath) tand() (in module bumps.pmath) tanh() (in module bumps.pmath) theory() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method)

thinning (bumps.dream.core.Dream attribute) TimedUpdate (class in bumps.monitor) title (bumps.dream.state.MCMCDraw attribute) Trace (class in bumps.history)

U

Unbounded (class in bumps.bounds) unique() (in module bumps.parameter) update() (bumps.curve.Curve method) (bumps.curve.PoissonCurve method) (bumps.dream.crossover.AdaptiveCrossover method) (bumps.dream.crossover.Crossover method) (bumps.dream.crossover.LogAdaptiveCrossover method) (bumps.fitproblem.Fitness method) (bumps.history.History method) (bumps.parameter.Alias method)

use_delayed_rejection (bumps.dream.core.Dream attribute)

V

valid() (bumps.fitproblem.BaseFitProblem method) (bumps.fitproblem.MultiFitProblem method) (bumps.parameter.BaseParameter method) (bumps.parameter.Constant method) (bumps.parameter.Function method) (bumps.parameter.IntegerParameter method) (bumps.parameter.OperatorAdd method) (bumps.parameter.OperatorDiv method) (bumps.parameter.OperatorMul method) (bumps.parameter.OperatorPow method) (bumps.parameter.OperatorSub method) (bumps.parameter.Parameter method) (bumps.parameter.Reference method) value (bumps.parameter.Constant attribute) (bumps.parameter.Function attribute) (bumps.parameter.IntegerParameter attribute) (bumps.parameter.OperatorAdd attribute) (bumps.parameter.OperatorDiv attribute) (bumps.parameter.OperatorMul attribute) (bumps.parameter.OperatorPow attribute) (bumps.parameter.OperatorSub attribute) (bumps.parameter.Reference attribute)

values (bumps.parameter.ParameterSet attribute) var (bumps.wsolve.LinearModel attribute) (bumps.wsolve.PolynomialModel attribute) var_stats() (in module bumps.dream.stats) VarStats (class in bumps.dream.stats) varying() (in module bumps.parameter) VectorPDF (class in bumps.pdfwrapper)

W

wpolyfit() (in module bumps.wsolve)

wsolve() (in module bumps.wsolve)

X

x (bumps.wsolve.LinearModel attribute)