Index

_

__call__() (bayesmsd.fit.Fit.MinTarget method)

B

bar (bayesmsd.profiler.Profiler attribute) bayesmsd module bayesmsd.deco module bayesmsd.fit module bayesmsd.gp module

bayesmsd.lib module bayesmsd.parameters module bayesmsd.profiler module best_estimate (bayesmsd.profiler.Profiler property)

C

check_point_estimate_against() (bayesmsd.profiler.Profiler method) compactify() (bayesmsd.lib.NPXFit method) (bayesmsd.lib.SplineFit method) constraint_Cpositive() (bayesmsd.fit.Fit method) constraint_dx() (bayesmsd.lib.NPXFit method) (bayesmsd.lib.SplineFit method)

constraint_logmsd() (bayesmsd.lib.NPXFit method) (bayesmsd.lib.SplineFit method) constraints (bayesmsd.fit.Fit attribute) cur_param (bayesmsd.profiler.Profiler attribute)

D

d (bayesmsd.fit.Fit attribute) data (bayesmsd.fit.Fit attribute) decompactify_log() (bayesmsd.lib.NPXFit method) (bayesmsd.lib.SplineFit method)

distance() (bayesmsd.parameters.Linearize.ABC method) ds_logL() (bayesmsd.gp.GP method)

E

expand_fix_values() (bayesmsd.fit.Fit method)

F

find_bracket_point() (bayesmsd.profiler.Profiler method) find_closest_res() (bayesmsd.profiler.Profiler method) find_MCI() (bayesmsd.profiler.Profiler method) find_single_MCI() (bayesmsd.profiler.Profiler method) fit (bayesmsd.fit.Fit.MinTarget attribute) (bayesmsd.profiler.Profiler attribute) Fit (class in bayesmsd.fit)

Fit.MinTarget (class in bayesmsd.fit) fix_values (bayesmsd.fit.Fit.MinTarget attribute) fix_values_resolution_order (bayesmsd.fit.Fit.MinTarget attribute) from_linear() (bayesmsd.parameters.Linearize.ABC method) (bayesmsd.parameters.Linearize.Bounded method) (bayesmsd.parameters.Linearize.Exponential method) (bayesmsd.parameters.Linearize.Multiplicative method)

G

generate() (in module bayesmsd.gp) generate_dataset_like() (in module bayesmsd.gp)

GP (class in bayesmsd.gp) GP.BadCovarianceError

I

imaging() (in module bayesmsd.deco) independent_parameters() (bayesmsd.fit.Fit method) initial_bracket_points() (bayesmsd.profiler.Profiler method) initial_offset() (bayesmsd.fit.Fit method) (bayesmsd.lib.NPXFit method) (bayesmsd.lib.SplineFit method)

initial_params() (bayesmsd.fit.Fit method) (bayesmsd.lib.NPXFit method) (bayesmsd.lib.SplineFit method) (bayesmsd.lib.TwoLocusRouseFit method)

L

likelihood_significantly_greater() (bayesmsd.profiler.Profiler static method) Linearize (class in bayesmsd.parameters) Linearize.ABC (class in bayesmsd.parameters) Linearize.Bounded (class in bayesmsd.parameters) Linearize.Exponential (class in bayesmsd.parameters) Linearize.Multiplicative (class in bayesmsd.parameters)

logL() (bayesmsd.gp.GP method) logprior() (bayesmsd.fit.Fit method) logT (bayesmsd.lib.NPXFit attribute) (bayesmsd.lib.SplineFit attribute) LR_interval (bayesmsd.profiler.Profiler attribute) LR_target (bayesmsd.profiler.Profiler attribute)

M

max_fit_runs (bayesmsd.profiler.Profiler attribute) max_penalty (bayesmsd.fit.Fit attribute) max_restarts_per_parameters (bayesmsd.profiler.Profiler attribute) mean() (bayesmsd.parameters.Linearize.ABC method) method_verbosity_patch() (in module bayesmsd.deco) min_target_from_fit (bayesmsd.profiler.Profiler attribute) module bayesmsd bayesmsd.deco bayesmsd.fit bayesmsd.gp bayesmsd.lib bayesmsd.parameters bayesmsd.profiler

motion_blur_f (bayesmsd.lib.NPXFit attribute) (bayesmsd.lib.SplineFit attribute) move() (bayesmsd.parameters.Linearize.ABC method) MSD() (bayesmsd.fit.Fit method) msd2C_fun() (in module bayesmsd.gp) MSDfun() (in module bayesmsd.deco)

N

n (bayesmsd.lib.NPXFit attribute) (bayesmsd.lib.SplineFit attribute)

NPXFit (class in bayesmsd.lib)

O

offset (bayesmsd.fit.Fit.MinTarget attribute)

P

param (bayesmsd.parameters.Linearize.ABC attribute) param_names (bayesmsd.fit.Fit.MinTarget attribute) Parameter (class in bayesmsd.parameters) parameters (bayesmsd.fit.Fit attribute) params2msdm() (bayesmsd.fit.Fit method) (bayesmsd.lib.NPXFit method) (bayesmsd.lib.SplineFit method) (bayesmsd.lib.TwoLocusRouseFit method) params_array2dict() (bayesmsd.fit.Fit.MinTarget method)

params_dict2array() (bayesmsd.fit.Fit.MinTarget method) point_estimate (bayesmsd.profiler.Profiler attribute) prev_fit (bayesmsd.lib.NPXFit attribute) (bayesmsd.lib.SplineFit attribute) profile_likelihood() (bayesmsd.profiler.Profiler method) Profiler (class in bayesmsd.profiler) Profiler.FoundBetterPointEstimate profiling (bayesmsd.profiler.Profiler attribute) (bayesmsd.profiler.Profiler property)

R

ress (bayesmsd.profiler.Profiler attribute) restart_if_better_pe_found() (bayesmsd.profiler.Profiler method) restart_on_better_point_estimate (bayesmsd.profiler.Profiler attribute)

run() (bayesmsd.fit.Fit method) run_count (bayesmsd.profiler.Profiler attribute) run_fit() (bayesmsd.profiler.Profiler method)

S

solve_bisection() (bayesmsd.profiler.Profiler method) SplineFit (class in bayesmsd.lib) ss_order (bayesmsd.fit.Fit attribute) (bayesmsd.lib.NPXFit attribute) (bayesmsd.lib.SplineFit attribute)

suggest_linearization() (bayesmsd.parameters.Parameter method)

T

T (bayesmsd.fit.Fit attribute) to_linear() (bayesmsd.parameters.Linearize.ABC method) (bayesmsd.parameters.Linearize.Bounded method) (bayesmsd.parameters.Linearize.Exponential method) (bayesmsd.parameters.Linearize.Multiplicative method)

TwoLocusRouseFit (class in bayesmsd.lib)

U

upper_bc_type (bayesmsd.lib.NPXFit attribute) (bayesmsd.lib.SplineFit attribute)

V

verbosity (bayesmsd.fit.Fit attribute) (bayesmsd.profiler.Profiler attribute)

vprint() (bayesmsd.fit.Fit method) (bayesmsd.profiler.Profiler method)

X

x_last (bayesmsd.lib.NPXFit attribute) (bayesmsd.lib.SplineFit attribute)

x_max (bayesmsd.lib.NPXFit attribute) (bayesmsd.lib.SplineFit attribute)