Index Symbols | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y Symbols --acid-scale ppr-tecan command line option --add ppr-tecan command line option --all ppr-tecan command line option --band fit-titration-spec command line option --band-name ppr-enspire command line option --bg ppr-tecan command line option --bg-adj ppr-tecan command line option --bg-mth ppr-tecan command line option --boot fit-titration-glob command line option --buffer ppr-enspire command line option ppr-enspire-batch command line option --chains ppr-enspire command line option --cl ppr-tecan command line option --components ppr-enspire command line option --cores ppr-enspire command line option --ctr-free-k ppr-tecan command line option --ctr-shared-k ppr-tecan command line option --ctr-sigma-w ppr-tecan command line option --detect-bad ppr-tecan command line option --draws ppr-enspire command line option --dry-run ppr-tecan command line option --fit ppr-tecan command line option --fit-method ppr-tecan command line option --fit-noise ppr-tecan command line option --is-ph fit-titration command line option --label ppr-tecan command line option --labels note_to_csv command line option --lim ppr-tecan command line option --mask-outliers ppr-tecan command line option --max-k-se ppr-tecan command line option --mcmc ppr-tecan command line option --mcmc-chains ppr-tecan command line option --mcmc-noise ppr-tecan command line option --mcmc-robust ppr-tecan command line option --mcmc-robust-likelihood ppr-tecan command line option --mcmc-samples ppr-tecan command line option --mcmc-seed ppr-tecan command line option --mcmc-target-accept ppr-tecan command line option --mcmc-tune ppr-tecan command line option --mcmc-x-error ppr-tecan command line option --mcmc-x-start-between ppr-tecan command line option --mcmc-x-start-between-learn ppr-tecan command line option --method ppr-enspire command line option --min-rho ppr-enspire command line option ppr-enspire-batch command line option --no-buffer ppr-enspire command line option ppr-enspire-batch command line option --no-detect-bad ppr-tecan command line option --no-fit ppr-tecan command line option --no-is-ph fit-titration command line option --no-mask-outliers ppr-tecan command line option --no-mcmc-robust ppr-tecan command line option --no-noise-ye-mag ppr-tecan command line option --no-per-well-ye-mags ppr-tecan command line option --no-png ppr-tecan command line option --no-weight fit-titration-glob command line option --noise-alpha ppr-tecan command line option --noise-alpha-mode ppr-tecan command line option --noise-floor ppr-tecan command line option --noise-floor-mode ppr-tecan command line option --noise-floor-ref-gain ppr-tecan command line option --noise-gain ppr-tecan command line option --noise-gain-mode ppr-tecan command line option --noise-mode ppr-tecan command line option --noise-ye-mag ppr-tecan command line option --nrm ppr-tecan command line option --nuts-sampler ppr-tecan command line option --out fit-titration command line option ppr command line option --outlier ppr-tecan command line option --outlier-threshold ppr-tecan command line option --output note_to_csv command line option --per-well-ye-mags ppr-tecan command line option --plate-fit ppr-tecan command line option --plate-noise ppr-tecan command line option --plate-screen-frac ppr-tecan command line option --plate-screen-noise ppr-tecan command line option --plate-screen-z ppr-tecan command line option --png ppr-tecan command line option --print-spec ppr-tecan command line option --quiet ppr command line option --raw-dir ppr-tecan command line option --scan ppr-enspire command line option --sch ppr-tecan command line option --screen ppr-enspire command line option ppr-enspire-batch command line option --seed ppr-enspire command line option --student-t-nu ppr-tecan command line option --target-accept ppr-enspire command line option --temp note_to_csv command line option --title ppr-tecan command line option --verbose fit-titration command line option ppr command line option --version clop command line option fit-titration command line option ppr command line option --weight fit-titration-glob command line option --x-sigma ppr-enspire command line option --ye-mag-parameterization ppr-tecan command line option -b fit-titration-glob command line option fit-titration-spec command line option ppr-enspire command line option -l note_to_csv command line option -o fit-titration command line option note_to_csv command line option ppr command line option -q ppr command line option -t note_to_csv command line option ppr-tecan command line option -v fit-titration command line option ppr command line option A acid_scale (clophfit.prtecan.titration.McmcSpec attribute) (clophfit.prtecan.titration.TitrationConfig attribute) acid_step() (in module clophfit.fitting.models) add_robust_scores() (in module clophfit.fitting.utils) additions (clophfit.prtecan.titration.Titration property) all_computed() (clophfit.prtecan.titration.TitrationResults static method) allequal (clophfit.prtecan.models.LabelblocksGroup attribute) almost_equal() (clophfit.prtecan.models.Labelblock method) alpha (clophfit.fitting.data_structures.NoiseModelParams attribute) (clophfit.fitting.data_structures.PlateNoiseModel property) analysis (clophfit.fitting.model_validation.ResidualDiagnostics property) analyze_spectra() (in module clophfit.fitting.core) analyze_spectra_glob() (in module clophfit.fitting.core) annotate() (clophfit.fitting.model_validation.ResidualDiagnostics method) apply_blocks() (in module clophfit.fitting.grid) apply_combination() (in module clophfit.prtecan.export) apply_excluded_points() (in module clophfit.fitting.plate_lm) apply_exclusions() (in module clophfit.fitting.model_validation) apply_mask() (clophfit.fitting.data_structures.Dataset method) apply_outlier_mask() (in module clophfit.fitting.utils) apply_tecan_combination() (in module clophfit.testing.fitter_test_utils) apply_to() (clophfit.fitting.data_structures.PlateNoiseModel method) apply_to_plate() (clophfit.fitting.data_structures.PlateNoiseModel method) B b (clophfit.prenspire.thermo.VanthoffFit attribute) band_rho() (in module clophfit.prenspire.bands) band_values() (in module clophfit.prenspire.bands) BandFit (class in clophfit.prenspire.bands) bands (clophfit.fitting.data_structures.SpectraGlobResults attribute) bg (clophfit.prtecan.titration.Buffer property) (clophfit.prtecan.titration.Titration property) bg_err (clophfit.prtecan.titration.Buffer property) (clophfit.prtecan.titration.Titration property) bg_noise (clophfit.prtecan.titration.Buffer property) (clophfit.prtecan.titration.Titration property) bg_read_noise (clophfit.prtecan.titration.Buffer property) (clophfit.prtecan.titration.Titration property) binding_1site() (in module clophfit.fitting.models) blank_rows() (in module clophfit.prenspire.bands) bonferroni_threshold() (in module clophfit.fitting.utils) breusch_pagan() (in module clophfit.fitting.residual_tests) Buffer (class in clophfit.prtecan.titration) buffer (clophfit.prtecan.models.PlateScheme property) (clophfit.prtecan.titration.Titration attribute) BufferFit (class in clophfit.prtecan.titration) build_factorized_tecan_fit_combinations() (in module clophfit.testing.fitter_test_utils) build_fitters() (in module clophfit.testing.fitter_test_utils) build_tecan_fit_combinations() (in module clophfit.testing.fitter_test_utils) build_titrations() (clophfit.prenspire.prenspire.Note method) C c (clophfit.prenspire.mcr.McrFit attribute) calculate_bias() (in module clophfit.testing.evaluation) calculate_conc() (in module clophfit.prtecan.parsers) calculate_coverage() (in module clophfit.testing.evaluation) calculate_rmse() (in module clophfit.testing.evaluation) calibrate_gain() (in module clophfit.fitting.gain_calibration) calibrate_noise_robust() (in module clophfit.fitting.noise_calibration) calibrate_plate_lm() (in module clophfit.fitting.gain_calibration) calibrate_single_well() (in module clophfit.fitting.gain_calibration) cap_by_min_keep() (in module clophfit.fitting.utils) check_unique_signature() (in module clophfit.fitting.grid) classical_ctr_holdout_rows() (in module clophfit.fitting.ctr_validation) classify() (in module clophfit.prenspire.bands) clean_data() (clophfit.fitting.data_structures.Dataset method) clear_all_data_results() (clophfit.prtecan.titration.Titration method) CLIError clop command line option --version clop-eq1 command line option KD1 PH PKA clophfit module clophfit.clophfit_types module clophfit.fitting module clophfit.fitting.bayes module clophfit.fitting.bayes_config module clophfit.fitting.core module clophfit.fitting.ctr_validation module clophfit.fitting.data_structures module clophfit.fitting.diagnostic_plots module clophfit.fitting.diagnostics module clophfit.fitting.errors module clophfit.fitting.gain_calibration module clophfit.fitting.grid module clophfit.fitting.model_validation module clophfit.fitting.models module clophfit.fitting.noise_calibration module clophfit.fitting.odr module clophfit.fitting.plate_lm module clophfit.fitting.plate_odr module clophfit.fitting.plotting module clophfit.fitting.residual_tests module clophfit.fitting.residuals module clophfit.fitting.robust_se module clophfit.fitting.spectral module clophfit.fitting.utils module clophfit.prenspire module clophfit.prenspire.bands module clophfit.prenspire.mcr module clophfit.prenspire.prenspire module clophfit.prenspire.spectral module clophfit.prenspire.thermo module clophfit.prenspire.thermo_plot module clophfit.prtecan module clophfit.prtecan.export module clophfit.prtecan.models module clophfit.prtecan.parsers module clophfit.prtecan.titration module clophfit.testing module clophfit.testing.evaluation module clophfit.testing.fitter_test_utils module clophfit.testing.synthetic module clophfit.utils module ClopHfitError compare_methods_statistical() (in module clophfit.testing.evaluation) component_pka() (in module clophfit.prenspire.mcr) compute_all() (clophfit.prtecan.titration.TitrationResults method) compute_binding_slope() (in module clophfit.fitting.noise_calibration) compute_noise_variance() (in module clophfit.fitting.data_structures) compute_plate_slopes() (in module clophfit.fitting.noise_calibration) compute_y_err() (clophfit.fitting.data_structures.NoiseModelParams method) concatenate_data() (clophfit.fitting.data_structures.Dataset method) converged (clophfit.fitting.gain_calibration.GainCalibration attribute) ConvergenceError copy() (clophfit.fitting.data_structures.Dataset method) correlation() (clophfit.fitting.model_validation.ResidualAnalysis method) covariance() (clophfit.fitting.model_validation.ResidualAnalysis method) create_dataset_dict() (clophfit.prtecan.titration.Titration method) create_ds() (clophfit.prtecan.titration.Titration method) create_global_ds() (clophfit.prtecan.titration.Titration method) CSV_F fit-titration-spec command line option ppr-enspire command line option CsvLineError ctr_free_k (clophfit.prtecan.titration.TecanConfig attribute) ctr_holdout_odr() (in module clophfit.fitting.plate_odr) ctr_param_name() (in module clophfit.fitting.ctr_validation) ctrl (clophfit.prtecan.models.PlateScheme property) curve_turnover() (in module clophfit.fitting.diagnostics) D data (clophfit.prenspire.mcr.StackedScans attribute) (clophfit.prtecan.models.Labelblock attribute) (clophfit.prtecan.models.LabelblocksGroup property) (clophfit.prtecan.titration.Titration property) data_nrm (clophfit.prtecan.models.Labelblock attribute) (clophfit.prtecan.models.LabelblocksGroup property) DataArray (class in clophfit.fitting.data_structures) dataframe (clophfit.prtecan.titration.TitrationResults property) dataframes (clophfit.prtecan.titration.Buffer property) dataframes_nrm (clophfit.prtecan.titration.Buffer property) Dataset (class in clophfit.fitting.data_structures) dataset (clophfit.fitting.data_structures.FitResult attribute) DataValidationError dead_components (clophfit.prenspire.mcr.McrFit attribute) dead_components() (in module clophfit.prenspire.mcr) degenerate (clophfit.prenspire.mcr.McrFit property) detect_adjacent_correlation() (in module clophfit.fitting.residuals) detect_and_discard_bad_wells() (clophfit.prtecan.titration.Titration method) detect_bad (clophfit.prtecan.titration.TecanConfig attribute) detect_bad_wells() (in module clophfit.fitting.diagnostics) dilution_correction() (in module clophfit.prtecan.parsers) direct_kwargs() (in module clophfit.fitting.grid) discard (clophfit.prtecan.models.PlateScheme property) distribute_axes() (in module clophfit.fitting.plotting) distribution_summary() (clophfit.fitting.model_validation.ResidualAnalysis method) dof_scale() (in module clophfit.fitting.noise_calibration) ds (clophfit.prenspire.thermo.VanthoffFit attribute) durbin_watson() (in module clophfit.fitting.residual_tests) durbin_watson_null() (in module clophfit.fitting.residual_tests) E empty (clophfit.prtecan.titration.BufferFit property) EnspireFile (class in clophfit.prenspire.prenspire) estimate_x_shift_statistics() (in module clophfit.fitting.residuals) evaluate() (clophfit.fitting.model_validation.OutlierCriterion method) (clophfit.fitting.model_validation.OutlierProbability method) (clophfit.fitting.model_validation.ResidualTail method) (clophfit.fitting.model_validation.RobustZMad method) evaluate_residuals() (in module clophfit.testing.evaluation) excess_tail_outlier_mask() (in module clophfit.fitting.model_validation) exclude_label() (clophfit.prtecan.titration.Titration method) excluded_labels (clophfit.prtecan.titration.Titration property) export() (clophfit.fitting.data_structures.Dataset method) export_data() (clophfit.prtecan.titration.TitrationResults method) export_data_fit() (in module clophfit.prtecan.export) export_fit() (in module clophfit.prtecan.export) export_measurements() (clophfit.prenspire.prenspire.EnspireFile method) export_plate_fit() (in module clophfit.prtecan.export) export_pngs() (clophfit.prtecan.titration.TitrationResults method) export_residuals() (in module clophfit.prtecan.export) export_trace_summary() (in module clophfit.prtecan.export) extract_metadata() (in module clophfit.prtecan.parsers) extract_params() (in module clophfit.testing.evaluation) extract_residual_points() (in module clophfit.fitting.residuals) extract_sigma_df() (in module clophfit.fitting.plotting) F fgls_fit_plate() (clophfit.prtecan.titration.Titration method) figure (clophfit.fitting.data_structures.FitResult attribute) FILE fit-titration-glob command line option FileFormatError filename (clophfit.prtecan.models.Labelblock attribute) fit-titration command line option --is-ph --no-is-ph --out --verbose --version -o -v fit-titration-glob command line option --boot --no-weight --weight -b FILE fit-titration-spec command line option --band -b CSV_F NOTE_F fit_bands() (in module clophfit.prenspire.bands) fit_binding_glob() (in module clophfit.fitting.core) fit_binding_odr() (in module clophfit.fitting.odr) fit_binding_pymc() (in module clophfit.fitting.bayes) fit_binding_pymc_multi() (in module clophfit.fitting.bayes) fit_gain_and_floor() (in module clophfit.fitting.noise_calibration) fit_gain_floor_fixed() (in module clophfit.fitting.noise_calibration) fit_gain_from_residuals() (in module clophfit.fitting.noise_calibration) fit_gain_nnls() (in module clophfit.fitting.noise_calibration) fit_keys (clophfit.prtecan.titration.Titration property) fit_noise (clophfit.prtecan.titration.TecanConfig attribute) fit_noise_model_merged() (in module clophfit.fitting.noise_calibration) fit_noise_model_nnls() (in module clophfit.fitting.noise_calibration) fit_ph_slope_noise() (in module clophfit.fitting.noise_calibration) fit_plate() (clophfit.prtecan.titration.Titration method) fit_plate_lm() (in module clophfit.fitting.plate_lm) fit_plate_lm_screened() (in module clophfit.fitting.plate_lm) fit_plate_odr() (in module clophfit.fitting.plate_odr) fit_rel_error_from_residuals() (in module clophfit.fitting.noise_calibration) fit_single_mcmc() (in module clophfit.prtecan.export) fit_spectra_global() (in module clophfit.fitting.spectral) fit_titrations() (in module clophfit.prenspire.bands) fit_titrations_spectral() (in module clophfit.prenspire.spectral) fit_trendline() (in module clophfit.fitting.utils) fit_vanthoff_model() (in module clophfit.prenspire.thermo) FitError FitResult (class in clophfit.fitting.data_structures) fits (clophfit.fitting.gain_calibration.GainCalibration attribute) flag_trend_outliers() (in module clophfit.fitting.utils) format_estimate() (in module clophfit.fitting.odr) fractional_outliers() (in module clophfit.fitting.plate_lm) free_ctr_param_name() (in module clophfit.fitting.ctr_validation) from_da() (clophfit.fitting.data_structures.Dataset class method) from_fit_results() (clophfit.fitting.model_validation.ResidualComparison class method) (clophfit.fitting.model_validation.ResidualDiagnostics class method) fromlistfile() (clophfit.prtecan.titration.Titration class method) G gain (clophfit.fitting.data_structures.NoiseModelParams attribute) (clophfit.fitting.data_structures.PlateNoiseModel property) GainCalibration (class in clophfit.fitting.gain_calibration) generalized_combined_model() (in module clophfit.fitting.odr) generate_combinations() (in module clophfit.prtecan.export) gsvd (clophfit.fitting.data_structures.SpectraGlobResults attribute) H hc_covariance() (in module clophfit.fitting.robust_se) hill (clophfit.fitting.spectral.SpectralFit attribute) history (clophfit.fitting.gain_calibration.GainCalibration attribute) I identify_outliers_mad() (in module clophfit.fitting.utils) inert_knobs() (in module clophfit.fitting.grid) InitConfig (class in clophfit.fitting.bayes_config) InsufficientDataError InvalidDataError is_ph (clophfit.fitting.data_structures.Dataset attribute) (clophfit.prenspire.thermo.VanthoffModel attribute) (clophfit.prtecan.titration.Titration attribute) is_valid() (clophfit.fitting.data_structures.FitResult method) iter_ctr_holdouts() (in module clophfit.fitting.ctr_validation) K K (clophfit.fitting.spectral.SpectralFit attribute) k_by_temp (clophfit.prenspire.thermo.VanthoffFit attribute) k_from_result() (in module clophfit.testing.fitter_test_utils) k_verdicts() (in module clophfit.prtecan.export) kd() (in module clophfit.fitting.models) KD1 clop-eq1 command line option kd_bounds() (in module clophfit.fitting.models) kd_lower_bound() (in module clophfit.prtecan.export) key (clophfit.fitting.grid.Knob property) Knob (class in clophfit.fitting.grid) L label (clophfit.fitting.residuals.ResidualPoint attribute) label_bias() (clophfit.fitting.model_validation.ResidualAnalysis method) label_is_uninformative() (in module clophfit.prtecan.titration) label_scaled() (clophfit.fitting.model_validation.ResidualDiagnostics method) Labelblock (class in clophfit.prtecan.models) labelblocks (clophfit.prtecan.models.Tecanfile attribute) LabelblocksGroup (class in clophfit.prtecan.models) labelblocksgroups (clophfit.prtecan.models.TecanfilesGroup attribute) lag1_autocorrelation() (clophfit.fitting.model_validation.ResidualAnalysis method) left_log (clophfit.prenspire.thermo_plot.VanthoffAxes attribute) left_x (clophfit.prenspire.thermo_plot.VanthoffAxes attribute) left_y (clophfit.prenspire.thermo_plot.VanthoffAxes attribute) likelihood_res (clophfit.fitting.residuals.ResidualPoint attribute) likelihood_residual_table() (in module clophfit.prtecan.export) lines (clophfit.prtecan.models.Labelblock attribute) LIST_FILE ppr-tecan command line option load_additions() (clophfit.prtecan.titration.Titration method) load_real_data_paths() (in module clophfit.testing.evaluation) load_scheme() (clophfit.prtecan.titration.Titration method) lookup_listoflines() (in module clophfit.utils) M m (clophfit.prenspire.thermo.VanthoffFit attribute) make_benchmark_dataset() (in module clophfit.testing.synthetic) make_ctr_holdout_scheme() (in module clophfit.fitting.ctr_validation) make_dataset() (in module clophfit.testing.synthetic) make_simple_dataset() (in module clophfit.testing.synthetic) ManyLinesFoundError mark_outliers() (in module clophfit.fitting.model_validation) mask (clophfit.fitting.data_structures.DataArray property) mask_label_steps() (clophfit.fitting.data_structures.Dataset method) mask_outliers (clophfit.prtecan.titration.TitrationConfig attribute) mask_steps() (clophfit.fitting.data_structures.DataArray method) masks (clophfit.prenspire.bands.BandFit attribute) max_k_se (clophfit.prtecan.titration.TecanConfig attribute) McmcSpec (class in clophfit.prtecan.titration) mcr_als() (in module clophfit.prenspire.mcr) mcr_titration() (in module clophfit.prenspire.mcr) McrFit (class in clophfit.prenspire.mcr) measurements (clophfit.prenspire.prenspire.EnspireFile attribute) merge_log_likelihoods() (in module clophfit.fitting.model_validation) merge_md() (in module clophfit.prtecan.parsers) Metadata (class in clophfit.prtecan.parsers) metadata (clophfit.prenspire.prenspire.EnspireFile attribute) (clophfit.prtecan.models.Labelblock attribute) (clophfit.prtecan.models.LabelblocksGroup attribute) (clophfit.prtecan.models.Tecanfile attribute) (clophfit.prtecan.models.TecanfilesGroup attribute) mini (clophfit.fitting.data_structures.FitResult attribute) MissingDependencyError mixture_params_from_trace() (in module clophfit.fitting.model_validation) model_fraction() (in module clophfit.prenspire.mcr) model_residual_score_table() (in module clophfit.fitting.model_validation) model_signature() (in module clophfit.fitting.grid) module clophfit clophfit.clophfit_types clophfit.fitting clophfit.fitting.bayes clophfit.fitting.bayes_config clophfit.fitting.core clophfit.fitting.ctr_validation clophfit.fitting.data_structures clophfit.fitting.diagnostic_plots clophfit.fitting.diagnostics clophfit.fitting.errors clophfit.fitting.gain_calibration clophfit.fitting.grid clophfit.fitting.model_validation clophfit.fitting.models clophfit.fitting.noise_calibration clophfit.fitting.odr clophfit.fitting.plate_lm clophfit.fitting.plate_odr clophfit.fitting.plotting clophfit.fitting.residual_tests clophfit.fitting.residuals clophfit.fitting.robust_se clophfit.fitting.spectral clophfit.fitting.utils clophfit.prenspire clophfit.prenspire.bands clophfit.prenspire.mcr clophfit.prenspire.prenspire clophfit.prenspire.spectral clophfit.prenspire.thermo clophfit.prenspire.thermo_plot clophfit.prtecan clophfit.prtecan.export clophfit.prtecan.models clophfit.prtecan.parsers clophfit.prtecan.titration clophfit.testing clophfit.testing.evaluation clophfit.testing.fitter_test_utils clophfit.testing.synthetic clophfit.utils MultiFitResult (class in clophfit.fitting.data_structures) N n (clophfit.prenspire.thermo.VanthoffFit attribute) n_iter (clophfit.fitting.gain_calibration.GainCalibration attribute) n_sd() (clophfit.prtecan.titration.TitrationResults method) n_wells (clophfit.fitting.spectral.SpectralFit attribute) names (clophfit.prtecan.models.PlateScheme property) no_binding_k() (in module clophfit.prtecan.export) nofit_keys (clophfit.prtecan.models.PlateScheme property) noise (clophfit.fitting.gain_calibration.GainCalibration attribute) noise_alpha (clophfit.prtecan.titration.TitrationConfig attribute) noise_floor (clophfit.prtecan.titration.TitrationConfig attribute) noise_floor_ref_gain (clophfit.prtecan.titration.TitrationConfig attribute) noise_gain (clophfit.prtecan.titration.TitrationConfig attribute) noise_ye_mag (clophfit.prtecan.titration.McmcSpec attribute) NoiseConfig (class in clophfit.fitting.bayes_config) NoiseModelParams (class in clophfit.fitting.data_structures) normality() (clophfit.fitting.model_validation.ResidualDiagnostics method) normality_tests() (in module clophfit.fitting.residual_tests) NOTE note_to_csv command line option Note (class in clophfit.prenspire.prenspire) note (clophfit.prenspire.prenspire.Note property) NOTE_F fit-titration-spec command line option ppr-enspire command line option note_to_csv command line option --labels --output --temp -l -o -t NOTE O odr (clophfit.fitting.data_structures.FitResult attribute) ok (clophfit.prenspire.thermo.VanthoffFit attribute) outlier() (in module clophfit.fitting.odr) outlier_scores_extended() (in module clophfit.fitting.utils) outlier_threshold (clophfit.prtecan.titration.TitrationConfig attribute) OutlierCriterion (class in clophfit.fitting.model_validation) OutlierProbability (class in clophfit.fitting.model_validation) P params (clophfit.prtecan.titration.Titration property) pareto_k_summary() (in module clophfit.fitting.model_validation) pareto_k_table() (in module clophfit.fitting.model_validation) parse_remove_outliers() (in module clophfit.fitting.utils) PH clop-eq1 command line option PKA clop-eq1 command line option plate_lm_residuals() (in module clophfit.fitting.gain_calibration) plate_noise (clophfit.prtecan.titration.TecanConfig attribute) plate_screen_frac (clophfit.prtecan.titration.TecanConfig attribute) plate_screen_noise (clophfit.prtecan.titration.TecanConfig attribute) plate_screen_z (clophfit.prtecan.titration.TecanConfig attribute) plateaus (clophfit.prenspire.thermo.VanthoffFit attribute) PlateLMResult (class in clophfit.fitting.plate_lm) PlateNoiseModel (class in clophfit.fitting.data_structures) PlateODRResult (class in clophfit.fitting.plate_odr) PlateScheme (class in clophfit.prtecan.models) plot() (clophfit.fitting.data_structures.Dataset method) (clophfit.prtecan.titration.Buffer method) plot_autovalues() (in module clophfit.fitting.plotting) plot_autovectors() (in module clophfit.fitting.plotting) plot_col() (clophfit.fitting.model_validation.ResidualDiagnostics method) plot_emcee() (in module clophfit.fitting.plotting) plot_emcee_k_on_ax() (in module clophfit.fitting.plotting) plot_fit() (in module clophfit.fitting.plotting) plot_fit_gemini() (in module clophfit.fitting.plotting) plot_hist_qq() (clophfit.fitting.model_validation.ResidualDiagnostics method) plot_k() (clophfit.prtecan.titration.TitrationResults method) plot_pca() (in module clophfit.fitting.plotting) plot_qc_mean_vs_std() (in module clophfit.fitting.plotting) plot_qc_span_vs_center() (in module clophfit.fitting.plotting) plot_qc_span_vs_center_titration() (in module clophfit.fitting.plotting) plot_residual_distribution() (in module clophfit.fitting.residuals) plot_residual_overview() (in module clophfit.fitting.diagnostic_plots) plot_residual_vs_predicted() (in module clophfit.fitting.residuals) plot_residual_vs_yerr() (in module clophfit.fitting.residuals) plot_role() (clophfit.fitting.model_validation.ResidualDiagnostics method) plot_sample() (in module clophfit.prenspire.bands) plot_spectra() (in module clophfit.fitting.plotting) plot_spectra_distributed() (in module clophfit.fitting.plotting) plot_step() (clophfit.fitting.model_validation.ResidualDiagnostics method) plot_temperature() (clophfit.prtecan.titration.Titration method) plot_well_summary() (clophfit.fitting.model_validation.ResidualDiagnostics method) PlotParameters (class in clophfit.fitting.plotting) position_summary() (clophfit.fitting.model_validation.ResidualDiagnostics method) posterior_dataset() (in module clophfit.fitting.model_validation) ppr command line option --out --quiet --verbose --version -o -q -v ppr-enspire command line option --band-name --buffer --chains --components --cores --draws --method --min-rho --no-buffer --scan --screen --seed --target-accept --x-sigma -b CSV_F NOTE_F ppr-enspire-batch command line option --buffer --min-rho --no-buffer --screen ROOT ppr-tecan command line option --acid-scale --add --all --bg --bg-adj --bg-mth --cl --ctr-free-k --ctr-shared-k --ctr-sigma-w --detect-bad --dry-run --fit --fit-method --fit-noise --label --lim --mask-outliers --max-k-se --mcmc --mcmc-chains --mcmc-noise --mcmc-robust --mcmc-robust-likelihood --mcmc-samples --mcmc-seed --mcmc-target-accept --mcmc-tune --mcmc-x-error --mcmc-x-start-between --mcmc-x-start-between-learn --no-detect-bad --no-fit --no-mask-outliers --no-mcmc-robust --no-noise-ye-mag --no-per-well-ye-mags --no-png --noise-alpha --noise-alpha-mode --noise-floor --noise-floor-mode --noise-floor-ref-gain --noise-gain --noise-gain-mode --noise-mode --noise-ye-mag --nrm --nuts-sampler --outlier --outlier-threshold --per-well-ye-mags --plate-fit --plate-noise --plate-screen-frac --plate-screen-noise --plate-screen-z --png --print-spec --raw-dir --sch --student-t-nu --title --ye-mag-parameterization -t LIST_FILE pprint() (clophfit.fitting.data_structures.FitResult method) prepare_output_folder() (in module clophfit.prtecan.export) press_statistics() (in module clophfit.fitting.residual_tests) print_emcee() (in module clophfit.fitting.plotting) process_trace() (in module clophfit.fitting.bayes) profile_k_intervals() (in module clophfit.fitting.plate_lm) proposal_moved (clophfit.fitting.gain_calibration.GainCalibration attribute) Q qc_flag_bad_wells() (in module clophfit.fitting.plotting) qc_flag_bad_wells_titration() (in module clophfit.fitting.plotting) qq_fit() (in module clophfit.fitting.residuals) R ratiometric_exempt() (in module clophfit.fitting.plate_lm) raw_i (clophfit.fitting.residuals.ResidualPoint attribute) raw_res (clophfit.fitting.residuals.ResidualPoint attribute) read_xls() (in module clophfit.utils) Readout (class in clophfit.prenspire.bands) record_post_fit() (in module clophfit.prtecan.export) rel_err (clophfit.prenspire.mcr.McrFit attribute) residual_dataframe() (in module clophfit.fitting.residuals) residual_normal_scores() (in module clophfit.fitting.model_validation) residual_statistics() (in module clophfit.fitting.residuals) residual_sv (clophfit.fitting.spectral.SpectralFit attribute) residual_table() (clophfit.fitting.data_structures.FitResult method) (clophfit.fitting.data_structures.MultiFitResult method) (clophfit.fitting.data_structures.ResidualsMixin method) (clophfit.prtecan.titration.TitrationResults method) residual_tests() (in module clophfit.fitting.residual_tests) ResidualAnalysis (class in clophfit.fitting.model_validation) ResidualComparison (class in clophfit.fitting.model_validation) ResidualDiagnostics (class in clophfit.fitting.model_validation) ResidualPoint (class in clophfit.fitting.residuals) residuals (clophfit.fitting.data_structures.ResidualsMixin property) residuals_from_fit_results() (in module clophfit.fitting.model_validation) residuals_from_multifit() (in module clophfit.fitting.model_validation) ResidualsMixin (class in clophfit.fitting.data_structures) ResidualTail (class in clophfit.fitting.model_validation) resolve_y_err() (in module clophfit.fitting.utils) result (clophfit.fitting.data_structures.FitResult attribute) reweight_from_residuals() (in module clophfit.fitting.utils) right_log (clophfit.prenspire.thermo_plot.VanthoffAxes attribute) right_y (clophfit.prenspire.thermo_plot.VanthoffAxes attribute) rms (clophfit.fitting.spectral.SpectralFit attribute) robust_k_se() (in module clophfit.fitting.robust_se) robust_likelihood_from_trace() (in module clophfit.fitting.model_validation) robust_residual_outlier_mask() (in module clophfit.fitting.model_validation) robust_scale() (in module clophfit.fitting.utils) robust_settings_from_trace() (in module clophfit.fitting.model_validation) robust_z_scores() (in module clophfit.fitting.utils) RobustConfig (class in clophfit.fitting.bayes_config) RobustZMad (class in clophfit.fitting.model_validation) ROOT ppr-enspire-batch command line option roughness() (in module clophfit.fitting.utils) run_pre_fit_detection() (in module clophfit.prtecan.export) runs_test() (in module clophfit.fitting.residual_tests) runs_test_null() (in module clophfit.fitting.residual_tests) S s (clophfit.prenspire.mcr.McrFit attribute) s_from_result() (in module clophfit.testing.fitter_test_utils) sample_spectra() (in module clophfit.prenspire.spectral) sample_stats_dataset() (in module clophfit.fitting.model_validation) SamplerConfig (class in clophfit.fitting.bayes_config) sandwich_se() (in module clophfit.fitting.robust_se) scan_blocks() (in module clophfit.prenspire.mcr) scan_name() (in module clophfit.prenspire.spectral) scheme (clophfit.prtecan.titration.Titration property) screen_atypical_wells() (in module clophfit.prtecan.export) screen_bands() (in module clophfit.prenspire.bands) screen_wells() (in module clophfit.fitting.diagnostics) screening_sigma_floor() (in module clophfit.fitting.plate_lm) se (clophfit.fitting.spectral.SpectralFit attribute) se_naive (clophfit.fitting.spectral.SpectralFit attribute) set_callback() (clophfit.prtecan.titration.TitrationConfig method) sigma (clophfit.fitting.residuals.ResidualPoint attribute) sigma_floor (clophfit.fitting.data_structures.NoiseModelParams attribute) (clophfit.fitting.data_structures.PlateNoiseModel property) (clophfit.prtecan.titration.Titration property) sigma_ph (clophfit.fitting.data_structures.NoiseModelParams attribute) single_well_residuals() (in module clophfit.fitting.gain_calibration) smoothness() (in module clophfit.fitting.utils) species (clophfit.fitting.spectral.SpectralFit attribute) species_by_scan() (in module clophfit.prenspire.mcr) SpectraGlobResults (class in clophfit.fitting.data_structures) SpectralFit (class in clophfit.fitting.spectral) stack_scans() (in module clophfit.prenspire.mcr) StackedScans (class in clophfit.prenspire.mcr) std_res (clophfit.fitting.residuals.ResidualPoint attribute) step_centered() (clophfit.fitting.model_validation.ResidualDiagnostics method) step_summary() (clophfit.fitting.model_validation.ResidualDiagnostics method) strip_lines() (in module clophfit.utils) structured() (clophfit.fitting.bayes_config.NoiseConfig class method) studentized_outliers() (in module clophfit.fitting.residual_tests) studentized_scores() (in module clophfit.fitting.utils) subtract_buffer() (in module clophfit.prenspire.bands) summarize_bayesian_ctr_holdout() (in module clophfit.fitting.ctr_validation) summarize_ctr_loo_table() (in module clophfit.fitting.ctr_validation) svd (clophfit.fitting.data_structures.SpectraGlobResults attribute) T tags (clophfit.prenspire.mcr.StackedScans attribute) tail_rows() (clophfit.fitting.model_validation.ResidualDiagnostics method) TecanConfig (class in clophfit.prtecan.titration) Tecanfile (class in clophfit.prtecan.models) TecanfilesGroup (class in clophfit.prtecan.models) TecanFitCombination (class in clophfit.testing.fitter_test_utils) titrant_kind() (in module clophfit.prenspire.thermo) Titration (class in clophfit.prtecan.titration) TitrationConfig (class in clophfit.prtecan.titration) TitrationResults (class in clophfit.prtecan.titration) titrations (clophfit.prenspire.prenspire.Note attribute) trace (clophfit.fitting.data_structures.FitResult attribute) trace_diagnostics() (in module clophfit.fitting.model_validation) trace_parameter_summary() (in module clophfit.fitting.model_validation) TruthParams (class in clophfit.testing.synthetic) U undetermined_k() (in module clophfit.prtecan.export) unit (clophfit.prtecan.parsers.Metadata attribute) V validate() (clophfit.fitting.model_validation.ResidualAnalysis method) vanthoff_axes() (in module clophfit.prenspire.thermo_plot) vanthoff_curve() (in module clophfit.prenspire.thermo_plot) vanthoff_enthalpy() (in module clophfit.prenspire.thermo_plot) vanthoff_right_line() (in module clophfit.prenspire.thermo_plot) vanthoff_right_point() (in module clophfit.prenspire.thermo_plot) vanthoff_titration() (in module clophfit.prenspire.thermo) VanthoffAxes (class in clophfit.prenspire.thermo_plot) VanthoffFit (class in clophfit.prenspire.thermo) VanthoffModel (class in clophfit.prenspire.thermo) verbose (clophfit.prenspire.prenspire.EnspireFile attribute) (clophfit.prenspire.prenspire.Note attribute) verbose_print() (in module clophfit.prenspire.prenspire) W wavelengths (clophfit.fitting.spectral.SpectralFit attribute) (clophfit.prenspire.mcr.StackedScans attribute) weight_da() (in module clophfit.fitting.core) weight_multi_ds_titration() (in module clophfit.fitting.core) weighted_mean_reference() (in module clophfit.fitting.ctr_validation) weights_from_sigma() (in module clophfit.utils) well_leverage() (in module clophfit.fitting.residual_tests) well_scale (clophfit.fitting.spectral.SpectralFit attribute) well_scaled() (clophfit.fitting.model_validation.ResidualDiagnostics method) well_summary() (clophfit.fitting.model_validation.ResidualDiagnostics method) wells (clophfit.prenspire.prenspire.EnspireFile attribute) (clophfit.prenspire.prenspire.Note attribute) (clophfit.prtecan.titration.Buffer property) white_test() (in module clophfit.fitting.residual_tests) widen_heldout_k_prior() (in module clophfit.fitting.ctr_validation) with_relative_residuals() (clophfit.fitting.model_validation.ResidualDiagnostics method) with_value() (clophfit.fitting.model_validation.ResidualComparison method) X x (clophfit.fitting.data_structures.DataArray property) (clophfit.fitting.residuals.ResidualPoint attribute) x_axis_sanity() (in module clophfit.fitting.model_validation) x_correlation() (clophfit.fitting.model_validation.ResidualAnalysis method) x_err (clophfit.fitting.data_structures.DataArray property) (clophfit.prtecan.titration.Titration attribute) Y y (clophfit.fitting.data_structures.DataArray property) (clophfit.fitting.residuals.ResidualPoint attribute) y_err (clophfit.fitting.data_structures.DataArray property) ye_mag() (clophfit.fitting.bayes_config.NoiseConfig class method) yhat (clophfit.fitting.residuals.ResidualPoint attribute)