Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z _ __eq__() (BasePrior method) __getitem__() (NormativeModel method) __setitem__() (NormativeModel method) __slots__ (NormData attribute) _migrations (MigrationRegistry attribute) A active_job_ids (JobObserver attribute) active_jobs (Runner attribute) adjust_outliers (Scaler attribute) AGE_FP_POWER_PRESETS (FractionalPolynomialBasisFunction attribute) all_job_ids (JobObserver attribute) alpha (BetaLikelihood attribute) apply_mapping() (BasePrior method) ard (BLR attribute) autoscale() (in module pcntoolkit.util.autoscale_plot) B backward() (BetaLikelihood method) (BLR method) (HBR method) (Likelihood method) (NormalLikelihood method) (RegressionModel method) (SHASHbLikelihood method) (SHASHo2Likelihood method) (SHASHoLikelihood method) (TestModel method) BasePrior (class in pcntoolkit.math_functions.prior) basis_column (BasisFunction attribute) basis_function (LinearPrior attribute) basis_function_mean (BLR attribute) basis_function_var (BLR attribute) basis_name (BasisFunction attribute) (BsplineBasisFunction attribute) (FractionalPolynomialBasisFunction attribute) (LinearBasisFunction attribute) (PolynomialBasisFunction attribute) BasisFunction (class in pcntoolkit.math_functions.basis_function) batch_effect_counts (NormativeModel attribute) batch_effect_covariate_ranges (NormativeModel attribute) batch_effect_dims (NormativeModel property) batch_effects (NormData attribute) batch_effects_maps (NormativeModel attribute) batch_effects_split() (NormData method) batch_size (Runner attribute) BATCH_SIZE_AND_N_BATCHES_SPECIFIED (Warnings attribute) be_idx_gen() (BLR method) be_maps (HBR attribute) beta (BetaLikelihood attribute) BetaLikelihood (class in pcntoolkit.math_functions.likelihood) BLR (class in pcntoolkit.regression_model.blr) BLR_BATCH_EFFECTS_NOT_PROVIDED (Warnings attribute) BLR_CG_NOT_SUPPORTED_WITH_HETEROSKEDASTIC (Warnings attribute) BLR_CG_NOT_SUPPORTED_WITH_WARP (Warnings attribute) BLR_ERROR_NO_DESIGN_MATRIX_CREATED (Errors attribute) BLR_ESTIMATION_OF_POSTERIOR_DISTRIBUTION_FAILED (Warnings attribute) BLR_HYPERPARAMETER_VECTOR_INVALID_LENGTH (Errors attribute) BLR_HYPERPARAMETERS_HAVE_NOT_CHANGED (Messages attribute) BLR_MODEL_NOT_FITTED (Errors attribute) BLR_RESTARTING_ESTIMATION_AT_HYP (Messages attribute) BLR_VAR_X_NOT_PROVIDED (Warnings attribute) BLR_X_NOT_PROVIDED (Errors attribute) BLR_Y_NOT_PROVIDED (Warnings attribute) BsplineBasisFunction (class in pcntoolkit.math_functions.basis_function) C calculate_new_limit() (in module pcntoolkit.util.autoscale_plot) CenteredRandomPrior (class in pcntoolkit.math_functions.prior) centiles (NormData attribute) CENTILES_ALREADY_COMPUTED_FOR_CENTILES (Warnings attribute) chains (HBR attribute) check_compatibility() (NormativeModel method) (NormData method) check_forward_compatibility() (in module pcntoolkit.util.migration) check_job_status() (Runner method) check_jobs_status() (Runner method) check_success_file() (JobObserver method) chunk() (NormData method) CIFTI_MAPPINGS (in module pcntoolkit.dataio.fileio) CIFTI_VOL_ATLAS (in module pcntoolkit.dataio.fileio) compare_hbr_models() (in module pcntoolkit.util.model_comparison) compile() (BasePrior method) (Likelihood method) compile_params() (BetaLikelihood method) (Likelihood method) (NormalLikelihood method) (SHASHbLikelihood method) ComponentName (in module pcntoolkit.util.migration) CompositeBasisFunction (class in pcntoolkit.math_functions.basis_function) compute_baseline_logp() (NormativeModel method) compute_centiles() (NormativeModel method) compute_correlation_matrix() (NormativeModel method) compute_logp() (NormativeModel method) compute_max (BasisFunction attribute) compute_min (BasisFunction attribute) compute_thrivelines() (NormativeModel method) compute_yhat() (HBR method) (NormativeModel method) (RegressionModel method) compute_zscores() (NormativeModel method) COMPUTING_CENTILES (Messages attribute) COMPUTING_CENTILES_MODEL (Messages attribute) COMPUTING_LOGP (Messages attribute) COMPUTING_LOGP_MODEL (Messages attribute) COMPUTING_YHAT (Messages attribute) COMPUTING_YHAT_MODEL (Messages attribute) COMPUTING_ZSCORES (Messages attribute) COMPUTING_ZSCORES_MODEL (Messages attribute) concatenate_string_arrays() (NormData method) CONST1 (in module pcntoolkit.math_functions.shash) CONST2 (in module pcntoolkit.math_functions.shash) cores (HBR attribute) correlation_matrix (NormativeModel attribute) covariate_ranges (NormativeModel attribute) covariates (NormativeModel attribute) create_basis_function() (in module pcntoolkit.math_functions.basis_function) create_design_matrix() (in module pcntoolkit.regression_model.blr) create_incremental_backup() (in module pcntoolkit.dataio.fileio) create_mask() (in module pcntoolkit.dataio.fileio) create_model_with_data() (Likelihood method) create_statistics_group() (Evaluator method) (NormData method) create_temp_and_log_dir() (Runner method) cross_validate (Runner attribute) cv_folds (Runner attribute) D DATA_ALREADY_SCALED (Warnings attribute) DATA_NOT_SCALED (Warnings attribute) DATASET_CREATED (Messages attribute) DEFAULT_POWER_SET (FractionalPolynomialBasisFunction attribute) DEFAULT_PRIOR_ARGS (in module pcntoolkit.math_functions.prior) degree (BsplineBasisFunction attribute) (PolynomialBasisFunction attribute) delta (SHASHbLikelihood attribute) (SHASHo2Likelihood attribute) (SHASHoLikelihood attribute) design_matrix() (in module pcntoolkit.math_functions.thrive) df() (WarpAffine method) (WarpBase method) (WarpBoxCox method) (WarpCompose method) (WarpLog method) (WarpSinhArcsinh method) dimension (BasisFunction property) (BsplineBasisFunction property) (CompositeBasisFunction property) (FractionalPolynomialBasisFunction property) (LinearBasisFunction property) (PolynomialBasisFunction property) dims (BasePrior property) (CenteredRandomPrior property) (LinearPrior property) (RandomPrior property) DIR_DOES_NOT_EXIST (Warnings attribute) dist() (SHASH class method) (SHASHb class method) (SHASHo class method) (SHASHo2 class method) dist_name (Prior attribute) dist_params (Prior attribute) dloglik() (BLR method) draws (HBR attribute) dtype (SHASHbRV attribute) (SHASHo2RV attribute) (SHASHoRV attribute) (SHASHrv attribute) E elemwise_logp() (BLR method) (HBR method) (RegressionModel method) (TestModel method) elemwise_logp_baseline_model() (NormativeModel static method) empty_statistic() (Evaluator method) ensure_dir_exists() (in module pcntoolkit.util.paths) ENSURE_POSITIVE_DISTRIBUTION (Errors attribute) entrypoint() (in module pcntoolkit.normative) environment (Runner attribute) eps (FractionalPolynomialBasisFunction attribute) epsilon (SHASHbLikelihood attribute) (SHASHo2Likelihood attribute) (SHASHoLikelihood attribute) error() (Output class method) ERROR_ARGUMENT_SPECIFIED_TWICE (Errors attribute) ERROR_BASIS_FUNCTION_NOT_FITTED (Errors attribute) ERROR_BATCH_EFFECTS_NOT_LIST (Errors attribute) ERROR_BATCH_SIZE_AND_N_BATCHES_MISMATCH (Errors attribute) ERROR_BLR_CG_NOT_SUPPORTED_WITH_WARP (Errors attribute) ERROR_BLR_HYPERPARAMETER_VECTOR_INVALID_LENGTH (Errors attribute) ERROR_BLR_PENALTY_NOT_RECOGNIZED (Errors attribute) ERROR_BLR_POWELL (Errors attribute) ERROR_BLR_TRANSFER_NOT_IMPLEMENTED (Errors attribute) ERROR_BLR_VAR_X_NOT_PROVIDED (Errors attribute) ERROR_BLR_WARPS_NOT_PROVIDED (Errors attribute) ERROR_CDF_SHAPE (Errors attribute) ERROR_CROSS_VALIDATION_FOLDS (Errors attribute) ERROR_DATA_MUST_BE_1D (Errors attribute) ERROR_ENVIRONMENT_NOT_FOUND (Errors attribute) ERROR_FILE_NOT_FOUND (Errors attribute) ERROR_GETTING_JOB_STATUSES (Warnings attribute) ERROR_HBR_COULD_NOT_LOAD_IDATA (Errors attribute) ERROR_HBR_FITTED_BUT_NO_IDATA (Errors attribute) ERROR_HBR_Y_NOT_PROVIDED (Errors attribute) ERROR_HBRDATA_X_NOT_PROVIDED (Errors attribute) ERROR_MODEL_NOT_FITTED (Errors attribute) ERROR_MULTIPLE_COVARIATE_DIMS (Errors attribute) ERROR_NO_ENVIRONMENT_SPECIFIED (Errors attribute) ERROR_PARSING_JOB_STATUS_LINE (Warnings attribute) ERROR_PARSING_TIME_LIMIT (Errors attribute) ERROR_PREDICT_DATA_NOT_SUPPORTED_FOR_CROSS_VALIDATION (Errors attribute) ERROR_PREDICT_DATA_REQUIRED (Errors attribute) ERROR_PREDICT_DATA_REQUIRED_FOR_FIT_PREDICT_WITHOUT_CROSS_VALIDATION (Errors attribute) ERROR_SCALER_NOT_FITTED (Errors attribute) ERROR_SCALER_TYPE_NOT_FOUND (Errors attribute) ERROR_SOURCE_ARRAY_NOT_FOUND (Errors attribute) ERROR_SUBMITTING_JOB (Errors attribute) (Warnings attribute) ERROR_UNKNOWN_CLASS (Errors attribute) ERROR_UNKNOWN_DISTRIBUTION (Errors attribute) ERROR_UNKNOWN_FUNCTION (Errors attribute) ERROR_UNKNOWN_LIKELIHOOD (Errors attribute) ERROR_UNKNOWN_MAPPING (Errors attribute) ERROR_UNKNOWN_SCALER_TYPE (Errors attribute) ERROR_WARP_STRING_INVALID (Errors attribute) ERROR_Y_NOT_FOUND (Errors attribute) ERROR_ZSCORES_INVERSE (Errors attribute) Errors (class in pcntoolkit.util.output) evaluate() (Evaluator method) (NormativeModel method) evaluate_bic() (Evaluator method) evaluate_expv() (Evaluator method) evaluate_kurt() (Evaluator method) evaluate_mace() (Evaluator method) evaluate_mape() (Evaluator method) evaluate_mll() (Evaluator method) evaluate_model (NormativeModel attribute) evaluate_msll() (Evaluator method) evaluate_R2() (Evaluator method) evaluate_rho() (Evaluator method) evaluate_rmse() (Evaluator method) evaluate_shapiro_w() (Evaluator method) evaluate_skew() (Evaluator method) evaluate_smse() (Evaluator method) Evaluator (class in pcntoolkit.util.evaluator) evaluator (NormativeModel attribute) EXECUTING_CALLABLE (Messages attribute) EXECUTION_FAILED (Messages attribute) EXECUTION_SUCCESSFUL (Messages attribute) extend() (NormativeModel method) (Runner method) extend_predict() (NormativeModel method) (Runner method) EXTRA_COVARIATES (Warnings attribute) EXTRA_RESPONSE_VARS (Warnings attribute) extract_and_reshape() (HBR method) extract_data() (NormativeModel method) EXTRACTING_CIFTI_SURFACE_DATA (Messages attribute) EXTRACTING_CIFTI_VOLUME_DATA (Messages attribute) F f() (WarpAffine method) (WarpBase method) (WarpBoxCox method) (WarpCompose method) (WarpLog method) (WarpSinhArcsinh method) factorize_exponential() (in module pcntoolkit.math_functions.factorize) factorize_gamma() (in module pcntoolkit.math_functions.factorize) factorize_halfnormal() (in module pcntoolkit.math_functions.factorize) factorize_lognormal() (in module pcntoolkit.math_functions.factorize) factorize_normal() (in module pcntoolkit.math_functions.factorize) factorize_uniform() (in module pcntoolkit.math_functions.factorize) failed_jobs (Runner attribute) file_extension() (in module pcntoolkit.dataio.fileio) file_stem() (in module pcntoolkit.dataio.fileio) file_type() (in module pcntoolkit.dataio.fileio) fill_missing() (in module pcntoolkit.math_functions.thrive) fisher_transform() (in module pcntoolkit.math_functions.thrive) fit() (BasisFunction method) (BLR method) (CompositeBasisFunction method) (HBR method) (IdentityScaler method) (in module pcntoolkit.normative) (MinMaxScaler method) (NormativeModel method) (RegressionModel method) (RobustMinMaxScaler method) (Runner method) (Scaler method) (StandardScaler method) (TestModel method) fit_predict() (in module pcntoolkit.normative) (NormativeModel method) (Runner method) fit_transform() (Scaler method) FITTING_AND_PREDICTING_MODEL (Messages attribute) FITTING_AND_PREDICTING_MODELS (Messages attribute) FITTING_MODEL (Messages attribute) FITTING_MODELS (Messages attribute) fixed_effect (BLR attribute) fixed_effect_slope (BLR attribute) fixed_effect_slope_indices (BLR attribute) fixed_effect_var (BLR attribute) fixed_effect_var_slope (BLR attribute) fixed_effect_var_slope_indices (BLR attribute) forward() (BetaLikelihood method) (BLR method) (HBR method) (Likelihood method) (NormalLikelihood method) (RegressionModel method) (SHASHbLikelihood method) (SHASHo2Likelihood method) (SHASHoLikelihood method) (TestModel method) FractionalPolynomialBasisFunction (class in pcntoolkit.math_functions.basis_function) from_args() (BasisFunction class method) (BLR class method) (HBR class method) (Likelihood static method) (NormativeModel class method) (RegressionModel class method) (Runner class method) (TestModel class method) from_bids() (NormData class method) from_dataframe() (NormData class method) from_dict() (BasePrior class method) (BasisFunction class method) (BLR class method) (CenteredRandomPrior class method) (HBR class method) (IdentityScaler class method) (Likelihood static method) (LinearPrior class method) (MinMaxScaler class method) (Prior class method) (RandomPrior class method) (RegressionModel class method) (RobustMinMaxScaler class method) (Scaler class method) (StandardScaler class method) (TestModel class method) from_fsl() (NormData class method) from_ndarrays() (NormData class method) from_netcdf() (NormData class method) from_paths() (NormData class method) from_string() (Scaler static method) from_xarray() (NormData class method) G gamma (BLR attribute) GENERATING_MASK_AUTOMATICALLY (Messages attribute) generic_MCMC_apply() (HBR method) get_all_job_file_paths() (Runner method) get_argparser() (in module pcntoolkit.normative) get_conf_dict_from_args() (in module pcntoolkit.normative) get_correlation_matrix() (in module pcntoolkit.math_functions.thrive) get_data_path() (Runner method) get_default_home_dir() (in module pcntoolkit.util.paths) get_default_log_dir() (in module pcntoolkit.util.paths) get_default_normal_likelihood() (in module pcntoolkit.math_functions.likelihood) get_default_save_dir() (in module pcntoolkit.util.paths) get_default_temp_dir() (in module pcntoolkit.util.paths) get_extend_chunk_fn() (Runner method) get_extend_predict_chunk_fn() (Runner method) get_fit_chunk_fn() (Runner method) get_fit_predict_chunk_fn() (Runner method) get_job_statuses() (JobObserver method) get_n_params() (WarpBase method) get_predict_chunk_fn() (Runner method) get_python_callable_path() (Runner method) get_save_subdirs() (in module pcntoolkit.util.paths) get_show_messages() (Output class method) get_show_pid() (Output class method) get_show_timestamp() (Output class method) get_show_warnings() (Output class method) get_single_batch_effect() (NormData method) get_statistics_df() (NormData method) get_thrive_Z_X() (in module pcntoolkit.math_functions.thrive) get_transfer_chunk_fn() (Runner method) get_transfer_predict_chunk_fn() (Runner method) get_var_names() (BetaLikelihood method) (SHASHbLikelihood method) (SHASHo2Likelihood method) (SHASHoLikelihood method) get_warp() (BLR method) get_xy() (in module pcntoolkit.util.autoscale_plot) grad() (Kv method) H harmonize() (NormativeModel method) HARMONIZING_DATA (Messages attribute) HARMONIZING_DATA_MODEL (Messages attribute) has_batch_effect (BLR property) (NormativeModel property) (RegressionModel property) (TestModel property) has_batch_effect() (HBR method) has_random_effect (BasePrior property) (CenteredRandomPrior property) (LinearPrior property) (Prior property) (RandomPrior property) has_random_effect() (BetaLikelihood method) (Likelihood method) (NormalLikelihood method) (SHASHbLikelihood method) (SHASHo2Likelihood method) (SHASHoLikelihood method) has_registered_metadata() (NormData method) HBR (class in pcntoolkit.regression_model.hbr) HBR_BATCH_EFFECTS_NOT_PROVIDED (Warnings attribute) HBR_MODEL_NOT_FITTED (Errors attribute) heteroskedastic (BLR attribute) hyp (BLR attribute) hyp0 (BLR attribute) I idata (HBR attribute) IdentityScaler (class in pcntoolkit.math_functions.scaler) impl() (Kv method) init (HBR attribute) init_hyp() (BLR method) initialize_warp() (BLR method) inscaler (NormativeModel attribute) inscalers (NormativeModel attribute) intercept (LinearPrior attribute) INVALID_ENVIRONMENT (Errors attribute) inverse_transform() (IdentityScaler method) (MinMaxScaler method) (Scaler method) (StandardScaler method) invf() (WarpAffine method) (WarpBase method) (WarpBoxCox method) (WarpCompose method) (WarpLog method) (WarpSinhArcsinh method) is_fitted (BasisFunction attribute) (NormativeModel attribute) (RegressionModel attribute), [1] is_from_dict (RegressionModel attribute) iter_batch_combinations() (in module pcntoolkit.util.data_utils) J job_commands (Runner attribute) job_id (JobStatus attribute) job_id_to_name (JobObserver attribute) job_observer (Runner attribute) JOB_STATUS_LINE (Messages attribute) JOB_STATUS_MONITOR (Messages attribute) JOB_STATUS_SUMMARY (Messages attribute) job_type (JobObserver attribute) (Runner attribute) JobObserver (class in pcntoolkit.util.job_observer) JobStatus (class in pcntoolkit.util.job_observer) K K() (in module pcntoolkit.math_functions.shash) kfold_split() (NormData method) knot_method (BsplineBasisFunction attribute) Kv (class in pcntoolkit.math_functions.shash) kv (in module pcntoolkit.math_functions.shash) KV_GRADIENT_DP (in module pcntoolkit.math_functions.shash) L l_bfgs_b_epsilon (BLR attribute) l_bfgs_b_l (BLR attribute) l_bfgs_b_norm (BLR attribute) left_expand (BsplineBasisFunction attribute) Likelihood (class in pcntoolkit.math_functions.likelihood) likelihood (HBR attribute) linear_BLR() (in module pcntoolkit.regression_model.factory) LinearBasisFunction (class in pcntoolkit.math_functions.basis_function) LinearPrior (class in pcntoolkit.math_functions.prior) load() (in module pcntoolkit.dataio.fileio) (NormativeModel class method) load_and_execute() (in module pcntoolkit.util.runner) load_ascii() (in module pcntoolkit.dataio.fileio) load_centiles() (NormData method) load_cifti() (in module pcntoolkit.dataio.fileio) LOAD_CIFTI_GENERIC_EXCEPTION (Warnings attribute) load_data() (in module pcntoolkit.normative) (Runner method) load_fcon1000() (in module pcntoolkit.dataio.data_factory) load_from_state() (Runner class method) load_idata() (HBR method) load_lifespan_big() (in module pcntoolkit.dataio.data_factory) load_logp() (NormData method) load_model() (Runner method) load_nifti() (in module pcntoolkit.dataio.fileio) LOAD_NIFTI_GENERIC_EXCEPTION (Warnings attribute) load_pd() (in module pcntoolkit.dataio.fileio) load_response_vars() (in module pcntoolkit.normative) load_results() (NormData method) load_statistics() (NormData method) load_test_data() (in module pcntoolkit.normative) load_zscores() (NormData method) LOADING_CALLABLE (Messages attribute) LOADING_DATA (Messages attribute) LOADING_DATA_NOT_SUPPORTED_FOR_CROSS_VALIDATION (Warnings attribute) LOADING_DATA_UNDER_KFOLD_CV (Messages attribute) LOADING_ROI_MASK (Messages attribute) LOADING_RUNNER_STATE (Messages attribute) log_dir (JobObserver attribute) (Runner attribute) LOG_DIR_CREATED (Messages attribute) loglik() (BLR method) logp() (SHASH method) (SHASHb method) (SHASHo method) (SHASHo2 method) M m (StandardScaler attribute), [1] m() (in module pcntoolkit.math_functions.shash) m1() (SHASH static method) m1m2() (in module pcntoolkit.math_functions.shash) (SHASH static method) m2() (SHASH static method) main() (in module pcntoolkit.normative) make_compatible() (NormData method) make_prior() (in module pcntoolkit.math_functions.prior) make_synthetic_data() (in module pcntoolkit.normative) map_batch_effects() (NormativeModel method) mapping (BasePrior attribute) mapping_params (BasePrior attribute) max (BasisFunction attribute) (MinMaxScaler attribute), [1] (RobustMinMaxScaler attribute) max_retries (Runner attribute) memory (Runner attribute) merge() (NormativeModel class method) (NormData method) Messages (class in pcntoolkit.util.output) migrate() (MigrationRegistry method) MigrationRegistry (class in pcntoolkit.util.migration) min (BasisFunction attribute) (MinMaxScaler attribute), [1] (RobustMinMaxScaler attribute) MinMaxScaler (class in pcntoolkit.math_functions.scaler) MISSING_COVARIATES (Warnings attribute) MODEL_MIGRATION_APPLIED (Warnings attribute) MODEL_SAVED_WITH_NEWER_VERSION (Warnings attribute) model_specific_evaluation() (BLR method) (HBR method) (NormativeModel method) (RegressionModel method) models_variance (BLR attribute) module pcntoolkit pcntoolkit.dataio pcntoolkit.dataio.data_factory pcntoolkit.dataio.fileio pcntoolkit.dataio.norm_data pcntoolkit.math_functions pcntoolkit.math_functions.basis_function pcntoolkit.math_functions.factorize pcntoolkit.math_functions.likelihood pcntoolkit.math_functions.prior pcntoolkit.math_functions.scaler pcntoolkit.math_functions.shash pcntoolkit.math_functions.thrive pcntoolkit.math_functions.warp pcntoolkit.normative pcntoolkit.normative_model pcntoolkit.regression_model pcntoolkit.regression_model.blr pcntoolkit.regression_model.factory pcntoolkit.regression_model.hbr pcntoolkit.regression_model.regression_model pcntoolkit.regression_model.test_model pcntoolkit.util pcntoolkit.util.autoscale_plot pcntoolkit.util.data_utils pcntoolkit.util.evaluator pcntoolkit.util.job_observer pcntoolkit.util.migration pcntoolkit.util.model_comparison pcntoolkit.util.output pcntoolkit.util.paths pcntoolkit.util.plotter pcntoolkit.util.runner mu (CenteredRandomPrior attribute) (NormalLikelihood attribute) (RandomPrior attribute) (SHASHbLikelihood attribute) (SHASHo2Likelihood attribute) (SHASHoLikelihood attribute) MULTIPLE_BATCH_EFFECT_SUMMARY (Warnings attribute) MULTIPLE_JOBS_FOUND_FOR_JOB_ID (Warnings attribute) my_K (SHASH attribute) N n_batches (Runner attribute) n_cores (Runner attribute) n_fit_observations (NormativeModel property) n_iter (BLR attribute) n_params (WarpAffine attribute) (WarpBase attribute) (WarpBoxCox attribute) (WarpCompose attribute) (WarpLog attribute) (WarpSinhArcsinh attribute) n_params() (Evaluator method) name (BasePrior attribute) (JobStatus attribute) (Likelihood attribute) (NormativeModel attribute) (NormData property) (RegressionModel property) (SHASHbRV attribute) (SHASHo2RV attribute) (SHASHoRV attribute) (SHASHrv attribute) nfunc_spec (Kv attribute) nknots (BsplineBasisFunction attribute) NO_COVARIATES (Warnings attribute) NO_FLOAT_DATA_TYPE (Errors attribute) NO_LOG_DIR_SPECIFIED (Messages attribute) NO_MORE_RUNNING_JOBS (Messages attribute) NO_PYTHON_PATH_SPECIFIED (Messages attribute) NO_RESPONSE_VARS (Warnings attribute) NO_TEMP_DIR_SPECIFIED (Messages attribute) nodes (JobStatus attribute) Normal_HBR() (in module pcntoolkit.regression_model.factory) NormalLikelihood (class in pcntoolkit.math_functions.likelihood) NORMATIVE_MODEL_CONFIGURATION_PROBLEMS (Errors attribute) NORMATIVE_MODEL_CONFIGURATION_VALID (Messages attribute) NormativeModel (class in pcntoolkit.normative_model) NormData (class in pcntoolkit.dataio.norm_data) nuts_sampler (HBR attribute) O offset_indices() (in module pcntoolkit.math_functions.thrive) OFFSET_NOT_VALID (Errors attribute) offsets (CenteredRandomPrior attribute) (RandomPrior attribute) OFFSETS_NOT_1D (Errors attribute) optimizer (BLR attribute) order (FractionalPolynomialBasisFunction attribute) Output (class in pcntoolkit.util.output) outscaler (NormativeModel attribute) outscalers (NormativeModel attribute) P P() (in module pcntoolkit.math_functions.shash) (SHASH static method) parallelize (Runner attribute) parse_hyps() (BLR method) parseWarpString() (in module pcntoolkit.math_functions.warp) parts (CompositeBasisFunction attribute) path (in module pcntoolkit.dataio.fileio), [1] pcntoolkit module pcntoolkit.dataio module pcntoolkit.dataio.data_factory module pcntoolkit.dataio.fileio module pcntoolkit.dataio.norm_data module pcntoolkit.math_functions module pcntoolkit.math_functions.basis_function module pcntoolkit.math_functions.factorize module pcntoolkit.math_functions.likelihood module pcntoolkit.math_functions.prior module pcntoolkit.math_functions.scaler module pcntoolkit.math_functions.shash module pcntoolkit.math_functions.thrive module pcntoolkit.math_functions.warp module pcntoolkit.normative module pcntoolkit.normative_model module pcntoolkit.regression_model module pcntoolkit.regression_model.blr module pcntoolkit.regression_model.factory module pcntoolkit.regression_model.hbr module pcntoolkit.regression_model.regression_model module pcntoolkit.regression_model.test_model module pcntoolkit.util module pcntoolkit.util.autoscale_plot module pcntoolkit.util.data_utils module pcntoolkit.util.evaluator module pcntoolkit.util.job_observer module pcntoolkit.util.migration module pcntoolkit.util.model_comparison module pcntoolkit.util.output module pcntoolkit.util.paths module pcntoolkit.util.plotter module pcntoolkit.util.runner module penalized_loglik() (BLR method) Phi_Phi_var() (BLR method) plot_centiles() (in module pcntoolkit.util.plotter) plot_centiles_advanced() (in module pcntoolkit.util.plotter) plot_qq() (in module pcntoolkit.util.plotter) plot_ridge() (in module pcntoolkit.util.plotter) PM_DISTMAP (in module pcntoolkit.math_functions.prior) PolynomialBasisFunction (class in pcntoolkit.math_functions.basis_function) post() (BLR method) postprocess() (NormativeModel method) power_set (FractionalPolynomialBasisFunction attribute) preamble (Runner attribute) predict() (in module pcntoolkit.normative) (NormativeModel method) (Runner method) predict_and_adjust() (BLR method) PREDICT_DATA_NOT_USED_IN_KFOLD_CROSS_VALIDATION (Warnings attribute) PREDICTING_MODEL (Messages attribute) PREDICTING_MODELS (Messages attribute) prepare() (Evaluator method) preprocess() (NormativeModel method) print() (Output class method) Prior (class in pcntoolkit.math_functions.prior) prior_from_args() (in module pcntoolkit.math_functions.prior) progressbar (HBR attribute) pymc_model (HBR attribute) R RandomPrior (class in pcntoolkit.math_functions.prior) re_submit_failed_jobs() (Runner method) register() (MigrationRegistry method) register_batch_effects() (NormativeModel method) (NormData method) register_data_info() (NormativeModel method) register_fold_indices() (Runner method) registry (in module pcntoolkit.util.migration) regmodel_dict (RegressionModel property) REGRESSION_MODEL_CONFIGURATION_PROBLEMS (Errors attribute) REGRESSION_MODEL_CONFIGURATION_VALID (Messages attribute) regression_models (NormativeModel attribute) RegressionModel (class in pcntoolkit.regression_model.regression_model) remove_nan() (NormData class method) REMOVE_NAN_SET_TO_FALSE (Warnings attribute) remove_outliers() (NormData class method) RENAMED (Warnings attribute) reset() (Evaluator method) response_var_list (NormData property) RESPONSE_VAR_NOT_FOUND (Warnings attribute) response_vars (Evaluator attribute), [1] (NormativeModel attribute) right_expand (BsplineBasisFunction attribute) rng_fn() (SHASHbRV class method) (SHASHo2RV class method) (SHASHoRV class method) (SHASHrv class method) RobustMinMaxScaler (class in pcntoolkit.math_functions.scaler) Runner (class in pcntoolkit.util.runner) RUNNER_LOADED (Messages attribute) rv_op (SHASH attribute) (SHASHb attribute) (SHASHo attribute) (SHASHo2 attribute) S s (StandardScaler attribute), [1] S() (in module pcntoolkit.math_functions.shash) S_inv() (in module pcntoolkit.math_functions.shash) SAMPLE_BATCH_EFFECTS (Errors attribute) sample_batch_effects() (NormativeModel method) sample_covariates() (NormativeModel method) sample_dims (BasePrior attribute) (CenteredRandomPrior attribute) (LinearPrior attribute) (Prior attribute) (RandomPrior attribute) save() (in module pcntoolkit.dataio.fileio) (NormativeModel method) (Runner method) save_ascii() (in module pcntoolkit.dataio.fileio) save_callable_and_data() (Runner method) save_centiles() (NormData method) save_cifti() (in module pcntoolkit.dataio.fileio) save_dir (NormativeModel property) (Runner attribute) save_idata() (HBR method) save_logp() (NormData method) save_nifti() (in module pcntoolkit.dataio.fileio) save_pd() (in module pcntoolkit.dataio.fileio) save_results() (NormData method) save_statistics() (NormData method) save_zscores() (NormData method) savemodel (NormativeModel attribute) saveplots (NormativeModel attribute) saveresults (NormativeModel attribute) SAVING_CENTILES (Messages attribute) SAVING_MODEL (Messages attribute) SAVING_RESULTS (Messages attribute) SAVING_RUNNER_STATE (Messages attribute) SAVING_STATISTICS (Messages attribute) SAVING_ZSCORES (Messages attribute) scale_backward() (NormativeModel method) (NormData method) scale_forward() (NormativeModel method) (NormData method) scaled_offsets (CenteredRandomPrior attribute) (RandomPrior attribute) Scaler (class in pcntoolkit.math_functions.scaler) select_batch_effects() (NormData method) set_ensure_save_dirs() (NormativeModel method) set_name() (BasePrior method) (CenteredRandomPrior method) (LinearPrior method) (Prior method) (RandomPrior method) set_save_dir() (NormativeModel method) set_show_messages() (Output class method) set_show_pid() (Output class method) set_show_timestamp() (Output class method) set_show_warnings() (Output class method) set_task_id() (Runner method) SHASH (class in pcntoolkit.math_functions.shash) shash (in module pcntoolkit.math_functions.shash) SHASHb (class in pcntoolkit.math_functions.shash) shashb (in module pcntoolkit.math_functions.shash) SHASHb1_HBR() (in module pcntoolkit.regression_model.factory) SHASHb2_HBR() (in module pcntoolkit.regression_model.factory) SHASHbLikelihood (class in pcntoolkit.math_functions.likelihood) SHASHbRV (class in pcntoolkit.math_functions.shash) SHASHo (class in pcntoolkit.math_functions.shash) shasho (in module pcntoolkit.math_functions.shash) SHASHo2 (class in pcntoolkit.math_functions.shash) shasho2 (in module pcntoolkit.math_functions.shash) SHASHo2Likelihood (class in pcntoolkit.math_functions.likelihood) SHASHo2RV (class in pcntoolkit.math_functions.shash) SHASHoLikelihood (class in pcntoolkit.math_functions.likelihood) SHASHoRV (class in pcntoolkit.math_functions.shash) SHASHrv (class in pcntoolkit.math_functions.shash) show_job_status_monitor() (JobObserver method) sigma (CenteredRandomPrior attribute) (NormalLikelihood attribute) (RandomPrior attribute) (SHASHbLikelihood attribute) (SHASHo2Likelihood attribute) (SHASHoLikelihood attribute) sigmas (CenteredRandomPrior attribute) (RandomPrior attribute) signature (SHASHbRV attribute) (SHASHo2RV attribute) (SHASHoRV attribute) (SHASHrv attribute) slope (LinearPrior attribute) st_impl() (Kv static method) StandardScaler (class in pcntoolkit.math_functions.scaler) state (JobStatus attribute) SUBJECT_ID_MULTIPLE_COLUMNS (Warnings attribute) SUBJECT_ID_UNEXPECTED_SHAPE (Warnings attribute) submit_jobs() (Runner method) success_file_exists (JobStatus attribute) success_ratio (TestModel attribute) synthesize() (NormativeModel method) SYNTHESIZE_N_SAMPLES_IGNORED (Warnings attribute) SYNTHESIZING_DATA (Messages attribute) SYNTHESIZING_DATA_MODEL (Messages attribute) T tail (RobustMinMaxScaler attribute), [1] task_id (JobObserver attribute) (Runner attribute) TASK_ID_CREATED (Messages attribute) temp_dir (Runner attribute) TEMP_DIR_CREATED (Messages attribute) template_regression_model (NormativeModel attribute) TestModel (class in pcntoolkit.regression_model.test_model) thrive_covariate (NormativeModel attribute) THRIVELINES_ALREADY_COMPUTED_FOR (Warnings attribute) time (JobStatus attribute) time_limit_seconds (Runner attribute) time_limit_str (Runner attribute) to_dataframe() (NormData method) to_dict() (BasePrior method) (BasisFunction method) (BetaLikelihood method) (BLR method) (BsplineBasisFunction method) (CenteredRandomPrior method) (CompositeBasisFunction method) (FractionalPolynomialBasisFunction method) (HBR method) (IdentityScaler method) (Likelihood method) (LinearPrior method) (MinMaxScaler method) (NormalLikelihood method) (NormativeModel method) (Prior method) (RandomPrior method) (RegressionModel method) (RobustMinMaxScaler method) (Scaler method) (SHASHbLikelihood method) (SHASHo2Likelihood method) (SHASHoLikelihood method) (StandardScaler method) (TestModel method) to_netcdf() (NormData method) tol (BLR attribute) TOO_FEW_OBSERVATIONS (Warnings attribute) train_test_split() (NormData method) transfer() (BasePrior method) (BetaLikelihood method) (BLR method) (CenteredRandomPrior method) (HBR method) (Likelihood method) (LinearPrior method) (NormalLikelihood method) (NormativeModel method) (Prior method) (RandomPrior method) (RegressionModel method) (Runner method) (SHASHbLikelihood method) (TestModel method) TRANSFER_DATA_FEWER_BATCH_EFFECTS (Warnings attribute) transfer_predict() (NormativeModel method) (Runner method) transfered (RegressionModel attribute) TRANSFERRING_MODEL (Messages attribute) TRANSFERRING_MODELS (Messages attribute) transform() (BasisFunction method) (CompositeBasisFunction method) (IdentityScaler method) (MinMaxScaler method) (Scaler method) (StandardScaler method) tune (HBR attribute) U unique_batch_effects (NormativeModel attribute) unique_log_dir (Runner attribute) unique_temp_dir (Runner attribute) UNKNOWN_BATCH_EFFECTS (Warnings attribute) UNKNOWN_FILE_TYPE (Errors attribute) update_data() (BasePrior method) (CenteredRandomPrior method) (Likelihood method) (LinearPrior method) (Prior method) (RandomPrior method) V vol2vec() (in module pcntoolkit.dataio.fileio) W wait_for_jobs() (JobObserver method) wait_or_finish() (Runner method) warning() (Output class method) Warnings (class in pcntoolkit.util.output) warp_name (BLR attribute) warp_predictions() (WarpBase method) warp_reparam (BLR attribute) WarpAffine (class in pcntoolkit.math_functions.warp) WarpBase (class in pcntoolkit.math_functions.warp) WarpBoxCox (class in pcntoolkit.math_functions.warp) WarpCompose (class in pcntoolkit.math_functions.warp) warped_BLR() (in module pcntoolkit.regression_model.factory) WarpLog (class in pcntoolkit.math_functions.warp) warps (WarpCompose attribute) WarpSinhArcsinh (class in pcntoolkit.math_functions.warp) WB_COMMAND_FAILED (Errors attribute) WB_COMMAND_NOT_FOUND (Errors attribute) wrap_in_job() (Runner method) wrap_in_slurm_job() (Runner method) wrap_in_torque_job() (Runner method) X X (NormData attribute) Y y (NormData attribute) y_transform (NormativeModel attribute) yhat() (BetaLikelihood method) (Likelihood method) (NormalLikelihood method) (SHASHbLikelihood method) ys_s2() (BLR method) Z Z (NormData attribute)
