CDR package documentation

Documentation for the cdr Python package.

Contents:

• Introduction
  • Installation (PyPI)
  • Installation (Anaconda)
  • Basic Usage
  • References
• Getting Started
  • Configuring CDR Experiments
  • Running CDR executables
  • Training CDR Models
  • Evaluating and Testing CDR Models
• CDR Configuration Files
  • Section: [data]
  • Section: [global_settings]
  • Section: [cdr_settings]
    • All Models
    • Variational Bayes
    • Neural Network Components
    • Variational Bayesian Neural Network Components
  • Section: [irf_name_map]
  • Sections: [model_CDR_*]
• CDR Model Formulas
  • Basic Overview
  • CDR Model Formulas
    • Linear (DiracDelta) Predictors
    • Defining an Impulse Response Function (IRF)
    • Supported Parametric IRFs
    • Interactions in CDR
    • Automatic Term Expansion
    • Random Effects
    • Parameter Initialization
    • Using Constant (Non-trainable) Parameters
    • Parameter Tying
    • Transforming Variables
    • Pseudo Non-Parametric IRFs
    • IRF Composition
  • Neural Network Components
  • Multivariate Responses
• IRF Trees in CDR
  • Factorization
  • IRF composition
  • Parameter tying
  • CDR tree summaries
• CDR Package API
  • cdr.backend module
  • cdr.config module
    • Config
      • Config.build_cdr_settings()
      • Config.expand_submodels()
      • Config.set_model()
    • PlotConfig
      • PlotConfig.build_plot_settings()
  • cdr.data module
    • add_responses()
    • build_CDR_impulse_data()
    • build_CDR_response_data()
    • c()
    • compare_elementwise_perf()
    • compute_filter()
    • compute_filters()
    • compute_partition()
    • compute_splitID()
    • compute_time_mask()
    • corr_cdr()
    • expand_impulse_sequence()
    • filter_invalid_responses()
    • get_first_last_obs_lists()
    • get_rangf_array()
    • get_time_windows()
    • preprocess_data()
    • s()
    • split_cdr_outputs()
    • z()
  • cdr.formula module
    • Formula
      • Formula.ablate_impulses()
      • Formula.apply_formula()
      • Formula.apply_op()
      • Formula.apply_op_2d()
      • Formula.apply_ops()
      • Formula.apply_ops_2d()
      • Formula.bases()
      • Formula.build()
      • Formula.categorical_transform()
      • Formula.compute_2d_predictor()
      • Formula.initialize_nns()
      • Formula.insert_impulses()
      • Formula.irf_params()
      • Formula.is_LCG()
      • Formula.pc_transform()
      • Formula.process_ast()
      • Formula.process_irf()
      • Formula.re_transform()
      • Formula.remove_impulses()
      • Formula.response_names()
      • Formula.responses()
      • Formula.to_lmer_formula_string()
      • Formula.to_string()
      • Formula.unablate_impulses()
    • IRFNode
      • IRFNode.ablate_impulses()
      • IRFNode.add_child()
      • IRFNode.add_interactions()
      • IRFNode.add_rangf()
      • IRFNode.atomic_irf_by_family()
      • IRFNode.atomic_irf_param_init_by_family()
      • IRFNode.atomic_irf_param_trainable_by_family()
      • IRFNode.bases()
      • IRFNode.categorical_transform()
      • IRFNode.coef2impulse()
      • IRFNode.coef2terminal()
      • IRFNode.coef_by_rangf()
      • IRFNode.coef_id()
      • IRFNode.coef_names()
      • IRFNode.depth()
      • IRFNode.fixed_coef_names()
      • IRFNode.fixed_interaction_names()
      • IRFNode.formula_terms()
      • IRFNode.has_coefficient()
      • IRFNode.has_composed_irf()
      • IRFNode.has_irf()
      • IRFNode.impulse2coef()
      • IRFNode.impulse2terminal()
      • IRFNode.impulse_names()
      • IRFNode.impulse_set()
      • IRFNode.impulses()
      • IRFNode.impulses_by_name()
      • IRFNode.impulses_from_response_interaction()
      • IRFNode.interaction_by_rangf()
      • IRFNode.interaction_names()
      • IRFNode.interactions()
      • IRFNode.interactions2inputs()
      • IRFNode.irf_by_rangf()
      • IRFNode.irf_id()
      • IRFNode.irf_to_formula()
      • IRFNode.is_LCG()
      • IRFNode.local_name()
      • IRFNode.name()
      • IRFNode.nns_by_key()
      • IRFNode.node_table()
      • IRFNode.nonparametric_coef_names()
      • IRFNode.pointers2namemmaps()
      • IRFNode.re_transform()
      • IRFNode.remove_impulses()
      • IRFNode.supports_non_causal()
      • IRFNode.terminal()
      • IRFNode.terminal2coef()
      • IRFNode.terminal2impulse()
      • IRFNode.terminal_names()
      • IRFNode.terminals()
      • IRFNode.terminals_by_name()
      • IRFNode.unablate_impulses()
      • IRFNode.unary_nonparametric_coef_names()
    • Impulse
      • Impulse.categorical()
      • Impulse.expand_categorical()
      • Impulse.expand_re()
      • Impulse.get_matcher()
      • Impulse.is_nn_impulse()
      • Impulse.name()
    • ImpulseInteraction
      • ImpulseInteraction.expand_categorical()
      • ImpulseInteraction.expand_re()
      • ImpulseInteraction.impulses()
      • ImpulseInteraction.is_nn_impulse()
      • ImpulseInteraction.name()
    • NN
      • NN.all_impulse_names()
      • NN.input_impulse_names()
      • NN.name()
      • NN.output_impulse_names()
    • NNImpulse
      • NNImpulse.expand_categorical()
      • NNImpulse.expand_re()
      • NNImpulse.impulses()
      • NNImpulse.is_nn_impulse()
      • NNImpulse.name()
    • ResponseInteraction
      • ResponseInteraction.add_rangf()
      • ResponseInteraction.contains_member()
      • ResponseInteraction.dirac_delta_responses()
      • ResponseInteraction.irf_responses()
      • ResponseInteraction.name()
      • ResponseInteraction.nn_impulse_responses()
      • ResponseInteraction.replace()
      • ResponseInteraction.responses()
    • pythonize_string()
    • standardize_formula_string()
  • cdr.io module
    • read_tabular_data()
  • cdr.kwargs module
    • Kwarg
      • Kwarg.dtypes_str()
      • Kwarg.get_type_name()
      • Kwarg.in_settings()
      • Kwarg.kwarg_from_config()
      • Kwarg.type_comparator()
    • cdr_kwarg_docstring()
    • docstring_from_kwarg()
    • plot_kwarg_docstring()
  • cdr.model module
  • cdr.opt module
  • cdr.plot module
    • plot_heatmap()
    • plot_irf()
    • plot_irf_as_heatmap()
    • plot_qq()
    • plot_surface()
  • cdr.signif module
    • correlation_test()
    • permutation_test()
  • cdr.synth module
    • SyntheticModel
      • SyntheticModel.convolve()
      • SyntheticModel.convolve_v2()
      • SyntheticModel.get_curves()
      • SyntheticModel.irf()
      • SyntheticModel.plot_irf()
      • SyntheticModel.sample_data()
  • cdr.util module
    • filter_models()
    • filter_names()
    • get_random_permutation()
    • load_cdr()
    • mae()
    • mse()
    • names2ix()
    • nested()
    • pca()
    • percent_variance_explained()
    • reg_name()
    • sn()
• CDR Visualizer

Indices

• Index