Tools for Applying Catalytic Priors in Statistical Modeling

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Documentation for package ‘catalytic’ version 0.1.0

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cat_cox Catalytic Cox Proportional Hazards Model (COX) Fitting Function with Fixed Tau
cat_cox_bayes Bayesian Estimation for Catalytic Cox Proportional-Hazards Model (COX) with Fixed tau
cat_cox_bayes_joint Bayesian Estimation for Catalytic Cox Proportional-Hazards Model (COX) with adaptive tau
cat_cox_initialization Initialization for Catalytic Cox proportional hazards model (COX)
cat_cox_tune Catalytic Cox Proportional-Hazards Model (COX) Fitting Function by Tuning tau from a Sequence of tau Values
cat_glm Catalytic Generalized Linear Models (GLMs) Fitting Function with Fixed Tau
cat_glm_bayes Bayesian Estimation for Catalytic Generalized Linear Models (GLMs) with Fixed tau
cat_glm_bayes_joint Bayesian Estimation for Catalytic Generalized Linear Models (GLMs) with adaptive tau
cat_glm_bayes_joint_gibbs Bayesian Estimation with Gibbs Sampling for Catalytic Generalized Linear Models (GLMs) Binomial Family for Coefficients and tau
cat_glm_initialization Initialization for Catalytic Generalized Linear Models (GLMs)
cat_glm_tune Catalytic Generalized Linear Models (GLMs) Fitting Function by Tuning tau from a Sequence of tau Values
cat_lmm Catalytic Linear Mixed Model (LMM) Fitting Function with fixed tau
cat_lmm_initialization Initialization for Catalytic Linear Mixed Model (LMM)
cat_lmm_tune Catalytic Linear Mixed Model (LMM) Fitting Function by Tuning tau from a Sequence of tau Values
cross_validation Perform Cross-Validation for Model Estimation
cross_validation_cox Perform Cross-Validation for Catalytic Cox Proportional-Hazards Model (COX) to Select Optimal tau
cross_validation_lmm Perform Cross-Validation for Catalytic Linear Mixed Model (LMM) to Select Optimal tau
extract_coefs Extract and Format Model Coefficients
extract_dim Extract Dimension Information from Model Initialization
extract_stan_summary Extract and Format Summary of Stan Model Results
extract_tau_seq Extract and Format Sequence of Tau Values
get_adjusted_cat_init Adjusted Cat Initialization
get_cox_gradient Compute the Gradient for Cox Proportional Hazards Model
get_cox_hessian Compute the Hessian Matrix for Cox Proportional Hazards Model
get_cox_kappa Estimate the kappa value for the synthetic Cox proportional hazards model
get_cox_partial_likelihood Compute the Partial Likelihood for the Cox Proportional Hazards Model
get_cox_qr_solve Solve Linear System using QR Decomposition
get_cox_risk_and_failure_sets Calculate Risk and Failure Sets for Cox Proportional Hazards Model
get_cox_risk_set_idx Identify the risk set indices for Cox proportional hazards model
get_cox_syn_gradient Compute the gradient of the synthetic Cox proportional hazards model
get_cox_syn_hessian Compute the Synthetic Hessian Matrix for Cox Proportional Hazards Model
get_discrepancy Compute Discrepancy Measures
get_formula_lhs Extract Left-Hand Side of Formula as String
get_formula_rhs Extract the Right-Hand Side of a Formula
get_formula_string Convert Formula to String
get_glm_custom_var Get Custom Variance for Generalized Linear Model (GLM)
get_glm_diag_approx_cov Compute Diagonal Approximate Covariance Matrix
get_glm_family_string Retrieve GLM Family Name or Name with Link Function
get_glm_lambda Compute Lambda Based on Discrepancy Method
get_glm_log_density Compute Log Density Based on GLM Family
get_glm_log_density_grad Compute Gradient of Log Density for GLM Families
get_glm_mean Compute Mean Based on GLM Family
get_glm_sample_data Generate Sample Data for GLM
get_hmc_mcmc_result Run Hamiltonian Monte Carlo to Get MCMC Sample Result
get_linear_predictor Compute Linear Predictor
get_resampled_df Resampling Methods for Data Processing
get_standardized_data Standardize Data
get_stan_model Generate Stan Model Based on Specified Parameters
hmc_neal_2010 Hamiltonian Monte Carlo (HMC) Implementation
is.continuous Check if a Variable is Continuous
mallowian_estimate Perform Mallowian Estimate for Model Risk (Only Applicable for Gaussian Family)
parametric_bootstrap Perform Parametric Bootstrap for Model Risk Estimation
plot.cat_tune Plot Likelihood or Risk Estimate vs. Tau for Tuning Model
predict.cat_cox Predict Linear Predictor for New Data Using a Fitted Cox Model
predict.cat_glm Predict Outcome for New Data Using a Fitted GLM Model
predict.cat_lmm Predict Linear Predictor for New Data Using a Fitted Linear Mixed Model
print.cat Print Method for 'cat' Object
print.cat_bayes Print Summary of 'cat_bayes' Model
print.cat_gibbs Print Summary of 'cat_gibbs' Model
print.cat_initialization Print Summary for Catalytic Initialization Model
print.cat_tune Print Method for 'cat_tune' Object
print_df_head_tail Print Data Frame with Head and Tail Rows
print_glm_bayes_joint_binomial_suggestion Generate Suggestions for Bayesian Joint Binomial GLM Parameter Estimation
steinian_estimate Perform Steinian Estimate for Model Risk (Only Applicable for Binomial Family)
swim Simulated SWIM Dataset with Binary Response
traceplot Traceplot for Bayesian Model Sampling
traceplot.cat_bayes Traceplot for Bayesian Sampling Model
traceplot.cat_gibbs Traceplot for Gibbs Sampling Model
update_lmm_variance Calculates the log-likelihood for linear mixed models (LMMs) by combining observed and synthetic log-likelihoods based on the variance parameters.
validate_cox_initialization_input Validate Inputs for Catalytic Cox proportional hazards model (COX) Initialization
validate_cox_input Validate Inputs for Catalytic Cox Model
validate_glm_initialization_input Validate Inputs for Catalytic Generalized Linear Models (GLMs) Initialization
validate_glm_input Validate Inputs for Catalytic Generalized Linear Models (GLMs)
validate_lmm_initialization_input Validate Inputs for Catalytic Linear Mixed Model (LMM) Initialization
validate_lmm_input Validate Inputs for Catalytic Linear Mixed Model (LMM)
validate_positive Validate Positive or Non-negative Parameter