Experimental Design and Inference

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Documentation for package ‘EDI’ version 1.0.2

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B C D E F G I K L M P R S T U

EDI-package Experimental Design and Inference

-- B --

build_cox_data_cache_cpp Build a Reusable Unstratified Cox Data Cache (C++ Backend)
build_stratified_cox_data_cache_cpp Build a Reusable Stratified Cox Data Cache (C++ Backend)

-- C --

clear_local_EDI_optimization Delete this machine's saved EDI tuning and return to shipped defaults

-- D --

DesignFixedBernoulli A Fixed-Sample-Size Bernoulli (Independent-Coin-Flip) Randomized Design
DesignFixedBinaryMatch A Fixed, Non-Bipartite-Matched-Pair Design with Within-Pair Randomization
DesignFixedBlockedCluster A Fixed, Blocked-and-Clustered Randomized Design
DesignFixedBlocking A Fixed, Stratified-Block Randomized Design
DesignFixedCluster A Fixed, Unblocked Cluster Randomized Design
DesignFixedFactorial A Fixed, Balanced Two-Arm Factorial Design
DesignFixedGreedy A Fixed, Covariate-Balanced Design via Greedy Pairwise-Swap Search
DesignFixedGreedyDOptimal A Fixed, Model-Based Optimal Design via Greedy Pairwise-Exchange Search
DesignFixediBCRD A Fixed, Individually Balanced Completely Randomized Design (iBCRD)
DesignFixedMatchingGreedyPairSwitching A Fixed, Matched-Pair Design with Greedy Which-Member-Treated Optimization
DesignFixedOptimal A Fixed, Deterministic Single-Allocation Optimal Design
DesignFixedOptimalBlocks A Fixed, Covariate-Homogeneous-Block Randomized Design
DesignFixedRerandomization A Fixed Rerandomization Design (Rejection-Sampled on Covariate Balance)
DesignSeqOneByOneAtkinson Atkinson's (1982) Covariate-Adjusted Biased Coin Sequential Design
DesignSeqOneByOneBernoulli A Sequential Bernoulli (Independent-Coin-Flip) Randomized Design
DesignSeqOneByOneEfron Efron's (1971) Biased Coin Sequential Design
DesignSeqOneByOneiBCRD A Sequential Design Guaranteeing Exact Terminal Balance (Random Allocation Rule)
DesignSeqOneByOneKK14 Kapelner and Krieger's (2014) Sequential "Matching-on-the-Fly" Design
DesignSeqOneByOneKK21 Kapelner and Krieger's (2021) Outcome-Weighted Sequential Matching-on-the-Fly Design
DesignSeqOneByOneKK21stepwise Stepwise Variant of the KK21 Outcome-Weighted Sequential Matching Design
DesignSeqOneByOnePocockSimon Pocock and Simon's (1975) Minimization Sequential Design
DesignSeqOneByOneRandomBlockSize A Sequential Permuted-Block Design with Randomly Varying Block Sizes
DesignSeqOneByOneSPBR A Stratified Permuted-Block Sequential Design (SPBR) with Fixed Block Size
DesignSeqOneByOneUrn Wei's (1977, 1978) Adaptive Urn Sequential Design, UD(alpha, beta)

-- E --

EDI Experimental Design and Inference
edi_build_info_cpp Return EDI Build Information (C++ Backend)
EDI_COMPREHENSIVE_SLOW_PATHS Comprehensive-test slow-path registry
exact_jonckheere_terpstra_pval_cpp Exact Two-Group Jonckheere-Terpstra Test via Full Randomization Enumeration (C++ Backend)

-- F --

fast_beta_regression Fast Beta Regression (R Wrapper)
fast_beta_regression_with_var Fast Beta Regression with Variance Calculation (R Wrapper)
fast_coxph_regression Fast Cox Proportional Hazards Regression (R Wrapper)
fast_coxph_regression_cpp Fast Cox Proportional Hazards Regression, One-Shot Fit (C++ Backend)
fast_coxph_regression_prebuilt_cpp Fast Cox Proportional Hazards Regression, Cache-Reusing Fit (C++ Backend)
fast_logistic_regression Fast Logistic Regression, Estimate Only (R Wrapper)
fast_logistic_regression_cpp Fast Logistic Regression, Estimate Only (C++ Backend)
fast_logistic_regression_weighted_cpp Fast Weighted Logistic Regression, Estimate Only (C++ Backend)
fast_logistic_regression_with_var Fast Logistic Regression with Variance, Auto-Retrying on Separation (R Wrapper)
fast_logistic_regression_with_var_cpp Fast Logistic Regression with Targeted Variance (C++ Backend)
fast_negbin_regression Fast Negative Binomial Regression, Estimate-Only (R Wrapper)
fast_negbin_regression_with_var Fast Negative Binomial Regression with Variance Calculation (R Wrapper)
fast_ols_cpp Fast Ordinary Least Squares (OLS) Regression, Estimate-Only (C++ Backend)
fast_ols_with_var_cpp Fast Ordinary Least Squares (OLS) Regression with Variance (C++ Backend)
fast_poisson_regression_cpp Fast Poisson Regression, Estimate-Only (C++ Backend)
fast_poisson_regression_weighted_cpp Fast Weighted Poisson Regression (C++ Backend)
fast_poisson_regression_with_var_cpp Fast Poisson Regression with Variance Calculation (C++ Backend)
fast_quasipoisson_regression_with_var_cpp Fast Quasi-Poisson Regression with Variance Calculation (C++ Backend)
fast_weibull_regression Fast Weibull AFT Regression (R Wrapper: Rcpp Backend or 'survival')

-- G --

generate_covariate_dataset Generate Synthetic Simulation Covariates and Continuous Response
get_bootstrap_dispatch_policy Get the default bootstrap dispatch policy
get_cold_start_dispatch_policy Get the default cold-start dispatch policy
get_local_EDI_optimization Show this machine's saved EDI tuning, if any
get_optimization_dispatch_policy Get the default optimization dispatch policy
get_parallel_dispatch_policy Get the default parallel dispatch policy
get_warm_start_dispatch_policy Get the default warm-start dispatch policy

-- I --

InferenceAllKKMeanDiffIVWC Mean-Difference IVWC Inference for KK Matching-on-the-Fly Designs
InferenceAllKKWilcoxIVWC Non-parametric Wilcoxon-based Compound Inference for KK Matching-on-the-Fly Designs
InferenceAllSimpleAverageDiff Simple Mean-Difference Inference for Continuous Responses
InferenceAllSimpleMeanDiffPooledVar Simple Mean-Difference Inference with Pooled Variance
InferenceAllSimpleWilcox Simple Wilcoxon Rank-Sum (Hodges-Lehmann) Inference
InferenceBaiAdjustedTKK14 Bai Adjusted-t Mean-Difference Inference for KK14 Designs
InferenceBaiAdjustedTKK21 Bai Adjusted-t Mean-Difference Inference for KK21 Designs
InferenceContinKKGLMM Linear Mixed Model Inference for KK Designs with Continuous Response
InferenceContinKKOLSIVWC OLS IVWC Compound Inference for KK Designs
InferenceContinKKOLSOneLik OLS Combined-Likelihood Inference for KK Designs
InferenceContinKKQuantileRegrIVWC Quantile Regression Compound Estimator for KK Matching-on-the-Fly Designs
InferenceContinKKQuantileRegrOneLik Quantile Regression Combined-Likelihood Compound Estimator for KK Designs (Continuous)
InferenceContinKKRobustRegrIVWC Robust-Regression IVWC Compound Inference for KK Designs
InferenceContinKKRobustRegrOneLik Robust-Regression Combined-Likelihood Inference for KK Designs
InferenceContinLin Lin (2013) Covariate-Adjusted OLS Inference for Continuous Responses
InferenceContinOLS OLS Inference for Continuous Responses
InferenceContinQuantileRegr Quantile Regression Inference for Continuous Responses
InferenceContinRobustRegr Robust (M/MM-Estimator) Regression Inference for Continuous Responses
InferenceCountHurdleNegBin Hurdle Negative Binomial Regression Inference for Count Responses
InferenceCountHurdlePoisson Hurdle Poisson Regression Inference for Count Responses
InferenceCountKKCondPoissonOneLik One-Likelihood Conditional-Poisson Inference for KK Count Designs
InferenceCountKKGLMM GLMM Inference for KK Designs with Count Response
InferenceCountKKHurdlePoissonIVWC KK Hurdle Poisson IVWC Inference for Count Responses
InferenceCountKKHurdlePoissonOneLik KK Hurdle-Poisson Combined-Likelihood Inference for Count Responses
InferenceCountNegBin Negative Binomial Regression Inference for Count Responses
InferenceCountPoisson Poisson Regression Inference for Count Responses
InferenceCountPoissonKKGEE GEE Inference for KK Designs with Count Response
InferenceCountQuasiPoisson Quasi-Poisson Regression Inference for Count Responses
InferenceCountRobustPoisson Robust (Sandwich-Variance) Poisson Regression Inference for Count Responses
InferenceCountZeroInflatedNegBin Zero-Inflated Negative Binomial Regression Inference for Count Responses
InferenceCountZeroInflatedPoisson Zero-Inflated Poisson Regression Inference for Count Responses
InferenceIncidBinomialIdentityRiskDiff Binomial Identity Risk Difference Inference for Incidence Responses
InferenceIncidCMH CMH Blocked Incidence Inference
InferenceIncidExactBinomial Exact Binomial (McNemar-Type) Incidence Inference for Matched-Pair Designs
InferenceIncidExactFisher Exact Fisher (Conditional Hypergeometric) Incidence Inference
InferenceIncidExactZhang Exact Zhang Combined-Test Incidence Inference
InferenceIncidExtendedRobins Extended Robins Blocked Incidence Inference
InferenceIncidGCompRiskDiff G-Computation Risk-Difference Inference for Binary Responses
InferenceIncidGCompRiskRatio G-Computation Risk-Ratio Inference for Binary Responses
InferenceIncidKKCondLogitGLMMIVWC Conditional Logistic Plus GLMM IVWC Inference for KK Designs
InferenceIncidKKCondLogitGLMMOneLik Conditional Logistic Plus GLMM Combined-Likelihood Inference for KK Designs
InferenceIncidKKCondLogitIVWC Conditional Logistic IVWC Inference (KK Designs, Binary Response)
InferenceIncidKKCondLogitOneLik One-Likelihood Conditional-Logistic Inference for KK Binary Designs
InferenceIncidKKGCompRiskDiff G-Computation Risk-Difference Inference for KK Designs with Binary Responses
InferenceIncidKKGCompRiskRatio G-Computation Risk-Ratio Inference for KK Designs with Binary Responses
InferenceIncidKKGEE GEE Inference for KK Designs with Binary Response
InferenceIncidKKModifiedPoisson Modified-Poisson Inference for KK Designs with Binary Responses
InferenceIncidKKNewcombeRiskDiff KK Newcombe Risk-Difference IVWC Inference for Binary Responses
InferenceIncidLogBinomial Log-Binomial Regression Inference for Incidence Responses
InferenceIncidLogRegr Logistic Regression Inference for Incidence Responses
InferenceIncidMiettinenNurminenRiskDiff Miettinen-Nurminen Risk-Difference Inference for Binary Responses
InferenceIncidModifiedPoisson Modified Poisson Regression Inference for Incidence Responses
InferenceIncidNewcombeRiskDiff Newcombe Risk-Difference Inference for Binary Responses
InferenceIncidProbitRegr Probit Regression Inference for Incidence Responses
InferenceIncidRiskDiff Risk Difference Inference for Incidence Responses
InferenceIncidWald Wald Incidence Inference
InferenceOrdinalAdjCatLogitRegr Adjacent Category Logit Regression Inference for Ordinal Responses
InferenceOrdinalCauchitRegr Cauchit Regression Inference for Ordinal Responses
InferenceOrdinalCloglogRegr Cumulative Cloglog Inference for Ordinal Responses
InferenceOrdinalContRatioRegr Continuation Ratio Regression Inference for Ordinal Responses
InferenceOrdinalGCompMeanDiff G-Computation Mean-Difference Inference for Ordinal Responses
InferenceOrdinalJonckheereTerpstraTest Jonckheere-Terpstra (JT) Test for Ordinal Responses
InferenceOrdinalKKCLMM Ordinal KK CLMM (Proportional Odds / logit link)
InferenceOrdinalKKCLMMCauchit Ordinal KK CLMM (Cauchit link)
InferenceOrdinalKKCLMMCloglog Ordinal KK CLMM (Complementary log-log link)
InferenceOrdinalKKCLMMProbit Ordinal KK CLMM (Probit link)
InferenceOrdinalKKCondAdjCatLogitRegr Adjacent Category Logit Inference for KK Matching-on-the-fly Designs
InferenceOrdinalKKGEE GEE Inference for KK Designs with Ordinal Response
InferenceOrdinalKKGLMM GLMM Inference for KK Designs with Ordinal Response
InferenceOrdinalOrderedProbitRegr Ordered Probit Regression Inference for Ordinal Responses
InferenceOrdinalPairedSignTest Paired Sign Test Inference for KK Designs with Ordinal Response
InferenceOrdinalPartialProportionalOddsRegr Partial Proportional-Odds Regression Inference for Ordinal Responses
InferenceOrdinalPropOddsRegr Proportional Odds Regression Inference for Ordinal Responses
InferenceOrdinalRidit Ridit Analysis for Ordinal Responses
InferenceOrdinalStereotypeLogitRegr Stereotype Logit Regression Inference for Ordinal Responses
InferencePropBetaRegr Beta Regression Inference for Proportion Responses
InferencePropFractionalLogit Fractional Logit Inference for Proportion Responses
InferencePropGCompMeanDiff G-Computation Mean-Difference Inference for Proportion Responses
InferencePropKKGEE GEE Inference for KK Designs with Proportion Response
InferencePropKKGLMM KK GLMM Inference for Proportion Responses
InferencePropKKQuantileRegrIVWC Quantile Regression Compound Estimator for KK Matching-on-the-Fly Designs (Proportion Outcomes)
InferencePropKKQuantileRegrOneLik Quantile Regression Combined-Likelihood Compound Estimator for KK Designs (Proportion)
InferencePropQuantileRegr Quantile Regression Inference for Proportion Responses
InferencePropZeroOneInflatedBetaRegr Zero/One-Inflated Beta Inference for Proportion Responses
InferenceRandCustom Randomization test/CI on a user-supplied statistic
InferenceSuite Inference Suite: Discover and Bundle Every Applicable Inference Class for a Design
InferenceSurvivalCoxPHRegr Cox Proportional Hazards Regression Inference for Survival Responses
InferenceSurvivalDepCensTransformRegr Dependent-Censoring Transformation Inference for Survival Responses
InferenceSurvivalGehanWilcox Gehan-Wilcoxon (Peto-Prentice) Inference for Survival Data with Censoring
InferenceSurvivalGLMMWeibullFrailtyLoggammaIVWC Clayton Copula / Standard Weibull Compound Inference for KK Designs
InferenceSurvivalGLMMWeibullFrailtyLoggammaOneLik One-Likelihood Clayton-Copula Weibull AFT Inference for KK Survival Designs
InferenceSurvivalGLMMWeibullFrailtyNormalIVWC Weibull Frailty IVWC Inference for KK Designs
InferenceSurvivalGLMMWeibullFrailtyNormalOneLik Weibull Frailty Combined-Likelihood Inference for KK Designs
InferenceSurvivalKKLWACoxPHIVWC LWA-style Marginal Cox IVWC Compound Inference for KK Designs
InferenceSurvivalKKLWACoxPHOneLik LWA-style Marginal Cox Combined-Likelihood Inference for KK Designs
InferenceSurvivalKKRankRegrIVWC Rank Regression Inference for Survival Responses under KK Designs
InferenceSurvivalKKStratCoxPHIVWC Stratified Cox / Standard Cox Compound Inference for KK Designs
InferenceSurvivalKKStratCoxPHOneLik Stratified Cox Combined-Likelihood Compound Inference for KK Designs
InferenceSurvivalKKWeibullMarginal Marginal (Cluster-Robust) Weibull Inference for KK Matched-Pair Survival Designs
InferenceSurvivalKMDiff Kaplan-Meier Median-Difference Inference for Survival Responses
InferenceSurvivalLogRank Log-Rank Inference for Survival Data with Censoring
InferenceSurvivalRestrictedMeanDiff Restricted Mean Survival Time (RMST) Difference Inference for Survival Responses
InferenceSurvivalStratCoxPHRegr Stratified Cox PH Inference for Survival Responses
InferenceSurvivalWeibullRegr Weibull AFT Inference for Survival Responses
inv_logit Inverse Logit (Logistic) Function

-- K --

KKNewcombeRiskDiffIVWCSource KK Newcombe Risk-Difference IVWC Inference for Binary Responses

-- L --

logit Logit (Log-Odds) Transform

-- M --

mn_pvalue_cpp Export of C++ function mn_pvalue_cpp

-- P --

print.EDIInferenceSuiteResults Prints the results table from an 'InferenceSuite' 'run_all_inference()' call - the same table 'screen = TRUE' prints during the call itself, so a user who assigned the return value and later types its name (or calls 'print()' on it) sees a readable table rather than a raw nested list dump. The table itself is rendered by 'run_all_inference_format_pretty_table()': rows sorted by 'estimand', with a double rule under the header and a single rule between 'estimand' groups and at the bottom, class names and 'estimand' values shortened for display (never the underlying 'results_table' values), and a 'cov_model' letter-key legend appended when applicable - see that function's own documentation for the exact column-by-column rendering rules.
print.summary.EDIInferenceSuiteResults Summarizes an 'InferenceSuite' 'run_all_inference()' result: counts by 'status', the estimate range across 'status == "ok"' classes, and how many reject at 'alpha'.

-- R --

robust_negbinreg Robust Negative Binomial Regression with Backward Column-Dropping Fallback
robust_survreg Robust Parametric Survival Regression from Response/Censoring Vectors
robust_survreg_with_surv_object Robust Parametric Survival Regression (AFT) with Warm-Start and Random-Restart Fallback

-- S --

sample_mode Sample Mode
set_cold_start_dispatch_policy Update the cold-start dispatch policy
set_num_cores Set the number of cores for parallelization
set_optimization_dispatch_policy Update the optimization dispatch policy
set_parallel_dispatch_policy Update the parallel dispatch policy
set_warm_start_dispatch_policy Update the warm-start dispatch policy
SimulationFramework Simulation Framework for Experimental Designs and Inference Methods
SimulationFrameworkReport Reporting class for SimulationFramework results
summary.EDIInferenceSuiteResults Summarizes an 'InferenceSuite' 'run_all_inference()' result: counts by 'status', the estimate range across 'status == "ok"' classes, and how many reject at 'alpha'.
summary_glm_lean Lean GLM Summary (Skips Deviance Residual Quantiles)
SurvivalKKWeibullMarginalSource Marginal (Cluster-Robust) Weibull Inference for KK Matched-Pair Survival Designs

-- T --

transform_cont_y_based_on_response_type Transform continuous latent signal to the response type scale
tune_EDI_for_this_machine Benchmark this machine and tune EDI's performance-policy defaults to it

-- U --

unset_num_cores Unset the number of cores and stop parallel clusters