arXiv subjects

Stephen R Cole

Publications and source records attributed to Stephen R Cole.

12 recordsLinked to original sources

arXiv2026

Delicatessen: Automated Estimating Equations in Python

Estimating equation theory provides a unified framework for statistical modeling and inference. Applying estimating equations has historically involved extensive matrix algebra and by-hand differentiation of complex functions. Here, we introduce delicatessen, a Python library that automates those tedious calculations, lowering the barrier to adoption in quantitative biological and life science research. To highlight the utility of delicatessen for the acceleration of scientific research, we provide illustrative examples of linear regression with outliers, estimation of a dose-response curve, and standardization of the mean. Across these and other settings, delicatessen streamlines transparent and reproducible advanced statistical procedures for modern data analysis.

stat.ME↗

arXiv2026

Estimating equations for causal survival analysis with pooled logistic regression

Background: Pooled logistic regression models are commonly applied in survival analysis. However, the standard implementation can be computationally demanding, which is further exacerbated when using the nonparametric bootstrap for inference. To ease these computational burdens, investigators often coarsen time intervals or assume a parametric functional form for time. These approaches impose restrictive assumptions, which may not always have a well-motivated substantive justification. Methods: Here, the pooled logistic regression model is re-framed using estimating equations to simplify computations and allow for inference via the empirical sandwich variance estimator, thus avoiding the more computationally demanding bootstrap. The proposed implementation is demonstrated using two examples with publicly available data. The performance of the empirical sandwich variance estimator is illustrated using a Monte Carlo simulation study. Results: As shown in the applied examples, the proposed implementation substantially reduced run-times and could be applied without needing to coarsen the data. In the simulation study, the empirical sandwich variance estimator results in nominal confidence interval coverage. Conclusions: The implementation proposed here offers a less computationally demanding alternative to the standard implementation of pooled logistic regression without needing to impose restrictive constraints on time.

stat.ME↗

arXiv2025

Accounting for Missing Data in Public Health Research Using a Synthesis of Statistical and Mathematical Models

Introduction: Accounting for missing data by imputing or weighting conditional on covariates relies on the variable with missingness being observed at least some of the time for all unique covariate values. This requirement is referred to as positivity and positivity violations can result in bias. Here, we review a novel approach to addressing positivity violations in the context of systolic blood pressure. Methods: To illustrate the proposed approach, we estimate the mean systolic blood pressure among children and adolescents aged 2-17 years old in the United States using data from the 2017-2018 National Health and Nutrition Examination Survey (NHANES). As blood pressure was not measured for those aged 2-7, there exists a positivity violation by design. Using a recently proposed synthesis of statistical and mathematical models, we integrate external information with NHANES to address our motivating question. Results: With the synthesis model, the estimated mean systolic blood pressure was 100.5 (95% confidence interval: 99.9, 101.0), which is notably lower than either a complete-case analysis or extrapolation from a statistical model. The synthesis results were supported by a diagnostic comparing the performance of the mathematical model in the positive region. Discussion: Positivity violations pose a threat to quantitative medical research, and standard approaches to addressing nonpositivity rely on restrictive untestable assumptions. Using a synthesis model, like the one detailed here, offers a viable alternative.

stat.AP↗

arXiv2025

Confidence Regions for Multiple Outcomes, Effect Modifiers, and Other Multiple Comparisons

In epidemiology, some have argued that multiple comparison corrections are not necessary as there is rarely interest in the universal null hypothesis. From a parameter estimation perspective, epidemiologists may still be interested in multiple parameters. In this context, standard confidence intervals are not guaranteed to provide simultaneous coverage of more than one parameter. In other words, use of confidence intervals in these cases will understate the uncertainty due to random error. To address this challenge, one can use confidence bands, an extension of confidence intervals to parameter vectors. We illustrate the use of confidence bands in three case studies: estimation of multiple causal effects, effect measure modification by a binary variable, and effect measure modification by a continuous variable. Each example uses publicly available data is accompanied by SAS, R, and Python code. The type of confidence region reported by epidemiologists should depend on whether scientific interest is in a single parameter or a set of parameters. For sets of parameters, like in cases where multiple actions or outcomes, effect measure modification, dose-response, or other functions are of interest, sup-t confidence bands are preferred due to their statistical properties, computational simplicity, and ease of presentation.

stat.ME↗

arXiv2024

Empirical sandwich variance estimator for iterated conditional expectation g-computation

Iterated conditional expectation (ICE) g-computation is an estimation approach for addressing time-varying confounding for both longitudinal and time-to-event data. Unlike other g-computation implementations, ICE avoids the need to specify models for each time-varying covariate. For variance estimation, previous work has suggested the bootstrap. However, bootstrapping can be computationally intense. Here, we present ICE g-computation as a set of stacked estimating equations. Therefore, the variance for the ICE g-computation estimator can be consistently estimated using the empirical sandwich variance estimator. Performance of the variance estimator was evaluated empirically with a simulation study. The proposed approach is also demonstrated with an illustrative example on the effect of cigarette smoking on the prevalence of hypertension. In the simulation study, the empirical sandwich variance estimator appropriately estimated the variance. When comparing runtimes between the sandwich variance estimator and the bootstrap for the applied example, the sandwich estimator was substantially faster, even when bootstraps were run in parallel. The empirical sandwich variance estimator is a viable option for variance estimation with ICE g-computation.

stat.ME↗

arXiv2024

Synthesis estimators for positivity violations with a continuous covariate

Studies intended to estimate the effect of a treatment, like randomized trials, may not be sampled from the desired target population. To correct for this discrepancy, estimates can be transported to the target population. Methods for transporting between populations are often premised on a positivity assumption, such that all relevant covariate patterns in one population are also present in the other. However, eligibility criteria, particularly in the case of trials, can result in violations of positivity when transporting to external populations. To address nonpositivity, a synthesis of statistical and mathematical models can be considered. This approach integrates multiple data sources (e.g. trials, observational, pharmacokinetic studies) to estimate treatment effects, leveraging mathematical models to handle positivity violations. This approach was previously demonstrated for positivity violations by a single binary covariate. Here, we extend the synthesis approach for positivity violations with a continuous covariate. For estimation, two novel augmented inverse probability weighting estimators are proposed. Both estimators are contrasted with other common approaches for addressing nonpositivity. Empirical performance is compared via Monte Carlo simulation. Finally, the competing approaches are illustrated with an example in the context of two-drug versus one-drug antiretroviral therapy on CD4 T cell counts among women with HIV.

stat.ME↗

arXiv2024

Transportability without positivity: a synthesis of statistical and simulation modeling

When estimating an effect of an action with a randomized or observational study, that study is often not a random sample of the desired target population. Instead, estimates from that study can be transported to the target population. However, transportability methods generally rely on a positivity assumption, such that all relevant covariate patterns in the target population are also observed in the study sample. Strict eligibility criteria, particularly in the context of randomized trials, may lead to violations of this assumption. Two common approaches to address positivity violations are restricting the target population and restricting the relevant covariate set. As neither of these restrictions are ideal, we instead propose a synthesis of statistical and simulation models to address positivity violations. We propose corresponding g-computation and inverse probability weighting estimators. The restriction and synthesis approaches to addressing positivity violations are contrasted with a simulation experiment and an illustrative example in the context of sexually transmitted infection testing uptake. In both cases, the proposed synthesis approach accurately addressed the original research question when paired with a thoughtfully selected simulation model. Neither of the restriction approaches were able to accurately address the motivating question. As public health decisions must often be made with imperfect target population information, model synthesis is a viable approach given a combination of empirical data and external information based on the best available knowledge.

stat.ME↗

arXiv2023

The Metropolis algorithm: A useful tool for epidemiologists

The Metropolis algorithm is a Markov chain Monte Carlo (MCMC) algorithm used to simulate from parameter distributions of interest, such as generalized linear model parameters. The "Metropolis step" is a keystone concept that underlies classical and modern MCMC methods and facilitates simple analysis of complex statistical models. Beyond Bayesian analysis, MCMC is useful for generating uncertainty intervals, even under the common scenario in causal inference in which the target parameter is not directly estimated by a single, fitted statistical model. We demonstrate, with a worked example, pseudo-code, and R code, the basic mechanics of the Metropolis algorithm. We use the Metropolis algorithm to estimate the odds ratio and risk difference contrasting the risk of childhood leukemia among those exposed to high versus low level magnetic fields. This approach can be used for inference from Bayesian and frequentist paradigms and, in small samples, offers advantages over large-sample methods like the bootstrap.

stat.CO↗

arXiv2023

Bridged treatment comparisons: an illustrative application in HIV treatment

Comparisons of treatments, interventions, or exposures are of central interest in epidemiology, but direct comparisons are not always possible due to practical or ethical reasons. Here, we detail a fusion approach to compare treatments across studies. The motivating example entails comparing the risk of the composite outcome of death, AIDS, or greater than a 50% CD4 cell count decline in people with HIV when assigned triple versus mono antiretroviral therapy, using data from the AIDS Clinical Trial Group (ACTG) 175 (mono versus dual therapy) and ACTG 320 (dual versus triple therapy). We review a set of identification assumptions and estimate the risk difference using an inverse probability weighting estimator that leverages the shared trial arms (dual therapy). A fusion diagnostic based on comparing the shared arms is proposed that may indicate violation of the identification assumptions. Application of the data fusion estimator and diagnostic to the ACTG trials indicates triple therapy results in a reduction in risk compared to monotherapy in individuals with baseline CD4 counts between 50 and 300 cells/mm$^3$. Bridged treatment comparisons address questions that none of the constituent data sources could address alone, but valid fusion-based inference requires careful consideration of the underlying assumptions.

stat.ME↗

arXiv2023

A Causal Inference Framework for Leveraging External Controls in Hybrid Trials

We consider the challenges associated with causal inference in settings where data from a randomized trial is augmented with control data from an external source to improve efficiency in estimating the average treatment effect (ATE). Through the development of a formal causal inference framework, we outline sufficient causal assumptions about the exchangeability between the internal and external controls to identify the ATE and establish the connection to a novel graphical criteria. We propose estimators, review efficiency bounds, develop an approach for efficient doubly-robust estimation even when unknown nuisance models are estimated with flexible machine learning methods, and demonstrate finite-sample performance through a simulation study. To illustrate the ideas and methods, we apply the framework to a trial investigating the effect of risdisplam on motor function in patients with spinal muscular atrophy for which there exists an external set of control patients from a previous trial.

stat.ME↗

arXiv2022

Positivity: Identifiability and Estimability

Positivity, the assumption that every unique combination of confounding variables that occurs in a population has a non-zero probability of an action, can be further delineated as deterministic positivity and stochastic positivity. Here, we revisit this distinction, examine its relation to nonparametric identifiability and estimability, and discuss how to address violations of positivity assumptions. Finally, we relate positivity to recent interest in machine learning, as well as the limitations of data-adaptive algorithms for causal inference. Positivity may often be overlooked, but it remains important for inference.

stat.ME↗

arXiv2019

Super learning in the SAS system

Background and objective: Stacking is an ensemble machine learning method that averages predictions from multiple other algorithms, such as generalized linear models and regression trees. An implementation of stacking, called super learning, has been developed as a general approach to supervised learning and has seen frequent usage, in part due to the availability of an R package. We develop super learning in the SAS software system using a new macro, and demonstrate its performance relative to the R package. Methods: Following previous work using the R SuperLearner package we assess the performance of super learning in a number of domains. We compare the R package with the new SAS macro in a small set of simulations assessing curve fitting in a predictive model as well in a set of 14 publicly available datasets to assess cross-validated accuracy. Results: Across the simulated data and the publicly available data, the SAS macro performed similarly to the R package, despite a different set of potential algorithms available natively in R and SAS. Conclusions: Our super learner macro performs as well as the R package at a number of tasks. Further, by extending the macro to include the use of R packages, the macro can leverage both the robust, enterprise oriented procedures in SAS and the nimble, cutting edge packages in R. In the spirit of ensemble learning, this macro extends the potential library of algorithms beyond a single software system and provides a simple avenue into machine learning in SAS.

stat.ML↗