arXiv subjects

Marlena Bannick

Publications and source records attributed to Marlena Bannick.

6 recordsLinked to original sources

arXiv2026

The RobinCar Family: R Tools for Robust Covariate Adjustment in Randomized Clinical Trials

Purpose: Covariate adjustment is a powerful statistical technique that can increase efficiency in clinical trials. Recent guidance from the U.S. FDA provided recommendations and best practices for using covariate adjustment. However, there has existed a gap between the extensive statistical literature on covariate adjustment and software that is easy to use and abides by these best practices. Methods: We have developed the RobinCar Family, which is comprised of RobinCar and RobinCar2. These two R packages enable covariate-adjusted analyses for continuous, discrete, and time-to-event outcomes that follow best practices. For continuous and discrete outcomes, the functions in the RobinCar Family facilitate traditional forms of covariate adjustment such as ANCOVA as well as more recent approaches like ANHECOVA, G-computation with generalized linear models and machine learning models, and adjustment for a super-covariate (as in PROCOVA(TM)). Functions for time-to-event outcomes implement the covariate-adjusted log-rank test, the stratified covariate-adjusted log-rank test, and the marginal covariate-adjusted hazard ratio. The RobinCar Family is supported by the ASA Biopharmaceutical Section Covariate Adjustment Scientific Working Group. Results: We provide an accessible overview of the covariate-adjusted statistical methods, and describe how they are implemented in RobinCar and RobinCar2. We highlight important usage notes for clinical trial practitioners. Conclusion: We apply RobinCar and RobinCar2 functions by analyzing data from the AIDS Clinical Trials Group Study 175, demonstrating that they are straightforward and user-friendly.

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arXiv2024

Estimating HIV Cross-sectional Incidence Using Recency Tests from a Non-representative Sample

Cross-sectional incidence estimation based on recency testing has become a widely used tool in HIV research. Recently, this method has gained prominence in HIV prevention trials to estimate the "placebo" incidence that participants might experience without preventive treatment. The application of this approach faces challenges due to non-representative sampling, as individuals aware of their HIV-positive status may be less likely to participate in screening for an HIV prevention trial. To address this, a recent phase 3 trial excluded individuals based on whether they have had a recent HIV test. To the best of our knowledge, the validity of this approach has yet to be studied. In our work, we investigate the performance of cross-sectional HIV incidence estimation when excluding individuals based on prior HIV tests in realistic trial settings. We develop a statistical framework that incorporates a testing-based criterion and possible non-representative sampling. We introduce a metric we call the effective mean duration of recent infection (MDRI) that mathematically quantifies bias in incidence estimation. We conduct an extensive simulation study to evaluate incidence estimator performance under various scenarios. Our findings reveal that when screening attendance is affected by knowledge of HIV status, incidence estimators become unreliable unless all individuals with recent HIV tests are excluded. Additionally, we identified a trade-off between bias and variability: excluding more individuals reduces bias from non-representative sampling but in many cases increases the variability of incidence estimates. These findings highlight the need for caution when applying testing-based criteria and emphasize the importance of refining incidence estimation methods to improve the design and evaluation of future HIV prevention trials.

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arXiv2024

Robust Nonparametric Stochastic Frontier Analysis

Benchmarking tools, including stochastic frontier analysis (SFA), data envelopment analysis (DEA), and its stochastic extension (StoNED) are core tools in economics used to estimate an efficiency envelope and production inefficiencies from data. The problem appears in a wide range of fields -- for example, in global health the frontier can quantify efficiency of interventions and funding of health initiatives. Despite their wide use, classic benchmarking approaches have key limitations that preclude even wider applicability. Here we propose a robust non-parametric stochastic frontier meta-analysis (SFMA) approach that fills these gaps. First, we use flexible basis splines and shape constraints to model the frontier function, so specifying a functional form of the frontier as in classic SFA is no longer necessary. Second, the user can specify relative errors on input datapoints, enabling population-level analyses. Third, we develop a likelihood-based trimming strategy to robustify the approach to outliers, which otherwise break available benchmarking methods. We provide a custom optimization algorithm for fast and reliable performance. We implement the approach and algorithm in an open source Python package `sfma'. Synthetic and real examples show the new capabilities of the method, and are used to compare SFMA to state of the art benchmarking packages that implement DEA, SFA, and StoNED.

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arXiv2023

An Enhanced Cross-Sectional HIV Incidence Estimator that Incorporates Prior HIV Test Results

Incidence estimation of HIV infection can be performed using recent infection testing algorithm (RITA) results from a cross-sectional sample. This allows practitioners to understand population trends in the HIV epidemic without having to perform longitudinal follow-up on a cohort of individuals. The utility of the approach is limited by its precision, driven by the (low) sensitivity of the RITA at identifying recent infection. By utilizing results of previous HIV tests that individuals may have taken, we consider an enhanced RITA with increased sensitivity (and specificity). We use it to propose an enhanced estimator for incidence estimation. We prove the theoretical properties of the enhanced estimator and illustrate its numerical performance in simulation studies. We apply the estimator to data from a cluster-randomized trial to study the effect of community-level HIV interventions on HIV incidence. We demonstrate that the enhanced estimator provides a more precise estimate of HIV incidence compared to the standard estimator.

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arXiv2023

Robust Variance Estimation for Covariate-Adjusted Unconditional Treatment Effect in Randomized Clinical Trials with Binary Outcomes

To improve precision of estimation and power of testing hypothesis for an unconditional treatment effect in randomized clinical trials with binary outcomes, researchers and regulatory agencies recommend using g-computation as a reliable method of covariate adjustment. However, the practical application of g-computation is hindered by the lack of an explicit robust variance formula that can be used for different unconditional treatment effects of interest. To fill this gap, we provide explicit and robust variance estimators for g-computation estimators and demonstrate through simulations that the variance estimators can be reliably applied in practice.

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arXiv2021

Analysis and Methods to Mitigate Effects of Under-reporting in Count Data

Under-reporting of count data poses a major roadblock for prediction and inference. In this paper, we focus on the Pogit model, which deconvolves the generating Poisson process from the censuring process controlling under-reporting using a generalized linear modeling framework. We highlight the limitations of the Pogit model and address them by adding constraints to the estimation framework. We also develop uncertainty quantification techniques that are robust to model mis-specification. Our approach is evaluated using synthetic data and applied to real healthcare datasets, where we treat in-patient data as `reported' counts and use held-out total injuries to validate the results. The methods make it possible to separate the Poisson process from the under-reporting process, given sufficient expert information. Codes to implement the approach are available via an open source Python package.

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