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Randomization-based confidence intervals for cluster randomized trials.

ABSTRACT: In a cluster randomized trial (CRT), groups of people are randomly assigned to different interventions. Existing parametric and semiparametric methods for CRTs rely on distributional assumptions or a large number of clusters to maintain nominal confidence interval (CI) coverage. Randomization-based inference is an alternative approach that is distribution-free and does not require a large number of clusters to be valid. Although it is well-known that a CI can be obtained by inverting a randomization test, this requires testing a non-zero null hypothesis, which is challenging with non-continuous and survival outcomes. In this article, we propose a general method for randomization-based CIs using individual-level data from a CRT. This approach accommodates various outcome types, can account for design features such as matching or stratification, and employs a computationally efficient algorithm. We evaluate this method's performance through simulations and apply it to the Botswana Combination Prevention Project, a large HIV prevention trial with an interval-censored time-to-event outcome.

SUBMITTER: Rabideau DJ

PROVIDER: S-EPMC8511941 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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Randomization-based confidence intervals for cluster randomized trials.

Rabideau Dustin J DJ Wang Rui R

Biostatistics (Oxford, England) 20211001 4

In a cluster randomized trial (CRT), groups of people are randomly assigned to different interventions. Existing parametric and semiparametric methods for CRTs rely on distributional assumptions or a large number of clusters to maintain nominal confidence interval (CI) coverage. Randomization-based inference is an alternative approach that is distribution-free and does not require a large number of clusters to be valid. Although it is well-known that a CI can be obtained by inverting a randomiza ...[more]

PMID: 32112077

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Project description:BackgroundIn cluster-randomized controlled trials (C-RCTs), covariate-constrained randomization (CCR) methods efficiently control imbalance in multiple baseline cluster-level variables, but the choice of imbalance metric to define the subset of "adequately balanced" possible allocation schemes for C-RCTs involving more than two arms and continuous variables is unclear. In an ongoing three-armed C-RCT, we chose the min(three Kruskal-Wallis [KW] test P values) > 0.30 as our metric. We use simulation studies to explore the performance of this and other metrics of baseline variable imbalance in CCR.MethodsWe simulated three continuous variables across three arms under varying allocation ratios and assumptions. We compared the performance of min(analysis of variance [ANOVA] P value) > 0.30, min(KW P value) > 0.30, multivariate analysis of variance (MANOVA) P value > 0.30, min(nine possible t test P values) > 0.30, and min(Wilcoxon rank-sum [WRS] P values) > 0.30.ResultsPairwise comparison metrics (t test and WRS) tended to be the most conservative, providing the smallest subset of allocation schemes (10%-13%) meeting criteria for acceptable balance. Sensitivity of the min(t test P values) > 0.30 for detecting non-trivial imbalance was 100% for both hypothetical and resampled simulation scenarios. The KW criterion maintained higher sensitivity than both the MANOVA and ANOVA criteria (89% to over 99%) but was not as sensitive as pairwise criteria.ConclusionsOur criterion, the KW P value > 0.30, to signify "acceptable" balance was not the most conservative, but it appropriately identified imbalance in the majority of simulations. Since all are related, CCR algorithms involving any of these imbalance metrics for continuous baseline variables will ensure robust simultaneous control over multiple continuous baseline variables, but we recommend care in determining the threshold of "acceptable" levels of (im)balance.Trial registrationThis trial is registered on ClinicalTrials.gov (initial post: December 1, 2016; identifier: NCT02979444 ).

Project description:In the analysis of networks we frequently require the statistical significance of some network statistic, such as measures of similarity for the properties of interacting nodes. The structure of the network may introduce dependencies among the nodes and it will in general be necessary to account for these dependencies in the statistical analysis. To this end we require some form of Null model of the network: generally rewired replicates of the network are generated which preserve only the degree (number of interactions) of each node. We show that this can fail to capture important features of network structure, and may result in unrealistic significance levels, when potentially confounding additional information is available.We present a new network resampling Null model which takes into account the degree sequence as well as available biological annotations. Using gene ontology information as an illustration we show how this information can be accounted for in the resampling approach, and the impact such information has on the assessment of statistical significance of correlations and motif-abundances in the Saccharomyces cerevisiae protein interaction network. An algorithm, GOcardShuffle, is introduced to allow for the efficient construction of an improved Null model for network data.We use the protein interaction network of S. cerevisiae; correlations between the evolutionary rates and expression levels of interacting proteins and their statistical significance were assessed for Null models which condition on different aspects of the available data. The novel GOcardShuffle approach results in a Null model for annotated network data which appears better to describe the properties of real biological networks.An improved statistical approach for the statistical analysis of biological network data, which conditions on the available biological information, leads to qualitatively different results compared to approaches which ignore such annotations. In particular we demonstrate the effects of the biological organization of the network can be sufficient to explain the observed similarity of interacting proteins.

Project description:BackgroundFor the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes. Its application as an in-silico replacement for DDH was recently introduced. The main challenge in the implementation of such an application is to produce digital DDH values that must mimic the wet-lab DDH values as close as possible to ensure consistency in the Prokaryotic species concept.ResultsCorrelation and regression analyses were used to determine the best-performing methods and the most influential parameters. GBDP was further enriched with a set of new features such as confidence intervals for intergenomic distances obtained via resampling or via the statistical models for DDH prediction and an additional family of distance functions. As in previous analyses, GBDP obtained the highest agreement with wet-lab DDH among all tested methods, but improved models led to a further increase in the accuracy of DDH prediction. Confidence intervals yielded stable results when inferred from the statistical models, whereas those obtained via resampling showed marked differences between the underlying distance functions.ConclusionsDespite the high accuracy of GBDP-based DDH prediction, inferences from limited empirical data are always associated with a certain degree of uncertainty. It is thus crucial to enrich in-silico DDH replacements with confidence-interval estimation, enabling the user to statistically evaluate the outcomes. Such methodological advancements, easily accessible through the web service at http://ggdc.dsmz.de, are crucial steps towards a consistent and truly genome sequence-based classification of microorganisms.

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Randomization-based confidence intervals for cluster randomized trials.

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Randomization-based confidence intervals for cluster randomized trials.

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