Randomization-based confidence intervals for cluster randomized trials.
Ontology highlight
ABSTRACT:
SUBMITTER: Rabideau DJ
PROVIDER: S-EPMC8511941 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The log-rank test is widely used to compare two survival distributions in a randomized clinical trial, while partial likelihood (Cox, 1975) is the method of choice for making inference about the hazard ratio under the Cox (1972) proportional hazards model. The Wald 95% confidence interval of the hazard ratio may include the null value of 1 when the p-value of the log-rank test is less than 0.05. Peto et al. (1977) provided an estimator for the hazard ratio based on the log-rank statistic; the corresponding 95% confidence interval excludes the null value of 1 if and only if the p-value of the log-rank test is less than 0.05. However, Peto's estimator is not consistent, and the corresponding confidence interval does not have correct coverage probability. In this article, we construct the confidence interval by inverting the score test under the (possibly stratified) Cox model, and we modify the variance estimator such that the resulting score test for the null hypothesis of no treatment difference is identical to the log-rank test in the possible presence of ties. Like Peto's method, the proposed confidence interval excludes the null value if and only if the log-rank test is significant. Unlike Peto's method, however, this interval has correct coverage probability. An added benefit of the proposed confidence interval is that it tends to be more accurate and narrower than the Wald confidence interval. We demonstrate the advantages of the proposed method through extensive simulation studies and a colon cancer study.
| S-EPMC5085885 | biostudies-literature
Project description:It is a challenge to design randomized trials when it is suspected that a treatment may benefit only certain subsets of the target population. In such situations, trial designs have been proposed that modify the population enrolled based on an interim analysis, in a preplanned manner. For example, if there is early evidence during the trial that the treatment only benefits a certain subset of the population, enrollment may then be restricted to this subset. At the end of such a trial, it is desirable to draw inferences about the selected population. We focus on constructing confidence intervals for the average treatment effect in the selected population. Confidence interval methods that fail to account for the adaptive nature of the design may fail to have the desired coverage probability. We provide a new procedure for constructing confidence intervals having at least 95% coverage probability, uniformly over a large class Q of possible data generating distributions. Our method involves computing the minimum factor c by which a standard confidence interval must be expanded in order to have, asymptotically, at least 95% coverage probability, uniformly over Q. Computing the expansion factor c is not trivial, since it is not a priori clear, for a given decision rule, for which data generating distribution leads to the worst-case coverage probability. We give an algorithm that computes c, and then prove an optimality property for the resulting confidence interval procedure.
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Project description:Although Cohen's d and the growth modeling analysis (GMA) d from linear models are common standardized effect sizes used to convey treatment effects, popular statistical software packages do not include them in their standard outputs. This article demonstrated the use of statistical software with user-prescribed parameter functions (e.g., Mplus) to produce d for treatment effects from both classical analysis and GMA--along with their associated standard errors (SEs) and confidence intervals (CIs). A Monte Carlo study was conducted to examine bias in the SE and CI for GMA d obtained with Mplus and found that both estimates were more accurate when calculated by the software with the standard bootstrap than with the delta method, but the delta method estimates were less biased than respective estimates from extant post hoc equations. Thus, users of many statistical software packages (including SAS, R, and LISREL) should obtain d or GMA d and associated CIs directly. Researchers employing less versatile software--and meta-analysts including ds and GMA ds in their syntheses of treatment effects--should continue to use the conventional post hoc equations. Biases in SEs and CIs for effect sizes obtained with them are ignorable and point estimates of d and GMA d are the same whether obtained directly from the software or with post hoc equations.
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Project description:Interval estimates - estimates of parameters that include an allowance for sampling uncertainty - have long been touted as a key component of statistical analyses. There are several kinds of interval estimates, but the most popular are confidence intervals (CIs): intervals that contain the true parameter value in some known proportion of repeated samples, on average. The width of confidence intervals is thought to index the precision of an estimate; CIs are thought to be a guide to which parameter values are plausible or reasonable; and the confidence coefficient of the interval (e.g., 95 %) is thought to index the plausibility that the true parameter is included in the interval. We show in a number of examples that CIs do not necessarily have any of these properties, and can lead to unjustified or arbitrary inferences. For this reason, we caution against relying upon confidence interval theory to justify interval estimates, and suggest that other theories of interval estimation should be used instead.
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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 ).
| S-EPMC6537428 | biostudies-literature
Project description:Covariate constrained randomization (CCR) is a method of controlling imbalance in important baseline covariates in cluster-randomized trials (CRT). We use simulated CRTs to investigate the performance (control of imbalance) of CCR relative to simple randomization (SR) under conditions of misspecification of the cluster-level variable used in the CCR algorithm. We use data from a Patient-Centered Outcomes Research Institute (PCORI)-funded CRT evaluating the Mothers and Babies (MB) intervention (AD-1507-31,473). CCR methodology was used in the MB study to control imbalance in, among other baseline variables, the percent minority (i.e., non-White) participants at each study site. Simulation schemes explored variation in degree of misspecification in the baseline covariate of interest, and include correct report, observed misspecification, and a range of simulated misspecification for intervals within and beyond that observed in the MB study. We also consider three within-site sample size scenarios: that observed in the MB study, small (mean 10) and large (mean 50). Simulations at every level of baseline covariate misspecification suggest that use of the CCR strategy provides between-arm imbalance that is simultaneously lower and less variable, on average, than that produced from the SR strategy. We find that the gains to using CCR over SR are nearly twice as high with accurate reporting (Δ = -5.33) compared to the observed study-level misspecification (Δ = -3.03). Although CCR still outperforms SR as the level of misspecification increases, the gains to using CCR over SR decrease; thus, every effort should still be made to obtain high-quality baseline data.
| S-EPMC7941091 | biostudies-literature
Project description:Within cluster randomized trials no algorithms exist to generate a full enumeration of a block randomization, balancing for covariates across treatment arms. Furthermore, often for practical reasons multiple blocks are required to fully randomize a study, which may not have been well balanced within blocks.We present a convenient and easy to use randomization tool to undertake allocation concealed block randomization. Our algorithm highlights allocations that minimize imbalance between treatment groups across multiple baseline covariates. We demonstrate the algorithm using a cluster randomized trial in primary care (the PRE-EMPT Study) and show that the software incorporates a trade off between independent random allocations that were likely to be imbalanced, and predictable deterministic approaches that would minimise imbalance. We extend the methodology of single block randomization to allocate to multiple blocks conditioning on previous allocations.The algorithm is included as Additional file 1 and we advocate its use for robust randomization within cluster randomized trials.
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Project description:a- Self –Self Hybridisation were used to set confidence 99% interval using RNA from non-tethered cell lines that is both labelled in with cy3 cy5 (theoretically identical cDNA populations) to compared technical errors associated with such experiments Keywords: comparative hybridization to access expression profiles between Cy3 and Cy5 uniformally labelled template.
2008-03-04 | GSE10697 | GEO
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.
| S-EPMC2241843 | biostudies-other
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.
| S-EPMC3665452 | biostudies-literature