Diagnostic test accuracy: application and practice using R software.
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ABSTRACT:
SUBMITTER: Shim SR
PROVIDER: S-EPMC6545496 | biostudies-literature | 2019
REPOSITORIES: biostudies-literature
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Project description:The objective of this study was to describe general approaches for intervention meta-analysis available for quantitative data synthesis using the R software. We conducted an intervention meta-analysis using two types of data, continuous and binary, characterized by mean difference and odds ratio, respectively. The package commands for the R software were "metacont", "metabin", and "metagen" for the overall effect size, "forest" for forest plot, "metareg" for meta-regression analysis, and "funnel" and "metabias" for the publication bias. The estimated overall effect sizes, test for heterogeneity and moderator effect, and the publication bias were reported using the R software. In particular, the authors indicated methods for calculating the effect sizes of the target studies in intervention meta-analysis. This study focused on the practical methods of intervention meta-analysis, rather than the theoretical concepts, for researchers with no major in statistics. Through this study, the authors hope that many researchers will use the R software to more readily perform the intervention meta-analysis and that this will in turn generate further related research.
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Project description:The objective of this study is to describe the general approaches to network meta-analysis that are available for quantitative data synthesis using R software. We conducted a network meta-analysis using two approaches: Bayesian and frequentist methods. The corresponding R packages were "gemtc" for the Bayesian approach and "netmeta" for the frequentist approach. In estimating a network meta-analysis model using a Bayesian framework, the "rjags" package is a common tool. "rjags" implements Markov chain Monte Carlo simulation with a graphical output. The estimated overall effect sizes, test for heterogeneity, moderator effects, and publication bias were reported using R software. The authors focus on two flexible models, Bayesian and frequentist, to determine overall effect sizes in network meta-analysis. This study focused on the practical methods of network meta-analysis rather than theoretical concepts, making the material easy to understand for Korean researchers who did not major in statistics. The authors hope that this study will help many Korean researchers to perform network meta-analyses and conduct related research more easily with R software.
| S-EPMC6635665 | biostudies-literature
Project description:The objective of this study was to describe the general approaches of dose-response meta-analysis (DRMA) available for the quantitative synthesis of data using the R software. We conducted a DRMA using two types of data, the difference of means in continuous data and the odds ratio in binary data. The package commands of the R software were "doseresmeta" for the overall effect sizes that were separated into a linear model, quadratic model, and restricted cubic split model for better understanding. The effect sizes according to the dose and a test for linearity were demonstrated and interpreted by analyzing one-stage and two-stage DRMA. The authors examined several flexible models of exposure to pool study-specific trends and made a graphical presentation of the dose-response trend. This study focused on practical methods of DRMA rather than theoretical concepts for researchers who did not major in statistics. The authors hope that this study will help many researchers use the R software to perform DRMAs more easily, and that related research will be pursued.
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Project description:In 1996, shortly after the founding of The Cochrane Collaboration, leading figures in test evaluation research established a Methods Group to focus on the relatively new and rapidly evolving methods for the systematic review of studies of diagnostic tests. Seven years later, the Collaboration decided it was time to develop a publication format and methodology for Diagnostic Test Accuracy (DTA) reviews, as well as the software needed to implement these reviews in The Cochrane Library. A meeting hosted by the German Cochrane Centre in 2004 brought together key methodologists in the area, many of whom became closely involved in the subsequent development of the methodological framework for DTA reviews. DTA reviews first appeared in The Cochrane Library in 2008 and are now an integral part of the work of the Collaboration.
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Project description:BackgroundSystematic reviews and meta-analyses of test accuracy studies are increasingly being recognised as central in guiding clinical practice. However, there is currently no dedicated and comprehensive software for meta-analysis of diagnostic data. In this article, we present Meta-DiSc, a Windows-based, user-friendly, freely available (for academic use) software that we have developed, piloted, and validated to perform diagnostic meta-analysis.ResultsMeta-DiSc a) allows exploration of heterogeneity, with a variety of statistics including chi-square, I-squared and Spearman correlation tests, b) implements meta-regression techniques to explore the relationships between study characteristics and accuracy estimates, c) performs statistical pooling of sensitivities, specificities, likelihood ratios and diagnostic odds ratios using fixed and random effects models, both overall and in subgroups and d) produces high quality figures, including forest plots and summary receiver operating characteristic curves that can be exported for use in manuscripts for publication. All computational algorithms have been validated through comparison with different statistical tools and published meta-analyses. Meta-DiSc has a Graphical User Interface with roll-down menus, dialog boxes, and online help facilities.ConclusionMeta-DiSc is a comprehensive and dedicated test accuracy meta-analysis software. It has already been used and cited in several meta-analyses published in high-ranking journals. The software is publicly available at http://www.hrc.es/investigacion/metadisc_en.htm.
| S-EPMC1552081 | biostudies-literature
Project description:IntroductionIdentification of people who have or are at risk of frailty enables targeted interventions, and the use of tools that screen for frailty using electronic records (which we term as validated electronic frailty measures (VEFMs)) within primary care is incentivised by NHS England. We carried out a systematic review to establish the sensitivity and specificity of available primary care VEFMs when compared to a reference standard in-person assessment.MethodsMedline, Pubmed, CENTRAL, CINHAL and Embase searches identified studies comparing a primary care VEFM with in-person assessment. Studies were quality assessed using Quality Assessment of Diagnostic Accuracy Studies revised tool. Sensitivity and specificity values were extracted or were calculated and pooled using StatsDirect.ResultsThere were 2,245 titles screened, with 10 studies included. These described three different index tests: electronic frailty index (eFI), claims-based frailty index (cFI) and polypharmacy. Frailty Phenotype was the reference standard in each study. One study of 60 patients examined the eFI, reporting a sensitivity of 0.84 (95% CI = 0.55, 0.98) and a specificity of 0.78 (0.64, 0.89). Two studies of 7,679 patients examined cFI, with a pooled sensitivity of 0.48 (95% CI = 0.23, 0.74) and a specificity of 0.80 (0.53, 0.98). Seven studies of 34,328 patients examined a polypharmacy as a screening tool (defined as more than or equal to five medications) with a pooled sensitivity of 0.61 (95% CI = 0.50, 0.72) and a specificity of 0.66 (0.58, 0.73).ConclusionseFI is the best-performing VEFM; however, based on our analysis of an average UK GP practice, it would return a high number of false-positive results. In conclusion, existing electronic frailty tools may not be appropriate for primary care-based population screening.
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Project description:Screening and diagnostic tests are applied for the classification of people into diseased and non-diseased populations. Although diagnostic accuracy measures are used to evaluate the correctness of classification in clinical research and practice, there has been limited research on their uncertainty. The objective for this work was to develop a tool for calculating the uncertainty of diagnostic accuracy measures, as diagnostic accuracy is fundamental to clinical decision-making. For this reason, the freely available interactive program Diagnostic Uncertainty has been developed in the Wolfram language. The program provides six modules with nine submodules for calculating and plotting the standard measurement, sampling and combined uncertainty and the resultant confidence intervals of various diagnostic accuracy measures of screening or diagnostic tests, which measure a normally distributed measurand, applied at a single point in time in samples of non-diseased and diseased populations. This is done for differing sample sizes, mean and standard deviation of the measurand, diagnostic threshold and standard measurement uncertainty of the test. The application of the program is demonstrated with an illustrative example of glucose measurements in samples of diabetic and non-diabetic populations, that shows the calculation of the uncertainty of diagnostic accuracy measures. The presented interactive program is user-friendly and can be used as a flexible educational and research tool in medical decision-making, to calculate and explore the uncertainty of diagnostic accuracy measures.
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Project description:Despite the high prevalence of traumatic brain injuries (TBI), there are few rapid and straightforward tests to improve its assessment. To this end, we developed a tablet-based software battery ("BrainCheck") for concussion detection that is well suited to sports, emergency department, and clinical settings. This article is a study of the diagnostic accuracy of BrainCheck. We administered BrainCheck to 30 TBI patients and 30 pain-matched controls at a hospital Emergency Department (ED), and 538 healthy individuals at 10 control test sites. We compared the results of the tablet-based assessment against physician diagnoses derived from brain scans, clinical examination, and the SCAT3 test, a traditional measure of TBI. We found consistent distributions of normative data and high test-retest reliability. Based on these assessments, we defined a composite score that distinguishes TBI from non-TBI individuals with high sensitivity (83%) and specificity (87%). We conclude that our testing application provides a rapid, portable testing method for TBI.
| S-EPMC5501428 | biostudies-literature
Project description:AimsTo validate the diagnostic accuracy of the Augurix SARS-CoV-2 IgM/IgG rapid immunoassay diagnostic test (RDT) for COVID-19.MethodsIn this unmatched 1:1 case-control study, blood samples from 46 real-time RT-PCR-confirmed SARS-CoV-2 hospitalized cases and 45 healthy donors (negative controls) were studied. Diagnostic accuracy of the IgG RDT was assessed against both an in-house recombinant spike-expressing immunofluorescence assay (rIFA), as an established reference method (primary endpoint), and the Euroimmun SARS-CoV-2 IgG enzyme-linked immunosorbent assays (ELISA) (secondary endpoint).ResultsCOVID-19 patients were more likely to be male (61% vs 20%; P = .0001) and older (median 66 vs 47 years old; P < .001) than controls. Whole blood IgG-RDT results showed 86% and 93% overall Kendall concordance with rIFA and IgG ELISA, respectively. IgG RDT performances were similar between plasma and whole blood. Overall, RDT sensitivity was 88% (95% confidence interval [95%CI]: 70-96), specificity 98% (95%CI: 90-100), PPV 97% (95%CI: 80-100) and NPV 94% (95%CI: 84-98). The IgG-RDT carried out from 0 to 6 days, 7 to 14 days and > 14 days after the SARS-CoV-2 RT-PCR test displayed 30%, 73% and 100% positivity rates in the COVID-19 group, respectively. When considering samples taken >14 days after RT-PCR diagnosis, NPV was 100% (95%CI:90-100), and PPV was 100% (95%CI:72-100).ConclusionsThe Augurix IgG-RDT done in whole blood displays a high diagnostic accuracy for SARS-CoV-2 IgG in high COVID-19 prevalence settings, where its use could be considered in the absence of routine diagnostic serology facilities.
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Project description:BackgroundThe head impulse test (HIT) is a useful bedside test to identify peripheral vestibular deficits. However, such a deficit of the vestibulo-ocular reflex (VOR) may not be diagnosed because corrective saccades cannot always be detected by simple observation. The scleral search coil technique is the gold standard for HIT measurements, but it is not practical for routine testing or for acute patients, because they are required to wear an uncomfortable contact lens.ObjectiveTo develop an easy-to-use video HIT system (vHIT) as a clinical tool for identifying peripheral vestibular deficits. To validate the diagnostic accuracy of vHIT by simultaneous measures with video and search coil recordings across healthy subjects and patients with a wide range of previously identified peripheral vestibular deficits.MethodsHorizontal HIT was recorded simultaneously with vHIT (250 Hz) and search coils (1,000 Hz) in 8 normal subjects, 6 patients with vestibular neuritis, 1 patient after unilateral intratympanic gentamicin, and 1 patient with bilateral gentamicin vestibulotoxicity.ResultsSimultaneous video and search coil recordings of eye movements were closely comparable (average concordance correlation coefficient r(c) = 0.930). Mean VOR gains measured with search coils and video were not significantly different in normal (p = 0.107) and patients (p = 0.073). With these groups, the sensitivity and specificity of both the reference and index test were 1.0 (95% confidence interval 0.69-1.0). vHIT measures detected both overt and covert saccades as accurately as coils.ConclusionsThe video head impulse test is equivalent to search coils in identifying peripheral vestibular deficits but easier to use in clinics, even in patients with acute vestibular neuritis.
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