scholarly journals How to perform a meta-analysis with R: a practical tutorial

2019 ◽  
Vol 22 (4) ◽  
pp. 153-160 ◽  
Author(s):  
Sara Balduzzi ◽  
Gerta Rücker ◽  
Guido Schwarzer
Keyword(s):  
Mental Health ◽  
Meta Analysis ◽  
R Package ◽  
Outcome Data ◽  
Sensitivity Analyses ◽  
Binary Outcome ◽  
Software Environment ◽  
Flexible Tool ◽  
Funnel Plot ◽  
Meta Analyses

ObjectiveMeta-analysis is of fundamental importance to obtain an unbiased assessment of the available evidence. In general, the use of meta-analysis has been increasing over the last three decades with mental health as a major research topic. It is then essential to well understand its methodology and interpret its results. In this publication, we describe how to perform a meta-analysis with the freely available statistical software environment R, using a working example taken from the field of mental health.MethodsR package meta is used to conduct standard meta-analysis. Sensitivity analyses for missing binary outcome data and potential selection bias are conducted with R package metasens. All essential R commands are provided and clearly described to conduct and report analyses.ResultsThe working example considers a binary outcome: we show how to conduct a fixed effect and random effects meta-analysis and subgroup analysis, produce a forest and funnel plot and to test and adjust for funnel plot asymmetry. All these steps work similar for other outcome types.ConclusionsR represents a powerful and flexible tool to conduct meta-analyses. This publication gives a brief glimpse into the topic and provides directions to more advanced meta-analysis methods available in R.

scholarly journals Sensitivity analysis for publication bias in meta-analyses

2019 ◽  
Author(s):  
Maya B Mathur ◽  
Tyler VanderWeele
Keyword(s):  
Publication Bias ◽  
Normal Population ◽  
Meta Analysis ◽  
Real Life ◽  
R Package ◽  
Sensitivity Analyses ◽  
Point Estimate ◽  
Worst Case ◽  
Null Value ◽  
Meta Analyses

We propose sensitivity analyses for publication bias in meta-analyses. We consider a publication process such that "statistically significant" results are more likely to be published than negative or "nonsignificant" results by an unknown ratio, eta. Our proposed methods also accommodate some plausible forms of selection based on a study's standard error. Using inverse-probability weighting and robust estimation that accommodates non-normal population effects, small meta-analyses, and clustering, we develop sensitivity analyses that enable statements such as: "For publication bias to shift the observed point estimate to the null, 'significant' results would need to be at least 30-fold more likely to be published than negative or 'nonsignificant' results." Comparable statements can be made regarding shifting to a chosen non-null value or shifting the confidence interval. To aid interpretation, we describe empirical benchmarks for plausible values of eta across disciplines. We show that a worst-case meta-analytic point estimate for maximal publication bias under the selection model can be obtained simply by conducting a standard meta-analysis of only the negative and "nonsignificant" studies; this method sometimes indicates that no amount of such publication bias could "explain away" the results. We illustrate the proposed methods using real-life meta-analyses and provide an R package, PublicationBias.

scholarly journals Systemic Corticosteroid Administration in Coronavirus Disease 2019 Outcomes: An Umbrella Meta-Analysis Incorporating Both Mild and Pulmonary Fibrosis–Manifested Severe Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Bin Cheng ◽  
Jinxiu Ma ◽  
Yani Yang ◽  
Tingting Shao ◽  
Binghao Zhao ◽  
...  
Keyword(s):  
Critically Ill ◽  
Meta Analysis ◽  
Severe Disease ◽  
Outcome Data ◽  
Sensitivity Analyses ◽  
Corticosteroid Administration ◽  
Random Effects Models ◽  
Hospital Stays ◽  
Meta Analyses ◽  
Negative Conversion

Background: Effective treatments for coronavirus disease 2019 (COVID-19) are urgently needed. The real role of corticosteroid use in COVID-19 has long been of interest and is disputable.Methods: We aimed to quantitatively reevaluate the efficacy of corticosteroids on COVID-19. Databases were searched for eligible meta-analyses/systematic reviews with available outcome data. For each association, we estimated the summary effect size with fixed- and random-effects models, 95% confidence intervals, and 95% prediction intervals. Heterogeneity, Egger’s test, evidence of small-study effects and excess significance bias, and subgroup analyses were rigorously evaluated.Results: Intended outcomes of 12 eligible studies were mortality, clinical improvement, hospitalization, mechanical ventilation (MV), adverse events (AEs), intensive care unit (ICU) stay, hospital stay, virus clearance time (VCT), and negative conversion. Corticosteroid administration was associated with a 27% risk reduction in MV [hazard ratio (HR): 0.73 (0.64–0.83)] and a 20% reduction in mortality of critically ill/severe COVID-19 patients [HR: 0.80 (0.65–0.98)]. Interestingly, shorter ICU stays and, conversely, potentially longer hospital stays, a longer VCT, and a longer time to negative conversion were associated with corticosteroid use. There was no significant impact of different corticosteroid doses on mortality. Only one study showed slightly excess significant bias. Caution should be applied given the weak nature of the evidence, and it has been confirmed by sensitivity analyses too.Conclusion: This umbrella study found benefits from corticosteroids on MV and especially the mortality of critically ill/severe patients with shorter ICU stays but prolonged hospital stays and VCT. The benefits and harms should be reevaluated and balanced before corticosteroids are cautiously prescribed in clinical practice.

Power-Enhanced Funnel Plots for Meta-Analysis

2020 ◽  
Vol 228 (1) ◽  
pp. 43-49 ◽  
Author(s):  
Michael Kossmeier ◽  
Ulrich S. Tran ◽  
Martin Voracek
Keyword(s):  
Statistical Power ◽  
Meta Analysis ◽  
Relevant Information ◽  
Selective Reporting ◽  
Graphical Display ◽  
Funnel Plot ◽  
Evidential Value ◽  
Graphical Displays ◽  
Funnel Plots ◽  
Meta Analyses

Abstract. Currently, dedicated graphical displays to depict study-level statistical power in the context of meta-analysis are unavailable. Here, we introduce the sunset (power-enhanced) funnel plot to visualize this relevant information for assessing the credibility, or evidential value, of a set of studies. The sunset funnel plot highlights the statistical power of primary studies to detect an underlying true effect of interest in the well-known funnel display with color-coded power regions and a second power axis. This graphical display allows meta-analysts to incorporate power considerations into classic funnel plot assessments of small-study effects. Nominally significant, but low-powered, studies might be seen as less credible and as more likely being affected by selective reporting. We exemplify the application of the sunset funnel plot with two published meta-analyses from medicine and psychology. Software to create this variation of the funnel plot is provided via a tailored R function. In conclusion, the sunset (power-enhanced) funnel plot is a novel and useful graphical display to critically examine and to present study-level power in the context of meta-analysis.

The Orchard Plot: Cultivating a Forest Plot for Use in Ecology, Evolution and Beyond

2019 ◽  
Author(s):  
Shinichi Nakagawa ◽  
Malgorzata Lagisz ◽  
Rose E O'Dea ◽  
Joanna Rutkowska ◽  
Yefeng Yang ◽  
...  
Keyword(s):  
Meta Analysis ◽  
R Package ◽  
Effect Sizes ◽  
Forest Plot ◽  
Point Estimates ◽  
Aggregate Effect ◽  
The Individual ◽  
Meta Analyses ◽  
Heterogeneous Effect ◽  
Intuitive Interpretation

‘Classic’ forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a ‘forest-like plot’, showing point estimates (with 95% confidence intervals; CIs) from a series of subgroups or categories in a meta-regression. We propose a modification of the forest-like plot, which we name the ‘orchard plot’. Orchard plots, in addition to showing overall mean effects and CIs from meta-analyses/regressions, also includes 95% prediction intervals (PIs), and the individual effect sizes scaled by their precision. The PI allows the user and reader to see the range in which an effect size from a future study may be expected to fall. The PI, therefore, provides an intuitive interpretation of any heterogeneity in the data. Supplementing the PI, the inclusion of underlying effect sizes also allows the user to see any influential or outlying effect sizes. We showcase the orchard plot with example datasets from ecology and evolution, using the R package, orchard, including several functions for visualizing meta-analytic data using forest-plot derivatives. We consider the orchard plot as a variant on the classic forest plot, cultivated to the needs of meta-analysts in ecology and evolution. Hopefully, the orchard plot will prove fruitful for visualizing large collections of heterogeneous effect sizes regardless of the field of study.

scholarly journals Comparative efficacy and safety of oral or transdermal opioids in the treatment of knee or hip osteoarthritis: a systematic review and Bayesian network meta-analysis protocol

BMJ Open ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. e022142
Author(s):  
Jun Wang ◽  
Yin Wang ◽  
Hui Zhang ◽  
Ming Lu ◽  
Weilu Gao ◽  
...  
Keyword(s):  
Bayesian Network ◽  
Meta Analysis ◽  
Hip Osteoarthritis ◽  
Sensitivity Analyses ◽  
Cochrane Library ◽  
Efficacy And Safety ◽  
Meta Analyses ◽  
Transdermal Opioids ◽  
And Function

IntroductionOsteoarthritis is a common degenerative joint disease that eventually leads to disability and poor quality of life. The main symptoms are joint pain and mobility disorders. If the patient has severe pain or other analgesics are contraindicated, opioids may be a viable treatment option. To evaluate and compare the efficacy and safety of opioids in the treatment of knee or hip osteoarthritis, we will integrate direct and indirect evidence using a Bayesian network meta-analysis to establish hierarchies of these drugs.Methods and analysisWe will search the Medical Literature Analysis and Retrieval System Online, Excerpta Medica database, Cumulative Index to Nursing and Allied Health Literature, Cochrane Library, Web of Science and PsycINFO databases as well as published and unpublished research in international registries and regulatory agency websites for osteoarthritis reports published prior to 5 January 2018. There will be no restrictions on the language. Randomised clinical trials that compare oral or transdermal opioids with other various opioids, placebo or no treatment for patients with knee or hip osteoarthritis will be included. The primary outcomes of efficacy will be pain and function. We will use pain and function scales to evaluate the main outcomes. The secondary outcomes of safety will be defined as the proportion of patients who have stopped treatment due to side effects. Pairwise meta-analyses and Bayesian network meta-analyses will be performed for all related outcome measures. We will conduct subgroup analyses and sensitivity analyses to assess the robustness of our findings. The Grading of Recommendations, Assessment, Development and Evaluations framework will be used to assess the quality of the evidence contributing to each network assessment.Ethics and disseminationThis study does not require formal ethical approval because individual patient data will not be included. The findings will be disseminated through peer-reviewed publications or conference presentations.PROSPERO registration numberCRD42018085503.

scholarly journals Leishmanicidal effects of resveratrol and its derivatives: a systematic review and meta-Analysis

2020 ◽  
Author(s):  
Nasrin Amiri Dashatan ◽  
Marzieh Ashrafmansouri ◽  
Mehdi Koushki ◽  
Nayebali Ahmadi
Keyword(s):  
Systematic Review ◽  
Publication Bias ◽  
Data Extraction ◽  
Meta Analysis ◽  
Sensitivity Analyses ◽  
Protective Effects ◽  
Random Effects Models ◽  
Important Health ◽  
Mean Differences ◽  
Meta Analyses

Abstract Background Leishmaniasis is one of the most important health problems worldwide. The evidence has suggested that resveratrol and its derivatives have anti-leishmanial effects; however, the results are inconsistent and inconclusive. The aim of this study was to assess the effect of resveratrol and its derivatives on the Leishmania viability through a systematic review and meta-analysis of available relevant studies. Methods The electronic databases PubMed, ScienceDirect, Embase, Web of Science and Scopus were queried between October 2000 and April 2020 using a comprehensive search strategy. The eligible articles selected and data extraction conducted by two reviewers. Mean differences of IC50 (concentration leading to reduction of 50% of Leishmania) for each outcome was calculated using random-effects models. Sensitivity analyses and prespecified subgroup were conducted to evaluate potential heterogeneity and the stability of the pooled results. Publication bias was evaluated using the Egger’s and Begg’s tests. We also followed the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines for this review. Results Ten studies were included in the meta-analysis. We observed that RSV and its derivatives had significant reducing effects on Leishmania viability in promastigote [24.02 µg/ml; (95% CI 17.1, 30.8); P < 0.05; I2 = 99.8%; P heterogeneity = 0.00] and amastigote [18.3 µg/ml; (95% CI 13.5, 23.2); P < 0.05; I2 = 99.6%; P heterogeneity = 0.00] stages of Leishmania. A significant publication bias was observed in the meta-analysis. Sensitivity analyses showed a similar effect size while reducing the heterogeneity. Subgroup analysis indicated that the pooled effects of leishmanicidal of resveratrol and its derivatives were affected by type of stilbenes and Leishmania species. Conclusions Our findings clearly suggest that the strategies for the treatment of leishmaniasis should be focused on natural products such as RSV and its derivatives. Further study is needed to identify the mechanisms mediating this protective effects of RSV and its derivatives in leishmaniasis.

scholarly journals When the Bough Breaks: A Systematic Review and Meta-Analysis of Mental Health Symptoms in Mothers of Young Children during the COVID-19 Pandemic

2021 ◽  
Author(s):  
Nicole Racine ◽  
Rachel Eirich ◽  
Jessica Cookee ◽  
Jenney Zhu ◽  
Paolo Pador ◽  
...  
Keyword(s):  
Mental Health ◽  
Young Children ◽  
Maternal Mental Health ◽  
Meta Analysis ◽  
Random Effect ◽  
Well Being ◽  
Anxiety Symptoms ◽  
Study Quality ◽  
Depression And Anxiety ◽  
Meta Analyses

Parents have experienced considerable challenges and stress during the COVID-19 pandemic, which may impact their well-being. This meta-analysis sought to identify: 1) the prevalence of depression and anxiety in parents of young children (&lt; age 5) during the COVID-19 pandemic, and 2) sociodemographic (e.g., parent age, minority status) and methodological moderators (e.g., study quality) that explain heterogeneity among studies. A systematic search was conducted across four databases from January 1st, 2020 to March 3st, 2021. A total of 18 non-overlapping studies (9,101 participants), all focused on maternal mental health, met inclusion criteria. Random-effect meta-analyses were conducted. Pooled prevalence estimates for clinically significant depression and anxiety symptoms for mothers of young children during the COVID-19 pandemic were 27.4% (95% CI: 21.5-34.3) and 43.5% (95% CI:27.5-60.9), respectively. Prevalence of clinically elevated depression and anxiety symptoms were higher in Europe and North America and among older mothers. Clinically elevated depressive symptoms were lower in studies with a higher percentage of racial and ethnic minority individuals. In comparison, clinically elevated anxiety symptoms were higher among studies of low study quality and in samples with highly educated mothers. Policies and resources targeting improvements in maternal mental health are essential.

scholarly journals Robust metrics and sensitivity analyses for meta-analyses of heterogeneous effects

2020 ◽  
Author(s):  
Maya B Mathur ◽  
Tyler VanderWeele
Keyword(s):  
R Package ◽  
Point Estimation ◽  
Effect Sizes ◽  
Sensitivity Analyses ◽  
Robust Methods ◽  
Heterogeneous Effects ◽  
Evidence Strength ◽  
Meta Analyses ◽  
Effect Heterogeneity ◽  
Statistical Metrics

We recently suggested new statistical metrics for routine reporting in random-effects meta-analyses to convey evidence strength for scientifically meaningful effects under effect heterogeneity. First, given a chosen threshold of meaningful effect size, we suggested reporting the estimated proportion of true effect sizes above this threshold. Second, we suggested reporting the proportion of effect sizes below a second, possibly symmetric, threshold in the opposite direction from the estimated mean. Our previous methods applied when the true effects are approximately normal, when the number of studies is relatively large, and when the proportion is between approximately 0.15 and 0.85. Here, we additionally describe robust methods for point estimation and inference that perform well under considerably more general conditions, as we validate in an extensive simulation study. The methods are implemented in the R package MetaUtility (function prop_stronger). We describe application of the robust methods to conducting sensitivity analyses for unmeasured confounding in meta-analyses.

scholarly journals Clinical course of pain and disability following primary lumbar discectomy: systematic review and meta-analysis

2020 ◽  
Vol 29 (7) ◽  
pp. 1660-1670 ◽  
Author(s):  
A. Rushton ◽  
N. R. Heneghan ◽  
M. W. Heymans ◽  
J. B. Staal ◽  
P. Goodwin
Keyword(s):  
Back Pain ◽  
Clinical Course ◽  
Meta Analysis ◽  
A Priori ◽  
Random Effect ◽  
Outcome Data ◽  
Lumbar Discectomy ◽  
Risk Of Bias ◽  
Leg Pain ◽  
Meta Analyses

Abstract Purpose To conduct a meta-analysis to describe clinical course of pain and disability in adult patients post-lumbar discectomy (PROSPERO: CRD42015020806). Methods Sensitive topic-based search strategy designed for individual databases was conducted. Patients (> 16 years) following first-time lumbar discectomy for sciatica/radiculopathy with no complications, investigated in inception (point of surgery) prospective cohort studies, were included. Studies including revision surgery or not published in English were excluded. Two reviewers independently searched information sources, assessed eligibility at title/abstract and full-text stages, extracted data, assessed risk of bias (modified QUIPs) and assessed GRADE. Authors were contacted to request raw data where data/variance data were missing. Meta-analyses evaluated outcomes at all available time points using the variance-weighted mean in random-effect meta-analyses. Means and 95% CIs were plotted over time for measurements reported on outcomes of leg pain, back pain and disability. Results A total of 87 studies (n = 31,034) at risk of bias (49 moderate, 38 high) were included. Clinically relevant improvements immediately following surgery (> MCID) for leg pain (0–10, mean before surgery 7.04, 50 studies, n = 14,910 participants) and disability were identified (0–100, mean before surgery 53.33, 48 studies, n = 15,037). Back pain also improved (0–10, mean before surgery 4.72, 53 studies, n = 14,877). Improvement in all outcomes was maintained (to 7 years). Meta-regression analyses to assess the relationship between outcome data and a priori potential covariates found preoperative back pain and disability predictive for outcome. Conclusion Moderate-level evidence supports clinically relevant immediate improvement in leg pain and disability following lumbar discectomy with accompanying improvements in back pain. Graphic abstract These slides can be retrieved under Electronic Supplementary Material.

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