Cited by 1,125Data Analysis with RScientific Computing and Data ManagementMeta-analysis and systematic reviews

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Closing the Gap between Methodologists and End-Users: R as a Computational Back-End

Open access

Wallace, Byron C., Dahabreh, Issa J., Trikalinos, Thomas A., Lau, Joseph, Trow, Paul, Schmid, Christopher H.·2012·Journal of Statistical Software

DOI 10.18637/jss.v049.i05

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Abstract

The R environment provides a natural platform for developing new statistical methods due to the mathematical expressiveness of the language, the large number of existing libraries, and the active developer community. One drawback to R, however, is the learning curve; programming is a deterrent to non-technical users, who typically prefer graphical user interfaces (GUIs) to command line environments. Thus, while statisticians develop new methods in R, practitioners are often behind in terms of the statistical techniques they use as they rely on GUI applications. Meta-analysis is an instructive example; cutting-edge meta-analysis methods are often ignored by the overwhelming majority of practitioners, in part because they have no easy way of applying them. This paper proposes a strategy to close the gap between the statistical state-of-the-science and what is applied in practice. We present open-source meta-analysis software that uses R as the underlying statistical engine, and Python for the GUI. We present a framework that allows methodologists to implement new methods in R that are then automatically integrated into the GUI for use by end-users, so long as the programmer conforms to our interface. Such an approach allows an intuitive interface for non-technical users while leveraging the latest advanced statistical methods implemented by methodologists.

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Meta-analysis in clinical trials
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“A striking example is the almost universal use of the DerSimonian-Laird method for random eﬀects univariate meta-analysis (DerSimonian and Laird 1986) (the default or only method in the aforementioned programs), irrespective of good data that alternative random eﬀect methods have better statistical…”
Method
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“Line 2 is the call out to the random eﬀects as implemented by the metafor package (Viechtbauer 2010).”
MethodInfluential
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Kendall, M. (1937) · Nature · doi:10.1038/139737d0 · Cited by 9,676 · cited 1×
“…disciplines, including the natural sciences, such as physics, astronomy (Airy 1875) and ecology (Osenberg, Sarnelle, and Goldberg 1999), as well as medicine (Simpson and Pearson 1904; Fisher 1925), epidemiology (Stroup et al. 2000), psychology (Glass 1976), and education (Kulik and Kulik 1989).”
Background
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“…disciplines, including the natural sciences, such as physics, astronomy (Airy 1875) and ecology (Osenberg, Sarnelle, and Goldberg 1999), as well as medicine (Simpson and Pearson 1904; Fisher 1925), epidemiology (Stroup et al. 2000), psychology (Glass 1976), and education (Kulik and Kulik 1989).”
Background
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Viechtbauer, W. (2005) · Journal of Educational and Behavioral Statistics · doi:10.3102/10769986030003261 · Cited by 1,699 · cited 2×
“…random eﬀects univariate meta-analysis (DerSimonian and Laird 1986) (the default or only method in the aforementioned programs), irrespective of good data that alternative random eﬀect methods have better statistical properties (Turner, Omar, Yang, Goldstein, and Thompson 2000; Viechtbauer 2005).”
Method
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Fox, J. (2005) · Journal of Statistical Software · doi:10.18637/jss.v014.i09 · Cited by 1,098 · cited 1×
“Our approach is similar in spirit to the R Commander package ( Rcmdr ), which provides an “easy-to-use, cross-platform, extensible GUI” with enough functionality to span a basic statistics course (Fox 2005).”
Method
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“Currently, meta-analysis methods are implemented in many statistical packages, including Stata (Sterne 2009), SPSS (Lipsey and Wilson 2001), SAS (Arthur, Bennett, Huﬀcutt, Arthur, and Bennett 2001) and R (Schwarzer 2012; Lumley 2009; Viechtbauer 2010), in addition to Microsoft Excel plug-ins, such as MIX (Bax, Yu, Ike…”
Method
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Simpson, L. (1904) · British medical journal · doi:10.1136/bmj.2.2288.1243 · Cited by 283 · cited 1×
“…disciplines, including the natural sciences, such as physics, astronomy (Airy 1875) and ecology (Osenberg, Sarnelle, and Goldberg 1999), as well as medicine (Simpson and Pearson 1904; Fisher 1925), epidemiology (Stroup et al. 2000), psychology (Glass 1976), and education (Kulik and Kulik 1989).”
Background

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Midterm outcomes of 146 EVOLVE Proline modular radial head prostheses: a systematic review
Laumonerie, P., Raad, M., Tibbo, M., Kerezoudis, P., Bonnevialle, N., & Mansat, P. (2019) · Shoulder & Elbow · doi:10.1177/1758573219850111 · Cited by 3
Polymorphisms of anti-Müllerian hormone signaling pathway in healthy Singapore women: population differences, endocrine effects and reproductive outcomes
Yu, E., Zhu, H., Li, Y., Chua, S. E., Indran, I. R., Li, J., & Yong, E. (2016) · Gynecological Endocrinology · doi:10.3109/09513590.2015.1117068 · Cited by 3
“Pooled data analysis was performed with OpenMetaAnalyst software (Brown University, Providence, RI) [10].”
Method
21. Graphical Presentation of Results
Lortie, C., Lau, J., & Lajeunesse, M. (2013) · Princeton University Press eBooks · doi:10.1515/9781400846184-023 · Cited by 3
Self-citation
Data Curation: Towards a Tool for All
Dias, J., Cunha, J., & Pereira, R. (2020) · Interacción · doi:10.1007/978-3-030-60700-5_23 · Cited by 3
“Wallace et al. propose a tool to allow users with less statistical skills to make use of advanced models written using the R language [20].”
Method
Effects of Inhaled β 2 ‐ AR Agonists in Athletes According to the WADA 2025 List: New Insights From a Systematic Review and Meta‐Analysis
Calzetta, L., Pistocchini, E., Manzetti, G. M., Gholamalishahi, S., Cammarata, M., Muscoli, S., Ora, J., & Rogliani, P. (2025) · Scandinavian Journal of Medicine and Science in Sports · doi:10.1111/sms.70197 · Cited by 2
A systematic review and meta-analysis exploring the recruitment hurdles and nonparticipation rate in noninvasive brain stimulation for addictive disorders
Sevda, P., Saha, P., Sarkar, S., Verma, R., & Nebhinani, N. (2025) · Journal of Addictive Diseases · doi:10.1080/10550887.2025.2564446 · Cited by 2
Outpatient total elbow arthroplasty—outcomes and complications: a systematic review and meta-analysis
Singh, V., Nazar, N., Wiyono, L., Paul, A. J., & Phadnis, J. (2025) · JSES Reviews Reports and Techniques · doi:10.1016/j.xrrt.2025.100592 · Cited by 1
“27 The confidence interval (CI) was set at 95% ( P value is significant if it is less than .05).”
Efficacy of Sialendoscopy with Steroid Irrigation for Non-Lithiasic Chronic Sialadenitis: A Systematic Review and Proportional Meta-Analysis
Tsikopoulos, A., Garefis, K., Sidiropoulos, K., Triaridis, S., Nikolaidis, V., & Konstantinidis, I. (2025) · Journal of Clinical Medicine · doi:10.3390/jcm14155202 · Cited by 2
“The binary random-effect (DerSimonian and Laird) method was implemented [33].”
Esophageal stenting and endoscopic vacuum therapy for esophageal defects: a systematic review and meta-analysis of observational studies
Saqib, M., Iftikhar, M., Ahmed, K., Shahid, H., Shehr, I., Khan, Y., Iqbal, M. A., & Mumtaz, H. (2025) · Annals of Medicine and Surgery · doi:10.1097/ms9.0000000000003525 · Cited by 2
“Meta-analyses were conducted using OpenMeta Analyst software [ 16 ] under a random-effects model to account for inter-study variability.”
Genomic profiling of head and neck adenoid cystic carcinoma: A systematic review and meta-analysis.
Sharma, M., Narwal, A., Kamboj, M., Devi, A., Kumar, A., & Vijayakumar, G. (2025) · Journal of Cancer Research and Therapeutics · doi:10.4103/jcrt.jcrt_908_25 · Cited by 2
GLOSSA : A user‐friendly R Shiny application for Bayesian machine learning analysis of marine species distribution
Mestre‐Tomás, J., Fuster‐Alonso, A., Bellido-Millán, J. M., & Marta Coll, M. (2025) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.70167 · Cited by 4
“Environmental variables should be in raster format and can be sourced from databases such as the National Oceanic and Atmospheric Administration (NOAA, https://www.noaa.gov/ ), the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP, https://www.isimip.org/ ), or Bio-ORACLE (…”
A systematic review supporting the Society for Vascular Surgery guideline update on the management of intermittent claudication
Saadi, S. M., Nayfeh, T., Rajjoub, R., Hasan, B., Firwana, M., Jawaid, T., Hazem, W., Shah, S. H., Alsawaf, Y., Seisa, M. O., et al. (2025) · Journal of Vascular Surgery · doi:10.1016/j.jvs.2024.12.135 · Cited by 4
Endotension following endovascular aortic repair: systematic review and meta-analysis on occurrence rate, treatment approaches and outcomes.
Cicala, N., Massoni, C. B., Meroni, P., Catasta, A., Freyrie, A., & Perini, P. (2025) · International Angiology · doi:10.23736/s0392-9590.25.05373-8 · Cited by 2
Bypass is associated with lower treatment failure than stricturoplasty in duodenal Crohn's disease: a systematic review with pairwise and network meta-analyses.
Dourado, J., Wignakumar, A., Emile, S., Rogers, P., Weiss, B., Khan, S. M., Aeschbacher, P., & Wexner, S. (2025) · Journal of Gastrointestinal Surgery · doi:10.1016/j.gassur.2025.102041 · Cited by 2
Nepafenac role in macular swelling prevention and in visual outcome after cataract surgery – a systematic review and meta-analysis
Almasri, M., Ghareeb, A., Ismaiel, A., Leucuța, D., & Nicoară, S. (2025) · European Journal of Ophthalmology · doi:10.1177/11206721251317652 · Cited by 2
“24,25 Between-study heterogeneity was checked using the χ ²-based Q-test and I².”
Efficacy of Transcutaneous Electrical Nerve Stimulation in Management of Cancer Pain: a Meta Analysis
Kaye, A., Allen, K. E., Shah, S. S., Smith, S. A., Plaisance, T. R., Brouillette, A. E., Despanie, D. J., Payton, T. D., Rieger, R., Singh, N., et al. (2025) · Current Pain and Headache Reports · doi:10.1007/s11916-024-01337-0 · Cited by 2
Single‐arm interventional versus observational studies for assessing efficacy: A meta‐epidemiological study
Chappell, M., Watkins, D., Sanderson, A., di Ruffano, L. F., Miller, P., Fewster, H., Fitzgerald, A., Edwards, M., & McCool, R. (2025) · Cochrane evidence synthesis and methods · doi:10.1002/cesm.70016 · Cited by 2
“For each included review, sub ‐ group analysis was conducted on dichotomous outcome data for SATs and single ‐ arm cohorts in OpenMeta [12] using DerSimonian ‐ Laird random effects meta ‐ analysis.”
HIV-1 Antiretroviral Drug Resistance in Mozambique: A Systematic Review and Meta-Analysis
Gonçalves, P., Mascarenhas, P., Marcelino, R., Mabunda, N., Kroidl, A., Buck, W., Jani, I., Palladino, C., & Taveira, N. (2024) · Viruses · doi:10.3390/v16121808 · Cited by 2
Effect of TED Talks on University Students' Speaking Skill Competency: A Meta-Analysis
Patty, J. (2024) · International Journal of Multidisciplinary Approach Research and Science · doi:10.59653/ijmars.v2i03.923 · Cited by 2
“The effect size data from the individual studies were synthesized using the openMEE software (Wallace et al., 2012).”
Method
Fast absorbing gut sutures in dermatologic surgery: a systematic review and meta-analysis
Seger, E. W., McClure, S. P., Neill, B. C., & Jibbe, A. (2024) · Archives of Dermatological Research · doi:10.1007/s00403-024-02973-7 · Cited by 2
“Statistical comparisons were made using Open Meta-Analyst software [12].”
Efficacy of Split Versus Full-Body Resistance Training on Strength and Muscle Growth: A Systematic Review With Meta-Analysis
Ramos‐Campo, D. J., Benito-Peinado, P. J., Andreu‐Caravaca, L., Rojo‐Tirado, M. Á., & Rubio‐Arias, J. Á. (2024) · The Journal of Strength and Conditioning Research · doi:10.1519/jsc.0000000000004774 · Cited by 4
“In addition, a sensitivity analysis was performed using the leave-1-out method (37) with OpenMetaAnalyst.”
Method
Pro- and Anti-inflammatory Biomarkers Responses after Aerobic Training in Heart Transplant Recipients: A Systematic Review and Meta-analysis
Franzoni, L., da Motta, S. B., Carvalho, G., Costa, R. R., Ahner, M. M., Saffi, M., Pereira, A. A., Pereira, A. H., da Silveira, A. D., & Stein, R. (2024) · Current Cardiology Reviews · doi:10.2174/011573403x269909240320061952 · Cited by 2
“All analyses were performed using OpenMeta Analyst Software, version 10.10 [18-21].”
Influential
Deap-seated infection and nonunion following internal fixation for Charcot foot deformity correction. A proportional meta-analysis of level 4 evidence.
Tsikopoulos, K., Sidiropoulos, K., Meroni, G., Christofilos, S., Kazamias, K., Abbas, K. S., Papaioannou, P., Mavridis, D., Kavarthapu, V., & Givissis, P. (2024) · Journal of Orthopaedic Science · doi:10.1016/j.jos.2024.03.004 · Cited by 2
Rhinoplasty for Sinonasal Deformities in Granulomatosis with Polyangiitis: A Systematic Review and Meta-Analysis
Alanazi, F., Alenezi, M., Alanazy, S., & Yahya, B. (2023) · The Journal of craniofacial surgery (Print) · doi:10.1097/scs.0000000000009721 · Cited by 2
“27”
Incidence and Comparison of Suicide in Various Phases of the Menstrual Cycle: a Systematic Review and Meta-analysis
Alnashwan, Y. A., Rashid, A. M., Javaid, S. S., Kharoshah, M., Arun, M., Dsouza, H., Atreya, A., & Menezes, R. (2023) · Acta Informatica Medica · doi:10.5455/aim.2023.31.76-83 · Cited by 2
“I2 was used to assess the heterogeneity between the studies and a value of I2 = 25%–50% was considered mild, 50%–75% as moderate, and > 75% as severe (15).”
Method
Next Generation Sequencing of Human Platelet Antigens for Routine Clinical Investigations and Donor Screening.
Guglielmino, J., & Jackson, D. (2022) · Transfusion Medicine Reviews · doi:10.1016/j.tmrv.2022.01.001 · Cited by 2
Preoperative predictors for a successful return to sport following anterior cruciate ligament reconstruction (ACLR): a protocol for a systematic review and meta-analysis
Carter, H., Lewis, G., & Smith, B. E. (2021) · BMJ Open · doi:10.1136/bmjopen-2020-048295 · Cited by 2
“37 Subgroup analysis Subgroup analysis may be performed, if possible, according to the predictors associated with a RTS compared with those associated with a return to preinjury level of physical activity.”
Is livestock husbandry more stressing than other anthropic activities to wild carnivores?
Arzabe, A., Retamal, P., & Simonetti, J. A. (2021) · Applied Animal Behaviour Science · doi:10.1016/j.applanim.2021.105380 · Cited by 2
Systematic Review and Pooled Meta-analysis of the Current Status of Coronary Revascularization Surgery in Bangladesh
Sazzad, F., Ler, A., Ganesh, G., Kung, M., & Kofidis, T. (2021) · doi:10.3329/bhj.v35i2.52894 · Cited by 2
Evaluating the Efficacy and Safety of the Existing Repurposed Pharmacological Agents for Treating COVID-19: A Meta-analysis and Systematic Review of Clinical Trials
Choupoo, N. S., Das, S. K., Haldar, R., Sarkar, H., Tewari, R., & Ray, S. (2020) · Indian Journal of Critical Care Medicine · doi:10.5005/jp-journals-10071-23664 · Cited by 2
Comparison of Glycemic Control between Intensive Insulin Regimen and Continuous Subcutaneous Insulin infusion: A Meta-Analysis Report of Type-1 Diabetics from Randomized Controlled Trials
Aziz, K., & Othman, A. (2020) · medRxiv · doi:10.1101/2020.06.01.20119693 · Cited by 2
Methicillin-Resistant Staphylococcus Aureus colonization in Iranian Health Care Workers: A Systemic Review and Meta-Analysis
Mohammadi, N., Danesh, M. A. P., & Allami, A. (2019) · The Journal of Qazvin University of Medical Sciences · doi:10.32598/jqums.23.5.452 · Cited by 2
The Development of Web-based Graphical User Interface for Unified Modeling Data with Multi (Correlated) Responses
Tirta, I., & Anggraeni, D. (2018) · Journal of Physics Conference Series · doi:10.1088/1742-6596/1008/1/012003 · Cited by 2
SLEEP DEFICITS AND EXECUTIVE FUNCTIONS AT DIFFERENT DEVELOPMENTAL STAGES - METAANALYSIS
Molińska, M., & Złotogórska, A. (2016) · The Polish Journal of Aviation Medicine Bioengineering and Psychology · doi:10.13174/pjambp.31.12.2016.03 · Cited by 2
Reply: Left atrial appendage occlusion devices versus pharmacological agents for stroke prevention in atrial fibrillation: testing the noninferiority margins.
Parashar, A., Agarwal, S., Bajaj, N., Tuzcu, E., & Kapadia, S. (2014) · JACC: Cardiovascular Interventions · doi:10.1016/j.jcin.2014.05.010 · Cited by 2
Arabic Location Named Entity Recognition for Tweets using a Deep Learning Approach
Alzaidi, B. S., Abushark, Y. B., & Khan, A. I. (2022) · International Journal of Advanced Computer Science and Applications · doi:10.14569/ijacsa.2022.0131211 · Cited by 2
“The prototype implementation is based on open-source tools using R and Python which support rapid development and fast prototyping [30].”
Method
HCI International 2020 – Late Breaking Posters: 22nd International Conference, HCII 2020, Copenhagen, Denmark, July 19–24, 2020, Proceedings, Part I
Dahiya, A. (2020) · Interacción · doi:10.1007/978-3-030-60700-5 · Cited by 2
Influence of Imaging Modality on the Detection of Periapical Lesions in Root-Filled Teeth: A Systematic Review and Meta-Analysis.
Segura-Egea, J., Segura-Raya, C., Martín-González, J., Cabrera-Fernández, A., Areal-Quecuty, V., & Cabanillas-Balsera, D. (2026) · International Endodontic Journal · doi:10.1111/iej.70245 · Cited by 1
Cerebral amyloid angiopathy-related inflammation (CAA-ri): an updated systematic review and meta-analysis
Laterza, V., Magro, G., Tosto, F., & Quattrone, A. (2026) · Journal of Neurology · doi:10.1007/s00415-026-13969-w · Cited by 1
The effect of bilevel ventilation or modified continuous positive airway pressure on treatment adherence in adults with obstructive sleep apnea: a systematic review and meta-analysis
Messineo, L., Bakker, J. P., Noah, W. H., & White, D. P. (2026) · EClinicalMedicine · doi:10.1016/j.eclinm.2026.103993 · Cited by 1
Radiolabeled FAPI PET versus 18 F-FDG PET for diagnosing breast cancer: A systematic review and meta-analysis
Ruan, D., Zhao, L., Fu, H., Chen, H.-J., & Herrmann, K. (2026) · Journal of Nuclear Medicine and Molecular Imaging · doi:10.65457/jnmmi-2026-0030 · Cited by 1
Direct oral anticoagulants versus vitamin K antagonists for atrial fibrillation patients on dialysis: A systematic review and meta-analysis of randomized controlled trials and real-world evidence
Shaheen, O., Hamdy, M., Afifi, I. A., Hassan, A. A., Kassar, O., Ismail, A., Bedwany, S. S., Elhalawany, B. A. E., & Diab, R. A. (2026) · Journal of Thrombosis and Thrombolysis · doi:10.1007/s11239-026-03322-3 · Cited by 1
“Analysis was done using R software version 4.5.0 and OpenMeta[Analyst] software [ 30 ].”
Influential
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Authors: Wallace, B. C., Dahabreh, I. J., Trikalinos, T. A., Lau, J., Trow, P., & Schmid, C. H.
Affiliations: Tufts University (US)
ORCID: Wallace, Byron C.
Dahabreh, Issa J.
Trikalinos, Thomas A.
Lau, Joseph
Schmid, Christopher H.
Venue: Journal of Statistical Software
Publisher: Foundation for Open Access Statistic
Published: 2012
Volume: 49
Issue: 5
ISSN: 1548-7660 (ISSN-L)
DOI: 10.18637/jss.v049.i05
OpenAlex: W2120771911
Cited by: 1,125
References: 27
Citations by year: 2026: 50 · 2025: 89 · 2024: 115 · 2023: 105 · 2022: 127 · 2021: 143 · 2020: 133 · 2019: 94 · 2018: 76 · 2017: 68 · 2016: 65 · 2015: 37 · 2014: 17 · 2013: 4 · 2012: 1
FWCI: 18.44
Type: journal article
Language: en
Open access: diamond
doi.org
Licence: cc-by
Locations: Journal of Statistical Software (publishedVersion, cc-by)
RePEc: Research Papers in Economics (submittedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics: Physical Sciences › Mathematics › Statistics and Probability › Data Analysis with R
Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
Social Sciences › Decision Sciences › Statistics, Probability and Uncertainty › Meta-analysis and systematic reviews
Keywords: R, meta-analysis software, graphical user interface, Python, open source software, software integration, statistical software development, non-technical users

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Closing the Gap between Methodologists and End-Users: R as a Computational Back-End

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