Closing the Gap between Methodologists and End-Users: R as a Computational Back-End
Open accessAbstract
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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Riesel, A. (2019) · Psychophysiology · doi:10.1111/psyp.13348 · Cited by 170 · see citing works
Rogliani, P., Calzetta, L., Cavalli, F., Matera, M. G., & Cazzola, M. (2016) · Pulmonary Pharmacology & Therapeutics · doi:10.1016/j.pupt.2016.07.009 · Cited by 168 · see citing works
Clamor, A., Lincoln, T. M., Thayer, J. F., & Koenig, J. (2016) · British Journal of Psychiatry · doi:10.1192/bjp.bp.114.160762 · Cited by 167 · see citing works
Lajeunesse, M. (2013) · Princeton University Press eBooks · doi:10.1515/9781400846184-015 · Cited by 164 · see citing works
Tariq, R., Pardi, D. S., Bartlett, M. G., & Khanna, S. (2018) · Clinical Infectious Diseases · doi:10.1093/cid/ciy721 · Cited by 175 · see citing works
Stellingwerf, M., van Praag, E. V., Tozer, P., Bemelman, W., & Buskens, C. (2019) · BJS Open · doi:10.1002/bjs5.50129 · Cited by 160 · see citing works
Bellolio, M., Gilani, W. I., Barrionuevo, P., Murad, M., Erwin, P., Anderson, J. R., Miner, J., & Hess, E. (2016) · Academic Emergency Medicine · doi:10.1111/acem.12875 · Cited by 159 · see citing works
Paul, S., Dickstein, A. M., Saxena, A., Terrin, N., Viveiros, K., Balk, E., & Wong, J. B. (2017) · Hepatology · doi:10.1002/hep.29082 · Cited by 154 · see citing works
“Statistical analyses were performed with OpenMetaAnalyst(18) and the metafor package in R, version 3.2.1 (R Foundation for Statistical Computing).”
MethodInfluentialBora, E., & Özerdem, A. (2017) · Psychological Medicine · doi:10.1017/s0033291717001490 · Cited by 173 · see citing works
“Meta-analyses were performed using packages in R environment (OpenMetaAnalyst, Metafor) (Viechtbauer, 2010; Wallace et al. 2012).”
MethodSocial cognition in schizophrenia in comparison to bipolar disorder: A meta-analysis.
Bora, E., & Pantelis, C. (2016) · Schizophrenia Research · doi:10.1016/j.schres.2016.04.018 · Cited by 151 · see citing works
“7 on a Windows platform (Bax et al., 2006; Viechtbauer, 2010; Wallace et al., 2012).”
MethodMaternal body mass index and pregnancy outcomes: a systematic review and metaanalysis
D’Souza, R., Horyn, I., Pavalagantharajah, S., Zaffar, N., & Jacob, C.-E. (2019) · American Journal of Obstetrics & Gynecology MFM · doi:10.1016/j.ajogmf.2019.100041 · Cited by 150 · see citing works
Vijayvargiya, P., Camilleri, M., Chedid, V. G., Mandawat, A., Erwin, P., & Murad, M. (2019) · Gastroenterology · doi:10.1053/j.gastro.2019.01.249 · Cited by 147 · see citing works
Social cognition in alcohol use disorder: a meta-analysis
Bora, E., & Zorlu, N. (2016) · Addiction · doi:10.1111/add.13486 · Cited by 158 · see citing works
“Meta-analyses were performed using packages in the R environment (OpenMetaAnalyst, Metafor) [52,53].”
MethodBulluck, H., Chan, M., Paradies, V., Yellon, R., Ho, H., Chan, M., Chin, C., Tan, J. W., & Hausenloy, D. (2018) · Journal of Cardiovascular Magnetic Resonance · doi:10.1186/s12968-018-0494-3 · Cited by 142 · see citing works
Dubosh, N. M., Bellolio, M., Rabinstein, A., & Edlow, J. (2016) · Stroke · doi:10.1161/strokeaha.115.011386 · Cited by 141
Memory and executive functions in persons with type 2 diabetes: a meta‐analysis
Sadanand, S., Balachandar, R., & Bharath, S. (2016) · Diabetes/Metabolism Research Reviews · doi:10.1002/dmrr.2664 · Cited by 141 · see citing works
“Using ‘OpenMetaAnalyst’ [40,41], combined d values were calculated for each sub-domain using continuous random effects model.”
MethodInfluentialBora, E., & Köse, S. (2016) · International Journal of Eating Disorders · doi:10.1002/eat.22572 · Cited by 139 · see citing works
Salmasi, S., Loewen, P. S., Tandun, R., Andrade, J. G., & Vera, M. A. D. (2020) · BMJ Open · doi:10.1136/bmjopen-2019-034778 · Cited by 154 · see citing works
Social cognition in Huntington's disease: A meta-analysis.
Bora, E., Velakoulis, D., & Walterfang, M. (2016) · Behavioural Brain Research · doi:10.1016/j.bbr.2015.10.001 · Cited by 138 · see citing works
Smith, B. E., Hendrick, P., Smith, T. O., Bateman, M., Moffatt, F., Rathleff, M., Selfe, J., & Logan, P. (2017) · British Journal of Sports Medicine · doi:10.1136/bjsports-2016-097383 · Cited by 137 · see citing works
Libânio, D., Costa, M., Pimentel-Nunes, P., & Dinis-Ribeiro, M. (2016) · Gastrointestinal Endoscopy · doi:10.1016/j.gie.2016.06.033 · Cited by 134
Tomşa, R., Gutu, S., Cojocaru, D., Gutiérrez-Bermejo, B., Flores, N., & Jenaro, C. (2021) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph18041980 · Cited by 132 · see citing works
“We used OpenMeta-Analyst [58] and Jamovi software [59] and a Bayesian random-effects model with a 95% credible interval (95% CI).”
MethodThe Impact of SARS‐CoV ‐2 on Stroke Epidemiology and Care: A Meta‐Analysis
Katsanos, A. H., Palaiodimou, L., Zand, R., Yaghi, S. R., Kamel, H., Navi, B. B., Turc, G., Romoli, M., Sharma, V. K., Mavridis, D., et al. (2020) · Annals of Neurology · doi:10.1002/ana.25967 · Cited by 138 · see citing works
Bellolio, M., Puls, H., Anderson, J. L., Gilani, W. I., Murad, M., Barrionuevo, P., Erwin, P., Wang, Z., & Hess, E. (2016) · BMJ Open · doi:10.1136/bmjopen-2016-011384 · Cited by 132 · see citing works
Meta-analysis of cognitive performance in fibromyalgia
Bell, T. R., Trost, Z., Buelow, M. T., Clay, O. J., Younger, J., Moore, D., & Crowe, M. G. (2018) · Journal of Clinical and Experimental Neuropsychology · doi:10.1080/13803395.2017.1422699 · Cited by 162 · see citing works
Varghese, A., Joseph, J., Vijay, V., Khakha, D. C., Dhandapani, M., Gigini, G., & Kaimal, R. (2021) · Journal of Clinical Nursing · doi:10.1111/jocn.15987 · Cited by 129 · see citing works
Cazzola, M., Rogliani, P., Calzetta, L., & Matera, M. (2018) · European Respiratory Journal · doi:10.1183/13993003.01586-2018 · Cited by 127 · see citing works
Cham, C. Q., Ibrahim, N., Siau, C. S., Kalaman, C. R., Ho, M. C., Yahya, A. N., Visvalingam, U., Roslan, S. B., Rahman, F. N. A., & Lee, K. W. (2022) · Healthcare · doi:10.3390/healthcare10122423 · Cited by 166 · see citing works
“Open Meta (Analyst) [38] was used to conduct the meta-analysis for this study.”
MethodLee, J. K. H., Lam, G., Shin, T., Kim, J., Krishnan, A., Greenberg, D. P., & Chit, A. (2018) · Expert Review of Vaccines · doi:10.1080/14760584.2018.1471989 · Cited by 143 · see citing works
Ospina, N. S., Rodríguez-Gutiérrez, R., Maraka, S., Ycaza, A. E. E. D., Jasim, S., Castañeda-Guarderas, A., Gionfriddo, M., Nofal, A. A., Brito, J. P., Erwin, P., et al. (2016) · World Journal of Surgery · doi:10.1007/s00268-016-3514-1 · Cited by 124 · see citing works
“All statistical analyses were performed using Open-Meta [16].”
MethodBeckwée, D., Leysen, L., Meuwis, K., & Adriaenssens, N. (2017) · Supportive Care in Cancer · doi:10.1007/s00520-017-3613-z · Cited by 123 · see citing works
The effects of ketamine on the mismatch negativity (MMN) in humans - A meta-analysis.
Rosburg, T., & Kreitschmann-Andermahr, I. (2016) · Clinical Neurophysiology · doi:10.1016/j.clinph.2015.10.062 · Cited by 123 · see citing works
“For the analysis of the drug effects, the mean amplitude and latencies (± SD) of each study were entered into OpenMeta Analyst (Brown University, Wallace et al., 2012) and effects sizes of the ketamine effects were calculated.”
Treatment of Thyroid Dysfunction and Serum Lipids: A Systematic Review and Meta-analysis
Kotwal, A., CORTES, T. M., Genere, N., Hamidi, O., Jasim, S., Newman, C. B., Prokop, L. J., Murad, M. H., & Alahdab, F. (2020) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/clinem/dgaa672 · Cited by 168 · see citing works
Jiritano, F., Serraino, G. F., Cate, H. T., Fina, D., Matteucci, M., Mastroroberto, P., & Lorusso, R. (2020) · Intensive Care Medicine · doi:10.1007/s00134-020-06031-4 · Cited by 159 · see citing works
Frequency of self-reported drug allergy: A systematic review and meta-analysis with meta-regression.
Sousa-Pinto, B., Fonseca, J., & Gomes, E. (2017) · Annals of Allergy, Asthma & Immunology · doi:10.1016/j.anai.2017.07.009 · Cited by 122 · see citing works
Ali, N., Tian, H., Thabane, L., Ma, J., Wu, H., Zhong, Q., Gao, Y., Sun, C., Zhu, Y., & Wang, T. (2022) · The journal of prevention of Alzheimer's disease · doi:10.14283/jpad.2022.16 · Cited by 121 · see citing works
“10), was used for data processing (31), while RevMan V5.”
MethodKishita, N., Hammond, L., Dietrich, C. M., Mioshi, E., Haapala, I., Biggs, S., & Kurrle, S. (2018) · International Psychogeriatrics · doi:10.1017/s1041610218000947 · Cited by 119 · see citing works
“All data were analyzed using the Open MetaAnalyst (Wallace et al., 2012).”
MethodPalaiodimou, L., Stefanou, M.-I., Katsanos, A., Fragkou, P., Papadopoulou, M., Moschovos, C., Michopoulos, I., Kokotis, P., Bakirtzis, C., Naska, A., et al. (2021) · European Journal of Neurology · doi:10.1111/ene.14860 · Cited by 116 · see citing works
“All statistical analyses were conducted using the OpenMetaAnalyst [23] and Stata Statistical Software Release 13 for Windows (StataCorp LP).”
MethodChrcanovic, B., Albrektsson, T., & Wennerberg, A. (2015) · E -journal of dentistry · doi:10.1016/j.jdent.2014.11.007 · Cited by 115
“The data were analyzed using OpenMeta[Analyst] [9].”
Willcutts, K. F., Chung, M. C., Erenberg, C. L., Finn, K. L., Schirmer, B. D., & Byham-Gray, L. D. (2016) · Annals of Surgery · doi:10.1097/sla.0000000000001644 · Cited by 115 · see citing works
“The data for each study were exported to OpenMeta-Analyst (Brown University, RI) for statistical analysis.(23) If there were 2 or more studies and the degree of clinical heterogeneity was determined to be logical by the research team, the overall pooled odds ratios (ORs) for dichotomous outcomes and difference in mean…”
MethodAlahdab, F., Arwani, R., Pasha, A. K., Razouki, Z. A., Prokop, L. J., Huber, T. S., & Murad, M. H. (2018) · Journal of Vascular Surgery · doi:10.1016/j.jvs.2017.12.046 · Cited by 114 · see citing works
“Statistical analyses were conducted using OpenMeta[Analyst].(14) All values were two tailed, and a P < .”
MethodKrivicich, L. M., Kunze, K., Parvaresh, K. C., Jan, K., Devinney, A., Vadhera, A. S., LaPrade, R., & Chahla, J. (2021) · American Journal of Sports Medicine · doi:10.1177/03635465211017514 · Cited by 114 · see citing works
Prevalence, awareness and control of hypertension in Ghana: A systematic review and meta-analysis
Bosu, W., & Bosu, D. K. (2021) · PLoS ONE · doi:10.1371/journal.pone.0248137 · Cited by 114 · see citing works
“Except for the leave-one-out influence analysis performed with OpenMeta (analyst) software [38], all statistical analyses were performed in Stata version 15 for windows [39].”
MethodBora, E., Velakoulis, D., & Walterfang, M. (2016) · Journal of Geriatric Psychiatry and Neurology · doi:10.1177/0891988716640375 · Cited by 110 · see citing works
“7 on a Windows platform andpackages in R environment (OpenMetaAnalyst, Metafor).(39-41) Effect sizes were weighted using the inverse variance method, and a random effects model (DerSimonian–Laird estimate) was used because the distributions of effect sizes were heterogeneous for the number of variables.”
MethodInfluentialHealth Literacy and Outcomes among Patients with Heart Failure A Systematic Review and Meta-Analysis
Fabbri, M., Murad, M., Wennberg, A., Turcano, P., Erwin, P., Alahdab, F., Berti, A., Manemann, S., Yost, K., Rutten, L. F. F., et al. (2020) · JACC. Heart failure · doi:10.1016/j.jchf.2019.11.007 · Cited by 110 · see citing works
“All the analyses were performed with Open-meta (30).”
Method
- Authors
- Wallace, B. C., Dahabreh, I. J., Trikalinos, T. A., Lau, J., Trow, P., & Schmid, C. H.
- Affiliations
- Tufts University (US)
- Venue
- Journal of Statistical Software
- Publisher
- Foundation for Open Access Statistic
- Published
- 2012
- Volume
- 49
- Issue
- 5
- ISSN
- 1548-7660 (ISSN-L)
- 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 › Computer Science › Artificial Intelligence › 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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