April 3, 2018
Nearly every scientist will have to do a literature review at some point. Many will have to do this quantitatively. In this lecture we explore the concept of the meta-analysis - what they are, what they’re for, and how to do them well.
- Systematic vs. unsystematic literature reviews
- Introduction to the term “Meta-Analysis”
- Basic logic of MA, including effect sizes
- PRISMA and MA reporting
By the end of this class
- Harrison, F. (2011). Getting started with meta‐analysis. Methods in Ecology and Evolution, 2(1), 1-10.
- Moher, D., Liberati, A., Tetzlaff, J., Altman, D. G., & Prisma Group. (2009). Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS medicine, 6(7), e1000097.
- Cox, K., Brennan, L. P., Gerwing, T. G., Dudas, S. E., & Juanes, F. (2018). Sound the Alarm: A Meta‐Analysis on the Effect of Aquatic Noise on Fish Behavior and Physiology. Global change biology.
There are several R packages that can be used to conduct meta-analysis. I’ve used the first one, and dabbled in the second. I have no experience with the third, but it looks good.
- Viechtbauer, W. (2010). Conducting meta-analyses in R with the metafor package. J Stat Softw, 36(3), 1-48.
- Lajeunesse, M. J. (2016). Facilitating systematic reviews, data extraction and meta‐analysis with the metagear package for R. Methods in Ecology and Evolution, 7(3), 323-330.
- Kossmeier et al. (2018). Visualizing meta-analytic data with R package metaviz
This textbook is godlike, and is a must-have if you intend to embark on a meta-analysis:
- Koricheva, J., Gurevitch, J., and Mengersen, K. (2013). Handbook of meta-analysis in ecology and evolution
Additional handy resources:
- Calculating effect sizes with escalc() in the metafor package
- Sterne, J. A., & Egger, M. (2001). Funnel plots for detecting bias in meta-analysis: guidelines on choice of axis. Journal of clinical epidemiology, 54(10), 1046-1055.
- Rosenberg, M. S. (2005). The file-drawer problem revisited: a general weighted method for calculating fail-safe numbers in meta-analysis. Evolution, 59(2), 464-468.
- Nakagawa, S., Poulin, R., Mengersen, K., Reinhold, K., Engqvist, L., Lagisz, M., & Senior, A. M. (2015). Meta‐analysis of variation: ecological and evolutionary applications and beyond. Methods in Ecology and Evolution, 6(2), 143-152.
- Leimu, R., & Koricheva, J. (2004). Cumulative meta–analysis: a new tool for detection of temporal trends and publication bias in ecology. Proceedings of the Royal Society of London B: Biological Sciences, 271(1551), 1961-1966.
And some food-for-thought about MA drawbacks:
Define your MA properly:
- Vetter, D., Rücker, G., & Storch, I. (2013). Meta‐analysis: A need for well‐defined usage in ecology and conservation biology. Ecosphere, 4(6), 1-24.
Don’t ask silly MA questions:
- Smith, G. C., & Pell, J. P. (2003). Parachute use to prevent death and major trauma related to gravitational challenge: systematic review of randomised controlled trials. BMJ: British Medical Journal, 327(7429), 1459.
Bonus points if you download and cite my MA from my Ph.D (kidding) (not really) (no, really I am kidding) (or am I?) Note especially our supplementary material, including a tracking spreadsheet for the literature included and excluded in the MA.
- Favaro, B., & Côté, I. M. (2015). Do by‐catch reduction devices in longline fisheries reduce capture of sharks and rays? A global meta‐analysis. Fish and fisheries, 16(2), 300-309.
No R code this week.
Slides available on Speakerdeck