orchaRd 2.0: An R package for visualising meta‐analyses with orchard plots

Journal article

S Nakagawa, M. Lagisz, R. E. O’Dea, Patrice Pottier, Joanna Rutkowska, A. Senior, Yefeng Yang, D. Noble
Methods in Ecology and Evolution, 2023

Semantic Scholar DOI

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APA Click to copy
Nakagawa, S., Lagisz, M., O’Dea, R. E., Pottier, P., Rutkowska, J., Senior, A., … Noble, D. (2023). orchaRd 2.0: An R package for visualising meta‐analyses with orchard plots. Methods in Ecology and Evolution.

Chicago/Turabian Click to copy
Nakagawa, S, M. Lagisz, R. E. O’Dea, Patrice Pottier, Joanna Rutkowska, A. Senior, Yefeng Yang, and D. Noble. “OrchaRd 2.0: An R Package for Visualising Meta‐Analyses with Orchard Plots.” Methods in Ecology and Evolution (2023).

MLA Click to copy
Nakagawa, S., et al. “OrchaRd 2.0: An R Package for Visualising Meta‐Analyses with Orchard Plots.” Methods in Ecology and Evolution, 2023.

BibTeX Click to copy

@article{s2023a,
  title = {orchaRd 2.0: An R package for visualising meta‐analyses with orchard plots},
  year = {2023},
  journal = {Methods in Ecology and Evolution},
  author = {Nakagawa, S and Lagisz, M. and O’Dea, R. E. and Pottier, Patrice and Rutkowska, Joanna and Senior, A. and Yang, Yefeng and Noble, D.}
}

Abstract

Although meta‐analysis has become an essential tool in ecology and evolution, reporting of meta‐analytic results can still be much improved. To aid this, we have introduced the orchard plot, which presents not only overall estimates and their confidence intervals, but also shows corresponding heterogeneity (as prediction intervals) and individual effect sizes. Here, we have added significant enhancements by integrating many new functionalities into orchaRd 2.0. This updated version allows the visualisation of heteroscedasticity (different variances across levels of a categorical moderator), marginal estimates (e.g. marginalising out effects other than the one visualised), conditional estimates (i.e. estimates of different groups conditioned upon specific values of a continuous variable) and visualisations of all types of interactions between two categorical/continuous moderators. orchaRd 2.0 has additional functions which calculate key statistics from multilevel meta‐analytic models such as I2 and R2. Importantly, orchaRd 2.0 contributes to better reporting by complying with PRISMA‐EcoEvo (preferred reporting items for systematic reviews and meta‐analyses in ecology and evolution). Taken together, orchaRd 2.0 can improve the presentation of meta‐analytic results and facilitate the exploration of previously neglected patterns. In addition, as a part of a literature survey, we found that graphical packages are rarely cited (~3%). We plea that researchers credit developers and maintainers of graphical packages, for example, by citations in a figure legend, acknowledging the use of relevant packages.