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

Nakagawa, Shinichi; Lagisz, Malgorzata; Pottier, Patrice; Rutkowska, Joanna; Senior, Alistair M.; Yang, Yefeng; Noble, Daniel W. A.

doi:10.1111/2041-210x.14152

Cited by 37 publications

(14 citation statements)

References 35 publications

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“…However, because there were few estimates for treatments involving olfactory cues either on their own or in combination with other cue types (see Results), we also constructed models that were restricted to estimates from studies based on A, V and AV treatment levels. Although we did not have a priori predictions regarding how multimodal cue integration would affect variance in response to manipulations of perceived predation risk, visualisations using orchard plots revealed a clear difference in variability among different treatment levels 171 , 172 . Therefore, we considered both homoscedastic and heteroscedastic models, as recommended by ref.…”

Section: Methodsmentioning

confidence: 84%

“…For all models, we assessed the importance of moderators by calculating marginal R 2 sensu 174 . We visualised meta-analytic results as well as other relevant results mainly using the R packages ggplot2 175 , orchaRd 171 , 172 , ggalluvial 176 and ggtree 177 . Data and reproducible analyses are provided in Supplementary Information S5 ( https://itchyshin.github.io/multimodality/ ).…”

Section: Methodsmentioning

confidence: 99%

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A systematic review and meta-analysis of unimodal and multimodal predation risk assessment in birds

Mathot,

Arteaga-Torres,

Besson

et al. 2024

Nat Commun

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Despite a wealth of studies documenting prey responses to perceived predation risk, researchers have only recently begun to consider how prey integrate information from multiple cues in their assessment of risk. We conduct a systematic review and meta-analysis of studies that experimentally manipulated perceived predation risk in birds and evaluate support for three alternative models of cue integration: redundancy/equivalence, enhancement, and antagonism. One key insight from our analysis is that the current theory, generally applied to study cue integration in animals, is incomplete. These theories specify the effects of increasing information level on mean, but not variance, in responses. In contrast, we show that providing multiple complementary cues of predation risk simultaneously does not affect mean response. Instead, as information richness increases, populations appear to assess risk more accurately, resulting in lower among-population variance in response to manipulations of perceived predation risk. We show that this may arise via a statistical process called maximum-likelihood estimation (MLE) integration. Our meta-analysis illustrates how explicit consideration of variance in responses can yield important biological insights.

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Section: Methodsmentioning

confidence: 84%

Section: Methodsmentioning

confidence: 99%

A systematic review and meta-analysis of unimodal and multimodal predation risk assessment in birds

Mathot,

Arteaga-Torres,

Besson

et al. 2024

Nat Commun

Self Cite

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“…The metafor package version 4.2 (Viechtbauer, 2010) was used for effect size calculation, fitting meta regression models and investigating publication bias. The orchaRd 2.0 package (Nakagawa et al, 2023) was used for creating the orchard plot and calculating I 2 .…”

Section: Discussionmentioning

confidence: 99%

Effects of dissolved organic matter and ecocorona formation on the toxicity of micro- and nanoplastic particles to Daphnia - A meta-analysis

Salomon,

Grubmüller,

Kropf

et al. 2023

Preprint

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Significant quantities of micro- and nanoplastic particles (MNP) end up in theenvironment, either due to larger plastic debris breaking down or by entering directlyas MNPs. Effects of MNPs on organisms have been increasingly reported in recentyears, with a large number of studies conducted on water fleas of the genus Daphnia.Most of the available studies used pristine particles that have not been exposed to theenvironment or to organic substances. In natural environments, however, proteins,organic substances and, if the particles are large enough, bacteria attach to MNP,forming an ecocorona or biofilm on the particles’ surface. How the formation of anecocorona influences MNP toxicity is still uncertain. While some studies suggest thatecocorona formation can mitigate the negative effects of MNP on organisms, otherstudies did not find such associations. In addition, it is unclear whether the ecocoronaitself is attenuating the effects of MNP or whether dissolved organic matter (DOM)affects toxicity indirectly such as by increasing Daphnia‘s resilience to stressors ingeneral. To draw more solid conclusions about the direction and size of the mediatingeffect of DOM and ecocorona formation on MNP-associated immobilization in Daphniaspp., we synthesized evidence from the published literature and compiled 305 datapoints from 13 independent studies. The results of our meta-analysis show that thetoxic effects of MNP are likely reduced in the presence of certain types of DOM. Weobserved similar mediating effects when MNP were incubated in media containingDOM before the exposure experiments, although to a lesser extent. Future studiesdesigned to disentangle the effects of the ecocorona itself from the general effects ofDOM will contribute to a deeper mechanistic understanding of MNP toxicity in natureand enhance the reliability of MNP risk assessment.

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“…We used the metafor 64 package to build all meta-analytical models. We visualised the results from the models using scatterplots (for numeric moderators) and orchard plots (for categorical moderators) from the orchaRd 65 package, using 95% confidence intervals to indicate the most likely location of the cross-study average effect. We visualised the geographic distribution of studies using the rnaturalearth 66 package.…”

Section: Methodsmentioning

confidence: 99%

Global meta-analysis reveals overall higher nocturnal than diurnal activity in insect communities

Wong,

Didham

2024

Nat Commun

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Insects sustain key ecosystem functions, but how their activity varies across the day–night cycle and the underlying drivers are poorly understood. Although entomologists generally expect that more insects are active at night, this notion has not been tested with empirical data at the global scale. Here, we assemble 331 quantitative comparisons of the abundances of insects between day and night periods from 78 studies worldwide and use multi-level meta-analytical models to show that insect activity is on average 31.4% (CI: −6.3%–84.3%) higher at night than in the day. We reveal diel preferences of major insect taxa, and observe higher nocturnal activity in aquatic taxa than in terrestrial ones, as well as in warmer environments. In a separate analysis of the small subset of studies quantifying diel patterns in taxonomic richness (31 comparisons from 13 studies), we detect preliminary evidence of higher nocturnal richness in tropical than temperate communities. The higher overall (but variable) nocturnal activity in insect communities underscores the need to address threats such as light pollution and climate warming that may disproportionately impact nocturnal insects.

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

Cited by 37 publications

References 35 publications

A systematic review and meta-analysis of unimodal and multimodal predation risk assessment in birds

A systematic review and meta-analysis of unimodal and multimodal predation risk assessment in birds

Effects of dissolved organic matter and ecocorona formation on the toxicity of micro- and nanoplastic particles to Daphnia - A meta-analysis

Global meta-analysis reveals overall higher nocturnal than diurnal activity in insect communities

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