Costello and Fox 2022; Yang et al 2023, 2024 (ecology and evolution)

Note

To download only this data file: CostelloFox.rds (2.3 MB); Yang.rds (255 KB)

To download all BEAR datasets, click here.

Costello and Fox 2022; Yang et al 2023, 2024 (ecology and evolution)

Reference: these two datasets come from the same replication package and shared data processing pipeline in Yang et al. 2024 (Yang et al. 2024). Original references for the datasets are Yang et al. 2023 and Costello and Fox 2022 (Yang et al. 2023; Costello and Fox 2022).

Research question: decline effects in ecology (Costello and Fox) and publication bias and performance of empirical research (Yang et al)

Data collection: Costello and Fox look at 466 meta-analyses obtained through searching Web of Science. Reproducibility dataset includes 88,000 rows among 466 analyses in 232 papers. Subsequently, Yang et al removed duplicated studies and zeroes, which meant discarding about 20% of rows. Yang et al collect 102 meta-analyses published 2010-2019 in relevant journals, de-duplicated against Costello and Fox dataset.

Data availability: two datasets may be downloaded from https://github.com/Yefeng0920/replication_EcoEvo_git/. Available under CC BY 4.0 licence.

Data processing: no additional data processing other than cleaning up study years. Signed z-values were computed as effect sizes divided by their standard errors. Note that the replication package for Yang et al does not include meta-analysis indicators.

Additional variables used: we retained a measure variable (“lnRR”, “SMD”, “Zr” or “uncommon”)

Model of z-values

This documentation page covers more than one fitted dataset, so the fitted models are shown separately. The fitted mixture model is shown over the empirical distribution of absolute z-values. The solid line is a mixture of half-normals, with selection. The dashed line shows the distribution without selection. If there are inequalities (e.g. studies reporting p < 0.05) the histogram resamples values from the appropriate set.

Costello and Fox: ecology & evolution

Costello and Fox: ecology & evolution mixture model plot

Yang et al: ecology & evolution

Yang et al: ecology & evolution mixture model plot

References

Costello, Laura, and Jeremy W Fox. 2022. “Decline Effects Are Rare in Ecology.” Ecology 103 (6): e3680.
Yang, Yefeng, Alfredo Sánchez-Tójar, Rose E O’Dea, et al. 2023. “Publication Bias Impacts on Effect Size, Statistical Power, and Magnitude (Type M) and Sign (Type S) Errors in Ecology and Evolutionary Biology.” BMC Biology 21 (1): 71.
Yang, Yefeng, Erik van Zwet, Nikolaos Ignatiadis, and Shinichi Nakagawa. 2024. “A Large-Scale in Silico Replication of Ecological and Evolutionary Studies.” Nature Ecology & Evolution, 1–5.