Computationally reproducing results from meta-analyses in ecology and evolutionary biology using shared code and data

Kambouris, Steven; Wilkinson, David P.; Smith, Eden T.; Fidler, Fiona

doi:10.1371/journal.pone.0300333

PLoS ONE

2024

DOI: 10.1371/journal.pone.0300333

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Computationally reproducing results from meta-analyses in ecology and evolutionary biology using shared code and data

Steven Kambouris,

David P. Wilkinson,

Eden T. Smith

et al.

Abstract: Many journals in ecology and evolutionary biology encourage or require authors to make their data and code available alongside articles. In this study we investigated how often this data and code could be used together, when both were available, to computationally reproduce results published in articles. We surveyed the data and code sharing practices of 177 meta-analyses published in ecology and evolutionary biology journals published between 2015–17: 60% of articles shared data only, 1% shared code only, and… Show more

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A review on exploring pyrolysis potential of invasive aquatic plants

Palai,

Sahoo,

Senapati

et al. 2024

Journal of Environmental Management

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A review on exploring pyrolysis potential of invasive aquatic plants

Palai,

Sahoo,

Senapati

et al. 2024

Journal of Environmental Management

View full text Add to dashboard Cite

Transparent reporting items for simulation studies evaluating statistical methods: Foundations for reproducibility and reliability

Williams,

Yang,

Lagisz

et al. 2024

Methods Ecol Evol

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Simulation studies are essential tools to assess statistical methods. Functioning as controlled experiments, simulations generate data from known underlying processes. However, unclear or incomplete reporting of simulation studies can impact their interpretability and reproducibility, potentially leading to the misuse of statistical methods. While Morris et al. (2019, Stat Med, 38, p. 2074) recently provided guidance on the planning and conduct of simulation studies for statistical method evaluation, there is currently no comprehensive set of reporting guidelines in ecology and evolutionary biology. Here, we propose 11 reporting items for statistical simulation studies extending on Morris and colleagues' guidance. These items span across three stages: planning, coding and analysis. We also clarify the terminology related to statistical components and the broad purposes of statistical simulation studies. To highlight our proposed reporting items with current practices, we surveyed 100 articles in ecology and evolution journals that included a simulation study evaluating a statistical method. Our survey found room for improvement in more transparent reporting to ensure clear evaluation of statistical methods. Most notably, only a small proportion of articles reported a Monte Carlo uncertainty (17%; 17 out of 98), and 32% (32 out of 100) articles did not provide code. Beyond the proposed reporting items, we discuss the benefits of open science tools to enhance the reproducibility of simulation studies. Specifically, we propose the registration of statistical simulation studies to enhance planning, reporting and collaboration. We aim to instigate discussions to improve the reporting of simulation studies for statistical method research. The reporting items we propose, along with open science tools, serve as a template for developing standards and guidelines for simulation studies evaluating statistical methods. These reporting guidelines will help enhance reproducibility and indirectly encourage more consideration in the design and conduct of these simulation studies.

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Synthesis of sexual selection: a systematic map of meta‐analyses with bibliometric analysis

Pollo,

Lagisz,

Yang

et al. 2024

Biological Reviews

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Sexual selection has been a popular subject within evolutionary biology because of its central role in explaining odd and counterintuitive traits observed in nature. Consequently, the literature associated with this field of study became vast. Meta‐analytical studies attempting to draw inferences from this literature have now accumulated, varying in scope and quality, thus calling for a synthesis of these syntheses. We conducted a systematic literature search to create a systematic map with a report appraisal of meta‐analyses on topics associated with sexual selection, aiming to identify the conceptual and methodological gaps in this secondary literature. We also conducted bibliometric analyses to explore whether these gaps are associated with the gender and origin of the authors of these meta‐analyses. We included 152 meta‐analytical studies in our systematic map. We found that most meta‐analyses focused on males and on certain animal groups (e.g. birds), indicating severe sex and taxonomic biases. The topics in these studies varied greatly, from proximate (e.g. relationship of ornaments with other traits) to ultimate questions (e.g. formal estimates of sexual selection strength), although the former were more common. We also observed several common methodological issues in these studies, such as lack of detailed information regarding searches, screening, and analyses, which ultimately impairs the reliability of many of these meta‐analyses. In addition, most of the meta‐analyses' authors were men affiliated to institutions from developed countries, pointing to both gender and geographical authorship biases. Most importantly, we found that certain authorship aspects were associated with conceptual and methodological issues in meta‐analytical studies. Many of our findings might simply reflect patterns in the current state of the primary literature and academia, suggesting that our study can serve as an indicator of issues within the field of sexual selection at large. Based on our findings, we provide both conceptual and analytical recommendations to improve future studies in the field of sexual selection.

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Computationally reproducing results from meta-analyses in ecology and evolutionary biology using shared code and data

Cited by 4 publications

References 65 publications

A review on exploring pyrolysis potential of invasive aquatic plants

A review on exploring pyrolysis potential of invasive aquatic plants

Transparent reporting items for simulation studies evaluating statistical methods: Foundations for reproducibility and reliability

Synthesis of sexual selection: a systematic map of meta‐analyses with bibliometric analysis

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