Filtering by Subject: Statistics and Probability

A pluralistic framework for measuring and stratifying heterogeneity in meta-analyses

Yefeng Yang, Daniel W.A. Noble, Rebecca Spake, et al.

Published: 2023-11-24
Subjects: Ecology and Evolutionary Biology, Statistics and Probability

  1. Measuring heterogeneity, or inconsistency, among effect sizes is a crucial step for interpreting the meta-analytic evidence across diverse taxonomic groups and spatiotemporal contexts. However, ecologists and evolutionary biologists often interpret mean population effects (i.e., meta-analytic mean effect size) as consistent, either explicitly or implicitly, without proper [...]

Robust point and variance estimation for ecological and evolutionary meta-analyses with selective reporting and dependent effect sizes

Yefeng Yang, Malgorzata Lagisz, Coralie Williams, et al.

Published: 2023-10-03
Subjects: Life Sciences, Medicine and Health Sciences, Statistics and Probability

Meta-analysis produces a quantitative synthesis of evidence-based knowledge, shaping not only research trends but also policy and practices in ecology and evolution. However, two statistical issues, selective reporting and statistical dependence, can severally distort meta-analytic evidence. Here, we propose a two-step procedure to tackle these challenges concurrently and re-analyse 448 [...]

Multi-species dependencies improve forecasts of population dynamics in a long-term monitoring study

Nicholas Joshua Clark, SKM Ernest, Henry Senyondo, et al.

Published: 2023-03-13
Subjects: Desert Ecology, Ecology and Evolutionary Biology, Life Sciences, Multivariate Analysis, Population Biology, Statistical Methodology, Statistical Models, Statistics and Probability

Forecasts of community dynamics are essential for the management of biodiversity. Theory suggests these predictions can be improved by leveraging multi-species dependencies to improve models, but empirical support for this is lacking. We test whether models that learn from multiple species, both to estimate nonlinear environmental effects and temporal dependence, improve forecasts for a semi-arid [...]

Publication bias impacts on effect size, statistical power, and magnitude (Type M) and sign (Type S) errors in ecology and evolutionary biology

Yefeng Yang, Alfredo Sánchez-Tójar, Rose E O'Dea, et al.

Published: 2022-09-12
Subjects: Biology, Ecology and Evolutionary Biology, Environmental Sciences, Life Sciences, Physical Sciences and Mathematics, Statistics and Probability

Collaborative assessments of direct replicability of empirical studies in the medical and social sciences have exposed alarmingly low rates of replicability, a phenomenon dubbed the ‘replication crisis’. Poor replicability has spurred cultural changes targeted at improving reliability in these disciplines. Given the absence of equivalent replication projects in ecology and evolutionary biology, [...]

Decline effects are rare in ecology: Comment

Yefeng Yang, Malgorzata Lagisz, Shinichi Nakagawa

Published: 2022-06-06
Subjects: Ecology and Evolutionary Biology, Life Sciences, Physical Sciences and Mathematics, Statistical Methodology, Statistical Models, Statistics and Probability

Recently, Costello and Fox (2022) tested, with a large dataset, the hypothesis of whether there is a widespread decline effect in the discipline of ecology. In other words, the magnitude of the reported ecological effect sizes declines over time (Leimu and Koricheva 2004). Contrary to early results from much smaller datasets (Jennions and Møller 2002, Barto and Rillig 2012), Costello and Fox [...]

Multi-population analysis reveals spatial consistency in drivers of population dynamics of a declining migratory bird

Chloé Rebecca Nater, Malcolm D. Burgess, Peter Coffey, et al.

Published: 2022-04-21
Subjects: Biodiversity, Biology, Biostatistics, Ecology and Evolutionary Biology, Life Sciences, Longitudinal Data Analysis and Time Series, Physical Sciences and Mathematics, Population Biology, Research Methods in Life Sciences, Statistical Methodology, Statistical Models, Statistics and Probability, Survival Analysis, Terrestrial and Aquatic Ecology

Many migratory species are in decline across their geographical ranges. Single-population studies can provide important insights into drivers at a local scale, but effective conservation requires multi-population perspectives. This is challenging because relevant data are often hard to consolidate, and state-of-the-art analytical tools are typically tailored to specific datasets. We capitalized [...]

Interpolation of temporal biodiversity change, loss, and gain across scales: a machine learning approach

Petr Keil, Jonathan Chase

Published: 2022-03-15
Subjects: Applied Statistics, Biodiversity, Ecology and Evolutionary Biology, Life Sciences, Physical Sciences and Mathematics, Statistics and Probability

1. Estimates of temporal change of biodiversity, and its components loss and gain, are needed at local and geographical scales. However, we lack them because of data in-completeness, heterogeneity, and lack of temporal replication. Hence, we need a tool to integrate heterogeneous data and to account for their incompleteness. 2. We introduce spatiotemporal machine learning interpolation that can [...]

Estimating complex ecological variables at high resolution in heterogeneous terrain using multivariate matching algorithms

Rachel Renne, Daniel Schlaepfer, Kyle Palmquist, et al.

Published: 2021-04-16
Subjects: Ecology and Evolutionary Biology, Life Sciences, Multivariate Analysis, Physical Sciences and Mathematics, Research Methods in Life Sciences, Statistics and Probability

1. Simulation models are valuable tools for estimating ecosystem structure and function under various climatic and environmental conditions and disturbance regimes, and are particularly relevant for investigating the potential impacts of climate change on ecosystems. However, because computational requirements can restrict the number of feasible simulations, they are often run at coarse scales or [...]

BetaBayes - A Bayesian approach for comparing ecological communities

Filipe S. Dias, Michael Betancourt, Patricia María Rodríguez-González, et al.

Published: 2021-04-08
Subjects: Biodiversity, Biology, Ecology and Evolutionary Biology, Life Sciences, Physical Sciences and Mathematics, Statistics and Probability

Ecological communities change due to both natural and human factors. Distinguishing between the two is critical to ecology and conservation science. One of the most common approaches for modelling species composition changes is calculating Beta diversity indices and then relating index changes to covariates changes. The main difficulty with these analyses is that Beta diversity indices are paired [...]

ausplotsR: An R package for rapid extraction and analysis of vegetation and soil data collected by Australia’s Terrestrial Ecosystem Research Network

Samantha Munroe, Greg Guerin, Tom Saleeba, et al.

Published: 2020-12-14
Subjects: Biostatistics, Botany, Life Sciences, Other Plant Sciences, Physical Sciences and Mathematics, Plant Biology, Plant Sciences, Statistics and Probability

The Terrestrial Ecosystem Research Network (TERN), Australia’s national land ecosystem monitoring program, measures critical environmental attributes from local to continental scale and generates quality data for research and land management. Since 2011, TERN has performed standardised field surveys and sampling across a national plot network. At each plot, TERN records vegetation structure, [...]

Phylogenetic multilevel meta-analysis: A simulation study on the importance of modeling the phylogeny

Ozan Cinar, Shinichi Nakagawa, Wolfgang Viechtbauer

Published: 2020-11-23
Subjects: Ecology and Evolutionary Biology, Life Sciences, Physical Sciences and Mathematics, Statistical Models, Statistics and Probability

1. Meta-analyses in ecology and evolution require special attention due to certain study characteristics in these fields. First, the primary articles in these fields usually report results that are observed from studies conducted with different species, and the phylogeny among the species violates the independence assumption. Second, articles frequently allow the computation of multiple effect [...]

Motif: an open-source R tool for pattern-based spatial analysis

Jakub Nowosad

Published: 2020-10-17
Subjects: Categorical Data Analysis, Earth Sciences, Ecology and Evolutionary Biology, Environmental Sciences, Life Sciences, Physical Sciences and Mathematics, Statistics and Probability, Terrestrial and Aquatic Ecology

*Context* Pattern-based spatial analysis provides methods to describe and quantitatively compare spatial patterns for categorical raster datasets. It allows for spatial search, change detection, and clustering of areas with similar patterns. *Objectives* We developed an R package **motif** as a set of open-source tools for pattern-based spatial analysis. *Methods* This package provides [...]

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