Search Results - "Methods in ecology and evolution"

Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package by Lai, Jiangshan, Zou, Yi, Zhang, Jinlong, Peres‐Neto, Pedro R.

“…Canonical analysis, a generalization of multiple regression to multiple‐response variables, is widely used in ecology. Because these models often involve many…”
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raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML by Edler, Daniel, Klein, Johannes, Antonelli, Alexandre, Silvestro, Daniele, Matschiner, Michael

“…raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood. Here we…”
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Robustness of linear mixed‐effects models to violations of distributional assumptions by Schielzeth, Holger, Dingemanse, Niels J., Nakagawa, Shinichi, Westneat, David F., Allegue, Hassen, Teplitsky, Céline, Réale, Denis, Dochtermann, Ned A., Garamszegi, László Zsolt, Araya‐Ajoy, Yimen G., Sutherland, Chris

“…Linear mixed‐effects models are powerful tools for analysing complex datasets with repeated or clustered observations, a common data structure in ecology and…”
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ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions by Kass, Jamie M., Muscarella, Robert, Galante, Peter J., Bohl, Corentin L., Pinilla‐Buitrago, Gonzalo E., Boria, Robert A., Soley‐Guardia, Mariano, Anderson, Robert P.

“…Quantitative evaluations to optimize complexity have become standard for avoiding overfitting of ecological niche models (ENMs) that estimate species’…”
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metan: An R package for multi‐environment trial analysis by Olivoto, Tiago, Lúcio, Alessandro Dal'Col, Jarman, Simon

“…Multi‐environment trials (MET) are crucial steps in plant breeding programs that aim at increasing crop productivity to ensure global food security. The…”
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The use of focus group discussion methodology: Insights from two decades of application in conservation by O.Nyumba, Tobias, Wilson, Kerrie, Derrick, Christina J., Mukherjee, Nibedita, Geneletti, Davide

“…Focus group discussion is frequently used as a qualitative approach to gain an in‐depth understanding of social issues. The method aims to obtain data from a…”
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geomorph v4.0 and gmShiny: Enhanced analytics and a new graphical interface for a comprehensive morphometric experience by Baken, Erica K., Collyer, Michael L., Kaliontzopoulou, Antigoni, Adams, Dean C.

“…Geometric morphometric (GM) tools are essential for meaningfully quantifying and understanding patterns of variation in complex traits like shape. In this…”
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CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases by Zizka, Alexander, Silvestro, Daniele, Andermann, Tobias, Azevedo, Josué, Duarte Ritter, Camila, Edler, Daniel, Farooq, Harith, Herdean, Andrei, Ariza, María, Scharn, Ruud, Svantesson, Sten, Wengström, Niklas, Zizka, Vera, Antonelli, Alexandre, Quental, Tiago

“…Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues…”
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ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data by Yu, Guangchuang, Smith, David K., Zhu, Huachen, Guan, Yi, Lam, Tommy Tsan‐Yuk, McInerny, Greg

“…Summary We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats…”
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iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers) by Hsieh, T. C., Ma, K. H., Chao, Anne, McInerny, Greg

“…Summary Hill numbers (or the effective number of species) have been increasingly used to quantify the species/taxonomic diversity of an assemblage. The…”
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rptR: repeatability estimation and variance decomposition by generalized linear mixed‐effects models by Stoffel, Martin A., Nakagawa, Shinichi, Schielzeth, Holger, Goslee, Sarah

“…Summary Intra‐class correlations (ICC) and repeatabilities (R) are fundamental statistics for quantifying the reproducibility of measurements and for…”
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BORIS: a free, versatile open‐source event‐logging software for video/audio coding and live observations by Friard, Olivier, Gamba, Marco, Fitzjohn, Richard

“…Summary Quantitative aspects of the study of animal and human behaviour are increasingly relevant to test hypotheses and find empirical support for them. At…”
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Analysing continuous proportions in ecology and evolution: A practical introduction to beta and Dirichlet regression by Douma, Jacob C., Weedon, James T., Warton, David

“…Proportional data, in which response variables are expressed as percentages or fractions of a whole, are analysed in many subfields of ecology and evolution…”
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piecewiseSEM: Piecewise structural equation modelling in r for ecology, evolution, and systematics by Lefcheck, Jonathan S., Freckleton, Robert

“…Summary Ecologists and evolutionary biologists rely on an increasingly sophisticated set of statistical tools to describe complex natural systems. One such…”
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popart: full‐feature software for haplotype network construction by Leigh, Jessica W., Bryant, David, Nakagawa, Shinichi

“…Summary Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. Here, we present popart,…”
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Joint species distribution modelling with the r‐package Hmsc by Tikhonov, Gleb, Opedal, Øystein H., Abrego, Nerea, Lehikoinen, Aleksi, Jonge, Melinda M. J., Oksanen, Jari, Ovaskainen, Otso, Golding, Nick

“…Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analysing data in community ecology. Hierarchical…”
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ntbox: An r package with graphical user interface for modelling and evaluating multidimensional ecological niches by Osorio‐Olvera, Luis, Lira‐Noriega, Andrés, Soberón, Jorge, Peterson, Andrew Townsend, Falconi, Manuel, Contreras‐Díaz, Rusby G., Martínez‐Meyer, Enrique, Barve, Vijay, Barve, Narayani, Qiao, Huijie

“…Biodiversity studies rely heavily on estimates of species' distributions often obtained through ecological niche modelling. Numerous software packages exist…”
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SIMR: an R package for power analysis of generalized linear mixed models by simulation by Green, Peter, MacLeod, Catriona J., Nakagawa, Shinichi

“…Summary The r package simr allows users to calculate power for generalized linear mixed models from the lme4 package. The power calculations are based on Monte…”
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Predicting into unknown space? Estimating the area of applicability of spatial prediction models by Meyer, Hanna, Pebesma, Edzer

“…Machine learning algorithms have become very popular for spatial mapping of the environment due to their ability to fit nonlinear and complex relationships…”
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RRPP: An r package for fitting linear models to high‐dimensional data using residual randomization by Collyer, Michael L., Adams, Dean C., Freckleton, Robert

“…Residual randomization in permutation procedures (RRPP) is an appropriate means of generating empirical sampling distributions for ANOVA statistics and linear…”
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