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Can time-to-detection models with fewer survey replicates provide a robust alternative to traditional site-occupancy models?
Dominic A. W. Henry, Alan T. K. Lee, Res Altwegg , Methods in Ecology and Evolution , 2020RFree
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An r package and online resource for macroevolutionary studies using the ray-finned fish tree of life
Jonathan Chang, Daniel L. Rabosky, Stephen A. Smith, Michael E. Alfaro , Methods in Ecology and Evolution , 2019RFree
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Recombination rate plasticity: revealing mechanisms by design
Laurie S. Stevison , Stephen Sefick , Chase Rushton and Rita M. Graze , Methods in Ecology and Evolution , 2017RFree
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For everything there is a season: Analysing periodic mortality patterns with the cyclomortr package
Eliezer Gurarie, Peter R. Thompson, Allicia P. Kelly, Nicholas C. Larter, William F. Fagan, Kyle Joly , Methods in Ecology and Evolution , 2019RFree
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Point density and spatial resolution limit estimation of Leaf Area Index using discrete return LiDAR
Milodowski, David ; Swinfield, Thomas ; Coomes, David ; Williams, Mathew , Methods in Ecology and Evolution , 2018PythonFree
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Environmental drivers of variability in the movement ecology of turkey vultures (Cathartes aura) in North and South America
Somayeh Dodge , Gil Bohrer , Keith Bildstein , Sarah C. Davidson , Rolf Weinzierl , Marc J. Bechard , David Barber , Roland Kays , David Brandes , Jiawei Han and Martin Wikelski , Methods in Ecology and Evolution , 2014RFree
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When can we trust population trends? A method for quantifying the effects of sampling interval and duration
Hannah S. Wauchope, Tatsuya Amano, William J. Sutherland, Alison Johnston , Methods in Ecology and Evolution , 2019RFree
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momentuHMM: R package for generalized hidden Markov models of animal movement
Brett T. McClintock, Théo Michelot , Methods in Ecology and Evolution , 2018RFree
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Estimating species richness and accumulation by modelling species occurrence and detectability.
Robert M. Dorazio, J. Andrew Royle, Bo Söderström, Anders Glimskär , Methods in Ecology and Evolution , 2016PythonFree
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Estimating recruitment from capture–recapture data by modelling spatio-temporal variation in birth and age-specific survival rates
Richard B. Chandler, Kristin Engebretsen, Michael J. Cherry, Elina P. Garrison, Karl V. Miller , Methods in Ecology and Evolution , 2018RFree
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raptr: Representative and adequate prioritization toolkit in R
Jeffrey O. Hanson, Jonathan R. Rhodes, Hugh P. Possingham, Richard A. Fuller , Methods in Ecology and Evolution , 2017RFree
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Performance of multistate mark–recapture models for temporary emigration in the presence of survival costs
Klaus Henle, Bernd Gruber , Methods in Ecology and Evolution , 2017C++Free
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Imperfect pathogen detection from non-invasive skin swabs biases disease inference
Graziella V. DiRenzo, Evan H. Campbell Grant, Ana V. Longo, Christian Che-Castaldo, Kelly R. Zamudio, Karen R. Lips , Methods in Ecology and Evolution , 2017RFree
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Ecological resistance surfaces predict fine-scale genetic differentiation in a terrestrial woodland salamander
William E. Peterman, Grant M. Connette, Raymond D. Semlitsch, Lori S. Eggert , Methods in Ecology and Evolution , 2014RFree
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Active learning for classifying long-duration audio recordings of the environment
Mahnoosh Kholghi, Yvonne Phillips, Michael Towsey, Laurianne Sitbon, Paul Roe , Methods in Ecology and Evolution , 2018JavaFree
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Sensitivity of binomial N-mixture models to overdispersion: The importance of assessing model fit
Jonas Knape, Debora Arlt, Frédéric Barraquand, Åke Berg, Mathieu Chevalier, Tomas Pärt, Alejandro Ruete, Michał Żmihorski , Methods in Ecology and Evolution , 2018RFree
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Dealing with high uncertainty in qualitative network models using Boolean analysis
Nadiah P. Kristensen, Ryan A. Chisholm, Eve McDonald-Madden , Methods in Ecology and Evolution , 2019RFree
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Non-specific amplification compromises environmental DNA metabarcoding with COI
Rupert A. Collins, Judith Bakker, Owen S. Wangensteen, Ana Z. Soto, Laura Corrigan, David W. Sims, Martin J. Genner, Stefano Mariani , Methods in Ecology and Evolution , 2019RFree
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Using machine vision to estimate fish length from images using regional convolutional neural networks
Graham G. Monkman, Kieran Hyder, Michel J. Kaiser, Franck P. Vidal , Methods in Ecology and Evolution , 2019PythonFree
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Use of a filter cartridge combined with intra-cartridge bead-beating improves detection of microbial DNA from water samples
Masayuki Ushio , Methods in Ecology and Evolution , 2019RFree
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An r package and online resource for macroevolutionary studies using the ray-finned fish tree of life
Jonathan Chang, Daniel L. Rabosky, Stephen A. Smith, Michael E. Alfaro , Methods in Ecology and Evolution , 2019RFree
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Rapid spatial risk modelling for management of early weed invasions: Balancing ecological complexity and operational needs
Jens G. Froese, Alan R. Pearse, Grant Hamilton , Methods in Ecology and Evolution , 2019RFree
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tRophicPosition, an r package for the Bayesian estimation of trophic position from consumer stable isotope ratios
Claudio Quezada-Romegialli, Andrew L. Jackson, Brian Hayden, Kimmo K. Kahilainen, Christelle Lopes, Chris Harrod , Methods in Ecology and Evolution , 2018RFree
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Drones and convolutional neural networks facilitate automated and accurate cetacean species identification and photogrammetry
Patrick C. Gray, Kevin C. Bierlich, Sydney A. Mantell, Ari S. Friedlaender, Jeremy A. Goldbogen, David W. Johnston , Methods in Ecology and Evolution , 2019Jupyter NotebookFree
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How should we estimate diversity in the fossil record? Testing richness estimators using sampling-standardised discovery curves
Roger A. Close, Serjoscha W. Evers, John Alroy, Richard J. Butler , Methods in Ecology and Evolution , 2018RFree
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raptr: Representative and adequate prioritization toolkit in R
Jeffrey O. Hanson, Jonathan R. Rhodes, Hugh P. Possingham, Richard A. Fuller , Methods in Ecology and Evolution , 2017RFree
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Clustering and correlations: Inferring resilience from spatial patterns in ecosystems
Sumithra Sankaran, Sabiha Majumder, Ashwin Viswanathan, Vishwesha Guttal , Methods in Ecology and Evolution , 2019RFree
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A simulation tool to scrutinise the behaviour of functional diversity metrics
Jana M. McPherson, Lauren A. Yeager, Julia K. Baum , Methods in Ecology and Evolution , 2017RFree
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A quantitative framework for investigating the reliability of empirical network construction
Alyssa R. Cirtwill, Anna Eklöf, Tomas Roslin, Kate Wootton, Dominique Gravel , Methods in Ecology and Evolution , 2019RFree
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A practical guide to structured expert elicitation using the IDEA protocol
Victoria Hemming, Mark A. Burgman, Anca M. Hanea, Marissa F. McBride, Bonnie C. Wintle , Methods in Ecology and Evolution , 2017RFree
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babette: BEAUti 2, BEAST2 and Tracer for R
Richèl J. C. Bilderbeek, Rampal S. Etienne , Methods in Ecology and Evolution , 2018RFree
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Differentiating the Lévy walk from a composite correlated random walk
Marie Auger-Méthé, Andrew E. Derocher, Michael J. Plank, Edward A. Codling, Mark A. Lewis , Methods in Ecology and Evolution , 2015RFree
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babette: BEAUti 2, BEAST2 and Tracer for R
Richèl J. C. Bilderbeek, Rampal S. Etienne , Methods in Ecology and Evolution , 2018RFree
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A practical method to account for variation in detection range in acoustic telemetry arrays to accurately quantify the spatial ecology of aquatic animals
Jacob W. Brownscombe, Lucas P. Griffin, Jacqueline M. Chapman, Danielle Morley, Alejandro Acosta, Glenn T. Crossin, Sara J. Iverson, Aaron J. Adams, Steven J. Cooke, Andy J. Danylchuk , Methods in Ecology and Evolution , 2019RFree
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NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R
Marco Sciaini, Matthias Fritsch, Cédric Scherer, Craig Eric Simpkins , Methods in Ecology and Evolution , 2018NetLogoFree
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mfSBA: Multifractal analysis of spatial patterns in ecological communities
Leonardo A. Saravia , Methods in Ecology and Evolution , 2014C++Free
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A convolutional neural network for detecting sea turtles in drone imagery
Patrick C. Gray, Abram B. Fleishman, David J. Klein, Matthew W. McKown, Vanessa S. Bézy, Kenneth J. Lohmann, David W. Johnston , Methods in Ecology and Evolution , 2018PythonFree
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Paleontological baselines for evaluating extinction risk in the modern oceans
Seth Dinnegan, Sean C. Anderson, Paul G. Harnik, Carl Suimpson, Derek P. Tittensor , Methods in Ecology and Evolution , 2015Jupyter NotebookFree
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embarcadero: Species distribution modelling with Bayesian additive regression trees in r
Colin J. Carlson , Methods in Ecology and Evolution , 2020RFree
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dispRity: A modular R package for measuring disparity
Thomas Guillerme , Methods in Ecology and Evolution , 2019HTMLFree
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Functional ecology and imperfect detection of species
Tobias Roth, Eric Allan, Peter B. Pearman, Valentin Amrhein , Methods in Ecology and Evolution , 2017RFree
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Identifying animal species in camera trap images using deep learning and citizen science
Marco Willi, Ross T. Pitman, Anabelle W. Cardoso, Christina Locke, Alexandra Swanson, Amy Boyer, Marten Veldthuis, Lucy Fortson , Methods in Ecology and Evolution , 2018PythonFree
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GRAPHITE: A graphical environment for scalable in situ video tracking of moving insects
Blair J. Rossetti, Travis Dynes, Berry Brosi, Jacobus C. de Roode, Jun Kong , Methods in Ecology and Evolution , 2017MatlabFree
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Machine learning to classify animal species in camera trap images: Applications in ecology
Michael A. Tabak, Mohammad S. Norouzzadeh, David W. Wolfson, Steven J. Sweeney, Kurt C. Vercauteren, Nathan P. Snow, Joseph M. Halseth, Paul A. Di Salvo , Methods in Ecology and Evolution , 2018RFree
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Continuous traits and speciation rates: Alternatives to state-dependent diversification models
Michael G. Harvey, Daniel L. Rabosky , Methods in Ecology and Evolution , 2017RFree
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A guide to the application of Hill numbers to DNA-based diversity analyses
Antton Alberdi, M. Thomas P. Gilbert , Methods in Ecology and Evolution , 2019RFree
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Mechanistic model predicts tissue–environment relationships and trophic shifts in animal hydrogen and oxygen isotope ratios
Sarah Magozzi, Hannah B. Vander Zanden, Michael B. Wunder & Gabriel J. Bowen , Oecologia , 2019RFree
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Recursive anisotropy: a spatial taphonomic study of the Early Pleistocene vertebrate assemblage of Tsiotra Vryssi, Mygdonia Basin, Greece
Recursive anisotropy: a spatial taphonomic study of the Early Pleistocene vertebrate assemblage of Tsiotra Vryssi, Mygdonia Basin, Greece , Boreas , 2019RFree
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Algorithmic approaches to aid species' delimitation in multidimensional morphospace
Thomas HG Ezard, Paul N Pearson & Andy Purvis , BMC Evolutionary Biology , 2020RFree
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Diversity and evolution of the transposable element repertoire in insects
Malte Petersen, David Armisén, Richard A. Gibbs, Lars Hering, Abderrahman Khila, Georg Mayer, Stephen Richards, Oliver Niehuis & Bernhard Misof , BMC Evolutionary Biology , 2019PerlFree
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Early modern human lithic technology from Jerimalai, East Timor
Ben Marwick,Chris Clarkson,Sue O'Connor, Sophie Collins , Journal of Human Evolution , 2016HTMLFree
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A current affair: entanglement of humpback whales in coastal shark-control nets
Jessica A. Bolin, David S. Schoeman, Carme Pizà-Roca, Kylie L. Scales , Remote Sensing in Ecology and Conservation , 2019RFree
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Contributions toward understanding the biodiversity of Passiflora in North America: Updates and a new combination from the Baja California Peninsula, Mexico and vicinity
Harlan T. Svoboda, AJ Harris , Journal of Systematics and Evolution , 2018RFree
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Testing species assemblage predictions from stacked and joint species distribution models
Damaris Zurell, Niklaus E. Zimmermann, Helge Gross, Andri Baltensweiler, Thomas Sattler, Rafael O. Wüest , Journal of Biogeography , 2019RFree
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A Humboldtian approach to life and climate of the geological past: Estimating palaeotemperature from dental traits of mammalian communities
Otto Oksanen, Indrė Žliobaitė, Juha Saarinen, A. Michelle Lawing, Mikael Fortelius , Journal of Biogeography , 2019RFree
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Phylogenetic structure of geographical co-occurrence among New World Triatominae species, vectors of Chagas disease
Soledad Ceccarelli, Silvia A. Justi, Jorge E. Rabinovich, José Alexandre F. Diniz Filho, Fabricio Villalobos , Journal of Biogeography , 2020RFree
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A world of sequences: can we use georeferenced nucleotide databases for a robust automated phylogeography?
Paolo Gratton, Silvio Marta, Gaëlle Bocksberger, Marten Winter, Emiliano Trucchi, Hjalmar Kühl , Journal of Biogeography , 2016RFree
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Validating dispersal distances inferred from autoregressive occupancy models with genetic parentage assignments
Laurie A. Hall, Nathan D. Van Schmidt, Steven R. Beissinger , Oikos , 2018RFree
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Picky hitch-hikers: vector choice leads to directed dispersal and fat-tailed kernels in a passively dispersing mite
Emanuel A. Fronhofer, Ellen B. Sperr, Anna Kreis, Manfred Ayasse, Hans Joachim Poethke, Marco Tschapka , Oikos , 2013PascalFree
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Are variations of direct and indirect plant interactions along a climatic gradient dependent on species’ strategies? An experiment on tree seedlings
Emmanuel Defossez, Benoît Courbaud, Olivier Lasbouygues, Katja Schiffers, Georges Kunstler , Oikos , 2015RFree
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Individual-based modelling of resource competition to predict density-dependent population dynamics: a case study with white storks
Damaris Zurell, Ute Eggers, Michael Kaatz, Shay Rotics, Nir Sapir, Martin Wikelski, Ran Nathan, Florian Jeltsch , Oikos , 2014C++Free
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Suite of simple metrics reveals common movement syndromes across vertebrate taxa
Briana Abrahms, Dana P. Seidel, Eric Dougherty, Elliott L. Hazen, Steven J. Bograd, Alan M. Wilson, J. Weldon McNutt, Daniel P. Costa, Stephen Blake, Justin S. Brashares & Wayne M. Getz , Movement Ecology , 2017RFree
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A novel method for assessing climate change impacts in ecotron experiments
Inne Vanderkelen, Jakob Zscheischler, Lukas Gudmundsson, Klaus Keuler, Francois Rineau, Natalie Beenaerts, Jaco Vangronsveld, Sara Vicca & Wim Thiery , Biogeosciences , 2020MATLABFree
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Examining the evidence for decoupling between photosynthesis and transpiration during heat extremes
Martin G. De Kauwe, Martin G. De Kauwe, Andrew J. Pitman, John E. Drake, Anna Ukkola, Anne Griebel, Elise Pendall, Suzanne Prober, Michael Roderick , Biogeosciences , 2019PythonFree
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Global biosphere–climate interaction: a causal appraisal of observations and models over multiple temporal scales
Jeroen Claessen, Annalisa Molini, Brecht Martens, Matteo Detto, Matthias Demuzere,Diego G. Miralles. , Biogeosciences , 2019MATLABFree
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Improving North American terrestrial CO2 flux diagnosis using spatial structure in land surface model residuals
T. W. Hilton, K. J. Davis, N. M. Urban , Biogeosciences , 2013RFree
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Predicting vegetation type through physiological and environmental interactions with leaf traits: evergreen and deciduous forests in an earth system modeling framework
Ensheng Weng, Caroline E. Farrior, Ray Dybzinski, Stephen W. Pacala , Biogeosciences , 2016FortranFree
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Kinetics and Identities of Extracellular Peptidases in Subsurface Sediments of the White Oak River Estuary, North Carolina
Andrew D. Steen, Richard T. Kevorkian, Jordan T. Bird, Nina Dombrowski et al , Environmental Microbiology , 2019RFree
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Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources
Julie M. Cridland, Stuart J. Macdonald, Anthony D. Long, Kevin R. Thornton , Genome Biology and Evolution , 2013C++Free
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Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp
Cyril Matthey-Doret, Casper J van der Kooi, Daniel L Jeffries, Jens Bast, Alice B Dennis, Christoph Vorburger, Tanja Schwander , Genome Biology and Evolution , 2019ShellFree
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Evolution of Dosage Compensation in Anolis carolinensis, a Reptile with XX/XY Chromosomal Sex Determination
Shawn M. Rupp, Timothy H. Webster, Kimberly C. Olney, Elizabeth D. Hutchins, Kenro Kusumi, Melissa A. Wilson Sayres , Genome Biology and Evolution , 2016PythonFree
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Predicting to new environments: tools for visualising model behaviour and impacts on mapped distributions
Damaris Zurell, Jane Elith, Boris Schröder , Diversity and Distributions , 2012RFree
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Trade-Offs and Coexistence: A Lottery Model Applied to Fig Wasp Communities
A. Bradley Duthie, Karen C. Abbott and John D. Nason , American Naturalist , 2014CFree
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Warming increases the cost of growth in a model vertebrate
Diego R. Barneche, Miki Jahn, Frank Seebacher , Functional Ecology , 2019RFree
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Habitat and fishing control grazing potential on coral reefs
James P. W. Robinson, Jamie M. McDevitt-Irwin, Jan-Claas Dajka, Jeneen Hadj-Hammou, Samantha Howlett, Alexia Graba-Landry, Andrew S. Hoey, Kirsty L. Nash , Functional Ecology , 2019RFree
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Among-strain consistency in the pace and shape of senescence in duckweed
Patrick M. Barks, Zach W. Dempsey, Theresa M. Burg, Robert A. Laird , Journal of Ecology , 2018RFree
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Fire history and plant community composition outweigh decadal multi-factor global change as drivers of microbial composition in an annual grassland
Clara Qin, Kai Zhu, Nona R. Chiariello, Christopher B. Field, Kabir G. Peay , Journal of Ecology , 2019RFree
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Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
Matthew E. MacGilvray , Evgenia Shishkova , Deborah Chasman, Michael Place, Anthony Gitter, Joshua J. Coon, Audrey P. Gasch , PLoS Computational Biology , 2018GAMSFree
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A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system
Andrea K. Barreiro, Shree Hari Gautam, Woodrow L. Shew, Cheng Ly , PLoS Computational Biology , 2017MatlabFree
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Prefrontal Cortical Mechanisms Underlying Individual Differences in Cognitive Flexibility and Stability
Diana J. N. Armbruster, Kai Ueltzhöffer, Ulrike Basten, Christian J. Fiebach , PLoS Computational Biology , 2012ScilabFree
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External Drive to Inhibitory Cells Induces Alternating Episodes of High- and Low-Amplitude Oscillations
Oscar J. Avella Gonzalez, Karlijn I. van Aerde, Ronald A. J. van Elburg, Simon-Shlomo Poil, Huibert D. Mansvelder, Klaus Linkenkaer-Hansen, Jaap van Pelt, Arjen van Ooyen , PLoS Computational Biology , 2012MATLABFree
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Spike and burst coding in thalamocortical relay cells.
Fleur Zeldenrust , Pascal Chameau, Wytse J. Wadman , PLoS Computational Biology , 2018AMPLFree
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STDP Allows Fast Rate-Modulated Coding with Poisson-Like Spike Trains
Matthieu Gilson , Timothée Masquelier , Etienne Hugues , PLoS Computational Biology , 2011PythonFree
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A Voltage-Based STDP Rule Combined with Fast BCM-Like Metaplasticity Accounts for LTP and Concurrent “Heterosynaptic” LTD in the Dentate Gyrus In Vivo
Peter Jedlicka , Lubica Benuskova , Wickliffe C. Abraham , PLoS Computational Biology , 2015AMPLFree
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Top-down inputs drive neuronal network rewiring and context-enhanced sensory processing in olfaction
Wayne Adams , James N. Graham , Xuchen Han , Hermann Riecke , PLoS Computational Biology , 2019MATLABFree
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Dendritic Nonlinearities Reduce Network Size Requirements and Mediate ON and OFF States of Persistent Activity in a PFC Microcircuit Model
Athanasia Papoutsi, Kyriaki Sidiropoulou, Panayiota Poirazi , PLoS Computational Biology , 2014AMPLFree
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Communication through Resonance in Spiking Neuronal Networks
Gerald Hahn , Alejandro F. Bujan , Yves Frégnac, Ad Aertsen, Arvind Kumar , PLoS Computational Biology , 2014PythonFree
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Odorant mixtures elicit less variable and faster responses than pure odorants
Ho Ka Chan , Fabian Hersperger, Emiliano Marachlian, Brian H. Smith, Fernando Locatelli, Paul Szyszka, Thomas Nowotny , PLoS Computational Biology , 2018C++Free
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Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons
Elisabetta Iavarone , Jane Yi, Ying Shi, Bas-Jan Zandt, Christian O’Reilly, Werner Van Geit, Christian Rössert, Henry Markram, Sean L. Hill , PLoS Computational Biology , 2019AGS ScriptFree
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Cerebellar Nuclear Neurons Use Time and Rate Coding to Transmit Purkinje Neuron Pauses
Shyam Kumar Sudhakar, Benjamin Torben-Nielsen, Erik De Schutter , PLoS Computational Biology , 2015AMPLFree
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Dynamic Mechanisms of Neocortical Focal Seizure Onset
Yujiang Wang, Marc Goodfellow, Peter Neal Taylor, Gerold Baier , PLoS Computational Biology , 2014MATLABFree
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Contribution of synchronized GABAergic neurons to dopaminergic neuron firing and bursting
Ekaterina O. Morozova, Maxym Myroshnychenko, Denis Zakharov , PLoS Computational Biology , 2016C++Free
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Computational Models Describing Possible Mechanisms for Generation of Excessive Beta Oscillations in Parkinson’s Disease
Alex Pavlides, S. John Hogan, Rafal Bogacz , PLoS Computational Biology , 2015MATLABFree
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Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties
Etay Hay , Sean Hill, Felix Schürmann, Henry Markram, Idan Segev , PLoS Computational Biology , 2011AGS ScriptFree
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Synaptic Plasticity Can Produce and Enhance Direction Selectivity
Sean Carver , Eatai Roth, Noah J Cowan, Eric S Fortune , PLoS Computational Biology , 2008MATLABFree
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A Learning Theory for Reward-Modulated Spike-Timing-Dependent Plasticity with Application to Biofeedback
Robert Legenstein , Dejan Pecevski , Wolfgang Maass , PLoS Computational Biology , 2008PythonFree
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Emergence of spontaneous assembly activity in developing neural networks without afferent input
Marcus A. Triplett, Lilach Avitan, Geoffrey J. Goodhill , PLoS Computational Biology , 2018MatlabFree
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Emergence of Functional Specificity in Balanced Networks with Synaptic Plasticity
Sadra Sadeh , Claudia Clopath , Stefan Rotter , PLoS Computational Biology , 2015PythonFree
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Power-Law Dynamics of Membrane Conductances Increase Spiking Diversity in a Hodgkin-Huxley Model
Wondimu Teka, David Stockton, Fidel Santamaria , PLoS Computational Biology , 2016MATLABFree
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Function and energy consumption constrain neuronal biophysics in a canonical computation: Coincidence detection
Michiel W. H. Remme , John Rinzel, Susanne Schreiber , PLoS Computational Biology , 2018MATLABFree
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