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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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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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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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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 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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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 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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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
-
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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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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momentuHMM: R package for generalized hidden Markov models of animal movement
Brett T. McClintock, Théo Michelot , Methods in Ecology and Evolution , 2018RFree
-
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
-
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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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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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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Recombination rate plasticity: revealing mechanisms by design
Laurie S. Stevison , Stephen Sefick , Chase Rushton and Rita M. Graze , Methods in Ecology and Evolution , 2017RFree
-
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
-
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
-
pavo2: New tools for the spectral and spatial analysis of colour in r
Rafael Maia, Hugo Gruson, John A. Endler, Thomas E. White , Methods in Ecology and Evolution , 2019RFree
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BA3-SNPs: Contemporary migration reconfigured in BayesAss for next-generation sequence data
Steven M. Mussmann, Marlis R. Douglas, Tyler K. Chafin, Michael E. Douglas , Methods in Ecology and Evolution , 2019PythonFree
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Using taxonomic consistency with semi-automated data pre-processing for high quality DNA barcodes
Björn Rulik, Jonas Eberle, Laura von der Mark, Jana Thormann, Manfred Jung, Frank Köhler, Wolfgang Apfel, Andreas Weigel, Andreas Kopetz, Jonas Köhler, Frank Fritzlar , Methods in Ecology and Evolution , 2017RFree
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Fast evaluation of study designs for spatially explicit capture–recapture
Murray G. Efford, John Boulanger , Methods in Ecology and Evolution , 2019RFree
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Plants In Trait Analysis (PITA)
Nicole Diaz; Jordan Holmes , Methods in Ecology and Evolution , 2019ShellFree
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A package for motif analyses of bipartite networks
Benno I. Simmons, Michelle J. M. Sweering, Maybritt Schillinger, Lynn V. Dicks, William J. Sutherland, Riccardo Di Clemente , Methods in Ecology and Evolution , 2019RFree
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Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions
Jonathan Chang, Daniel L Rabosky, Michael E Alfaro , Methods in Ecology and Evolution , 2019PythonFree
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Data from: A comparative analysis of common methods to identify waterbird hotspots
Allison L. Sussman, Beth Gardner, Evan M. Adams, Leo Salas, Kevin P. Kenow, David R. Luukkonen , Methods in Ecology and Evolution , 2019RFree
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Towards an ecological trait-data standard
Florian D. Schneider, David Fichtmueller, Martin M. Gossner, Anton Güntsch, Malte Jochum, Birgitta König-Ries, Gaëtane Le Provost, Peter Manning, Andreas Ostrowski , Methods in Ecology and Evolution , 2019RFree
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Parallel Likelihood Calculation for Phylogenetic Comparative Models: the SPLITT C++ Library
Venelin Mitov, Tanja Stadler , Methods in Ecology and Evolution , 2019ShellFree
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Filling reference gaps via assembling DNA barcodes using high-throughput sequencing—moving toward barcoding the world
Shanlin Liu, Chentao Yang, Chengran Zhou, Xin Zhou , Methods in Ecology and Evolution , 2017PythonFree
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Estimating dispersal kernels using genetic parentage data
Michael Bode, David H. Williamson, Hugo B. Harrison, Nick Outram, Geoffrey P. Jones , Methods in Ecology and Evolution , 2017MatlabFree
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The multiple population genetic and demographic routes to islands of genomic divergence
Claudio S. Quilodrán, Kristen Ruegg, Ashley T. Sendell-Price, Eric C. Anderson, Tim Coulson, Sonya M. Clegg , Methods in Ecology and Evolution , 2019RFree
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Incorporating fine-scale environmental heterogeneity into broad-extent models
Laura J. Graham, Rebecca Spake, Simon Gillings, Kevin Watts, Felix Eigenbrod , Methods in Ecology and Evolution , 2019RFree
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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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Reliable species distributions are obtainable with sparse, patchy and biased data by leveraging over species and data types
Samantha L. Peel, Nicole A. Hill, Scott D. Foster, Simon J. Wotherspoon, Claudio Ghiglione, Stefano Schiaparelli , Methods in Ecology and Evolution , 2019RFree
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Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models
Venelin Mitov, Krzysztof Bartoszek, and Tanja Stadler , Methods in Ecology and Evolution , 2019RFree
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Assessing adequacy of models of phyletic evolution in the fossil record
Kjetil Lysne Voje , Methods in Ecology and Evolution , 2018RFree
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performance: An R Package for Assessment, Comparison and Testing of Statistical Models
Daniel Lüdecke, Mattan S. Ben-Shachar, Indrajeet Patil, Philip Waggoner, and Dominique Makowski , Methods in Ecology and Evolution , 2021RFree
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Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2
Michael A. Tabak, Mohammad S. Norouzzadeh, David W. Wolfson, Erica J. Newton, Raoul K. Boughton, Jacob S. Ivan, Eric A. Odell, Eric S. Newkirk, Reesa Y. Conrey, Jennifer Stenglein , Methods in Ecology and Evolution , 2020RFree
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The r package divDyn for quantifying diversity dynamics using fossil sampling data
Ádám T. Kocsis, Carl J. Reddin, John Alroy, Wolfgang Kiessling , Methods in Ecology and Evolution , 2019RFree
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DYNAMITE: a phylogenetic tool for identification of dynamic transmission epicenters
Brittany Rife Magalis, Simone Marini, Marco Salemi, Mattia Prosperi , Methods in Ecology and Evolution , 2021RFree
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The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections
Alisa O. Vershinina, Joshua D. Kapp, Gennady F. Baryshnikov, Beth Shapiro , Molecular Ecology Resources , 2019ShellFree
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Local temperature and ecological similarity drive distributional dynamics of tropical mammals worldwide
Lydia Beaudrot, Miguel A. Acevedo, Jean-Philippe Lessard, Alex Zvoleff, Patrick A. Jansen, Douglas Sheil, Francesco Rovero, Timothy O’Brien, Eileen Larney, Christine Fletcher, Sandy Andelman, Jorge Ahumada , Global Ecology and Biogeography , 2019RFree
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Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods
Bernd Hänfling, Lori Lawson Handley, Daniel S. Read, Christoph Hahn, Jianlong Li, Paul Nichols, Rosetta C. Blackman, Anna Oliver, Ian J. Winfield , Molecular Ecology , 2016RFree
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RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)
Laura Benestan, Thierry Gosselin, Charles Perrier, Bernard Sainte-Marie, Rémy Rochette, Louis Bernatchez , Molecular Ecology , 2015HTMLFree
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Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes
Guillem Salazar, Francisco M. Cornejo-Castillo, Encarna Borrull, Cristina Díez-Vives, Elena Lara, Dolors Vaqué, Jesús M. Arrieta, Carlos M. Duarte, Josep M. Gasol, Silvia G. Acinas , Molecular Ecology , 2015RFree
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Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA
Brandon M. Lind, Christopher J. Friedline, Jill L. Wegrzyn, Patricia E. Maloney, Detlev R. Vogler, David B. Neale, Andrew J. Eckert , Molecular Ecology , 2017Jupyter NotebookFree
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Comparative genomics in the Asteraceae reveals little evidence for parallel evolutionary change in invasive taxa
Kathryn A. Hodgins, Dan G. Bock, Min A. Hahn, Sylvia M. Heredia, Kathryn G. Turner, Loren H. Rieseberg , Molecular Ecology , 2014RFree
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Detecting host–parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding
James J. N. Kitson, Christoph Hahn, Richard J. Sands, Nigel A. Straw, Darren M. Evans, David H. Lunt , Molecular Ecology , 2018HTMLFree
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The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding
Jianlong Li, Lori-Jayne Lawson Handley, Daniel S. Read, Bernd Hänfling , Molecular Ecology , 2018RFree
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Allelic diversity for neutral markers retains a higher adaptive potential for quantitative traits than expected heterozygosity
Ana Vilas, Andrés Pérez-Figueroa, Humberto Quesada, Armando Caballero , Molecular Ecology , 2015ShellFree
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Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations
Michael D. Martin, Flora Jay, Sergi Castellano, Montgomery Slatkin , Molecular Ecology , 2017PythonFree
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Decision-support tools for dynamic management
Heather Welch, Stephanie Brodie, Michael G. Jacox, Steven J. Bograd, Elliott L. Hazen , Conservation Biology , 2019RFree
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Untangling the proximate causes and underlying drivers of deforestation and forest degradation in Myanmar
Cheng Ling Lim, Graham W. Prescott, Jose Don T. De Alban, Alan D. Ziegler, Edward L. Webb , Conservation Biology , 2017QMLFree
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Why are metapopulations so rare?
Emanuel A. Fronhofer, Alexander Kubisch, Frank M. Hilker, Thomas Hovestadt, Hans Joachim Poethke , Conservation Biology , 2012PascalFree
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Deep convolutional models improve predictions of macaque V1 responses to natural images
Santiago A. Cadena , George H. Denfield, Edgar Y. Walker, Leon A. Gatys, Andreas S. Tolias , Matthias Bethge , Alexander S. Ecker , PLoS Computational Biology , 2019PythonFree
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Seizure pathways: A model-based investigation
Philippa J. Karoly , Levin Kuhlmann, Daniel Soudry, David B. Grayden, Mark J. Cook, Dean R. Freestone , PLoS Computational Biology , 2018MATLABFree
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JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets
Michael E. Hughes, John B. Hogenesch, Karl Kornacker , PLoS Computational Biology , 2010PythonFree
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Fast Reconstruction of Compact Context-Specific Metabolic Network Models
Nikos Vlassis , Maria Pires Pacheco , Thomas Sauter , PLoS Computational Biology , 2014PythonFree
-
Gap junction plasticity as a mechanism to regulate network-wide oscillations
Guillaume Pernelle, Wilten Nicola, Claudia Clopath , PLoS Computational Biology , 2018HTMLFree
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Deterministic response strategies in trial-and-error learning
Holger Mohr, Katharina Zwosta, Dimitrije Markovic, Sebastian Bitzer, Uta Wolfensteller, Hannes Ruge , PLoS Computational Biology , 2018MATLABFree
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Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model
Wondimu Teka, Toma M. Marinov, Fidel Santamaria , PLoS Computational Biology , 2014MATLABFree
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A Sparse Coding Model with Synaptically Local Plasticity and Spiking Neurons Can Account for the Diverse Shapes of V1 Simple Cell Receptive Fields
Joel Zylberberg , Jason Timothy Murphy, Michael Robert DeWeese , PLoS Computational Biology , 2011PythonFree
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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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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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Emergence of Functional Specificity in Balanced Networks with Synaptic Plasticity
Sadra Sadeh , Claudia Clopath , Stefan Rotter , PLoS Computational Biology , 2015PythonFree
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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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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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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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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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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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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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Dynamic Mechanisms of Neocortical Focal Seizure Onset
Yujiang Wang, Marc Goodfellow, Peter Neal Taylor, Gerold Baier , PLoS Computational Biology , 2014MATLABFree
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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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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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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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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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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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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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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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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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Spike and burst coding in thalamocortical relay cells.
Fleur Zeldenrust , Pascal Chameau, Wytse J. Wadman , PLoS Computational Biology , 2018AMPLFree
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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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