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Single-cell transcriptomics unveils gene regulatory network plasticity
Giovanni Iancono, Ramon Massoni-Badosa, Holger Heyn , Genome Biology , 2019HTMLFree
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Comparison of computational methods for the identification of topologically assocaiting domains
Marie Zufferey, Daniele Tavernari, Elisa Oricchio, Giovanni Ciriello , Genome Biology , 2018RFree
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An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BedArray
Lucas A. Salas, Devin C. Koestler, Rondi A. Butler, Helen M.Hansen, John K. Wiencke, Karl T. Kelsey, Brock C. Christensen , Genome Biology , 2018RFree
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Comparative assessment of methods for aligning multiple genome sequences
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The somatic mutation landscape of the human body
Pablo E. García-Nieto, Ashby J. Morrison, Hunter B. Fraser , Genome Biology , 2019RFree
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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 , 2016PythonFree
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Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp
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Moderm computational approaches for analysing molecular genetic variation data
Paul Marjoram, Simon Tavaré , Annual Review of Ecology, Evolution, and Systematics , 2006PythonFree
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Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers
Anne Chao, Chun-Huo Chiu, Lou Jost , Annual Review of Ecology, Evolution, and Systematics , 2014RFree
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Time to get moving: assisted gene flow of forest trees
Sally N. Aitken, Jordan B. Bemmels , Annual Review of Ecology, Evolution, and Systematics , 2015RebolFree
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On Fitting the Poisson Lognormal Distribution to Species-Abundance Data
M.G. Bulmer , Annual Review of Ecology, Evolution, and Systematics , 1974PascalFree
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Do baseline glucocorticoids presict fitness? Trends in Ecology and Evolution
Frances Bonier, Paul R. Martin, Ignacio T. Moore, John C. Wingfield , Trends in Ecology and Evolution , 2009HTMLFree
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ENMTools 1.0: an R package for comparative ecological biogeography
Dan L. Warren, Nicholas J. Matzke, Marcel Cardillo, John B. Baumartner , Trends in Ecology and Evolution , 2021RFree
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Blobal photsynthetic capacity is optimized to the environment
Nicholas G. Smith, Trevor F. Keenan, I.Colin Prentice, Han Wang , Ecology Letters , 2019RFree
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Abunance of common species, not species richness, drives delivery of a real-world ecosystem service
Rachael Winfree, Jeremy W. Fox, Neal M. Williams, James R. Reilly, Daniel P.Cariveau , Ecology Letters , 2015RFree
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Network spandrels reflect ecological assembly
Daniel S. Maynard, Carlos A. Serván, Stefano Allesina , Ecology Letters , 2018RFree
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Predicting the spread of all invasive forest pests in the United States
Emma J. Hudgins, Andrew M. Liebhlod, Brian Leung , Ecology Letters , 2017RFree
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Trasnlucent windows: how uncertainty in competitive interactions impacts detection of community pattern
Rafael D'Andrea, Annette Ostling, James P. O'Dwyer , Ecology Letters , 2018RFree
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Traits linked with species invasivness and community invasiblity vary with time, stage and indicator of invasion in a long-term grassland experiment
Jane A. Catford, Annabel L. Smith, Peter D. Wragg, et al , Ecology Letters , 2019RFree
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The ecohydrological context of drought and classification of plant responses
Xue Feng, David D. Sckerly, Todd E. Dawson, Stefano Manzoni, Rob P.Skelton, Giulia Vico, Sally E. Thompson , Ecology Letters , 2018PythonFree
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Scaling metabolism from individuals to reef-fish communities at broad spatial scales
D.R. Barneche, M.Kulbicki, S.R. Floeter, A.M. Friendlander, J.Maina, A.P Allen , Ecology Letters , 2014RFree
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Metabloic compensation constrains the temperature dependence of gross primary production
Daniel Padfield, Chris Lowe, Angus Buckling, Richard Ffrench-Constant , Ecology Letters , 2017RFree
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Size-based ecological interactions drive food web responses to climate warming
Max Lindmark, Jan Ohlberger, Magnus Huss, Anna Gårdmark , Ecology Letters , 2019RFree
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Ecology Under Lake Ice
Stephaine E. Hamptopn, Aaron W. E. Galloway, et al , Ecology Letters , 2016RFree
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Linking phytoplankton community metabolism to the individual size distribution
Daneil Padfield, Angus Buckling, Ruth Warfield, Chris Lowe, Gabriel Yvon-Durocher , Ecology Letters , 2018RFree
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A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences
Tal Pupko, Itsik Pe, Ron Shamir, Dan Graur , Molecular Biology and Evolution , 2000PythonFree
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Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens
Jing Wang, Nathaniel R. Street, Douglas G. Scofield, Pär K. Ingvarsson , Molecular Biology and Evolution , 2016ShellFree
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Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata)
Stuart V. Nielsen , Irán Andira Guzmán-Méndez , Tony Gamble , Madison Blumer , Brendan J. Pinto , Lukáš Kratochvíl, Michail Rovatsos , Molecular Biology and Evolution , 2019PythonFree
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Accounting for Phylogenetic Uncertainty in Biogeography: A Bayesian Approach to Dispersal-Vicariance Analysis of the Thrushes
Johan A A Nylander,Urban Olsson,Per Alström,Isabel Sanmartín , Systematic Biology , 2008PerlFree
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Widespread inhibition of daytime ecosystem respiration
Trevor F. Keenan, Mirco Migliavacca, Dario Papale, Dennis Baldocchi, Markus Reichstein, Margaret Torn & Thomas Wutzler , Nature Ecology and Evolution , 2019MATLABFree
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Social support drives female dominance in the spotted hyaena
Colin Vullioud, Eve Davidian, Bettina Wachter, François Rousset, Alexandre Courtiol, Oliver P. Höner , Nature Ecology and Evolution , 2018RFree
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Tipping points in the dynamics of speciation
Patrik Nosil, Jeffrey L. Feder, Samuel M. Flaxman, Zachariah Gompert , Nature Ecology and Evolution , 2017MathematicaFree
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Root microbiota assembly and adaptive differentiation among European Arabidopsis populations
Thorsten Thiergart, Paloma Durán, Thomas Ellis, Nathan Vannier, Ruben Garrido-Oter, Eric Kemen , Nature Ecology and Evolution , 2019RFree
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Individual immune selection pressure has limited impact on seasonal influenza virus evolution
Alvin X. Han, Sebastian Maurer-Stroh,Colin A. Russell , Nature Ecology and Evolution , 2018Jupyter NotebookFree
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A meta-analysis of changes in bacterial and archaeal communities with time
Ashley Shade, J Gregory Caporaso, Jo Handelsman, Rob Knight, Noah Fierer , ISME Journal , 2013RFree
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Time and ecological resilience: can diurnal animals compensate for climate change by shifting to nocturnal activity?
Ofir Levy, Tamar Dayan, Warren P. Porter, Noga Kronfeld-Schor , Ecological Monographs , 2018FortranFree
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Local snow melt and temperature—but not regional sea ice—explain variation in spring phenology in coastal Arctic tundra
Jakob J. Assmann, Isla H. Myers-Smith, Albert B. Phillimore, Anne D. Bjorkman, Richard E. Ennos, Janet S. Prevéy, Greg H. R. Henry, Niels M. Schmidt, Robert D. Hollister , Ecological Monographs , 2019RFree
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Disentangling herbivore impacts in primary succession by refocusing the plant stress and vigor hypotheses on phenology
Christian Che-Castaldo, Charlie M. Crisafulli, John G. Bishop, Elise F. Zipkin, William F. Fagan , Ecological Monographs , 2019HTMLFree
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Estimating the volume and age of water stored in global lakes using a geo-statistical approach
Mathis Loïc Messager, Bernhard Lehner, Günther Grill, Irena Nedeva, Oliver Schmitt , Frontiers in Ecology and the Environment , 2016PythonFree
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ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms
William E. Peterman , Methods in Ecology and Evolution , 2018RFree
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Microclima: An r package for modelling meso- and microclimate
Ilya M. D. Maclean, Jonathan R. Mosedale, Jonathan J. Bennie , Methods in Ecology and Evolution , 2018RFree
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A New Method for Estimation of Resource Selection Probability Function
SUBHASH R. LELE , Methods in Ecology and Evolution , 2010RFree
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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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Measuring microenvironments for global change: DIY environmental microcontroller units (EMUs)
James G. Mickley, Timothy E. Moore, Carl D. Schlichting, Amber DeRobertis, Emilia N. Pfisterer, Robert Bagchi , Methods in Ecology and Evolution , 2018LuaFree
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Phylogenomics from low-coverage whole-genome sequencing
Feng Zhang, Yinhuan Ding, Chao-Dong Zhu, Xin Zhou, Michael C. Orr, Stefan Scheu, Yun-Xia Luan , Methods in Ecology and Evolution , 2019ShellFree
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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 , Methods in Ecology and Evolution , 2019RFree
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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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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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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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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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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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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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dispRity: A modular R package for measuring disparity
Thomas Guillerme , Methods in Ecology and Evolution , 2019HTMLFree
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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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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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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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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
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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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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
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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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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
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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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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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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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