Methods in Ecology and Evolution

Papers
(The median citation count of Methods in Ecology and Evolution is 4. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-08-01 to 2025-08-01.)
ArticleCitations
Cover Picture and Issue Information727
Cover Picture and Issue Information410
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Incidence‐data‐based species richness estimation via a Beta‐Binomial model204
poems: R package for simulating species' range dynamics using pattern‐oriented validation154
Cover Picture and Issue Information136
Cover Picture and Issue Information126
A network theoretic method for the basic reproductive number for infectious diseases112
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses104
Empirical dynamic programming for model‐free ecosystem‐based management92
Exploring congruent diversification histories with flexibility and parsimony92
Filtering heart rates using data densities: The boxfilter R package89
Revticulate: An R framework for interaction with RevBayes83
plantR: An R package and workflow for managing species records from biological collections82
AF‐vapeR: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors79
Nighthawk: Acoustic monitoring of nocturnal bird migration in the Americas76
How to get the most out of phylogenetic imputation without abusing it75
Using cloud radar to investigate the effect of rainfall on migratory insect flight74
FlywayNet: A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data73
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records72
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution71
Beneath the buzz: Quantifying nest locations and densities of ground‐nesting wild bees (Hymenoptera: Anthophila)70
Individual tree extraction through 3D promptable segmentation networks69
Exploring noise, degeneracy and determinism in biological networks with the einet package69
A new centrality index designed for multilayer networks64
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation63
ECOGEN: Bird sounds generation using deep learning59
Toward a unified approach to modelling adaptation among demographers and evolutionary ecologists59
From anarchy to clarity, data pre‐processing and statistical choices influence quantitative environmental DNA (eDNA) analyses59
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occupancyTuts: Occupancy modelling tutorials with RPresence57
Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources57
BATScan: A radar classification tool reveals large‐scale bat migration patterns57
Cover Picture and Issue Information55
Towards biologically realistic estimates of home range and spatial exposure for colonial animals55
Long‐term automated visual monitoring of Antarctic benthic fauna53
Going beyond richness: Modelling the BEF relationship using species identity, evenness, richness and species interactions via the DImodels R package52
Integrated movement models for individual tracking and species distribution data52
Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity50
Measuring reflectance of tiny organisms: The promise of species level biocrust remote sensing48
A systematic method for hypothesis synthesis and conceptual model development48
A 3D modelling approach to measuring structural characteristics of bird nest interiors47
Benchmarking imputation methods for categorical biological data46
Multi‐trait point pattern reconstruction of plant ecosystems44
Classifying the activity states of small vertebrates using automated VHF telemetry42
Continuous on‐board behaviour classification using accelerometry: A case study with a new GPS‐3G‐Bluetooth system in Pacific black ducks42
An open future for MEE41
Gone with the wind: Inferring bird migration with light‐level geolocation, wind and activity measurements41
treetop: A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and conservationists40
Dynamic visualisation of million‐tip trees: The OneZoom project39
A general framework for jointly modelling thermal and hydric constraints on developing eggs39
MoonShine: A software‐hardware system for simulating moonlight ground illuminance and re‐creating artificial moonlight cycles in a laboratory environment39
Navigating through space and time: A methodological approach to quantify spatiotemporal connectivity using stream flow data as a case study38
EcoEnsemble: A general framework for combining ecosystem models in R38
Scalable semantic 3D mapping of coral reefs with deep learning37
Moving‐resting process with measurement error in animal movement modeling36
The ecological forecast limit revisited: Potential, absolute and relative system predictability36
Plant biodiversity assessment through soil eDNA reflects temporal and local diversity36
Cover Picture and Issue Information35
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Corrigendum35
When to monitor or control: Informed invasive species management using a partially observable Markov decision process (POMDP) framework34
Using causal diagrams and superpopulation models to correct geographic biases in biodiversity monitoring data33
PleistoDist: A toolbox for visualising and quantifying the effects of Pleistocene sea‐level change on island archipelagos32
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An aquaria set‐up for long‐term, multiple‐stressor research in marine organisms32
Same data, different results? Machine learning approaches in bioacoustics31
The r package enerscape: A general energy landscape framework for terrestrial movement ecology31
Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management30
Handbook of protocols for standardized measurements of floral traits for pollinators in temperate communities30
treats: A modular R package for simulating trees and traits30
The Benthic Underwater Microscope imaging PAM (BUMP): A non‐invasive tool for in situ assessment of microstructure and photosynthetic efficiency30
Retrodiction of forest demography: Backward simulation with reverse matrix models29
Overall dynamic body acceleration measures activity differently on large versus small aquatic animals29
Using standardized fish‐specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities29
Sourcing high tissue quality brains from deceased wild primates with known socio‐ecology29
Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA29
Food web reconstruction through phylogenetic transfer of low‐rank network representation28
The Wayqecha Amazon Cloud Curtain Ecosystem Experiment: A new experimental method to manipulate fog water inputs in terrestrial systems28
Existing and emerging uses of drones in restoration ecology28
Measuring understorey vegetation structure using a novel mixed‐reality device28
RFIDeep: Unfolding the potential of deep learning for radio‐frequency identification28
qad: An R‐package to detect asymmetric and directed dependence in bivariate samples28
A Double machine learning trend model for citizen science data27
Building ecological networks with local ecological knowledge in hyper‐diverse and logistically challenging ecosystems27
Detecting and reducing heterogeneity of error in acoustic classification27
Hidden Markov models: Pitfalls and opportunities in ecology27
TinyCO2: High‐performance, low‐cost CO2 enrichment for field‐grown plants27
Parasitic flowering plant collections embody the extended specimen26
Introducing recurrent event analyses to assess species interactions based on camera‐trap data: A comparison with time‐to‐first‐event approaches26
Accelerating advances in landscape connectivity modelling with the ConScape library26
Generating spatially realistic environmental null models with the shift‐&‐rotate approach helps evaluate false positives in species distribution modelling25
Automated identification of diverse Neotropical pollen samples using convolutional neural networks25
Methods for testing publication bias in ecological and evolutionary meta‐analyses25
Issues in calibrating models with multiple unbalanced constraints: the significance of systematic model and data errors25
PicoCam: High‐resolution 3D imaging of live animals and preserved specimens25
RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes25
Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves25
In situ estimation of active dispersal abilities in reef fish early life stages using tracking technologies24
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species24
TreeCompR: Tree competition indices for inventory data and 3D point clouds24
Detecting seasonal episodic‐like spatio‐temporal memory patterns using animal movement modelling23
A wireless, remotely operable and easily customizable robotic flower system23
Optimising sampling designs for habitat fragmentation studies23
TaxoNERD: Deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature23
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning23
A cost‐effective method to passively sample communities at the forest canopy–aerosphere interface23
A process approach to quality management doublesNEONsensor data quality23
Correction to: Quantifying degradation in animal acoustic signals with the R package baRulho22
Addressing spatial confounding in geostatistical regression models: An R‐INLA approach22
Tracking the frequency of phytoplankton clonal lineages using multispectral image flow cytometry and neural networks22
Writing a massively multi‐authored paper: Overcoming barriers to meaningful authorship for all21
The Movebank system for studying global animal movement and demography21
The power of forecasts to advance ecological theory21
An automatic classifier of bat sonotypes around the world20
The CV is dead, long live the CV!20
Estimating process‐based model parameters from species distribution data using the evolutionary algorithm CMA‐ES20
OpenSoundscape: An open‐source bioacoustics analysis package for Python20
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sabinaNSDM: An R package for spatially nested hierarchical species distribution modelling19
starve: An R package for spatio‐temporal analysis of research survey data using nearest‐neighbour Gaussian processes19
Cover Picture and Issue Information19
Using ensemble methods to improve the robustness of deep learning for image classification in marine environments19
The uniform AUC: Dealing with the representativeness effect in presence–absence models19
tidysdm: Leveraging the flexibility of tidymodels for species distribution modelling in R19
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation19
Towards scalable insect monitoring: Ultra‐lightweight CNNs as on‐device triggers for insect camera traps19
poolHelper: An R package to help in designing Pool‐Seq studies19
Monitoring fast‐moving animals—Building a customized camera system and evaluation toolset19
Synthesizing forecasts to inform decision‐making and advance ecological theory18
ipsecr: An R package for awkward spatial capture–recapture data18
The Latent Dirichlet Allocation model applied to airborne LiDAR data: A case study on mapping forest degradation associated with fragmentation and fire in the Amazon region18
Precise tactile stimulation of worker ants by a robotic manipulator reveals that individual responses are density‐ and context‐dependent18
Estimating interaction strengths for diverse horizontal systems using performance data18
Design and performance of an ecosystem‐scale forest soil warming experiment with infrared heater arrays18
Estimating species misclassification with occupancy dynamics and encounter rates: A semi‐supervised, individual‐level approach18
Scalable phylogenetic Gaussian process models improve the detectability of environmental signals on local extinctions for many Red List species18
How to generate accurate continuous thermal regimes from sparse but regular temperature measurements18
A framework to model a web of linkage disequilibria for natural allotetraploid populations18
PhycoCanopy: An R Shiny tool for exploring primary production in macroalgal canopies18
Methods to account for incomplete viewsheds in distance sampling17
NAPS: Integrating pose estimation and tag‐based tracking17
Cover Picture and Issue Information17
Evo‐Scope: Fully automated assessment of correlated evolution on phylogenetic trees17
Practical guidelines and the EMLN R package for handling ecological multilayer networks17
Impact of sampling strategy on inference of community assembly processes in phylogenetic island biogeography17
Cover Picture and Issue Information17
Guidelines for the prediction of species interactions through binary classification17
Managing risk and uncertainty in systematic conservation planning with insufficient information17
soundscape_IR: A source separation toolbox for exploring acoustic diversity in soundscapes17
Unifying individual differences in personality, predictability and plasticity: A practical guide17
Cover Picture and Issue Information17
Temporal design for aquatic organismal sampling across the National Ecological Observatory Network17
soundClass: An automatic sound classification tool for biodiversity monitoring using machine learning17
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Correction to ‘The Aquatic Metatron: A large‐scale experimental facility to study the combined effects of habitat fragmentation and climate change on aquatic meta‐ecosystems’16
ecochange: An R‐package to derive ecosystem change indicators from freely available earth observation products16
PiCAM: A Raspberry Pi‐based open‐source, low‐power camera system for monitoring plant phenology in Arctic environments16
Introducing the combined atlas framework for large‐scale web‐based data visualization: The GloNAF atlas of plant invasion16
Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring16
Hard tissue thin‐sectioning techniques in vertebrate paleohistology: Review, synthesis and improvements16
Long‐term collar deployment leads to bias in soil respiration measurements16
A low‐cost IoT network to monitor microclimate variables in ecosystems16
A framework for post‐processing bird tracks from automated tracking radar systems16
Acoustic and archival technologies join forces: A combination tag16
A GLMM approach for combining multiple relative abundance surfaces16
Quantifying the utilisation of blue, green and brown resources by riparian predators: A combined use of amino acid isotopes and fatty acids16
The use of weighted averages of Hedges' d in meta‐analysis: Is it worth it?16
Extending isolation by resistance to predict genetic connectivity16
Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data16
Including the invisible fraction in whole population studies: A guide to the genetic sampling of unhatched bird eggs16
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A conceptual framework for host‐associated microbiomes of hybrid organisms15
Stable isotope fingerprinting traces essential amino acid assimilation and multichannel feeding in a vertebrate consumer15
CaptuRING: A do‐it‐yourself tool for wood sample digitization15
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits15
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Pitfalls arising from site selection bias in population monitoring defy simple heuristics15
Streamlining analysis methods for large acoustic surveys using automatic detectors with operator validation15
Improved order selection method for hidden Markov models: A case study with movement data15
Cover Picture and Issue Information15
TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups15
Cover Picture and Issue Information15
allodb: An R package for biomass estimation at globally distributed extratropical forest plots15
Real‐time alerts from AI‐enabled camera traps using the Iridium satellite network: A case‐study in Gabon, Central Africa15
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PoolDilutionR: An R package for easy optimization of isotope pool dilution calculations15
Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?14
Clustering and unconstrained ordination with Dirichlet process mixture models14
HSC3D: A Python package to quantify three‐dimensional habitat structural complexity14
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap14
Ten practical guidelines for microclimate research in terrestrial ecosystems14
Impact of acoustic index parameters on soundscape comparisons14
ISSRseq: An extensible method for reduced representation sequencing14
A continuous‐score occupancy model that incorporates uncertain machine learning output from autonomous biodiversity surveys14
CATS: A high‐performance software framework for simulating plant migration in changing environments14
3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass14
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward14
isotracer: An R package for the analysis of tracer addition experiments14
Sap Flow Analyzer: A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method14
Realising the promise of large data and complex models14
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs14
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot14
Corrigendum13
The geodiv r package: Tools for calculating gradient surface metrics13
Investigating soil mesofauna cryptic diversity: Current challenges and perspectives13
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes13
Continuous‐surface geographic assignment of migratory animals using strontium isotopes: A case study with monarch butterflies13
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions13
Wellcounter: Automated high‐throughput phenotyping for aquatic microinvertebrates13
mpmsim: An R package for simulating matrix population models13
Cover Picture and Issue Information13
Correction to ‘PhyBaSE: A Bayesian structural equation model approach to causal inference in phylogenetic comparative analyses’13
Cost‐effective seafloor habitat mapping using a portable speedy sea scanner and deep‐learning‐based segmentation: A sea trial at Pujada Bay, Philippines13
Connectivity conservation planning through deep reinforcement learning13
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metaRange: A framework to build mechanistic range models13
Decoding the footsteps of the African savanna: Classifying wildlife using seismic signals and machine learning13
An RGB‐D framework for capturing soft‐sediment microtopography13
Cover Picture and Issue Information13
Estimating animal density for a community of species using information obtained only from camera‐traps13
Generating continuous maps of genetic diversity using moving windows13
ChirpArray: A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring13
Applying computer vision to digitised natural history collections for climate change research: Temperature‐size responses in British butterflies13
ENphylo: A new method to model the distribution of extremely rare species13
A model selection approach to structural equation modelling: A critical evaluation and a road map for ecologists13
High‐magnification platform for characterising microscopic communities13
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods12
plantTracker: An R package to translate maps of plant occurrence into demographic data12
Simple assay quantifying sediment resuspension effects on marine carbon storage12
A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats12
AMMonitor 2: Remote monitoring of biodiversity in an adaptive framework in R12
Robust passive sampling of airborne environmental DNA to monitor plants and animals12
A new tool to improve the estimates of interaction rewiring considering the whole community composition12
USE it: Uniformly sampling pseudo‐absences within the environmental space for applications in habitat suitability models12
Avoiding confusion: Modelling image identification surveys with classification errors12
Bioregionalization analyses with the bioregion R package12
ohun: An R package for diagnosing and optimizing automatic sound event detection12
EEMtoolbox: A user‐friendly R package for flexible ensemble ecosystem modelling12
Navigating the temporal continuum of effective population size12
Systematic review and best practices for drone remote sensing of invasive plants12
A Monte Carlo resampling framework for implementing goodness‐of‐fit tests in spatial capture‐recapture models12
A multi‐property assessment of intensity of use provides a functional understanding of animal movement12
Deep reinforcement learning for conservation decisions12
Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model12
patter: Particle algorithms for animal tracking in R and Julia12
A new method for voxel‐based modelling of three‐dimensional forest scenes with integration of terrestrial and airborne LiDAR data12
Integrating eco‐evolutionary dynamics into matrix population models for structured populations: Discrete and continuous frameworks11
Detecting stochasticity in population time series using a non‐parametric test of intrinsic predictability11
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