Methods in Ecology and Evolution

Article	Citations
	821
Cover Picture and Issue Information	256
Cover Picture and Issue Information	246
	166
A new centrality index designed for multilayer networks	153
A network theoretic method for the basic reproductive number for infectious diseases	151
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Individual tree extraction through 3D promptable segmentation networks	114
Empirical dynamic programming for model‐free ecosystem‐based management	108
Incidence‐data‐based species richness estimation via a Beta‐Binomial model	108
occupancyTuts: Occupancy modelling tutorials with RPresence	96
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	94
Toward a unified approach to modelling adaptation among demographers and evolutionary ecologists	92
Beneath the buzz: Quantifying nest locations and densities of ground‐nesting wild bees (Hymenoptera: Anthophila)	89
A pluralistic framework for measuring, interpreting and decomposing heterogeneity in meta‐analysis	83
How to get the most out of phylogenetic imputation without abusing it	83
Nighthawk: Acoustic monitoring of nocturnal bird migration in the Americas	81
Exploring noise, degeneracy and determinism in biological networks with the einet package	80
From anarchy to clarity, data pre‐processing and statistical choices influence quantitative environmental DNA (eDNA) analyses	79
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation	78
Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources	72
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records	71
Cover Picture and Issue Information	67
Cover Picture and Issue Information	65
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses	63

Revticulate: An R framework for interaction with RevBayes	62
Filtering heart rates using data densities: The boxfilter R package	62
AF‐vapeR: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors	59
ECOGEN: Bird sounds generation using deep learning	58
plantR: An R package and workflow for managing species records from biological collections	58
Exploring congruent diversification histories with flexibility and parsimony	56
FlywayNet: A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data	56
Using cloud radar to investigate the effect of rainfall on migratory insect flight	54
BATScan: A radar classification tool reveals large‐scale bat migration patterns	53
Cover Picture and Issue Information	52
A 3D modelling approach to measuring structural characteristics of bird nest interiors	49
Gone with the wind: Inferring bird migration with light‐level geolocation, wind and activity measurements	47
An open future for MEE	46
Multi‐trait point pattern reconstruction of plant ecosystems	43
The ecological forecast limit revisited: Potential, absolute and relative system predictability	41
Integrated movement models for individual tracking and species distribution data	40
A general framework for jointly modelling thermal and hydric constraints on developing eggs	40
Continuous on‐board behaviour classification using accelerometry: A case study with a new GPS‐3G‐Bluetooth system in Pacific black ducks	40
EcoEnsemble: A general framework for combining ecosystem models in R	39
Towards biologically realistic estimates of home range and spatial exposure for colonial animals	38
lacunr: Efficient 3D lacunarity for voxelized LiDAR data from forested ecosystems	38
Classifying the activity states of small vertebrates using automated VHF telemetry	38
A systematic method for hypothesis synthesis and conceptual model development	38
MoonShine: A software‐hardware system for simulating moonlight ground illuminance and re‐creating artificial moonlight cycles in a laboratory environment	38
Long‐term automated visual monitoring of Antarctic benthic fauna	37
Plant biodiversity assessment through soil eDNA reflects temporal and local diversity	37
Benchmarking imputation methods for categorical biological data	36
Navigating through space and time: A methodological approach to quantify spatiotemporal connectivity using stream flow data as a case study	34
treetop: A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and conservationists	34
Going beyond richness: Modelling the BEF relationship using species identity, evenness, richness and species interactions via the DImodels R package	34
Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity	33
Scalable semantic 3D mapping of coral reefs with deep learning	33
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Dynamic visualisation of million‐tip trees: The OneZoom project	32
Corrigendum	31
Cover Picture and Issue Information	31
PicoCam: High‐resolution 3D imaging of live animals and preserved specimens	31
Introducing recurrent event analyses to assess species interactions based on camera‐trap data: A comparison with time‐to‐first‐event approaches	31
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Cover Picture and Issue Information	31
Automated identification of diverse Neotropical pollen samples using convolutional neural networks	30
Sensors versus surveyors: Comparing passive acoustic monitoring, camera trapping and observer‐based monitoring for terrestrial mammals	30
Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA	30
PleistoDist: A toolbox for visualising and quantifying the effects of Pleistocene sea‐level change on island archipelagos	30
Same data, different results? Machine learning approaches in bioacoustics	30
Detecting and reducing heterogeneity of error in acoustic classification	30
The Benthic Underwater Microscope imaging PAM (BUMP): A non‐invasive tool for in situ assessment of microstructure and photosynthetic efficiency	29
Issues in calibrating models with multiple unbalanced constraints: the significance of systematic model and data errors	29
TinyCO2: High‐performance, low‐cost CO2 enrichment for field‐grown plants	29
Measuring understorey vegetation structure using a novel mixed‐reality device	29

Sourcing high tissue quality brains from deceased wild primates with known socio‐ecology	28
Parasitic flowering plant collections embody the extended specimen	28
An aquaria set‐up for long‐term, multiple‐stressor research in marine organisms	28
RFIDeep: Unfolding the potential of deep learning for radio‐frequency identification	28
Retrodiction of forest demography: Backward simulation with reverse matrix models	27
Using standardized fish‐specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities	27
Using causal diagrams and superpopulation models to correct geographic biases in biodiversity monitoring data	26
The Wayqecha Amazon Cloud Curtain Ecosystem Experiment: A new experimental method to manipulate fog water inputs in terrestrial systems	26
Overall dynamic body acceleration measures activity differently on large versus small aquatic animals	26
qad: An R‐package to detect asymmetric and directed dependence in bivariate samples	26
A Double machine learning trend model for citizen science data	26
Handbook of protocols for standardized measurements of floral traits for pollinators in temperate communities	25
Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management	25
The r package enerscape: A general energy landscape framework for terrestrial movement ecology	25
Hidden Markov models: Pitfalls and opportunities in ecology	25
When to monitor or control: Informed invasive species management using a partially observable Markov decision process (POMDP) framework	24
Methods for testing publication bias in ecological and evolutionary meta‐analyses	24
Food web reconstruction through phylogenetic transfer of low‐rank network representation	24
RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes	24
Generating spatially realistic environmental null models with the shift‐&‐rotate approach helps evaluate false positives in species distribution modelling	23
Existing and emerging uses of drones in restoration ecology	23
treats: A modular R package for simulating trees and traits	23
Accelerating advances in landscape connectivity modelling with the ConScape library	23
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species	23
Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves	23
In situ estimation of active dispersal abilities in reef fish early life stages using tracking technologies	22
A wireless, remotely operable and easily customizable robotic flower system	21
Tracking the frequency of phytoplankton clonal lineages using multispectral image flow cytometry and neural networks	21
Correction to: Quantifying degradation in animal acoustic signals with the R package baRulho	21
Addressing spatial confounding in geostatistical regression models: An R‐INLA approach	21
Writing a massively multi‐authored paper: Overcoming barriers to meaningful authorship for all	21
TreeCompR: Tree competition indices for inventory data and 3D point clouds	21
TaxoNERD: Deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature	20
A cost‐effective method to passively sample communities at the forest canopy–aerosphere interface	20
Detecting seasonal episodic‐like spatio‐temporal memory patterns using animal movement modelling	20
Estimating process‐based model parameters from species distribution data using the evolutionary algorithm CMA‐ES	20
The Movebank system for studying global animal movement and demography	20
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning	20
A process approach to quality management doublesNEONsensor data quality	20
The power of forecasts to advance ecological theory	20
OpenSoundscape: An open‐source bioacoustics analysis package for Python	20
The CV is dead, long live the CV!	20
Cover Picture and Issue Information	19
Estimating interaction strengths for diverse horizontal systems using performance data	19
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Towards scalable insect monitoring: Ultra‐lightweight CNNs as on‐device triggers for insect camera traps	19
Estimating species misclassification with occupancy dynamics and encounter rates: A semi‐supervised, individual‐level approach	19
starve: An R package for spatio‐temporal analysis of research survey data using nearest‐neighbour Gaussian processes	19
Design and performance of an ecosystem‐scale forest soil warming experiment with infrared heater arrays	19
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 region	18
How to generate accurate continuous thermal regimes from sparse but regular temperature measurements	18
ipsecr: An R package for awkward spatial capture–recapture data	18
Evo‐Scope: Fully automated assessment of correlated evolution on phylogenetic trees	18
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation	18
The uniform AUC: Dealing with the representativeness effect in presence–absence models	18
soundscape_IR: A source separation toolbox for exploring acoustic diversity in soundscapes	18
Scalable phylogenetic Gaussian process models improve the detectability of environmental signals on local extinctions for many Red List species	18
poolHelper: An R package to help in designing Pool‐Seq studies	18
A framework to model a web of linkage disequilibria for natural allotetraploid populations	18
sabinaNSDM: An R package for spatially nested hierarchical species distribution modelling	18
Precise tactile stimulation of worker ants by a robotic manipulator reveals that individual responses are density‐ and context‐dependent	18
Using ensemble methods to improve the robustness of deep learning for image classification in marine environments	18
NAPS: Integrating pose estimation and tag‐based tracking	18
Impact of sampling strategy on inference of community assembly processes in phylogenetic island biogeography	18
Monitoring fast‐moving animals—Building a customized camera system and evaluation toolset	18
PhycoCanopy: An R Shiny tool for exploring primary production in macroalgal canopies	18
soundClass: An automatic sound classification tool for biodiversity monitoring using machine learning	18
Methods to account for incomplete viewsheds in distance sampling	18
Temporal design for aquatic organismal sampling across the National Ecological Observatory Network	18
DeepDiveR—A software for deep learning estimation of palaeodiversity from fossil occurrences	17
Unifying individual differences in personality, predictability and plasticity: A practical guide	17
Cover Picture and Issue Information	17
ecochange: An R‐package to derive ecosystem change indicators from freely available earth observation products	17
Synthesizing forecasts to inform decision‐making and advance ecological theory	17
Practical guidelines and the EMLN R package for handling ecological multilayer networks	17
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Cover Picture and Issue Information	17
Guidelines for the prediction of species interactions through binary classification	17
tidysdm: Leveraging the flexibility of tidymodels for species distribution modelling in R	17
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Hard tissue thin‐sectioning techniques in vertebrate paleohistology: Review, synthesis and improvements	17
Acoustic and archival technologies join forces: A combination tag	16
A conceptual framework for host‐associated microbiomes of hybrid organisms	16
Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring	16
A framework for post‐processing bird tracks from automated tracking radar systems	16
The use of weighted averages of Hedges' d in meta‐analysis: Is it worth it?	16
A GLMM approach for combining multiple relative abundance surfaces	16
Quantifying the utilisation of blue, green and brown resources by riparian predators: A combined use of amino acid isotopes and fatty acids	16
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
Including the invisible fraction in whole population studies: A guide to the genetic sampling of unhatched bird eggs	16
Introducing the combined atlas framework for large‐scale web‐based data visualization: The GloNAF atlas of plant invasion	16
PiCAM: A Raspberry Pi‐based open‐source, low‐power camera system for monitoring plant phenology in Arctic environments	16
Improved order selection method for hidden Markov models: A case study with movement data	16
Extending isolation by resistance to predict genetic connectivity	16
CaptuRING: A do‐it‐yourself tool for wood sample digitization	16
Advancing aquatic biodiversity assessments of invertebrates using eDNA metabarcoding: A systematic evaluation of primers for marine and freshwater communities	16
Streamlining analysis methods for large acoustic surveys using automatic detectors with operator validation	15
Pitfalls arising from site selection bias in population monitoring defy simple heuristics	15
A low‐cost IoT network to monitor microclimate variables in ecosystems	15
Stable isotope fingerprinting traces essential amino acid assimilation and multichannel feeding in a vertebrate consumer	15
Modelling approaches for meta‐analyses with dependent effect sizes in ecology and evolution: A simulation study	15
Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data	15
Real‐time alerts from AI‐enabled camera traps using the Iridium satellite network: A case‐study in Gabon, Central Africa	15
Long‐term collar deployment leads to bias in soil respiration measurements	15
Studying collective animal behaviour with drones and computer vision	15
Sap Flow Analyzer: A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method	14
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isotracer: An R package for the analysis of tracer addition experiments	14
A model selection approach to structural equation modelling: A critical evaluation and a road map for ecologists	14
Connectivity conservation planning through deep reinforcement learning	14
Cover Picture and Issue Information	14
ChirpArray: A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring	14
Correction to ‘PhyBaSE: A Bayesian structural equation model approach to causal inference in phylogenetic comparative analyses’	14
HSC3D: A Python package to quantify three‐dimensional habitat structural complexity	14
3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass	14
PoolDilutionR: An R package for easy optimization of isotope pool dilution calculations	14
CATS: A high‐performance software framework for simulating plant migration in changing environments	14
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TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups	14
ISSRseq: An extensible method for reduced representation sequencing	14
Generating continuous maps of genetic diversity using moving windows	14
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	14
Clustering and unconstrained ordination with Dirichlet process mixture models	14
allodb: An R package for biomass estimation at globally distributed extratropical forest plots	14
A continuous‐score occupancy model that incorporates uncertain machine learning output from autonomous biodiversity surveys	13
Cover Picture and Issue Information	13
Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?	13
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits	13
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward	13
Time‐lapse cameras bridge the gap between remote sensing and in situ observations of tundra phenology	13
Applying computer vision to digitised natural history collections for climate change research: Temperature‐size responses in British butterflies	13
Realising the promise of large data and complex models	13
Impact of acoustic index parameters on soundscape comparisons	13
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot	13
Estimating animal density for a community of species using information obtained only from camera‐traps	13
ENphylo: A new method to model the distribution of extremely rare species	13
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	13
Quantifying macro‐evolutionary patterns of trait mean and variance with phylogenetic location–scale models	13
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap	13
Investigating soil mesofauna cryptic diversity: Current challenges and perspectives	13
Ten practical guidelines for microclimate research in terrestrial ecosystems	13
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs	13
Cover Picture and Issue Information	13
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods	12
mpmsim: An R package for simulating matrix population models	12
metaRange: A framework to build mechanistic range models	12
Avoiding confusion: Modelling image identification surveys with classification errors	12
Decoding the footsteps of the African savanna: Classifying wildlife using seismic signals and machine learning	12
Distinguishing passive and driven trait evolution in the presence of boundaries	12
patter: Particle algorithms for animal tracking in R and Julia	12
A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats	12
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A new method for voxel‐based modelling of three‐dimensional forest scenes with integration of terrestrial and airborne LiDAR data	12
A new tool to improve the estimates of interaction rewiring considering the whole community composition	12
AMMonitor 2: Remote monitoring of biodiversity in an adaptive framework in R	12
A Monte Carlo resampling framework for implementing goodness‐of‐fit tests in spatial capture‐recapture models	12
An RGB‐D framework for capturing soft‐sediment microtopography	12
High‐magnification platform for characterising microscopic communities	12
Corrigendum	12
plantTracker: An R package to translate maps of plant occurrence into demographic data	12
EEMtoolbox: A user‐friendly R package for flexible ensemble ecosystem modelling	12
Robust passive sampling of airborne environmental DNA to monitor plants and animals	12
Systematic review and best practices for drone remote sensing of invasive plants	11
Home‐range spillover in habitats with impassable boundaries: Causes, biases and corrections using autocorrelated kernel density estimation	11
Bioregionalization analyses with the bioregion R package	11
Wellcounter: Automated high‐throughput phenotyping for aquatic microinvertebrates	11
A multi‐property assessment of intensity of use provides a functional understanding of animal movement	11
Simple assay quantifying sediment resuspension effects on marine carbon storage	11
USE it: Uniformly sampling pseudo‐absences within the environmental space for applications in habitat suitability models	11
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Mitigating pseudoreplication and bias in resource selection functions with autocorrelation‐informed weighting	11
Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model	11
ohun: An R package for diagnosing and optimizing automatic sound event detection	11
Cover Picture and Issue Information	11