Methods in Ecology and Evolution

Article	Citations
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Cover Picture and Issue Information	220
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Cover Picture and Issue Information	128
Cover Picture and Issue Information	105
A network theoretic method for the basic reproductive number for infectious diseases	100
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses	97
FlywayNet : A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data	85
Nighthawk : Acoustic monitoring of nocturnal bird migration in the Americas	84
A new centrality index designed for multilayer networks	84
Exploring congruent diversification histories with flexibility and parsimony	82
Beneath the buzz: Quantifying nest locations and densities of ground‐nesting wild bees (Hymenoptera: Anthophila)	74
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	74
BATScan: A radar classification tool reveals large‐scale bat migration patterns	71
Empirical dynamic programming for model‐free ecosystem‐based management	61
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records	56
State‐space models and inference approaches for aquatic animal tracking with passive acoustic telemetry and biologging sensors	53
Using cloud radar to investigate the effect of rainfall on migratory insect flight	53
Filtering heart rates using data densities: The boxfilter R package	53
Incidence‐data‐based species richness estimation via a Beta‐Binomial model	52
Goby gummies: A customizable and edible assay to quantify predation in aquatic ecosystems	50
Inferring state‐dependent diversification rates using approximate Bayesian computation	50
Toward a unified approach to modelling adaptation among demographers and evolutionary ecologists	50

A pluralistic framework for measuring, interpreting and decomposing heterogeneity in meta‐analysis	49
Individualised niches in a variable environment—Consequences for environmental change responses	48
ECOGEN : Bird sounds generation using deep learning	48
From anarchy to clarity, data pre‐processing and statistical choices influence quantitative environmental DNA ( eDNA	47
How to get the most out of phylogenetic imputation without abusing it	45
Individual tree extraction through 3D promptable segmentation networks	45
Towards biologically realistic estimates of home range and spatial exposure for colonial animals	42
AF‐vapeR : A multivariate genome scan for detecting parallel evolution using allele frequency change vectors	42
occupancyTuts : Occupancy modelling tutorials with RPresence	42
A systematic method for hypothesis synthesis and conceptual model development	42
An open future for MEE	41
Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity	39
Integrated movement models for individual tracking and species distribution data	38
M oon S hine : A software‐hardware system for simulating moonlight ground illuminance and re‐creat	38
A 3D modelling approach to measuring structural characteristics of bird nest interiors	38
EcoEnsemble: A general framework for combining ecosystem models in R	38
Classifying the activity states of small vertebrates using automated VHF telemetry	38
lacunr: Efficient 3D lacunarity for voxelized LiDAR data from forested ecosystems	37
Towards ‘digital ecology’: Advances in integrating artificial intelligence from data generation to ecological insight	36
Data reconciliation in multi‐trait experiments with kinship ordination	35
‘But I can't preregister my research’: Improving the reproducibility and transparency of ecology and conservation with adaptive preregistration for model‐based research	35
Going beyond richness: Modelling the BEF relationship using species identity, evenness, richness and species interactions via the DImodels R package	35
Navigating through space and time: A methodological approach to quantify spatiotemporal connectivity using stream flow data as a case study	33
A general framework for jointly modelling thermal and hydric constraints on developing eggs	33
Multi‐trait point pattern reconstruction of plant ecosystems	32
Long‐term automated visual monitoring of Antarctic benthic fauna	31
Scalable semantic 3D mapping of coral reefs with deep learning	31
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Benchmarking imputation methods for categorical biological data	31
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The ecological forecast limit revisited: Potential, absolute and relative system predictability	31
Sensors versus surveyors: Comparing passive acoustic monitoring, camera trapping and observer‐based monitoring for terrestrial mammals	30
Cover Picture and Issue Information	30
Issues in calibrating models with multiple unbalanced constraints: the significance of systematic model and data errors	30
Microclimf: Fast modelling of microclimate across real landscapes in R	30
RFIDeep: Unfolding the potential of deep learning for radio‐frequency identification	30
Trait coevolution and causal inference using generalized dynamic phylogenetic models	30
A global estimator of C and N isotope baselines for fresh waters	29
Using standardized fish‐specific autonomous reef monitoring structures ( FARMS ) to quantify cryptobenthic fish communities	29
Handbook of protocols for standardized measurements of floral traits for pollinators in temperate communities	29
Using causal diagrams and superpopulation models to correct geographic biases in biodiversity monitoring data	29
Measuring understorey vegetation structure using a novel mixed‐reality device	28
PleistoDist : A toolbox for visualising and quantifying the effects of Pleistocene sea‐level change on island archipelagos	28
qad : An R‐package to detect asymmetric and directed dependence in bivariate samples	28
When to monitor or control: Informed invasive species management using a partially observable Markov decision process ( POMDP ) framework	28
TinyCO 2 : High‐performance, low‐cost CO	28
Retrodiction of forest demography: Backward simulation with reverse matrix models	27
The Benthic Underwater Microscope imaging PAM ( BUMP ): A non‐invasive tool for in situ assessment	27
PicoCam: High‐resolution 3D imaging of live animals and preserved specimens	26
Same data, different results? Machine learning approaches in bioacoustics	26

Automated identification of diverse Neotropical pollen samples using convolutional neural networks	26
An aquaria set‐up for long‐term, multiple‐stressor research in marine organisms	26
Sourcing high tissue quality brains from deceased wild primates with known socio‐ecology	26
Existing and emerging uses of drones in restoration ecology	26
The Wayqecha Amazon Cloud Curtain Ecosystem Experiment: A new experimental method to manipulate fog water inputs in terrestrial systems	26
A Double machine learning trend model for citizen science data	26
Correction to: Quantifying degradation in animal acoustic signals with the R package baRulho	25
treats: A modular R package for simulating trees and traits	25
Detecting and reducing heterogeneity of error in acoustic classification	25
Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves	25
Introducing recurrent event analyses to assess species interactions based on camera‐trap data: A comparison with time‐to‐first‐event approaches	25
A cost‐effective method to passively sample communities at the forest canopy–aerosphere interface	24
Estimating process‐based model parameters from species distribution data using the evolutionary algorithm CMA‐ES	24
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species	24
A wireless, remotely operable and easily customizable robotic flower system	24
Writing a massively multi‐authored paper: Overcoming barriers to meaningful authorship for all	24
In situ estimation of active dispersal abilities in reef fish early life stages using tracking technologies	24
Cover Picture and Issue Information	23
A terrestrial laser scanning‐based workflow for component‐wise estimation of individual tree above‐ground biomass	23
A short guide for effective field data collection	23
Addressing spatial confounding in geostatistical regression models: An R‐ INLA approach	23
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning	23
The power of forecasts to advance ecological theory	23
Data‐driven discovery of mechanistic ecosystem models with LLMs	23
Tracking the frequency of phytoplankton clonal lineages using multispectral image flow cytometry and neural networks	23
Vegetation patterns pinpoint the least resilient dryland sites	23
The CV is dead, long live the CV !	23
A process approach to quality management doubles NEON sensor data quality	22
Generating spatially realistic environmental null models with the shift‐&‐rotate approach helps evaluate false positives in species distribution modelling	22
Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees	22
Paying attention to other animal detections improves camera trap classification models	22
TreeCompR : Tree competition indices for inventory data and 3D point clouds	22
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OpenSoundscape: An open‐source bioacoustics analysis package for Python	22
Cover Picture and Issue Information	22
starve: An R package for spatio‐temporal analysis of research survey data using nearest‐neighbour Gaussian processes	21
Scalable phylogenetic Gaussian process models improve the detectability of environmental signals on local extinctions for many Red List species	21
Animal geolocation with convolution algorithms in Julia and R via Wahoo.jl	21
sound C lass : An automatic sound classification tool for biodiversity monitoring using machine learning	21
How to generate accurate continuous thermal regimes from sparse but regular temperature measurements	21
Guidelines for the prediction of species interactions through binary classification	21
Temporal design for aquatic organismal sampling across the National Ecological Observatory Network	21
Methods to account for incomplete viewsheds in distance sampling	21
poolHelper : An R package to help in designing Pool‐Seq studies	21
ipsecr: An R package for awkward spatial capture–recapture data	20
Estimating interaction strengths for diverse horizontal systems using performance data	20
Synthesizing forecasts to inform decision‐making and advance ecological theory	20
sabinaNSDM : An R package for spatially nested hierarchical species distribution modelling	20
Precise tactile stimulation of worker ants by a robotic manipulator reveals that individual responses are density‐ and context‐dependent	20
Reconstructing Langevin systems from high‐ and low‐resolution time series using Euler and Hermite reconstructions	20
COPIS : A robust and versatile robotic imaging system for the 3D digitization of natural history specimens with photog	20
Impact of sampling strategy on inference of community assembly processes in phylogenetic island biogeography	20
Design and performance of an ecosystem‐scale forest soil warming experiment with infrared heater arrays	20
DeepDiveR—A software for deep learning estimation of palaeodiversity from fossil occurrences	20
tidysdm : Leveraging the flexibility of tidymodels for species distribution modelling in R	20
NAPS : Integrating pose estimation and tag‐based tracking	19
Monitoring fast‐moving animals—Building a customized camera system and evaluation toolset	19
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation	19
Cover Picture and Issue Information	19
Practical guidelines and the EMLN R package for handling ecological multilayer networks	19
Towards scalable insect monitoring: Ultra‐lightweight CNNs as on‐device triggers for insect camera traps	19
Cover Picture and Issue Information	19
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’	19
soundscape_IR: A source separation toolbox for exploring acoustic diversity in soundscapes	19
ForestForTrees : An R package to infer forest structure from remote sensing data	19
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Cover Picture and Issue Information	19
Correction to ‘An evaluation of multi‐species occupancy models with correlated species occurrences’	18
Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring	18
3D photogrammetry as a low‐cost and non‐invasive method for acoustic modelling of animal hearing	18
Including the invisible fraction in whole population studies: A guide to the genetic sampling of unhatched bird eggs	18
A low‐cost IoT network to monitor microclimate variables in ecosystems	18
Hard tissue thin‐sectioning techniques in vertebrate paleohistology: Review, synthesis and improvements	18
Acoustic and archival technologies join forces: A combination tag	18
A GLMM approach for combining multiple relative abundance surfaces	18
Improved order selection method for hidden Markov models: A case study with movement data	18
PiCAM : A Raspberry Pi‐based open‐source, low‐power camera system for monitoring plant phenology in Arctic environments	18
Modelling approaches for meta‐analyses with dependent effect sizes in ecology and evolution: A simulation study	18
Pitfalls arising from site selection bias in population monitoring defy simple heuristics	18
Quantifying the utilisation of blue, green and brown resources by riparian predators: A combined use of amino acid isotopes and fatty acids	18

Stable isotope fingerprinting traces essential amino acid assimilation and multichannel feeding in a vertebrate consumer	17
Non‐invasive reconstruction of complete mitochondrial genomes from aquatic environmental DNA using PCR‐free long‐read sequencing	17
Studying collective animal behaviour with drones and computer vision	17
A conceptual framework for host‐associated microbiomes of hybrid organisms	17
ecochange: An R‐package to derive ecosystem change indicators from freely available earth observation products	17
Computationally efficient Bayesian capture–mark–recapture models with transients, applied to survival of hand‐reared African Penguins	17
A framework for post‐processing bird tracks from automated tracking radar systems	17
Streamlining analysis methods for large acoustic surveys using automatic detectors with operator validation	17
Estimating spatiotemporal reproductive dynamics of fish populations with passive acoustic monitoring: A state‐space model approach	17
A novel generalized spatial mark‐resight model that accounts for group associations	16
Long‐term collar deployment leads to bias in soil respiration measurements	16
Real‐time alerts from AI‐enabled camera traps using the Iridium satellite network: A case‐study in Gabon, Central Africa	16
Advancing aquatic biodiversity assessments of invertebrates using eDNA metabarcoding: A systematic evaluation of primers for marine and freshwater co	16
The persistent advantage of model‐based phylogenetic methods for single‐trait prediction	16
Applying the maximum entropy principle to neural networks enhances multi‐species distribution models	16
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Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data	16
Rapid construction of insect–plant interaction networks via multiplexed long‐fragment DNA metabarcoding and NGS	16
Extending isolation by resistance to predict genetic connectivity	16
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TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups	15
Time‐lapse cameras bridge the gap between remote sensing and in situ observations of tundra phenology	15
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits	15
3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass	15
Connectivity conservation planning through deep reinforcement learning	15
Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?	15
Sap Flow Analyzer : A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method	15
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap	15
CATS : A high‐performance software framework for simulating plant migration in changing environments	15
Cover Picture and Issue Information	15
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Clustering and unconstrained ordination with Dirichlet process mixture models	15
ChirpArray : A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring	15
Generating continuous maps of genetic diversity using moving windows	15
Correction to ‘ PhyBaSE : A Bayesian structural equation model approach to causal inference in phylogenetic comparative analyses’	15
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One number to rule them all: The Wildlife Sperm Index for standardized gamete assessment	14
Investigating soil mesofauna cryptic diversity: Current challenges and perspectives	14
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward	14
Cover Picture and Issue Information	14
PoolDilutionR : An R package for easy optimization of isotope pool dilution calculations	14
HSC 3 D : A Python package to quantify three‐dimensional habitat structural complexity	14
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot	14
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	14
A continuous‐score occupancy model that incorporates uncertain machine learning output from autonomous biodiversity surveys	14
theRmalUAV: An R package to clean and correct thermal UAV data for accurate land surface temperatures	14
Estimating animal density for a community of species using information obtained only from camera‐traps	13
A multi‐property assessment of intensity of use provides a functional understanding of animal movement	13
A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats	13
plantTracker : An R package to translate maps of plant occurrence into demographic data	13
patter: Particle algorithms for animal tracking in R and Julia	13
Cover Picture and Issue Information	13
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs	13
Quantifying macro‐evolutionary patterns of trait mean and variance with phylogenetic location–scale models	13
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	13
Robust passive sampling of airborne environmental DNA to monitor plants and animals	13
Deep reinforcement learning for conservation decisions	13
mpmsim: An R package for simulating matrix population models	13
AMMonitor 2: Remote monitoring of biodiversity in an adaptive framework in R	13
Ten practical guidelines for microclimate research in terrestrial ecosystems	13
ENphylo : A new method to model the distribution of extremely rare species	13
Realising the promise of large data and complex models	13
Cover Picture and Issue Information	13
Wellcounter: Automated high‐throughput phenotyping for aquatic microinvertebrates	13
Distinguishing passive and driven trait evolution in the presence of boundaries	13
High‐magnification platform for characterising microscopic communities	13
Impact of acoustic index parameters on soundscape comparisons	13
An intuitive method to calculate the utilization distribution of an animal from step‐selection analysis	13
Simple assay quantifying sediment resuspension effects on marine carbon storage	12
EEMtoolbox : A user‐friendly R package for flexible ensemble ecosystem modelling	12
Avoiding confusion: Modelling image identification surveys with classification errors	12
ohun: An R package for diagnosing and optimizing automatic sound event detection	12
A new method for voxel‐based modelling of three‐dimensional forest scenes with integration of terrestrial and airborne LiDAR data	12
Fine‐scale reconstruction of pelagic fish migration by iso‐logging of eye lens	12
A Monte Carlo resampling framework for implementing goodness‐of‐fit tests in spatial capture‐recapture models	12
Bioregionalization analyses with the bioregion R package	12
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods	12
Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model	12
Decoding the footsteps of the African savanna: Classifying wildlife using seismic signals and machine learning	12
Home‐range spillover in habitats with impassable boundaries: Causes, biases and corrections using autocorrelated kernel density estimation	12
metaRange : A framework to build mechanistic range models	12
USE it: Uniformly sampling pseudo‐absences within the environmental space for applications in habitat suitability models	12
Systematic review and best practices for drone remote sensing of invasive plants	12
Beyond the next step: A multi‐criteria generative validation framework for step selection functions	12
DImodelsMulti: An R package for fitting Diversity‐Interactions models to repeated measures or multivariate data	11
Spatially explicit management of genetic diversity using ancestry probability surfaces	11
Introduction to deep learning methods for multi‐species predictions	11
dentist: Quantifying uncertainty by sampling points around maximum likelihood estimates	11
Ecoacoustics for context‐rich direct and indirect trophic interaction data and ecological network construction	11
STbayes : An R package for creating, fitting and understanding Bayesian models of social transmission	11
Differentiating siliceous particulate matter in the diets of mammalian herbivores	11
A new tool to improve the estimates of interaction rewiring considering the whole community composition	11
Validating ATLAS : A regional‐scale high‐throughput tracking system	11
Fieldwork in conservation organisations–A review of methodological challenges, opportunities and ethics	11
The RadOrgMiner pipeline: Automated genotyping of organellar loci from RADseq data	11