Methods in Ecology and Evolution

Article	Citations
	856
Cover Picture and Issue Information	260
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Cover Picture and Issue Information	130
Cover Picture and Issue Information	117
Exploring congruent diversification histories with flexibility and parsimony	114
A pluralistic framework for measuring, interpreting and decomposing heterogeneity in meta‐analysis	113
Empirical dynamic programming for model‐free ecosystem‐based management	103
Revticulate: An R framework for interaction with RevBayes	100
How to get the most out of phylogenetic imputation without abusing it	96
occupancyTuts : Occupancy modelling tutorials with RPresence	94
Filtering heart rates using data densities: The boxfilter R package	91
plantR: An R package and workflow for managing species records from biological collections	85
From anarchy to clarity, data pre‐processing and statistical choices influence quantitative environmental DNA ( eDNA	85
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses	84
A new centrality index designed for multilayer networks	83
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	74
Toward a unified approach to modelling adaptation among demographers and evolutionary ecologists	72
FlywayNet : A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data	69
Using cloud radar to investigate the effect of rainfall on migratory insect flight	67
AF‐vapeR : A multivariate genome scan for detecting parallel evolution using allele frequency change vectors	64
ECOGEN : Bird sounds generation using deep learning	62
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records	60

Beneath the buzz: Quantifying nest locations and densities of ground‐nesting wild bees (Hymenoptera: Anthophila)	59
A network theoretic method for the basic reproductive number for infectious diseases	57
Individual tree extraction through 3D promptable segmentation networks	57
Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources	55
Nighthawk : Acoustic monitoring of nocturnal bird migration in the Americas	54
Incidence‐data‐based species richness estimation via a Beta‐Binomial model	53
Exploring noise, degeneracy and determinism in biological networks with the einet package	50
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation	47
Multi‐trait point pattern reconstruction of plant ecosystems	44
BATScan: A radar classification tool reveals large‐scale bat migration patterns	44
A systematic method for hypothesis synthesis and conceptual model development	43
Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity	42
The ecological forecast limit revisited: Potential, absolute and relative system predictability	42
lacunr: Efficient 3D lacunarity for voxelized LiDAR data from forested ecosystems	42
Dynamic visualisation of million‐tip trees: The OneZoom project	41
Integrated movement models for individual tracking and species distribution data	41
A 3D modelling approach to measuring structural characteristics of bird nest interiors	40
Gone with the wind: Inferring bird migration with light‐level geolocation, wind and activity measurements	40
Long‐term automated visual monitoring of Antarctic benthic fauna	40
treetop : A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and	40
Classifying the activity states of small vertebrates using automated VHF telemetry	38
M oon S hine : A software‐hardware system for simulating moonlight ground illuminance and re‐creat	37
Towards biologically realistic estimates of home range and spatial exposure for colonial animals	36
An open future for MEE	35
Continuous on‐board behaviour classification using accelerometry: A case study with a new GPS‐3G‐Bluetooth system in Pacific black ducks	35
Plant biodiversity assessment through soil eDNA reflects temporal and local diversity	35
Scalable semantic 3D mapping of coral reefs with deep learning	34
A general framework for jointly modelling thermal and hydric constraints on developing eggs	34
Going beyond richness: Modelling the BEF relationship using species identity, evenness, richness and species interactions via the DImodels R package	34
Benchmarking imputation methods for categorical biological data	34
EcoEnsemble: A general framework for combining ecosystem models in R	33
Navigating through space and time: A methodological approach to quantify spatiotemporal connectivity using stream flow data as a case study	32
Cover Picture and Issue Information	32
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Corrigendum	31
Cover Picture and Issue Information	31
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Accelerating advances in landscape connectivity modelling with the ConScape library	31
An aquaria set‐up for long‐term, multiple‐stressor research in marine organisms	30
Parasitic flowering plant collections embody the extended specimen	30
Retrodiction of forest demography: Backward simulation with reverse matrix models	30
RFIDeep: Unfolding the potential of deep learning for radio‐frequency identification	30
TinyCO 2 : High‐performance, low‐cost CO	30
Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves	30
Using standardized fish‐specific autonomous reef monitoring structures ( FARMS ) to quantify cryptobenthic fish communities	29
Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA	29
PleistoDist : A toolbox for visualising and quantifying the effects of Pleistocene sea‐level change on island archipelagos	29
Automated identification of diverse Neotropical pollen samples using convolutional neural networks	28
PicoCam: High‐resolution 3D imaging of live animals and preserved specimens	28
Same data, different results? Machine learning approaches in bioacoustics	28

qad : An R‐package to detect asymmetric and directed dependence in bivariate samples	28
The Benthic Underwater Microscope imaging PAM ( BUMP ): A non‐invasive tool for in situ assessment	27
Handbook of protocols for standardized measurements of floral traits for pollinators in temperate communities	27
Using causal diagrams and superpopulation models to correct geographic biases in biodiversity monitoring data	27
The Wayqecha Amazon Cloud Curtain Ecosystem Experiment: A new experimental method to manipulate fog water inputs in terrestrial systems	27
Measuring understorey vegetation structure using a novel mixed‐reality device	26
Sensors versus surveyors: Comparing passive acoustic monitoring, camera trapping and observer‐based monitoring for terrestrial mammals	26
Issues in calibrating models with multiple unbalanced constraints: the significance of systematic model and data errors	25
Hidden Markov models: Pitfalls and opportunities in ecology	25
Existing and emerging uses of drones in restoration ecology	25
When to monitor or control: Informed invasive species management using a partially observable Markov decision process ( POMDP ) framework	25
Introducing recurrent event analyses to assess species interactions based on camera‐trap data: A comparison with time‐to‐first‐event approaches	24
Detecting and reducing heterogeneity of error in acoustic classification	24
Food web reconstruction through phylogenetic transfer of low‐rank network representation	24
A Double machine learning trend model for citizen science data	24
Sourcing high tissue quality brains from deceased wild primates with known socio‐ecology	24
treats: A modular R package for simulating trees and traits	23
Correction to: Quantifying degradation in animal acoustic signals with the R package baRulho	23
Generating spatially realistic environmental null models with the shift‐&‐rotate approach helps evaluate false positives in species distribution modelling	22
The power of forecasts to advance ecological theory	22
Tracking the frequency of phytoplankton clonal lineages using multispectral image flow cytometry and neural networks	22
A process approach to quality management doubles NEON sensor data quality	22
A cost‐effective method to passively sample communities at the forest canopy–aerosphere interface	22
A wireless, remotely operable and easily customizable robotic flower system	21
OpenSoundscape: An open‐source bioacoustics analysis package for Python	21
Vegetation patterns pinpoint the least resilient dryland sites	21
TreeCompR : Tree competition indices for inventory data and 3D point clouds	21
In situ estimation of active dispersal abilities in reef fish early life stages using tracking technologies	21
Addressing spatial confounding in geostatistical regression models: An R‐ INLA approach	21
Estimating process‐based model parameters from species distribution data using the evolutionary algorithm CMA‐ES	21
TaxoNERD: Deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature	21
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning	21
The CV is dead, long live the CV !	21
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species	20
Scalable phylogenetic Gaussian process models improve the detectability of environmental signals on local extinctions for many Red List species	20
poolHelper : An R package to help in designing Pool‐Seq studies	20
sabinaNSDM : An R package for spatially nested hierarchical species distribution modelling	20
The Movebank system for studying global animal movement and demography	20
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Cover Picture and Issue Information	20
How to generate accurate continuous thermal regimes from sparse but regular temperature measurements	20
Writing a massively multi‐authored paper: Overcoming barriers to meaningful authorship for all	20
starve: An R package for spatio‐temporal analysis of research survey data using nearest‐neighbour Gaussian processes	20
Impact of sampling strategy on inference of community assembly processes in phylogenetic island biogeography	20
The Latent Dirichlet Allocation model applied to airborne LiDAR data: A case study on mapping forest degradation associated with fragmentation and fi	20
soundscape_IR: A source separation toolbox for exploring acoustic diversity in soundscapes	19
Synthesizing forecasts to inform decision‐making and advance ecological theory	19
Using ensemble methods to improve the robustness of deep learning for image classification in marine environments	19
ipsecr: An R package for awkward spatial capture–recapture data	19
Methods to account for incomplete viewsheds in distance sampling	19
Estimating interaction strengths for diverse horizontal systems using performance data	19
sound C lass : An automatic sound classification tool for biodiversity monitoring using machine learning	19
The uniform AUC: Dealing with the representativeness effect in presence–absence models	19
Temporal design for aquatic organismal sampling across the National Ecological Observatory Network	19
Guidelines for the prediction of species interactions through binary classification	18
NAPS : Integrating pose estimation and tag‐based tracking	18
Estimating species misclassification with occupancy dynamics and encounter rates: A semi‐supervised, individual‐level approach	18
Precise tactile stimulation of worker ants by a robotic manipulator reveals that individual responses are density‐ and context‐dependent	18
Towards scalable insect monitoring: Ultra‐lightweight CNNs as on‐device triggers for insect camera traps	18
Reconstructing Langevin systems from high‐ and low‐resolution time series using Euler and Hermite reconstructions	18
Monitoring fast‐moving animals—Building a customized camera system and evaluation toolset	18
Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees	18
PhycoCanopy : An R Shiny tool for exploring primary production in macroalgal canopies	18
DeepDiveR—A software for deep learning estimation of palaeodiversity from fossil occurrences	18
tidysdm : Leveraging the flexibility of tidymodels for species distribution modelling in R	17
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Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring	17
Introducing the combined atlas framework for large‐scale web‐based data visualization: The GloNAF atlas of plant invasion	17
Design and performance of an ecosystem‐scale forest soil warming experiment with infrared heater arrays	17
Cover Picture and Issue Information	17
Practical guidelines and the EMLN R package for handling ecological multilayer networks	17
Stable isotope fingerprinting traces essential amino acid assimilation and multichannel feeding in a vertebrate consumer	17
Cover Picture and Issue Information	17
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation	17
Cover Picture and Issue Information	17
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’	17
A low‐cost IoT network to monitor microclimate variables in ecosystems	17
Including the invisible fraction in whole population studies: A guide to the genetic sampling of unhatched bird eggs	16
Pitfalls arising from site selection bias in population monitoring defy simple heuristics	16
Long‐term collar deployment leads to bias in soil respiration measurements	16

CaptuRING: A do‐it‐yourself tool for wood sample digitization	16
A GLMM approach for combining multiple relative abundance surfaces	16
Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data	16
3D photogrammetry as a low‐cost and non‐invasive method for acoustic modelling of animal hearing	16
The use of weighted averages of Hedges' d in meta‐analysis: Is it worth it?	16
Modelling approaches for meta‐analyses with dependent effect sizes in ecology and evolution: A simulation study	16
Hard tissue thin‐sectioning techniques in vertebrate paleohistology: Review, synthesis and improvements	16
A conceptual framework for host‐associated microbiomes of hybrid organisms	16
Real‐time alerts from AI‐enabled camera traps using the Iridium satellite network: A case‐study in Gabon, Central Africa	16
Streamlining analysis methods for large acoustic surveys using automatic detectors with operator validation	16
ecochange: An R‐package to derive ecosystem change indicators from freely available earth observation products	16
Quantifying the utilisation of blue, green and brown resources by riparian predators: A combined use of amino acid isotopes and fatty acids	16
Improved order selection method for hidden Markov models: A case study with movement data	15
Extending isolation by resistance to predict genetic connectivity	15
A framework for post‐processing bird tracks from automated tracking radar systems	15
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Acoustic and archival technologies join forces: A combination tag	15
Non‐invasive reconstruction of complete mitochondrial genomes from aquatic environmental DNA using PCR‐free long‐read sequencing	15
Correction to ‘PhyBaSE: A Bayesian structural equation model approach to causal inference in phylogenetic comparative analyses’	15
Studying collective animal behaviour with drones and computer vision	15
Advancing aquatic biodiversity assessments of invertebrates using eDNA metabarcoding: A systematic evaluation of primers for marine and freshwater co	15
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PiCAM : A Raspberry Pi‐based open‐source, low‐power camera system for monitoring plant phenology in Arctic environments	15
Cover Picture and Issue Information	14
Quantifying macro‐evolutionary patterns of trait mean and variance with phylogenetic location–scale models	14
Investigating soil mesofauna cryptic diversity: Current challenges and perspectives	14
CATS : A high‐performance software framework for simulating plant migration in changing environments	14
Realising the promise of large data and complex models	14
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot	14
PoolDilutionR : An R package for easy optimization of isotope pool dilution calculations	14
ISSRseq: An extensible method for reduced representation sequencing	14
Cover Picture and Issue Information	14
Time‐lapse cameras bridge the gap between remote sensing and in situ observations of tundra phenology	14
isotracer: An R package for the analysis of tracer addition experiments	14
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits	14
TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups	14
ChirpArray : A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring	14
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A continuous‐score occupancy model that incorporates uncertain machine learning output from autonomous biodiversity surveys	14
Clustering and unconstrained ordination with Dirichlet process mixture models	14
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward	14
Applying computer vision to digitised natural history collections for climate change research: Temperature‐size responses in British butterflies	14
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap	14
Sap Flow Analyzer : A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method	14
Cover Picture and Issue Information	13
A Monte Carlo resampling framework for implementing goodness‐of‐fit tests in spatial capture‐recapture models	13
An RGB‐D framework for capturing soft‐sediment microtopography	13
A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats	13
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	13
Generating continuous maps of genetic diversity using moving windows	13
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs	13
Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?	13
ENphylo : A new method to model the distribution of extremely rare species	13
Fine‐scale reconstruction of pelagic fish migration by iso‐logging of eye lens	13
Corrigendum	13
Ten practical guidelines for microclimate research in terrestrial ecosystems	13
Impact of acoustic index parameters on soundscape comparisons	13
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	13
Mitigating pseudoreplication and bias in resource selection functions with autocorrelation‐informed weighting	13
Wellcounter: Automated high‐throughput phenotyping for aquatic microinvertebrates	13
High‐magnification platform for characterising microscopic communities	13
Cover Picture and Issue Information	13
3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass	13
Estimating animal density for a community of species using information obtained only from camera‐traps	13
Connectivity conservation planning through deep reinforcement learning	13
HSC 3 D : A Python package to quantify three‐dimensional habitat structural complexity	13
Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model	12
Robust passive sampling of airborne environmental DNA to monitor plants and animals	12
Decoding the footsteps of the African savanna: Classifying wildlife using seismic signals and machine learning	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
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
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods	12
A new tool to improve the estimates of interaction rewiring considering the whole community composition	12
A multi‐property assessment of intensity of use provides a functional understanding of animal movement	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
mpmsim: An R package for simulating matrix population models	12
Avoiding confusion: Modelling image identification surveys with classification errors	12
Distinguishing passive and driven trait evolution in the presence of boundaries	12
Differentiating siliceous particulate matter in the diets of mammalian herbivores	11
Fieldwork in conservation organisations–A review of methodological challenges, opportunities and ethics	11
patter: Particle algorithms for animal tracking in R and Julia	11
Systematic review and best practices for drone remote sensing of invasive plants	11
The RadOrgMiner pipeline: Automated genotyping of organellar loci from RADseq data	11
Adaptive sampling by citizen scientists improves species distribution model performance: A simulation study	11
Know what you don't know: Embracing state uncertainty in disease‐structured multistate models	11
Simple assay quantifying sediment resuspension effects on marine carbon storage	11
Spatially explicit management of genetic diversity using ancestry probability surfaces	11
Resin‐coated urea effectively simulates the chronic dynamics of natural nitrogen deposition	11
Detecting stochasticity in population time series using a non‐parametric test of intrinsic predictability	11
USE it: Uniformly sampling pseudo‐absences within the environmental space for applications in habitat suitability models	11
Managing ecosystems with resist–accept–direct (RAD)	11
dentist: Quantifying uncertainty by sampling points around maximum likelihood estimates	11