Methods in Ecology and Evolution

Article	Citations
Geographic principles applied to population dynamics: A spatially interpolated integrated population model	630
	382
	358
Cover Picture and Issue Information	240
	193
Food web visualisation: Heat map, interactive graph and animated flow network	170
The fallacy of single imputation for trait databases: Use multiple imputation instead	155
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward	132
Correction to ‘Sap Flow Analyzer: A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method’	127
Sap Flow Analyzer: A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method	113
Exploring noise, degeneracy and determinism in biological networks with the einet package	106
Using cloud radar to investigate the effect of rainfall on migratory insect flight	102
	89
ECOGEN: Bird sounds generation using deep learning	88
Challenges and opportunities for data integration to improve estimation of migratory connectivity	84
Single‐egg comet assay: A protocol to quantify DNA damage in natural bioarchives	82
Infectious disease phylodynamics with occurrence data	80
Understanding the reliability of citizen science observational data using item response models	73
	73
	72
Cover Picture and Issue Information	71
ChirpArray: A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring	69
Ten practical guidelines for microclimate research in terrestrial ecosystems	67
	64
Cover Picture and Issue Information	63

A framework for computer‐aided design and manufacturing of habitat structures for cavity‐dependent animals	62
Cover Picture and Issue Information	61
	61
3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass	60
Guidelines for estimating occupancy from autocorrelated camera trap detections	59
ngsLCA—A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data	58
Signalling in groups: New tools for the integration of animal communication and collective movement	56
Bootstrapping outperforms community‐weighted approaches for estimating the shapes of phenotypic distributions	55
optimLanduse: A package for multiobjective land‐cover composition optimization under uncertainty	54
Impact of acoustic index parameters on soundscape comparisons	54
Applying computer vision to digitised natural history collections for climate change research: Temperature‐size responses in British butterflies	53
A toolbox to explore the composition of species dynamics behind multi‐species indices	52
scikit‐maad: An open‐source and modular toolbox for quantitative soundscape analysis in Python	52
occupancyTuts: Occupancy modelling tutorials with RPresence	51
Optimizing stable isotope sampling design in terrestrial movement ecology research	51
TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups	50
	50
A comparison of photographic and spectrometric methods to quantify the colours seen by animal eyes	50
PoolDilutionR: An R package for easy optimization of isotope pool dilution calculations	49
	49
BarKeeper—a versatile web framework to assemble, analyse and manage DNA barcoding data and metadata	47
	47
Response to Discretising and validating Keyfitz' entropy for any demographic classification	45
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	45
Accounting for observation noise in equation‐free forecasting: The hidden‐Markov S‐map	45
Inferring time of infection from field data using dynamic models of antibody decay	45
Macrophenological dynamics from citizen science plant occurrence data	43
Filtering heart rates using data densities: The boxfilter R package	42
LC‐ICP‐MS analysis of inositol phosphate isomers in soil offers improved sensitivity and fine‐scale mapping of inositol phosphate distribution	41
A flexible Bayesian approach for estimating survival probabilities from age‐at‐harvest data	41
Performance of five statistical methods to infer interactions among moving individuals in a predator–prey system	38
CATS: A high‐performance software framework for simulating plant migration in changing environments	38
Estimating the cumulative impact and zone of influence of anthropogenic features on biodiversity	37
Individual‐based models of avian migration for estimating behavioural traits and predicting ecological interactions	36
Using identity calls to detect structure in acoustic datasets	36
How to get the most out of phylogenetic imputation without abusing it	35
Revticulate: An R framework for interaction with RevBayes	34
BoomBox: An Automated Behavioural Response (ABR) camera trap module for wildlife playback experiments	34
Cover Picture and Issue Information	34
Importance sampling and Bayesian model comparison in ecology and evolution	34
Single‐fit bootstrapping: A simple alternative to the delta method	34
Application of active acoustic transducers in monitoring and assessment of terrestrial ecosystem health—A review	33
A network theoretic method for the basic reproductive number for infectious diseases	30
Rapid alignment updating with Extensiphy	30
FlywayNet: A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data	30
Bayesian models for spatially explicit interactions between neighbouring plants	30
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses	29
AF‐vapeR: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors	29
isotracer: An R package for the analysis of tracer addition experiments	29
TiPS: Rapidly simulating trajectories and phylogenies from compartmental models	28

bistro: An R package for vector bloodmeal identification by short tandem repeat overlap	28
HSC3D: A Python package to quantify three‐dimensional habitat structural complexity	27
Cover Picture and Issue Information	26
plantR: An R package and workflow for managing species records from biological collections	26
Robust rhythm reporting will advance ecological and evolutionary research	26
The Aquatic Metatron: A large‐scale experimental facility to study the combined effects of habitat fragmentation and climate change on aquatic meta‐ecosystems	26
Empirical dynamic programming for model‐free ecosystem‐based management	26
Quantifying surface topography of biological systems from 3D scans	26
Three methods to measure parasite aggregation using examples from Australian fish parasites	26
Cover Picture and Issue Information	26
Bayesian views of generalized additive modelling	25
Cover Picture and Issue Information	25
Percolation threshold analyses can detect community assembly processes in simulated and natural tree communities	25
Correlating variables with different scale types: A new framework based on matrix comparisons	24
Calcification accretion units (CAUs): A standardized approach for quantifying recruitment and calcium carbonate accretion in marine habitats	24
Reconstruction of small subunit ribosomal RNA from high‐throughput sequencing data: A comparative study of metagenomics and total RNA sequencing	24
An approach for estimating haplotype diversity from sequences with unequal lengths	24
Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources	24
classecol: Classifiers to understand public opinions of nature	24
Exploring congruent diversification histories with flexibility and parsimony	24
Quantitative photography for rapid, reliable measurement of marine macro‐plastic pollution	24
Uncertainty propagation in matrix population models: Gaps, importance and guidelines	23
Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?	23
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits	23
Nighthawk: Acoustic monitoring of nocturnal bird migration in the Americas	23
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records	22
Controlling critical mistag‐associated false discoveries in metagenetic data	22
A critical examination of models of annual‐plant population dynamics and density‐dependent fecundity	22
A method for sampling the living wood microbiome	22
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	22
Realising the promise of large data and complex models	22
Fast fitting of neural ordinary differential equations by Bayesian neural gradient matching to infer ecological interactions from time‐series data	22
Druid Drone—A portable unmanned aerial vehicle with a multifunctional manipulator for forest canopy and mistletoe research and management	22
Evaluation and redesign of the primers for detecting nitrogen cycling genes in environments	22
ImprovingICESat‐2‐based boreal forest height estimation by a multivariate sample quality control approach	21
Extension of Pradel capture–recapture survival‐recruitment model accounting for transients	21
Discovering and measuring giant trees through the integration of multi‐platform lidar data	21
Connectivity conservation planning through deep reinforcement learning	21
Cover Picture and Issue Information	21
SpatMCDA: An R package for assessing areas at risk of infectious diseases based on spatial multi‐criteria decision analysis	20
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation	20
Incidence‐data‐based species richness estimation via a Beta‐Binomial model	20
Higher‐order dissimilarity in biodiversity: Identifying dissimilarities of spatial or temporal dissimilarity structures	20
Clustering and unconstrained ordination with Dirichlet process mixture models	20
A machine learning approach for classifying and quantifying acoustic diversity	20
The geodiv r package: Tools for calculating gradient surface metrics	20
ISSRseq: An extensible method for reduced representation sequencing	20
A method for characterizing disease emergence curves from paired pathogen detection and serology data	20
Automatic detection of migrating soaring bird flocks using weather radars by deep learning	20
FEISTY Fortran library and R package to integrate fish and fisheries with biogeochemical models	20
Improving estimations of life history parameters of small animals in mesocosm experiments: A case study on mosquitoes	20
Microbial lag calculator: A shiny‐based application and an R package for calculating the duration of microbial lag phase	20
Improving ecological data science with workflow management software	20
A deep Generative Artificial Intelligence system to predict species coexistence patterns	19
smartsnp, an r package for fast multivariate analyses of big genomic data	19
Occupancy–detection models with museum specimen data: Promise and pitfalls	19
Generating continuous maps of genetic diversity using moving windows	19
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot	19
Body condition changes at sea: Onboard calculation and telemetry of body density in diving animals	19
Using camera traps and N‐mixture models to estimate population abundance: Model selection really matters	18
Circular–linear copulae for animal movement data	18
	18
good: An R package for modelling count data	18
Correction to: Circular–linear copulae for animal movement data	18
Correction to: An automatic classifier of bat sonotypes around the world	18
Integrated population models poorly estimate the demographic contribution of immigration	18
Estimating animal density for a community of species using information obtained only from camera‐traps	17
Estimating species relative abundances from museum records	17
Effects of outliers on remote sensing‐assisted forest biomass estimation: A case study from the United States national forest inventory	17
Continuous‐surface geographic assignment of migratory animals using strontium isotopes: A case study with monarch butterflies	17
The Flora Incognita app – Interactive plant species identification	17
BATScan: A radar classification tool reveals large‐scale bat migration patterns	17
A novel and efficient method for wood–leaf separation from terrestrial laser scanning point clouds at the forest plot level	16
A standardized effect size for evaluating and comparing the strength of phylogenetic signal	16
A joint likelihood estimator of relatedness and allele frequencies from a small sample of individuals	16
Replication in field ecology: Identifying challenges and proposing solutions	16
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	16
Pedigree accumulation analysis: Combining methods from community ecology and population genetics for breeding adult estimation	16
A comparison of design‐based and model‐based approaches for finite population spatial sampling and inference	16
Broad‐scale applications of the Raspberry Pi: A review and guide for biologists	16

Scale dependency of lidar‐derived forest structural diversity	15
eDITH: An R‐package to spatially project eDNA‐based biodiversity across river networks with minimal prior information	15
A new centrality index designed for multilayer networks	15
Concurrent ordination: Simultaneous unconstrained and constrained latent variable modelling	15
“Fractional replication” in single‐visit multi‐season occupancy models: Impacts of spatiotemporal autocorrelation on identifiability	15
Analysing economic costs of invasive alien species with the invacost r package	15
spOccupancy: An R package for single‐species, multi‐species, and integrated spatial occupancy models	15
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs	15
Physically based modelling of spectral transmittance through forest canopies	15
hydrographr: An R package for scalable hydrographic data processing	15
Cost‐effective seafloor habitat mapping using a portable speedy sea scanner and deep‐learning‐based segmentation: A sea trial at Pujada Bay, Philippines	15
ENphylo: A new method to model the distribution of extremely rare species	15
poems: R package for simulating species' range dynamics using pattern‐oriented validation	14
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods	14
A general framework for jointly modelling thermal and hydric constraints on developing eggs	14
The Australian Acoustic Observatory	14
Spectrogram cross‐correlation can be used to measure the complexity of bird vocalizations	14
Argos: A toolkit for tracking multiple animals in complex visual environments	14
Cover Picture and Issue Information	14
A model selection approach to structural equation modelling: A critical evaluation and a road map for ecologists	14
An open future for MEE	14
A continuous‐score occupancy model that incorporates uncertain machine learning output from autonomous biodiversity surveys	14
A motion‐detection based camera trap for small nocturnal mammals with low latency and high signal‐to‐noise ratio	14
Cover Picture and Issue Information	14
paleobuddy: An R package for flexible simulations of diversification and fossil sampling	14
Positional errors in species distribution modelling are not overcome by the coarser grains of analysis	14
Implementing GitHub Actions continuous integration to reduce error rates in ecological data collection	14
A systematic method for hypothesis synthesis and conceptual model development	14
Deep learning and satellite imagery predict genetic diversity and differentiation	14
A hierarchical approach for estimating state‐specific mortality and state transition in dispersing animals with incomplete death records	13
A new tool to improve the estimates of interaction rewiring considering the whole community composition	13
Discretizing and validating Keyfitz' entropy for any demographic classification	13
Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication	12
AMMonitor 2: Remote monitoring of biodiversity in an adaptive framework in R	12
Rapid ecological data collection from 360‐degree imagery using visualisation and immersive sampling in the R pannotator package	12
Bayesian hierarchical modelling of size spectra	12
Cover Picture and Issue Information	12
Avoiding confusion: Modelling image identification surveys with classification errors	12
bayesTPC: Bayesian inference for thermal performance curves in R	12
BatRack: An open‐source multi‐sensor device for wildlife research	12
Estimation of additive genetic variance when there are gene–environment correlations: Pitfalls, solutions and unexplored questions	12
Moving‐resting process with measurement error in animal movement modeling	12
BEE‐STEWARD: A research and decision‐support software for effective land management to promote bumblebee populations	12
A comparison and evaluation of strategies for bulk sequencing of mitogenomes from museum collections	12
Repairing gaps in ecological time series	12
Cover Picture and Issue Information	12
Multi‐trait point pattern reconstruction of plant ecosystems	12
Fragmented landscape generator (flsgen): A neutral landscape generator with control of landscape structure and fragmentation indices	11
Permutation tests for hypothesis testing with animal social network data: Problems and potential solutions	11
An ethical assessment of the use of old and new methods to study sociality in wild animals	11
Inferring species absence from zero‐sighting records using analytical Bayesian models with population growth	11
SimpleMetaPipeline: Breaking the bioinformatics bottleneck in metabarcoding	11
TLS2trees: A scalable tree segmentation pipeline forTLSdata	11
Systematic review and best practices for drone remote sensing of invasive plants	11
Correction to: Characterising menotactic behaviours in movement data using hidden Markov models	11
Estimating reproductive and juvenile survival rates when offspring ages are uncertain: A novel multievent mark‐resight model with beluga whale case study	11
An RGB‐D framework for capturing soft‐sediment microtopography	11
Linking relative suitability to probability of occurrence in presence‐only species distribution models: Implications for global change projections	11
Life on the edge: A new toolbox for population‐level climate change vulnerability assessments	11
Completing 3D point clouds of individual trees using deep learning	11
A statistical framework for modelling migration corridors	11
	11
Overcoming data gaps using integrated models to estimate migratory species' dynamics during cryptic periods of the annual cycle	11
Detection method for diel vertical migration pattern using 2D cross‐correlation with ADCP backscatter time‐series data	11
Assessing repeatability of spatial trajectories	11
Cover Picture and Issue Information	11
Measuring reflectance of tiny organisms: The promise of species level biocrust remote sensing	10
Measuring overall functional diversity by aggregating its multiple facets: Functional richness, biomass evenness, trait evenness and dispersion	10
Modelling internal stem damage in savanna trees: Error in aboveground biomass with terrestrial laser scanning and allometry	10
CRABS: Congruent rate analyses in birth–death scenarios	10
Exploring deep learning techniques for wild animal behaviour classification using animal‐borne accelerometers	10
	10
A multi‐property assessment of intensity of use provides a functional understanding of animal movement	10
Pressure to publish introduces large‐language model risks	10
plantTracker: An R package to translate maps of plant occurrence into demographic data	10
Constructing a multiple‐part morphospace using a multiblock method	10
Simpson's tachytely or bradytely? The importance of quantifying rate uncertainty	10
Wellcounter: Automated high‐throughput phenotyping for aquatic microinvertebrates	10
A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats	10
A Monte Carlo resampling framework for implementing goodness‐of‐fit tests in spatial capture‐recapture models	10
treetop: A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and conservationists	10
Cover Picture and Issue Information	10
Yes, they're all individuals: Hierarchical models for repeat survey data improve estimates of tree growth and size	10
Continuous on‐board behaviour classification using accelerometry: A case study with a new GPS‐3G‐Bluetooth system in Pacific black ducks	10
Statistical inference methods for n‐dimensional hypervolumes: Applications to niches and functional diversity	10
Predicting adaptation and evolution of plasticity from temporal environmental change	10
Gone with the wind: Inferring bird migration with light‐level geolocation, wind and activity measurements	10
Towards understanding interactions in a complex world: Design and analysis of multi‐species functional response experiments	10
Learning to predict spatiotemporal movement dynamics from weather radar networks	10
Decoding the footsteps of the African savanna: Classifying wildlife using seismic signals and machine learning	10
Dynamic visualisation of million‐tip trees: The OneZoom project	10
Benchmarking imputation methods for categorical biological data	10
metaRange: A framework to build mechanistic range models	10
Correcting a bias in the computation of behavioural time budgets that are based on supervised learning	10