Methods in Ecology and Evolution

Article	Citations
poems: R package for simulating species' range dynamics using pattern‐oriented validation	539
Geographic principles applied to population dynamics: A spatially interpolated integrated population model	328
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Cover Picture and Issue Information	174
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Bayesian views of generalized additive modelling	135
Food web visualisation: Heat map, interactive graph and animated flow network	124
ngsLCA—A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data	117
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward	104
Identifying flow modules in ecological networks using Infomap	94
Concurrent ordination: Simultaneous unconstrained and constrained latent variable modelling	89
spOccupancy: An R package for single‐species, multi‐species, and integrated spatial occupancy models	85
Spot size, distance and emissivity errors in field applications of infrared thermography	84
A machine learning approach for classifying and quantifying acoustic diversity	82
Signalling in groups: New tools for the integration of animal communication and collective movement	76
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ECOGEN: Bird sounds generation using deep learning	70
Cover Picture and Issue Information	68
Estimating the cumulative impact and zone of influence of anthropogenic features on biodiversity	58
A framework for computer‐aided design and manufacturing of habitat structures for cavity‐dependent animals	58
Cover Picture and Issue Information	55
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“Fractional replication” in single‐visit multi‐season occupancy models: Impacts of spatiotemporal autocorrelation on identifiability	51

CATS: A high‐performance software framework for simulating plant migration in changing environments	50
3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass	49
Individual‐based models of avian migration for estimating behavioural traits and predicting ecological interactions	47
Continuous‐surface geographic assignment of migratory animals using strontium isotopes: A case study with monarch butterflies	47
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optimLanduse: A package for multiobjective land‐cover composition optimization under uncertainty	45
Development of a new low‐cost device to measure calcium carbonate content, reactive surface area in solid samples and dissolved inorganic carbon content in water samples	45
Applying computer vision to digitised natural history collections for climate change research: Temperature‐size responses in British butterflies	45
A standardised biologging approach to infer parturition: An application in large herbivores across the hider‐follower continuum	45
scikit‐maad: An open‐source and modular toolbox for quantitative soundscape analysis in Python	44
Implementing GitHub Actions continuous integration to reduce error rates in ecological data collection	44
Cover Picture and Issue Information	44
TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups	43
Optimizing stable isotope sampling design in terrestrial movement ecology research	43
A comparison of design‐based and model‐based approaches for finite population spatial sampling and inference	43
PoolDilutionR: An R package for easy optimization of isotope pool dilution calculations	42
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A comparison of photographic and spectrometric methods to quantify the colours seen by animal eyes	42
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Inferring time of infection from field data using dynamic models of antibody decay	39
BarKeeper—a versatile web framework to assemble, analyse and manage DNA barcoding data and metadata	39
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	38
Response to Discretising and validating Keyfitz' entropy for any demographic classification	38
Accounting for observation noise in equation‐free forecasting: The hidden‐Markov S‐map	36
Macrophenological dynamics from citizen science plant occurrence data	35
Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources	34
A flexible Bayesian approach for estimating survival probabilities from age‐at‐harvest data	34
Filtering heart rates using data densities: The boxfilter R package	34
occupancyTuts: Occupancy modelling tutorials with RPresence	33
A toolbox to explore the composition of species dynamics behind multi‐species indices	33
Using identity calls to detect structure in acoustic datasets	33
Performance of five statistical methods to infer interactions among moving individuals in a predator–prey system	33
BoomBox: An Automated Behavioural Response (ABR) camera trap module for wildlife playback experiments	32
Importance sampling and Bayesian model comparison in ecology and evolution	32
How to get the most out of phylogenetic imputation without abusing it	32
Cover Picture and Issue Information	32
Revticulate: An R framework for interaction with RevBayes	31
Application of active acoustic transducers in monitoring and assessment of terrestrial ecosystem health—A review	30
Bayesian models for spatially explicit interactions between neighbouring plants	30
Rapid alignment updating with Extensiphy	30
Single‐fit bootstrapping: A simple alternative to the delta method	30
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses	29
A network theoretic method for the basic reproductive number for infectious diseases	29
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap	29
AF‐vapeR: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors	29
FlywayNet: A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data	29
isotracer: An R package for the analysis of tracer addition experiments	29
A new centrality index designed for multilayer networks	29
TiPS: Rapidly simulating trajectories and phylogenies from compartmental models	28

Cover Picture and Issue Information	27
HSC3D: A Python package to quantify three‐dimensional habitat structural complexity	27
Cover Picture and Issue Information	26
Robust rhythm reporting will advance ecological and evolutionary research	26
Quantifying surface topography of biological systems from 3D scans	26
Empirical dynamic programming for model‐free ecosystem‐based management	26
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs	25
plantR: An R package and workflow for managing species records from biological collections	25
classecol: Classifiers to understand public opinions of nature	25
Calcification accretion units (CAUs): A standardized approach for quantifying recruitment and calcium carbonate accretion in marine habitats	24
An approach for estimating haplotype diversity from sequences with unequal lengths	24
Correlating variables with different scale types: A new framework based on matrix comparisons	24
Exploring noise, degeneracy and determinism in biological networks with the einet package	24
Exploring congruent diversification histories with flexibility and parsimony	24
Reconstruction of small subunit ribosomal RNA from high‐throughput sequencing data: A comparative study of metagenomics and total RNA sequencing	24
ChirpArray: A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring	23
Pedigree accumulation analysis: Combining methods from community ecology and population genetics for breeding adult estimation	23
Ten practical guidelines for microclimate research in terrestrial ecosystems	23
Revisiting animal photo‐identification using deep metric learning and network analysis	23
Nighthawk: Acoustic monitoring of nocturnal bird migration in the Americas	22
Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?	22
eDITH: An R‐package to spatially project eDNA‐based biodiversity across river networks with minimal prior information	22
Broad‐scale applications of the Raspberry Pi: A review and guide for biologists	22
Fast fitting of neural ordinary differential equations by Bayesian neural gradient matching to infer ecological interactions from time‐series data	21
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records	21
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits	21
A standardized effect size for evaluating and comparing the strength of phylogenetic signal	21
Uncertainty propagation in matrix population models: Gaps, importance and guidelines	21
A method for sampling the living wood microbiome	20
ENphylo: A new method to model the distribution of extremely rare species	20
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	20
Controlling critical mistag‐associated false discoveries in metagenetic data	20
Three methods to measure parasite aggregation using examples from Australian fish parasites	20
A five‐channel LED display to investigate UV perception	20
Cost‐effective seafloor habitat mapping using a portable speedy sea scanner and deep‐learning‐based segmentation: A sea trial at Pujada Bay, Philippines	20
Druid Drone—A portable unmanned aerial vehicle with a multifunctional manipulator for forest canopy and mistletoe research and management	20
hydrographr: An R package for scalable hydrographic data processing	20
Realising the promise of large data and complex models	20
Guidelines for estimating occupancy from autocorrelated camera trap detections	20
Evaluation and redesign of the primers for detecting nitrogen cycling genes in environments	19
A critical examination of models of annual‐plant population dynamics and density‐dependent fecundity	19
Extension of Pradel capture–recapture survival‐recruitment model accounting for transients	19
A continuous‐score occupancy model that incorporates uncertain machine learning output from autonomous biodiversity surveys	19
Cover Picture and Issue Information	19
Understanding the reliability of citizen science observational data using item response models	19
Connectivity conservation planning through deep reinforcement learning	19
Bootstrapping outperforms community‐weighted approaches for estimating the shapes of phenotypic distributions	19
ImprovingICESat‐2‐based boreal forest height estimation by a multivariate sample quality control approach	18
Improving ecological data science with workflow management software	18
Effects of outliers on remote sensing‐assisted forest biomass estimation: A case study from the United States national forest inventory	18
Quantitative photography for rapid, reliable measurement of marine macro‐plastic pollution	18
Discovering and measuring giant trees through the integration of multi‐platform lidar data	18
Automatic detection of migrating soaring bird flocks using weather radars by deep learning	18
Physically based modelling of spectral transmittance through forest canopies	18
SpatMCDA: An R package for assessing areas at risk of infectious diseases based on spatial multi‐criteria decision analysis	18
FEISTY Fortran library and R package to integrate fish and fisheries with biogeochemical models	17
The Aquatic Metatron: A large‐scale experimental facility to study the combined effects of habitat fragmentation and climate change on aquatic meta‐ecosystems	17
Challenges and opportunities for data integration to improve estimation of migratory connectivity	17
A method for characterizing disease emergence curves from paired pathogen detection and serology data	16
Microbial lag calculator: A shiny‐based application and an R package for calculating the duration of microbial lag phase	16
Higher‐order dissimilarity in biodiversity: Identifying dissimilarities of spatial or temporal dissimilarity structures	16
GPSeqClus: An R package for sequential clustering of animal location data for model building, model application and field site investigations	16
Sap Flow Analyzer: A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method	16
Clustering and unconstrained ordination with Dirichlet process mixture models	16
Incidence‐data‐based species richness estimation via a Beta‐Binomial model	15
The geodiv r package: Tools for calculating gradient surface metrics	15
Improving estimations of life history parameters of small animals in mesocosm experiments: A case study on mosquitoes	15
A novel and efficient method for wood–leaf separation from terrestrial laser scanning point clouds at the forest plot level	15
The Australian Acoustic Observatory	15
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation	15
Replication in field ecology: Identifying challenges and proposing solutions	14
Generating continuous maps of genetic diversity using moving windows	14
Percolation threshold analyses can detect community assembly processes in simulated and natural tree communities	14
Estimating species relative abundances from museum records	14
Infectious disease phylodynamics with occurrence data	14
Integrated population models poorly estimate the demographic contribution of immigration	14
LC‐ICP‐MS analysis of inositol phosphate isomers in soil offers improved sensitivity and fine‐scale mapping of inositol phosphate distribution	14
ISSRseq: An extensible method for reduced representation sequencing	14
A model selection approach to structural equation modelling: A critical evaluation and a road map for ecologists	14
A joint likelihood estimator of relatedness and allele frequencies from a small sample of individuals	14

Body condition changes at sea: Onboard calculation and telemetry of body density in diving animals	14
BATScan: A radar classification tool reveals large‐scale bat migration patterns	14
Using cloud radar to investigate the effect of rainfall on migratory insect flight	14
smartsnp, an r package for fast multivariate analyses of big genomic data	14
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot	13
A deep Generative Artificial Intelligence system to predict species coexistence patterns	13
Using camera traps and N‐mixture models to estimate population abundance: Model selection really matters	13
Correction to: Circular–linear copulae for animal movement data	13
Estimating animal density for a community of species using information obtained only from camera‐traps	13
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	13
Improving Landsat predictions of rangeland fractional cover with multitask learning and uncertainty	13
Analysing economic costs of invasive alien species with the invacost r package	13
Circular–linear copulae for animal movement data	13
Scale dependency of lidar‐derived forest structural diversity	13
Occupancy–detection models with museum specimen data: Promise and pitfalls	13
The Flora Incognita app – Interactive plant species identification	13
Correction to: An automatic classifier of bat sonotypes around the world	13
good: An R package for modelling count data	13
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Single‐egg comet assay: A protocol to quantify DNA damage in natural bioarchives	12
BatRack: An open‐source multi‐sensor device for wildlife research	12
paleobuddy: An R package for flexible simulations of diversification and fossil sampling	12
An open future for MEE	12
Deep learning and satellite imagery predict genetic diversity and differentiation	12
Argos: A toolkit for tracking multiple animals in complex visual environments	12
Cover Picture and Issue Information	12
A systematic method for hypothesis synthesis and conceptual model development	12
The effects of climate change on Australia’s only endemic Pokémon: Measuring bias in species distribution models	12
Cover Picture and Issue Information	12
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods	12
Instrumental variable methods in structural equation models	11
euka: Robust tetrapodic and arthropodic taxa detection from modern and ancient environmental DNA using pangenomic reference graphs	11
Bayesian hierarchical modelling of size spectra	11
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A hierarchical approach for estimating state‐specific mortality and state transition in dispersing animals with incomplete death records	11
Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication	11
A new tool to improve the estimates of interaction rewiring considering the whole community composition	11
Estimation of additive genetic variance when there are gene–environment correlations: Pitfalls, solutions and unexplored questions	11
Moving‐resting process with measurement error in animal movement modeling	11
Imputation of incomplete large‐scale monitoring count data via penalized estimation	11
Discretizing and validating Keyfitz' entropy for any demographic classification	11
FINDeM: A CRISPR‐based, molecular method for rapid, inexpensive and field‐deployable organism detection	11
Deep reinforcement learning for conservation decisions	11
A motion‐detection based camera trap for small nocturnal mammals with low latency and high signal‐to‐noise ratio	11
Cover Picture and Issue Information	11
Multi‐trait point pattern reconstruction of plant ecosystems	11
Using unmanned aerial vehicles to estimate body volume at scale for ecological monitoring	11
Spectrogram cross‐correlation can be used to measure the complexity of bird vocalizations	11
Multi‐species hotspots detection using self‐organizing maps: Simulation and application to purse seine tuna fisheries management	11
Overcoming data gaps using integrated models to estimate migratory species' dynamics during cryptic periods of the annual cycle	10
A statistical framework for modelling migration corridors	10
Autocorrelation‐informed home range estimation: A review and practical guide	10
Integrated movement models for individual tracking and species distribution data	10
An ethical assessment of the use of old and new methods to study sociality in wild animals	10
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Cover Picture and Issue Information	10
A low‐cost, long‐running, open‐source stereo camera for tracking aquatic species and their behaviours	10
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Systematic review and best practices for drone remote sensing of invasive plants	10
A theoretical framework for upscaling species distribution models	10
Permutation tests for hypothesis testing with animal social network data: Problems and potential solutions	10
Effectiveness of joint species distribution models in the presence of imperfect detection	10
Detection method for diel vertical migration pattern using 2D cross‐correlation with ADCP backscatter time‐series data	10
Machine learning is a powerful tool to study the effect of cancer on species and ecosystems	10
Fine‐tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches	10
Dynamic visualisation of million‐tip trees: The OneZoom project	10
ohun: An R package for diagnosing and optimizing automatic sound event detection	10
Estimating reproductive and juvenile survival rates when offspring ages are uncertain: A novel multievent mark‐resight model with beluga whale case study	10
Decomposing dark diversity affinities of species and sites using Bayesian method: What accounts for absences of species at suitable sites?	10
Spatial conservation planning: Proposing clustering methods to improve connectivity protection	10
Inferring species absence from zero‐sighting records using analytical Bayesian models with population growth	10
Going beyond richness: Modelling the BEF relationship using species identity, evenness, richness and species interactions via the DImodels R package	10
An RGB‐D framework for capturing soft‐sediment microtopography	10
treetop: A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and conservationists	10
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Cover Picture and Issue Information	10
Fragmented landscape generator (flsgen): A neutral landscape generator with control of landscape structure and fragmentation indices	10
Spatio‐temporal data integration for species distribution modelling in R‐INLA	10
Predicting adaptation and evolution of plasticity from temporal environmental change	9
Statistical inference methods for n‐dimensional hypervolumes: Applications to niches and functional diversity	9
Correcting a bias in the computation of behavioural time budgets that are based on supervised learning	9
Spanning scales: The airborne spatial and temporal sampling design of the National Ecological Observatory Network	9
BEE‐STEWARD: A research and decision‐support software for effective land management to promote bumblebee populations	9
Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models	9
Benchmarking imputation methods for categorical biological data	9
Widespread analytical pitfalls in empirical coexistence studies and a checklist for improving their statistical robustness	9
A novel red‐edge spectral index for retrieving the leaf chlorophyll content	9
Long‐term automated visual monitoring of Antarctic benthic fauna	9
Individual‐based simulations of genome evolution with ancestry: The GenomeAdmixR R package	9
Modelling internal stem damage in savanna trees: Error in aboveground biomass with terrestrial laser scanning and allometry	9
A multi‐property assessment of intensity of use provides a functional understanding of animal movement	9
Continuous on‐board behaviour classification using accelerometry: A case study with a new GPS‐3G‐Bluetooth system in Pacific black ducks	9
Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model	9
Domain‐specific neural networks improve automated bird sound recognition already with small amount of local data	9
plantTracker: An R package to translate maps of plant occurrence into demographic data	9