Methods in Ecology and Evolution

Article	Citations
Robustness of linear mixed‐effects models to violations of distributional assumptions	523
raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML	388
Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package	341
metan: An R package for multi‐environment trial analysis	291
geomorph v4.0 and gmShiny: Enhanced analytics and a new graphical interface for a comprehensive morphometric experience	220
ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions	200
ntbox: An r package with graphical user interface for modelling and evaluating multidimensional ecological niches	182
Predicting into unknown space? Estimating the area of applicability of spatial prediction models	139
An empirical evaluation of camera trap study design: How many, how long and when?	112
Methods for testing publication bias in ecological and evolutionary meta‐analyses	103
Improving Landsat predictions of rangeland fractional cover with multitask learning and uncertainty	103
Redundancy analysis: A Swiss Army Knife for landscape genomics	102
A field and video annotation guide for baited remote underwater stereo‐video surveys of demersal fish assemblages	98
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish	96
Deep learning‐based methods for individual recognition in small birds	96
Broad‐scale applications of the Raspberry Pi: A review and guide for biologists	93
Towards a more balanced combination of multiple traits when computing functional differences between species	85
A deep active learning system for species identification and counting in camera trap images	81
phyr: An r package for phylogenetic species‐distribution modelling in ecological communities	79
rTPC and nls.multstart: A new pipeline to fit thermal performance curves in r	74
phyloregion: R package for biogeographical regionalization and macroecology	68
Functional diversity metrics using kernel density n‐dimensional hypervolumes	68
SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology	64
adiv: An r package to analyse biodiversity in ecology	63
The Movebank system for studying global animal movement and demography	61

Unbiased population heterozygosity estimates from genome‐wide sequence data	57
Deep learning as a tool for ecology and evolution	57
Generalized hidden Markov models for phylogenetic comparative datasets	57
The welfare and ethics of research involving wild animals: A primer	55
Automatic image‐based identification and biomass estimation of invertebrates	55
On the measurement of microclimate	55
The use of Bayesian priors in Ecology: The good, the bad and the not great	54
embarcadero: Species distribution modelling with Bayesian additive regression trees in r	52
Plant and root‐zone water isotopes are difficult to measure, explain, and predict: Some practical recommendations for determining plant water sources	49
DeepForest: A Python package for RGB deep learning tree crown delineation	48
Automated detection of wildlife using drones: Synthesis, opportunities and constraints	47
Spatial thinning and class balancing: Key choices lead to variation in the performance of species distribution models with citizen science data	46
Quality control for modern bone collagen stable carbon and nitrogen isotope measurements	44
Machine learning and deep learning—A review for ecologists	44
Outstanding challenges and future directions for biodiversity monitoring using citizen science data	42
A quick, easy and non‐invasive method to quantify coral growth rates using photogrammetry and 3D model comparisons	42
An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data	42
A practical guide to question formation, systematic searching and study screening for literature reviews in ecology and evolution	41
The Flora Incognita app – Interactive plant species identification	41
Inferring individual fate from aquatic acoustic telemetry data	40
dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture	40
Autocorrelation‐informed home range estimation: A review and practical guide	39
Meta‐analysis of primary producer amino acid δ15N values and their influence on trophic position estimation	39
Common datastream permutations of animal social network data are not appropriate for hypothesis testing using regression models	38
The potential and practice of arboreal camera trapping	37
ALPACA: A fast and accurate computer vision approach for automated landmarking of three‐dimensional biological structures	35
ubms: An R package for fitting hierarchical occupancy and N‐mixture abundance models in a Bayesian framework	35
RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes	35
Navigating the temporal continuum of effective population size	34
A standardisation framework for bio‐logging data to advance ecological research and conservation	34
spOccupancy: An R package for single‐species, multi‐species, and integrated spatial occupancy models	34
Robust ecological analysis of camera trap data labelled by a machine learning model	34
Replication in field ecology: Identifying challenges and proposing solutions	34
rasterdiv—An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back	33
Integrating airborne remote sensing and field campaigns for ecology and Earth system science	33
Acoustic indices perform better when applied at ecologically meaningful time and frequency scales	33
dsmextra: Extrapolation assessment tools for density surface models	33
track2KBA: An R package for identifying important sites for biodiversity from tracking data	33
Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices	33
Phylogenetically aligned component analysis	32
Permutation tests for hypothesis testing with animal social network data: Problems and potential solutions	32
assignR: An r package for isotope‐based geographic assignment	32
The Australian Acoustic Observatory	32
Detecting plant species in the field with deep learning and drone technology	31
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	31
HaplowebMaker and CoMa: Two web tools to delimit species using haplowebs and conspecificity matrices	30
A protocol for the large‐scale analysis of reefs using Structure from Motion photogrammetry	30
Measuring temporal change in alpha diversity: A framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT.3D standardization	30
Parametrizing diffusion‐taxis equations from animal movement trajectories using step selection analysis	29
The accuracy of phenology estimators for use with sparsely sampled presence‐only observations	29

Survey coverage, recording duration and community composition affect observed species richness in passive acoustic surveys	29
metabaR: An r package for the evaluation and improvement of DNA metabarcoding data quality	29
Defining and evaluating predictions of joint species distribution models	29
Spot size, distance and emissivity errors in field applications of infrared thermography	29
The Purr‐fect Catch: Using accelerometers and audio recorders to document kill rates and hunting behaviour of a small prey specialist	28
Unifying individual differences in personality, predictability and plasticity: A practical guide	28
PICT: A low‐cost, modular, open‐source camera trap system to study plant–insect interactions	27
Novel methods for spatial prioritization with applications in conservation, land use planning and ecological impact avoidance	27
Overcoming the pitfalls of merging dietary metabarcoding into ecological networks	27
Including intraspecific trait variability to avoid distortion of functional diversity and ecological inference: Lessons from natural assemblages	27
Unsupervised acoustic classification of individual gibbon females and the implications for passive acoustic monitoring	26
Scaling methods in ecological modelling	26
Detection dogs in nature conservation: A database on their world‐wide deployment with a review on breeds used and their performance compared to other methods	26
Phylogenetic multilevel meta‐analysis: A simulation study on the importance of modelling the phylogeny	26
actel: Standardised analysis of acoustic telemetry data from animals moving through receiver arrays	26
Analysing economic costs of invasive alien species with the invacost r package	26
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation	26
Determination of optimal flight altitude to minimise acoustic drone disturbance to wildlife using species audiograms	25
Leaving the area under the receiving operating characteristic curve behind: An evaluation method for species distribution modelling applications based on presence‐only data	25
phenofit: An R package for extracting vegetation phenology from time series remote sensing	25
The way bioclimatic variables are calculated has impact on potential distribution models	25
A new joint species distribution model for faster and more accurate inference of species associations from big community data	25
Hidden Markov models: Pitfalls and opportunities in ecology	25
A workflow for accurate metabarcoding using nanopore MinION sequencing	24
Double‐tagging scores of seabirds reveals that light‐level geolocator accuracy is limited by species idiosyncrasies and equatorial solar profiles	24
Existing and emerging uses of drones in restoration ecology	23
ForestScanner: A mobile application for measuring and mapping trees with LiDAR‐equipped iPhone and iPad	23
r3PG – An r package for simulating forest growth using the 3‐PG process‐based model	23
Convergence assessment for Bayesian phylogenetic analysis using MCMC simulation	23
Calculating effect sizes in animal social network analysis	23
Refined Shortest Paths (RSP): Incorporation of topography in space use estimation from node‐based telemetry data	23
viewshed3d: An r package for quantifying 3D visibility using terrestrial lidar data	23
Efficient, automated and robust pollen analysis using deep learning	22
Incorporating climate velocity into the design of climate‐smart networks of marine protected areas	22
graph4lg: A package for constructing and analysing graphs for landscape genetics in R	22
An evaluation of platforms for processing camera‐trap data using artificial intelligence	22
scikit‐maad: An open‐source and modular toolbox for quantitative soundscape analysis in Python	22
Interactions in statistical models: Three things to know	21
AIDE: Accelerating image‐based ecological surveys with interactive machine learning	21
A model selection approach to structural equation modelling: A critical evaluation and a road map for ecologists	21
Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms	21
Telemetry‐validated nitrogen stable isotope clocks identify ocean‐to‐estuarine habitat shifts in mobile organisms	21
The power of forecasts to advance ecological theory	21
Estimating encounter location distributions from animal tracking data	21
A methodological guide for translating study instruments in cross‐cultural research: Adapting the ‘connectedness to nature’ scale into Chinese	20
Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction	20
Reliably predicting pollinator abundance: Challenges of calibrating process‐based ecological models	20
Congruence of local ecological knowledge (LEK)‐based methods and line‐transect surveys in estimating wildlife abundance in tropical forests	20
Fine‐tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches	20
Marine artificial light at night: An empirical and technical guide	20
A roadmap for sampling and scaling biological nitrogen fixation in terrestrial ecosystems	20
A spatial capture–recapture model to estimate call rate and population density from passive acoustic surveys	20
Animal social networks: Towards an integrative framework embedding social interactions, space and time	20
Identifying flow modules in ecological networks using Infomap	20
nosoi: A stochastic agent‐based transmission chain simulation framework in r	19
Opportunities and risks in the use of drones for studying animal behaviour	19
A cost‐effective video system for a rapid appraisal of deep‐sea benthic habitats: The Azor drift‐cam	19
Schrödinger's phenotypes: Herbarium specimens show two‐dimensional images are both good and (not so) bad sources of morphological data	19
Why did the animal turn? Time‐varying step selection analysis for inference between observed turning‐points in high frequency data	18
Determining marine bioregions: A comparison of quantitative approaches	18
The consequences of checking for zero‐inflation and overdispersion in the analysis of count data	18
flexsdm: An r package for supporting a comprehensive and flexible species distribution modelling workflow	18
Null models for animal social network analysis and data collected via focal sampling: Pre‐network or node network permutation?	18
On the relationship of fractal geometry and tree–stand metrics on point clouds derived from terrestrial laser scanning	18
The In situ Plankton Assemblage eXplorer (IPAX): An inexpensive underwater imaging system for zooplankton study	18
Multi‐output Gaussian processes for species distribution modelling	18
Assimilate, process and analyse thermal dissipation sap flow data using the TREX r package	17
Study becomes insight: Ecological learning from machine learning	17
A unifying framework for quantifying and comparing n‐dimensional hypervolumes	17
Bulk arthropod abundance, biomass and diversity estimation using deep learning for computer vision	17
HumBug – An Acoustic Mosquito Monitoring Tool for use on budget smartphones	17
Nemo‐age: Spatially explicit simulations of eco‐evolutionary dynamics in stage‐structured populations under changing environments	17
TaxoNERD: Deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature	16
Internet on animals: Wi‐Fi‐enabled devices provide a solution for big data transmission in biologging	16
SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets	16
Plant biodiversity assessment through soil eDNA reflects temporal and local diversity	16
Continuous‐surface geographic assignment of migratory animals using strontium isotopes: A case study with monarch butterflies	16
Exploiting the full potential of Bayesian networks in predictive ecology	16
Disentangling effects of climate and land use on biodiversity and ecosystem services—A multi‐scale experimental design	16
Machine learning applications in river research: Trends, opportunities and challenges	16

Automated retrieval of information on threatened species from online sources using machine learning	16
A novel red‐edge spectral index for retrieving the leaf chlorophyll content	16
Protein quantification in ecological studies: A literature review and empirical comparisons of standard methodologies	16
bdc: A toolkit for standardizing, integrating and cleaning biodiversity data	16
Optimising sample sizes for animal distribution analysis using tracking data	16
treetop: A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and conservationists	16
A machine learning approach for classifying and quantifying acoustic diversity	16
Innovations in movement and behavioural ecology from camera traps: Day range as model parameter	15
Neural ordinary differential equations for ecological and evolutionary time‐series analysis	15
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation	15
Quantifying effects of tracking data bias on species distribution models	15
Optimizing aerial imagery collection and processing parameters for drone‐based individual tree mapping in structurally complex conifer forests	15
Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance	15
State‐space models for ecological time‐series data: Practical model‐fitting	15
A primer on partially observable Markov decision processes (POMDPs)	15
A practical approach to measuring the biodiversity impacts of land conversion	15
The omnistat: A flexible continuous‐culture system for prolonged experimental evolution	15
Tracking the temporal dynamics of insect defoliation by high‐resolution radar satellite data	15
Rcompadre and Rage—Two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life‐history traits from matrix population models	14
Methodology matters for comparing coarse wood and bark decay rates across tree species	14
MEDI: Macronutrient Extraction and Determination from invertebrates, a rapid, cheap and streamlined protocol	14
TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution	14
Modelling the joint effects of body size and microclimate on heat budgets and foraging opportunities of ectotherms	14
Quantifying carbon in tree bark: The importance of bark morphology and tree size	14
Infectious disease phylodynamics with occurrence data	14
The unmarked R package: Twelve years of advances in occurrence and abundance modelling in ecology	14
Advancing diet reconstruction in fish eye lenses	14
A novel and efficient method for wood–leaf separation from terrestrial laser scanning point clouds at the forest plot level	14
Revisiting animal photo‐identification using deep metric learning and network analysis	14
Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management	13
Assessing the performance and efficiency of environmental DNA/RNA capture methodologies under controlled experimental conditions	13
poems: R package for simulating species' range dynamics using pattern‐oriented validation	13
ROBITT: A tool for assessing the risk‐of‐bias in studies of temporal trends in ecology	13
Validating ATLAS: A regional‐scale high‐throughput tracking system	13
Standardized nuclear markers improve and homogenize species delimitation in Metazoa	13
A guide to sampling design for GPS‐based studies of animal societies	13
Conditional repeatability and the variance explained by reaction norm variation in random slope models	13
A standardised biologging approach to infer parturition: An application in large herbivores across the hider‐follower continuum	13
Count transformation models	13
msocc: Fit and analyse computationally efficient multi‐scale occupancy models in r	12
One leaf for all: Chemical traits of single leaves measured at the leaf surface using near‐infrared reflectance spectroscopy	12
Lights, camera, pliman! An R package for plant image analysis	12
mcera5: Driving microclimate models with ERA5 global gridded climate data	12
Calibration chain transformation improves the comparability of organic hydrogen and oxygen stable isotope data	12
Instrumental variable methods in structural equation models	12
Estimating species relative abundances from museum records	12
bRacatus: A method to estimate the accuracy and biogeographical status of georeferenced biological data	12
cxr: A toolbox for modelling species coexistence in R	12
Sashimi: A toolkit for facilitating high‐throughput organismal image segmentation using deep learning	12
Extending Bayesian Elo‐rating to quantify the steepness of dominance hierarchies	12
Shannon entropy as a robust estimator of Zipf's Law in animal vocal communication repertoires	12
Positional errors in species distribution modelling are not overcome by the coarser grains of analysis	12
A customizable, low‐cost optomotor apparatus: A powerful tool for behaviourally measuring visual capability	12
A multi‐platform package for the analysis of intra‐ and interspecific trait evolution	12
Comparing traditional and Bayesian approaches to ecological meta‐analysis	12
Incorporating time into the traditional correlational distributional modelling framework: A proof‐of‐concept using the Wood Thrush Hylocichla mustelina	12
Impact network analysis and the ina r package: Decision support for regional management interventions	12
Dynamic visualisation of million‐tip trees: The OneZoom project	12
SAFE Acoustics: An open‐source, real‐time eco‐acoustic monitoring network in the tropical rainforests of Borneo	12
An automatic classifier of bat sonotypes around the world	11
Analytical models for β‐diversity and the power‐law scaling of β‐deviation	11
maxnodf: An R package for fair and fast comparisons of nestedness between networks	11
Using acoustic indices in ecology: Guidance on study design, analyses and interpretation	11
allodb: An R package for biomass estimation at globally distributed extratropical forest plots	11
RUbble Biodiversity Samplers: 3D‐printed coral models to standardize biodiversity censuses	11
A practical method for evaluating spatial biodiversity offset scenarios based on spatial conservation prioritization outputs	11
Solving the sample size problem for resource selection functions	11
Mooring scientific instruments on the seabed—Design, deployment protocol and performance of a recoverable frame for acoustic receivers	11
A Raspberry Pi‐based camera system and image processing procedure for low cost and long‐term monitoring of forest canopy dynamics	11
Ecological inference using data from accelerometers needs careful protocols	11
Revisiting the minimum set cover, the maximal coverage problems and a maximum benefit area selection problem to make climate‐change‐concerned conservation plans effective	11
CollembolAI, a macrophotography and computer vision workflow to digitize and characterize samples of soil invertebrate communities preserved in fluid	11
Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models	11
Complementary sampling methods for coral histology, metabolomics and microbiome	11
SuessR: Regional corrections for the effects of anthropogenic CO2 on δ13C data from marine organisms	11
Recent developments in empirical dynamic modelling	11
Physics‐based model to predict the acoustic detection distance of terrestrial autonomous recording units over the diel cycle and across seasons: Insights from an Alpine and a Neotropical forest	11
Stable isotope fingerprinting traces essential amino acid assimilation and multichannel feeding in a vertebrate consumer	10
Non‐invasive surveys of mammalian viruses using environmental DNA	10
Fast model‐based ordination with copulas	10
Assessing the predictive power of step selection functions: How social and environmental interactions affect animal space use	10
ngsLCA—A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data	10
Estimating animal density for a community of species using information obtained only from camera‐traps	10
orchaRd 2.0: An R package for visualising meta‐analyses with orchard plots	10
Mapping forest leaf area density from multiview terrestrial lidar	10
Network structure and the optimization of proximity‐based association criteria	10
Seek and learn: Automated identification of microevents in animal behaviour using envelopes of acceleration data and machine learning	10
Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources	10
Modelling and inference for the movement of interacting animals	10
Worth the effort? A practical examination of random effects in hidden Markov models for animal telemetry data	10
A framework for quantifying soundscape diversity using Hill numbers	10
Merging computational fluid dynamics and machine learning to reveal animal migration strategies	10
Terrestrial laser scanning to reconstruct branch architecture from harvested branches	10
Signalling in groups: New tools for the integration of animal communication and collective movement	10
CMRnet: An r package to derive networks of social interactions and movement from mark–recapture data	10