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A guide to state–space modeling of ecological time series
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Parameter Identifiability and Model Selection in Capture-Recapture Models: A Numerical Approach
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Overcoming Equifinality: Leveraging Long Time Series for Stream Metabolism Estimation
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Identifiable state‐space models: A case study of the Bay of Fundy sea scallop fishery
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A need for speed in Bayesian population models: a practical guide to marginalizing and recovering discrete latent states
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Estimating range expansion of wildlife in heterogeneous landscapes: A spatially explicit state‐space matrix model coupled with an improved numerical integration technique
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The BUGS project: Evolution, critique and future directions
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WinBUGS for Population Ecologists: Bayesian Modeling Using Markov Chain Monte Carlo Methods
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Weak Identifiability in Models for Mark-Recapture-Recovery Data
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An Introduction to Sequential Monte Carlo Methods
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Modelling Population Dynamics : Model Formulation, Fitting and Assessment using State-Space Methods
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Recursive residuals and model diagnostics for normal and non-normal state space models
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Population diversity in Pacific herring of the Puget Sound, USA
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Towards built-in capture–recapture mixed models in program E-SURGE
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Frequentist analysis of hierarchical models for population dynamics and demographic data
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Validation of ecological state space models using the Laplace approximation
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Understanding predictive information criteria for Bayesian models
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Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC
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Conditional vs marginal estimation of the predictive loss of hierarchical models using WAIC and cross-validation
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Variational Bayes with synthetic likelihood
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Bayesian Comparison of Latent Variable Models: Conditional Versus Marginal Likelihoods
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Selecting the Number of States in Hidden Markov Models: Pragmatic Solutions Illustrated Using Animal Movement
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Parameter redundancy and identifiability in hidden Markov models
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An improved Akaike information criterion for state-space model selection
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An ANOVA test for parameter estimability using data cloning with application to statistical inference for dynamic systems
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State-space models for bio-loggers: A methodological road map
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State-space models for the dynamics of wild animal populations
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Using Bayesian state-space modelling to assess the recovery and harvest potential of the Hawaiian green sea turtle stock
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State-space modelling of data on marked individuals
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Estimation methods for nonlinear state-space models in ecology
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State-space methods for more completely capturing behavioral dynamics from animal tracks
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Effects of model complexity and priors on estimation using sequential importance sampling/resampling for species conservation
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Bayesian state-space models reveal unobserved off-shore nocturnal migration from Motus data
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Performance of deviance information criterion model selection in statistical catch-at-age analysis
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Estimation of time-varying selectivity in stock assessments using state-space models
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Model selection and multi-model inference for Bayesian surplus production models: A case study for Pacific blue and striped marlin
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Performance evaluation of information criteria for estimating a shape parameter in a Bayesian state-space biomass dynamics model
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Parameterizations for Bayesian state-space surplus production models
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Estimating total net primary productivity of managed grasslands by a state-space modeling approach in a small catchment on the Loess Plateau, China
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On the use of cross-validation for time series predictor evaluation
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Determining the parametric structure of models
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A hybrid symbolic-numerical method for determining model structure
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Time is an affliction: Why ecology cannot be as predictive as physics and why it needs time series
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State–space models of individual animal movement
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Generalized linear mixed models: a practical guide for ecology and evolution
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Approximate Bayesian Computation (ABC) in practice
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Overcoming the Data Crisis in Biodiversity Conservation
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A Critique of the Space-for-Time Substitution Practice in Community Ecology
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Out-of-sample tests of forecasting accuracy: an analysis and review
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Forecasting, Structural Time Series Models and the Kalman Filter
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WinBUGS - A Bayesian modelling framework: Concepts, structure, and extensibility
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Joint estimation over multiple individuals improves behavioural state inference from animal movement data
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State-space models’ dirty little secrets: even simple linear Gaussian models can have estimation problems
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Novel approach to nonlinear/non-Gaussian Bayesian state estimation
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Inference for dynamic and latent variable models via iterated, perturbed Bayes maps
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A Hellinger distance approach to MCMC diagnostics
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Approximate leave-future-out cross-validation for Bayesian time series models
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Non-Gaussian State-Space Modeling of Nonstationary Time Series
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State-Space Analysis of Wildlife Telemetry Data
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Markov Chain Monte Carlo Convergence Diagnostics: A Comparative Review
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The Selection of Prior Distributions by Formal Rules
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Identifiability, Improper Priors, and Gibbs Sampling for Generalized Linear Models
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Filtering via Simulation: Auxiliary Particle Filters
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Tracking Epidemics With Google Flu Trends Data and a State-Space SEIR Model
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AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models
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Programming With Models: Writing Statistical Algorithms for General Model Structures With NIMBLE
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Monitoring Joint Convergence of MCMC Samplers
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Time Series Analysis by State Space Methods
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Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
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Efficient Generalized Cross-Validation for State Space Models
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A Cross-Validation Filter for Time Series Models
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On Gibbs sampling for state space models
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Bayesian Estimation of Movement and Survival Probabilities from Capture- Recapture Data
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Detecting parameter redundancy
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Miscellanea. Estimation in parameter-redundant models
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Conditional Akaike information for mixed-effects models
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Accounting for correlated observations in an age-based state-space stock assessment model
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A state-space modeling approach to estimating canopy conductance and associated uncertainties from sap flux density data
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A review of Bayesian state-space modelling of capture–recapture–recovery data
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Avoidable errors in the modelling of outbreaks of emerging pathogens, with special reference to Ebola
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Applications of Kalman Filtering in Aerospace 1960 to the Present [Historical Perspectives]
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Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo
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momentuHMM: R package for generalized hidden Markov models of animal movement
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Exact Inference for Integrated Population Modelling
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Improving inference for nonlinear state‐space models of animal population dynamics given biased sequential life stage data
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Cross‐validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure
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Changes in the diet and body size of a small herbivorous mammal (hispid cotton rat, Sigmodon hispidus ) following the late Pleistocene megafauna extinction
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Temporal ecology in the Anthropocene
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Uncovering ecological state dynamics with hidden Markov models
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Latent Class Model Diagnosis
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On the Near-Singularity of Models for Animal Recovery Data
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Integrating Mark-Recapture-Recovery and Census Data to Estimate Animal Abundance and Demographic Parameters
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Climate change vulnerability of forest biodiversity: climate and competition tracking of demographic rates
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Geographical gradients in the population dynamics of North American prairie ducks
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Population dynamics of an Arctiid caterpillar–tachinid parasitoid system using state‐space models
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On observation distributions for state space models of population survey data
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Inferring spatial structure from time‐series data: using multivariate state‐space models to detect metapopulation structure of California sea lions in the Gulf of California, Mexico
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Estimation of immigration rate using integrated population models
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Addressing challenges when studying mobile or episodic species: hierarchical Bayes estimation of occupancy and use
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Bayesian state‐space model of fin whale abundance trends from a 1991–2008 time series of line‐transect surveys in the California Current
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Particle Markov Chain Monte Carlo Methods
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The Use of Bayesian Model Averaging to Better Represent Uncertainty in Ecological Models
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Modeling Individual Effects in the Cormack–Jolly–Seber Model: A State–Space Formulation
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Comparison of Hierarchical Bayesian Models for Overdispersed Count Data using DIC and Bayes' Factors
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Estimating environmental effects on population dynamics: consequences of observation error
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Optimal spatio‐temporal hybrid sampling designs for ecological monitoring
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State‐space framework for estimating measurement error from double‐tagging telemetry experiments
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A NON‐GAUSSIAN FAMILY OF STATE‐SPACE MODELS WITH EXACT MARGINAL LIKELIHOOD
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Moving beyond noninformative priors: why and how to choose weakly informative priors in Bayesian analyses
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New Results in Linear Filtering and Prediction Theory
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A New Approach to Linear Filtering and Prediction Problems
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Shark baselines and the conservation role of remote coral reef ecosystems
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BUGS in Bayesian stock assessments
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Reference priors for Bayesian fisheries models
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A Bayesian statespace markrecapture model to estimate exploitation rates in mixed-stock fisheries
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A state–space multistage life cycle model to evaluate population impacts in the presence of density dependence: illustrated with application to delta smelt (Hyposmesus transpacificus)
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Review of State-Space Models for Fisheries Science
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Parameter and structural identifiability concepts and ambiguities: a critical review and analysis
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When to be discrete: the importance of time formulation in understanding animal movement
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Monte Carlo State-Space Likelihoods by Weighted Posterior Kernel Density Estimation
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Time Series Analysis and Its Applications: With R Examples
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Estimability and Likelihood Inference for Generalized Linear Mixed Models Using Data Cloning
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Bringing Bayesian Models to Life
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MCMC Using Hamiltonian Dynamics
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Introduction to Markov Chain Monte Carlo
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A review of Bayesian variable selection methods: what, how and which
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Consistency of the maximum likelihood estimator for general hidden Markov models
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Model Selection in Linear Mixed Models
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A Comparison of Inferential Methods for Highly Nonlinear State Space Models in Ecology and Epidemiology
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Multivariate State Hidden Markov Models for Mark-Recapture Data
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Inference from Iterative Simulation Using Multiple Sequences
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A Disease-Mediated Trophic Cascade in the Serengeti and its Implications for Ecosystem C
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Accuracy of ARGOS Locations of Pinnipeds at-Sea Estimated Using Fastloc GPS
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Hierarchical State-Space Estimation of Leatherback Turtle Navigation Ability
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Effects of Temporal Resolution on an Inferential Model of Animal Movement
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Using Hierarchical Bayes to Understand Movement, Health, and Survival in the Endangered North Atlantic Right Whale
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The PIT-trap—A “model-free” bootstrap procedure for inference about regression models with discrete, multivariate responses
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Model selection for the North American Breeding Bird Survey: A comparison of methods
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An R Package for Dynamic Linear Models
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Statistical Inference for Partially Observed Markov Processes via theRPackagepomp
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TMB : Automatic Differentiation and Laplace Approximation
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MultiBUGS: A Parallel Implementation of the BUGS Modeling Framework for Faster Bayesian Inference
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FITTING POPULATION MODELS INCORPORATING PROCESS NOISE AND OBSERVATION ERROR
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ESTIMATING COMMUNITY STABILITY AND ECOLOGICAL INTERACTIONS FROM TIME-SERIES DATA
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ESTIMATING DENSITY DEPENDENCE, PROCESS NOISE, AND OBSERVATION ERROR
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DENSITY DEPENDENCE IN NORTH AMERICAN DUCKS
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ANALYSIS OF SIZE TRAJECTORY DATA USING AN ENERGETIC-BASED GROWTH MODEL
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ROBUST STATE–SPACE MODELING OF ANIMAL MOVEMENT DATA
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Accounting for uncertainty in ecological analysis: the strengths and limitations of hierarchical statistical modeling
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CONTINUOUS‐TIME CORRELATED RANDOM WALK MODEL FOR ANIMAL TELEMETRY DATA
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Species richness and occupancy estimation in communities subject to temporary emigration
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ESTIMABILITY OF DENSITY DEPENDENCE IN MODELS OF TIME SERIES DATA
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Replicated sampling increases efficiency in monitoring biological populations
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A general discrete‐time modeling framework for animal movement using multistate random walks
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Fitting complex population models by combining particle filters with Markov chain Monte Carlo
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R: A Language and Environment for Statistical Computing
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MARSS: Multivariate Autoregressive State-space Models for Analyzing Time-series Data
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The Prior Can Often Only Be Understood in the Context of the Likelihood
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A Conceptual Introduction to Hamiltonian Monte Carlo
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What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Peterman's productivity method for estimating dynamic reference points in changing ecosystems
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Regional differences in population trends and environmental drivers of population dynamics in an at-risk waterbird
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Conservation of Wildlife Populations
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Preface to Third Edition
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.002.0011openalex-snapshot
Preface to Second Edition
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.002.0012openalex-snapshot
Preface to First Edition
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.002.0014openalex-snapshot
Credits for Epigraphs
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Gaining reliable knowledge
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.003.0003openalex-snapshot
Genetic concepts and tools to support wildlife population ecology
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.003.0004openalex-snapshot
Estimating population size and vital rates
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.003.0005openalex-snapshot
Exponential (or geometric) change
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.003.0006openalex-snapshot
All stage classes are not equal in their effects on population growth
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.003.0007openalex-snapshot
Density-dependent population change
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.003.0008openalex-snapshot
Predation and wildlife populations
inferred← citeshttps://doi.org/10.1093/oso/9780192898166.003.0009openalex-snapshot
Genetic variation and fitness of wildlife populations
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Dynamics of multiple populations
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Population responses to human-caused stressors: Move, adjust, or die
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Dynamics of small and declining populations
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Sustainable harvest principles, models, and best practices
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Bottom-up effects of variable winter weather conditions on phytoplankton dynamics in an enclosed bay: implications for ecological responses to climate change
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Implementing measurement error models with mechanistic mathematical models in a likelihood-based framework for estimation, identifiability analysis and prediction in the life sciences
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Individualized survival predictions using state space model with longitudinal and survival data
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State-space modelling using wastewater virus and epidemiological data to estimate reported COVID-19 cases and the potential infection numbers
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Improved abundance trajectories with Bayesian population dynamics models: case study with a Hawaiian honeycreeper
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A Bayesian state-space model for estimating pup production in an asynchronous breeder: the grey seal (Halichoerus grypus)
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Towards a causal understanding of bidirectional effects in ecology and evolution
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A comprehensive framework for handling location error in animal tracking data
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Confronting population models with experimental microcosm data: from trajectory matching to state-space models
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Long-Term Forecasting of a Motor Outcome Following Rehabilitation in Chronic Stroke via a Hierarchical Bayesian Model of Motor Learning
inferred← citeshttps://doi.org/10.1101/2023.01.12.523862openalex-snapshot
Change in Monarch Butterfly Winter Abundance Over the Past Decade: A Red List Perspective
inferred← citeshttps://doi.org/10.1101/2024.03.02.581600openalex-snapshot
Inferring stability and persistence in the vaginal microbiome: A stochastic model of ecological dynamics
inferred← citeshttps://doi.org/10.1101/2025.05.15.654001openalex-snapshot
Using wingbeat frequency to estimate mass gained by seabirds
inferred← citeshttps://doi.org/10.1101/2025.06.13.659576openalex-snapshot
Forecasts for 80% of wild populations and communities predict no change, and why
inferred← citeshttps://doi.org/10.1101/2025.11.08.687336openalex-snapshot
Inferring the causes of animal social network structure from time-series data
inferred← citeshttps://doi.org/10.1109/access.2026.3671697openalex-snapshot
Integrated Diagnosis and Prognosis of Dynamic Systems Using Deep Learning: Case Study on a Welding Robot
inferred← citeshttps://doi.org/10.1109/acctcs66275.2025.00068openalex-snapshot
Risk Assessment of Cyberbullying Based on Improved Bayesian Networks
inferred← citeshttps://doi.org/10.1109/ithings-greencom-cpscom-smartdata-cybermatics67059.2025.00038openalex-snapshot
A Survey of Forecasting Methods for Irregular Time Series
inferred← citeshttps://doi.org/10.1109/tim.2025.3650236openalex-snapshot
Toward Continuous and Contactless Cardiac Monitoring: A State-Space Approach With FMCW Radar
inferred← citeshttps://doi.org/10.1111/1365-2656.13936openalex-snapshot
Tree and shrub expansion at treeline drive contrasting responses in a subarctic passerine community
inferred← citeshttps://doi.org/10.1111/1365-2656.70040openalex-snapshot
Understanding and predicting animal movements and distributions in the Anthropocene
inferred← citeshttps://doi.org/10.1111/1365-2656.70068openalex-snapshot
Body size, nutritional state and endocrine state are associated with calving probability in a long‐lived marine species
inferred← citeshttps://doi.org/10.1111/1365-2656.70176openalex-snapshot
An integrated integral projection model ( IPM 2 ) to disentangle size‐structured harvest and natural mortality
inferred← citeshttps://doi.org/10.1111/1365-2656.70177openalex-snapshot
Disentangling the influence of density dependence, size dependence and environmental effects on fish population dynamics
inferred← citeshttps://doi.org/10.1111/1365-2664.70505openalex-snapshot
Strategic dam management can offset climate‐driven declines in fish production
inferred← citeshttps://doi.org/10.1111/1365-2745.14289openalex-snapshot
Interacting effects of fire and hydroclimate on oak and beech community prevalence in the southern Great Lakes region
inferred← citeshttps://doi.org/10.1111/1752-1688.70134openalex-snapshot
Improving Living Resource Responses in Ecosystem Restoration: An Illustration Using the Chesapeake Bay
inferred← citeshttps://doi.org/10.1111/2041-210x.13788openalex-snapshot
Smoothed dynamic factor analysis for identifying trends in multivariate time series
inferred← citeshttps://doi.org/10.1111/2041-210x.13801openalex-snapshot
Hidden Markov models: Pitfalls and opportunities in ecology
inferred← citeshttps://doi.org/10.1111/2041-210x.13812openalex-snapshot
Predicting aquatic animal movements and behavioural states from acoustic telemetry arrays
inferred← citeshttps://doi.org/10.1111/2041-210x.13833openalex-snapshot
State‐space models for ecological time‐series data: Practical model‐fitting
inferred← citeshttps://doi.org/10.1111/2041-210x.13974openalex-snapshot
Dynamic generalised additive models ( DGAMs ) for forecasting discrete ecological time series
inferred← citeshttps://doi.org/10.1111/2041-210x.14046openalex-snapshot
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot
inferred← citeshttps://doi.org/10.1111/2041-210x.14050openalex-snapshot
Realising the promise of large data and complex models
inferred← citeshttps://doi.org/10.1111/2041-210x.14148openalex-snapshot
EcoEnsemble: A general framework for combining ecosystem models in R
inferred← citeshttps://doi.org/10.1111/2041-210x.14337openalex-snapshot
Accounting for observation noise in equation‐free forecasting: The hidden‐Markov S‐map
inferred← citeshttps://doi.org/10.1111/2041-210x.14361openalex-snapshot
Time series methods for the analysis of soundscapes and other cyclical ecological data
inferred← citeshttps://doi.org/10.1111/2041-210x.14423openalex-snapshot
Detecting stochasticity in population time series using a non‐parametric test of intrinsic predictability
inferred← citeshttps://doi.org/10.1111/2041-210x.70025openalex-snapshot
Improved order selection method for hidden Markov models: A case study with movement data
inferred← citeshttps://doi.org/10.1111/2041-210x.70071openalex-snapshot
TTR . PGM : An R package for modelling the distributions and dynamics of plants using the Thornley transport resistance plant growth model
inferred← citeshttps://doi.org/10.1111/2041-210x.70105openalex-snapshot
Assessing predictive accuracy of species abundance models in dynamic systems
inferred← citeshttps://doi.org/10.1111/2041-210x.70131openalex-snapshot
Advancing causal inference in ecology: Pathways for biodiversity change detection and attribution
inferred← citeshttps://doi.org/10.1111/2041-210x.70186openalex-snapshot
State‐space models and inference approaches for aquatic animal tracking with passive acoustic telemetry and biologging sensors
inferred← citeshttps://doi.org/10.1111/2041-210x.70190openalex-snapshot
A calibration framework to improve mechanistic forecasts with hybrid dynamic models
inferred← citeshttps://doi.org/10.1111/2041-210x.70244openalex-snapshot
Data‐driven discovery of mechanistic ecosystem models with LLMs
inferred← citeshttps://doi.org/10.1111/2041-210x.70273openalex-snapshot
movetrack: An R package to model flight paths from radio‐telemetry networks
inferred← citeshttps://doi.org/10.1111/2041-210x.70315openalex-snapshot
Statistical analyses of ecological multinomial time series to identify environmental drivers and biotic interactions
inferred← citeshttps://doi.org/10.1111/2041-210x.70319openalex-snapshot
Using wingbeat frequency to estimate mass gain
inferred← citeshttps://doi.org/10.1111/2041-210x.70343openalex-snapshot
Inferring alternative ecosystem states with field survey data
inferred← citeshttps://doi.org/10.1111/biom.13742openalex-snapshot
A Latent State Space Model for Estimating Brain Dynamics from Electroencephalogram (EEG) Data
inferred← citeshttps://doi.org/10.1111/cobi.14114openalex-snapshot
Incorporating multidimensional behavior into a risk management tool for a critically endangered and migratory species
inferred← citeshttps://doi.org/10.1111/csp2.70386openalex-snapshot
Thirty‐year elephant population trends across 93 South African reserves and the implications for conservation management
inferred← citeshttps://doi.org/10.1111/ele.14269openalex-snapshot
Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience
inferred← citeshttps://doi.org/10.1111/ele.70198openalex-snapshot
Understanding and Predicting Population Response to Anthropogenic Disturbance: Current Approaches and Novel Opportunities
inferred← citeshttps://doi.org/10.1111/ele.70261openalex-snapshot
Biotic Variability and Synchrony Across Hierarchical Levels and Freshwater Networks
inferred← citeshttps://doi.org/10.1111/ele.70359openalex-snapshot
Are Insect Populations Inherently More Variable? A Multi‐Taxa Approach to Characterising Interannual Fluctuations in Insect Time Series
inferred← citeshttps://doi.org/10.1111/ele.70364openalex-snapshot
Top‐Down and Bottom‐Up Processes Jointly Explain Mesopredator Movement and Foraging Ecology
inferred← citeshttps://doi.org/10.1111/ele.70375openalex-snapshot
Calibration, Sensitivity and Uncertainty Analysis of Complex Ecological Models—A Review
inferred← citeshttps://doi.org/10.1111/faf.12738openalex-snapshot
Fecundity trends of Chinook salmon in the Pacific Northwest
inferred← citeshttps://doi.org/10.1111/faf.12759openalex-snapshot
Using the best of two worlds: A bio‐economic stock assessment ( BESA ) method using catch and price data
inferred← citeshttps://doi.org/10.1111/faf.12910openalex-snapshot
Estimating Time‐Varying Productivity and Reference Points: A Case of North Sea Demersal Fish Stocks
inferred← citeshttps://doi.org/10.1111/gcb.17014openalex-snapshot
Disentangling the drivers of decadal body size decline in an insect population
inferred← citeshttps://doi.org/10.1111/gcb.17397openalex-snapshot
Predicting emergent animal biodiversity patterns across multiple scales
inferred← citeshttps://doi.org/10.1111/ggi.14543openalex-snapshot
Accelerated cognitive decline after the COVID ‐19 pandemic in a community population of older persons with cognitive impairment: A 4‐year time series analysis in the Tokyo Metropolis area
inferred← citeshttps://doi.org/10.1111/icad.12646openalex-snapshot
Change in monarch winter abundance over the past decade: A Red List perspective
inferred← citeshttps://doi.org/10.1111/jfb.14946openalex-snapshot
Predicting how environmental conditions and smolt body length when entering the marine environment impact individual Atlantic salmon Salmo salar adult return rates
inferred← citeshttps://doi.org/10.1111/mms.70258openalex-snapshot
Linking the Movement Behavior of the Laptev Sea Walrus to Sea Ice and Resource Dynamics
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