Uncovering ecological state dynamics with hidden Markov models

Anthropogenic disturbance drives dispersal syndromes, demography, and gene flow in amphibian populations

(2020) Hugo Cayuela et al.   ECOLOGICAL MONOGRAPHS

Multi‐event capture‐recapture analysis in Alpine chamois reveals contrasting responses to interspecific competition, within and between populations

(2020) Marlène Gamelon et al.   JOURNAL OF ANIMAL ECOLOGY

Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence

(2019) Manh Cuong Ngô et al.   PLoS Computational Biology

Exact inference for integrated population modelling

(2019) P. Besbeas et al.   BIOMETRICS

aphid: an R package for analysis with profile hidden Markov models

(2019) Shaun P Wilkinson   BIOINFORMATICS

Richness, diversity, and factors influencing occupancy of mammal communities across human-modified landscapes in Colombia

(2019) Valeria Boron et al.   BIOLOGICAL CONSERVATION

Open population maximum likelihood spatial capture‐recapture

(2019) R. Glennie et al.   BIOMETRICS

The Conditionally Autoregressive Hidden Markov Model (CarHMM): Inferring Behavioural States from Animal Tracking Data Exhibiting Conditional Autocorrelation

(2019) Ethan Lawler et al.   JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS

Markov models—Markov chains

(2019) Jasleen K. Grewal et al.   NATURE METHODS

Joint modelling of multi‐scale animal movement data using hierarchical hidden Markov models

(2019) Timo Adam et al.   Methods in Ecology and Evolution

Classifying grey seal behaviour in relation to environmental variability and commercial fishing activity - a multivariate hidden Markov model

(2019) Floris M. van Beest et al.   Scientific Reports

Scalable Bayesian Inference for Coupled Hidden Markov and Semi-Markov Models

(2019) Panayiota Touloupou et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

A hidden semi‐Markov model for characterizing regime shifts in ocean density variability

(2019) Theodoros Economou et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS

Inferring wildlife poaching in southeast Asia with multispecies dynamic occupancy models

(2019) Lucile Marescot et al.   ECOGRAPHY

Trade‐offs between age‐related breeding improvement and survival senescence in highly polygynous elephant seals: Dominant males always do better

(2019) Kyle J. Lloyd et al.   JOURNAL OF ANIMAL ECOLOGY

A low-cost, open-source inertial movement GPS logger for eco-physiology applications

(2019) James A. Fahlbusch et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

popler: An r package for extraction and synthesis of population time series from the long‐term ecological research (LTER) network

(2019) Aldo Compagnoni et al.   Methods in Ecology and Evolution

Ecosystem health monitoring in the Shanghai-Hangzhou Bay Metropolitan Area: A hidden Markov modeling approach

(2019) Rui Xiao et al.   ENVIRONMENT INTERNATIONAL

The handbook for standardized field and laboratory measurements in terrestrial climate change experiments and observational studies (ClimEx)

(2019) Aud H. Halbritter et al.   Methods in Ecology and Evolution

Use of ambiguous detections to improve estimates from species distribution models

(2018) Julie Louvrier et al.   CONSERVATION BIOLOGY

A general method for estimating seed dormancy and colonisation in annual plants from the observation of existing flora

(2018) Matthieu Pluntz et al.   ECOLOGY LETTERS

Ecological correlates of the spatial co-occurrence of sympatric mammalian carnivores worldwide

(2018) Courtney L. Davis et al.   ECOLOGY LETTERS

Social status mediates the fitness costs of infection with canine distemper virus in Serengeti spotted hyenas

(2018) Lucile Marescot et al.   FUNCTIONAL ECOLOGY

Lions and leopards coexist without spatial, temporal or demographic effects of interspecific competition

(2018) Jennifer R. B. Miller et al.   JOURNAL OF ANIMAL ECOLOGY

Understanding the ontogeny of foraging behaviour: insights from combining marine predator bio-logging with satellite-derived oceanography in hidden Markov models

(2018) W. James Grecian et al.   Journal of the Royal Society Interface

A comprehensive genomic history of extinct and living elephants

(2018) Eleftheria Palkopoulou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiont switching and alternative resource acquisition strategies drive mutualism breakdown

(2018) Gijsbert D. A. Werner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pacing of Paleozoic macroevolutionary rates by Milankovitch grand cycles

(2018) James S. Crampton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Iterative near-term ecological forecasting: Needs, opportunities, and challenges

(2018) Michael C. Dietze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural selection interacts with recombination to shape the evolution of hybrid genomes

(2018) Molly Schumer et al.   SCIENCE

Spline-based nonparametric inference in general state-switching models

(2018) Roland Langrock et al.   STATISTICA NEERLANDICA

momentuHMM : R package for generalized hidden Markov models of animal movement

(2018) Brett T. McClintock et al.   Methods in Ecology and Evolution

Optimal swimming strategies and behavioral plasticity of oceanic whitetip sharks

(2018) Yannis P. Papastamatiou et al.   Scientific Reports

Activity seascapes highlight central place foraging strategies in marine predators that never stop swimming

(2018) Yannis P. Papastamatiou et al.   Movement Ecology

Aerial-hawking bats adjust their use of space to the lunar cycle

(2018) Manuel Roeleke et al.   Movement Ecology

The spatial and temporal domains of modern ecology

(2018) Lyndon Estes et al.   Nature Ecology & Evolution

Accounting for misidentification and heterogeneity in occupancy studies using hidden Markov models

(2018) Julie Louvrier et al.   ECOLOGICAL MODELLING

Hidden state models improve state-dependent diversification approaches, including biogeographical models

(2018) Daniel S. Caetano et al.   EVOLUTION

Quantifying climate sensitivity and climate-driven change in North American amphibian communities

(2018) David A. W. Miller et al.   Nature Communications

Using camera traps to investigate spatial co-occurrence between exotic predators and native prey species: a case study from northeastern Madagascar

(2018) A. Murphy et al.   JOURNAL OF ZOOLOGY

Environmental DNA Time Series in Ecology

(2018) Miklós Bálint et al.   TRENDS IN ECOLOGY & EVOLUTION

A multistate dynamic occupancy model to estimate local colonization-extinction rates and patterns of co-occurrence between two or more interacting species

(2018) Mason Fidino et al.   Methods in Ecology and Evolution

Multi-scale Modeling of Animal Movement and General Behavior Data Using Hidden Markov Models with Hierarchical Structures

(2017) Vianey Leos-Barajas et al.   JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS

Selecting the Number of States in Hidden Markov Models: Pragmatic Solutions Illustrated Using Animal Movement

(2017) Jennifer Pohle et al.   JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS

LMest: An R Package for Latent Markov Models for Longitudinal Categorical Data

(2017) Francesco Bartolucci et al.   Journal of Statistical Software

Using Hidden Markov Models to characterise intermittent social behaviour in fish shoals

(2017) Nikolai W. F. Bode et al.   NATURWISSENSCHAFTEN

Estimating individual fitness in the wild using capture–recapture data

(2017) Olivier Gimenez et al.   POPULATION ECOLOGY

Survival, density, and abundance of common bottlenose dolphins in Barataria Bay (USA) following the Deepwater Horizon oil spill

(2017) TL McDonald et al.   Endangered Species Research

Using Hidden Markov Models to characterise intermittent social behaviour in fish shoals

(2017) Nikolai W. F. Bode et al.   Science of Nature

Extinction debt and colonization credit delay range shifts of eastern North American trees

(2017) Matthew V. Talluto et al.   Nature Ecology & Evolution

Hidden Markov models reveal complexity in the diving behaviour of short-finned pilot whales

(2017) Nicola J. Quick et al.   Scientific Reports

Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities

(2016) Gurutzeta Guillera-Arroita   ECOGRAPHY

What shapes fitness costs of reproduction in long-lived iteroparous species? A case study on the Alpine ibex

(2016) Alexandre Garnier et al.   ECOLOGY

Sex-specific and individual preferences for hunting strategies in white sharks

(2016) Alison V. Towner et al.   FUNCTIONAL ECOLOGY

Improving the Consistency of Multitemporal Land Cover Maps Using a Hidden Markov Model

(2016) S. Parker Abercrombie et al.   IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING

Using camera trapping and hierarchical occupancy modelling to evaluate the spatial ecology of an African mammal community

(2016) Lindsey N. Rich et al.   JOURNAL OF APPLIED ECOLOGY

Counting animal species with DNA barcodes: Canadian insects

(2016) Paul D. N. Hebert et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Differential and enhanced response to climate forcing in diarrheal disease due to rotavirus across a megacity of the developing world

(2016) Pamela P. Martinez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comparison of Inferential Methods for Highly Nonlinear State Space Models in Ecology and Epidemiology

(2016) Matteo Fasiolo et al.   STATISTICAL SCIENCE

Towards Process-based Range Modeling of Many Species

(2016) Margaret E.K. Evans et al.   TRENDS IN ECOLOGY & EVOLUTION

A multiregion community model for inference about geographic variation in species richness

(2016) Chris Sutherland et al.   Methods in Ecology and Evolution

A multispecies occupancy model for two or more interacting species

(2016) Christopher T. Rota et al.   Methods in Ecology and Evolution

Experimentally derived likelihoods for light-based geolocation

(2016) Marinelle Basson et al.   Methods in Ecology and Evolution

Analysis of animal accelerometer data using hidden Markov models

(2016) Vianey Leos-Barajas et al.   Methods in Ecology and Evolution

Life-history tradeoffs and reproductive cycles in Spotted Owls

(2015) Ricka E. Stoelting et al.   AUK

Semi-Markov Arnason-Schwarz models

(2015) Ruth King et al.   BIOMETRICS

Objective classification of latent behavioral states in bio-logging data using multivariate-normal hidden Markov models

(2015) Joe Scutt Phillips et al.   ECOLOGICAL APPLICATIONS

Estimating demographic parameters using a combination of known-fate and openN-mixture models

(2015) Joshua H. Schmidt et al.   ECOLOGY

Modeling spatiotemporal dynamics of outbreaking species: influence of environment and migration in a locust

(2015) Sophie Veran et al.   ECOLOGY

An open-population hierarchical distance sampling model

(2015) Rahel Sollmann et al.   ECOLOGY

Litter sex composition influences dominance status of Alpine marmots (Marmota marmota)

(2015) Pierre Dupont et al.   OECOLOGIA

A Hidden Markov Models Approach for Crop Classification: Linking Crop Phenology to Time Series of Multi-Sensor Remote Sensing Data

(2015) Sofia Siachalou et al.   Remote Sensing

A hidden Markov model for reconstructing animal paths from solar geolocation loggers using templates for light intensity

(2015) Eldar Rakhimberdiev et al.   Movement Ecology

depmixS4: AnRPackage for Hidden Markov Models

(2015) Ingmar Visser et al.   Journal of Statistical Software

Hidden Semi Markov Models for Multiple Observation Sequences: ThemhsmmPackage forR

(2015) Jared O'Connell et al.   Journal of Statistical Software

Multi-State Models for Panel Data: ThemsmPackage forR

(2015) Christopher H. Jackson   Journal of Statistical Software

Dynamics of Weeds in the Soil Seed Bank: A Hidden Markov Model to Estimate Life History Traits from Standing Plant Time Series

(2015) Benjamin Borgy et al.   PLoS One

Theoretical and Empirical Perspectives in Ecology and Evolution: A Survey

(2014) Benjamin C. Haller   BIOSCIENCE

Estimating dispersal among numerous sites using capture–recapture data

(2014) Paméla Lagrange et al.   ECOLOGY

Hidden semi-Markov models reveal multiphasic movement of the endangered Florida panther

(2014) Madelon van de Kerk et al.   JOURNAL OF ANIMAL ECOLOGY

Accounting for Imperfect Detection in Ecology: A Quantitative Review

(2014) Kenneth F. Kellner et al.   PLoS One

Volcano-induced regime shifts in millennial tree-ring chronologies from northeastern North America

(2014) F. Gennaretti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

A hidden Markov model combined with climate indices for multidecadal streamflow simulation

(2014) C. Bracken et al.   WATER RESOURCES RESEARCH

Accounting for imperfect detection in Hill numbers for biodiversity studies

(2014) Kristin M. Broms et al.   Methods in Ecology and Evolution

Fitting occupancy models with E-SURGE: hidden Markov modelling of presence-absence data

(2014) Olivier Gimenez et al.   Methods in Ecology and Evolution

Metapopulation Dynamics of Species with Cryptic Life Stages

(2013) Thomas Lamy et al.   AMERICAN NATURALIST

Multivariate methods using mixtures: Correspondence analysis, scaling and pattern-detection

(2013) Shirley Pledger et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Estimating transitions between states using measurements with imperfect detection: application to serological data

(2013) Rémi Choquet et al.   ECOLOGY

Modeling the Diving Behavior of Whales: A Latent-Variable Approach with Feedback and Semi-Markovian Components

(2013) Roland Langrock et al.   JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS

Imperfect detection is the rule rather than the exception in plant distribution studies

(2013) Guoke Chen et al.   JOURNAL OF ECOLOGY

Markov-Modulated Nonhomogeneous Poisson Processes for Modeling Detections in Surveys of Marine Mammal Abundance

(2013) Roland Langrock et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

A coupled hidden Markov model for disease interactions

(2013) Chris Sherlock et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS

Modelling group dynamic animal movement

(2013) Roland Langrock et al.   Methods in Ecology and Evolution

Behavioral signature of intraspecific competition and density dependence in colony-breeding marine predators

(2013) Greg A. Breed et al.   Ecology and Evolution

Value of long-term ecological studies

(2012) DAVID B. LINDENMAYER et al.   AUSTRAL ECOLOGY

A general discrete-time modeling framework for animal movement using multistate random walks

(2012) Brett T. McClintock et al.   ECOLOGICAL MONOGRAPHS

Combining individual animal movement and ancillary biotelemetry data to investigate population-level activity budgets

(2012) Brett T. McClintock et al.   ECOLOGY

C16S — A Hidden Markov Model based algorithm for taxonomic classification of 16S rRNA gene sequences

(2012) Tarini Shankar Ghosh et al.   GENOMICS

Exposure of black-legged kittiwakes to Lyme disease spirochetes: dynamics of the immune status of adult hosts and effects on their survival

(2012) Thierry Chambert et al.   JOURNAL OF ANIMAL ECOLOGY

Estimating demographic parameters using hidden process dynamic models

(2012) Olivier Gimenez et al.   THEORETICAL POPULATION BIOLOGY

On the application of mixed hidden Markov models to multiple behavioural time series

(2012) S. Schliehe-Diecks et al.   Interface Focus

Estimation methods for nonlinear state-space models in ecology

(2011) M.W. Pedersen et al.   ECOLOGICAL MODELLING

Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification

(2011) David A. Miller et al.   ECOLOGY

Estimating parameters of hidden Markov models based on marked individuals: use of robust design data

(2011) William L. Kendall et al.   ECOLOGY

Infection dynamics of endemic malaria in a wild bird population: parasite species-dependent drivers of spatial and temporal variation in transmission rates

(2011) Shelly Lachish et al.   JOURNAL OF ANIMAL ECOLOGY

Warming up for dinner: torpor and arousal in hibernating Natterer’s bats (Myotis nattereri) studied by radio telemetry

(2011) Paul R. Hope et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

Sampling errors create bias in Markov models for community dynamics: the problem and a method for its solution

(2011) Letitia L. Conway-Cranos et al.   OECOLOGIA

Estimating animal behavior and residency from movement data

(2011) M. W. Pedersen et al.   OIKOS

Bioinformatics tools in predictive ecology: applications to fisheries

(2011) A. Tucker et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Partitioning the Aggregation of Parasites on Hosts into Intrinsic and Extrinsic Components via an Extended Poisson-Gamma Mixture Model

(2011) Justin M. Calabrese et al.   PLoS One

Empirical Models of Transitions between Coral Reef States: Effects of Region, Protection, and Environmental Change

(2011) Phillip K. Lowe et al.   PLoS One

A semi-Markov model to assess reliably survival patterns from birth to death in free-ranging populations

(2011) Rémi Choquet et al.   Methods in Ecology and Evolution

Living dangerously with big fancy models1

(2010) Michael Lavine   ECOLOGY

Multistate modeling of habitat dynamics: factors affecting Florida scrub transition probabilities

(2010) David R. Breininger et al.   ECOLOGY

Models for inference in dynamic metacommunity systems

(2010) Robert M. Dorazio et al.   ECOLOGY

Seeking a second opinion: uncertainty in disease ecology

(2010) Brett T. McClintock et al.   ECOLOGY LETTERS

Integrated population models: a novel analysis framework for deeper insights into population dynamics

(2010) Michael Schaub et al.   JOURNAL OF ORNITHOLOGY

Bayesian non-parametric hidden Markov models with applications in genomics

(2010) C. Yau et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Behavioural switching in a central place forager: patterns of diving behaviour in the macaroni penguin (Eudyptes chrysolophus)

(2010) Tom Hart et al.   MARINE BIOLOGY

Statistical inference for noisy nonlinear ecological dynamic systems

(2010) Simon N. Wood   NATURE

Conceptual Synthesis in Community Ecology

(2010) Mark Vellend   QUARTERLY REVIEW OF BIOLOGY

Never mind the length, feel the quality: the impact of long-term epidemiological data sets on theory, application and policy

(2010) Pejman Rohani et al.   TRENDS IN ECOLOGY & EVOLUTION

A novel approach to detecting a regime shift in a lake ecosystem

(2010) Gideon Gal et al.   Methods in Ecology and Evolution

Estimating Population Size and Hidden Demographic Parameters with State‐Space Modeling

(2009) Giacomo Tavecchia et al.   AMERICAN NATURALIST

Dynamic multistate site occupancy models to evaluate hypotheses relevant to conservation of Golden Eagles in Denali National Park, Alaska

(2009) Julien Martin et al.   BIOLOGICAL CONSERVATION

Multi-species occurrence models to evaluate the effects of conservation and management actions

(2009) Elise F. Zipkin et al.   BIOLOGICAL CONSERVATION

Estimation of sex-specific survival with uncertainty in sex assessment

(2009) Roger Pradel et al.   CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE

Hidden Markov Models and their Applications in Biological Sequence Analysis

(2009) Byung-Jun Yoon   CURRENT GENOMICS

Modeling the effects of environmental disturbance on wildlife communities: avian responses to prescribed fire

(2009) Robin E. Russell et al.   ECOLOGICAL APPLICATIONS

Modeling species occurrence dynamics with multiple states and imperfect detection

(2009) Darryl I. MacKenzie et al.   ECOLOGY

Detecting Selective Sweeps: A New Approach Based on Hidden Markov Models

(2009) S. Boitard et al.   GENETICS

Classifying movement behaviour in relation to environmental conditions using hidden Markov models

(2009) Toby A. Patterson et al.   JOURNAL OF ANIMAL ECOLOGY

Landscape regularity modelling for environmental challenges in agriculture

(2009) El Ghali Lazrak et al.   LANDSCAPE ECOLOGY

Birds track their Grinnellian niche through a century of climate change

(2009) M. W. Tingley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geolocation of North Sea cod (Gadus morhua) using hidden Markov models and behavioural switching

(2008) M. W. Pedersen et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Imperfect detection and its consequences for monitoring for conservation

(2008) M. Kéry et al.   COMMUNITY ECOLOGY

A Markov model for assessing ecological stability properties

(2008) Christopher W. Pawlowski et al.   ECOLOGICAL MODELLING

Multistate capture-recapture analysis under imperfect state observation: an application to disease models

(2008) Paul B. Conn et al.   JOURNAL OF APPLIED ECOLOGY

Impact of a Century of Climate Change on Small-Mammal Communities in Yosemite National Park, USA

(2008) C. Moritz et al.   SCIENCE

State–space models of individual animal movement

(2008) T PATTERSON et al.   TRENDS IN ECOLOGY & EVOLUTION

Spatially Explicit Maximum Likelihood Methods for Capture-Recapture Studies

(2007) D. L. Borchers et al.   BIOMETRICS

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources