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

Detecting the Multiple Facets of Biodiversity

(2016) Marta A. Jarzyna et al.   TRENDS IN ECOLOGY & EVOLUTION

Uncertainty in biological monitoring: a framework for data collection and analysis to account for multiple sources of sampling bias

(2016) Viviana Ruiz-Gutierrez et al.   Methods in Ecology and Evolution

A guide to Bayesian model selection for ecologists

(2015) M. B. Hooten et al.   ECOLOGICAL MONOGRAPHS

Using multispecies occupancy models to improve the characterization and understanding of metacommunity structure

(2015) Joseph R. Mihaljevic et al.   ECOLOGY

To predict the niche, model colonization and extinction

(2015) Charles B. Yackulic et al.   ECOLOGY

Modeling false positive detections in species occurrence data under different study designs

(2015) Thierry Chambert et al.   ECOLOGY

Is my species distribution model fit for purpose? Matching data and models to applications

(2015) Gurutzeta Guillera-Arroita et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Spatial occupancy models for predicting metapopulation dynamics and viability following reintroduction

(2015) Richard B. Chandler et al.   JOURNAL OF APPLIED ECOLOGY

Statistical approaches to account for false-positive errors in environmental DNA samples

(2015) José J. Lahoz-Monfort et al.   Molecular Ecology Resources

So Many Variables: Joint Modeling in Community Ecology

(2015) David I. Warton et al.   TRENDS IN ECOLOGY & EVOLUTION

Performance of species occurrence estimators when basic assumptions are not met: a test using field data where true occupancy status is known

(2015) David A. W. Miller et al.   Methods in Ecology and Evolution

Estimates from non-replicated population surveys rely on critical assumptions

(2015) Jonas Knape et al.   Methods in Ecology and Evolution

Using latent variable models to identify large networks of species-to-species associations at different spatial scales

(2015) Otso Ovaskainen et al.   Methods in Ecology and Evolution

Uncovering hidden spatial structure in species communities with spatially explicit joint species distribution models

(2015) Otso Ovaskainen et al.   Methods in Ecology and Evolution

Valid auto-models for spatially autocorrelated occupancy and abundance data

(2015) David C. Bardos et al.   Methods in Ecology and Evolution

Point process models for presence-only analysis

(2015) Ian W. Renner et al.   Methods in Ecology and Evolution

unmarked: AnRPackage for Fitting Hierarchical Models of Wildlife Occurrence and Abundance

(2015) Ian Fiske et al.   Journal of Statistical Software

Estimating the Effects of Habitat and Biological Interactions in an Avian Community

(2015) Robert M. Dorazio et al.   PLoS One

A demographic, spatially explicit patch occupancy model of metapopulation dynamics and persistence

(2014) C. S. Sutherland et al.   ECOLOGY

Accounting for imperfect detection and survey bias in statistical analysis of presence-only data

(2014) Robert M. Dorazio   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Assessing the utility of statistical adjustments for imperfect detection in tropical conservation science

(2014) Cristina Banks-Leite et al.   JOURNAL OF APPLIED ECOLOGY

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

Ignoring Imperfect Detection in Biological Surveys Is Dangerous: A Response to ‘Fitting and Interpreting Occupancy Models'

(2014) Gurutzeta Guillera-Arroita et al.   PLoS One

Accounting for Imperfect Detection in Ecology: A Quantitative Review

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

Accounting for imperfect detection in Hill numbers for biodiversity studies

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

Studying phenology by flexible modelling of seasonal detectability peaks

(2014) Nicolas Strebel et al.   Methods in Ecology and Evolution

Hide-and-seek in vegetation: time-to-detection is an efficient design for estimating detectability and occurrence

(2014) Christophe N. Bornand 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

Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)

(2014) Laura J. Pollock et al.   Methods in Ecology and Evolution

Bias correction in species distribution models: pooling survey and collection data for multiple species

(2014) William Fithian et al.   Methods in Ecology and Evolution

A Bayesian model of metapopulation viability, with application to an endangered amphibian

(2013) Geoffrey W. Heard et al.   DIVERSITY AND DISTRIBUTIONS

Species distribution modelling and imperfect detection: comparing occupancy versus consensus methods

(2013) Lise Comte et al.   DIVERSITY AND DISTRIBUTIONS

Inference from presence-only data; the ongoing controversy

(2013) Trevor Hastie et al.   ECOGRAPHY

Spatial occupancy models applied to atlas data show Southern Ground Hornbills strongly depend on protected areas

(2013) Kristin M. Broms et al.   ECOLOGICAL APPLICATIONS

On estimating probability of presence from use–availability or presence–background data

(2013) Steven J. Phillips et al.   ECOLOGY

How long should we ignore imperfect detection of species in the marine environment when modelling their distribution?

(2013) Jacquomo Monk   FISH AND FISHERIES

Imperfect detection impacts the performance of species distribution models

(2013) José J. Lahoz-Monfort et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Opportunistic citizen science data of animal species produce reliable estimates of distribution trends if analysed with occupancy models

(2013) Arco J. van Strien et al.   JOURNAL OF APPLIED ECOLOGY

Analysing and mapping species range dynamics using occupancy models

(2013) Marc Kéry et al.   JOURNAL OF BIOGEOGRAPHY

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

(2013) Guoke Chen et al.   JOURNAL OF ECOLOGY

Fitting and Interpreting Occupancy Models

(2013) Alan H. Welsh et al.   PLoS One

Explaining Local-Scale Species Distributions: Relative Contributions of Spatial Autocorrelation and Landscape Heterogeneity for an Avian Assemblage

(2013) Brady J. Mattsson et al.   PLoS One

Determining Occurrence Dynamics when False Positives Occur: Estimating the Range Dynamics of Wolves from Public Survey Data

(2013) David A. W. Miller et al.   PLoS One

Understanding Linkage Rules in Plant-Pollinator Networks by Using Hierarchical Models That Incorporate Pollinator Detectability and Plant Traits

(2013) Ignasi Bartomeus   PLoS One

Model-Based Control of Observer Bias for the Analysis of Presence-Only Data in Ecology

(2013) David I. Warton et al.   PLoS One

Detecting diversity: emerging methods to estimate species diversity

(2013) Kelly J. Iknayan et al.   TRENDS IN ECOLOGY & EVOLUTION

Advances and applications of occupancy models

(2013) Larissa L. Bailey et al.   Methods in Ecology and Evolution

Statistical Ecology

(2013) Ruth King   Annual Review of Statistics and Its Application

Biodiversity of man-made open habitats in an underused country: a class of multispecies abundance models for count data

(2012) Yuichi Yamaura et al.   BIODIVERSITY AND CONSERVATION

Experimental investigation of false positive errors in auditory species occurrence surveys

(2012) David A. W. Miller et al.   ECOLOGICAL APPLICATIONS

Spatial occupancy models for large data sets

(2012) Devin S. Johnson et al.   ECOLOGY

Relaxing the closure assumption in occupancy models: staggered arrival and departure times

(2012) William L. Kendall et al.   ECOLOGY

Cryptic loss of montane avian richness and high community turnover over 100 years

(2012) Morgan W. Tingley et al.   ECOLOGY

Dealing with detection error in site occupancy surveys: what can we do with a single survey?

(2012) S. R. Lele et al.   Journal of Plant Ecology

Designing studies to detect differences in species occupancy: power analysis under imperfect detection

(2012) Gurutzeta Guillera-Arroita et al.   Methods in Ecology and Evolution

Integrating detection probabilities in species distribution models of amphibians breeding in Mediterranean temporary ponds

(2011) Carola Gómez-Rodríguez et al.   DIVERSITY AND DISTRIBUTIONS

The role of functional traits in species distributions revealed through a hierarchical model

(2011) Laura J. Pollock et al.   ECOGRAPHY

Does accounting for imperfect detection improve species distribution models?

(2011) Christopher T. Rota et al.   ECOGRAPHY

A robust-design formulation of the incidence function model of metapopulation dynamics applied to two species of rails

(2011) Benjamin B. Risk et al.   ECOLOGY

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

(2011) David A. Miller et al.   ECOLOGY

Species Occupancy Modeling for Detection Data Collected Along a Transect

(2011) Gurutzeta Guillera-Arroita et al.   JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS

Towards the modelling of true species distributions

(2011) Marc Kéry   JOURNAL OF BIOGEOGRAPHY

Impact of sampling with replacement in occupancy studies with spatial replication

(2011) Gurutzeta Guillera-Arroita   Methods in Ecology and Evolution

Models for species-detection data collected along transects in the presence of abundance-induced heterogeneity and clustering in the detection process

(2011) Gurutzeta Guillera-Arroita et al.   Methods in Ecology and Evolution

An integrated model of habitat and species occurrence dynamics

(2011) Darryl I. MacKenzie et al.   Methods in Ecology and Evolution

Detection biases yield misleading patterns of species persistence and colonization in fragmented landscapes

(2011) Viviana Ruiz-Gutiérrez et al.   Ecosphere

Poisson point process models solve the “pseudo-absence problem” for presence-only data in ecology

(2010) David I. Warton et al.   Annals of Applied Statistics

When have we looked hard enough? A novel method for setting minimum survey effort protocols for flora surveys

(2010) GEORGIA E. GARRARD et al.   AUSTRAL ECOLOGY

Site-Occupancy Distribution Modeling to Correct Population-Trend Estimates Derived from Opportunistic Observations

(2010) MARC KÉRY et al.   CONSERVATION BIOLOGY

A statistical explanation of MaxEnt for ecologists

(2010) Jane Elith et al.   DIVERSITY AND DISTRIBUTIONS

Tigers on trails: occupancy modeling for cluster sampling

(2010) J. E. Hines et al.   ECOLOGICAL APPLICATIONS

Hierarchical modeling of an invasive spread: the Eurasian Collared-Dove Streptopelia decaocto in the United States

(2010) Florent Bled et al.   ECOLOGICAL APPLICATIONS

Modeling species co-occurrence by multivariate logistic regression generates new hypotheses on fungal interactions

(2010) Otso Ovaskainen et al.   ECOLOGY

Models for inference in dynamic metacommunity systems

(2010) Robert M. Dorazio et al.   ECOLOGY

Making more out of sparse data: hierarchical modeling of species communities

(2010) Otso Ovaskainen et al.   ECOLOGY

Hierarchical dynamic modeling of outbreaks of mountain pine beetle using partial differential equations

(2010) Yanbing Zheng et al.   ENVIRONMETRICS

Modelling community dynamics based on species-level abundance models from detection/nondetection data

(2010) Yuichi Yamaura et al.   JOURNAL OF APPLIED ECOLOGY

Experimental Investigation of Observation Error in Anuran Call Surveys

(2010) Brett T. McClintock et al.   JOURNAL OF WILDLIFE MANAGEMENT

Testing the heterospecific attraction hypothesis with time-series data on species co-occurrence

(2010) E. Sebastian-Gonzalez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Design of occupancy studies with imperfect detection

(2010) Gurutzeta Guillera-Arroita et al.   Methods in Ecology and Evolution

Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data

(2009) Steven J. Phillips et al.   ECOLOGICAL APPLICATIONS

Modeling species occurrence dynamics with multiple states and imperfect detection

(2009) Darryl I. MacKenzie et al.   ECOLOGY

Species richness and occupancy estimation in communities subject to temporary emigration

(2009) Marc Kéry et al.   ECOLOGY

Mechanistic niche modelling: combining physiological and spatial data to predict species’ ranges

(2009) Michael Kearney et al.   ECOLOGY LETTERS

Impacts of forest fragmentation on species richness: a hierarchical approach to community modelling

(2009) Elise F. Zipkin et al.   JOURNAL OF APPLIED ECOLOGY

Trend estimation in populations with imperfect detection

(2009) Marc Kéry et al.   JOURNAL OF APPLIED ECOLOGY

Detecting range shifts from historical species occurrences: new perspectives on old data

(2009) Morgan W. Tingley et al.   TRENDS IN ECOLOGY & EVOLUTION

Climate and the range dynamics of species with imperfect detection

(2008) R. Altwegg et al.   Biology Letters

Imperfect detection and its consequences for monitoring for conservation

(2008) M. Kéry et al.   COMMUNITY ECOLOGY

Multi-scale occupancy estimation and modelling using multiple detection methods

(2008) James D. Nichols et al.   JOURNAL OF APPLIED ECOLOGY