ESTIMATING SITE OCCUPANCY, COLONIZATION, AND LOCAL EXTINCTION WHEN A SPECIES IS DETECTED IMPERFECTLY

@article{MacKenzie2003ESTIMATINGSO,
  title={ESTIMATING SITE OCCUPANCY, COLONIZATION, AND LOCAL EXTINCTION WHEN A SPECIES IS DETECTED IMPERFECTLY},
  author={Darryl I MacKenzie and James D. Nichols and James E Hines and Melinda G. Knutson and Alan B. Franklin},
  journal={Ecology},
  year={2003},
  volume={84},
  pages={2200-2207}
}
Few species are likely to be so evident that they will always be detected when present. Failing to allow for the possibility that a target species was present, but undetected, at a site will lead to biased estimates of site occupancy, colonization, and local extinction probabilities. These population vital rates are often of interest in long-term monitoring programs and metapopulation studies. We present a model that enables direct estimation of these parameters when the probability of… 

Tables from this paper

Comparing estimates of population change from occupancy and mark–recapture models for a territorial species

Monitoring studies often use marked animals to estimate population abundance at small spatial scales. However, at smaller scales, occupancy sampling, which uses detection/nondetection data, may be

Estimating species' absence, colonization and local extinction in patchy landscapes: an application of occupancy models with rodents

The distribution of two rodents Myodes glareolus and Mus musculus domesticus in a fragmented landscape in central Italy is analysed pointing out how it is possible to identify true absences, non-detections, extinctions/colonizations and determine seasonal values of detection probability.

Population Abundance Estimation Using Repeated Presence-Absence Observations : With or Without the Robust Design

  • Environmental Science
  • 2011
When animal monitoring efforts are concerned with estimating the total abundance of a species that is imperfectly detected, they typically collect at minimum point counts of the number of individuals

Climate and the range dynamics of species with imperfect detection

Recently developed occupancy models are drawn attention to, which can be used to examine colonization and local extinction or changes in occupancy over time, and the recent range expansion of hadeda ibises in South African protected areas is examined.

Small sample bias in dynamic occupancy models

Occupancy models may be used to estimate the probability that a randomly selected site in an area of interest is occupied by a species (c), given imperfect detection (p). This method can be extended,

Occupancy as a surrogate for abundance estimation

Some recent modelling developments that permit unbiased estimation of the proportion of area occupied, colonization and local extinction probabilities are reviewed and it is described how these models could be extended to incorporate information from marked individuals, which would enable finer questions of population dynamics to be addressed.

How biased are estimates of extinction probability in revisitation studies?

1 Extinction is a fundamental topic for population ecology and especially for conservation and metapopulation biology. Most empirical studies on extinction resurvey historically occupied sites and

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

It is shown that models that account for possible misidentification have greater support and can yield substantially different occupancy estimates than those that do not and can be used to improve estimates of occupancy for study designs where a subset of detections is of a type or method for which false positives can be assumed to not occur.

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

This model relaxes the closure assumption within a season by permitting staggered entry and exit times for the species of interest at each site, and permits comparison of phenology across sites, species, or years, by modeling variation in arrival or departure probabilities.

Cryptic wide‐ranging movements lead to upwardly biased occupancy in a territorial species

1. Occupancy modelling is useful for inferring population status and dynamics when occupancy reflects the presence of established individuals or populations, such as residents detected at breeding
...

Estimating rates of local extinction and colonization in colonial species and an extension to the metapopulation and community levels

Coloniality has mainly been studied from an evolutionary perspective, but relatively few studies have developed methods for modelling colony dynamics. Changes in number of colonies over time provide

ESTIMATING SITE OCCUPANCY RATES WHEN DETECTION PROBABILITIES ARE LESS THAN ONE

Nondetection of a species at a site does not imply that the species is absent unless the probability of detection is 1. We propose a model and likelihood-based method for estimating site occupancy

PATCH OCCUPANCY MODELS OF METAPOPULATION DYNAMICS: EFFICIENT PARAMETER ESTIMATION USING IMPLICIT STATISTICAL INFERENCE

The proposed method is based on Monte Carlo inference for implicit statistical models, and it can be adapted to any stochastic patch occupancy model of metapopulation dynamics, and allows the estimation of the amplitude of regional Stochasticity.

Pattern Does Not Equal Process: What Does Patch Occupancy Really Tell Us about Metapopulation Dynamics?

Simulations of effects of spatially correlated extinctions on patterns of patch occupancy among pikas at Bodie, California, using randomly located extinction disks to represent the likely effects of predation produced similar patterns to those cited as evidence of balanced metapopulation dynamics.

A Capture-Recapture Design Robust to Unequal Probability of Capture

A design for long-term studies that is robust to heterogeneity and/or trap response of the capture probabilities is described and an example is given in detail to illustrate the methodology for biologists.

INFERRING PROCESS FROM PATTERN: CAN TERRITORY OCCUPANCY PROVIDE INFORMATION ABOUT LIFE HISTORY PARAMETERS?

A significant problem in wildlife management is identifying "good" habitat for species within the short time frames demanded by policy makers. Statistical models of the response of species

Implications of empirical data quality to metapopulation model parameter estimation and application

It was found that mis-estimated areas influence the scaling of extinction risk with patch area; extinction probabilities for large patches become overestimated; and biases induced into metapopulation model parameter estimates by these three types of errors are investigated.

Extinction and Colonization Processes: Parameter Estimates from Sporadic Surveys

We discuss a simple method, based on maximum likelihood, to estimate the rates of extinction and recolonization of a species, for example, on an island. Our method applies to both regular and

ESTIMATING TEMPORARY EMIGRATION USING CAPTURE-RECAPTURE DATA WITH POLLOCK'S ROBUST DESIGN

A likelihood- based approach to dealing with temporary emigration is presented that permits estimation under different models of temporary em migration and yields tests for completely random and Markovian emigration.

Modeling Survival and Testing Biological Hypotheses Using Marked Animals: A Unified Approach with Case Studies

This paper synthesizes, using a common framework, recent developments of capture-recapture models oriented to estimation of survival rates together with new ones, with an emphasis on flexibility in modeling, model selection, and the analysis of multiple data sets.