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Occupancy modeling species-environment relationships with non-ignorable survey designs.

ABSTRACT: Statistical models supporting inferences about species occurrence patterns in relation to environmental gradients are fundamental to ecology and conservation biology. A common implicit assumption is that the sampling design is ignorable and does not need to be formally accounted for in analyses. The analyst assumes data are representative of the desired population and statistical modeling proceeds. However, if data sets from probability and non-probability surveys are combined or unequal selection probabilities are used, the design may be non-ignorable. We outline the use of pseudo-maximum likelihood estimation for site-occupancy models to account for such non-ignorable survey designs. This estimation method accounts for the survey design by properly weighting the pseudo-likelihood equation. In our empirical example, legacy and newer randomly selected locations were surveyed for bats to bridge a historic statewide effort with an ongoing nationwide program. We provide a worked example using bat acoustic detection/non-detection data and show how analysts can diagnose whether their design is ignorable. Using simulations we assessed whether our approach is viable for modeling data sets composed of sites contributed outside of a probability design. Pseudo-maximum likelihood estimates differed from the usual maximum likelihood occupancy estimates for some bat species. Using simulations we show the maximum likelihood estimator of species-environment relationships with non-ignorable sampling designs was biased, whereas the pseudo-likelihood estimator was design unbiased. However, in our simulation study the designs composed of a large proportion of legacy or non-probability sites resulted in estimation issues for standard errors. These issues were likely a result of highly variable weights confounded by small sample sizes (5% or 10% sampling intensity and four revisits). Aggregating data sets from multiple sources logically supports larger sample sizes and potentially increases spatial extents for statistical inferences. Our results suggest that ignoring the mechanism for how locations were selected for data collection (e.g., the sampling design) could result in erroneous model-based conclusions. Therefore, in order to ensure robust and defensible recommendations for evidence-based conservation decision-making, the survey design information in addition to the data themselves must be available for analysts. Details for constructing the weights used in estimation and code for implementation are provided.

SUBMITTER: Irvine KM

PROVIDER: S-EPMC6457115 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Occupancy modeling species-environment relationships with non-ignorable survey designs.

Irvine Kathryn M KM Rodhouse Thomas J TJ Wright Wilson J WJ Olsen Anthony R AR

Ecological applications : a publication of the Ecological Society of America 20180719 6

Statistical models supporting inferences about species occurrence patterns in relation to environmental gradients are fundamental to ecology and conservation biology. A common implicit assumption is that the sampling design is ignorable and does not need to be formally accounted for in analyses. The analyst assumes data are representative of the desired population and statistical modeling proceeds. However, if data sets from probability and non-probability surveys are combined or unequal selecti ...[more]

PMID: 29802750

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Project description:Motion-activated cameras are a versatile tool that wildlife biologists can use for sampling wild animal populations to estimate species occurrence. Occupancy modelling provides a flexible framework for the analysis of these data; explicitly recognizing that given a species occupies an area the probability of detecting it is often less than one. Despite the number of studies using camera data in an occupancy framework, there is only limited guidance from the scientific literature about survey design trade-offs when using motion-activated cameras. A fuller understanding of these trade-offs will allow researchers to maximise available resources and determine whether the objectives of a monitoring program or research study are achievable. We use an empirical dataset collected from 40 cameras deployed across 160 km(2) of the Western Slope of Colorado, USA to explore how survey effort (number of cameras deployed and the length of sampling period) affects the accuracy and precision (i.e., error) of the occupancy estimate for ten mammal and three virtual species. We do this using a simulation approach where species occupancy and detection parameters were informed by empirical data from motion-activated cameras. A total of 54 survey designs were considered by varying combinations of sites (10-120 cameras) and occasions (20-120 survey days). Our findings demonstrate that increasing total sampling effort generally decreases error associated with the occupancy estimate, but changing the number of sites or sampling duration can have very different results, depending on whether a species is spatially common or rare (occupancy = ψ) and easy or hard to detect when available (detection probability = p). For rare species with a low probability of detection (i.e., raccoon and spotted skunk) the required survey effort includes maximizing the number of sites and the number of survey days, often to a level that may be logistically unrealistic for many studies. For common species with low detection (i.e., bobcat and coyote) the most efficient sampling approach was to increase the number of occasions (survey days). However, for common species that are moderately detectable (i.e., cottontail rabbit and mule deer), occupancy could reliably be estimated with comparatively low numbers of cameras over a short sampling period. We provide general guidelines for reliably estimating occupancy across a range of terrestrial species (rare to common: ψ = 0.175-0.970, and low to moderate detectability: p = 0.003-0.200) using motion-activated cameras. Wildlife researchers/managers with limited knowledge of the relative abundance and likelihood of detection of a particular species can apply these guidelines regardless of location. We emphasize the importance of prior biological knowledge, defined objectives and detailed planning (e.g., simulating different study-design scenarios) for designing effective monitoring programs and research studies.

Project description:The use of camera traps as a tool for studying wildlife populations is commonplace. However, few have considered how the number of detections of wildlife differ depending upon the number of camera traps placed at cameras-sites, and how this impacts estimates of occupancy and community composition. During December 2015-February 2016, we deployed four camera traps per camera-site, separated into treatment groups of one, two, and four camera traps, in southern Illinois to compare whether estimates of wildlife community metrics and occupancy probabilities differed among survey methods. The overall number of species detected per camera-site was greatest with the four-camera survey method (P<0.0184). The four-camera survey method detected 1.25 additional species per camera-site than the one-camera survey method, and was the only survey method to completely detect the ground-dwelling silvicolous community. The four-camera survey method recorded individual species at 3.57 additional camera-sites (P = 0.003) and nearly doubled the number of camera-sites where white-tailed deer (Odocoileus virginianus) were detected compared to one- and two-camera survey methods. We also compared occupancy rates estimated by survey methods; as the number of cameras deployed per camera-site increased, occupancy estimates were closer to naïve estimates, detection probabilities increased, and standard errors of detection probabilities decreased. Additionally, each survey method resulted in differing top-ranked, species-specific occupancy models when habitat covariates were included. Underestimates of occurrence and misrepresented community metrics can have significant impacts on species of conservation concern, particularly in areas where habitat manipulation is likely. Having multiple camera traps per site revealed significant shortcomings with the common one-camera trap survey method. While we realize survey design is often constrained logistically, we suggest increasing effort to at least two camera traps facing opposite directions per camera-site in habitat association studies, and to utilize camera-trap arrays when restricted by equipment availability.

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Project description:Occupancy surveys should be designed to minimise false absences. This is commonly achieved by increasing replication or increasing the efficiency of surveys. In the case of destructive sampling designs, in which searches of individual microhabitats represent the repeat surveys, minimising false absences leads to an inherent trade-off. Surveyors can sample more low quality microhabitats, bearing the resultant financial costs and producing wider-spread impacts, or they can target high quality microhabitats were the focal species is more likely to be found and risk more severe impacts on local habitat quality. We show how this trade-off can be solved with a decision-theoretic approach, using the Millewa Skink Hemiergis millewae from southern Australia as a case study. Hemiergis millewae is an endangered reptile that is best detected using destructive sampling of grass hummocks. Within sites that were known to be occupied by H. millewae, logistic regression modelling revealed that lizards were more frequently detected in large hummocks. If this model is an accurate representation of the detection process, searching large hummocks is more efficient and requires less replication, but this strategy also entails destruction of the best microhabitats for the species. We developed an optimisation tool to calculate the minimum combination of the number and size of hummocks to search to achieve a given cumulative probability of detecting the species at a site, incorporating weights to reflect the sensitivity of the results to a surveyor's priorities. The optimisation showed that placing high weight on minimising volume necessitates impractical replication, whereas placing high weight on minimising replication requires searching very large hummocks which are less common and may be vital for H. millewae. While destructive sampling methods are sometimes necessary, surveyors must be conscious of the ecological impacts of these methods. This study provides a simple tool for identifying sampling strategies that minimise those impacts.

Dataset Information

Occupancy modeling species-environment relationships with non-ignorable survey designs.

Publications

Occupancy modeling species-environment relationships with non-ignorable survey designs.

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