共查询到20条相似文献，搜索用时 15 毫秒
1.
José J. Lahoz‐Monfort Gurutzeta Guillera‐Arroita Reid Tingley 《Molecular ecology resources》2016,16(3):673-685
Environmental DNA (eDNA) sampling is prone to both false‐positive and false‐negative errors. We review statistical methods to account for such errors in the analysis of eDNA data and use simulations to compare the performance of different modelling approaches. Our simulations illustrate that even low false‐positive rates can produce biased estimates of occupancy and detectability. We further show that removing or classifying single PCR detections in an ad hoc manner under the suspicion that such records represent false positives, as sometimes advocated in the eDNA literature, also results in biased estimation of occupancy, detectability and false‐positive rates. We advocate alternative approaches to account for false‐positive errors that rely on prior information, or the collection of ancillary detection data at a subset of sites using a sampling method that is not prone to false‐positive errors. We illustrate the advantages of these approaches over ad hoc classifications of detections and provide practical advice and code for fitting these models in maximum likelihood and Bayesian frameworks. Given the severe bias induced by false‐negative and false‐positive errors, the methods presented here should be more routinely adopted in eDNA studies. 相似文献
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Multispecies occupancy models can estimate species richness from spatially replicated multispecies detection/non‐detection survey data, while accounting for imperfect detection. A model extension using data augmentation allows inferring the total number of species in the community, including those completely missed by sampling (i.e., not detected in any survey, at any site). Here we investigate the robustness of these estimates. We review key model assumptions and test performance via simulations, under a range of scenarios of species characteristics and sampling regimes, exploring sensitivity to the Bayesian priors used for model fitting. We run tests when assumptions are perfectly met and when violated. We apply the model to a real dataset and contrast estimates obtained with and without predictors, and for different subsets of data. We find that, even with model assumptions perfectly met, estimation of the total number of species can be poor in scenarios where many species are missed (>15%–20%) and that commonly used priors can accentuate overestimation. Our tests show that estimation can often be robust to violations of assumptions about the statistical distributions describing variation of occupancy and detectability among species, but lower‐tail deviations can result in large biases. We obtain substantially different estimates from alternative analyses of our real dataset, with results suggesting that missing relevant predictors in the model can result in richness underestimation. In summary, estimates of total richness are sensitive to model structure and often uncertain. Appropriate selection of priors, testing of assumptions, and model refinement are all important to enhance estimator performance. Yet, these do not guarantee accurate estimation, particularly when many species remain undetected. While statistical models can provide useful insights, expectations about accuracy in this challenging prediction task should be realistic. Where knowledge about species numbers is considered truly critical for management or policy, survey effort should ideally be such that the chances of missing species altogether are low. 相似文献
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Assessments of spatial patterns of biodiversity change are essential to detect a signature of anthropogenic impacts, inform monitoring and conservation programs, and evaluate implications of biodiversity loss to humans. While taxonomic diversity (TD) is the most commonly assessed attribute of biodiversity, it misses the potential functional or phylogenetic implications of species losses or gains for ecosystems. Functional diversity (FD) and phylogenetic diversity (PD) are able to capture these important trait‐based and phylogenetic attributes of species, but their changes have to date only been evaluated over limited spatial and temporal extents. Employing a novel framework for addressing detectability, we here comprehensively assess a near half‐century of changes in local TD, FD, and PD of breeding birds across much of North America to examine levels of congruency in changes among these biodiversity facets and their variation across spatial and environmental gradients. Time‐series analysis showed significant and continuous increases in all three biodiversity attributes until ca. 2000, followed by a slow decline since. Comparison of avian diversity at the beginning and end of the temporal series revealed net increase in TD, FD, and PD, but changes in TD were larger than those in FD and PD, suggesting increasing biotic homogenization of avian assemblages throughout the United States. Changes were greatest at high elevations and latitudes – consistent with purported effects of ongoing climate change on biodiversity. Our findings highlight the potential of combining new types of data with novel statistical models to enable a more integrative monitoring and assessment of the multiple facets of biodiversity. 相似文献
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Joseph C. Gardiner Marianne Huebner James Jetton Cathy J. Bradley 《Biometrical journal. Biometrische Zeitschrift》2001,43(3):283-296
When comparing two competing interventions, confidence intervals for cost‐effectiveness ratios (CERs) provide information on the uncertainty in their point estimates. Techniques for constructing these confidence intervals are much debated. We provide a formal comparison of the Fieller, symmetric and Bonferroni methods for constructing confidence intervals for the CER using only the joint asymptotic distribution of the incremental cost and incremental effectiveness of the two interventions being compared. We prove the existence of a finite interval under the Fieller method when the incremental effectiveness is statistically significant. When this difference is not significant the Fieller method yields an unbounded confidence interval. The Fieller interval is always wider than the symmetric interval, but the latter is an approximation to the Fieller interval when the incremental effectiveness is highly significant. The Bonferroni method is shown to produce the widest interval. Because it accounts for the likely correlation between cost and effectiveness measures, and the intuitively appealing relationship between the existence of a bounded interval and the significance of the incremental effectiveness, the Fieller interval is to be preferred in reporting a confidence interval for the CER. 相似文献
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Kayla L. Davis Emily D. Silverman Allison L. Sussman R. Randy Wilson Elise F. Zipkin 《Ecology and evolution》2022,12(3)
Accurate estimates of animal abundance are essential for guiding effective management, and poor survey data can produce misleading inferences. Aerial surveys are an efficient survey platform, capable of collecting wildlife data across large spatial extents in short timeframes. However, these surveys can yield unreliable data if not carefully executed. Despite a long history of aerial survey use in ecological research, problems common to aerial surveys have not yet been adequately resolved. Through an extensive review of the aerial survey literature over the last 50 years, we evaluated how common problems encountered in the data (including nondetection, counting error, and species misidentification) can manifest, the potential difficulties conferred, and the history of how these challenges have been addressed. Additionally, we used a double‐observer case study focused on waterbird data collected via aerial surveys and an online group (flock) counting quiz to explore the potential extent of each challenge and possible resolutions. We found that nearly three quarters of the aerial survey methodology literature focused on accounting for nondetection errors, while issues of counting error and misidentification were less commonly addressed. Through our case study, we demonstrated how these challenges can prove problematic by detailing the extent and magnitude of potential errors. Using our online quiz, we showed that aerial observers typically undercount group size and that the magnitude of counting errors increases with group size. Our results illustrate how each issue can act to bias inferences, highlighting the importance of considering individual methods for mitigating potential problems separately during survey design and analysis. We synthesized the information gained from our analyses to evaluate strategies for overcoming the challenges of using aerial survey data to estimate wildlife abundance, such as digital data collection methods, pooling species records by family, and ordinal modeling using binned data. Recognizing conditions that can lead to data collection errors and having reasonable solutions for addressing errors can allow researchers to allocate resources effectively to mitigate the most significant challenges for obtaining reliable aerial survey data. 相似文献
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David S. L. Ramsey David M. Forsyth Mike Perry Pete Thomas Meredith McKay Elaine F. Wright 《The Journal of wildlife management》2022,86(6):e22252
Estimating the abundance and density of mountain ungulates is difficult because of rugged and remote terrain, high elevations, and rapidly changing weather. Helicopter surveys could overcome these problems, but researchers have seldom applied helicopter-based survey methods at large spatial scales in mountain terrain. We used helicopters to count introduced Himalayan tahr (Hemitragus jemlahicus) at 117 plots, each of 4 km2, in New Zealand's Southern Alps during 2016–2019. The sampling frame was 7,844 km2 and we located the plots at the vertices of an 8-km grid superimposed over the sampling frame (i.e., a systematic random sampling design). We conducted 3 repeat counts at each plot during summer–autumn. We used the repeat counts to estimate tahr abundance and density, corrected for imperfect detection, using a dynamic N-mixture model for open populations. We estimated the population of tahr in the sampling frame using design-based, finite sampling methods and model-based inference procedures. The mean estimated density of tahr on each plot varied from zero to 31.7 tahr/km2. The mean densities of tahr varied among management units, ranging from 0.3 to 10.7 tahr/km2, and exceeded specified intervention densities in 6 of the 7 management units. The total design-based estimate of tahr abundance in the sampling frame was 34,500 (95% CI = 27,750–42,900), with a coefficient of variation (CV) of 0.11. The corresponding model-based estimate of total abundance was similar (34,550, 95% CI = 30,250–38,700) but was substantially more precise (CV = 0.06) than the design-based estimate. The precision of the estimates for the individual management units was also better than that of the design-based estimates, with CVs of <0.20 for all but 1 management unit. Our study provides a repeatable method for sampling mountain ungulates. More generally, robust estimation of abundance and density of mountain ungulates is possible by combining aerial surveys and open population models with an objective, probabilistic sampling design. 相似文献
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Aims To determine the detectability of a global weedy perennial weed Hypochaeris radicata and its relationship with five common observer, species and environmental variables.Methods Trained independent observers conducted time-limited repeat surveys of H. radicata during autumn in an endangered grassy box-gum woodland ecosystem in south-east Australia. Single-species single-season site-occupancy modelling was used to determine if detectability of H. radicata was altered by five covariates, observer, litter height, grazing, maximum plant height and flowering state.Important findings Detectability for H. radicata varied significantly with observer, litter height, plant maximum height and flowering state, but not with grazing. Despite significant observer-specific variation, there was a consistent increase in detectability with plant height and when plants are in flower for all observers. Detectability generally decreased as litter height increases. Perfect or constant detection rates cannot be assumed in plant surveys, even for easily recognizable plants in simple survey conditions. Understanding how detectability is influenced by common survey variables can help improve the efficacy of plant monitoring programs by quantifying the extent of uncertainty in inferences made from survey data, or by determining optimal survey conditions to increase the reliability of collected data. For plants with traits similar to H. radicata, surveying when most plants are at maximum height or in flower, increasing search intensity when litter levels are high and minimizing observer-related heterogeneity are potentially simple and effective ways to reduce detection errors. We speculate that detection rates may be lower, more variable and involve additional covariates when surveying during the peak flowering spring season with the presence of more warm season and taller annual species. 相似文献
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GEORGIA E. GARRARD SARAH A. BEKESSY MICHAEL A. McCARTHY BRENDAN A. WINTLE 《Austral ecology》2008,33(8):986-998
There is now a substantial body of literature documenting the detectability of plants and animals under standard survey conditions. Despite the evidence that many flora and fauna species have detection probabilities of less than one, it is still the default assumption of most environmental impact assessment processes that if a species is present, it will be detected. Here we briefly review a number of existing studies that have estimated the survey effort necessary to detect animal species, based on what is known about their detection rates in standard surveys. We then propose a novel method, based on failure‐time analysis, for quantifying the detectability of and determining appropriate survey effort for plant species during flora surveys. We provide computer code for implementing the method in the Bayesian freeware WinBUGS. Methods for estimating detectability can be used to inform minimum survey requirements and have important applications in environmental impact assessment and monitoring. 相似文献
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Renée Hartley Wade Blanchard Nick Clemann Mel Schroder Martin Schulz David B. Lindenmayer Ben C. Scheele 《Austral ecology》2023,48(8):1921-1940
Wildfire and grazing by invasive herbivores can influence habitat suitability for ground-dwelling fauna, such as reptiles. Australia has a large and diverse reptile fauna, with the Australian Alps bioregion in the southeast of the continent supporting a disproportionately high number of threatened species. In this bioregion, many species are threatened by fire, habitat loss or modification, and invasive species. The range of one such threatened endemic lizard, Cyclodomorphus praealtus (family Scincidae), was impacted by the 2019–20 megafires and is also subject to widespread grazing by invasive species. We investigated the relationship between C. praealtus site occupancy and fire and grazing. We completed 2045 surveys across 120 sites over 4 years, detecting the species at 43% of sites and increasing the species' known geographic range. Using single season detection occupancy models, we found C. praealtus occupancy was not associated with elevation, vegetation height or whether the site was burnt, but was positively associated with grazing activity. Our results indicate that C. praealtus has the capacity to persist following a single fire in some cases, and that habitats with high occupancy probabilities are subject to high grazing pressure. However, our results do not rule out more nuanced impacts associated with these disturbances, which affect a large proportion of C. praealtus' habitat. Our cumulative detection probability calculations revealed that considerable survey effort is often required to determine C. praealtus site occupancy. We therefore recommend that impact assessments assume species presence within areas of suitable habitat within the species' range. Our study improves our understanding of disturbance impacts on C. praealtus' occupancy, while demonstrating the need for sufficiently resourced impact assessments for cryptic and threatened species. 相似文献
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Kathryn A. Williams Peter C. Frederick Paul S. Kubilis John C. Simon 《Journal of Field Ornithology》2008,79(4):438-447
ABSTRACT Estimating detection error, as well as the magnitude of other potential survey biases, is essential when sampling efforts play a role in the estimation of population size and management of wildlife populations. We quantified visual biases in aerial surveys of nesting wading birds (Ciconiiformes) in colonies in the Florida Everglades using a negative binomial count regression model to compare numbers of nests in quadrats counted on the ground with numbers estimated from aerial photographs of the same quadrats. The model also allowed the determination of degree of difference between monitoring results based upon such factors as nest density, vegetative cover, and nest turnover rates. Aerial surveys of White Ibis (Eudocimus albus) colonies underestimated the true number of nests found during ground counts by 11.1%, and underestimates were significantly greater (P= 0.047) in a colony with high nest turnover. Error rates did not differ for quadrats that varied in the density of White Ibis nests did not differ, and visual bias did not increase with vegetative complexity (P= 0.73). Estimates of nest density in colonies of Great Egrets (Ardea alba) based on aerial surveys were higher than ground counts for 38% of the quadrats sampled, and mean visual bias was 23.1%. Species misidentification likely contributed to visibility bias for Great Egrets in our study, with some Snowy Egrets almost certainly mistaken for Great Egrets in aerial photos. Biases of the magnitude we observed fro Great Egrets and White Ibises can mask true population trends in long‐term monitoring and, therefore, we recommend that detection probability be explicitly evaluated when conducting aerial surveys of nesting birds. 相似文献
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Gerd Rippin 《Biometrical journal. Biometrische Zeitschrift》2000,42(7):887-894
When a case‐control study is planned to include an internal validation study, the sample size of the study and the proportion of validated observations has to be calculated. There are a variety of alternative methods to accomplish this. In this article some possible procedures will be compared in order to clarify whether considerable differences in the suggested optimal designs occur, dependent on the used method. 相似文献
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Species abundance and community composition are affected not only by the local environment, but also by broader landscape and regional context. Yet, determining the spatial scales at which landscapes affect species remains a persistent challenge, hindering our ability to understand how environmental gradients shape communities. This problem is amplified by rare species and imperfect species detection. Here, we present a Bayesian framework that allows uncertainty surrounding the ‘true’ spatial scale of species’ responses (i.e. changes in presence/absence) to be integrated directly into a community hierarchical model. This scale‐selecting multispecies occupancy model (ssMSOM) estimates the scale of response, and shows high accuracy and correct levels of uncertainty in parameter estimates across a broad range of simulation conditions. An ssMSOM can be run in a matter of minutes, as opposed to the many hours required to run normal multispecies occupancy models at all queried spatial scales, and then conduct model selection – a problem that up to now has prohibited scale of response from being rigorously evaluated in an occupancy framework. Alternatives to the ssMSOM, such as GLM‐based approaches frequently fail to detect the correct spatial scale and magnitude of response, and are often falsely confident by favoring the incorrect parameter estimates, especially as species’ detection probabilities deviate from perfect. We further show how trait information can be leveraged to understand how individual species’ scales of response vary within communities. Integrating spatial scale selection directly into hierarchical community models provides a means of formally testing hypotheses regarding spatial scales of response, and more accurately determining the environmental drivers that shape communities. 相似文献
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Mário Ferreira Ana Filipa Filipe David C. Bardos Maria Filomena Magalhães Pedro Beja 《Ecology and evolution》2016,6(15):5530-5541
Controlling for imperfect detection is important for developing species distribution models (SDMs). Occupancy‐detection models based on the time needed to detect a species can be used to address this problem, but this is hindered when times to detection are not known precisely. Here, we extend the time‐to‐detection model to deal with detections recorded in time intervals and illustrate the method using a case study on stream fish distribution modeling. We collected electrofishing samples of six fish species across a Mediterranean watershed in Northeast Portugal. Based on a Bayesian hierarchical framework, we modeled the probability of water presence in stream channels, and the probability of species occupancy conditional on water presence, in relation to environmental and spatial variables. We also modeled time‐to‐first detection conditional on occupancy in relation to local factors, using modified interval‐censored exponential survival models. Posterior distributions of occupancy probabilities derived from the models were used to produce species distribution maps. Simulations indicated that the modified time‐to‐detection model provided unbiased parameter estimates despite interval‐censoring. There was a tendency for spatial variation in detection rates to be primarily influenced by depth and, to a lesser extent, stream width. Species occupancies were consistently affected by stream order, elevation, and annual precipitation. Bayesian P‐values and AUCs indicated that all models had adequate fit and high discrimination ability, respectively. Mapping of predicted occupancy probabilities showed widespread distribution by most species, but uncertainty was generally higher in tributaries and upper reaches. The interval‐censored time‐to‐detection model provides a practical solution to model occupancy‐detection when detections are recorded in time intervals. This modeling framework is useful for developing SDMs while controlling for variation in detection rates, as it uses simple data that can be readily collected by field ecologists. 相似文献
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DOUGLAS H. JOHNSON 《The Journal of wildlife management》2008,72(4):857-868
Abstract: Indices to population size have come under increasing criticism in recent years, on the grounds that indices might not faithfully represent the entire population. Most criticisms involve surveys of birds, particularly those based on point counts, which is my focus here. A variety of quantitative methods have been developed to reduce the bias of point counts, such as distance sampling, multiple-observer surveys, and time-of-detection methods. I argue that these developments are valuable, in that they enhance understanding of the detection process, but that their practical application may well be limited, likely to intensive studies focusing on a small number of species. These quantitative methods are not generally applicable to extensive, multiple-species surveys. Although criticism of the thoughtless use of indices is welcome, their wholesale rejection is not. 相似文献
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Bradley Law Gabriele Caccamo Paul Roe Anthony Truskinger Traecey Brassil Leroy Gonsalves Anna McConville Matthew Stanton 《Ecology and evolution》2017,7(18):7475-7489
Species distribution models have great potential to efficiently guide management for threatened species, especially for those that are rare or cryptic. We used MaxEnt to develop a regional‐scale model for the koala Phascolarctos cinereus at a resolution (250 m) that could be used to guide management. To ensure the model was fit for purpose, we placed emphasis on validating the model using independently‐collected field data. We reduced substantial spatial clustering of records in coastal urban areas using a 2‐km spatial filter and by modeling separately two subregions separated by the 500‐m elevational contour. A bias file was prepared that accounted for variable survey effort. Frequency of wildfire, soil type, floristics and elevation had the highest relative contribution to the model, while a number of other variables made minor contributions. The model was effective in discriminating different habitat suitability classes when compared with koala records not used in modeling. We validated the MaxEnt model at 65 ground‐truth sites using independent data on koala occupancy (acoustic sampling) and habitat quality (browse tree availability). Koala bellows (n = 276) were analyzed in an occupancy modeling framework, while site habitat quality was indexed based on browse trees. Field validation demonstrated a linear increase in koala occupancy with higher modeled habitat suitability at ground‐truth sites. Similarly, a site habitat quality index at ground‐truth sites was correlated positively with modeled habitat suitability. The MaxEnt model provided a better fit to estimated koala occupancy than the site‐based habitat quality index, probably because many variables were considered simultaneously by the model rather than just browse species. The positive relationship of the model with both site occupancy and habitat quality indicates that the model is fit for application at relevant management scales. Field‐validated models of similar resolution would assist in guiding management of conservation‐dependent species. 相似文献
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Targeted lek surveys, in which historically active lekking areas are surveyed over multiple years, are commonly used to monitor lek‐mating birds. Lek surveys are usually used in habitats and species in which individuals are not easily detected when they are not lekking. Unfortunately, lek surveys suffer from a number of shortcomings, most notably the failure to observe lekking individuals when they are near but not actively attending a lek. Like other sources of imperfect detection, inconsistency in lek attendance may bias estimates of annual population sizes or the proportion of lekking arenas active in a given year. In turn, this may result in unreliable estimates of trends, distributions or other parameters of interest. An improved understanding of the factors affecting lek attendance is crucial to improving the efficacy of many lek monitoring programmes and the utility of lek surveys in estimating population and distributional dynamics. We assess variation in lek attendance in the Lesser Prairie Chicken Tympanuchus pallidicinctus using a subset of data from a long‐term monitoring programme in eastern New Mexico, USA. Focusing on lek‐years in which at least one male was observed, we used generalized linear models to assess the influence of lek size and survey and environmental characteristics on the probability that at least one male was observed in attendance. Our best‐supported model provided evidence for influences of each of these sources of variation. Models suggested that surveyors may improve the likelihood of detecting lek attendance by making small changes to survey duration, targeted survey dates and by considering environmental factors such as weather, habitat and human disturbance. In addition to improving detection, consideration of lek attendance patterns and associated behaviours may improve estimation for more effective conservation in a variety of lekking bird species. 相似文献