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Occupancy models (Ecology, 2002; 83: 2248) were developed to infer the probability that a species under investigation occupies a site. Bayesian analysis of these models can be undertaken using statistical packages such as WinBUGS, OpenBUGS, JAGS, and more recently Stan, however, since these packages were not developed specifically to fit occupancy models, one often experiences long run times when undertaking an analysis. Bayesian spatial single‐season occupancy models can also be fit using the R package stocc. The approach assumes that the detection and occupancy regression effects are modeled using probit link functions. The use of the logistic link function, however, is algebraically more tractable and allows one to easily interpret the coefficient effects of an estimated model by using odds ratios, which is not easily done for a probit link function for models that do not include spatial random effects. We develop a Gibbs sampler to obtain posterior samples from the posterior distribution of the parameters of various occupancy models (nonspatial and spatial) when logit link functions are used to model the regression effects of the detection and occupancy processes. We apply our methods to data extracted from the 2nd Southern African Bird Atlas Project to produce a species distribution map of the Cape weaver (Ploceus capensis) and helmeted guineafowl (Numida meleagris) for South Africa. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using JAGS and Stan and that in certain cases the posterior chains mix much faster than those obtained when using JAGS, stocc, and Stan. Our algorithms are implemented in the R package, Rcppocc. The software is freely available and stored on GitHub ( https://github.com/AllanClark/Rcppocc ).  相似文献   

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Autonomously triggered cameras are a common wildlife survey technique. The use of attractants and surrounding microhabitats is likely to influence detection probabilities and survey outcomes; however, few studies consider these factors. We compared three attractants (peanut butter‐based, tuna‐based and a control) in a Latin square design through a coastal shrubland with high microhabitat variability at Cape Otway, Victoria, Australia (38º50?S, 143º30?E). Deployments involved 36 cameras for four days in each of five years. The percentage cover of each vegetation structural type (low [no or sparse cover], moderate [grass] or high [shrubs]) within 20 m of each camera was calculated and reduced to a single variable using PCA. Dynamic occupancy modelling, with lure type and vegetation structure as covariates of detection probability, found that peanut butter attracted the greatest diversity of species (24 of 35 species, 69%) and yielded the greatest number of detections (50% of 319) when compared with tuna oil (66% and 24%, respectively) and the control (43% and 26%, respectively). Peanut butter attracted more Macropodidae (wallabies) and Muridae (rats and mice); however, vegetation structural variables were the greatest influence on Corvidae/Artamidae (raven/currawong) detections with higher detectability in more open areas. Vegetation structure also influenced Muridae detections. This study reinforces the critical choice of appropriate attractants and camera placement when investigating vertebrate groups and highlights the role of microhabitat in the detection of small mammals and birds. We suggest future large‐scale camera surveys consider different bait types and microhabitats in their designs, to control for any biases and enable future advice on ‘optimal’ methods.  相似文献   

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  1. Predictive models of species distribution are useful tools to identify habitats of imperilled species for protection, inventory and restoration. Critical aspects of such models include the influence of scale, uncertainties associated with imperfect detection and spatial autocorrelation and transferability of model predictions.
  2. We addressed these issues in developing occupancy models of the imperilled eastern sand darter (Ammocrypta pellucida) based on surveys of the Grand and Thames Rivers, Ontario, Canada.
  3. Eastern sand darter detection probabilities were remarkably different between streams, but factors affecting site occupancy were similar. The proportion of sand and fine gravel was most important, but water clarity and biotic indices also received support in additive models. Accounting for spatial autocorrelation reduced the effect of important covariates.
  4. Occupancy was more closely related to substratum at the site level than factors at broader scales (reach and valley segment), further emphasising the substratum specificity of this species.
  5. Almost all of the top‐ranked site and reach occupancy models had good predictive performance based on assessments of transferability. These models indicate that three formerly occupied Ontario catchments have a high probability of supporting the species and deserve consideration for repatriation.
  6. Our methods demonstrate how a comprehensive approach to occupancy modelling can be used to help guide recovery efforts for imperilled species.
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6.
High rates of old growth (OG) forest destruction and difficult farming conditions result in increasing cover of secondary forests (SF) in the Amazon. In this setting, it is opportune to ask which animals use newly available SF and which stay restricted to OG. This study presents a comparison of SF and OG site occupancy by nocturnal birds in terra firme forests of the Amazon Guianan shield, north of Manaus, Brazil. We tested species-specific occupancy predictions for two owls ( Lophostrix cristata/Glaucidium hardyi ), two potoos ( Nyctibius leucopterus/Nyctibius griseus ) and two nightjars ( Caprimulgus nigrescens/Nyctidromus albicollis ). For each pair, we predicted that one species would have higher occupancy in OG while the other would either be indifferent to forest type or favor SF sites. Data were collected in 30 OG and 24 SF sites with monthly samples from December 2007 to December 2008. Our analytic approach accounts for the possibility of detection failure and for spatial autocorrelation in occupancy, thus leading to strong inferences about changes in occupancy between forest types and between species. Nocturnal bird richness and community composition were indistinguishable between OG and SF sites. Owls were relatively indifferent to forest type. Potoos followed the a priori predictions, and one of the nightjars ( C. nigrescens ) favored SF instead of OG as predicted. Only one species, Nyctib. leucopterus , clearly favored OG. The landscape context of our SF study sites, surrounded by a vast expanse of continuous OG forest, partially explains the resemblance between SF and OG fauna but leaves unexplained the higher occupancy for SF than OG sites for several study species. The causal explanation of high SF occupancy remains an open question, but the result itself motivates further comparisons for other groups, as well as recognition of the conservation potential of SF.  相似文献   

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祁兰兰  王敏  王卿  吴建强  张小乐  卢蒙  徐锐  黄晶心 《生态学报》2023,43(22):9527-9538
抚仙湖流域作为我国重要的战略水资源储备区,生态安全地位重要。本研究以该流域为研究对象,采用\"状态-隐患-响应\"模型,探索性空间分析法,基于格网尺度分析其1987-2020年生态安全空间分异特征。结果表明:(1)抚仙湖流域生态安全空间差异性明显,生态安全状况以中度安全(Ⅳ级)与高安全(Ⅴ级)状态为主,主要分布于流域四周,生态不安全(Ⅰ级)、较不安全(Ⅱ级)、临界安全(Ⅲ级)成片地集中于流域南北岸及东岸中部的人口农业密集区。(2)研究区生态安全空间集聚效应明显,全局空间自相关系数较高,且逐期上升,集聚效应增强,并以高高(HH),低低(LL)集聚为主,HH区域集中于流域西北,东南,西岸中部片区,LL区域分布于流域北岸人口密集区及南岸的农业地带。(3)研究区生态安全在不同土地利用类型、坡度、人口密度上空间分异规律明显,生态不安全(Ⅰ级)在建设用地分布居多,生态较不安全(Ⅱ级)和生态临界安全(Ⅲ级)以耕地分布为主,生态中度安全(Ⅳ)和高安全(Ⅴ级)主要分布在林地。生态安全分别与坡度、人口密度存在明显的分异特征,坡度增加,生态安全水平高,人口密度变大,生态安全质量越低。  相似文献   

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Environmental DNA (eDNA) is DNA that has been isolated from field samples, and it is increasingly used to infer the presence or absence of particular species in an ecosystem. However, the combination of sampling procedures and subsequent molecular amplification of eDNA can lead to spurious results. As such, it is imperative that eDNA studies include a statistical framework for interpreting eDNA presence/absence data. We reviewed published literature for studies that utilized eDNA where the species density was known and compared the probability of detecting the focal species to the sampling and analysis protocols. Although biomass of the target species and the volume per sample did not impact detectability, the number of field replicates and number of samples from each replicate were positively related to detection. Additionally, increased number of PCR replicates and increased primer specificity significantly increased detectability. Accordingly, we advocate for increased use of occupancy modelling as a method to incorporate effects of sampling effort and PCR sensitivity in eDNA study design. Based on simulation results and the hierarchical nature of occupancy models, we suggest that field replicates, as opposed to molecular replicates, result in better detection probabilities of target species.  相似文献   

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Tree cavities are used as shelter and breeding nests by numerous avian and mammalian species. In cold environments, tree cavities are often proposed as the best winter nest choice because of the superior protection they offer from precipitation, wind, cold temperatures, and predators. As such, they represent a critical resource, which has the potential to limit population size of non-excavating species. We assessed factors affecting site occupancy in the boreal forest by northern flying squirrels, a secondary user of tree cavities, and to identify which nest type is preferred during the colder days of the autumn–winter period. We trapped flying squirrels twice in 59 aspen-dominated stands in the autumn period using low- (1.5 m above ground-level) and high-mounted (4 m) traps to determine site occupancy. A total of 85 individuals were captured on 2,880 trap-nights. During the winter period, we radio-tracked 26 individuals to 87 diurnal nests in 220 locations. None of the habitat variables considered (cavity availability, woody debris, and lateral cover) explained site occupancy. Detectability decreased with precipitation, and was lower using high traps than low traps. Both females and males used tree cavities (26%), external nests (39%), and ground nests (35%). In cold weather, females preferred ground nests, whereas males preferred external nests. Our results do not support the hypothesis that tree cavities represent a limiting factor to northern flying squirrels in cold environments. Instead, this species seems to be a generalist and is opportunistic, using a variety of nest types. Nevertheless, practices ensuring the persistence of large diameter live cavity trees, providing better insulative properties, are likely to increase the relative use of tree cavities as nest sites by northern flying squirrels. © 2011 The Wildlife Society.  相似文献   

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Ecologists often seek to infer patterns of species occurrence or community structure from survey data. Hierarchical models, including multi‐species occupancy models (MSOMs), can improve inference by pooling information across multiple species via random effects. Originally developed for local‐scale survey data, MSOMs are increasingly applied to larger spatial scales that transcend major abiotic gradients and dispersal barriers. At biogeographic scales, the benefits of partial pooling in MSOMs trade off against the difficulty of incorporating sufficiently complex spatial effects to account for biogeographic variation in occupancy across multiple species simultaneously. We show how this challenge can be overcome by incorporating preexisting range information into MSOMs, yielding a “biogeographic multi‐species occupancy model” (bMSOM). We illustrate the bMSOM using two published datasets: Parulid warblers in the United States Breeding Bird Survey and entire avian communities in forests and pastures of Colombia''s West Andes. Compared with traditional MSOMs, the bMSOM provides dramatically better predictive performance at lower computational cost. The bMSOM avoids severe spatial biases in predictions of the traditional MSOM and provides principled species‐specific inference even for never‐observed species. Incorporating preexisting range data enables principled partial pooling of information across species in large‐scale MSOMs. Our biogeographic framework for multi‐species modeling should be broadly applicable in hierarchical models that predict species occurrences, whether or not false absences are modeled in an occupancy framework.  相似文献   

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ABSTRACT Capercaillie (Tetrao urogallus) is a large, endangered forest grouse species with narrow habitat preferences and large spatial requirements that make it susceptible to habitat changes at different spatial scales. Our aim was to evaluate the relative power of variables relating to forest versus landscape structure in predicting capercaillie occurrence at different spatial scales. We investigated capercaillie-habitat relationships at the scales of forest stand and forest-stand mosaic in 2 Swiss regions. We assessed forest structure from aerial photographs in 52 study plots each 5 km2. We classified plots into one of 3 categories denoting the observed local population trend (stable, declining, extinct), and we compared forest structure between categories. At the stand scale, we used presence-absence data for grid cells within the plots to build predictive habitat models based on logistic regression. At this scale, habitat models that included only variables relating to forest structure explained the occurrence of capercaillie only in part, whereas variables selected by the models differed between regions. Including variables relating to landscape features improved the models significantly. At the scale of stand mosaic, variables describing forest structure (e.g., mean canopy cover, proportion of open forest, and proportion of multistoried forest) differed between plot categories. We conclude that small-scale forest structure has limited power to predict capercaillie occurrence at the stand scale, but that it explains well at the scale of the stand mosaic. Including variables for landscape structure improves predictions at the forest-stand scale. Habitat models built with data from one region cannot be expected to predict the species occurrence in other regions well. Thus, multiscale approaches are necessary to better understand species-habitat relationships. Our results can help regional authorities and forest-management planners to identify areas where suitable habitat for capercaillie is not available in the required proportion and, thus, where management actions are needed to improve habitat suitability.  相似文献   

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The Carpentarian Pseudantechinus (Pseudantechinus mimulus) is a poorly studied dasyurid marsupial that inhabits rocky outcrops in the Mount Isa Inlier bioregion in Queensland and the Gulf Coastal and Gulf Fall and Uplands bioregions in the Northern Territory. It is readily detected by passive infrared triggered camera traps (‘camera traps’). Camera trap data can be used to develop detection probability estimates from which activity patterns can be inferred, but no effort has previously been made to determine changes in the detectability of P. mimulus throughout the year. We undertook a 13-month baited camera trap survey across nine sampling periods at 60 locations of known historic presence or nearby suitable habitat to assess the change in detection rates and detection probabilities of P. mimulus across a year. Detection probabilities were calculated from camera trap data within a single-species, multi-season occupancy framework to determine optimal survey timing. Detection probability data were used to calculate the likelihood of false absences to determine optimal survey duration. We recorded 2493 detections of P. mimulus over 10 966 camera days. Detection probability ranged from 0.009 to 0.179 and was significantly higher from April to October than from November to March. The likelihood of false absences varied by sampling period and desired level of confidence. We find that camera trap surveys for P. mimulus are best conducted from April to October, but optimal survey duration is dependent upon the time of year and desired level of confidence that an observed absence from a given site reflects a true absence at that site. Attaining a minimum of 80% confidence of absence requires as few as 9 days of survey effort in May to 16 days of survey effort in October.  相似文献   

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Pilot studies are often used to design short‐term research projects and long‐term ecological monitoring programs, but data are sometimes discarded when they do not match the eventual survey design. Bayesian hierarchical modeling provides a convenient framework for integrating multiple data sources while explicitly separating sample variation into observation and ecological state processes. Such an approach can better estimate state uncertainty and improve inferences from short‐term studies in dynamic systems. We used a dynamic multistate occupancy model to estimate the probabilities of occurrence and nesting for white‐headed woodpeckers Picoides albolarvatus in recent harvest units within managed forests of northern California, USA. Our objectives were to examine how occupancy states and state transitions were related to forest management practices, and how the probabilities changed over time. Using Gibbs variable selection, we made inferences using multiple model structures and generated model‐averaged estimates. Probabilities of white‐headed woodpecker occurrence and nesting were high in 2009 and 2010, and the probability that nesting persisted at a site was positively related to the snag density in harvest units. Prior‐year nesting resulted in higher probabilities of subsequent occurrence and nesting. We demonstrate the benefit of forest management practices that increase the density of retained snags in harvest units for providing white‐headed woodpecker nesting habitat. While including an additional year of data from our pilot study did not drastically alter management recommendations, it changed the interpretation of the mechanism behind the observed dynamics. Bayesian hierarchical modeling has the potential to maximize the utility of studies based on small sample sizes while fully accounting for measurement error and both estimation and model uncertainty, thereby improving the ability of observational data to inform conservation and management strategies.  相似文献   

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In the Appalachian portion of their breeding range, Golden‐winged Warblers (Vermivora chrysoptera) nest in shrubland and regenerating forest communities created and maintained by disturbance. Because populations of Golden‐winged Warblers have exhibited precipitous declines in population throughout their Appalachian breeding range, management activities that create or maintain early successional habitat are a priority for many natural resource agencies and their conservation partners. Within these early successional habitats, however, additional information is still needed concerning the relative importance of different vegetation features in selection of breeding territories by Golden‐winged Warblers. Our objective, therefore, was to use logistic regression to estimate the probability of territory‐level occupancy by Golden‐winged Warblers in north‐central Pennsylvania at two sites, each with its own early successional community, based on vegetation characteristics. Our communities were composed of shrublands and regenerating forest sites resulting from two disturbances: agriculture and forest fire. Despite differences in vegetation structure, portions of both study areas (regenerating forest and old field) supported territorial Golden‐winged Warblers. Probability of territory occupancy by Golden‐winged Warblers increased with percent blackberry (Rubus) cover in the regenerating forest community, and decreased as basal area and distance to microedge increased (i.e., as vegetation patchiness decreased) in both communities. These habitat features have also been found to influence other aspects of Golden‐winged Warbler breeding ecology such as nest‐site selection, pairing success, and territory abundance. Vegetation features influencing Golden‐winged Warbler territory establishment can differ among shrubland and regenerating forest communities, and management decisions and outcomes may be affected by these differences. Our study provides a starting point for a more comprehensive hypothesis‐driven occupancy survey to investigate features of the territories of Golden‐winged Warblers across a broader geographic range and in different vegetation communities.  相似文献   

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With reference to a stratified case–control (CC) procedure based on a binary variable of primary interest, we derive the expression of the distortion induced by the sampling design on the parameters of the logistic model of a secondary variable. This is particularly relevant when performing mediation analysis (possibly in a causal framework) with stratified case–control (SCC) data in settings where both the outcome and the mediator are binary. Despite being designed for parametric identification, our strategy is general and can be used also in a nonparametric context. With reference to parametric estimation, we derive the maximum likelihood (ML) estimator and the M-estimator of the joint outcome–mediator parameter vector. We then conduct a simulation study focusing on the main causal mediation quantities (i.e., natural effects) and comparing M- and ML estimation to existing methods, based on weighting. As an illustrative example, we reanalyze a German CC data set in order to investigate whether the effect of reduced immunocompetency on listeriosis onset is mediated by the intake of gastric acid suppressors.  相似文献   

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Spatial scale is fundamental in understanding species–landscape relationships because species’ responses to landscape characteristics typically vary across scales. Nonetheless, such scales are often unidentified or unreliably predicted by theory. Many landscapes worldwide are urbanizing, yet the spatial scaling of species’ responses to urbanization is poorly understood. We investigated the spatial scaling of urbanization effects on a community of 15 mammal species using ~60 000 wildlife detections collected from a constellation of 207 camera traps across an extensive urban park system. We embedded a bivariate Gaussian kernel in hierarchical multi-species models to determine two scales of effect (a scale of maximal effect and a broader scale of cumulative landscape effect) for two biological responses (occupancy and site visit frequency) across two seasons (winter and summer) for each species. We then assessed whether scales of effect varied according to theoretical predictions associated with biological responses and species traits (body size and mobility). Scales of effect ranged from < 50 m to > 9000 m and varied among species, but not as predicted by theory. Species’ occupancy generally showed a weak response to urbanization and the scale of this effect was both highly uncertain and consistent across species. We did not detect any relationship between scales of effect and species’ body size or mobility, nor was there any evident pattern of scaling across biological response or seasons. These results imply that 1) urbanization effects on mammals manifest across a very broad spectrum of spatial scales, and 2) current theories that a priori predict the scale at which urbanization affects mammals may be of limited use within a given system. Overall, this study suggests that developing general theory regarding the scaling of species–landscape relationships requires additional empirical work conducted across multiple species, systems and timescales.  相似文献   

18.
Declining fish health and the occurrence of large fish kills are some of the more publicly meaningful indicators of water quality in the impaired Neuse River Estuary, North Carolina. It is generally believed that such problems are caused by the widespread depletion of dissolved oxygen—an indirect result of anthropogenic nutrient pollution. However, the development of scientific simulation models to predict how improvements in oxygen conditions will improve the health of fish and reduce the frequency of fish kills has proven elusive. As a pragmatic solution to this problem, the expert opinion of estuarine fisheries scientists in possession of relevant data and experience was elicited. The relations between joint and conditional probabilities were exploited to translate quantities that are normally hard to assess into quantities that can be drawn more directly from the experiential knowledge of the experts. A combined model of expert opinion was constructed as an influence diagram, and Monte Carlo simulation was used to generate predictions of fish health and fish kills in the Neuse River Estuary under current and improved oxygen conditions. Full model results are expressed as probability distributions, capturing the effects of natural variability and knowledge uncertainty—both contributors to total ecological risk.  相似文献   

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Ruffed grouse (Bonasa umbellus) are a popular game bird and the management indicator species for quaking aspen (Populus tremuloides) in the Black Hills National Forest (BHNF), which requires development of a robust monitoring protocol to evaluate trends in ruffed grouse populations. We used roadside drumming surveys in spring 2007 and 2008 to estimate ruffed grouse occupancy and detection probabilities in the BHNF while simultaneously assessing the influence of sampling and site covariates on these processes. Ruffed grouse occupancy estimates were constant between spring 2007 and 2008 (Ψ = 0.12, SE = 0.03) and were positively influenced by the amount of aspen surrounding the site. Detection probability estimates were constant between spring 2007 and 2008 (p = 0.27, SE = 0.06) and were influenced by survey date in a quadratic form and negatively influenced by wind speed and time of the survey. Collectively, our results demonstrated that ruffed grouse occupancy and detection probabilities in the BHNF were low. Occupancy could be increased by increasing the extent of aspen. To improve monitoring efficiency and maximize probability of detecting ruffed grouse, ruffed grouse monitoring should be conducted during the peak of drumming (mid-May), during favorable weather conditions such as low wind speeds and little precipitation, and during early morning, near sunrise. © 2010 The Wildlife Society.  相似文献   

20.
以辽东山区次生林为研究对象,分析4 hm2样地Gleason丰富度指数、Simpson优势度指数、Shannon多样性指数和Pielou均匀度指数的空间分布特征及其与尺度的关系.结果表明: 4个多样性指数的空间分布均表现出较高的空间异质性;4个多样性指数的方差随尺度的增加其变化趋势有所差异;4个多样性指数的变异系数随尺度的增加呈下降趋势;乔木层的4个多样性指数值高于灌木层,且随尺度增加其变化趋势有所差异.在分析辽东山区次生林物种多样性时应考虑尺度效应.  相似文献   

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