Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
126
datasets available to search
ShareScore release 0.9.0
Dataset results
126 results for “occupancy modelling”
Data from: A model for non-equilibrium metapopulation dynamics utilizing data on species occupancy, patch ages and landscape history
1. The distribution pattern of many species reflects the past rather than the current structure of landscapes. Consequently, species are most often not in equilibrium with the current landscape structure. Yet this is a well-known fact, there is no appropriate approach to estimate the colonization rate of non-equilibrium species based on only data on the species occurrence pattern in the landscape. 2. We present an approach to estimate the colonization rate of non-equilibrium metapopulations. The approach requires only data on species presence/absence among its patches (occurrence pattern), data on patch ages and data on the historic distribution of the patches in the landscape. By estimating the past occurrence patterns and colonization events leading to the current pattern of occupied and non-occupied patches, we estimate the colonization rate, including the dispersal kernel. We also show how to estimate effects of local patch conditions and how to include an independent estimate of the local extinction rate based on other data. We use nine epiphytic lichen species confined to beech trees to illustrate the method. 3. Five species had restricted dispersal range, between 200 and 4700 m, and their colonization rate decreased with increasing fragmentation. Species colonization rates were related to niche width. Among the demographic parameters, the force of colonization was more important than the dispersal range in explaining the colonization rates. Local patch conditions did not explain the colonization probability of any species. In metapopulation projections that did not account for restricted dispersal range, higher future metapopulation sizes were projected. 4. Synthesis. The presented approach uses data on only species occurrence, patch age and landscape history to estimate the species colonization rate and dispersal kernel. It can also utilize independent data on local extinction rate. Rather than identifying factors explaining the occurrence pattern, the model estimates the rate of change in the occurrence pattern. This dynamic modelling allows testing general and applied questions on the dynamics or viability of metapopulations of sessile species. The approach is applicable for species whose distribution pattern reflects the past rather than the current landscape structure, e.g. certain epiphytes and ground-floor plants.
Data from: Distribution models and a dated phylogeny for Chilean Oxalis species reveal occupation of new habitats by different lineages, not rapid adaptive radiation
Among the World's most challenging environments for plant life is the Atacama Desert, an arid zone extending over 1300 km and from sea level to 2000/3000 m along the southwestern Andean foothills. Plants there and in the adjacent Mediterranean zone exhibit striking adaptations, and we here use a species-rich such group to address the question whether adaptations arose in parallel, at different times, or simultaneously. Answering this type of question has been a major concern of evolutionary biology over the past few years, with a growing consensus that lineages tend to be conservative in their vegetative traits and niche requirements. Combined nuclear and chloroplast DNA sequences for 112 species of Oxalidales (4900 aligned nucleotides) yielded a fossil-calibrated phylogeny that includes 43 of the 54 species of Oxalis occurring in Chile. Distribution models (SDMs) for these species that included precipitation, temperature, fog and/or vegetation types and the phylogeny were used to reconstruct ancestral habitat preferences, relying on likelihood and Bayesian techniques. Since uneven collecting can reduce the power of SDMs, we used a background sample from 1224 Chilean Oxalis collections to correct models for collecting effort. Models with just 10 of 19 bioclim parameters did as well as more parameter-rich models. Results reveal that the Oxalis flora of Chile consists of seven distant lineages that originated at different times prior to the last Andean uplift pulse and some of which had features pre-adapting them to seasonally arid or xeric conditions. The Mediterranean core zone, south of the Atacama, offered an ecological refuge for insufficiently arid-adapted species and harbors a mix of ancient and young groups. There is no evidence of rapid adaptive radiation.
Data from: Manipulating wetland hydroperiod to improve occupancy rates by an endangered amphibian: modelling management scenarios
Environmental managers have the difficult task of ensuring species persistence despite considerable uncertainty about their response to management. Spatially explicit population models provide one solution for simulating the dynamics of species and evaluating alternative management regimes. We used a Bayesian model to investigate wetland occupancy dynamics of the endangered growling grass frog Litoria raniformis at a wastewater treatment plant in southern Victoria, Australia. We coupled prior information from earlier research on this species with our survey data to quantify the effects of patch-scale variables and connectivity on the probabilities of occupancy, population extinction and colonization. Hydroperiods of 13 sites were experimentally enhanced to bolster occupancy rates by L. raniformis. We used simulations to assess the extent to which the enhanced hydroperiod regime improved the viability of the focal metapopulation. Occupancy rate increased by 15% among the enhanced sites in 2013–2014, whereas the rate of occupancy among unenhanced sites fell by 11% in that year. Forward simulation using the dynamic occupancy model suggested that the minimum occupancy rate across the metapopulation would be 18% higher if the enhanced hydroperiod regime was retained over the next 20 years. Mean posterior effects of patch-scale variables and connectivity on the occupancy dynamics of L. raniformis were consistent with the prior effect in all cases, with only small changes to the size of these effects. There was no clear effect of water chemistry on occupancy dynamics. Synthesis and applications. This work suggests that managing the hydroperiod of constructed wetlands can be an effective tool for the conservation of amphibians and demonstrates the utility of spatially explicit models for assessing metapopulation viability. We encourage managers to experimentally test the efficacy of manipulating patch-scale variables to improve occupancy rates within amphibian metapopulations.
Data from: Using camera trapping and hierarchical occupancy modelling to evaluate the spatial ecology of an African mammal community
Emerging conservation paradigms have shifted from single to multi-species approaches focused on sustaining biodiversity. Multi-species hierarchical occupancy modelling provides a method for assessing biodiversity while accounting for multiple sources of uncertainty. We analysed camera trapping data with multi-species models using a Bayesian approach to estimate the distributions of a terrestrial mammal community in northern Botswana and evaluate community, group, and species-specific responses to human disturbance and environmental variables. Groupings were based on two life-history traits: body size (small, medium, large and extra-large) and diet (carnivore, omnivore and herbivore). We photographed 44 species of mammals over 6607 trap nights. Camera station-specific estimates of species richness ranged from 8 to 27 unique species, and species had a mean occurrence probability of 0·32 (95% credible interval = 0·21–0·45). At the community level, our model revealed species richness was generally greatest in floodplains and grasslands and with increasing distances into protected wildlife areas. Variation among species' responses was explained in part by our species groupings. The positive influence of protected areas was strongest for extra-large species and herbivores, while medium-sized species actually increased in the non-protected areas. The positive effect of grassland/floodplain cover, alternatively, was strongest for large species and carnivores and weakest for small species and herbivores, suggesting herbivore diversity is promoted by habitat heterogeneity. Synthesis and applications. Our results highlight the importance of protected areas and grasslands in maintaining biodiversity in southern Africa. We demonstrate the utility of hierarchical Bayesian models for assessing community, group and individual species' responses to anthropogenic and environmental variables. This framework can be used to map areas of high conservation value and predict impacts of land-use change. Our approach is particularly applicable to the growing number of camera trap studies world-wide, and we suggest broader application globally will likely result in reduced costs, improved efficiency and increased knowledge of wildlife communities.
Data from: Novel application of explicit dynamics occupancy models to ongoing aquatic invasions
1. Identification of suitable habitat where invasive species can establish is an important step towards controlling their spread. Accurate identification is difficult for new or slow invaders because unoccupied habitats may be suitable given enough time for dispersal and occupied habitats may prove to be unsuitable for establishment. 2. To identify suitable habitat of a recent invader, I used an explicit dynamics occupancy modeling framework to evaluate habitat covariates related to successful and failed establishments of American bullfrogs (Lithobates catesbeianus) within the Yellowstone River floodplain of Montana, USA from 2012-2016. 3. During this 5-year period, bullfrogs failed to establish at most sites they colonized. Bullfrog establishment was most likely to occur and least likely to fail at sites closest to human-modified ponds and lakes and those with emergent vegetation. These habitat covariates were generally associated with the presence of permanent water. 4. Suitable habitat for bullfrog establishment is abundant in the Yellowstone River floodplain, though many sites with suitable habitat remain uncolonized. Thus, the maximum distribution of bullfrogs is much greater than their current distribution. 5. Synthesis and applications. Focused control efforts on habitats with or proximate to permanent waters are most likely to reduce the potential for bullfrog establishment and spread. The novel application of explicit dynamics occupancy models is a useful and widely applicable tool for guiding management efforts towards those habitats where new or slow invaders are most likely to establish and persist.07-Aug-2017
Nicaragua Occupancy Modeling
<p>The data and code provided here were used to produce the results contained in Jordan <em>et al</em>. (2016), submitted to PLOS ONE in August 2015.</p>
SITE OCCUPANCY AND ABUNDANCE MODELS FOR ANALYZING MULTIPLE-VISIT DETECTION/NONDETECTION DATA
<p>Data and R codes for the paper: Site occupancy and abundance models for analyzing multiple-visit detection/nondetection data.</p>
AN EXTENSION OF N-MIXTURE OCCUPANCY MODELS FOR COUNT DATA
Open the record for dataset details and reuse information.
Automated bird sound classifications of long-duration recordings produce occupancy model outputs similar to manually annotated data
<p>Occupancy modeling is used to evaluate avian distributions and habitat associations, yet it typically requires extensive survey effort because a minimum of three repeat samples are required for accurate parameter estimation. Autonomous recording units (ARUs) can reduce the need for surveyors on site, yet ARUs utility were limited by hardware costs and the time required to manually annotate recordings. Software that identifies bird vocalizations may reduce expert time needed, if classification is sufficiently accurate. We assessed the performance of BirdNET – an automated classifier capable of identifying vocalizations from >900 North American and European bird species – by comparing automated to manual annotations of recordings of 13 breeding bird species collected in northwestern California. We compared the parameter estimates of occupancy models evaluating habitat associations supplied with manually annotated data (9 min recording segments) to output from models supplied with BirdNET detections. We used three sets of BirdNET output to evaluate the duration of automatic annotation needed to approach manually annotated model parameter estimates: 9-min, 87-min, and 87-min of high-confidence detections. We incorporated 100 3-sec manually validated BirdNET detections per species to estimate true and false positive rates within an occupancy model. BirdNET correctly identified 90% and 65% of the bird species a human detected when data were restricted to detections exceeding a low or high confidence score threshold, respectively. Occupancy estimates, including habitat associations, were similar regardless of method. Precision (proportion of true positives to all detections) was >0.70 for 9 of 13 species, and a low of 0.29. However, processing of longer recordings was needed to rival manually annotated data. We conclude that BirdNET is suitable for annotating multispecies recordings for occupancy modeling when extended recording durations are used. Together, ARUs and BirdNET may benefit monitoring and, ultimately, conservation of bird populations by greatly increasing monitoring opportunities. </p>
Occupancy modeling of habitat use by white-tailed deer after more than a decade of exclusion in the boreal forest
<p>The exclusion of herbivores in forest areas is a strategy used to reduce the impact of selective browsing and increase the regeneration of desired plant species. On Anticosti Island (Québec, Canada), selective browsing by white-tailed deer prevents the regeneration of balsam fir – white birch forests leading to their conversion into white spruce forests. Large deer exclosures were established for ca . 10 to 12 years in clear-cuts with patches of residual forest from 2001 to 2006 to assist in the natural regeneration of fir stands and to provide shelter and food resources for deer. Our objective was to assess how deer use exclosures after the removal of fences according to their spatial configuration and habitat composition. We randomly distributed automatic cameras for periods of 14 days during summer in six exclosures ranging from 3.1 to 11.2 km2 (n=25 cameras per exclosure) from which deer were reduced for 10 to 12 years. We compared candidate occupancy models that included spatial configuration and food resource variables while simultaneously controlling for variables affecting detection probability. We obtained weak evidence that deer habitat use increased by 19% when forage resources, represented by the cover of <em>Cornus canadensis</em>, increased from 0 to 100%. None of the other variables (distance between the border of exclosures and cameras and distance between forest patches and cameras) was retained, suggesting that the use of regenerating forests by deer in summer after a period of exclusion is related to forage availability and therefore, any forest management that improves food production during summer should help maintain or increase habitat use by deer.</p>
Data from: Modelling the area of occupancy of habitat types with remote sensing
1. A current challenge of biodiversity and conservation is the estimation of the spatial extent of habitat types across broad territories. In the absence of fine-resolution maps, predictive modelling helps in assessing the spatial distribution of vegetation cover. However, such approaches are still uncommon in regional planning and management. Here, we present a framework for mapping the area of occupancy (AOO) of habitat types that allows highly suitable estimates at different scales. 2. We model the potential AOO with abiotic variables related to topography and climate, resulting in broad AOO estimates that are subsequently downscaled to the local AOO with remote sensing. The combination of individual local AOO estimates allows the defining of the realized AOO, comprising locations with a high likelihood of occurrence and low uncertainty for each habitat. We applied this framework to mapping 24 protected habitat types of Natura 2000 sites in northern Spain. 3. Local and realized AOO were highly accurate, with a 70% overall accuracy for the realized AOO. Remote sensing data, and especially LiDAR, were the most important predictors in habitat types related to forests and shrubs, followed by rock outcrops and pastures. Environmental variables were also relevant for specific habitats subject to abiotic constraints. 4. The combination of ecological modelling with remote sensing offers multiple advantages over traditional field surveys and image interpretation, allowing the harmonization of habitat maps across large regions and through time. This is particularly useful for implementing conservation actions under Natura 2000 principles or assessing IUCN criteria for ecosystems.
Bayesian N-mixture and occupancy modeling code for songbirds
<p>The proliferation of energy rights-of-way (pipelines and powerlines; ROWs) in the central Appalachian region has prompted wildlife management agencies to consider ways to use these features to manage and conserve at-risk songbird species. However, little empirical evidence exists regarding best management strategies to enhance habitat surrounding ROWs for the songbird community during stopover or breeding periods. We used a before-after-control-impact design to study cut-back border (linear tree cuttings along abrupt forest edges) harvest width (15 m, 30 m, and 45 m wide into the forest) and harvest intensity (14 m<sup>2</sup>/ha and 4.5 m<sup>2</sup>/ha basal area retention) prescriptions along ROWs and assessed their effects on mature forest and young forest songbird species and avian guilds (forest gap habitat, forest interior habitat, young forest habitat, and species of regional conservation priority) up to two years after treatment throughout West Virginia. Species richness during the spring stopover period initially decreased at one-year post-treatment but returned to pre-treatment levels by two-year post-treatment. Breeding season responses to cut-back border treatments varied across harvest width, harvest intensity, and time, but all responses of focal species abundance and guild richness were neutral or positive. Cut-back border harvest intensity had a stronger influence (i.e., more positive responses) than harvest width on breeding focal species abundances and guild richness. For harvest intensity, the more intense, 4.5 m<sup>2</sup>/ha retention treatment had a stronger influence (i.e., more positive responses) than the less intense, 14 m<sup>2</sup>/ha retention treatment. For harvest width, the narrowest treatment (15-m wide) had the strongest influence (i.e., more positive responses) of all width treatments, followed by the widest (45-m wide treatment) with the least influence from the 30-m wide treatment. Abundances and richness increased from pre-treatment to two-year post-treatment across all species and guilds that exhibited a response. These results suggest that cut-back borders increase breeding season habitat suitability along ROWs for the mature forest and young forest songbird community as well as for species of regional conservation priority in the short-term. These findings can aid development of management guidelines for the forest songbird community along abrupt forest edges of man-made habitat features in forest-dominated landscapes.</p>
Establishment of Sleep Quality, Physical and Mental Health and Occupational Burnout Management Model for Shift Nursing Staff and Evaluation of Its Effectiveness
ClinicalTrials.gov study NCT04423328. IPD Sharing: NO. Countries: 1. Publications: 1.
Occupancy modeling of habitat use by white-tailed deer after more than a decade of exclusion in the boreal forest
Open the record for dataset details and reuse information.
Data from: A multistate dynamic site occupancy model for spatially aggregated sessile communities
Open the record for dataset details and reuse information.
Data from: Predictive habitat occupancy models for North American river otters along inland streams in New Jersey
Open the record for dataset details and reuse information.
Data from: An integrated occupancy and space-use model to predict abundance of imperfectly detected, territorial vertebrates
Open the record for dataset details and reuse information.
Data from: Using occupancy modeling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species
Open the record for dataset details and reuse information.
Data from: Integrating over uncertainty in spatial scale of response within multispecies occupancy models yields more accurate assessments of community composition
Open the record for dataset details and reuse information.
Data from: A model for non-equilibrium metapopulation dynamics utilizing data on species occupancy, patch ages and landscape history
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.