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Dataset results
31 results for “nested models”
Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)
Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data for 130 samples of Chiromantis rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change, and periods of isolation and secondary contact. Species distribution models were used to identify regions of climatic stability that could have served as forest refugia since the Last Interglacial. Results: Population structure within Chiromantis rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent-based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene. Main conclusions: Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo-Congolian forest. Population demographic inferences help connect patterns of genetic variation to diversification model predictions. The diversification history of Chiromantis rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation, and adaptive evolution along environmental gradients.
Mechanisms for a record-breaking rainfall in the coastal metropolitan city of Guangzhou, China: observation analysis and nested very-large-eddy simulation with the WRF Model
<p>A video shows the processes of a record-breaking rainfall in the coastal metropolitan city of Guangzhou, China simulated by WRF nested very-large-eddy simulation.</p>
Figure 2 3D in A 3D model to illustrate the nest architecture of Acromyrmex balzani (Hymenoptera; Formicidae)
Figure 2 3D profile of nests 5 to 8, showing turret height and maximum depth. a: nest 5; b: nest 6; c: nest 7 and d: nest 8.
Figure 3 in A 3D model to illustrate the nest architecture of Acromyrmex balzani (Hymenoptera; Formicidae)
Figure 3 Pearson's Correlation between the number of workers and the number of chambers (a); between the number of workers and the nest volume (b) and between the number of chambers and the nest volume (c), with their respective r and p values.
NUMAC: Description of the Nested Unified Model with Aerosols and Chemistry, and evaluation with KORUS-AQ data: supporting data
<p>Simulated data presented in manuscript with title above, generated with the Met Office Unified Model, together with observations from KORUS-AQ and MODIS that are used in the model evaluation.</p> <p>The Terra/MODIS aerosol datasets were acquired from the Level-1 and Atmosphere Archive & Distribution<br> System (LAADS) Distributed Active Archive Center (DAAC), located in the Goddard Space Flight Center in Greenbelt, Maryland https://ladsweb.nascom.nasa.gov/. All surface and aircraft observation data is freely and publicly available at https://www-air.larc.nasa.gov/cgi-bin/ArcView/korusaq, last access 10 June 2022.</p>
Data from: Alternative forms of brook trout nest site selection alter modeled offspring thermal experience and emergence phenology in groundwater-influenced streambeds
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Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)
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Impact of Different Nesting Methods on the Simulation of a Severe Convective Event Over South Korea Using the Weather Research and Forecasting Model
<p>The data from various platforms (NCEP FNL, TRMM, ERA5, AWS) and WRF Model output utilised to generate the figures in the current study (https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020JD033084) are available at this Zenodo data repository.</p>
Data from: How well do embryo development rate models derived from laboratory data predict embryo development in sea turtle nests?
<p>Development rate of ectothermic animals varies with temperature. Here we use data derived from laboratory constant temperature incubation experiments to formulate development rate models that can be used to model embryonic development rate in sea turtle nests. We then use a novel method for detecting the time of hatching to measure the in situ incubation period of sea turtle clutches to test the accuracy of our models in predicting the incubation period from nest temperature traces. We found that all our models overestimated the incubation period. We hypothesize three possible explanations which are not mutually exclusive for the mismatch between our modeling and empirically measured in situ incubation period: (1) a difference in the way the incubation period is calculated in laboratory data and in our field nests, (2) inaccuracies in the assumptions made by our models at high incubation temperatures where there is no empirical laboratory data, and (3) a tendency for development rate in laboratory experiments to be progressively slower as temperature decreases compared with in situ incubation.</p>
Model sets and data used in the preprint "Evaluating functional dispersal and its eco-epidemiological implications in a nest ectoparasite"
<p>Model sets and data used in the preprint "Evaluating functional dispersal and its eco-epidemiological implications in a nest ectoparasite", reviewed and recommended by Peer Community In Ecology (https://dx.doi.org/10.24072/pci.ecology.100013). See preprint and supplementary materials.</p>
Wave-Cascade Nested Model: The Urban-rural Diffusion Model of Suzhou(Essays on Linguistics 2025(1))
<p>This is the high-resolution images (Figure 3) from published paper entitled Wave-Cascade Nested Model: The Urban-rural Diffusion Model of Suzhou (Essays on Linguistics 2025(1)) (in Chinese 波浪-级联嵌套模型”:苏州城乡方言的扩散模式 (《语言学论丛》2025年第1期)) . </p> <p>Given the journal doesn't provide color printing or needs to compress images due to size limitations, it offers readers access to the high-quality and full-color image.</p> <p>If you have any question, please contact me without any hesitation! Thank you very much!</p>
Data from: Short-billed Dowitcher (Limnodromus griseus hendersoni) nesting habitat preferences in Churchill, Manitoba, Canada: Habitat modelling and climate change implications
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Data from: How well do embryo development rate models derived from laboratory data predict embryo development in sea turtle nests?
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Data from: Nest survival modeling using a multi-species approach in forests managed for timber and biofuel feedstock
1. Switchgrass (Panicum virgatum) intercropping is a novel forest management practice for biomass production intended to generate cellulosic feedstocks within intensively managed loblolly pine-dominated landscapes. These pine plantations are important for early-successional bird species, as short rotation times continually maintain early successional habitat. We tested the efficacy of using community models compared to individual surrogate species models in understanding influences on nest survival. We analysed nest data to test for differences in habitat use for 14 bird species in plots managed for switchgrass intercropping and controls within loblolly pine (Pinus taeda) plantations in Mississippi, USA. 2. We adapted hierarchical models using hyper-parameters to incorporate information from both common and rare species to understand community-level nest survival. This approach incorporates rare species that are often discarded due to low sample sizes, but can inform community-level demographic parameter estimates. We illustrate use of this approach in generating both species-level and community-wide estimates of daily survival rates for songbird nests. We were able to include rare species with low sample size (minimum n = 5) to inform a hyper-prior, allowing us to estimate effects of covariates on daily survival at the community level, then compare this with a single-species approach using surrogate species. Using single species models, we were unable to generate estimates below a sample size of 21 nests per species. 3. Community model species-level survival and parameter estimates were similar to those generated by five single species models, with improved precision in community model parameters. 4. Covariates of nest placement indicated that switchgrass at the nest site (< 4 m) reduced daily nest survival, although intercropping at the forest stand level increased daily nest survival. 5. Synthesis and applications. Community models represent a viable method for estimating community nest survival rates and effects of covariates while incorporating limited data for rarely detected species. Intercropping switchgrass in loblolly pine plantations slightly increased daily nest survival at the research plot scale (0.1 km2), although at a local scale (50 m2) switchgrass negatively influenced nest survival. A likely explanation supported by previous research is intercropping shifted community composition, favouring species with greater disturbance tolerance.
input files for CROCO-WRF-OASIS3-MCT coupled model with a nest in CROCO
<p><span>This tar file contains all the input files needed to run the coupled model CROCO-WRF with OASIS3-MCT coupler with one 2-way nested domain in CROCO. This example configuration is based on the BENGUELA region at low resolution (this is the example of regional configuration of the CROCO model: see CROCO documentationa nd tutorials for more details</span>)</p>
Results and Validation of Global-Regional Nested model for polycyclic aromatic hydrocarbons.
<p>The repository is used to store data from the results and collected observations in the submitted paper "Modeling PAHs from Global to Regional Scales: Model Development and Investigation of Health risks in China 2013-2018," which was published in the Earth Science Model Development (GMD) journal.</p>
Evaluating the effects of nest management on a recovering raptor using integrated population modeling
<p>Data and code from Cappello et al. 2024 Ecosphere</p> <p>Evaluating the effects of nest management on a recovering raptor using integrated population modeling.</p> <p>Abstract: Evaluating population responses to management is a crucial component of successful conservation programs. Models predicting population growth under different management scenarios can provide key insights into the efficacy of specific management actions both in reversing population decline and in maintaining recovered populations. Bald eagle (Haliaeetus leucocephalus) conservation in the United States has seen many successes over the last 50 years, yet the extent to which the bald eagle population has recovered in Arizona, an important population within the Southwest region, remains an area of debate. Estimates of the species’ population trend and an evaluation of ongoing nest-level management practices are needed to inform management decisions. We developed a Bayesian integrated population model (IPM) and population viability analysis (PVA) using a 36-year dataset to assess Arizona bald eagle population dynamics and their underlying demographic rates under current and possible future management practices. We estimated that the population grew from 77 females in 1993 to 180 females in 2022, an average yearly increase of 3%. Breeding sites that had trained personnel (i.e., nestwatchers) stationed at active nests to mitigate human disturbance had 28% higher reproductive output than nests without this protection. Uncertainty around population trends was high, but scenarios that continued the nestwatcher program were less likely to predict abundance declines than scenarios without nestwatchers. Here, the IPM-PVA framework provides a useful tool both for estimating the effectiveness of past management actions and for exploring the management needs of a delisted population, highlighting that continued management action may be necessary to maintain population viability even after meeting certain recovery criteria.</p>
Data from: Nest survival modeling using a multi-species approach in forests managed for timber and biofuel feedstock
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Data from: Using dynamic N-mixture models to test cavity limitation on northern flying squirrel demographic parameters using experimental nest box supplementation.
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Data from: Model selection and parameter inference in phylogenetics using nested sampling
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in phylogenetics is the estimation of the marginal likelihood. This quantity is commonly used for comparing different evolutionary models, but its calculation, even for simple models, incurs high computational cost. Another interesting challenge relates to the estimation of the posterior distribution. Often, long Markov chains are required to get sufficient samples to carry out parameter inference, especially for tree distributions. In general, these problems are addressed separately by using different procedures. Nested sampling (NS) is a Bayesian computation algorithm which provides the means to estimate marginal likelihoods together with their uncertainties, and to sample from the posterior distribution at no extra cost. The methods currently used in phylogenetics for marginal likelihood estimation lack in practicality due to their dependence on many tuning parameters and their inability of most implementations to provide a direct way to calculate the uncertainties associated with the estimates, unlike NS. In this paper, we introduce NS to phylogenetics. Its performance is analysed under different scenarios and compared to established methods. We conclude that NS is a competitive and attractive algorithm for phylogenetic inference. An implementation is available as a package for BEAST 2 under the LGPL licence, accessible at https://github.com/BEAST2-Dev/nested-sampling.
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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.