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34 results for “Estimation Framework”
Datasets for "A unified framework to estimate the origins of atmospheric moisture and heat using Lagrangian models"
<p>This repository contains the post-processed model outputs from HAMSTER v1.2.0 as used in the following paper: </p> <p>Keune, J., Schumacher, D. L., and Miralles, D. G.: A unified framework to estimate the origins of atmospheric moisture and heat using Lagrangian models, Geosci. Model Dev., 15, 1875–1898, https://doi.org/10.5194/gmd-15-1875-2022, 2022.<br> <br> The data set contains (1) global validation statistics for the three fluxes (evaporation, precipitation, sensible heat), and (2) the climatological source regions of precipitation and heat for Denver, Beijing and Windhoek. The former are found in the directory 'validation/global', and the latter are found in the directories '1001' (Denver), '3001' (Beijing) and '5002' (Windhoek). Multiple experiments were performed to assess the uncertainty of the source regions. Thus, multiple files exist, that show the same variables but for multiple experiments (indicated by the names "ALLPBL", "RH-10-20", "SOD08-SCH19", "SCH20", "FAS19" in the file name). For the moisture source regions, the uncertainty of the attribution methodology was assessed; these are indicated by the different folders, i.e. 'linear_upscaled' and 'random2_upscaled'. For each city and each experiment, the climatologically averaged source regions ('_mean.nc') and the climatologically averaged individual backward day contributions ('_bwmean.nc') are provided. Data sets are in the netCDF format and contain metadata following the CF convention.</p>
Data for "Modelling soil carbon stocks following reduced tillage intensity: a framework to estimate decomposition rate constant modifiers for RothC-26.3, demonstrated in north-west Europe"
<p>Dataset of paired observations of conventional tillage (CT) with no tillage (NT) and reduced tillage (RT) from studies in temperate oceanic regions of Western Europe, extracted from a recent systematic review (Jordon et al. preprint, see DOI below).</p> <p>R code of modelling framework to estimate tillage rate modifiers (TRM) for simulating adoption of RT and NT using RothC-26.3, and meta-estimates of TRM across studies.</p>
Dataset - DeepWealth: A Generalizable Open-Source Deep Learning Framework using Satellite Images for Well-Being Estimation
<p>This dataset encapsulates the Checkpoints obtained during the training process of the Deep Learning model, which can be used for new estimations.</p> <p>The aim of the DeepWealth package is to provide a generalizable Deep Learning framework for the use of remote sensing in poverty estimation. The combination of Deep Learning and Earth Observation data is increasingly being used to estimate socioeconomic conditions at regional and global scales. The proposed framework aligns with the Sustainable Development Goal SDG1 of ending poverty. The framework provides open-source data, code, and training models (checkpoints) for reproducibility and replicability.</p> <ul> <li>The source code can be found in <a href="https://github.com/PARSECworld/DeepWealth" target="_blank" rel="noopener">https://github.com/PARSECworld/DeepWealth</a></li> <li>The metadata from source code can be found in <a href="https://github.com/PARSECworld/DeepWealth/blob/main/metadata.pdf" target="_blank" rel="noopener">https://github.com/PARSECworld/DeepWealth/blob/main/metadata.pdf</a></li> <li>The paper describing the development of this framework can be found at: Ben Abbes, A., Machicao, J., Corrêa, P. L. P., Specht, A., Devillers, R., Ometto, J. P., Kondo, Y., & Mouillot, D. (2024). DeepWealth: A generalizable open-source deep learning framework using satellite images for well-being estimation. <em>SoftwareX</em>, 27, 101785. <a href="https://doi.org/10.1016/j.softx.2024.101785">https://doi.org/10.1016/j.softx.2024.101785</a> </li> </ul>
Code and data for "KGML-ag: A Modeling Framework of Knowledge-Guided Machine Learning to Simulate Agroecosystems: A Case Study of Estimating N2O Emission using Data from Mesocosm Experiments "
<p>This is code and data for manuscript: <br> "KGML-ag: A Modeling Framework of Knowledge-Guided Machine Learning to Simulate Agroecosystems: <br> A Case Study of Estimating N<sub>2</sub>O Emission using Data from Mesocosm Experiments"<br> Licheng Liu, Shaoming Xu, Zhenong Jin*, Jinyun Tang, Kaiyu Guan, Timothy J. Griffis, <br> Matt D. Erickson, Alexander L. Frie, Xiaowei Jia, Taegon Kim, Lee T. Miller, Bin Peng, Shaowei Wu, Yufeng Yang, Wang Zhou, Vipin Kumar</p> <p>All the files belong to Prof. Zhenong Jin, University of Minnesota, UA. jinzn@umn.edu<br> "code" foler includes code for data processing, model training, and results plotting.<br> "trained_model_saved" includes all trained model so you can use to reproduce the results showed in the study;<br> "data" includes all data presented in the study. Finetuning data is refering to Miller, L.T. , Griffis, T. J., Erickson, M. D., Turner, P. A., Deventer, M. J., Chen, Z., Yu, Z., Venterea, R.T., Baker, J. M., and Frie, A. L. (2021). Response of nitrous oxide emissions to future changes in precipitation and individual rain events. Journal of Environmental Quality, In review</p>
A framework for estimating global river discharge from the Surface Water and Ocean Topography satellite mission example data
<p>These files contain the Confluence pipeline outputs, prior information (SOS) and Simulated SWOT shape files from the example in the "A framework for estimating global river discharge from the Surface Water and Ocean Topography satellite mission" manuscript. </p>
There and back to the present: a model-based framework to estimate phylogenetically constrained alpha diversity gradients
<p>The imprint left by niche evolution on the variation of biological diversity across spatial and environmental gradients is still debated among ecologists. Furthermore, understanding to what extent dispersal limitation may reinforce or blur such an imprint is still a gap in our ecological knowledge. In this article we introduce a simulation approach coupled to Approximate Bayesian Computation (ABC) that parameterizes both the adaptation rate of species' niche positions over the evolution of a monophyletic lineage and the intensity of dispersal limitation associated with the variation of species alpha diversity among assemblages distributed across spatial and environmental gradients. The analytical tool was implemented in the R package <em>mcfly</em>. We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate the adaptation rate parameter but showed to be less precise in relation to the dispersal limitation parameter. Also, we found that increased dispersal limitation levels improved the parameterization of the adaptation rate of species' niche positions in simulated datasets. Further, we evaluated the role played by niche evolution and dispersal limitation on species alpha diversity variation of Phyllostomidae bats across the Neotropics. The framework proposed here sheds light on the links between niche evolution, dispersal limitation and gradients of biological diversity, and thereby improved our understanding of evolutionary imprints on current biological diversity patterns.</p>
There and back to the present: a model-based framework to estimate phylogenetically constrained alpha diversity gradients
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A new Double Observer based census framework to improve abundance estimations in mountain ungulates and other gregarious species with a reduced effort
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Integrating multiple field measurements in a Bayesian parallel regression framework to estimate Tasmanian devil age
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A modeling framework for quantifying spatial recruitment dynamics using abundance estimation and sibship analysis: code and simulation study output
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A multi-state occupancy modeling framework for robust estimation of disease prevalence in multi-tissue disease systems
<p>1. Given the public health, economic, and conservation implications of zoonotic diseases, their effective surveillance is of paramount importance. The traditional approach to estimating pathogen prevalence as the proportion of infected individuals in the population is biased because it fails to account for imperfect detection. A statistically robust way to reduce bias in prevalence estimates is to obtain repeated samples (or sample many tissues in multi-tissue disease systems) and to apply statistical methods that account for imperfect detection and permit the interdependence of the infection process across multiple tissues.</p> <p>2. We developed a multi-state occupancy modeling framework which considers two scenarios about the infection process, one where no assumptions about the dependencies among the tissues are made (general), and another where dependence among tissues is not permitted (constrained).</p> <p>3. We applied this model to pseudorabies virus (PrV) DNA detection data obtained from whole blood; and oral, nasal, and genital mucosa of 510 feral swine (Sus scrofa) during the years 2014-2016 in Florida, USA.</p> <p>4. The constrained model was better supported by data. Estimated PrV prevalence varied among tissues, ranging from to 0.06 (CI: 0.02-0.14) in genital to 0.54 (CI: 0.14-0.82) in nasal tissue. Probability of PrV detection ranged from 0.11 (CI: 0.06-0.18) in nasal to 0.51 (CI: 0.21-0.81) in genital tissue. Estimates of PrV prevalence after accounting for imperfect detection were higher than the naïve estimates for all four tissues.</p> <p>5. PrV prevalence was not affected by the age or sex of the animal or the year of sampling, but prevalence increased as drought severity increased.</p> <p>6. The conditional probability of detecting PrV given infection in at least one tissue type within an individual was highest for nasal tissue, suggesting that nasal is the best tissue to sample for PrV surveillance if only one tissue can be sampled, at least for systems with tissue-specific prevalence and detection probabilities similar to ours.</p> <p>7. We found that pathogen prevalence in multi-tissue disease systems can vary across tissues. Our results emphasize the importance of sampling multiple tissues, and the application of robust statistical models to account for imperfect detection in the surveillance of systemic diseases. The multi-state modeling framework is broadly applicable to the surveillance of pathogens that infect multiple tissues and where the infection status or detection of the pathogen in one tissue may depend on the infection status of the pathogen in other tissues). 29-Jul-2020</p>
Dataset for "Recursive Input and State Estimation: A General Framework for Learning from Time Series with Missing Data"
<p>Dataset for "Recursive Input and State Estimation: A General Framework for Learning from Time Series with Missing Data"</p> <p> </p> <p>Missing values in the blood glucose datasets are represented with -2.</p>
Data from: Evaluating population receptive field estimation frameworks in terms of robustness and reproducibility
Within vision research retinotopic mapping and the more general receptive field estimation approach constitute not only an active field of research in itself but also underlie a plethora of interesting applications. This necessitates not only good estimation of population receptive fields (pRFs) but also that these receptive fields are consistent across time rather than dynamically changing. It is therefore of interest to maximize the accuracy with which population receptive fields can be estimated in a functional magnetic resonance imaging (fMRI) setting. This, in turn, requires an adequate estimation framework providing the data for population receptive field mapping. More specifically, adequate decisions with regard to stimulus choice and mode of presentation need to be made. Additionally, it needs to be evaluated whether the stimulation protocol should entail mean luminance periods and whether it is advantageous to average the blood oxygenation level dependent (BOLD) signal across stimulus cycles or not. By systematically studying the effects of these decisions on pRF estimates in an empirical as well as simulation setting we come to the conclusion that a bar stimulus presented at random positions and interspersed with mean luminance periods is generally most favorable. Finally, using this optimal estimation framework we furthermore tested the assumption of temporal consistency of population receptive fields. We show that the estimation of pRFs from two temporally separated sessions leads to highly similar pRF parameters.
Data for the manuscript 'Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework'.
<p>This zip file contains the data downloaded from external sources used to produce the results in the manuscript 'Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework'. Note that all of the data contained in this zip file was publicly available at the time of writing.</p> <p>The corresponding Github can be found here:<br> https://github.com/alan-turing-institute/jbc-turing-rss-testdebiasing</p> <p>The publication is available here:<br> https://doi.org/10.1038/s41564-021-01029-0</p>
Data for "The influence of internal variability on Earth's energy balance framework and implications for estimating climate sensitivity"
<p>This archive contains processed model output necessary for reproducing the figures in Dessler, Maurtisen, Stevens, ACP, 2018</p> <p>historicalEnsemble.nc contains data from the 100-member MPI historical ensemble</p> <p>forcing_aed_ensemble.nc contains the forcing for the historical runs</p> <p>model0001.nc is the control run of the MPI model<br> model0003.nc is an abrupt 4xCO2 run of the MPI model</p> <p>cmip5 contains data from individual CMIP5 models </p> <p>the folder "fig 5" contains zonal average fields necessary for that figure</p>
Data used in "A novel response priority framework for an urban coastal catchment using global weather forecasts-based improved flood risk estimates"
<p>The datasets used in "A novel response priority framework for an urban coastal catchment using global weather forecasts-based improved flood risk estimates" have been provided as rar files. Further details and instructions are provided in readme.txt in each folder of the rar file.</p>
Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images - Simulation Data
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Data from: From a line in the sand to a landscape of decisions: a Hierarchical Diversity Decision Framework (HiDDeF) for estimating and communicating biodiversity loss along anthropogenic gradients
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Data from: Evaluating population receptive field estimation frameworks in terms of robustness and reproducibility
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Data from: Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them
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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.