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310 results for “State Model”
Modeled maximum and mean lake depths for the contiguous United States
Depth regulates many attributes of aquatic ecosystems, but relatively few lakes are measured, and existing datasets are biased toward large lakes. To address this, we used a large dataset of maximum (Zmax; n = 16,831) and mean (Zmean; n = 5,881) depth observations to create new depth models, focusing on lakes < 1,000 ha. We then used the models to characterize patterns in lake basin shape and volume. We included terrain metrics, water temperature and reflectance, polygon attributes, and other predictors in a random forest model. Our final models generally outperformed existing models (Zmax R^2 = 0.35; RMSE = 8.1 m and Zmean R^2 = 0.36; RMSE = 3.0 m). Our models show that lake depth followed a Pareto distribution, with 2.8 orders of magnitude fewer lakes for an order of magnitude increase in depth. Additionally, despite orders of magnitude variation in surface area, most size classes had a modeled modal maximum depth of ~5 m. Concave (bowl-shaped) lake basins represented 79% of all lakes, but lakes were more convex (funnel-shaped) as surface area increased. Across the conterminous US, 9.8% of all lake water was within the top meter of the water column, and 48% in the top 10 m. Excluding the Laurentian Great Lakes, we estimate the total volume in the conterminous US is 1,068 to 1,298 km3, depending on whether Zmax or Zmean was modeled. Lake volume also exhibited substantial geographic variation, with high volumes in the upper Midwest, Northeast, and Florida and low volumes in the southwestern US.
Arctic Ocean state estimates for 2009 using the GECCO model
<p>The dataset contains the 2009 data of a 10-year ocean synthesis (2007-2016) obtained by assimilating available observations of sea ice and ocean parameters into the GECCO model. Data from, among others, several satellite programs such as AMSRE, SSMI, AMSR2, Envisat, Jason, Cryosat., AVHRR, and SMOS, and available moorings in the Davis Strait, the Bering Strait, the Fram Strait, the Barents Sea Opening, and by the Nansen and Amundsen Basins Observational System (NABOS), the North Pole Environmental Observatory (NPEO), and the Beaufort Gyre Exploration Project (BGEP) project. A detailed description can be found in Lyu et al., 2020.</p> <p>Guokun Lyu, Nuna Serra, Armin Koehl and Detlef Stammer, 2020. INTAROS Deliverable 6.4 Ice-ocean statistics and state estimation V1. https://intaros.nersc.no/sites/intaros.nersc.no/files/D6.4_INTAROS_Data_assimilation_v1.3.pdf </p>
Dataset for: African manatee (Trichechus senegalensis) habitat suitability at Lake Ossa, Cameroon using trophic state models and predictions of submerged aquatic vegetation
<p>See research article here: https://onlinelibrary.wiley.com/doi/epdf/10.1002/ece3.8202</p> <p>Aim: The present study aims at investigating the past and current trophic status of Lake Ossa and evaluating its potential impact on African manatee health.</p> <p>Location: Lake Ossa is known as a refuge for the threatened African manatees in Cameroon. Little information exists on the water quality and health of the ecosystem as reflected by its chemical and biological characteristics.</p> <p>Methods: Aquatic biotic and abiotic parameters including water clarity, nitrogen, phosphorous and chlorophyll concentrations were measured monthly during four months at each of 18 water sampling stations evenly distributed across the lake. These parameters were then compared with historical values obtained from the literature to examine the dynamic trophic state of Lake Ossa.</p> <p>Results: Results indicate that Lake Ossa’s trophic state parameters doubled in only three decades (from 1985 to 2016), moving from a mesotrophic to a eutrophic state. The decreasing nutrient gradient moving from the mouth of the lake (in the south) to the north indicates that the flow of the adjacent Sanaga River is the primary source of nutrient input. Further analysis suggests that the poor transparency of the lake is not associated with chlorophyll concentrations but rather with the suspended sediments brought-in by the Sanaga River. Consequently, our model demonstrated that despite nutrient enrichment, less than 5% of the lake bottom surface sustained submerged aquatic vegetation. Thus, shoreline emergent vegetation is the primary food available for the local manatee population. During the dry season, water recedes drastically and disconnects from the dominant shoreline emergent vegetation, decreasing accessibility for manatees.</p> <p>Main conclusions: The current study revealed major environmental concerns (eutrophication and sedimentation) that may negatively impact habitat quality for manatees. Efficient land use and water management across the entire watershed may be necessary to mitigate such issues.</p>
XIS: A daily spatiotemporal machine-learning model for environmental exposures in the contiguous United States
<p>These Parquet files contain the outputs used for many analyses and plots in the linked papers. For temperature and humidity, the full sets of observations for cross-validation aren't included because we used restricted-use MADIS data.</p>
Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets
<p>This archive contains the empirical data analysed in the paper 'Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets' by Touzalin et al. (https://doi.org/10.24072/pci.ecology.100416). The dataset is provided as a .Rdata file ('TLoss_GMdata.Rdata'), and full description of the content is provided in the file 'Readme_TLdata.csv'. All additional details are available in the main text (https://doi.org/10.24072/pci.ecology.100416) or in the supporting information (https://doi.org/10.5281/zenodo.10204538).</p>
An ensemble of 48 physically perturbed model estimates of the 1/8° terrestrial water budget over the conterminous United States, 1980–2015
<p>This dataset contains the 1980–2015 monthly terrestrial water budget simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include total evapotranspiration and its constituents (canopy evaporation, soil evaporation, and transpiration), runoff (the surface and subsurface components), as well as terrestrial water storage (snow water equivalent, four-layer soil water content from the surface down to 2 m, and the groundwater storage anomaly). The file name has four parts: the abbreviation for "terrestrial water budget", the used parameterization, the time scale, and the suffix.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
Distinguishing GUI Component States for Blind Users using Large Language Models
<p><strong># Data Code Repository</strong></p><p> </p><p>This repository contains open-source data code that provides utilities for the paper named "Here comes trouble! Distinguishing GUI Component States for Blind Users using Large Language Models". The code is designed to facilitate data-related tasks and promote reproducibility in research and data analysis projects.</p><p> </p><p><strong>## Features</strong></p><p> </p><p>- Attribute identification and extraction: Including real-time recognition and extraction of GUI components in the view type, resource-id, color, action of four attributes</p><p>- Components State Distinction: Provides the prompt needed for large language models, covering their specific design schemes and chain of thought reasoning processes as well as contextual learning content.</p><p>- Implementation: Offers specific methods to realize the process, including the setting of relevant parameters and the use of functions.</p><p> </p><p><strong>## Installation</strong></p><p> </p><p>To use the data code, you can down or clone the required code.</p><p>Notably, before using the code, make sure the necessary environment configuration is done.</p><p> </p><p><strong>## Dependencies</strong></p><p>The data code has the following dependencies:</p><p> </p><p>Python (version 3.6 or higher)</p><p>NumPy</p><p>Pandas</p><p>Seaborn</p><p>Scikit-learn</p><p>Openai</p><p>Android Studio (version 4.0)</p><p> </p><p>Install the required dependencies using pip:</p><p>pip install numpy..</p><p> </p><p><strong>##License</strong></p><p>This data code is distributed under the MIT License. See LICENSE for more information.</p><p> </p><p><strong>##Copyright</strong></p><p>All copyright of the tool is owned by the author of the paper.</p>
Novel disease state model finds most juvenile green turtles develop and recover from fibropapillomatosis
<p>Fibropapillomatosis (FP) is a sea turtle disease characterized by benign tumor development on skin, eyes, and/or internal organs. It primarily affects juvenile green turtles (Chelonia mydas) in coastal foraging sites. The Indian River Lagoon (IRL), Florida, USA, is a coastal green turtle foraging site where the observed FP annual rate averaged 49% between 1983 and 2018. FP is not a major cause of sea turtle mortality and most individuals fully recover; however, the overall dynamics of this disease are poorly understood because prior disease history is unknown for individuals without FP at capture time, and future disease outcome is unknown for individuals with FP at capture time. To better evaluate FP dynamics for green turtles in the IRL, we developed a hierarchical model for predicting disease state change. We used data from 4,149 captures of 3,700 individual green turtles captured in the IRL. The hierarchical disease state model contained two levels: level one modeled whether an individual would develop FP, and level two modeled disease state progression, including states for pre-FP affliction, active FP affliction, and full recovery from FP. From the hierarchical model, we estimated 99.8% (95% credibility intervals 99.1-100%) of juvenile green turtles in the IRL developed FP, indicating that nearly every individual in the IRL is affected by this disease. The model also suggested that turtles quickly developed FP upon recruitment to the IRL and then recovered at different rates, with most completely recovering before emigrating from the IRL as they mature. This is the first analysis of long-term sea turtle data suggesting nearly every turtle in an aggregation both develops and recovers from FP.</p>
Processed data and models in support of manuscript "Deciphering the state of the lower crust and upper mantle with multi-physics inversion"
<p>Data and model files in original format used in the manuscript "Deciphering the state of the lower crust and upper mantle with multi-physics inversion". These files are accompanied by a set of python scripts to reproduce several of the figures in the Manuscript. Please refer to the Manuscript and the included files for further information on data origin and how to use the scripts. A link will be added upon acceptance.</p>
Dataset for "WUS256: An Adjoint Waveform Tomography Model of the Crust and Upper Mantle of the Western United States for Improved Waveform Simulations"
<p>This dataset contains the WUS256 seismic model and auxiliary data used in the creation of the model (Rodgers et al., 2022). WUS256 is a three-dimensional model of the seismic properties of crust and upper mantle of the western United States. The WUS256 model is provided in NetCDF format (readable by for example, <em>xarray</em>, Hoyer & Hamman, <a href="https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JB022930#jgrb55516-bib-0057">2017</a>) and HDF5 format for viewing with <em>ParaView</em> (Ahrens et al., <a href="https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JB022930#jgrb55516-bib-0002">2005</a>) and interaction with <em>Salvus</em> (Afanasiev et al., <a href="https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JB022930#jgrb55516-bib-0001">2019</a>).</p> <p>Also included are the earthquake source parameters for the 72 inversion events and 18 validation events in ASCII text format. Lastly, we include a list of all waveforms used in the creation of WUS256. This is a simple ASCII file with the event name and receiver name (composed of the network_code and station_code).</p> <p>This effort was support by Lawrence Livermore National Laboratory’s Laboratory Directed Research and Development project 20-ERD-008. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-MI-833624</p>
An ensemble of 48 perturbed-physics model (Noah-MP) estimates of the 1/8° runoff over the conterminous United States, 1980–2015
<p>This dataset contains the 1980–2015 monthly evapotranspiration simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include the surface and subsurface runoff. The file name has four parts: the variable collection, the used parameterization, the time scale, and the suffix.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
An ensemble of 48 perturbed-physics model (Noah-MP) estimates of the 1/8° ET over the conterminous United States, 1980–2015
<p>This dataset contains the 1980–2015 monthly evapotranspiration simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include total evapotranspiration and its constituents (canopy evaporation, soil evaporation, and transpiration). The file name has four parts: the variable collection, the used parameterization, the time scale, and the suffix.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
An ensemble of 48 perturbed-physics model (Noah-MP) estimates of the 1/8° terrestrial water storage over the conterminous United States, 1980–2015
<p>This dataset contains the 1980–2015 monthly terrestrial water storage simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include the total terrestrial water storage and its constituents (snow water equivalent, four-layer soil water content from the surface down to 2 m, and the groundwater storage anomaly). The file name has four parts: the variable collection, the used parameterization, the time scale, and the suffix.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character's evolution: R scripts and simulated trees
<p>All R scripts used in this study, and the set of simulated phylogenetic trees used in the study.</p> <p>1. Modern methods of ancestral state estimation (ASE) incorporate branch length information, and it has been demonstrated that ASEs are more accurate when conducted on the branch lengths most correlated with a character's evolution; however, a reliable method for choosing between alternate branch length sets for discrete characters has not yet been proposed.<br><br>2. In this study, we simulate paired chronograms and phylograms, and generate binary characters that evolve in correlation with one of these. We then investigate (1) the effect of alternate branch lengths on ASE error, and (2) whether phylogenetic signal statistics and/or model-fit statistic can be used to select the branch lengths most correlated with a binary character.<br><br>3. In agreement with previous studies, we find that ASEs are more accurate when conducted on the branch lengths most correlated with the character. Phylogenetic signal statistics show limited utility for selecting the correct branch lengths, but model-fit statistics are found to be more accurate, with the correct branch lengths generally returning greater model-fit (lower AICc and BIC values). Using this method to choose between alternate branch length sets is more accurate when tree and character properties are more favorable for model optimization, and when shape differences between alternate phylogenies are greater.<br><br>4. Our results indicate that researchers conducting ASEs on discrete characters should carefully consider which branch lengths are appropriate, and, in the absence of other evidence, we suggest estimating model-fit values over alternate branch length sets and evolutionary models and choosing the branch length/model combination that returns better model fit.</p>
An ensemble of 48 perturbed-physics model (Noah-MP) estimates of the 1/8° runoff over the conterminous United States, 1980–2015 (time-merged version)
<p>This dataset contains the 1980–2015 monthly evapotranspiration simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include the surface and subsurface runoff. The file name has four parts: the variable collection, the used parameterization, the time period, the suffix, and the compression format.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
An ensemble of 48 perturbed-physics model (Noah-MP) estimates of the 1/8° ET over the conterminous United States, 1980–2015 (time-merged version)
<p>This dataset contains the 1980–2015 monthly evapotranspiration simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include total evapotranspiration and its constituents (canopy evaporation, soil evaporation, and transpiration). The file name has four parts: the variable collection, the used parameterization, the time period, the suffix, and the compression format.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
An ensemble of 48 perturbed-physics model (Noah-MP) estimates of the 1/8° terrestrial water storage over the conterminous United States, 1980–2015 (time-merged version)
<p>This dataset contains the 1980–2015 monthly terrestrial water storage simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include the total terrestrial water storage and its constituents (snow water equivalent, four-layer soil water content from the surface down to 2 m, and the groundwater storage anomaly). The file name has four parts: the variable collection, the used parameterization, the time period, the suffix, and the compression format.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
Multi-model Hydropower Projections for the United States Federal Power Marketing Areas under CMIP5 Climate Change Conditions
<p>This dataset contains an ensemble of monthly hydropower generation projections for the United States Federal Hydropower plants for the periods of 1966-2005 (historical period) and 2011-2050 (future period). The dataset includes the monthly hydropower projections developed in (Kao et al. 2016) based on the Watershed Runoff-Energy Storage (WRES) model and is complemented with another ensemble based on the process-based Water Management Power (WMP) model.</p> <p>The hydrologic projections are estimated through a cascading modeling toolchain that include ten global climate change model projections (ACCESS1-0, BCC-CSM1-1, CCSM4, CMCC-CM, GFDL-ESM2M, MIROC5, MPI-ESM-MR, MRI-CGCM3, NorESM1-M and IPSL-CM5A-LR) under RCP8.5 scenario, which are dynamically downscaled with a regional climate model (RegCM4) ( Pal et al. 2007, Giorgi et al. 2012)), which then inform the Variable Infiltration Capacity (VIC) hydrology model (Liang et al. 1994). The ensemble of hydrologic projections is then informing two processes to translate runoff into hydropower projections. First, WRES models monthly river routing and employs a non-linear statistical approach relating monthly natural flow to hydropower generation, including processes such as spilling. Second, MOSART-WM (Voisin et al. 2013), a large-scale river routing and water management model, provides daily reservoir storage and regulated release at dam locations as well as regulated flow at run-of-the-river power plants. The WMP model then translates reservoir and regulated river dynamics into hydropower projections (Zhou et al. 2018). Those projections are further calibrated to monthly generation provided by the federal utilities. The US federal hydropower plants analyzed in this study include 132 facilities that were built and/or are operated by the US Army Corps of Engineers (USACE), the Bureau of Reclamation (Reclamation), and the International Boundary and Water Commission (IBWC). The electricity generation projected for these hydropower plants were aggregated by four Power Marketing Administrations (PMAs), including Bonneville Power Administration (BPA), Southeastern Power Administration (SEPA), Southwestern Power Administration (SWPA), and Western Area Power Administration (WAPA), and their associate subregions.</p> <p>The two files, <em>SWA9505V2_Gsim_PMA_WRES.mat</em> and <em>SWA9505V2_Gsim_PMA_WMP.mat</em>, represent model outputs from the two hydropower models, WRES and WMP respectively.</p> <p>Each file contains 6 variables:</p> <p>1) “Models”: the 10 global climate models (GCMs).</p> <p>2) “PMA_areas”: the 18 subregions of PMAs as defined in (Kao et al. 2015).</p> <p>3) “PMA_G_mn_6605”: 1966-2005 projected monthly hydropower generation for each PMA sub-regions. Dimension: (12 [months], 40 [years], 18 [subregions], 10 [GCMs]). Unit: MWH.</p> <p>4) “PMA_G_mn_1150”: Same as “PMA_G_mn_6605”, but for 2011-2050 projected hydropower generation.</p> <p>5) “PMA_G_yr_6605”: 1966-2005 projected annual hydropower generation. Dimension: (40 [years], 18 [subregions], 10 [GCMs]) . Unit: MWH.</p> <p>6) “PMA_G_yr_1150”: Same as “PMA_G_yr_6605”, but for 2011-2050 projected hydropower generation.</p> <p>The following journal paper details the method in creating the dataset:</p> <p><strong>Impacts of Climate Change on Subannual Hydropower Generation: A Multi-model Assessment of the United States Federal Hydropower Plants</strong></p> <p><strong>Zhou et al. (2022) Preparing for submission to Environmental Research Letters.</strong></p>
Know what you don't know: Embracing state uncertainty in disease-structured multistate models
<p>Hidden Markov models (HMMs) are broadly applicable hierarchical models that derive their utility from separating state processes from observation processes yielding the data. Multistate models such as mark-recapture and dynamic multistate occupancy models are examples of HMMs that are frequently used in ecology. In their early formulations, states, such as pathogen infection status, were assumed to be perfectly observed without ambiguity in state assignment. However, state uncertainty is a pervasive feature of many ecological systems, and multievent models were developed to explicitly account for it.</p> <p>We developed a novel extended multievent mark-recapture model that incorporates state uncertainty at multiple levels of detection. Using a disease-structured example, both false-negative and false-positive state assignment errors are modeled at two levels of state assignment---the pathogen sampling process and the diagnostic process that samples are subjected to. We additionally describe methods to jointly model infection intensity to integrate heterogeneity in ecological parameters, such as survival, and the pathogen detection processes. We provide code to simulate and analyze datasets with various underlying ecological processes and fit our model to a mark-recapture dataset of <em>Mixophyes fleayi</em> (Fleay's barred frog) infected with the amphibian chytrid fungus (<em>Batrachochytrium dendrobatidis</em>, <em>Bd</em>).</p> <p>In our case study, we found evidence for various state assignment errors: the sampling protocol performed poorly in detecting <em>Bd</em>, pathogen detection was highly dependent on infection intensity, and false-positives were non-negligible. Incorporating state uncertainty yielded significantly higher estimates of infection prevalence and 4--5 times lower rates of infection state transitions compared to those obtained from a traditional multistate model.</p> <p>Our results highlight that incorporating state assignment errors improves inference on the ecological state process, especially when sensitivity and specificity of the state assignment processes are low. The general model structure can be applied to other HMMs, providing a foundation for modeling state uncertainty in a range of related models. --</p>
An ensemble of 48 physically perturbed model estimates of the 1/8° terrestrial water budget over the conterminous United States, 1980–2015
<p>This dataset contains the 1980–2015 monthly terrestrial water budget simulated by a 48-member perturbed-physics ensemble configured from the Noah LSM with multi-physics options (Noah‑MP v3.6). Simulation outputs include total evapotranspiration and its constituents (canopy evaporation, soil evaporation, and transpiration), runoff (the surface and subsurface components), as well as terrestrial water storage (snow water equivalent, four-layer soil water content from the surface down to 2 m, and the groundwater storage anomaly). The file name has four parts: the abbreviation for "terrestrial water budget", the used parameterization, the time scale, and the suffix.</p> <p>The 48 physics configurations are generated by combining four runoff parameterizations (run1: SIMGM, run2: SIMTOP, run3: NOAHR, run4: BATS), two parameterizations of stomatal conductance (can1: Ball–Berry, can2: Jarvis), three parameterizations of soil moisture stress factor (btr1:NOAHB, btr2: CLM, btr3: SSiB), and two parameterizations of near-surface atmospheric turbulence (tub1: M-O, tub2: Chen97).</p> <p>The simulation domain covers the all of conterminous United States (25°–53°N, 125°–67°W), which is also called the NLDAS-2 testbed (Xia et al., 2012a, b). The simulations were performed at a spatial resolution of 0.125°, which is the same as for NLDAS-2 models. Details of the simulation settings and spin-up run can be found in Section 2.3 of Zheng et al. (2019) and Section 2.2 of Fei et al. (2021).</p>
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.