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41 results for “Model America”
Validation of a new spatially-explicit process-based model (HETEROFOR) to simulate structurally and compositionally complex stands in Eastern North-America : Dataset
<p>This dataset is linked to the paper “Validation of a new spatially-explicit process-based model (HETEROFOR) to simulate structurally and compositionally complex stands in Eastern North-America" published in Geoscientific Model Development (https://doi.org/10.5194/gmd-16-1661-2023). It contains the installer of the model, its user guide, as well as all the input files (inventory, thinning, meteorology and soil horizons files for each stand used in the evaluation and calibration steps), the R scripts and associated data used to analyse the model outputs.</p>
Data from: Abundance models of endemic birds of the Sierra Nevada de Santa Marta, northern South America, suggest small population sizes and dependence on montane elevations
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The role of fire in the carbon dynamics of the boreal forest III. - North America model simulations of historical fire disturbance and carbon dynamics (1900-2100).
The boreal forest contains large reserves of carbon, and across this region wildfire is a common occurrence. To improve the understanding of how wildfire influences the carbon dynamics of this region, methods were developed to incorporate the spatial and temporal effects of fire into the Terrestrial ecosystem Model (TEM). The historical role of fire on carbon dynamics of the boreal region was evaluated within the context of ecosystem responses to changing atmospheric CO2 and climate. These results show that the role of historical fire on boreal carbon dynamics resulted in a net carbon sink; however, fire plays a major role in the interannual and decadal scale variation of source/sink relationships. To estimate the effects of future fire on boreal carbondynamics, spatially and temporally explicit empirical relationships between climate andfire were quantified. Fuel moisture, monthly severity rating, and air temperature explained a significant proportion of observed variability in annual area burned. These relationships were used to estimate annual area burned for future scenarios of climate change and were coupled to TEM to evaluate the role of future fire on the carbon dynamics of the North American boreal region for the 21st Century. Simulations with TEM indicate that boreal North America is a carbon sink in response to CO2 fertilization, climate variability, and fire, but an increase in fire leads to a decrease in the sink strength. While this study highlights the importance of fire on carbon dynamics in the boreal region, there are uncertainties in the effects of fire in TEM simulations. These uncertainties are associated with sparse fire data for northern Eurasia, uncertainty in estimating carbon consumption, and difficulty in verifying assumptions about the representation of fires that occurred prior to the start of the historical fire record. Future studies should incorporate the role of dynamic vegetation to more accurately represent post-fire successional pr
Data from: Postglacial recolonization of North America by spadefoot toads: integrating niche and corridor modeling to study species' range dynamics over geologic time
<p>Understanding the factors that shape species' distributions is a key topic in biogeography. As climates change, species can either cope with these changes through evolution, plasticity or by shifting their ranges to track the optimal climatic conditions. Ecological niche modeling (ENM) is a widespread technique in biogeography that estimates the niche of the organism by using occurrences and environmental data to estimate species' potential distributions. ENMs are often criticized for failing to take species' dispersal abilities into consideration. Here, we attempt to fill this gap by combining ENMs with dispersal and corridor modeling to study the range dynamics of North American spadefoot toads (Scaphiopodidae) over the Holocene. We first estimated the current and past distributions of spadefoot toads and then estimated their past distributions from the Last Glacial Maximum (LGM) to the present day. Then, we estimated how each taxon recolonized North American by using dispersal and corridor modeling. By combining these two modeling approaches we were able to 1) estimate the LGM refugia used by the North American spadefoot toads, 2) further refine these projections by estimating which of the putative LGM refugia contributed to the recolonization of North America via dispersal, and 3) estimate the relative influence of each LGM refugium to the current species' distributions. The models were tested using previously published phylogeographic data, revealing a high degree of congruence between our models and the genetic data. These results suggest that combining ENMs and dispersal modeling over time is a promising approach to investigate both historical and future species' range dynamics.</p>
Predicting time series of vegetation leaf area index across North America based on climate variables for land surface modeling using attention-enhanced LSTM
<p>We developed an attention-enhanced long and short memory (AELSTM) model for predicting vegetation LAI time series based on climatic data. The developed AELSTM model establishes the relationships between the time series of vegetation LAI and climatic variables. </p>
Evolution of Castanea in North America: RADseq and ecological modeling reveal a history of radiation, range shifts, and disease
<p><b>Premise of the Study: </b>Chestnuts and chinquapins are some of the best known and most widely loved of any plants in North America. Despite the fame of this clade, relatively little genomic sequencing has been done, and much is still unknown about their evolution. </p> <p><b>Methods: </b>Here we use ddRAD data to infer the species-level phylogeny for <i>Castanea </i>and assess the phylogeography of the North American species using samples collected from populations that span the full extent of the species' ranges. We also construct species distribution models using digitized herbarium specimens and observational data from field surveys. </p> <p><b>Key Results: </b>We identified strong population structure within <i>Castanea dentata</i> (American Chestnut) that reflects a stepwise northern migration since the last glacial maximum. Our species distribution models further confirm this scenario and match closely with the <i>Castanea</i> fossil pollen record. We also found significant structure within the <i>Castanea pumila</i> lineage, most notably a genetic cluster that corresponds to the frequently recognized "<i>Castanea pumila var. ozarkensis</i>."</p> <p><b>Conclusions: </b>The two North American <i>Castanea</i> species have contrasting patterns of population structure, but each is typical of plant phylogeography in North America. Within the <i>C. pumila</i> complex we find novel genetic structure that provides new insights to <i>C. pumila</i> taxonomy. Our results also identify a series of distinctive populations that will be valuable in on going efforts to conserve and restore the Chestnuts and Chinquapins in North America.</p>
A Modified Global Plate Model Including Quantitative Tomotectonic Plate Reconstruction of Western North America and the Eastern Pacific Basin
<p>This plate model is based on that of Clennett et al. (2020) (<a href="../records/10348271" target="_blank" rel="noopener">https://zenodo.org/records/10348271</a>). The Clennett et al. (2020) model was an extension of the global model of Müller et al. (2019) (<a href="../records/10525287" target="_blank" rel="noopener">https://zenodo.org/records/10525287</a>), with a focus on producing a more detailed tectonic reconstruction of the North American Cordillera. Further minor modifications were made to the model for a paper by Alfonso et al. (2024), using the <em>GPlates</em> software (<a href="https://url.au.m.mimecastprotect.com/s/JVvZCE8wmrt1kqgwPtNcn8j?domain=gplates.org/" target="_blank" rel="noopener">https://www.gplates.org/</a>). Firstly, several subduction zones in the published plate model have no associated motions, instead remaining entirely stationary relative to the mantle. This was judged to be incompatible with basic geodynamic principles, as geodynamic models indicate that trenches and subducting slabs are almost always in motion relative to the mantle, exhibiting retreat or, more rarely, advance (e.g. Capitanio, 2013; Capitanio et al., 2010; Schellart et al., 2007; Stegman et al., 2010). As trenches of intermediate length generally display relatively slow retreat (Schellart, 2008), a small amount of trench rollback was imposed on the subduction zones in this model, whilst ensuring that they remained located above their associated tomographically-imaged slabs. Additionally, the Orcas plate (170–130 Ma), located within the Cordilleran archipelago, was split into two sections separated by an east-west trending mid-ocean ridge, consistent with the subsequent plate configuration after 130 Ma. This was done to improve the consistency of the plate motion model, which appeared to indicate divergence within the Orcas plate and convergence at its boundaries. Finally, the reconstruction’s absolute plate motion model was recalculated using the iterative optimisation workflow developed by Tetley et al. (2019).</p> <p> </p> <p>The agegrids associated with this model can be accessed from: <a href="https://repo.gplates.org/webdav/PlateModel_Age_SR_Grids/Alfonso_etal_2024_modClennettMuller/" target="_blank" rel="noopener">https://repo.gplates.org/webdav/PlateModel_Age_SR_Grids/Alfonso_etal_2024_modClennettMuller/</a></p> <p> </p>
Code and Data: WRF v.3.9 sensitivity to land surface model and horizontal resolution changes over North America
<p>Data and code used to obtain results published in Garcia-Garcia et al 2021: WRF v.3.9 sensitivity to land surface model and horizontal resolution changes over North America. Submited to<em> Geosci. Model Dev</em>.</p>
Evolution of Castanea in North America: RADseq and ecological modeling reveal a history of radiation, range shifts, and disease
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Data from: Postglacial recolonization of North America by spadefoot toads: integrating niche and corridor modeling to study species’ range dynamics over geologic time
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Data from: An integrated population model for bird monitoring in North America
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Data from: High invasion potential of Hydrilla verticillata in the Americas predicted using ecological niche modeling combined with genetic data
Ecological niche modeling is an effective tool to characterize the spatial distribution of suitable areas for species, and it is especially useful for predicting the potential distribution of invasive species. The widespread submerged plant Hydrilla verticillata (hydrilla) has an obvious phylogeographical pattern: Four genetic lineages occupy distinct regions in native range, and only one lineage invades the Americas. Here, we aimed to evaluate climatic niche conservatism of hydrilla in North America at the intraspecific level and explore its invasion potential in the Americas by comparing climatic niches in a phylogenetic context. Niche shift was found in the invasion process of hydrilla in North America, which is probably mainly attributed to high levels of somatic mutation. Dramatic changes in range expansion in the Americas were predicted in the situation of all four genetic lineages invading the Americas or future climatic changes, especially in South America; this suggests that there is a high invasion potential of hydrilla in the Americas. Our findings provide useful information for the management of hydrilla in the Americas and give an example of exploring intraspecific climatic niche to better understand species invasion.
Data from: High invasion potential of Hydrilla verticillata in the Americas predicted using ecological niche modeling combined with genetic data
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Mechanistic Module for Soil Nitrogen Emissions for CMAQ Model, North America, 2011
This model product provides source code, input data files, and example model outputs for a new mechanistic soil nitrogen (N) module in-line with the Community Multiscale Air Quality (CMAQ) model 5.1 to simulate nitric oxide (NO), nitrous acid (HONO), nitrous oxide (N2O), and ammonia (NH3) soil emissions. The modeling domain covers the continental USA plus portions of northern Mexico and southern Canada, extending from 25 degrees north to 52 degrees north.The simulations use a 12-km spatial grid resolution. Input data are from high-quality reference sources for year 2011. Example model output data are provided for one day, April 21, 2011.
CMS: Simulated Physical-Biogeochemical Data, SABGOM Model, Gulf of America, 2005-2010
This dataset contains monthly mean ocean surface physical and biogeochemical data for the Gulf of America simulated by the South Atlantic Bight and Gulf of America (SABGOM) model on a 5-km grid from 2005 to 2010. The simulated data include ocean surface salinity, temperature, dissolved inorganic nitrogen (DIN), dissolved inorganic carbon (DIC), partial pressure of CO2 (pCO2), air-sea CO2 flux, surface currents, and primary production. The SABGOM model is a coupled physical-biogeochemical model for studying circulation and biochemical cycling for the entire Gulf of America to achieve an improved understanding of marine ecosystem variations and their relations with three-dimensional ocean circulation in a gulf-wide context.
CMS: Hourly Carbon Dioxide Estimated Using the WRF Model, North America, 2010
This data set contains estimated hourly CO2 atmospheric mole fractions and meteorological observations over North America for the year 2010 at a horizontal grid resolution of 27 km and vertical resolution from the surface to 50 hPa. The data are output from the Penn State WRF-Chem version of the Weather Research and Forecasting (WRF) model using lateral boundary conditions and surface fluxes from the CMS-Flux Inversion system.
Ecosystem Demography Model: Scaling Vegetation Dynamics Across South America
This model product contains the source code for the Ecosystem Demography Model (ED version 1.0) as well as model input and output data for a portion of South America including the Brazilian Amazon. The model output data are estimates of potential average live biomass (kg C/m2), potential average soil carbon (kg C/m2), and potential above-ground net primary production (NPP) (kg C/m2/yr) at 1.0 degree resolution. To produce these estimates, ED was forced with ISLSCP I data for 1987 and 1988, averaged into a single year (Moorcroft et al., 2001). Data for the three estimates are provided in both ASCII text and in NetCDF formatted files. ED is an individual-based terrestrial ecosystem model that predicts both ecosystem structure (e.g. above and below-ground biomass, vegetation height and basal area, and soil carbon stocks) and corresponding ecosystem fluxes (e.g. NPP, NEP and evapotranspiration) from climate, soil, and land-use inputs. The model consists of integrated sub-models governing processes such as leaf-level physiology, plant allocation, allometry, phenology, dispersal, the effects of fire disturbances, and below-ground sub-models for soil carbon dynamics and hydrology. Using a new method for scaling-up it is possible to predict ED's large-scale behavior without simulating the fate of every plant individually. ED is used to examine how climate and edaphic factors, natural disturbances, and human land-use practices affect ecosystem structure and fluxes. This data set contains six zip files which each uncompress into six unique subdirectories. Each subdirectory is described in detail in the Model Product Description section of this document. Installation and execution instructions are provided in the Model Documentation and User's Guide section of this document.
DATA for Land Surface Model influence on the simulated climatologies of temperature and precipitation extremes in the WRF v.3.9 model over North America
<p>Code and daily temperature and precipitation outputs used to estimate climate extreme indices in García-García et al. 2020.</p> <p> </p> <p>García-García A., Cuesta-Valero F.J., Beltrami H., González-Rouco J.F., García-Bustamante E., and Finnis J. "Land Surface Model influence on the simulated climatologies of temperature and precipitation extremes in the WRF v.3.9 model over North America" submitted to Geocientific Model Development. 2020. </p>
Arizona Building Aggregated Parameters: Model America v1.0 Data for 146,557 1kmx1km Grid Cells
<p>Oak Ridge National Laboratory (ORNL) has developed the Automatic Building Energy Modeling (AutoBEM) software suite to process multiple types of data, extract building-specific descriptors, generate building energy models, and simulate them on High Performance Computing (HPC) resources. For more information, see AutoBEM-related publications (<a href="https://bit.ly/AutoBEM">bit.ly/AutoBEM</a>).</p> <ul> <li>Building height</li> <li>Building footprint area</li> <li>Building total floor area</li> <li>Height-to-width ratio (height / [longest polygon vertex pair distance]) </li> <li>Number of buildings (ratio of each building type)</li> <li> Street orientation (longest polygon vertex pair's degree)</li> <li>Rooftop area density (total roof area / total cell area)</li> <li>Rooftop area density (total roof area / total cell area)</li> <li>Lambda_p (roof area / total cell area)</li> <li>Lambda_b (surface area of buildings (roof + vertical walls) / total cell area)</li> </ul> <p>Please note that certain parameters include the mean, median, mode, standard deviation, maximum, and minimum values.</p> <p>Three sets of data are provided for 2,555,153 buildings located within the boundary of Arizona in the United States:</p> <ol> <li><strong>Data (3.6MB *.csv) - Arizona 146,557 Grid Cell Locations.</strong></li> <li><strong>Data (15MB *.csv) - Arizona Building Aggregated Parameters Data developed for the Grid Cells.</strong></li> <li><strong>Data (2.5MB *.csv) - Arizona Building Aggregated Parameters Data developed for the Grid Cells (Selected Parameters).</strong></li> </ol> <p>This data is made free and openly available in hopes of stimulating any simulation-informed use case. Data is provided as-is with no warranties, express or implied, regarding fitness for a particular purpose. We wish to thank our sponsors which include Oak Ridge National Laboratory (ORNL), U.S. Dept. of Energy’s (DOE) Building Technologies Office (BTO), Office of Electricity (OE), and Biological and Environmental Research (BER).</p>
Model America - data for every U.S. building
<p> </p> <p><strong>DATA HAS BEEN MIGRATED TO <a href="https://data.ess-dive.lbl.gov/view/doi:10.15485/2283980">https://data.ess-dive.lbl.gov/view/doi:10.15485/2283980</a></strong></p> <p> </p> <p>The 5-year goal of the “Model America” concept was to generate a model of every building in the United States. This data repository delivers on that goal with "Model America v1".</p> <p>Oak Ridge National Laboratory (ORNL) has developed the Automatic Building Energy Modeling (AutoBEM) software suite to process multiple types of data, extract building-specific descriptors, generate building energy models, and simulate them on High Performance Computing (HPC) resources. For more information, see AutoBEM-related publications (<a href="https://bit.ly/AutoBEM">bit.ly/AutoBEM</a>).</p> <p>There were 125,715,609 buildings detected in the United States. Of this number, 122,146,671 (97.2%) buildings resulted in a successful generation and simulation of a building energy model. This dataset includes the full 125 million buildings. Future updates may include additional buildings, data improvements, or other algorithmic model enhancements in "Model America v2".</p> <ol> <li><strong>Data, separated by state - minimalist list of each building (rows) for the following fields (columns)</strong> <ol> <li>ID - unique building ID</li> <li>Footprint2D - lat/lon vertices of building footprint</li> <li>State_Abbrev - Abbreviation for the from which building is located</li> <li>Area - estimate of total conditioned floor area (ft<sup>2</sup>)</li> <li>Area2D - footprint area (ft<sup>2</sup>) </li> <li>CZ - ASHRAE Climate Zone designation</li> <li>Height - building height (ft)</li> <li>NumFloors - number of floors (above-grade) </li> <li>WWR_surfaces - percent of each facade (pair of points from Footprint2D) covered by fenestration/windows (average 14.5% for residential, 40% for commercial buildings)</li> <li>CZ - US climate zone designation</li> <li>BuildingType - DOE prototype building designation (IECC=residential) as implemented by OpenStudio-standards</li> <li>Standard - building vintage (determined by building age)</li> </ol> </li> </ol> <p>This data is made free and openly available in hopes of stimulating any simulation-informed use case. Data is provided as-is with no warranties, express or implied, regarding fitness for a particular purpose. We wish to thank our sponsors which include Oak Ridge National Laboratory (ORNL) Laboratory Directed Research and Development (LDRD), U.S. Dept. of Energy’s (DOE) Building Technologies Office (BTO), Office of Electricity (OE), Biological and Environmental Research (BER), and National Nuclear Security Administration (NNSA). </p>
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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.