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141 results for “ensemble; model”
Atmospheric and sea ice model fields from the perturbed parameter ensemble E3SMv0-HILAT used to examine emergent relationships among climate variables in the Arctic
<p>These files contain time series of several sea ice ad atmospheric fields produced in an ensemble of perturbed parameter simulations using the E3SMv0-HiLAT model. The time series are used to produced seasonal means, which are used to examine emerging relationships in the ensemble discussed in our manuscript, as of September 2019, in review at JGR</p>
Figure 2 in Ensemble distribution modeling of the Mesopotamian spiny-tailed lizard, Saara loricata (Blanford, 1874), in Iran: an insight into the impact of climate change
Figure 2. The habitat suitability map of the Mesopotamian spiny-tailed lizard in southwestern Iran.
Structural models of overlapping dinucleosome for SAXS-based ensemble modeling
<p>Around transcription start sites, chromatin remodelers form overlapping dinucleosomes (OLDNs). OLDNs contain two structural units, octasome and hexasome. In the octasome, the same histone octamer as a canonical nucleosome is wrapped by DNA. In the hexasome, a histone hexamer that lacks an H2A-H2B dimer is wrapped by DNA. Changes in positional relationship between structural units of a biomolecular complex resulting from molecular motion or fluctuation often have functional significance. To understand fluctuation of OLDNs, we conducted SAXS-based ensemble modeling. Here structural models of OLDNs for the ensemble modeling are uploaded. The structures were obtained by performing coarse-grained molecular dynamics simulations followed by reverse-mapping of the coarse-grained models to atomistic models.</p>
Downscaled North American Multi-Model Ensemble Forecast for the Pacific Northwest USA
<h1>Downscaled North American Multi-Model Ensemble Forecast of Meteorological Variables for the Pacific Northwest</h1> <p>Monthly retrospective hindcasts (1982-2010) and forecasts (2011-2020) of temperature and precipitation are acquired for the Pacific Northwest region of the United States from five models (CFSv2, NASA GEOS5v2, CanCM4i, GEM-NEMO, and NCAR-CCSM) participating in the North American Multi-Model Ensemble project <a href="https://www.zotero.org/google-docs/?WlFE7n">(Kirtman et al., 2014)</a>. These models, detailed in Table 1 with more recent information available in <a href="https://www.zotero.org/google-docs/?PjZZHw">(Becker et al., 2022)</a>, are initialized monthly to provide a forecast of 0-9 months at a 1.0̊ × 1.0̊ spatial resolution. The multi-model ensemble mean (ENSMEAN) is then generated for each initialization by simply averaging all considered models and their ensemble members. Monthly ENSMEAN forecast is bias-corrected and spatially downscaled to 1/24th degree using the methodology described in <a href="https://www.zotero.org/google-docs/?jwPLzP">Wood et al. (2002)</a> and <a href="https://www.zotero.org/google-docs/?2b3lkj">Barbero et al. (2017)</a> using historical meteorological data <a href="https://www.zotero.org/google-docs/?zN8gKh">(gridMET; Abatzoglou, 2013)</a> as the baseline. Then, the downscaled ENSMEAN data are temporally disaggregated to daily timescales using an analog approach. The closest analog month for the ENSMEAN forecast is found from the gridMET dataset by minimizing the root mean square error (RMSE) of monthly gridMET and forecast precipitation (excluding gridMET data for the target month). Other daily meteorological variables (such as maximum and minimum temperature, maximum and minimum relative humidity, wind speed, and specific humidity) are extracted from the same analog month to use as input for the coupled crop-hydrology model. As a last step to the analog approach, the process corrects the bias between the forecast and analog month to ensure that monthly mean temperature and accumulated precipitation match those of the original forecast. </p> <p>Table 1. List of NMME models used to create Ensemble Mean.</p> <div> <table> <tbody> <tr> <td>Model </td> <td>Model Expansion </td> <td>Ensemble Size </td> <td>References</td> </tr> <tr> <td>NCEP- CFSv2 </td> <td>Climate Forecast System, version 2 </td> <td>24 </td> <td><a href="https://www.zotero.org/google-docs/?XTr15U">(Saha et al., 2014)</a></td> </tr> <tr> <td>NASA GEOS5v2</td> <td>Goddard Earth Observing System, version 5 </td> <td>4</td> <td><a href="https://www.zotero.org/google-docs/?fQzQZL">(Molod et al., 2020)</a></td> </tr> <tr> <td>CanCM4i </td> <td>Fourth Generation Canadian Coupled Global Climate Model </td> <td>10 </td> <td><a href="https://www.zotero.org/google-docs/?AoXCO8">(Merryfield et al., 2013)</a></td> </tr> <tr> <td>GEM - NEMO </td> <td>Global Environmental Multiscale Model – Nucleus for European Modelling of the Ocean </td> <td>10 </td> <td><a href="https://www.zotero.org/google-docs/?N4JwM9">(Lin et al., 2020)</a></td> </tr> <tr> <td>NCAR - CCSM </td> <td>Community Climate System Model </td> <td>10 </td> <td><a href="https://www.zotero.org/google-docs/?NMkImR">(Kirtman & Min, 2009)</a></td> </tr> </tbody> </table> </div> <p>The dataset has *.mat files which are MATLAB data files. </p> <h3>References</h3> <ol> <li> <p>Abatzoglou, J. T. (2013). Development of gridded surface meteorological data for ecological applications and modelling. International Journal of Climatology, 33(1), 121–131. <a href="https://doi.org/10.1002/joc.3413">https://doi.org/10.1002/joc.3413</a></p> </li> <li> <p>Barbero, R., Abatzoglou, J. T., & Hegewisch, K. C. (2017). Evaluation of Statistical Downscaling of North American Multimodel Ensemble Forecasts over the Western United States. Weather and Forecasting, 32(1), 327–341. https://doi.org/10.1175/WAF-D-16-0117.1</p> </li> <li> <p>Becker, E. J., Kirtman, B. P., L’Heureux, M., Muñoz, Á. G., & Pegion, K. (2022). A Decade of the North American Multimodel Ensemble (NMME): Research, Application, and Future Directions. Bulletin of the American Meteorological Society, 103(3), E973–E995. <a href="https://doi.org/10.1175/BAMS-D-20-0327.1">https://doi.org/10.1175/BAMS-D-20-0327.1</a></p> </li> <li> <p>Kirtman, B. P., & Min, D. (2009). Multimodel Ensemble ENSO Prediction with CCSM and CFS. Monthly Weather Review, 137(9), 2908–2930. https://doi.org/10.1175/2009MWR2672.1</p> </li> <li> <p>Kirtman, B. P., Min, D., Infanti, J. M., Kinter, J. L., Paolino, D. A., Zhang, Q., Dool, H. van den, Saha, S., Mendez, M. P., Becker, E., Peng, P., Tripp, P., Huang, J., DeWitt, D. G., Tippett, M. K., Barnston, A. G., Li, S., Rosati, A., Schubert, S. D., … Wood, E. F. (2014). The North American Multimodel Ensemble: Phase-1 Seasonal-to-Interannual Prediction; Phase-2 toward Developing Intraseasonal Prediction. Bulletin of the American Meteorological Society, 95(4), 585–601. <a href="https://doi.org/10.1175/BAMS-D-12-00050.1">https://doi.org/10.1175/BAMS-D-12-00050.1</a></p> </li> <li> <p>Lin, H., Merryfield, W. J., Muncaster, R., Smith, G. C., Markovic, M., Dupont, F., Roy, F., Lemieux, J.-F., Dirkson, A., Kharin, V. V., Lee, W.-S., Charron, M., & Erfani, A. (2020). The Canadian Seasonal to Interannual Prediction System Version 2 (CanSIPSv2). Weather and Forecasting, 35(4), 1317–1343. <a href="https://doi.org/10.1175/WAF-D-19-0259.1">https://doi.org/10.1175/WAF-D-19-0259.1</a></p> </li> <li> <p>Merryfield, W. J., Lee, W.-S., Boer, G. J., Kharin, V. V., Scinocca, J. F., Flato, G. M., Ajayamohan, R. S., Fyfe, J. C., Tang, Y., & Polavarapu, S. (2013). The Canadian Seasonal to Interannual Prediction System. Part I: Models and Initialization. Monthly Weather Review, 141(8), 2910–2945. <a href="https://doi.org/10.1175/MWR-D-12-00216.1">https://doi.org/10.1175/MWR-D-12-00216.1</a></p> </li> <li> <p>Molod, A., Hackert, E., Vikhliaev, Y., Zhao, B., Barahona, D., Vernieres, G., Borovikov, A., Kovach, R. M., Marshak, J., Schubert, S., Li, Z., Lim, Y.-K., Andrews, L. C., Cullather, R., Koster, R., Achuthavarier, D., Carton, J., Coy, L., Friere, J. L. M., … Pawson, S. (2020). GEOS-S2S Version 2: The GMAO High-Resolution Coupled Model and Assimilation System for Seasonal Prediction. Journal of Geophysical Research: Atmospheres, 125(5), e2019JD031767. https://doi.org/10.1029/2019JD031767</p> </li> <li> <p>Saha, S., Moorthi, S., Wu, X., Wang, J., Nadiga, S., Tripp, P., Behringer, D., Hou, Y.-T., Chuang, H., Iredell, M., Ek, M., Meng, J., Yang, R., Mendez, M. P., Dool, H. van den, Zhang, Q., Wang, W., Chen, M., & Becker, E. (2014). The NCEP Climate Forecast System Version 2. Journal of Climate, 27(6), 2185–2208. https://doi.org/10.1175/JCLI-D-12-00823.1</p> </li> <li> <p>Wood, A. W., Maurer, E. P., Kumar, A., & Lettenmaier, D. P. (2002). Long-range experimental hydrologic forecasting for the eastern United States. Journal of Geophysical Research: Atmospheres, 107(D20), ACL 6-1-ACL 6-15. https://doi.org/10.1029/2001JD000659</p> </li> </ol>
Large ensemble climate modelling time series for the Rhine catchment, including drought2018 storylines
<p>Dataset associated with <strong>Van der Wiel, Lenderink, De Vries (2021): Physical storylines of future European drought events like 2018 based on ensemble climate modelling, <em>Weather and Climate Extremes, </em>DOI <a href="http://doi.org/10.1016/j.wace.2021.100350">10.1016/j.wace.2021.100350</a>.</strong></p> <p>Large ensemble climate modelling time series for the Rhine catchment. The dataset contains three ensembles (present-day, pre-industrial + 2C-warming, pre-industrial + 3C-warming) of 2000 years each, various variables related to drought are included. All data is derived from the EC-Earth global climate model (v2, Hazeleger et al. 2012, DOI <a href="https://doi.org/10.1007/s00382-011-1228-5">10.1007/s00382-011-1228-5</a>). Descriptions of large ensemble experimental setup can be found in Van der Wiel et al. (2019, DOI <a href="http://doi.org/10.1029/2019GL081967">10.1029/2019GL081967</a>). Files: *_d_ECEarth_??_Rhine.tar.gz</p> <p>Additionally, three sets of storylines of droughts similar to the western European drought of 2018 are included. These are the simulated events selected from the large ensembles, using metrics 1, 2 and 3 of Van der Wiel et al. (2021, DOI <a href="http://doi.org/10.1016/j.wace.2021.100350">10.1016/j.wace.2021.100350</a>). Files: drought18_m[123]_Rhine.tar.gz</p>
Hypothetical ensemble dispersion model runs with statistical verification
<p>This dataset contains output from the dispersion model NAME (Numerical Atmospheric-dispersion Modelling Environment) generated by modelling the hypothetical eruption of two volcanoes (Hekla and Oraefajokull both in Iceland) and a radiological release from 12 different locations across Europe. The hypothetical eruption of Hekla is a 12km eruption lasting 24 hours and the hypothetical eruption of Oraefajokull is a 25km eruption lasting 24 hours. Each of the radiological releases is a 1PBq Cs-137 release over 6 hours. The scenarios were modelling using three different sets of met data from the Met Office unified model; data from the global deterministic forecast, data from the global ensemble forecast and data constructed to form a global analysis. </p> <p>Output from the runs is stored in gzipped tar files labelled <name>_scenario_<year><month>.tar.gz where <name> is hekla, orae (short for oraefajokull) or radiological. Each of these tarballs contains the output from all the runs with a release start date in the year and month given in the file name. The data is stored in NetCDF format with each NetCDF file containing the run output from a single run with one type of met data. For example the NetCDF file: 20181109T1200Z_engl_members.nc contains all the output from the run started at 12 UTC on 9 November 2018 using the ensemble global forecast met data. </p> <p>For the radiological scenario output is the total integrated air concentration and the total deposition after 48 hours. For the volcanic eruption scenarios output is the hourly air concentration of volcanic ash on 22 vertical levels, hourly ash column load and hourly ash deposits.</p> <p>Two additional files are included. These contain the Brier skill score computed by comparing the ensemble and deterministic output to the analysis output and the maximum distance at which threshold concentrations are exceeded. Full details of the computation can be found in a paper submitted to Atmospheric Chemistry and Physics.</p> <p>@Crown Copyright, Met Office</p>
Replication Data for: CHEEREIO 1.0: a versatile and user-friendly ensemble-based chemical data assimilation and emissions inversion platform for the GEOS-Chem chemical transport model
<p>This dataset includes three files necessary for understanding CHEEREIO model output in the demo section of my initial submission to GMD for the paper: <em>CHEEREIO 1.0: a versatile and user-friendly ensemble-based chemical data assimilation and emissions inversion platform for the GEOS-Chem chemical transport model.</em> Detailed guides for how to handle these datasets are provided in the <a href="https://cheereio.readthedocs.io/en/latest/Postprocess-workflow.html">CHEEREIO documentation postprocessing page</a>.</p> <ul> <li>control_hemco_diagnostics.nc contains the source-separated prior methane emissions.</li> <li>combined_hemco_diagnostics.nc contains the source-separated and ensemble member separated posterior methane emissions.</li> <li>bigY.pkl contains a Python dictionary which aligns TROPOMI XCH4 with simulated prior and posterior GEOS-Chem XCH4.</li> </ul>
Data for: Ensemble-based data assimilation of significant wave height from Sofar Spotters and satellite altimeters with a global operational wave model
<p>An ensemble-based method for wave data assimilation is implemented using significant wave height observations from the globally distributed network of Sofar Spotter buoys and satellite altimeters. The Local Ensemble Transform Kalman Filter (LETKF) method generates skillful analysis fields resulting in reduced forecast errors out to 2.5 days when used as initial conditions in a cycled wave data assimilation system. The LETKF method provides more physically realistic model state updates that better reflect the underlying sea state dynamics and uncertainty compared to methods such as optimal interpolation. Skill assessment far from any included observations and inspection of specific storm events highlights the advantages of LETKF over an optimal interpolation method for data assimilation. This advancement has immediate value in improving predictions of the sea state and, more broadly, enabling future coupled data assimilation and utilization of global surface observations across domains (atmosphere-wave-ocean).</p>
Output files from SPEEDY v.42 ensembles described in the paper: "Multi-decadal pacemaker simulations with an intermediate-complexity climate model" by F. Molteni, F. Kucharski and R. Farneti (part 1 of 2)
<p>The monthly-mean output from SPEEDY v.42 ensembles (either driven by prescribed sea-surface temperature (SST) or coupled to the TOM3 model) consists of a series of IEEE little-endian binary files and metadata files in text format.<br> For each year of integration (indicated by a 4-digit number YYYY) and ensemble member (indicated by a 3-digit number NNN), two binary files are present, named:<br> • attmNNN_YYYY.grd, including data on the 120x60 grid-point atmospheric grid;<br> • sftmNNN_YYYY.grd, including data on the 360x180 grid-point surface grid.<br> The metadata for these files are contained in the text files <strong>attmEEE.ctl</strong> and <strong>sftmEEE.ctl</strong> respectively, where EEE is a 3-digit ensemble identifier (usually, but not necessarily, equal to one of the ensemble-member number NNN).</p> <p><br> This repository contains data from:</p> <ul> <li>(part 1) a 41-year 5-member ensemble (653) run with prescribed SST</li> <li>(part 2) a 70-year 5-member ensemble (104) run with the coupled SPEEDY-TOM3 model.</li> </ul> <p>Integration years are 1980 to 2020 for ensemble 653 and 1951 to 2020 for ensemble 104.</p> <p><br> The structure of the binary data and metadata files follows the conventions for gridded datasets set by the GrADS diagnostic and plotting package (developed by the Center for Ocean-Land-Atmosphere Studies of George Mason University), as described here:<br> http://cola.gmu.edu/grads/gadoc/aboutgriddeddata.html</p> <p><br> In addition to the COLA-GMU web site, free version of the GrADS package for different platforms can be downloaded from the OpenGrADS web site:<br> http://opengrads.org/</p> <p><br> Specifically, the SPEEDY v.42 output consists of sequential-access files where each record contains a two-dimensional field. Three-dimensional fields are stored as a sequence of consecutive records, one for each of the 8 pressure levels where model-level data are interpolated by the post-processing routines. For each month of the year:</p> <p><br> the <strong>attmNNN_YYYY.grd</strong> files contain a sequence of <strong>9 3-D variables and 26 2-D variables</strong>;<br> the <strong>sftmNNN_YYYY.grd</strong> files contain a sequence of <strong>21 2-D variables</strong>.</p> <p>Within each record, grid-point data are stored as a NLONxNLAT array with longitude varying from west to east and latitude varying from south to north. The list of variables and levels is specified in the <strong>attmEEE.ctl</strong> and s<strong>ftmEEE.ctl</strong> files. These files contain descriptors which allow the data of each ensemble to be accessed as a single dataset by the GrADS package.</p> <p>Although the metadata files are specific to the GrADS package, the binary data can be read by different types of code. As example of fortran90 instructions to read the content of the <strong>attmNNN_YYY.grd</strong> and <strong>sftmNNN_YYY.grd</strong> files for one year/ens.member is as follows:</p> <p>integer, parameter :: nlon=120<br> integer, parameter :: nlat=60<br> integer, parameter :: nlev=8<br> integer, parameter :: nlon0=360<br> integer, parameter :: nlat0=180</p> <p>integer :: jmonth, jvar3d, jvar2d, jlev<br> real :: fld3d(nlon,nlat,nlev)<br> real :: fld2d(nlon,nlat), fld0(nlon0,nlat0)</p> <p>open (unit=1, file=”attmNNN_YYY.grd”, form=”formatted”, access=”sequential”)<br> open (unit=2, file=”sftmNNN_YYY.grd”, form=”formatted”, access=”sequential”)</p> <p>do jmonth=1,12</p> <p> do jvar3d=1,9<br> do jlev=1,nlev<br> read (1) fld3d(:,:,jlev)<br> …………<br> enddo<br> enddo</p> <p> do jvar2d=1,26<br> read (1) fld2d(:,:)<br> ………<br> enddo</p> <p> do jvar2d=1,21<br> read (2) fld0(:,:)<br> ………<br> enddo</p> <p>enddo</p> <p>close (1)<br> close (2)</p> <p> </p> <p> </p>
Output files from SPEEDY v.42 ensembles described in the paper: "Multi-decadal pacemaker simulations with an intermediate-complexity climate model" by F. Molteni, F. Kucharski and R. Farneti (part 2 of 2)
<p>The monthly-mean output from SPEEDY v.42 ensembles (either driven by prescribed sea-surface temperature (SST) or coupled to the TOM3 model) consists of a series of IEEE little-endian binary files and metadata files in text format.<br> For each year of integration (indicated by a 4-digit number YYYY) and ensemble member (indicated by a 3-digit number NNN), two binary files are present, named:<br> • attmNNN_YYYY.grd, including data on the 120x60 grid-point atmospheric grid;<br> • sftmNNN_YYYY.grd, including data on the 360x180 grid-point surface grid.<br> The metadata for these files are contained in the text files <strong>attmEEE.ctl</strong> and <strong>sftmEEE.ctl</strong> respectively, where EEE is a 3-digit ensemble identifier (usually, but not necessarily, equal to one of the ensemble-member number NNN).</p> <p><br> This repository contains data from:</p> <ul> <li>(part 1) a 41-year 5-member ensemble (653) run with prescribed SST</li> <li>(part 2) a 70-year 5-member ensemble (104) run with the coupled SPEEDY-TOM3 model.</li> </ul> <p>Integration years are 1980 to 2020 for ensemble 653 and 1951 to 2020 for ensemble 104.</p> <p><br> The structure of the binary data and metadata files follows the conventions for gridded datasets set by the GrADS diagnostic and plotting package (developed by the Center for Ocean-Land-Atmosphere Studies of George Mason University), as described here:<br> http://cola.gmu.edu/grads/gadoc/aboutgriddeddata.html</p> <p><br> In addition to the COLA-GMU web site, free version of the GrADS package for different platforms can be downloaded from the OpenGrADS web site:<br> http://opengrads.org/</p> <p><br> Specifically, the SPEEDY v.42 output consists of sequential-access files where each record contains a two-dimensional field. Three-dimensional fields are stored as a sequence of consecutive records, one for each of the 8 pressure levels where model-level data are interpolated by the post-processing routines. For each month of the year:</p> <p><br> the <strong>attmNNN_YYYY.grd</strong> files contain a sequence of <strong>9 3-D variables and 26 2-D variables</strong>;<br> the <strong>sftmNNN_YYYY.grd</strong> files contain a sequence of <strong>21 2-D variables</strong>.</p> <p>Within each record, grid-point data are stored as a NLONxNLAT array with longitude varying from west to east and latitude varying from south to north. The list of variables and levels is specified in the <strong>attmEEE.ctl</strong> and s<strong>ftmEEE.ctl</strong> files. These files contain descriptors which allow the data of each ensemble to be accessed as a single dataset by the GrADS package.</p> <p>Although the metadata files are specific to the GrADS package, the binary data can be read by different types of code. As example of fortran90 instructions to read the content of the <strong>attmNNN_YYY.grd</strong> and <strong>sftmNNN_YYY.grd</strong> files for one year/ens.member is as follows:</p> <p>integer, parameter :: nlon=120<br> integer, parameter :: nlat=60<br> integer, parameter :: nlev=8<br> integer, parameter :: nlon0=360<br> integer, parameter :: nlat0=180</p> <p>integer :: jmonth, jvar3d, jvar2d, jlev<br> real :: fld3d(nlon,nlat,nlev)<br> real :: fld2d(nlon,nlat), fld0(nlon0,nlat0)</p> <p>open (unit=1, file=”attmNNN_YYY.grd”, form=”formatted”, access=”sequential”)<br> open (unit=2, file=”sftmNNN_YYY.grd”, form=”formatted”, access=”sequential”)</p> <p>do jmonth=1,12</p> <p> do jvar3d=1,9<br> do jlev=1,nlev<br> read (1) fld3d(:,:,jlev)<br> …………<br> enddo<br> enddo</p> <p> do jvar2d=1,26<br> read (1) fld2d(:,:)<br> ………<br> enddo</p> <p> do jvar2d=1,21<br> read (2) fld0(:,:)<br> ………<br> enddo</p> <p>enddo</p> <p>close (1)<br> close (2)</p>
Calibration Dataset - HPOSS: A hierarchical portfolio optimization stacking strategy to reduce the generalization error of ensembles of models
<p>Calibration dataset for the study case presented in the paper "HPOSS: A hierarchical portfolio optimization stacking strategy<br> to reduce the generalization error of ensembles of models".</p> <p>It encompasses a .h5 file with a dataset called "Calibrations_LHS", which consists of a 80x5 numpy array of float numbers corresponding to (d1(m),d2(m),d3(m),d4(m),zeta_max(Pa)), where d_i, i = 1,...,4 are dimensions (in meters) of the I-beam and zeta_max is the maximum bending stress (in Pascals) developed in a simply such supported beam with 1 m of length after a point load of 1000N is applied at its center.</p>
A multi-model ensemble of baseline and process-based models improves the predictive skill of near-term lake forecasts: data, forecasts, and scores
<p>This data publication contains zipped parquet from the Falling Creek Reservoir multi-model ensemble (MME) forecasting work using the FLARE (Forecasting Lake And Reservoir Ecosystems) system and baseline models: drivers.zip contains NOAA driver forecast files, targets.zip contains in-situ water temperature observations, forecasts.zip contains forecast parquet files generated from the MME workflow (FLARE & baseline models), and scores.zip contains forecast skill metrics required for analysis.</p>
Standard Error Estimates for ARRI Ensemble LM model outputs
<p>Summary</p> <p>Basal area per acre (BAA) standard error estimate (SEE) for all trees, pine trees, and non-pine trees across three diameter at breast height (DBH) size classes, 2- to 10-inch, 10- to 14-inch, and 14+ inch. Models were informed by relative density rasters from 2018 Light Detection and Ranging (lidar) point clouds.</p> <p>Description</p> <p>The LM_SEE_rasters are modelled basal area per acre standard error estimate single band rasters. The units for the rasters’ are square foot per acre. Rasters are divided into three tree species groups: 'All' trees, 'Pine' trees (defined as trees of the genus<em> Pinus)</em>, and 'No-Pine' trees, and three size classes: LT 10 for trees with DBH between 2- and 10-inches, 10-14 for trees with DBH between 10- and 14- inch DBH, and GT 14 for trees with DBH greater than 14-inches.</p> <p>Ensemble linear regression models (LM) of estimated tree basal area per DBH class were created from Restore field plots and relative density canopy cover rasters, or RDCC (St. Peter, et al., 2023). This ensemble LM model was created using a custom R script that was based off the work detailed in Hogland, 2021. The ensemble LM script was modified to use the lm() function in place of the GAM modelling functions. The parameters used were 0.75 for the percent of data used to train the model (selected using random sampling with replacement), 50 models, and using gaussian family. The estimated BAA for each of the 50 ensemble LM models for each cell were averaged (mean) to produce the LM estimate, additionally the variability between these estimates was used to create the standard error estimate (SEE) for each cell. </p> <p>The 246 Restore field plots used to train the LM model of basal area include measurements of all trees within four non-overlapping 9m radius circular subplots within a 36m square plot. Tree diameter at breast height (DBH), species, count, and condition measurements were recorded. Measurements were summarized to the plot and DBH (square inches) was converted to basal area per acre (square feet per acre) using the formula 0.005454 * DBH^2. Restore field plots were measured in the Spring of 2018. The RDCC metrics are 5m resolution multiband rasters produced by applying a custom r software function that uses the r software’s ‘lidR’ package to produce forest metrics summarized from Light Imaging Detection and Ranging (LiDAR) point clouds. ARSA LiDAR is a combination of three collections, Block 2 and 3 were collected in early 2018 and has a NPS of 0.7-m using a Riegl VQ-1560i lidar system. Leon county LiDAR data has a nominal pulse spacing (NPS) of 0.35-m and was acquired between February 05, 2018 and April 25, 2018 using the Leica ALS80 HP SN8137 and SN8235 lidar systems. Choctawhatchee data was acquired in early 2017, using the Riegl LMS-Q1560 lidar system and has a NPS of 0.7-m. Rasters were generated in their vendor provided spatial projection before being reprojected to UTM Zone 16.</p> <p>The 5m resolution RDCC bands were summarized to 40x40m to correspond with the area of our plots and used as predictor variables in the models of all trees basal area. Each 5m pixel value represents the estimated standard error of the basal area per acre estimate as if it was the center of a 40x40m (8x8 cells) plot surrounding that pixel. </p> <p>References:</p> <p>Hogland, J. (2021). Ensemble Generalized Additive Models (EGAM). Retrieved from Jupyter Notebook: <a href="https://colab.research.google.com/drive/1GnRagruTUCoPJQZSkZ2vMKS9aAKgnhEw?usp=sharing">https://colab.research.google.com/drive/1GnRagruTUCoPJQZSkZ2vMKS9aAKgnhEw?usp=sharing</a></p> <p>St. Peter, Joseph, Drake, Jason, Medley, Paul, & Ibeanusi, Victor. (2023). Relative Density Canopy Cover Outputs for Leon Lidar data in the Florida Panhandle 2018 [Data set]. In Remote Sensing (Vol. 13, Number 23, p. 4763). Zenodo. <a href="https://doi.org/10.5281/zenodo.8222114">https://doi.org/10.5281/zenodo.8222114</a></p> <p>Credits</p> <p>This dataset was built by Joseph St. Peter of FAMU’s Center for Spatial Ecology and Restoration using 2018 LiDAR data funded by Leon County, Northwest Florida Water Management District, US Geological Survey and the USDA Forest Service and processed using the r package lidR. Restore plots were funded by the Gulf Coast Ecosystem Restoration Council (RESTORE Council) through an interagency agreement with the USDA Forest Service (17-IA-11083150-001) for the Apalachicola Tate’s Hell Strategy 1 project.</p> <p>Use Limitations</p> <p>This spatial data is based on various data collection and processing techniques as well as on modeling or interpretation. While this data uses the most current and complete information available at the time of production, spatial data and derivative products may vary in accuracy. Spatial data are often developed from sources of differing accuracy which may be accurate only at certain scales. This data has been quality checked but may contain spurious errors or be incomplete or inappropriate for certain uses. Spatial data products used for purposes other than those for which they were created, may yield inaccurate or misleading results. The USDA Forest Service, Florida A&M University, and the Center for Spatial Ecology & Restoration (CSER) reserves the right to correct, update, modify, remove or replace GIS products at any time and without notification. This data may not be distributed without written permission from the Center for Spatial Ecology & Restoration (CSER) at Florida A&M University, and/or the USDA Forest Service.</p>
Data observed at Kawajima land subsidence observatory (Japan) and ensemble model
<p>This data set contains all data necessary to reproduce the results of the manuscript submitted by Akitaya & Aichi. The data set includes hydraulic head and land subsidence data observed at the Kawajima land subsidence observatory (Japan), and an ensemble model parameter set constructed using the evolutionary multimodal algorithm, ensemble simulation results, and predictive uncertainty analysis results obtained through ensemble model output statistics. Please refer to the "readme.txt" file provided in each individual folder for detailed instructions on how to read the data.</p>
Ensemble BLUP, Machine Learning, and Deep Learning Models Predict Maize Yield Better Than Each Model Alone.
<p>Data and scripts exploring ensembling strategies using the models developed in <a href="https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkad006/6982634">Kick et al., 2023</a> (see also <a href="https://zenodo.org/record/7401113">1</a>, <a href="https://zenodo.org/record/6916775">2</a>). Download all files to a single directory then run setup.sh or manually unzip using tar.</p> <p> </p> <table> <tbody> <tr> <td><strong>Filename</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>setup.sh</td> <td>Simple script that unzips zipped directories</td> </tr> <tr> <td>ext_data</td> <td>Reduced data from Kick et al. 2023</td> </tr> <tr> <td>ext_data_notebooks</td> <td>Contains python notebooks containing analysis and R markdown file containing visualization of results. Python and R data objects are written to allow results to be read in instead of re-generated.</td> </tr> <tr> <td>output</td> <td>Folder containing a placeholder file.</td> </tr> </tbody> </table> <p> </p> <p>This research used resources provided by the United States Department of Agriculture’s Agricultural Research Service (project number 5070-21000-041-000-D). The SCINet project of the USDA Agricultural Research Service (project number 0500-00093-001-00-D) was instrumental in the training of the models used in this work. In addition, we would like to acknowledge those presently and historically involved in generating data for the Genomes to Fields Initiative.</p> <p> </p> <p> </p> <p> </p>
K-model and H-gradient model ensemble averaged data (Version 1)
<p>It is the ensemble averaged data used in the creation of the manuscript "The impact of subgrid-scale turbulence model on tropical cyclone dynamics in convection-permitting simulations"</p>
Data for: Ensemble-based data assimilation of significant wave height from Sofar Spotters and satellite altimeters with a global operational wave model
Open the record for dataset details and reuse information.
Testing whether ensemble modelling is advantageous for maximising predictive performance of species distribution models
Open the record for dataset details and reuse information.
Data release for 'Ensemble Forecasting of Major Solar Flares: Methods for Combining Models'
<p>This is a release of the data that were used for validation in the paper 'Ensemble Forecasting of Major Solar Flares: Methods for Combining Models' by J. A. Guerra, S. A. Murray, D. S. Bloomfield, and P. T. Gallagher, that has been submitted to the Journal of Space Weather and Space Climate.</p> <p> </p> <ul> </ul> <p>The naming scheme for the files is in the format:</p> <pre><code>class_type_metric.dat</code></pre> <ul> <li>'class' denotes whether the forecast is for M- or X- class flares.</li> <li>'type' is what kind of forecast, i.e., the original ensemble members, an ensemble created from probabilistic validation metrics, or an ensemble created from categorical validation metrics.</li> <li>'metric' specifies the metric used to create the ensemble in the case of 'probabilistic' or 'categorical' types as above (see paper for further details), or in the case of the original ensemble members the name of the operational forecasting method.</li> </ul> <p> </p> <p>The data files are in the format:</p> <pre><code>obs,prob</code></pre> <ul> <li>'obs' denotes whether or not a flare was observed within 24 hours of the forecast issue time (1 for yes and 0 for no).</li> <li>'prob' gives the probabilistic forecast value (between 0.0 and 1.0).</li> </ul> <p> </p> <p>These data files can easily be read into the <a href="https://cran.r-project.org/web/packages/verification/verification.pdf">R verification package</a> to replicate the results presented in the paper.</p>
Cluster configurations of the Hegselmann-Krause model on network ensembles
<p>This is the raw data underlying the results of the preprint [arxiv:2102.10910](https://arxiv.org/abs/2102.10910).</p> <p> </p> <p>## Data</p> <p>For each measured combination of the confidence and system size, there is one gzipped<br> file. For different ensembles, we collected data in different ranges and quality.<br> The paramters are:</p> <p>* Number of samples `m` per parameter combination<br> * Range `r` of confidences epsilon<br> * Distances `d` between values of epsilon (basically the resolution of the data)<br> * Largest size `N_max`</p> <p>The single files follow a naming scheme of `n{N}_e{epsilon}.cluster.dat.gz`, where<br> `{N}` signals the system size of the simulation and `{epsilon}` is the confidence<br> value of the simulation (without a decimal point, i.e., `0050` corresponds to `epsilon = 0.050`).<br> The sizes `N` are usually powers of two (or for the lattices, perfect squares close to powers of two).</p> <p>We present the data for each ensemble in one archive.</p> <p><br> * Fully connected `full.tar`<br> * `m = 1000`, `r = [0.0, 0.6]`, `d = 0.001`, `N_max = 262144`<br> * Barabasi Albert with a mean degree of 4 `BA4.tar`<br> * `m = 1000`, `r = [0.0, 0.6]`, `d = 0.002`, `N_max = 32768`<br> * Barabasi Albert with a mean degree of 10 `BA10.tar`<br> * `m = 1000`, `r = [0.0, 0.6]`, `d = 0.001`, `N_max = 65536`<br> * Square lattice with first nearest neighbors `lat1.tar`<br> * `m = 1000`, `r = [0.0, 0.6]`, `d = 0.001`, `N_max = 16384`<br> * Square lattice with second nearest neighbors `lat2.tar`<br> * `m = 1000`, `r = [0.0, 0.6]`, `d = 0.001`, `N_max = 16384`<br> * Square lattice with third nearest neighbors `lat3.tar`<br> * `m = 1000`, `r = [0.0, 0.6]`, `d = 0.001`, `N_max = 65536`<br> * Square lattice with fourth nearest neighbors `lat4.tar`<br> * `m = 1000`, `r = [0.0, 0.6]`, `d = 0.001`, `N_max = 65536`<br> * Square lattice with third nearest neighbors and 1% rewired edges `lat3_ws.tar`<br> * `m = 1000`, `r = [0.0, 0.3]`, `d = 0.001`, `N_max = 16384`<br> * connected Erdos Renyi with mean degree of 10 `ER10.tar`<br> * `m = 1000`, `r = [0.0, 0.3]`, `d = 0.002`, `N_max = 32768`</p> <p> </p> <p>## Data format</p> <p>Each final state is encoded as three lines:</p> <p>* The convergence time is a single integer with a line prefix '# sweeps: '<br> * The positions of all clusters in opinion space with a line prefix '# ' (unsorted)<br> * The number of agents in each of the clusters without a line prefix</p> <p> </p> <p>## Python example for reading the format</p> <p>An example script, which visualizes the S vs eps graph for the largest size of the fully connected<br> case, with a function to read this format is given in `example.py`.</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.