Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
4,276
datasets available to search
ShareScore release 0.9.0
Dataset results
4,276 results for “Estimation”
Assessing tropospheric turbulence impact on VGOS telescope placement in the Indian subcontinent for the estimation of Earth Orientation Parameters
<p>The dataset accompanying this study is composed of three distinct files, each integral to the research conducted. The file, named 'Simulated Data', includes the results derived from the simulations performed within this investigation. This file serves as a repository of the computed outcomes. The file, named 'Data and Code', includes the MATLAB scripts utilized to compute the Cn value from the Zenith Wet Delay (ZWD). Additionally, this file encompasses the relevant datasets for both wind speed and ZWD at various station locations. The third file contains the geographical coordinates of the Indian stations that were used in the study. Together, these files constitute a complete dataset that supports the study’s objectives and verification of the findings. </p>
GloRESatE - Global Rainfall Erosivity from Reanalysis and Satellite Estimates
<p>Rainfall erosivity measures the impact of rainfall kinetic energy and intensity or its potential to cause soil erosion. The sparsely available gauge rainfall dataset limits reliable rainfall erosivity assessment globally. GloRESatE is a state-of-the-art global rainfall erosivity dataset with a high spatial resolution of 0.1° × 0.1°. It integrates satellite data (CMORPH, IMERG Final Run), reanalysis data (ERA5-Land), and observations from 6,170 gauge stations worldwide. Created using advanced Gaussian Process Regression, this dataset provides accurate and reliable rainfall erosivity information. It serves as a vital resource for hydrological research, aiding studies in soil erosion, water resource management, and climate change impact assessments on a global scale.</p> <p> </p> <p>Das, S., Jain, M.K., Gupta, V., McGehee, R.P., Yin, S., de Mello, C.R., Azari, M., Borrelli, P. and Panagos, P., 2024. GloRESatE: A dataset for global rainfall erosivity derived from multi-source data. <em>Scientific Data</em>, <strong>11</strong>:926. https://doi.org/10.1038/s41597-024-03756-5</p>
Accelerometer and Force/Torque Sensor Measurements for Parameter and State Estimation of an Unknown Robot End Effector
<h1>Introduction</h1> <p>This dataset was created as part of a study on the development of an estimator for the contact wrench (force and torque) of an unknown robot end effector. A conference paper from this study has been submitted and accepted for the 2024 IEEE International Conference on Real-time Computing and Robotics (RCAR 2024) [1]. </p> <p>A force/torque sensor (FTS) was attached to the robot wrist, and the unknown end effector was attached to the FTS. An inertial measurement unit (IMU) was in turn attached to the end effector. The FTS measurement can be decomposed into the (1) sensor bias, (2) contact wrench, and the effects from (3) gravity, (4) inertia, (5) vibrations, and (6) noise. Estimation of the contact wrench requires that the remaining effects are compensated for. The FTS and IMU sensor biases, as well as mass and mass center of the unknown end effector, were estimated as described by Vougioukas [2]. His method requires FTS and IMU samples from 24 specific orientations of the sensors. See his paper for a description of this calibration method.</p> <p>The hardware used to generate this dataset were:</p> <ul> <li>KUKA LBR Med 14 serial robot (KUKA AG, Germany)</li> <li>ATI Gamma FTS (ATI Industrial Automation, Inc., USA)</li> <li>ATI Netbox (ATI Industrial Automation, Inc., USA)</li> <li>MPU6886 IMU (M5Stack, China) </li> <li>Arduino Mega 2580 with a W5500 Ethernet Shield </li> </ul> <h1>Method</h1> <p>The robot was used to move the end effector, FTS, and IMU such that a trajectory could be replicated with high precision and accuracy. The trajectory was a simple rotation about the FTS y-axis. This trajectory and the resulting measurements were performed three times. The sensor signals were sampled during each iteration when:</p> <ol> <li>The robot moved freely without any kind of disturbance (<strong>basline</strong>).</li> <li>The robot moved freely with gentle taps to the robot body, using a rubber hammer (<strong>vibrations</strong>).</li> <li>The robot moved with gentle taps to the body using the hammer, and with a manual force exerted on the end effector (<strong>vibrations and contact</strong>).</li> </ol> <p>The IMU signal was obtained by the Arduino Mega using I2C, and the signal was sent from the Arduino to the external PC using the ethernet shield. This setup resulted in <strong>a phase of the IMU signal by 8416 μs</strong>. This was compensated for in the offline analysis of the study on the contact wrench estimator [1]. The sensor samplig rates were different for each sensor; they were approximately 100 Hz for the robot controller (FTS orientation measurements), 700 Hz for the FTS, and 254 Hz for the IMU. The frequency for each signal can be obtained through the timestamps in the dataset.</p> <h1>Dataset</h1> <p>Each CSV file has a row which serves as the header, which labels the columns of each file. The following nomenclature of the column labels were used:</p> <p><strong>t </strong> - Timestep in microseconds. Epoch time. <br><strong>fx,</strong> <strong>fy, fz</strong> - The force components as measured by the FTS.<br><strong>tx, ty, tz </strong>- The torque components as measured by the FTS.<br><strong>ax, ay, az </strong> - The acceleration components measured by the IMU.<br><strong>gx,gy,gz </strong>- The direction of the gravitational vector in the FTS frame.<br><strong>r11, r12, r13, r21, r22, r23, r31, r32, r33 </strong>- The components of the rotation matrix that represents the FTS orientation in the world frame. (R_wf)</p> <p>The measurements from the FTS and IMU signals from the 24 orientations (as required for the calibration method described by Vougioukas [2]), are stored in <strong>0-calibration_fts-accel.csv</strong>. Additionally, the files <strong>0-steady-state_wrench.csv </strong>and <strong>0-steady-state_accel.csv</strong> contains the continuous sensor signal from the FTS and IMU, respectively, while they were at rest; these two files can be used to calculate the sensor signal variances.</p> <p>After calibration, each sensor signal was recorded independently and stored in a separate file from the other sensors. The raw (biased) values were stored. Each test iteration produced three files:</p> <ol> <li>The end effector/FTS/IMU orientation in <strong>[test_iteration]_orientation.csv</strong></li> <li>The unbiased wrench as measured by the FTS in [<strong>test iteration]_wrench.csv</strong></li> <li>The unbiased acceleration as measured by the IMU in <strong>[test_iteration]_accel.csv</strong></li> </ol> <p>The test iteration prefix for these files are: <strong>1-baseline</strong>, <strong>2-vibrations, </strong>and <strong>3-vibrations-contact, </strong>as described in the previous section "Method". To obtain the relative time between samples across the test iteration files ([]<strong>_orientation</strong>, []<strong>_wrench</strong>, and []<strong>_accel.csv</strong>), load each dataset and determine which has the earliest timestamped sample on the first row. Then, subtract this initial timestamp value from all timestamps across the files for the respective test iteration.</p> <p>Note that the IMU frame does not align with the FTS frame (<strong>_accel.csv</strong> vs <strong>_wrench.csv</strong>), the following table describes the rotation matrix R_fa which can be used to transform the acceleration measurements from the IMU frame {a} to the FTS frame {f}. </p> <p>R_fa = </p> <table> <tbody> <tr> <td>0</td> <td>-1</td> <td>0</td> </tr> <tr> <td>0</td> <td>0</td> <td>1</td> </tr> <tr> <td>-1</td> <td>0</td> <td>0</td> </tr> </tbody> </table> <h1>References</h1> <p>[1] A. Skrede, "A Linear Discrete Kalman Filter to Estimate the Contact Wrench of an Unknown Robot End Effector", Accepted for the 2024 IEEE International Conference on Real-time Computing and Robotics (RCAR), Ålesund, Norway, June 2024 </p> <p>[2] S. Vougioukas, “Bias Estimation and Gravity Compensation For Force-Torque Sensors,” in Recent Advances in Simulation, Computational Methods and Soft Computing. WSEAS Press, 2001, pp. 82–85. </p>
The bearing capacity of asteroid (65803) Didymos estimated from boulder tracks
<p>This material constitutes the source data and codes used for the the computations and plots of the paper 'The bearing capacity of asteroid (65803) Didymos estimated from boulder tracks' by Bigot, Lombardo et al. This article has been published in Nature Communications on 30 July, 2024.</p> <p>The folder "Source Data" contains an Excel document that provides the raw data used to make the figures and supplementary figures. </p> <p>The folder "Codes" contains the Matlab codes used for the computations of the results, including comments on the figures produced by each code. It also contains a .mat file that consitutes the topographic data of Didymos from Barnouin et al. (2024), used in the code 'TopographyDidymos.m'.</p> <p>The folder "Images" contains the three DART images (DRACO) and the Moon image from LROC used in this article.</p> <p> </p>
Soil Bacteria Community-Weighted rrn Operon Copy Number Estimation
<p>Datasets and R-Scripts for estimating community-weighted rrn operon copy number for soil bacteria communities collected from the Yukon-Kuskokwim River Delta, AK, USA, and from La Selva Biological Station, Costa Rica. File descriptions follow:</p> <p>"rrnDB_copy_number_database.csv": The Ribosomal RNA Database downloaded from <a href="rrndb.umms.med.umich.edu.">rrndb.umms.med.umich.edu.</a> Citation: </p> <ul> <li>Stoddard S.F, Smith B.J., Hein R., Roller B.R.K. and Schmidt T.M. (2015) <em>rrn</em>DB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. <em>Nucleic Acids Research</em> 2014; doi: 10.1093/nar/gku1201 [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25414355">PMID:25414355</a></li> </ul> <p>"AK_16S_Genus_Abundance.csv": Count of ASVs by taxon (assigned to genus level) present in each soil sample collected in the Yukon_Kuskokwim River Delta, AK, USA.</p> <p>"Costa_Rica_16S_OTU_Abundance": Count of OTUs by taxon present in each soil sample collected in La Selva Biological Station, Costa Rica.</p> <p>"Alaska_rrn_copy_number_estimation_script.R": an R script for processing Alaska ASV count table and estimating community-weighted rrn operon copy numbers for each soil sample.</p> <p>"CostaRica_rrn_copy_number_estimation_script.R": an R script for processing Costa Rica OTU count table and estimating community-weighted rrn operon copy numbers for each soil sample.</p>
Transferring energy signatures across space and time to assess their viability for rapid urban energy demand estimation
<p>This data archive provides simulated hourly heating and cooling building energy demand for current and future RCP85 climate for 8 representative cities for a single-family and small office building archetype.</p> <p>The data forms part of the following publication:</p> <p><em>Eggimann S.; Fiorentini M. (2024): Transferring energy signatures across space and time to assess their viability for rapid urban energy demand estimation. Energy and Buildings. https://doi.org/10.1016/j.enbuild.2024.114348</em></p> <p><strong>Attributes</strong></p> <ul> <li>ID_origin: City ID of source city</li> <li>ID_destination: City ID of target city</li> <li>Signature_Cooling: Cooling demand determined by the signature approach</li> <li>Model_Cooling: Cooling demand determined by EnergyPlus</li> <li>Absolute_Diff: Absolute difference</li> <li>Percentage_Diff: Relative difference</li> <li>Daily_Tout: Average daily dry-bulb ambient temperature</li> </ul> <p><strong>Instruction</strong></p> <p>To obtain the simulation and energy signature-based results, it is required to filter the dataset and set the source ID to the destination ID. The city IDs are provided in the file city_table_ID.</p> <p><strong>Source</strong></p> <p>The archetypes are provided by the Office of Energy Efficiency & Renewable Energy: https://www.energycodes.gov/prototype-building-models</p>
Quantifying the basic reproduction number and the under-estimated fraction of mpox cases around the world at the onset of the outbreak: a mathematical modeling and machine learning- based study
<p><span>In 2022, there was a global resurgence of mpox, with different clinico-epidemiological features compared with previous</span><br><span>outbreaks. During this resurgence, sexual contact was hypothesized as the primary transmission route, with the community</span><br><span>of men having sex with men (MSM) being disproportionately affected. Because of the stigma associated with sexually</span><br><span>transmitted infections, especially those impacting MSM, the real burden of mpox could be masked.</span><br><span>We quantified the basic reproduction number (R</span><span>0</span><span>) and the under-estimated fraction of mpox cases in 16 countries, from the</span><br><span>onset of the outbreak until early September 2022, using Bayesian inference and a compartmentalized, risk-structured (high-</span><br><span>and low-risk populations), two-route (sexual and non-sexual transmission) mathematical model. Machine learning (ML) was</span><br><span>leveraged to identify under-estimation determinants.</span><br><span>Estimated R</span><span>0</span><span> </span><span>ranged between 1·37 (Canada) and 3·68 (Germany). The under-estimation rates for the high- and low-risk</span><br><span>populations varied between 25-93% and 65-85%, respectively. The estimated total number of mpox cases, relative to the</span><br><span>reported cases, is highest in Colombia (3·60) and lowest in Canada (1·08). In the ML analysis, two clusters of countries could</span><br><span>be identified, differing in terms of attitudes towards the 2SLGBTQIAP+ community and importance of religion.</span><br><span>Given the substantial mpox under-estimation, surveillance should be enhanced and campaigns against the stigmatization of</span><br><span>MSM should be organized. Countries have different social characteristics, potentially explaining the various degrees of under-</span><br><span>reporting in mpox cases, which should be considered by studies assessing the effectiveness of community-based</span><br><span>interventions.</span></p>
Monthly methane emissions estimated with the atmospheric inversion model CarbonTracker Europe - CH4
<p>Monthly estimates of global methane emissions from CarbonTracker Europe - CH4 (CTE-CH4). CTE-CH4 is a Bayesian inversion framework based on an ensemble Kalman filter algorithm using the Eulerian global atmospheric transport model TM5. The gridded fluxes are available with a resolution of 1.0x1.0 degrees and in units of kgCH4/m2/month. The gridded flux file contains variables for posterior fluxes from soils (bio_flux_opt) and anthropogenic sources (anth_flux_opt) and the total posterior flux (total_flux_opt). Priors used: Anthropogenic: EDGAR v6, biosphere/wetlands (soils): LPX-Bern DYPTOP v1.4, Ocean: Weber et al. (2019), Biomass burning: GFED v4.1, Termites: VISIT. A more detailed setup of the inversion is documented in Erkkilä, A., Tenkanen, M., Tsuruta, A., Rautiainen, K., and Aalto, T.: Environmental and Seasonal Variability of High Latitude Methane Emissions Based on Earth Observation Data and Atmospheric Inverse Modelling, Remote Sensing, 15, https://doi.org/10.3390/rs15245719, 2023. Note: Fluxes are optimised at 1.0x1.0 degrees in northern high latitudes (USA, Canada, Europe and Russia), but are also provided here at the same resolution for other regions.</p>
3D Stereo Body Pose Estimation - Evaluation Plots
<p>Evaluation plots for the "3D Stereo Body Pose Estimation" project, aimed at estimating 3d keypoints from humans captured using a OAK-D camera.</p> <p>The project is originated in the context of the activities of the postgraduate course IA904 - Model Project in Visual Computing, offered in the first semester of 2024, at Unicamp, under the supervision of Prof. Dr. Leticia Rittner and Prof. Paula D. Paro Costa, both from the Department of Computer and Automation Engineering (DCA) of the Faculty of Electrical and Computer Engineering (FEEC).</p> <p>The <a href="https://github.com/Disciplinas-FEEC/IA904-2024S1/tree/main/projetos/3DStereoBodyPoseEstimation">project page</a> have a full description of the project (portuguese).</p>
Dataset - DeepWealth: A Generalizable Open-Source Deep Learning Framework using Satellite Images for Well-Being Estimation
<p>This dataset encapsulates the Checkpoints obtained during the training process of the Deep Learning model, which can be used for new estimations.</p> <p>The aim of the DeepWealth package is to provide a generalizable Deep Learning framework for the use of remote sensing in poverty estimation. The combination of Deep Learning and Earth Observation data is increasingly being used to estimate socioeconomic conditions at regional and global scales. The proposed framework aligns with the Sustainable Development Goal SDG1 of ending poverty. The framework provides open-source data, code, and training models (checkpoints) for reproducibility and replicability.</p> <ul> <li>The source code can be found in <a href="https://github.com/PARSECworld/DeepWealth" target="_blank" rel="noopener">https://github.com/PARSECworld/DeepWealth</a></li> <li>The metadata from source code can be found in <a href="https://github.com/PARSECworld/DeepWealth/blob/main/metadata.pdf" target="_blank" rel="noopener">https://github.com/PARSECworld/DeepWealth/blob/main/metadata.pdf</a></li> <li>The paper describing the development of this framework can be found at: Ben Abbes, A., Machicao, J., Corrêa, P. L. P., Specht, A., Devillers, R., Ometto, J. P., Kondo, Y., & Mouillot, D. (2024). DeepWealth: A generalizable open-source deep learning framework using satellite images for well-being estimation. <em>SoftwareX</em>, 27, 101785. <a href="https://doi.org/10.1016/j.softx.2024.101785">https://doi.org/10.1016/j.softx.2024.101785</a> </li> </ul>
Estimated surface NO2 over Europe for the year 2019-2021
<p>These datasets consist of estimated daily surface NO<sub>2</sub> concentrations over Europe at ~1km spatial resolution in tiff file format generated using S-MESH model and is part of the research article https://doi.org/10.1016/j.rse.2024.114321. Files are zipped into 3 folders each corresponding to a year and can be unzipped from command line using "tar -xvzf filename.tar.gz". Each file represents surface NO<sub>2</sub> during the Sentinel-5P satellite overpass time and the file is named based on the date of measurement. Each tiff file is a single band image with an extent of 25°W-42.5°E & 29.9-74.28°N in EPSG:4326 - WGS 84 projection. The surface NO<sub>2</sub> concentrations are estimated using Sentinel-5P TROPOMI tropospheric column density and a XGBoost machine learning model. The overall median absolute error of the model predictions across Europe is 4.43μg/m<sup>3 </sup></p> <p><strong>Summary</strong></p> <ul> <li>Data: NO<sub>2</sub> concentrations over Europe at ~1km spatial resolution</li> <li>Time Period: 2019-2021</li> <li>Methodology: Using Sentinel-5P TROPOMI NO2 and XGBoost </li> </ul> <ul> <li><span>More information in the article </span><span><a href="https://www.sciencedirect.com/science/article/pii/S0034425724003390#s0155" target="_blank" rel="noopener"><span>https://authors.elsevier.com/sd/article/S0034-4257(24)00339-0</span></a></span><span> or </span><span><a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.rse.2024.114321" target="_blank" rel="noopener"><span>https://doi.org/10.1016/j.rse.2024.114321 </span></a></span></li> </ul>
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
<p>Bulk ATAC-seq data of tumour samples result in an averaged signal across different cell-types (cancer, stromal, vascular and immune cells). We propose a deconvolution framework called EPIC-ATAC (<a href="https://doi.org/10.7554/eLife.94833.1">https://doi.org/10.7554/eLife.94833.1</a>), which relies on newly identified cell-type specific ATAC-Seq marker peaks and reference profiles for all major cancer-relevant cell-types to predict the proportions of each cell-type.</p> <p>To evaluate EPIC-ATAC, we generated a bulk ATAC-Seq dataset from peripheral blood mononuclear cells (PBMCs) samples, from which the number of cells in each cell-type has been estimated using flow cytometry, as ground truth for cell proportions. The data provided in this Zenodo deposit correspond to:</p> <p>- The raw counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts.txt</p> <p>- The normalized (TPM-like) counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts_norm.txt</p> <p>- The cell fractions of each cell type in each sample: PBMC_cell_fractions.txt</p> <p>- The peaks called in each sample using MACS2 (*narrow.peaks): *_normalized.narrowPeak</p> <p>- Bed files listing ATAC-Seq fragments for each sample: *.bed</p> <p>We also evaluated EPIC-ATAC on multiple pseudobulks generated from single-cell ATAC-Seq data. We provide rds files containing the pseudobulks data used in our work for the evaluation of EPIC-ATAC. The rds files are located in the zip file "pseudobulks.zip".</p> <p>The file "additional_data.zip" contains additional files used to generate the reference profiles in EPIC-ATAC and to reproduce the main analyses performed in the manuscript: <a href="https://doi.org/10.7554/eLife.94833.1">https://doi.org/10.7554/eLife.94833.1</a>. These files are required to run the code available on the following GitHub repository: GfellerLab/EPIC-ATAC_manuscript. </p>
Supporting Datasets produced in Allen et al. (2018) Global Estimates of River Flow Wave Travel Times and Implications for Low-Latency Satellite Data"
<p><strong>Supporting datasets for Allen et al. (2018) - Global Estimates of River Flow Wave Travel Times and Implications for Low-Latency Satellite Data, <em>Geophysical Research Letters</em>, <a href="https://doi.org/10.1002/2018GL077914">https://doi.org/10.1002/2018GL077914</a></strong></p> <p>The code used to produce these data is available as a Github repository, permanently hosted on Zenodo: <a href="https://doi.org/10.5281/zenodo.1219784">https://doi.org/10.5281/zenodo.1219784</a></p> <p><strong>Abstract</strong></p> <p>Earth-orbiting satellites provide valuable observations of upstream river conditions worldwide. These observations can be used in real-time applications like early flood warning systems and reservoir operations, provided they are made available to users with sufficient lead time. Yet, the temporal requirements for access to satellite-based river data remain uncharacterized for time-sensitive applications. Here we present a global approximation of flow wave travel time to assess the utility of existing and future low-latency/near-real-time satellite products, with an emphasis on the forthcoming SWOT satellite. We apply a kinematic wave model to a global hydrography dataset and find that global flow waves traveling at their maximum speed take a median travel time of 6, 4 and 3 days to reach their basin terminus, the next downstream city and the next downstream dam respectively. Our findings suggest that a recently-proposed ≤2-day latency for a low-latency SWOT product is potentially useful for real-time river applications.</p> <p> </p> <p><strong>Description of repository datasets:</strong></p> <p>1. riverPolylines.zip contains ESRI shapefile polylines of river networks with outputs from main analysis. These continental-scale shapefiles contain the following attributes for each river segment:</p> <ul> <li>"ARCID" : unique identifier for each river segment line, defined as the river reach between river junctions/heads/mouths. The first 10 attributes are taken from Andreadis et al. (2013): https://doi.org/10.5281/zenodo.61758</li> <li>"UP_CELLS" : number of upstream cells (pixels)</li> <li>"AREA" : upstream drainage area (km<sup>2</sup>)</li> <li>"DISCHARGE" : discharge (m<sup>3</sup>/s)</li> <li>"WIDTH" : mean bankfull river width (m)</li> <li>"WIDTH5" : 5th percentile confidence interval bankfull river width (m)</li> <li>"WIDTH95" : 95th percentile confidence interval bankfull river width (m)</li> <li>"DEPTH" : mean bankfull river depth (m)</li> <li>"DEPTH5" : 5th percentile bankfull river depth (m)</li> <li>"DEPTH95" : 95th percentile confidence bankfull river depth (m)</li> <li>"LENGTH_KM" : segment length (km)</li> <li>"ORIG_FID" : original ID of segment</li> <li>"ELEV_M" : lowest elevation of segment (m). Derived from HydroSHEDS 15 sec hydrologically conditioned DEM: https://hydrosheds.cr.usgs.gov/datadownload.php?reqdata=15demg </li> <li>"POINT_X" : longitude of lowest point of segment (WGS84, decimal degrees)</li> <li>"POINT_Y" : latitude of lowest point of segment (WGS84, decimal degrees)</li> <li>"SLOPE" : average slope of segment (m/m)</li> <li>"CITY_JOINS" : an index associated with how likely a city/population center is located on the segment. Population center data from: http://web.ornl.gov/sci/landscan/ and http://www.naturalearthdata.com/downloads/10m-cultural-vectors/10m-populated-places/ </li> <li>"CITY_POP_M" : population of joined city (max N inhabitants) </li> <li>"DAM_JOINSC" : an index associated with how likely a dam is located on the segment. Dam data from Global Reservoir and Dam (GRanD) Database: http://www.gwsp.org/products/grand-database.html </li> <li>"DAM_AREA_S" : surface area of joined dam (m<sup>2</sup>)</li> <li>"DAM_CAP_MC" : volumetric capacity of joined dam (m<sup>3</sup>)</li> <li>"CELER_MPS" : modeled river flow wave celerity (m/s)</li> <li>"PROPTIME_D" : travel time of flow wave along segment (days)</li> <li>"hBASIN" : main basin UID for the hydroBASINS dataset: http://www.hydrosheds.org/page/hydrobasins</li> <li>"GLCC" : Global Land Cover Characterization at segment centroid: https://lta.cr.usgs.gov/glcc/globdoc2_0 </li> <li>"FLOODHAZAR" : flood hazard composite index from the DFO (via NASA Sedac): http://sedac.ciesin.columbia.edu/data/set/ndh-flood-hazard-frequency-distribution</li> <li>"SWOT_TRAC_" : SWOT track density (N overpasses per orbit cycle @ segment centroid). Created using SWOTtrack SWOTtracks_sciOrbit_sept15 polygon shapefile, uploaded here.</li> <li>"UPSTR_DIST" : upstream distance to the basin outlet (km) </li> <li>"UPSTR_TIME" : upstream flow wave travel time to the basin outlet (days)</li> <li>"CITY_UPSTR" : upstream flow wave travel time to the next downstream city (days)</li> <li>"DAM_UPSTR_" : upstream flow wave travel time to the next downstream dam (days)</li> <li>"MC_WIDTH" : mean of Monte Carlo simulated bankfull widths (m)</li> <li>"MC_DEPTH" : mean of Monte Carlo simulated bankfull depths (m)</li> <li>"MC_LENCOR" : mean of Monte Carlo simulated river length correction (km)</li> <li>"MC_LENGTH" : mean of Monte Carlo simulated river length (m)</li> <li>"MC_SLOPE" : mean of Monte Carlo simulated river slope (-)</li> <li>"MC_ZSLOPE" : mean of Monte Carlo simulated minimum slope threshold (m)</li> <li>"MC_N" : mean of Monte Carlo simulated Manning’s n (s/m^(1/3))</li> <li>"CONTINENT" : integer indicating the HydroSHEDS region of shapefile</li> </ul> <p>2. hydrosheds_connectivity.zip contains network connectivity CSVs for river polyline shapefiles. The tables do not contain headers:</p> <ul> <li>Col1: segment unique identifier (UID) corresponding to the ARCID column of the riverPolylines shapefiles</li> <li>Col2: Downstream UID</li> <li>Col3: Number of upstream UIDs</li> <li>Col4 – Col12: Upstream UIDs</li> </ul> <p>3. SWOTtracks_sciOrbit_sept15_density.zip contains a polygon shapefile derived from SWOTtracks_sciOrbit_sept15_completeOrbit containing the sampling frequency of SWOT (number of observations per complete orbit cycle). Polygon attributes correspond to each unique shape formed from overlapping swaths:</p> <ul> <li>FID : unique identifier of each polygon</li> <li>CENTROID_X : polygon centroid longitude (WGS84 - decimal degrees)</li> <li>CENTROID_Y : polygon centroid latitude (WGS84 - decimal degrees)</li> <li>COUNT_count: SWOT sampling frequency (N observations per complete orbit cycle)</li> </ul> <p>4. USGS_gauge_site_information.csv : table containing the list of USGS sites analyzed in the validation and obtained from http://nwis.waterdata.usgs.gov/nwis/dv Header descriptions contained within table. </p> <p>5. validation_gaugeBasedCelerity.zip contains polyline ESRI shapefiles covering North and Central America, where USGS gauges provided gauge-based celerity estimates. These files have FIDs and attributes corresponding to riverPolylines shapefiles described above and also contrain the folllowing fields:</p> <ul> <li>GAUGE_JOIN : an index associated with how likely a gauge is located on the segment. Gauge location information is contained in USGS_gauge_site_information.csv</li> <li>GAUGE_SITE: USGS gauge site number of joined gauge</li> <li>GAUGE_HUC8: which hydrological unit code the gauge is located in</li> <li>OBS_CEL_R: gauge-based correlation score (R). Upstream and downstream gauges were compared via lagged cross correlation analysis. The calculated celerity between the paired gauges were assigned to each segment between the two gauges. If there were multiple pairs of upstream and downstream gauges, the the mean celerity value was assigned, weighted by the quality of the correlation, R. Same weighted mean was applied in assigning R. </li> <li>OBS_CEL_MPS: gauge-based celerity estimate (m/s). </li> </ul> <p>6. tab1_latencies.csv contains data shown in Table 1 of the manuscript.</p> <p>7. figS3S4_monteCarloSim_global_runMeans.csv contains the mean of the Monte Carlo simulation inputs and outputs shown in Figure S3 and Figure S4. Column headers descriptions are given in riverPolylines (dataset #1 above). Some columns have rows with all the same value because these variables did not vary between ensemble runs.</p> <p>8. figS5_travelTimeEnsembleHistograms.zip contains data shown in Figure S5. Each csv corresponds to a figure component:</p> <ul> <li>tabdTT_b.csv : basin outlet travel times for all rivers</li> <li>tabdTT_b_swot.csv : basin outlet travel times for SWOT</li> <li>tabdTT_c.csv : next downstream city travel times for all rivers</li> <li>tabdTT_c_swot.csv : next downstream city travel times for SWOT</li> <li>tabdTT_d.csv : next downstream dam travel times for all rivers</li> <li>tabdTT_d_swot.csv : next downstream dam travel times for SWOT</li> </ul>
Estimation of the variation in specific discharge over large depth using Distributed Temperature Sensing (DTS) measurements of the heat pulse response
<p>The data contains measurements and derived values that are used for the manuscript "Estimation of the variation in specific discharge over large depth using Distributed Temperature Sensing (DTS) measurements of the heat pulse response, [Paper # 2018WR024171]" Currently under review at the Water Resources Research journal.</p> <p>The data is stored in netCDF files with xarray (Python), and should be readable with any other netCDF reader. </p> <ul> <li>TEMP is the measured temperature in degrees Celsius relative to the background temperature</li> <li>tempinfty is one of the calibration parameters. Represents the steady state temperature increase</li> <li>A is one of the calibration parameters. Represents the timescale in days</li> <li>b is one of the calibration parameters. Represents the scaled distance to the heat source</li> <li>err_alpha is one of the calibration parameters. Represents the autoregressive parameter</li> <li>TEMPmodel is the best fit temperature response in degrees Celsius relative to the background temperature</li> <li>Innovation is termed the noise in the article, in degrees Celsius.</li> <li>q is the estimated specific discharge in meters per day</li> <li>q_MC_XX are the confidence intervals of the estimated specific discharge calculated with Monte Carlo as presented in the article</li> <li>q_lmfit_XX are the confidence intervals of the estimated specific discharge calculated with LMFIT. Is a rough estimate for q_MC_XX calculated by lmfit (Python package).</li> </ul> <p>Time is measured in days with respect to when the heating cable is turned on.</p> <p>Additionally, a Jupyter notebook is supplemented to the article. It demonstrates the calibration routine and the calculation of the confidence interval for the temperature response at a single depth.</p>
Estimating heavy metal deposition in Germany using model calculations and biomonitoring data, link to research data and scientific software
<p>Research data and scientific software related to an investigation dealing with modelled data on Cd and Pb deposition (LOTOS-EUROS, EMEP/MSC-East) and monitoring data from the International Cooperative Programme on Effects of Air Pollution on Natural Vegetation and Crops (ICP Vegetation Moss Survey) and the German Environmental Specimen Bank (ESB) providing corresponding parameters on HM concentration in various biota. The study aimed at examining, whether an integrated use of model calculations and monitoring data can extend established methods for estimating and evaluating spatial patterns of atmospheric Pb and Cd deposition across Germany.</p>
Calving flux estimated from tsunami waves
<p>The following geophysical field data in July 2015 and July 2016 at Bowdoin Glacier in northwest Greenland is provided in this dataset: </p> <p>(1) Tsunami wave data: Low-pass filtered tsunami waves record in July 2015 and July 2016. The unit is meter. Local time.</p> <p>(2) UAV ortho-images and DEMs: Tiff format ortho-images and DEMs. Coordinates are in UTM19 north / WGS84.</p> <p>(3) Ice surface speed observed by GPS station near the glacier front. Coordinates are WGS 84. UTC time.</p> <p> </p>
Figure reproduction for "Accelerating small angle scattering experiments on anisotropic samples using kernel density estimation"
<p>These datasets and a Jupyter notebook reproduce figures in <a href="https://www.nature.com/articles/s41598-018-37345-5">a publication by Saito et al in Scientific Reports</a>. The notebook also serves as a demo for kernel density estimation (smoothing) of 2D data using Python. Details are described in the notebook. If you have no idea about ipynb format, please see HTML version with your web browser instead. It contains exactly the same codes and results as ipynb version.</p>
Estimating malaria disease burden in the Asia-Pacific
<p>This repository hosts all the Supplementary Material for the publication: Maude RJ, Mercado CEG, Rowley J, Ekapirat N, Dondorp AM. (2019) Estimating malaria disease burden in the Asia-Pacific (under review)</p>
Relate-estimated coalescence rates, allele ages, and selection p-values for the 1000 Genomes Project
<p><strong>Overview</strong></p> <p>Coalescence rates, allele ages, and p-values for evidence of positive selection calculated for 2478 samples of the 1000 Genomes Project using Relate.</p> <p>We estimated the joint genealogy of all 1000 GP populations and then extracted the embedded genealogy for each population.<br> For the genealogy of each population, we jointly estimated the population size history and branch lengths. <br> Variants segregating in more than one population therefore have correlated but different allele ages in each population.</p> <p>Please refer to <a href="https://www.nature.com/articles/s41588-019-0484-x">Speidel et al. Nature Genetics (2019)</a> for more details or email leo.speidel@outlook.com for any queries.</p> <p><strong>Coalescence rates</strong></p> <p>The zipped directory coalescence_rates.zip contains coalescence rates for 26 populations in the 1000 Genomes Project data set.</p> <ul> <li>The .coal files show the haploid coalescence rates, please refer to the <a href="https://myersgroup.github.io/relate/modules.html#PopulationSizeScript_FileFormats">Relate documentation</a> for the file format.</li> <li>The popsize.RData file is an R data frame storing the diploid population sizes (0.5/coalescence rate) calculated using the .coal files. The columns of this data frame, named "pop_size", are <ul> <li>gens_ago: Time in generations at which epoch starts. (To get years from generations, we multiply by 28.)</li> <li>population_size: Diploid population size in this epoch.</li> <li>population: Name of population </li> <li>region: Name of region (AFR, AMR, EAS, EUR, SAS)</li> </ul> </li> </ul> <p><strong>Allele ages and selection p-values</strong></p> <p>The zipped directories allele_ages_*.zip contain R data frames for each 1000GP population storing allele ages and selection p-values.<br> Please note that only mutations that segregate in the population and map to a unique branch in the Relate-estimated marginal trees are included. Selection p-values are only provided for mutations of DAF > 2 that pass quality filters (see Speidel et al., 2019). </p> <p>To get an age estimate for a neutral mutation, use 0.5*(lower_age + upper_age). To get years from generations, we multiply by 28.</p> <p>The columns of these data frames, named "allele_ages", are</p> <ul> <li>CHR: chromosome index</li> <li>BP: base-pair position (GRCh37)</li> <li>ID: id of SNP</li> <li>lower_age: Age in generations of coalescence event at the lower end of the branch onto which the mutation maps</li> <li>upper_age: Age in generations of coalescence event at the upper end of the branch onto which the mutation maps</li> <li>ancestral/derived: Ancestral/derived allele</li> <li>upstream: Upstream (5') allele</li> <li>downstream: Downstream (3') allele</li> <li>DAF: Derived-allele frequency</li> <li>pvalue: log10 p-value for selection evidence</li> </ul>
Rethinking the fundamental unit of ecological remote sensing: Estimating individual level plant traits at scale
<p>derived data of leaf and plant structural traits for two National Ecological Observatory Network (NEON) Airborne Observatory Platform (AOP) sites. Dataset contains spatial explicit information for 4.5 million trees, and include: Nitrogen (%mass), Phosphorus (%mass), Leaf mass per area (g m<sup>-2</sup>), diameter at breast height (cm), crown area (m2), tree height (m) and other physical topographic variables (Albedo, Elevation, Slope, Aspect). data are associated to the </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.