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Data inputs and results for "Mammal niches are not conserved over continental scales" by Goldstein et al.
<p>This data packet provides inputs and results for "Mammal niches are not conserved over continental scales" by Goldstein et al., currently in the submission process. This repository will eventually be updated to link to the published manuscript.</p> <p> </p> <p>===============================================================================<br>===============================================================================<br>Overview<br>===============================================================================<br>===============================================================================</p> <p>Data and model products associated with the manuscript "Mammal niches are not <br>conserved over continental scales" by Goldstein et al. </p> <p>Files are organized into two subdirectories. The first, "model_inputs/", <br>contains 8 data files intended to be used as part of the reproducible code <br>repository at https://github.com/dochvam/Mammal_SVCs_ISDM_reproducible. <br>The second subdirectory, "model_outputs/", contains modeled products giving<br>estimated spatially varying niche relationships and predictions of relative<br>abundance.</p> <p>Below, we describe the contents of each file type. See the main manuscript <br>for full methodology, data sources, and discussions of spatial scales.</p> <p>NOTE: Version 1 of this dataset contained some errors that have been corrected<br>in Version 2. Version 2 was used as the input dataset for the analyses in the<br>associated manuscript. Version 1 should not be used.</p> <p>===============================================================================<br>===============================================================================<br>Subdirectory 1: "model_inputs/"<br>===============================================================================<br>===============================================================================</p> <p>Two versions of each of four files are provided, corresponding to analyses <br>that do or do not consider ancient genetic lineages as potential sources of <br>spatial nonstationarity in mammal niches. Each file type is formatted the same,<br>and the versions are differentiated by either the suffix "nolineage" or <br>"lineage" in the filename. </p> <p>===============================================================================<br>File 1: gridcell_covars_lineage.csv and gridcell_covars_nolineage.csv<br>===============================================================================<br>These files are .csvs giving spatial covariate data for each scale 2 cell<br>in North America, summarized to 5000 m. All percentage values are given in <br>10ths of a percent (scale of 0-1000). The following columns are provided:</p> <p>- grid_cell: Scale 2 cell ID<br>- Arable: pct arable land (Jung et al. 2020)<br>- EVI_mean: mean enhanced vegetation index (Didan 2021)<br>- EVI_Q95: 95th quantile of EVI (Didan 2021)<br>- Forest: Pct forest cover (Jung et al. 2020)<br>- Grassland: pct grassland (Jung et al. 2020)<br>- Pastureland: pct pastureland (Jung et al. 2020)<br>- Pop_den: Human population density, from Gridded Population of the World (CIESIN 2018)<br>- Precipitation: avg annual precip. (Vega et al. 2017)<br>- Shrubland: pct shrubland (Jung et al. 2020)<br>- Temp_max: Average maximum daily temperature (Vega et al. 2017)<br>- Terrain_roughness (Amatulli et al. 2018)<br>- Wetlands: pct wetlands (Jung et al. 2020)<br>- is_land: Whether or not the cell is on land vs. ocean, used for filtering<br>- Agriculture: Pct. agricultural land (Jung et al. 2020)<br>- Pop_den_sqrt: Square root of human population density (CIESIN 2018)<br>- EVI_variability: Distance btw the 95% inner quantiles of EVI (Didan 2021)</p> <p> </p> <p>===============================================================================<br>File 2: inat_cts_lineage.csv and inat_cts_nolineage.csv<br>===============================================================================</p> <p>These files give summaries of iNaturalist sampling effort and detections<br>for target species. The following columns are provided:</p> <p>- grid_cell: Scale 3 cell ID<br>- n: Total iNaturalist effort in the cell (number of obs. of all mammals)<br>- The remaining columns are named for species. Each column gives the count<br> of observations of the species in the cell.</p> <p>===============================================================================<br>File 3: ct_datlist_lineage.RDS and ct_datlist_nolineage.RDS<br>===============================================================================</p> <p>The ct_datlist files contain R objects that are lists of lists. These objects ultimately<br>contain all of the camera detection histories and camera-level covariate data used<br>in modeling. We use the nice data type "unmarkedFrameOccu" from the unmarked R package<br>to organize these detection data.</p> <p>Each outer list is of length equal to the number of species. The ith element of each<br>list contains the following named slots:</p> <p>- species: a string giving the name of the ith species<br>- umf: an unmarkedFrameOccu object. This object has three important slots:<br> - y: a (# deployments) x (max # replicates) matrix giving 1s, 0s, or NAs indicating<br> whether the target species was observed in that 10-day window;<br> - siteCovs: a (# deployments) x 2 data frame with the following columns:<br> - site_ID: A unique ID of the exact location, shared by deployments with the same<br> coordinates<br> - subproject_ID: A unique ID indicating which camera array is associated <br> with this deployment<br> - obsCovs: a (# deployments * max # replicates) x 6 data frame with the following columns:<br> - year: the year of survey, relative to 2020 (zero-year is 2020)<br> - yday_scaled: the (scaled) Julian date of the beginning of the window<br> - yday_scaled_sq: yday_scaled^2, for use in estimating a quadratic effect<br> - log_roaddist_scaled: Scaled distance to nearest road (Meijer et al. 2018)<br> - Canopy_height_scaled: Scaled canopy height (Potapov et al. 2021)<br> - obs_len_scaled: Scaled duration of window, to account for some windows <br> being cut off at < 10 days<br>- coords: a data frame. Originally, this file gave the exact position for each camera,<br> but these exact locations have been scrubbed for privacy. See the original sources<br> cited in the manuscript for full details. This data frame contains the following column:<br> - scale2_grid_ID: the ID of the Scale-2 5000 m grid cell containing the camera</p> <p>===============================================================================<br>File 4: grid_translator_wspecs_nolineage.csv and grid_translator_wspecs_lineage.csv<br>===============================================================================</p> <p>These files are used for bookkeeping to track the relationships between the <br>three spatial scales in this study. Each row corresponds to a single "scale 2"<br>cell, giving the ID of the corresponding S3 and S4 grid and also an ID for each<br>species indicating whether and where it is in the species' range. </p> <p>Note that the scale names in the code don't match the manuscript. In the code,<br>"scale 1" is the level of an individual camera, "scale 2" is the 5 km intensity<br>grid, "scale 3" is the 50 km iNaturalist grid, and "scale 4" is the 100 km<br>SVC grid.</p> <p>The following columns are provided:<br>- scale2_grid_ID: unique ID for each cell in the 5 km intensity grid<br>- scale3_grid_ID: unique ID for each cell in the 50 km iNaturalist aggregation<br>- scale4_grid_ID: unique ID for each cell in the 100 km SVC grid<br>- GRID_ID_[species]: for each species, a column is provided on the S4 scale<br> counting each cell in the species' modeled range. NAs<br> indicate that the S2 cell defined in the row is not<br> included in the species' modeled range.</p> <p>===============================================================================<br>===============================================================================<br>Subdirectory 2: "model_outputs/"<br>===============================================================================<br>===============================================================================</p> <p>===============================================================================<br>File 1: svc_estimates.csv<br>===============================================================================</p> <p>This file gives an estimate of the effect of each covariate on each species'<br>intensity, and the uncertainty in that estimate, for each species/covariate<br>pair. Results correspond to lineage models for species with phylogeographies<br>and non-lineage species otherwise. Each row represents the effect of one <br>covariate on one species' relative intensity process within one 100 km cell g. <br>Note that many estimates of beta_g are uncertain even for strong spatial <br>effects---the model is often confident that a spatial process is supported <br>while estimates of the realized process are uncertain.</p> <p>The following columns are provided:<br>- x: the x-coordinate of the 100 km cell<br>- y: the y-coordinate of the 100 km cell<br>- species<br>- parname: the name of the covariate<br>- mean: the mean of the posterior samples of beta_g<br>- 2.5%: the 2.5th quantile of the posterior samples of beta_g<br>- 50%: the 50th quantile of the posterior samples of beta_g<br>- 97.5%: the 97.5th quantile of the posterior samples of beta_g</p> <p>The following spatial projection is used to define X/Y coordinates:<br>"+proj=aea +lat_1=20 +lat_2=60 +lat_0=40 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83"</p> <p>===============================================================================<br>File 2: predicted_intensity.tif<br>===============================================================================</p> <p>This file contains a raster "brick" giving the predicted intensity surface <br>and uncertainty in this surface for each species. All predictions are generated<br>using models that do *not* account for lineage information---this means that <br>predictions for species with lineages are not from the models reported in the<br>main manuscript. The reason for this is that we found that lineages were <br>overall unsupported, so better predictions can be arrived at by excluding this<br>source of uncertainty in the underlying intensity process.</p> <p>The raster brick has 66 layers. Each layer provides either the mean predicted<br>log intensity in each grid cell across the species range or else provides<br>the standard error of that predicted log intensity. Layer names indicate output<br>type and species associated with each layer.</p> <p><br>===============================================================================<br>===============================================================================<br>References<br>===============================================================================<br>===============================================================================</p> <p>Camera data are obtained from the following sources, which can be consulted to<br>obtain the original raw camera data</p> <p>- Cove, Michael V., et al. "SNAPSHOT USA 2019: a coordinated national camera trap survey of the United States." (2021): e03353.<br>- Kays, Roland, et al. "SNAPSHOT USA 2020: A second coordinated national camera trap survey of the United States during the COVID‐19 pandemic." (2022): e3775.<br>- Shamon, H., et al. “SNAPSHOT USA 2021: A third coordinated national camera trap survey of the United States.” Ecology, 105.6 (2024): e4318.<br>- Rooney, B., et al. “SNAPSHOT USA 2019–2023: The first five years of data from a coordinated camera trap survey of the United States.” In Press (2024).<br>- Kays, Roland, et al. "Does hunting or hiking affect wildlife communities in protected areas?." Journal of Applied Ecology 54.1 (2017): 242-252.<br>- Roberts, R. California Department of Fish and Wildlife, Bobcat Program Initiative. wildlifeinsights.org (2023).<br>- Lasky, Monica, et al. "CAROLINA CRITTERS: a collection of camera trap data from wildlife surveys across North Carolina." Ecology 102.7 (2021): e03372.<br>- Forrester, T. (2000). Urban to Wild Project. http://n2t.net/ark:/63614/w12004302. Accessed via wildlifeinsights.org on 2024-08-29.<br>- McMurry, S. et al. In review (2024).<br>- Forrester, T. (2011) Okaloosa S.C.I.E.N.C.E. Project. http://n2t.net/ark:/63614/w12004287. <br>- Myers, J. (2014) Tyson Research Center ForestGEO Project. http://n2t.net/ark:/63614/w12004295.<br>- McMurry, S., and Kays, R.(2023). Calloway Forest Preserve. http://n2t.net/ark:/63614/w12006449. Accessed via Wildlife Insights on 2024-08-29.<br>- McMurry, S., Parsons, A., Lasky, M., Luongo, K., Clark, J., McShea, W., Scher, L., Kays, R., Spurlin, J., Martin, G., Frech, G., Barajas-Salazar, K., Snider, M. (2022). Last updated October 2023. Calloway Forest Preserve. http://n2t.net/ark:/63614/w12004251. Accessed via wildlifeinsights.org on 2024-08-29.<br>- Kays, R.. (2008). Last updated March 2024. Albany Area Camera Trapping Project. http://n2t.net/ark:/63614/w12003860. Accessed via wildlifeinsights.org on 2024-08-29.<br>- Kays, R., Snider, M., McMurry, S., Alyetama, M. (2024). Last updated April 2024. Pilot Mountain Density 2024. http://n2t.net/ark:/63614/w12007160. Accessed via wildlifeinsights.org on 2024-08-29.<br>- Malleshappa, V., Smithsonian, E., Kays, R., Schuttler, S. (2015). Last updated December 2022. Museums Connect Mexico. http://n2t.net/ark:/63614/w12004298. Accessed via wildlifeinsights.org on 2024-08-29.</p> <p>Covariate data are obtained from the following sources:<br>- Vega, G. C., Pertierra, L. R. & Olalla-Tárraga, M. Á. MERRAclim, a high-resolution global dataset of remotely sensed bioclimatic variables for ecological modelling. Sci. Data 4, 170078 (2017).<br>- Jung, M. et al. A global map of terrestrial habitat types. Sci. Data 7, 256 (2020).<br>- Amatulli, G. et al. A suite of global, cross-scale topographic variables for environmental and biodiversity modeling. Sci. Data 5, 180040 (2018).<br>- Center For International Earth Science Information Network-CIESIN-Columbia University. Documentation for the Gridded Population of the World, Version 4 (GPWv4), Revision 11 Data Sets. (2018) doi:10.7927/H45Q4T5F.<br>- Didan, K. MODIS/Terra Vegetation Indices 16-Day L3 Global 1km SIN Grid V061. NASA EOSDIS Land Processes Distributed Active Archive Center https://doi.org/10.5067/MODIS/MOD13A2.061 (2021).<br>- Meijer, J. R., Huijbregts, M. A. J., Schotten, K. C. G. J. & Schipper, A. M. Global patterns of current and future road infrastructure. Environ. Res. Lett. 13, 064006 (2018).<br>- Potapov, P. et al. Mapping global forest canopy height through integration of GEDI and Landsat data. Remote Sens. Environ. 253, 112165 (2021).<br>- Jensen, A. J. et al. Geographic barriers but not life history traits shape the phylogeography of North American mammals. Glob. Ecol. Biogeogr. e13875 (2024).</p> <p>iNaturalist data are obtained from inaturalist.org via the data exporter (see manuscript for details).</p>
Effect of spatial input data quality on SWAT modelling in the Porijõgi catchment
<p>The Porijõgi Catchment near Tartu, Estonia is the study area for this research. Four model setups were created using global/regional level data (HWSD soil, CORINE), and local high-resolution spatial data including the new Estonian high-resolution EstSoil-EH soil dataset and the Estonian Topographic Database (ETAK). The study employed statistical criteria to assess SWAT model performance for monthly simulated stream flows from 2007 to 2019.</p> <p>Data deposit in preparation for article:</p> <p>Effect of spatial input data quality on the uncertainty of the<br> SWAT model, submitted 2022</p> <p>Alexander Kmoch, Desalew Meseret Moges, Mahdiyeh Sepehrar, Balaji Narasimhan and Evelyn<br> Uuemaa</p> <p>contact: alexander.kmoch@ut.ee</p>
Input data set for the statistical analsysis of rockfall reach probabilities
<p>These files contain reach probability values extracted from 3D rockfall simulations for field-mapped block deposits as well as a series of attributes characterising the deposits. They served for the statistical analysis of the reach probability values as a function of site, forest and rockfall characteristics. The results of the analysis are published in Dorren et al. 2022: Delimiting rockfall runout zones using reach probability values simulated with a Monte-Carlo based 3D trajectory model. Natural Hazards and Earth System Scienses.</p>
Southern African Power Pool GridPath Model Input Data
<p>This data repository holds GridPath model input data for the paper Chowdhury, A.K., Deshmukh, R., Wu, G., Uppal, A., Mileva, A., Curry, T., Armstrong, L., Galelli, S., and Kudakwashe, N. (2022) “Enabling a low-carbon electricity system for Southern Africa”, Joule. See Readme for more details. </p>
HANZE v2.0 exposure model input data
<p>This dataset provides all input data needed to run HANZE v2.0 model. The two ZIP files need to be downloaded and unpacked in the same directory, which has to be defined in "get_file.py" (variable "main_path" at the beginning of the file). For detailed description of the files, see the documentation provided with the code.</p>
Inputs of the Jupyter Notebook - Met Office UKV high-resolution atmosphere model data
<p>The dataset contains the inputs of the notebook "Met Office UKV high-resolution atmosphere model data" published in The Environmental Data Science Book.</p> <p>The input data refer to a subset of single sample data file for 1.5 m temperature as part of the Met Office contribution to the COVID 19 modelling effort.</p> <p>The full dataset was available for download from the Met Office Azure (https://metdatasa.blob.core.windows.net/covid19-response-non-commercial/). The full dataset was available for download under the terms of non-commercial purposes.</p> <p><strong>Contributions</strong></p> <p><em>Notebook</em></p> <ul> <li> <p>Samantha V. Adams (author), Met Office Informatics Lab, <a href="https://github.com/svadams">@svadams</a></p> </li> <li> <p>Alejandro Coca-Castro (reviewer), The Alan Turing Institute, <a href="https://github.com/acocac">@acocac</a></p> </li> </ul> <p><em>Dataset originator/creator</em></p> <ul> <li> <p>Met Office Informatics Lab (creator)</p> </li> <li> <p>Microsoft (support)</p> </li> <li> <p>European Regional Development Fund (support)</p> </li> </ul> <p><em>Dataset authors</em></p> <ul> <li> <p>Met Office</p> </li> </ul> <p><em>Dataset documentation</em></p> <ul> <li> <p>Theo McCaie. Met office and partners offer data and compute platform for covid-19 researchers. URL: <a href="https://medium.com/informatics-lab/met-office-and-partners-offer-data-and-compute-platform-for-covid-19-researchers-83848ac55f5f">https://medium.com/informatics-lab/met-office-and-partners-offer-data-and-compute-platform-for-covid-19-researchers-83848ac55f5f</a>.</p> </li> </ul> <p><strong>Note this data should be used only for non-commercial purposes.</strong></p>
Example input files and output data for 1D hydrodynamic simulations of shock compressed iron
<p>Example input files and output data for 1D hydrodynamic simulations of shock compressed iron. Input files consists of 3 examples from the SIMEX github wiki page for a 50 micron CH ablator with 5 micro Fe foil (laser pulse is a 6 ns flat top pulse, 1064 nm with 0.3 TW/cm<sup>2</sup>). Output data are from Esther hydrocode in .txt format and the SIMEX opmd.h5 format.</p>
HipFT Sample Input Dataset for Convective Flows and Data Assimilation
<p>This file package is a sample data set for running <a href="https://www.github.com/predsci/hipft">HipFT</a> with convective flows and data assimilation. </p> <p>The convective flows were generated with the <a href="https://www.github.com/predsci/conflow">ConFlow</a> code (soon to be released), while the data assimilation maps were processed from HMI M720s LOS data using the <a href="https://www.github.com/predsci/MagMAP">MagMAP</a> package (also soon to be released).</p> <p>See the enclosed README file on how to run an example included in the HipFT package that uses the two data sets.</p>
Input data files for the CPR-DINCAE project
<p>This dataset contains the netCDF files used as the input for [DINCAE](https://github.com/gher-uliege/DINCAE.jl)</p>
Fine-scale anthropogenic nutrient input data for 8 watersheds along the Saint Lawrence River (1981, 2021)
<p>We quantified Net Anthropogenic Nitrogen and Phosphorus Inputs (NANI-NAPI) at two scales (the finest one, the municipality, and a coarser one, the county) for all municipalities and counties of 8 watersheds in Québec, Canada, for 1981 and 2021.</p> <p>The datasets here report 1) watershed NANI and NAPI values accounted from both scales for 1981 and 2021, 2) municipality-scale NANI values for each municipality in the 8 watersheds, and 3) certain components of the municipality-scale NANI for all municipalities in the Yamaska watershed.</p>
Data set for "State-dependent cell-type-specific membrane potential dynamics and unitary synaptic inputs in awake mice"
<p>Data set for: Pala A, Petersen CCH (2018) State-dependent cell-type-specific membrane potential dynamics and unitary synaptic inputs in awake mice. eLife 7: e35869. DOI: https://doi.org/10.7554/eLife.35869.</p> <p>There are 12 files in this data upload:</p> <p>1. '2018_Pala_eLife.pdf' - this is a pdf version of the online publication: Pala & Petersen (2018).</p> <p>2. 'data.mat' - this is a Matlab data structure, which contains all the data for the publication.</p> <p>3. 'DataViewer.m' - this is a Matlab code for viewing the data.</p> <p>4. 'DataViewer.fig' - this is a Matlab figure file, which is the GUI layout for 'DataViewer.m'.</p> <p>5. 'PalaPetersen_Plot.m' - this is a Matlab code, which plots the figures for Pala & Petersen (2018).</p> <p>6. 'PalaPetersen_Analysis.m' - this is a Matlab code, which analyses the data for the figures of Pala & Petersen (2018).</p> <p>7. 'blankAPs.m' - this is a Matlab code, which blanks action potentials from the membrane potential trace.</p> <p>8. 'lowpassfilt.m' - this is a Matlab code, which low pass filters the LFP.</p> <p>9. 'medianFiltAPs.m' - this is a Matlab code, which median filters the membrane potential trace to remove action potentials.</p> <p>10. 'remTrialswithAPs.m' - this is a Matlab code, which removes trials with action potentials.</p> <p>11. 'retrieveSegDur.m' - this is a Matlab code, which retrieves chunks of the recording of a given length.</p> <p>12. 'suptitleAP.m' - this is a Matlab code, which puts titles above subplots.</p>
Dataset: Approximating input data to a snowmelt model using Weather Research and Forecasting model outputs in lieu of meteorological measurements
<p>The dataset presented is the companion data to the Journal of Hydrometeorology publication entitled “Approximating input data to a snowmelt model using Weather Research and Forecasting model outputs in lieu of meteorological measurements.” The data that follows contains everything needed to reproduce the spatial inputs for the meteorological station model run using the Spatial Modeling for Resources Framework (SMRF, Havens et al., 2017).</p> <p> </p> <p>Software versions used:</p> <ul> <li>Image Processing Workbench v2.2.0 (Marks et al., 2017)</li> <li>Spatial Modeling for Resources Framework v0.5.3 (Havens et al., 2019)</li> </ul> <p> </p> <p><strong>NOTE:</strong> Reproducing the spatial inputs will generate 10 netCDF files at ~80GB per file.</p> <p> </p> <p><strong>topo.nc</strong> – Contains multiple static layers that are required to run SMRF and iSnobal. The netCDF layers are:</p> <ul> <li>dem – digital elevation model at 100 meter resolution, aggregated from the 10 meter National Elevation Dataset (Archuleta et al., 2017)</li> <li>mask – basin mask for the Boise River Basin</li> <li>veg_height – vegetation height in meters from the National Land Cover Database (Homer et al., 2015)</li> <li>veg_type – vegetation type from the National Land Cover Database</li> <li>veg_tau – vegetation fractional transmissivity derived from the vegetation type</li> <li>veg_k – vegetation emissivity derived from the vegetation type</li> </ul> <p> </p> <p><strong>maxus.nc</strong> – maximum upwind slope netCDF that contains 72 images for all wind directions in 5 degree increments using the algorithm described in Winstral and Marks (2002)</p> <p> </p> <p><strong>Station data:</strong></p> <ul> <li>Contains hourly meteorological station data downloaded from Mesowest (Horel et al., 2002). Data was cleaned and filtered prior to running SMRF.</li> <li>metadata.csv – metadata for 40 stations</li> <li>air_temp.csv – 38 stations</li> <li>cloud_factor.csv – 7 stations</li> <li>precip.csv – 21 stations</li> <li>vapor_pressure.csv – 19 stations</li> <li>wind_direction.csv – 14 stations</li> <li>wind_speed.csv – 14 stations</li> </ul> <p> </p> <p><strong>smrf_config.ini</strong> – Configuration file needed to reproduce the spatial inputs using SMRF. The paths will need to be changed to reflect the data location.</p>
Personalized in silico model for radiation-induced pulmonary fibrosis | (source code, simulation input+output data)
<p>This repository concerns the supplementary material data of the research article entitled "<em>Personalised in silico model for radiation-induced pulmonary fibrosis</em>" that is published in the Royal Society Interface journal (rsif.royalsocietypublishing.org). More specifically, the repository contains the source code of the radiation-induced pulmonary fibrosis simulator, the results produced from the medical image analysis of this study (CT scans and RT dosage maps) for each patient case, the input files necessary to run the simulator and the corresponding output produced respectively. Each patient ID corresponds to each case documented in the research article.</p>
Model input data for the FACETS downscaling simulation with the CAM-MPAS model
<p>The archived file contains input data necessary to reproduce the set of simulations described in Sakaguchi et al., submitted to GWD, "Technical descriptions of the experimental dynamical downscaling simulations over North America by the CAM-MPAS variable-resolution model", using the experimental CAM-MPAS code further modified by Sakaguchi and Harrop (2022) for long-term AMIP-type simulations.</p>
Historical (1979 - 2020) data for anthropogenic inputs to a catchment and riverine mainstem exports for carbon, nitrogen, and phosphorus
<p>We estimated the difference in Net Anthropogenic Nitrogen and Phosphorus Inputs (NANI-NAPI) at the finest scale possible (the municipality) in the <em>Rivière du Nord</em> watershed (Québec, Canada) between 1981 and 2016. The dataset here reports the delta between those two years for each municipality in the watershed.</p> <p>Three sites along the mainstem of <em>Rivière du Nord </em>have been sampled ~bi-monthly from ~1979 - 2020 for dissolved organic carbon (DOC), total nitrogen (TN), and total phosphorus (TP), from which we estimated annual riverine export at each site. We also include annual precipitation (as the sum of rain and snow), and NANI-NAPI interpolated for each sub-watershed for 1981, 1986, 1991, 1996, 2001, 2006, 2011, and 2016.</p> <p> </p> <p> </p>
Input and output data for Experiment B2 (Deliverable 3.3 - Data assimilation in process-based models for algae bloom forecasting - Section 2)
<p>The dataset contains:</p> <p>i. the meteorological forcing, hydrological boundary condition and chlorophyll-a files used as an input</p> <p>ii. the model output and skill produced</p> <p>for Experiment B2 (Deliverable 3.3 - Data assimilation in process-based models for algae bloom forecasting - Section 2)</p>
Input and output data for Experiment B2 (Deliverable 3.3 - Data assimilation in process-based models for algae bloom forecasting - Section 1)
<p>The dataset contains:</p> <p>i. the meteorological forcing, hydrological boundary condition and chlorophyll-a files used as an input</p> <p>ii. the model output and skill produced</p> <p>for Experiment B2 (Deliverable 3.3 - Data assimilation in process-based models for algae bloom forecasting - Section 1)</p>
Input and output data for Experiment B2 (Deliverable 3.3 - Data assimilation in process-based models for algae bloom forecasting - Section 3)
<p>The dataset contains:</p> <p>i. the meteorological forcing, hydrological boundary condition and chlorophyll-a files used as an input</p> <p>ii. the model output and skill produced</p> <p>for Experiment B2 (Deliverable 3.3 - Data assimilation in process-based models for algae bloom forecasting - Section 3)</p>
Input and output data (images + boulder labels, model setup, model weights and more) for the manuscript "Automatic characterization of boulders on planetary surfaces from high-resolution satellite images"
<p><strong>File 1:</strong> raw_data_BOULDERING.zip</p> <p><strong>Size:</strong> 8.8 GB</p> <p><strong>Summary: </strong>It contains all of the rasters (planetary images) and labeled boulders (raw data):</p> <ul> <li> <p>a boulder-mapping file, which is the manually digitized outline of boulders.</p> </li> <li> <p>a ROM file (stands for Region of Mapping), which depicts the image patches on which the boulder mapping has been conducted.</p> </li> <li> <p>a global-tiles file, which shows all of the image patches within a raster.</p> </li> </ul> <p>There are multiple locations/images per planetary body.</p> <p><strong>Structure:</strong></p> <pre>. └── raw_data/ ├── earth/ │ └── image_name/ │ ├── shp/ │ │ ├── <image_name>-ROM.shp │ │ ├── <image_name>-boulder-mapping.shp │ │ └── <image_name>-global-tiles.shp │ └── raster/ │ └── <image_name>.tif ├── mars/ │ └── image_name/ │ ├── shp/ │ │ ├── <image_name>-ROM.shp │ │ ├── <image_name>-boulder-mapping.shp │ │ └── <image_name>-global-tiles.shp │ └── raster/ │ └── <image_name>.tif └── moon/ └── image_name/ ├── shp/ │ ├── <image_name>-ROM.shp │ ├── <image_name>-boulder-mapping.shp │ └── <image_name>-global-tiles.shp └── raster/ └── <image_name>.tif</pre> <p> </p> <p><strong>File 2:</strong> best_model.zip</p> <p><strong>Size:</strong> 624.7 MB</p> <p><strong>Summary:</strong></p> <p>This zip file contains all of the inputs and outputs required/obtained from the training of the BoulderNet Mask R-CNN model (model setup, augmentation pipeline, model weights, log during training, logged metrics):</p> <ul> <li> <p>augmentation_pipeline.json (required as inputs for the training of the algorithm to apply augmentations). See <a href="https://github.com/astroNils">https://github.com/astroNils</a> and the MLtools repository for more information.</p> </li> </ul> <ul> <li> <p>Base-RCNN-FPN.yaml (base model setup file).</p> </li> <li> <p>config.yaml (complete model setup file, merge of the base and Mars-Moon-Earth setup file).</p> </li> <li> <p>Mars-MoonEarth-v050...yaml (model setup file).</p> </li> <li> <p>log.txt (log during training of the algorithm).</p> </li> <li> <p>model_0055999.pth (model weights at second last saving step)</p> </li> <li> <p>model_0063999.pth (model weights at last saving step)</p> </li> </ul> <p>We advice the use of model weights model_0055999.pth (to avoid slight overfitting).</p> <p><strong>File 3:</strong> Apr2023-Mars-Moon-Earth-mask-5px.zip (pre-processed input images)</p> <p><strong>Size:</strong> 252.8 MB</p> <p><strong>Summary:</strong></p> <p>This zip files contains the input data (images and boulder outlines) for the train, validation and test datasets. See <a href="https://github.com/astroNils">https://github.com/astroNils</a> and the MLtools repository for more information in how-to-use the different files.</p> <ul> <li> <p>The json folder contains json files that can be given as input (as a custom dataset) to the Detectron2 platform. The only differences between the two files is how the bounding boxes around masks have been generated. We advised to use "Apr2023-Mars-Moon-Earth-mask-5px.json".</p> </li> <li> <p>The pkl folder and pickle file includes some informations about the 950 image patches in our boulder dataset.</p> </li> <li> <p>The pre-processing folder contains all of the training, validation and test image patches and corresponding shapefiles.</p> </li> <li> <p>The shapefile folder is actually empty (it should not be there!).</p> </li> </ul> <p><strong>Structure:</strong></p> <pre>. └── preprocessed_inputs/ ├── json ├── pkl ├── preprocessing/ │ ├── train/ │ │ ├── images │ │ └── labels │ ├── validation/ │ │ ├── images │ │ └── labels │ └── test/ │ ├── images │ └── labels └── shp</pre> <p> </p>
Input data for: Reconstruction of hourly coastal water levels and counterfactuals without sea level rise for impact attribution
<p>This Zenodo archive contains essential input datasets utilized in our <a href="https://doi.org/10.5194/essd-2023-112">research study</a> titled "Reconstruction of hourly coastal water levels and counterfactuals without sea level rise for impact attribution". </p><p>This archive contains only input data. The Hourly Coastal water levels with Counterfactual (HCC) dataset is published in the <a href="https://doi.org/10.48364/ISIMIP.749905">ISIMIP repository</a>.</p><p><strong>Datasets Included</strong>:</p><p><strong>CoDEC (Coastal Dataset for the Evaluation of Climate Impact)</strong>:</p><ul><li>This dataset is described in<a href="https://doi.org/10.3389/fmars.2020.00263"> Muis et al. (2020)</a></li><li><strong>cf_esl folder</strong>: Contains data representing total CoDEC water levels. Individual NetCDF files store data for each grid point.</li><li><strong>cf_tides folder</strong>: This folder holds data related to tidal elevation.</li><li><strong>coor_coastal.nc</strong>: A NetCDF file featuring the spatial grid utilized in CoDEC. This dataset comprises only coastal grid points.</li></ul><ol><li><strong>HR (Hybrid Reconstructions)</strong>:<ul><li><strong>HybridRec_Upd0422.mat</strong>: This file contains data from the Hybrid Reconstructions dataset (<a href="https://doi.org/10.1038/s41558-019-0531-8">Dangendorf et al 2019</a>), aligned to the CoDEC grid, and includes satellite altimetry integral to producing the Hybrid Reconstructions dataset. Each row corresponds to one grid point on the CoDEC grid. For ease of use in our applications, we offer a preprocessing script in our <a href="https://doi.org/10.5281/zenodo.7771501">source code</a> named split_hr_dataset_to_stations.py.</li></ul></li></ol><p>We here provide the specific versions of HR and CoDEC that are used in our study to ensure accurate replication.</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.