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Title: Model Output: Nemo-Cice With An Emergent Sea Ice Floe Size Distribution

NEMO-CICE model output from experiments with and without an emergent sea ice floe size distribution.

See README for further details

 
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Award ID(s):
1643431
NSF-PAR ID:
10342669
Author(s) / Creator(s):
Publisher / Repository:
Zenodo
Date Published:
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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  1. Data Description:

    To improve SOC estimation in the United States, we upscaled site-based SOC measurements to the continental scale using multivariate geographic clustering (MGC) approach coupled with machine learning models. First, we used the MGC approach to segment the United States at 30 arc second resolution based on principal component information from environmental covariates (gNATSGO soil properties, WorldClim bioclimatic variables, MODIS biological variables, and physiographic variables) to 20 SOC regions. We then trained separate random forest model ensembles for each of the SOC regions identified using environmental covariates and soil profile measurements from the International Soil Carbon Network (ISCN) and an Alaska soil profile data. We estimated United States SOC for 0-30 cm and 0-100 cm depths were 52.6 + 3.2 and 108.3 + 8.2 Pg C, respectively.

    Files in collection (32):

    Collection contains 22 soil properties geospatial rasters, 4 soil SOC geospatial rasters, 2 ISCN site SOC observations csv files, and 4 R scripts

    gNATSGO TIF files:

    ├── available_water_storage_30arc_30cm_us.tif                   [30 cm depth soil available water storage]
    ├── available_water_storage_30arc_100cm_us.tif                 [100 cm depth soil available water storage]
    ├── caco3_30arc_30cm_us.tif                                                 [30 cm depth soil CaCO3 content]
    ├── caco3_30arc_100cm_us.tif                                               [100 cm depth soil CaCO3 content]
    ├── cec_30arc_30cm_us.tif                                                     [30 cm depth soil cation exchange capacity]
    ├── cec_30arc_100cm_us.tif                                                   [100 cm depth soil cation exchange capacity]
    ├── clay_30arc_30cm_us.tif                                                     [30 cm depth soil clay content]
    ├── clay_30arc_100cm_us.tif                                                   [100 cm depth soil clay content]
    ├── depthWT_30arc_us.tif                                                        [depth to water table]
    ├── kfactor_30arc_30cm_us.tif                                                 [30 cm depth soil erosion factor]
    ├── kfactor_30arc_100cm_us.tif                                               [100 cm depth soil erosion factor]
    ├── ph_30arc_100cm_us.tif                                                      [100 cm depth soil pH]
    ├── ph_30arc_100cm_us.tif                                                      [30 cm depth soil pH]
    ├── pondingFre_30arc_us.tif                                                     [ponding frequency]
    ├── sand_30arc_30cm_us.tif                                                    [30 cm depth soil sand content]
    ├── sand_30arc_100cm_us.tif                                                  [100 cm depth soil sand content]
    ├── silt_30arc_30cm_us.tif                                                        [30 cm depth soil silt content]
    ├── silt_30arc_100cm_us.tif                                                      [100 cm depth soil silt content]
    ├── water_content_30arc_30cm_us.tif                                      [30 cm depth soil water content]
    └── water_content_30arc_100cm_us.tif                                   [100 cm depth soil water content]

    SOC TIF files:

    ├──30cm SOC mean.tif                             [30 cm depth soil SOC]
    ├──100cm SOC mean.tif                           [100 cm depth soil SOC]
    ├──30cm SOC CV.tif                                 [30 cm depth soil SOC coefficient of variation]
    └──100cm SOC CV.tif                              [100 cm depth soil SOC coefficient of variation]

    site observations csv files:

    ISCN_rmNRCS_addNCSS_30cm.csv       30cm ISCN sites SOC replaced NRCS sites with NCSS centroid removed data

    ISCN_rmNRCS_addNCSS_100cm.csv       100cm ISCN sites SOC replaced NRCS sites with NCSS centroid removed data


    Data format:

    Geospatial files are provided in Geotiff format in Lat/Lon WGS84 EPSG: 4326 projection at 30 arc second resolution.

    Geospatial projection

    GEOGCS["GCS_WGS_1984", DATUM["D_WGS_1984", SPHEROID["WGS_1984",6378137,298.257223563]], PRIMEM["Greenwich",0], UNIT["Degree",0.017453292519943295]] (base) [jbk@theseus ltar_regionalization]$ g.proj -w GEOGCS["wgs84", DATUM["WGS_1984", SPHEROID["WGS_1984",6378137,298.257223563]], PRIMEM["Greenwich",0], UNIT["degree",0.0174532925199433]]

     

     
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  2. A biodiversity dataset graph: UCSB-IZC

    The intended use of this archive is to facilitate (meta-)analysis of the UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC). UCSB-IZC is a natural history collection of invertebrate zoology at Cheadle Center of Biodiversity and Ecological Restoration, University of California Santa Barbara.

    This dataset provides versioned snapshots of the UCSB-IZC network as tracked by Preston [2,3] between 2021-10-08 and 2021-11-04 using [preston track "https://api.gbif.org/v1/occurrence/search/?datasetKey=d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0"].

    This archive contains 14349 images related to 32533 occurrence/specimen records. See included sample-image.jpg and their associated meta-data sample-image.json [4].

    The images were counted using:

    $ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\
     | grep -o -P ".*depict"\
     | sort\
     | uniq\
     | wc -l

    And the occurrences were counted using:

    $ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\
     | grep -o -P "occurrence/([0-9])+"\
     | sort\
     | uniq\
     | wc -l

    The archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance files and data files. Only two index and provenance files are included and have been individually included in this dataset publication. Index files provide a way to links provenance files in time to establish a versioning mechanism.

    To retrieve and verify the downloaded UCSB-IZC biodiversity dataset graph, first download preston-*.tar.gz. Then, extract the archives into a "data" folder. Alternatively, you can use the Preston [2,3] command-line tool to "clone" this dataset using:

    $ java -jar preston.jar clone --remote https://archive.org/download/preston-ucsb-izc/data.zip/,https://zenodo.org/record/5557670/files,https://zenodo.org/record/5557670/files/5660088

    After that, verify the index of the archive by reproducing the following provenance log history:

    $ java -jar preston.jar history
    <urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .
    <hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c> <http://purl.org/pav/previousVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .

    To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.

    $ java -jar preston.jar verify
    hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    file:/home/jhpoelen/ucsb-izc/data/ce/1d/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    OK    CONTENT_PRESENT_VALID_HASH    66438    hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c
    hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    file:/home/jhpoelen/ucsb-izc/data/f6/8d/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    OK    CONTENT_PRESENT_VALID_HASH    4093    hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844
    hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    file:/home/jhpoelen/ucsb-izc/data/3e/70/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    OK    CONTENT_PRESENT_VALID_HASH    5746    hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef
    hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    file:/home/jhpoelen/ucsb-izc/data/99/58/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    OK    CONTENT_PRESENT_VALID_HASH    6147    hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b

    Note that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".

    Files in this data publication:

    --- start of file descriptions ---

    -- description of archive and its contents (this file) --
    README

    -- executable java jar containing preston [2,3] v0.3.1. --
    preston.jar

    -- preston archive containing UCSB-IZC (meta-)data/image files, associated provenance logs and a provenance index --
    preston-[00-ff].tar.gz

    -- individual provenance index files --
    2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a

    -- example image and meta-data --
    sample-image.jpg (with hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c)
    sample-image.json (with hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844)

    --- end of file descriptions ---


    References

    [1] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-11-04 as indexed by the Global Biodiversity Informatics Facility (GBIF) with provenance hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36 hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c.
    [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .
    [3] MJ Elliott, JH Poelen, JAB Fortes (2020). Toward Reliable Biodiversity Dataset References. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2020.101132
    [4] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-10-08. https://www.gbif.org/occurrence/3323647301 . hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c

    This work is funded in part by grant NSF OAC 1839201 and NSF DBI 2102006 from the National Science Foundation. 
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  3. We are conducting nutrient manipulations in three study sites in the White Mountain National Forest in New Hampshire: Bartlett Experimental Forest, Hubbard Brook Experimental Forest, and Jeffers Brook. We monitored foliar chemistry in 12 of our stands (excluding C3) pre-treatment (2008-2010) and post-treatment (2014-2016). In general, we found that foliar N concentrations were higher with N addition and foliar P concentrations were higher with P addition. More interestingly, P addition reduced foliar N concentrations and N addition reduced foliar P concentrations. Some interactive effects were observed (i.e. NxP, Species x N, Species x P, Species x N x P). This dataset contains pre- and post- treatment foliar chemistry data, and data from the analysis of quality control standard samples. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station. 
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  4. Abstract

    The NeonTreeCrowns dataset is a set of individual level crown estimates for 100 million trees at 37 geographic sites across the United States surveyed by the National Ecological Observation Network’s Airborne Observation Platform. Each rectangular bounding box crown prediction includes height, crown area, and spatial location. 

    How can I see the data?

    A web server to look through predictions is available through idtrees.org

    Dataset Organization

    The shapefiles.zip contains 11,000 shapefiles, each corresponding to a 1km^2 RGB tile from NEON (ID: DP3.30010.001). For example "2019_SOAP_4_302000_4100000_image.shp" are the predictions from "2019_SOAP_4_302000_4100000_image.tif" available from the NEON data portal: https://data.neonscience.org/data-products/explore?search=camera. NEON's file convention refers to the year of data collection (2019), the four letter site code (SOAP), the sampling event (4), and the utm coordinate of the top left corner (302000_4100000). For NEON site abbreviations and utm zones see https://www.neonscience.org/field-sites/field-sites-map. 

    The predictions are also available as a single csv for each file. All available tiles for that site and year are combined into one large site. These data are not projected, but contain the utm coordinates for each bounding box (left, bottom, right, top). For both file types the following fields are available:

    Height: The crown height measured in meters. Crown height is defined as the 99th quartile of all canopy height pixels from a LiDAR height model (ID: DP3.30015.001)

    Area: The crown area in m2 of the rectangular bounding box.

    Label: All data in this release are "Tree".

    Score: The confidence score from the DeepForest deep learning algorithm. The score ranges from 0 (low confidence) to 1 (high confidence)

    How were predictions made?

    The DeepForest algorithm is available as a python package: https://deepforest.readthedocs.io/. Predictions were overlaid on the LiDAR-derived canopy height model. Predictions with heights less than 3m were removed.

    How were predictions validated?

    Please see

    Weinstein, B. G., Marconi, S., Bohlman, S. A., Zare, A., & White, E. P. (2020). Cross-site learning in deep learning RGB tree crown detection. Ecological Informatics56, 101061.

    Weinstein, B., Marconi, S., Aubry-Kientz, M., Vincent, G., Senyondo, H., & White, E. (2020). DeepForest: A Python package for RGB deep learning tree crown delineation. bioRxiv.

    Weinstein, Ben G., et al. "Individual tree-crown detection in RGB imagery using semi-supervised deep learning neural networks." Remote Sensing 11.11 (2019): 1309.

    Were any sites removed?

    Several sites were removed due to poor NEON data quality. GRSM and PUUM both had lower quality RGB data that made them unsuitable for prediction. NEON surveys are updated annually and we expect future flights to correct these errors. We removed the GUIL puerto rico site due to its very steep topography and poor sunangle during data collection. The DeepForest algorithm responded poorly to predicting crowns in intensely shaded areas where there was very little sun penetration. We are happy to make these data are available upon request.

    # Contact

    We welcome questions, ideas and general inquiries. The data can be used for many applications and we look forward to hearing from you. Contact ben.weinstein@weecology.org. 

    Gordon and Betty Moore Foundation: GBMF4563 
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  5. Model output from experiments described in Cooper et al 2022.

    Includes WW3 output of ice concentration and significant wave height (hourly) for 2018-01-01 through 2018-12-31.

    Includes WW3 1-D wave spectra (hourly) for 2018-07.

    Includes CICE output of representative radius (daily) for 2018-01-01 through 2018-12-31.

    Note: uncompressed file size is 2x the tar.gz file size.

     
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