Joint Ecosystem Modeling

Software Requirements

Java 11 or later
Operating system:
  • Windows - 64 bit
  • Mac OS - Intel 64 bit
  • Linux - 64 bit with GTK

JEM Small Fish Density Model Change Log

v2.1.0 - 2021-01-14
  • Add --psus-required option to CLI, which is enabled by default and requires all PSUs to map to input grid(s).

v2.0.0 - 2020-10-19
  • Update for Java 11
  • Move Software Requirements to README.txt file
  • Update to supporting libraries that have been migrated to Java 11
  • Add javax.annotation to dependencies
  • Update org.eclipse.jdt.core.prefs and org.eclipse.jdt.ui.prefs for Java 11 and warn on missing javadocs for private visibility

v1.1.4 - 2020-08-14
  • Library updates (some may not apply):
    • edu.ucar.unidata.netcdf;bundle-version="5.3.3",
    • gov.usgs.jem.cerp.netcdf;bundle-version="3.0.0",
    • gov.usgs.jem.spatial.model;bundle-version="2.0.0",
    • gov.usgs.jem.spatial.expressions;bundle-version="2.0.0",
    • gov.usgs.jem.hydro.processing;bundle-version="2.0.0",
    • gov.usgs.jem.netcdf.depthcreator.ui;bundle-version="2.0.0",
    • gov.usgs.jem.netcdf.ncmlcreator.ui;bundle-version="2.0.0",
    • gov.usgs.jem.thredds.ui;bundle-version="2.0.0"
  • Attempt to resolve the majority of compiler warnings through a combination of mechanisms:
    • refactor deprecated to current usage where possible, suppress deprecation otherwise;
    • add javadocs in some cases, but suppress where documentation was largely ignored or code is not otherwise actively maintained;
    • suppress or address other compiler warnings (e.g. resource; unused)

v1.1.3 - 2020-06-16
  • guava;bundle-version="29.0.0",
  • org.geotools.plugin;bundle-version="23.0.0",
  • edu.ucar.unidata.netcdf;bundle-version="5.1.0",
  • gov.usgs.jem.cerp.netcdf;bundle-version="2.0.0",
  • org.apache.commons.csv;bundle-version="1.8.0",
  • gov.usgs.jem.spatial.model;bundle-version="1.4.0",
  • gov.usgs.jem.hydro.processing;bundle-version="1.4.0"

v1.1.2 - 2018-03-21
  • Removed invalid parameters (i.e regions: HOLEY,LO,PENN,PM) from modeling_parameters.xml file.

v1.1.1 - 2018-01-22
  • Upgraded SQLite to latest version (v3.21.0) to fix issue on MacOS when running large / multiple input files

v1.1.0 - 2017-10-02
  • Load button click shows user three choices:
  • 1. NetCDFs Folder Scan: Allows the user to browse to a folder containing multiple NetCDF scenarios files.

    2. NcMLs Folder Scan: Allows the user to browse to a folder containing multiple NcML files.

    3. NetCDF Timeseries: Allows the user to select multiple NetCDF timeseries files. The application will create NcML file

    from the selected timeseries NetCDF files (files ordered on time ranges).

  • Allow users to add additional NetCDf or NcML files to table viewer without removing previously added files
  • Preferences page includes text boxes to edit default file names of Modeling parameters file, Region shape file, and
  • PSU CSV file (requires restart for these changes to take effect).

  • Help documentation is updated with three choices of load button and Preferences page text boxes
  • Update to help documentation with invalid OutputFiles link in index html page
  • Headless: Renamed "--input-folder" option to "--input-nc-folder"
  • Headless: --input-file option now also accepts ncml file
  • Headless: Added two new options
    • --input-ncml-folder: Specify input folder containing multiple ncml files which the application will scan for.
    • --input-timeseries-nc-files : Specify multiple NetCDF files from the same timeseries to create a new aggregated scenario

v1.0.0 - 2017-08-29
  • Initial release of application
  • Output includes:
    • DSD & TOTFISH CSV files for PSUs
    • TOTFISH change and % change (scenario - baseline) CSV files for PSUs
    • DSD (change and % change, scenario - baseline) CSV files for regions
    • TOTFISH (change and % change, scenario - baseline) CSV files for regions
    • TOTFISH landscape average CSV files
    • TOTFISH time series average CSV files
    • DSD differences by region (scenario - baseline) time series charts
    • TOTFISH, cumulative TOTFISH, and cumulative TOTFISH difference (scenario - baseline) time series charts
    • TOTFISH temporal average, change, and % change (scenario - baseline) maps for PSUs