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 Alligator Production Probability Model Change Log

v3.0.0 - 2020-10-16
  • 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

v2.6.4 - 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)

v2.6.3 - 2020-06-11
  • Library updates:
    • guava;bundle-version="29.0.0",
    • edu.ucar.unidata.netcdf;bundle-version="5.1.0",
    • gov.usgs.jem.cerp.netcdf;bundle-version="2.0.0",
    • org.geotools.plugin;bundle-version="23.0.0",
    • gov.usgs.jem.spatial.model;bundle-version="1.4.0",
    • org.apache.commons.csv;bundle-version="1.8.0"

v2.6.2 - 2019-07-01
  • Fix for grid artifacts in some locations across the output due to a problematic method of determining the input grid
  • index, which would lead to a duplication of the neighbor cell's calculated values

  • Fix so that if an input grid cell has fill value, the output grid cell for that variable will also have fill value

v2.6.1 - 2018-02-08
  • Fix for command line year range: make sure lower & upper years are valid and adjust as necessary, like UI does

v2.6.0 - 2018-01-16
  • Further improved modeling time by reading input data in even more efficient chunks
  • Fix for command line year range option being +1 year in the future

v2.5.0 - 2017-08-14
  • Tree island heights file now optional; added selectors for CSV columns
  • Gator holes file now optional; added selectors for CSV columns
  • Percent Edge Habitat can now be disabled
  • Automatically determine output file name
  • Indicate which files are required on the UI & update layout slightly
  • More descriptive errors when files are missing & better exception trapping

v2.4.2 - 2017-05-26
  • Ensure parent folders of specified output file exist or can be created
  • Change zip and extracted folder name for easier integration with headless scripting tools

v2.4.1 - 2017-04-12
  • Bug fix: do not require salinity file to run the model

v2.4.0 - 2017-03-29
  • Allow running on partial season data and to produce a subset of metrics when data are available
  • Allow selection of NcML files for depth data
  • Automatically convert units of input depth data (e.g. cm -> mm)
  • Detect coordinate axes order for depth and salinity data (e.g. t,y,x vs. t,x,y)
  • UI: Expand text controls for output parameters, remove tab folder
  • Fix for date ranges: use closed interval instead of open interval

v2.3.0 - 2017-02-17
  • Update to allow headless execution (see --headless --help)
  • Improved modeling time by reading input data in more efficient chunks
  • More granular reporting of modeling progress
  • Fix for potential resource problems (files left open in the event of errors)
  • Fix for "duplicate salinity" error when loading parameters file
  • Fix for salinity file not resetting when loading from parameters file
  • Fix for year range choice from user occasionally not being retained
  • Fix for occasional errors when saving parameters file

v2.2.0 - 2014-02-14
  • Added bug reporting capability (Help > Report Bug); integrated "Report Bug..." button to Eclipse error dialog
  • Bug fix: inter year dates (breeding start to nest flooding end) are now hh:mm:ss adjusted to the
  • depth input dates. If an exact match between dates cannot be found during processing, a close

    match is found and used

  • More verbose logging in model processor:
    • layer names & variable names;
    • output variable names, types, and units;
    • output spatial parameters, time parameter;
    • dates read from depth file and salinity file (if provided);
    • inter year dates used; inexact date matches logged;
  • Log CDL of input depth file (

v2.1.2 - 2013-10-18
  • Updated mean clutch top height equation in nest building component as requested by the modeler
  • Bug fix: changed constant value in same clutch height equation from 25 cm to 42 cm to represent typical
  • height of clutch

v2.1.1 - 2013-05-13
  • Fixed bug where gator holes spatial extent might extend beyond output grid extent, causing a nondescript error
  • Fixed bug where model year range may not be set properly when loading from parameters file
  • Allow salinity input file to be optional

v2.1 - 2013-04-24
  • Updated to Eclipse 4 platform
  • Update to NetCDF-Java 4.3
  • Defer reading of output parameters from depth file until "Run" is clicked or requested by the user
  • Fixed bug where output parameters were not being properly updated to the model before running
  • Fixed bug where multiple dialogs were being displayed when model run completed

v2.0.2 - 2013-04-03
  • Bug fix: do not require output file to exist before running

v2.0.1 - 2013-04-02
  • Allow selection of data variable from NetCDF if default is not found

v2.0.0 - 2013-03-25
  • Converted to cross-platform GUI application

  • CLI application created