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 Everglades Landscape Vegetation Succession Model (ELVeS) Change Log

v3.0.0 - 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

v2.5.2 - 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)

v2.5.1, 2020-06-16
  • 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",
  • org.apache.httpcomponents;bundle-version="4.5.12",
  • org.apache.commons.csv;bundle-version="1.8.0"

v2.5.0, 2019-09-24
  • Update to allow initial vegetation layer to come from a NetCDF grid (prior options were only 'random' or 'computed')
  • Ensure progress dialog is displayed (override "run in background")
  • Add checks to require that any vegetation class in NetCDF layer must exist in defined communities
  • Update parameters file for new initial vegetation type
  • Add "Check for Updates..." menu entry

v2.4.1, 2018-05-11
  • Bug fix for output file path error if parameters file contains a file name only

v2.4.0, 2017-03-09
  • Update to allow headless execution (see --headless --help)
  • Ensure file handles are closed in the event of an error

v2.3.1, 2014-10-20
  • Bug fix for "highest only" succession option when there are no communities with higher joint
  • instantaneous probability than the current (NoSuchElementException)

v2.3.0, 2014-10-14
  • Added new default option for vegetation succession: allow intermediate communities with higher
  • joint instantaneous probabilities than the current to be considered, instead of just the highest.

  • Added logging to Runtime tab
  • Bug fix for probability of replacement not being calculated from the favored community
  • Bug fix to reset the replacement index for each community during a new monte carlo iteration
  • Bug fix to update the replacement index of all unfavored communites. When a new community
  • replaces the current, reset the new community's replacement index.

v2.2.2, 2014-09-05
  • Expanded allowed input CSV file formats: can consume files output from NetCDF to CSV tool
    • Allow "x" as height column name
    • Allow "y" as width column name
    • Allow "time" as an additional time column name and format (assumes "yyyy-MM-dd'T'kk:mm:ss'Z'")
    • Automatically determine cell width and height if missing from first two nonequal x's, y's
  • Updated to show status line
  • Process dates using UTC timezone
  • Bug fix for determining the correct index for a given coordinate, which could also lead to NaN values
  • Bug fix for default veg class output being 0 instead of "fill value" when p_succession = 0 or NaN
  • Bug fix for order of site, year not matching between iprob and lag outputs (CSV)
  • Bug fix for lag parameters switch min, max not being used in evaluating succession (was using 0.001 and 3.5 always)
  • Bug fix for retrieving dates from nc files: use CERP NetCDFVarReader.getDates
  • Bug fix for different handling of out-of-bounds dates between CSV and NetCDF input files
  • Bug fix for determining the name and path of the output intermediate probability files
  • More descriptive error messages when validating output grid parameters

v2.2.1, 2014-03-10
  • Disable easting, northing, x max, y max, and cell size output parameter boxes when coordinates
  • output is being used since the coordinates are not being aligned to the output parameter grid

  • Bug fix: intermediate vegetation probability files (CSV output) had coordinates that were
  • still being aligned to the output parameter grid, resulting in incorrect coordinate values

  • Bug fix: Coordinate ordering for parameters file was not being preserved

v2.2.0, 2014-03-05
  • Improved bug reporting capability (Help > Report Bug); integrated "Report Bug..." button to
  • Eclipse error dialog

  • Output points are no longer aligned / moved to output parameter grid
  • If output to CSV is used, input coordinate ordering is preserved in output
  • If folder path to output file doesn't exist, create it
  • Added vertical scroll to output coordinates area so that the control doesn't get hidden for
  • large amounts of points

v2.1.1, 2013-08-30
  • Bug fix in CERP NetCDF library to allow dashes and dots in NetCDF variable names, as per
  • Unidata CDL syntax primer.


v2.1.0, 2013-08-30
  • Updated to Eclipse 4 platform
  • Update to NetCDF-Java 4.3
  • Added beta distributions for vegetation community responses
  • Added support for point-based (CSV) data layer files. See Help > Using the Application >
  • Modifying the Parameters > Data Layers page for information about required formatting

  • Added support for point-based (CSV) output. See Help > Using the Application >
  • Output page for more information

  • Include initial vegetation layer type in parameter file input / output

v2.0.1, 2012-11-28
  • Bug fix for the Evaluation -> Logistic tab, the X2 column gets input from the X1 text box
  • rather than the X2 text box

  • Bug fix for File -> Save not remembering parameters path

v2.0.0, 2012-09-29
  • Converted to cross-platform executable using Eclipse RCP, updated GUI
  • Includes help documentation
  • Improved run time
  • Allow user to specify community vegetation ID
  • Now uses CERP NetCDF libraries
  • Bug fix for iterations parameter being hard-coded at 100
  • Bug fix for progress dialog showing inaccurate percentage of work completed
  • Other minor bug fixes

v1.0.0, prior to 2012-06-26
  • Initial version of the application bundled as a jar with a Java Swing GUI