JEM Everglades Landscape Vegetation Succession Model (ELVeS) Change Log

• 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

• 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.cerp.netcdf.ug;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)

• 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"

• 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

• Bug fix for output file path error if parameters file contains a file name only

• Update to allow headless execution (see --headless --help)
• Ensure file handles are closed in the event of an error

• Bug fix for "highest only" succession option when there are no communities with higher joint

instantaneous probability than the current (NoSuchElementException)

• 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.

• 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

• 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

• 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

• Bug fix in CERP NetCDF library to allow dashes and dots in NetCDF variable names, as per

Unidata CDL syntax primer.

(See http://www.unidata.ucar.edu/software/netcdf/docs/netcdf/CDL-Syntax.html)

• 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

• 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

• 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

• Initial version of the application bundled as a jar with a Java Swing GUI