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 Apple Snail Change log

v3.1.0 - 2021-01-14
  • Relax grid overlap check between water and temperature to not require same starting x & y
  • Allow water coordinates to drive output dataset footprint

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

v2.5.2 - 2020-08-17
  • Set time variable as "unlimited" to fix errors like "Variable starting pos=3434677996 may not exceed 2147483647"

v2.5.1 - 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)

v2.5.0 - 2020-06-25
  • Javadocs, address compiler warnings, use primitives, general refactoring
  • Remove IDataWriter & DataWriter, refactor to use CERP NetCDF library in AppleSnailProcessor
  • Move AlleeFunctionType & AleeParameter to constants package
  • Add NcVariable, NcVariableImpl, and NcVariables
  • Add OutputNcVariable
  • Summarize variable mins and maxes after processing
  • Add "min", "max" attributes to output variables
  • Add "title", "summary", "keywords" attributes to global attributes
  • Log model parameterization (input files, variables, selected dates, output file, variables)
  • Log output file header and run time after processing
  • Add CLI option "--output-variables" to allow limiting output variables produced
  • Fix potential bug when comparing cell sizes of hydro and temp datasets
  • Add org.geotools.plugin;bundle-version="23.0.0"

v2.4.2 - 2020-06-18
  • Fix bug (since 2.4.0) that caused eggPopulation and snailPopulationJuveniles to be 0

v2.4.1 - 2020-06-15
  • 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",
    • gov.usgs.jem.spatial.model;bundle-version="1.4.0",

v2.4.0 - 2018-04-17
  • Refactored the Parameters tab to use ExpandBar and Expand Items with a vertical scroll bar.
  • Added a new Allee option to select which type of allee function to use, Hill (previous) or Log.

v2.3.0 - 2018-01-24
  • Improved modeling time significantly by restructuring the way data are read, processed, and written
  • Update UI to use list control for date selection instead of combo control
  • Updated command line options with --date-range (remove --date-index-range) to specify YYYYMMDD lower and upper
  • bounds for model run

v2.2.0 - 2017-12-18
  • Added fish mortality simulation and unit tests; New parameters: Dsd min water level, minimum days above water level,
  • and the fish mortality factor

  • Minor folder structure change: moved the tests to its own test source folder.
  • Added Reproduction delay to the UI
  • Added Allee Factors to the UI and the reproduction simulation

v2.1.0 - 2017-06-05
  • Headless: better model validation and setting of automatic defaults (variable names, output folder, date range)

v2.0.0 - 2017-02-22
  • Update to allow headless execution (see --headless --help)
  • Fixes for changes in NetCDF library and fill value
  • Minor bug fix related to dates in NetCDFReaderModel
  • Adjustment of kgrowth parameter default value from 0. 05 to 0.1
  • Bug fix to survival equation in SurvivalSimulation
  • Added the ability to have a negative date index to indicate the min / max of that index
  • Include default parameters XML file

v1.0.0 - 2012
  • Update to Eclipse 4 framework
  • Update to NetCDF-Java 4.3
  • pre-1.0

  • Initial release