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mouse GIT repository by nlighthart
Model Optimization Uncertainty SEnsitivity toolbox
Clone: Last push: Oct 07 2019 14:26
Push: Size: 140.6 MB
Forks: 0 Pull requests: 0 pending
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Author Comment Items
Nathan Lighthart <Nathan.lighthart@ars.usda.gov>
Oct 04 2019 08:19

Pusher:  nlighthart
Oct 07 2019 14:26
Upgrade Netbeans project files

- Netbeans 11.1 auto-updated project files
c839b5f611b7274ca7445c78425a9d8ac664b8b6 branches: master
  • modified
    nbproject/build-impl.xml
  • modified
    nbproject/genfiles.properties
  • modified
    nbproject/project.properties
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Nathan Lighthart <Nathan.lighthart@ars.usda.gov>
Oct 04 2019 08:08

Pusher:  nlighthart
Oct 07 2019 14:26
Update beansbinding library

- Netbeans 9+ removed internal beansbinding library so replaced internal
Netbeans library with jar file
4a4b1c604f7e3342e2aa6d69cd0f2f31465005ed branches: master
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Holm Kipka <holm.kipka@ars.usda.gov>
Mar 04 2019 14:09

Pusher:  GeoInfoHolm
Mar 04 2019 14:09
cha: code adapt. for KGE
473f2b9a453f949a44b2730be0f829ca4d991cf5 branches: master
  • modified
    src/optas/efficiencies/KGE.java
  • modified
    src/optimization/efficiencies/EfficiencyLibrary.java
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Holm Kipka <holm.kipka@ars.usda.gov>
Mar 04 2019 13:44

Pusher:  GeoInfoHolm
Mar 04 2019 13:44
new: KGE efficiency
ee34b2dd1ba540418fc8a13ca796e5b0fefe70a9 branches: master
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Oct 04 2017 08:44

Pusher:  nlighthart
Jan 28 2019 12:30
Fix gitignore

- Add only root data directory to ignore file
c94618a2a6a6e17d27256b46ffedd8dc4e2b4451 branches: master
  • modified
    .gitignore
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Sep 21 2017 09:23

Pusher:  nlighthart
Jan 28 2019 12:30
Update SCE2

- Add the ability to compute the parameter values for the number of memeplexes, the size of a memeplex, and the minimum number of generations
- Update parameter to logging to show the SCE parameters in the log file
3825c9ee3ea522cbc6c35661e853054381044aff branches: master
  • modified
    src/optas/optimizer/SCE2.java
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Jul 26 2017 14:31

Pusher:  nlighthart
Jan 28 2019 12:30
Fix date utilities

- Use chronounit between method instead of a period as days and months are rolled
96d2c3bf1863c7b873cc28213f9456d5cc3fe740 branches: master
  • modified
    src/util/DateUtil.java
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
May 08 2017 08:27

Pusher:  nlighthart
Jan 28 2019 12:30
Remove joda time library

- Replace joda time library with java 8 date and time library
- Replace use of org.joda.time.LocalDate with java.time.LocalDate
- Add time conversion utilties
c3afcfadde774cd0b3bfb0e1e834588741dddd15 branches: master
  • deleted
    lib/joda-time-2.3.jar
  • modified
    nbproject/project.properties
  • modified
    src/core/persistence/SaverLoader.java
  • modified
    src/core/persistence/converters/JAMSCalendarConverter.java
  • modified
    src/core/persistence/converters/LocalDateConverter.java
  • modified
    src/data/model/Configuration.java
  • modified
    src/gui/configurations/main/MainConfigurationView.java
  • modified
    src/jams/data/JAMSCalendar.java
  • modified
    src/jams/data/JAMSTimeInterval.java
  • modified
    src/jams/explorer/gui/DataCollectionView.java
  • modified
    src/optas/data/TimeFilterFactory.java
  • modified
    src/util/DateUtil.java
  • added
    src/util/TimeConversions.java
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Nov 30 2016 13:34

Pusher:  nlighthart
Jan 28 2019 12:30
Update Model Running to be more robust to failures

- Add checking that observed data and simulated data match the alotted time interval
- Add popup window for when failures occur with a message of what the failure is
- Make sure any samples that were previously computed are not lost and are written to file if possible
- Fixed exception being printed when the user canceled a run
055a9b4e98b1c9ac6dff4e403fc2f94b1b183cbb branches: master
  • modified
    src/optimization/UniversalSO.java
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Nov 14 2016 13:44

Pusher:  nlighthart
Jan 28 2019 12:30
Apply formatting rules

- Format all source files according to project formatting rules
81dfec5a1f3cbc2c36d42a3433cb6f1a395dad32 branches: master
  • ...
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Nov 14 2016 13:21

Pusher:  nlighthart
Jan 28 2019 12:30
Add project specific formatting properties

- Update netbeans profile to contain project specific formatting rules
73d586f1e760c4fa079399325ab1b01ae4226ca0 branches: master
  • modified
    nbproject/project.properties
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Nov 14 2016 12:41

Pusher:  nlighthart
Jan 28 2019 12:30
Add log and trace files

- Add a trace file that displays input parameters and efficiency values for each sample in real time
- Add log file that captures optimization specific log values
cc93bc15f686d230fcd25904ed30ff03aab187f5 branches: master
  • modified
    src/optimization/UniversalSO.java
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Nov 10 2016 10:51

Pusher:  nlighthart
Jan 28 2019 12:30
Updates to optimizer

- Add gasdev random sampling to optimizer
- Minor parameter adjustments to SCE
- Add new SCE2 which should be easier to parameterize and use
517ae45c57d5643b7111c77a5ccf4ae7feeea86e branches: master
  • modified
    src/optas/optimizer/Optimizer.java
  • modified
    src/optas/optimizer/SCE.java
  • added
    src/optas/optimizer/SCE2.java
  • modified
    src/optimization/optimizer/OptimizerLibrary.java
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Oct 07 2016 14:54

Pusher:  nlighthart
Jan 28 2019 12:30
Update SCE

- During evolution avoid generating 3 samples at every time step if one sample is found to be better than the worst sample
d946e8bd3d1ff7fd723f1ced11912d50c130c3e6 branches: master
  • modified
    src/optas/optimizer/SCE.java
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Oct 07 2016 14:49

Pusher:  nlighthart
Jan 28 2019 12:30
Update netbeans files

- Netbeans 8.2 updated project files
6bd09aaeb07651083f817b7c3d5f8fbbf23575a7 branches: master
  • modified
    nbproject/build-impl.xml
  • modified
    nbproject/genfiles.properties
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Mar 04 2016 10:54

Pusher:  nlighthart
Jan 28 2019 12:30
Fix XStreamAnnotations path in preprocessor settings

- Change "\\" to "/" in file path
85d7188a0ac86502ef9c59bdac83e8cda86cc5bf branches: master
  • modified
    nbproject/project.properties
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Mar 03 2016 08:54

Pusher:  nlighthart
Jan 28 2019 12:30
Normalize all the line endings
54f96af48e3b420bd96ad2a1113902d7cd9525a5 branches: master
  • modified
    MOUSE.bat
  • modified
    build.xml
  • modified
    lib/interpreter.properties
  • modified
    manifest.mf
  • modified
    nbproject/build-impl.xml
  • modified
    nbproject/genfiles.properties
  • modified
    nbproject/project.properties
  • modified
    nbproject/project.xml
  • modified
    resources/XStreamAnnotations
  • modified
    src/gui/components/ButtonTabComponent.java
  • modified
    src/jams/JAMSFileFilter.java
  • modified
    src/jams/explorer/spreadsheet/CTSPlot.java
  • modified
    src/jams/explorer/spreadsheet/GraphProperties.java
  • modified
    src/jams/explorer/spreadsheet/JAMSSpreadSheet.java
  • modified
    src/jams/explorer/spreadsheet/JAMSTableModel.java
  • modified
    src/jams/explorer/spreadsheet/JAMSTimePlot.java
  • modified
    src/jams/explorer/spreadsheet/JAMSXYPlot.java
  • modified
    src/jams/explorer/spreadsheet/JTSConfigurator.java
  • modified
    src/jams/explorer/spreadsheet/JXYConfigurator.java
  • modified
    src/jams/gui/tools/GUIHelper.java
  • modified
    src/optas/core/AbstractDataSerie.java
  • modified
    src/optas/core/AbstractFunction.java
  • modified
    src/optas/core/AbstractModel.java
  • modified
    src/optas/data/TimeFilterCollection.java
  • modified
    src/optas/gui/wizard/OPTASWizardException.java
  • modified
    src/optas/gui/wizard/ObjectiveDescription.java
  • modified
    src/optas/gui/wizard/TimeFilterTableInput.java
  • modified
    src/optas/regression/GaussianProcessRegression.java
  • modified
    src/optas/regression/gaussian/HyperParameter.java
  • modified
    src/optas/regression/gaussian/cov/CovarianceFunction.java
  • modified
    src/optas/regression/gaussian/cov/covNNiso.java
  • modified
    src/optas/regression/gaussian/cov/covSEard.java
  • modified
    src/optas/regression/gaussian/cov/covSEiso.java
  • modified
    src/optas/regression/gaussian/inf/Inference.java
  • modified
    src/optas/regression/gaussian/inf/infExact.java
  • modified
    src/optas/regression/gaussian/mean/Constant.java
  • modified
    src/optas/regression/gaussian/mean/Linear.java
  • modified
    src/optas/regression/gaussian/mean/MeanFunction.java
  • modified
    src/optas/regression/gaussian/mean/Sum.java
  • modified
    src/optas/regression/likelihood/Gaussian.java
  • modified
    src/optas/regression/likelihood/LikelihoodFunction.java
  • modified
    src/optas/tools/PatchedChartPanel.java
  • modified
    src/optas/tools/Tools.java
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Mar 03 2016 08:53

Pusher:  nlighthart
Jan 28 2019 12:30
Add line feed normalization

- Create .gitattributes file
- Add * text=auto to automatically convert LF to CRLF on Windows
5b6ec29834b6d57230e94f8fa9651b7af14fc406 branches: master
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Feb 25 2016 09:07

Pusher:  nlighthart
Jan 28 2019 12:30
Fix MOUSE bug where data directory is assumed to present which is not the case on a freshly cloned git repository

- Change model presenter to not only create model and run directories but also any parent directories that do not exist
8299bd82366420c9f5274adf35f7957d3b57c72a branches: master
  • modified
    src/gui/configurations/model/ModelPresenter.java
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Nathan Lighthart <Nathan.Lighthart@ars.usda.gov>
Feb 25 2016 09:02

Pusher:  nlighthart
Jan 28 2019 12:30
Create common git files

- Create git ignore file
- Create README file
3569dc5a2b8b6ccaadc61261a8ac82c2069e268f branches: master
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