├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── Format-GUESS.R ├── Format-NetCDF.R ├── Format-aDGVM.R ├── Format-aDGVM2.R ├── Standard-Quantities.R ├── addArea.R ├── addStandardSpatialAttributes.R ├── addTo.R ├── aggregateSpatial.R ├── aggregateSubannual.R ├── aggregateYears.R ├── availableQuantities.R ├── averageFields.R ├── benchmarking.R ├── byIDfromList.R ├── calcNewField.R ├── checkSTAMatches.R ├── classes.R ├── classification-schemes.R ├── commonSTAInfo.R ├── compareLayers.R ├── copyLayers.R ├── crop-methods.R ├── defineLayer.R ├── defineQuantity.R ├── defineSource.R ├── determinePFTs.R ├── export-methods.R ├── extent-methods.R ├── getDimInfo.R ├── getField.R ├── getScheme.R ├── is-methods.R ├── layerOp.R ├── lookupQuantity.R ├── makeFieldID.R ├── makePlotTitle.R ├── names-methods.R ├── package-documentation.R ├── periods.R ├── plotScatter.R ├── plotSpatial.R ├── plotSpatialComparison.R ├── plotSubannual.R ├── plotTemporal.R ├── plotTemporalComparison.R ├── plotting-framework-functions.R ├── read-netcdf-utility-functions.R ├── renameLayers.R ├── selectDays.R ├── selectGridcells.R ├── selectLayers.R ├── selectMonths.R ├── selectSeasons.R ├── selectYears.R ├── show-methods.R ├── small-utility-functions.R ├── summary-methods.R ├── whichLayers.R ├── writeField-methods.R └── writeNetCDF-methods.R ├── README.md ├── inst └── extdata │ ├── LPJ-GUESS_Runs │ ├── CentralAfrica │ │ └── cmass.out.gz │ └── CentralEurope │ │ ├── lai.out.gz │ │ └── mlai.out.gz │ └── NetCDF │ ├── HandP_PNV │ └── HD │ │ ├── .gitignore │ │ └── Smith2014.nc.gz │ └── Saatchi2011 │ └── HD │ └── vegC_std.nc.gz ├── man ├── BiomeScheme-class.Rd ├── Comparison-class.Rd ├── DGVMTools-package.Rd ├── FPCMegaBiomeRules.Rd ├── Field-class.Rd ├── FieldToArray.Rd ├── FireMIPBiomeRules.Rd ├── Format-class.Rd ├── Forrest2015MegaBiomeRules.Rd ├── GrowthFormAdgvm2BiomeRules.Rd ├── Hickler2012Rules.Rd ├── LPJQuantFromFilename.Rd ├── Layer-class.Rd ├── LondonCentre.Rd ├── MeditBiomeRules.Rd ├── MegaBiomeRules_dev.Rd ├── Period-class.Rd ├── PhenologyAdgvm2BiomeRules.Rd ├── Quantity-class.Rd ├── STAInfo-class.Rd ├── Scheme-class.Rd ├── SimpleAdgvm2BiomeRules.Rd ├── SimpleHeightAdgvm2BiomeRules.Rd ├── Smith2014BiomeRules.Rd ├── Source-class.Rd ├── Summary-methods.Rd ├── aDGVMBiomeRules.Rd ├── addArea.Rd ├── addMapOverlay.Rd ├── addStandardSpatialAttributes.Rd ├── addTo.Rd ├── aggregateSpatial.Rd ├── aggregateSpatial.uncompiled.Rd ├── aggregateSubannual.Rd ├── aggregateSubannual.uncompiled.Rd ├── aggregateYears.Rd ├── aggregateYears.uncompiled.Rd ├── availableQuantities.Rd ├── availableQuantities_GUESS.Rd ├── availableQuantities_NetCDF.Rd ├── availableQuantities_aDGVM.Rd ├── availableQuantities_aDGVM2.Rd ├── averageFields.Rd ├── byIDfromList.Rd ├── calcNME.Rd ├── calcNMSE.Rd ├── calcNewField.Rd ├── categoricalComparison.Rd ├── checkDimensionValues.Rd ├── checkSTAMatches.Rd ├── checkSource.Rd ├── commonSTAInfo.Rd ├── compareLayers.Rd ├── continuousComparison.Rd ├── copyLayers.Rd ├── crop-methods.Rd ├── defineLayer.Rd ├── defineQuantity.Rd ├── defineSource.Rd ├── determinePFTs.Rd ├── equivalentQuantities.Rd ├── export-methods.Rd ├── extent-methods.Rd ├── extract.seq.Rd ├── extractRasterExtent.Rd ├── getDailyField_aDGVM.Rd ├── getDimInfo.Rd ├── getField.Rd ├── getField_GUESS.Rd ├── getField_NetCDF.Rd ├── getField_aDGVM.Rd ├── getField_aDGVM2.Rd ├── getQuantity_aDGVM2_Scheme1.Rd ├── getQuantity_aDGVM2_Scheme2.Rd ├── getScheme.Rd ├── getStandardQuantity_LPJ.Rd ├── getStandardQuantity_aDGVM.Rd ├── getYearlyField_aDGVM.Rd ├── grapes-slash-0-grapes.Rd ├── gridarea1d.Rd ├── gridarea2d.Rd ├── is.leapyear.Rd ├── is.object-methods.Rd ├── layerOp.Rd ├── lm_eqn.Rd ├── lookupQuantity.Rd ├── makeFieldID.Rd ├── makePlotTitle.Rd ├── makeSPDFfromDT.Rd ├── makeYAxis.Rd ├── matchLayerCols.Rd ├── mergeFieldsForPlotting.Rd ├── names.Rd ├── openLPJOutputFile.Rd ├── openLPJOutputFile_FireMIP.Rd ├── parseStartDate.Rd ├── plotScatter.Rd ├── plotSpatial.Rd ├── plotSpatialComparison.Rd ├── plotSubannual.Rd ├── plotTemporal.Rd ├── plotTemporalComparison.Rd ├── processDailyNCAxis.Rd ├── processDailyRelativeNCAxis.Rd ├── processMonthlyNCAxis.Rd ├── processYearlyNCAxis.Rd ├── promoteToRaster.Rd ├── proportionsComparison.Rd ├── readRegularASCII.Rd ├── renameLayers.Rd ├── santiseComparisonsForPlotting.Rd ├── santiseDimensionsForPlotting.Rd ├── santiseFieldsForPlotting.Rd ├── santiseLayersForPlotting.Rd ├── seasonalComparison.Rd ├── selectDays.Rd ├── selectGridcells.Rd ├── selectLayers.Rd ├── selectMonths.Rd ├── selectSeasons.Rd ├── selectYears.Rd ├── setKeyDGVM.Rd ├── show.Rd ├── stats_mode.Rd ├── supported.classification.schemes.Rd ├── trimFieldsForPlotting.Rd ├── whichLayers.Rd ├── writeField-methods.Rd └── writeNetCDF-methods.Rd ├── tests ├── testthat.R └── testthat │ └── test_DGVMTools.R └── vignettes ├── DGVMTools_Introduction.R ├── DGVMTools_Introduction.Rmd ├── DGVMTools_Introduction.html ├── 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