Man pages for MagicForrest/DGVMTools
DGVM Processing, Analysis and Plotting Tools
| addArea | Adds the gridcell area to a spatial Field or... |
| addMapOverlay | Make a map overlay for ggplot2 |
| addStandardSpatialAttributes | Adds standard spatial attributes to a netCDF file |
| addTo | Add Layer/Quantity to a Format/Source/Field |
| aDGVMBiomeRules | Rules to classify tropical biomes from aDGVM1 output |
| aggregateSpatial | Spatially aggregate a Field |
| aggregateSpatial.uncompiled | Spatially aggregate a Field |
| aggregateSubannual | Sub-annual aggregation |
| aggregateSubannual.uncompiled | Sub-annual aggregation |
| aggregateYears | Aggregate years |
| aggregateYears.uncompiled | Aggregate years |
| availableQuantities | List available quantities |
| availableQuantities_aDGVM | List available aDGVM Quantities in a run |
| availableQuantities_aDGVM2 | List aDGVM2 quantities avialable |
| availableQuantities_GUESS | List all LPJ-GUESS *.out files in a run directory |
| availableQuantities_NetCDF | List all LPJ-GUESS *.out files in a source directory |
| averageFields | Average Fields |
| BiomeScheme-class | Smith et al 2014 *Smith2014BiomeScheme* Classification of... |
| byIDfromList | Retrieves an object from a list based on it's 'id' slot |
| calcNewField | Simple calculation of new Fields |
| calcNME | Calculate Normalised Mean Error |
| calcNMSE | Calculate Normalised Mean Square Error |
| categoricalComparison | Comparison between two datasets of categorical variables |
| checkDimensionValues | Check values of a particular dimension |
| checkSource | Checks validity of a 'Source'. |
| checkSTAMatches | Checks if STAInfo matches between Fields |
| commonSTAInfo | Checks common for STAInfo object |
| compareLayers | Compare layers to each other |
| Comparison-class | Contains a comparison between two layers |
| continuousComparison | Compare continuous data |
| copyLayers | Copy layers from one Field to another |
| crop-methods | Crop methods |
| defineLayer | Define a Layer object |
| defineQuantity | Define a Quantity object |
| defineSource | Define a Source object that represents a model run or data... |
| determinePFTs | Get PFTs present |
| DGVMTools-package | An overview of the DGVMTools package |
| equivalentQuantities | Check if two Quantity objects are equivalent |
| export-methods | Coerce from Fields and Comparisons |
| extent-methods | Extent methods |
| extractRasterExtent | Get an extent from anything |
| extract.seq | Extract a regular sequence from unique values in a vector |
| Field-class | Field-class contains data |
| FieldToArray | Convert a Field to Arrays |
| FireMIPBiomeRules | Rules to classify FireMIP biomes from fractionalcover of PFTs |
| Format-class | Format class |
| Forrest2015MegaBiomeRules | Rules to classify coarses "mega biomes" as per Forrest et al.... |
| FPCMegaBiomeRules | Rules for biome scheme based on FPC |
| getDailyField_aDGVM | Get a 'daily' aDGVM Field |
| getDimInfo | Returns the spatio-temporal information |
| getField | Get a 'Field' from a 'Source' |
| getField_aDGVM | Get a Field for aDGVM |
| getField_aDGVM2 | Get a Field for aDGVM2 |
| getField_GUESS | Get a Field for LPJ-GUESS |
| getField_NetCDF | Get a Field for NetCDF |
| getQuantity_aDGVM2_Scheme1 | Read aDGVM2 quantities from pop file |
| getQuantity_aDGVM2_Scheme2 | Read aDGVM2 quantities from trait file |
| getScheme | Get a Classification 'Field' from a 'Source' |
| getStandardQuantity_aDGVM | Returns the data from one aDGVM output variable as a... |
| getStandardQuantity_LPJ | Returns the data from one LPJ-GUESS output variable as a... |
| getYearlyField_aDGVM | Get a yearly aDGVM Field |
| grapes-slash-0-grapes | Safe division |
| gridarea1d | grid cell area along a vector of latitudes |
| gridarea2d | Returns the area for a lon/lat grid. |
| GrowthFormAdgvm2BiomeRules | Rules to classify coarse tropical biomes |
| Hickler2012Rules | Rules to classify biomes as per Hickler et al. 2012 |
| is.leapyear | check if a given year is a leap year |
| is.object-methods | Check if an object is a particular type of DGVMTools object. |
| Layer-class | Class to hold the metadata for a "Layer" |
| layerOp | Layer Operation |
| lm_eqn | Make linear fit equation string |
| LondonCentre | London centre a gridcell |
| lookupQuantity | Retrieve a Quantity from the standard list. |
| LPJQuantFromFilename | Helper function to raster::trim the ".out" or the ".out.gz"... |
| makeFieldID | Make an ID string for a 'Field' |
| makePlotTitle | Make a plot titles |
| makeSPDFfromDT | Make SpatialPixelDataFrame from a data.table |
| makeYAxis | Make y-axis |
| matchLayerCols | Make a LAyer colour list |
| MeditBiomeRules | Rules to classify coarses Mediterranean biomes |
| MegaBiomeRules_dev | Rules to classify coarser "mega biomes" from LAI, latitude... |
| mergeFieldsForPlotting | Merge data from Field for plotting |
| names | Layer name methods |
| openLPJOutputFile | Open an LPJ-GUESS .out file |
| openLPJOutputFile_FireMIP | Open an LPJ-GUESS .out file |
| parseStartDate | Parse start date |
| Period-class | Time periods - eg. a month or a season or a year. |
| PhenologyAdgvm2BiomeRules | Rules to classify coarse tropical biomes |
| plotScatter | Make a scatter plot |
| plotSpatial | Plot maps from a 'Field' or a lists of 'Field' |
| plotSpatialComparison | Plot a comparison between two spatial layers |
| plotSubannual | Plots sub-annual cycles |
| plotTemporal | Plot temporal data |
| plotTemporalComparison | Plot a comparison between two Temporal layers |
| processDailyNCAxis | processDailyNCAxis This function processes a time axis which... |
| processDailyRelativeNCAxis | processDailyRelativeNCAXis This function processes a relative... |
| processMonthlyNCAxis | processMonthlyNCAxis This function processes a time axis... |
| processYearlyNCAxis | processYearlyNCAxis This function processes a time axis which... |
| promoteToRaster | Convert to Raster |
| proportionsComparison | Compare relative proportions data |
| Quantity-class | Class to hold meta-data for a vegetation quantity |
| readRegularASCII | Read ASCII table |
| renameLayers | Rename layers |
| santiseComparisonsForPlotting | Sanitise input Comparisons for plotting |
| santiseDimensionsForPlotting | Sanitise STAInfo for plotting |
| santiseFieldsForPlotting | This is an internal helper function which checks the inputs... |
| santiseLayersForPlotting | Sanitise input layers for plotting |
| Scheme-class | A classification scheme |
| seasonalComparison | Compare seasonal data |
| selectDays | Select days from a Field |
| selectGridcells | Select gridcells |
| selectLayers | Select layers |
| selectMonths | Select months from a Field |
| selectSeasons | Select seasons from a Field |
| selectYears | Select years from a Field |
| setKeyDGVM | Sets keys on data.table based in the spatial (Lon, Lat) and... |
| show | Show a DGVMTools object |
| SimpleAdgvm2BiomeRules | Rules to classify coarse tropical biomes |
| SimpleHeightAdgvm2BiomeRules | Rules to classify coarse tropical biomes |
| Smith2014BiomeRules | Rules to classify biomes as per Smith et al. 2014 |
| Source-class | Metadata for a data source |
| STAInfo-class | STAInfo class |
| stats_mode | Statistical mode |
| Summary-methods | Summary methods |
| supported.classification.schemes | Currently supported classification schemes |
| trimFieldsForPlotting | Subsets data from Field for plotting |
| whichLayers | Select Layers |
| writeField-methods | Write methods |
| writeNetCDF-methods | writeNetCDF methods |
