Function reference • LandR

All functions
`CASFRItoSpRasts()`	`CASFRItoSpRasts`
`makeVegTypeMap()`	Make a vegetation type map from a stack of species abundances
`LandR-package`	`LandR` package
`addNoPixel2CohortData()`	Add number of pixels per `pixelGroup` and add it has a new column to `cohortData`
`addPixels2CohortData()`	Generate `cohortData` table per pixel:
`asInteger()`	Convert numeric values to rounded integers
`assertSpeciesEcoregionCohortDataMatch()`	Assert that the `cohortData` `speciesEcoregion` have matching classes
`assert1()` `assert2()` `assertUniqueCohortData()` `assertERGs()` `assertColumns()` `assertCohortData()` `assertPixelCohortData()` `assertSpeciesPlotLabels()` `assertFireToleranceDif()` `assertSpeciesLayers()` `assertRstLCChange()`	Assertions
`assignLightProb()`	Assign light probability
`calcSiteShade()`	Calculate site shade
`calculateClimateEffect()`	Null climate effect
`checkSpeciesTraits()`	Check if all species in have trait values
`columnsForPixelGroups`	Default columns that define pixel groups
`convertUnwantedLCC()`	Convert Land Cover Classes (LCC) to another value in its neighbourhood
`defineFlammable()`	Define flammability map
`describeCohortData()`	Summary for `cohortData`
`doResprouting()`	Activate resprouting after a (fire) disturbance
`doSerotiny()`	Activate serotiny after a (fire) disturbance
`.cleanLandWebStudyArea()`	Clean up the LandWeb study area from David Andison
`.interpolateLightProb()`	Find interpolated value of light probability
`makeDummyEcoregionMap()` `makeDummyRawBiomassMap()` `makeDummyStandAgeMap()` `makeDummyRstLCC()` `makeDummyEcoregionFiles()`	Create dummy inputs for test simulations
`ecoregionProducer()`	Make `ecoregionMap` and `ecoregion` table
`equivalentName()`	Return equivalent name from a `data.frame` of equivalencies
`fasterizeFromSp()`	Rasterize polygons using `fasterize`
`generatePixelGroups()`	Add the correct `pixelGroups` to a `pixelDataTable` object
`loadCASFRI()`	Load CASFRI data
`loadkNNSpeciesLayers()`	Load kNN species layers from online data repository
`loadkNNSpeciesLayersValidation()`	Load kNN species layers from online data repository
`makeAndCleanInitialCohortData()`	Generate initial `cohortData` table
`makeBiomassMap()`	Create `biomassMap`
`makeCohortDataFiles()`	Make the `cohortData` table, while modifying the temporary `pixelCohortData` that will be used to prepare other files.
`makeEcoregionDT()`	Make the `ecoregion` table
`makeEcoregionMap()`	Make the `ecoregionMap` raster
`makeMinRelativeB()`	Create `minRelativeB` table
`makePickellStack()`	`makePickellStack`
`makePixelGroupMap()`	Create `makePixelGroupMap`
`makePixelTable()`	Make `pixelTable` from biomass, age, land-cover and species cover data
`makeSpeciesEcoregion()`	Create `speciesEcoregion`
`overlayLCCs()`	Overlay different LCC data sources
`overlayStacks()`	Overlay layers within raster stacks
`pixelFate()`	Create or amend data to a `pixelFateDT` object
`plantNewCohorts()`	Create new cohorts based on provenance table with unique `pixelGroup` and add to `cohortData`
`plotVTM()`	Summary plots of leading vegetation types
`polygonClean()`	Do an arbitrary set of operations on a polygon
`prepEcoregions()`	Prepare ecoregions objects
`prepInputsEcoregion()`	Prepare ecoregion table
`prepInputsLCC()`	Simple `prepInputs` for LCC2005 or LCC2010 data
`prepInputsSpecies()` `prepInputsMainInput()`	Download and prepare a species traits table for use with `Biomass_core` module
`prepInputsSpeciesEcoregion()`	Prepare species ecoregion table
`prepSpeciesLayers_KNN()` `prepSpeciesLayers_CASFRI()` `prepSpeciesLayers_Pickell()` `prepSpeciesLayers_ForestInventory()` `prepSpeciesLayers_KNN2011()`	Prepare species layers
`randomStudyArea()`	Create default study areas for use with LandR modules
`rmMissingCohorts()`	Remove missing cohorts from `cohortData` based on `pixelGroupMap`
`scheduleDisturbance()`	Test whether disturbance should be scheduled
`speciesEcoregionLatestYear()`	Pull out the values from `speciesEcoregion` table for current time
`getSpeciesTable()` `prepSpeciesTable()`	Download and prepare a species traits table for use with `Biomass_core` module
`speciesTableUpdate()`	Change species table of parameters/traits
`sppColors()`	Create species colour vector from a `sppEquiv` table
`sppEquivalencies_CA`	Table of species name equivalencies for Canadian trees
`statsModel()`	The generic statistical model to run (`lmer` or `glmer`)
`subsetDT()`	Subset a `data.table` with random subsampling within `by` groups
`sumRastersBySpecies()`	Function to sum rasters of species layers
`uniqueCohortDefinition` `uniqueSpeciesEcoregionDefinition`	The columns in a `cohortData` that define "unique"
`updateCohortData()` `.initiateNewCohorts()`	Add cohorts to `cohortData` and `pixelGroupMap`
`updateCohortDataPostHarvest()`	Add cohorts to `cohortData` and `pixelGroupMap`
`updateSpeciesTable()`	Customize species trait table values
`vegTypeGenerator()`	Generate and add vegetation type column to `cohortData`
`vegTypeMapGenerator()`	Generate vegetation type map

Reference

All functions