Man pages for PredictiveEcology/LandR
Landscape Ecosystem Modelling in R
| addNoPixel2CohortData | Add number of pixels per 'pixelGroup' and add it has a new... |
| addPixels2CohortData | Generate 'cohortData' table per pixel: |
| aggregateRasByDT | Aggregate a raster |
| asInteger | Convert numeric values to rounded integers |
| assertions | Assertions |
| assertPostPartialDist | Assert post-fire disturbance mortality and regeneration |
| assignLightProb | Assign light probability |
| biomodEnsembleFrcstWrapper | Simple wrapper around 'biomod2::BIOMOD_EnsembleForecasting()' |
| biomodEnsembleProjMaps | Make maps from 'BIOMOD_EnsembleForecasting()' results |
| biomodEnsembleWrapper | BIOMOD_EnsembleModeling wrapper |
| biomodModelingWrapper | BIOMOD_Modeling wrapper |
| biomodProjWrapper | BIOMOD_Projection wrapper |
| BioSIM_extractPoints | Extract point locations from DEM raster to pass to 'BioSIM'... |
| BioSIM_getMPBSLR | Get annual historic and projected MPB climate suitability... |
| BioSIM_getWindAnnual | Get annual historic and projected wind maps from 'BioSIM' |
| BioSIM_getWindMonthly | Get monthly historic and projected wind maps from 'BioSIM' |
| calcSeverityB | Calculate fire severity |
| calcSiteShade | Calculate site shade |
| calculateClimateEffect | Null climate effect |
| CASFRItoSpRasts | 'CASFRItoSpRasts' |
| checkSpeciesTraits | Check if all species in have trait values |
| Colors | Helper for setting Raster or 'SpatRaster' colors |
| columnsForPixelGroups | Default columns that define pixel groups |
| compare | Compare raster properties |
| convertUnwantedLCC | Convert Land Cover Classes (LCC) to another value in its... |
| convertUnwantedLCC2 | Convert Land Cover Classes (LCC) to another value in its... |
| defineFlammable | Define flammability map |
| describeCohortData | Summary for 'cohortData' |
| Disturbances | Disturbance functions |
| doResprouting | Activate resprouting after a (fire) disturbance |
| doSerotiny | Activate serotiny after a (fire) disturbance |
| dot-createCohortData | Generate template 'cohortData' table |
| dot-fitNLMwCovariates | Fit non-linear growth model under various starting conditions |
| dot-getMaxBCoefs | Get maximum biomass coefficient names |
| dot-interpolateLightProb | Find interpolated value of light probability |
| dot-logFloor | Log-transformed values, with a floor (> 0) |
| dot-MLLMaxBPartialPlotData | Prepare data for model plotting |
| dot-MLLMaxBplotData | Prepare data for model plotting |
| dot-overlay | Overlaying function |
| dot-speciesTableColNames | Species Table Column Names |
| dropTerm | Drop factor term including interactions from a model formula |
| dummy-inputs | Create dummy inputs for test simulations |
| ecoregionProducer | Make 'ecoregionMap' and 'ecoregion' table |
| equivalentName | Return equivalent name from a 'data.frame' of equivalencies |
| extractMaxB | Maximum biomass estimator |
| fasterizeFromSp | Rasterize polygons using 'fasterize' |
| fitNLMModels | FUNCTIONS TO FIT NON-LINEAR MODELS TO ESTIMATE MAXB Wrapper... |
| generatePixelGroups | Add the correct 'pixelGroups' to a 'pixelDataTable' object |
| genericExtract | Generic extract points |
| genPGsPostDisturbance | Re-generate new 'pixelGroup's in partially disturbed pixels. |
| getWildfire_NFI | Download and prepare raster fire data from NFI |
| ggplotMLL_maxB | Plot estimated maximum biomass by age |
| installBioSIM | Install 'BioSIM' to retrieve climate and other projections... |
| LANDISDisp | Simulate a LANDIS-II dispersal process on a landscape. |
| landisIIrepo | Default LANDIS-II project repo url |
| LandR-deprecated | Make a vegetation type map from a stack of species abundances |
| LandR-package | 'LandR' package |
| loadCASFRI | Load CASFRI data |
| loadkNNSpeciesLayers | 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... |
| 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... |
| makeSpeciesEcoregion | Create 'speciesEcoregion' |
| mergeSppRaster | Merge species percent-cover rasters |
| minRelativeBDefaults | minRelativeB defaults for Western Boreal Forest Canada |
| modifySpeciesAndSpeciesEcoregionTable | Update 'species' and 'speciesEcoregion' tables |
| NAcover2zero | Convert 'NA' values in 'speciesLayers' to zeros |
| nonForestedPixels | Assess non-forested pixels based on species cover data and... |
| overlayLCCs | Overlay different LCC data sources |
| overlayStacks | Overlay layers within raster stacks |
| partialggplotMLL_maxB | Partial effect plots of maximum biomass estimates by age |
| partitionBiomass | Partition biomass according to cover estimates |
| pixelFate | Create or amend data to a 'pixelFateDT' object |
| pkgEnv | The 'LandR' package environment |
| plantNewCohorts | Create new cohorts based on provenance table with unique... |
| plotLeadingSpecies | Leading species plots |
| plotSpatial | Create a 'ggplot' of a raster or 'sf' object. |
| plotVTM | Summary plots of leading vegetation types |
| prepEcoregions | Prepare ecoregions objects |
| prepEcozonesRst | Prepare ecozones raster |
| prepInputsCanDEM | Get digital elevation map of Canada |
| prepInputsEcoregion | Prepare ecoregion table |
| prepInputsFireYear | Create a raster of fire perimeters |
| prepInputsLCC | Simple 'prepInputs' for Canadian LCC data |
| prepInputs_NTEMS_LCC_FAO | Obtain an LCC layer for a given year from NTEMS, with forest... |
| prepInputs_NTEMS_Nonforest | Reclassify non-flammable pixels that become flammable -... |
| prepInputsSpecies | Download and prepare a species traits table for use with... |
| prepInputsSpeciesEcoregion | Prepare species ecoregion table |
| prepInputsStandAgeMap | Create 'standAgeMap' |
| prepRasterToMatch | Create 'rasterToMatch' and 'rasterToMatchLarge' |
| prepRawBiomassMap | Create 'rawBiomassMap' |
| prepSpeciesLayers | Prepare species layers |
| randomStudyArea | Create default study areas for use with LandR modules |
| rasterRead | Wrapper to read a raster using a specific package function |
| rasterTerraHelpers | Set NA values in 'Raster' or 'SpatRaster' |
| replaceAgeInFires | Replace stand age with time since last fire |
| resample | Resample |
| rescale | Rescale function (as in 'scales::rescale') |
| rmMissingCohorts | Remove missing cohorts from 'cohortData' based on... |
| scheduleDisturbance | Test whether disturbance should be scheduled |
| speciesEcoregionLatestYear | Pull out the values from 'speciesEcoregion' table for current... |
| speciesEcoregionStack | Create Stacks of the 'speciesEcoregion' content |
| speciesPresent | Make a species factor raster |
| speciesTable | Download and prepare a species traits table for use with... |
| 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 |
| sppEquivCheck | Check and expand 'sppEquiv' |
| sppHarmonize | Harmonize the three components that bring species into... |
| standAgeMapGenerator | Produce stand age map based on 'cohortData' |
| statsModel | The generic statistical model to run ('lmer' or 'glmer') |
| subsetDT | Subset a 'data.table' with random subsampling within 'by'... |
| sumRastersBySpecies | Function to sum rasters of species layers |
| uniqueDefinitions | The columns in a 'cohortData' that define "unique" |
| updateCohortData | 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 |
| WardKernel | Ward Dispersal Kernel - vectorized, optimized for speed |
