LandR-deprecated: Make a vegetation type map from a stack of species abundances
In PredictiveEcology/LandR: Landscape Ecosystem Modelling in R

makeVegTypeMap

R Documentation

Make a vegetation type map from a stack of species abundances

Description

makeVegTypeMap is a wrapper around vegTypeMapGenerator that works from a species stack of percent cover. These do not have to sum to 100%%

Downloads the 2011 kNN species cover layers from the Canadian Forestry Service, National Inventory System, for validation.

Usage

makeVegTypeMap(speciesStack, vegLeadingProportion, mixed, ...)

loadkNNSpeciesLayersValidation(
  dPath,
  rasterToMatch,
  studyArea,
  sppEquiv,
  knnNamesCol = "KNN",
  sppEquivCol,
  thresh = 1,
  url,
  ...
)

prepSpeciesLayers_KNN2011(
  destinationPath,
  outputPath,
  url = NULL,
  studyArea,
  rasterToMatch,
  sppEquiv,
  sppEquivCol,
  thresh = 10,
  ...
)

Arguments

`speciesStack`	A `RasterStack` of species abundances. This must be one `RasterLayer` per species.
`vegLeadingProportion`	Numeric between 0-1, determining the relative biomass threshold a species needs to pass to be considered "leading".
`mixed`	Deprecated. See `mixedType` argument to vegTypeMapGenerator.
`...`	Additional arguments passed to `reproducible::Cache()` and `equivalentName()`.
`dPath`	path to the data directory
`rasterToMatch`	A `RasterLayer` objects to use as the template for all subsequent raster operations (i.e., the one used throughout the simulation).
`studyArea`	A `⁠SpatialPolygons*⁠` object used as the principle study region, passed to `reproducible::prepInputs()`.
`sppEquiv`	table with species name equivalencies between the kNN and final naming formats. See `data("sppEquivalencies_CA", "LandR")`. For functions that have `mixedType`, this only necessary if `mixedType == 2`. If not provided and `mixedType == 2`, will attempt to use `data("sppEquivalencies_CA", "LandR")`.
`knnNamesCol`	character string indicating the column in `sppEquiv` containing kNN species names. Default `"KNN"` for when `sppEquivalencies_CA` is used.
`sppEquivCol`	the column name to use from `sppEquiv`. For functions that have `mixedType`, only necessary if `mixedType == 2`. If not provided and `mixedType == 2`, will attempt to use "Boreal".
`thresh`	the minimum number of pixels where the species must have `biomass > 0` to be considered present in the study area. Defaults to 1.
`url`	the source url for the data, passed to `reproducible::prepInputs()`
`destinationPath`	path to data directory where objects will be downloaded or saved to
`outputPath`	path to output directory