Harmonize the three components that bring species into Biomass_** modules

Source: R/sppHarmonize.R

This function will attempt to harmonize many potential issues/conflicts that may arise under different combinations of supplied objects to the three arguments. See manual for details.

sppHarmonize(
  sppEquiv,
  sppNameVector,
  sppEquivCol,
  sppColorVect,
  vegLeadingProportion = 0,
  studyArea,
  dPath = getOption("reproducible.destinationPath")
)

Arguments

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").

sppNameVector

A character vector of species to use. These species must all be from one naming convention, i.e., from one column in the sppEquiv.

sppEquivCol

A character string normally provided from the P(sim)$sppEquivCol (see manual). If NA, the default, then this will try to determine which column the sppNameVector used and use that. If sppNameVector is NULL, then it will default to "Boreal".

sppColorVect

A named vector of colours to use for plotting. The names must conform with species name convention used (see sppEquivalencies_CA for possible naming conventions) and should also contain a colour for 'Mixed', when a mixed forest type is supported (see vegLeadingProportion parameter in vegTypeGenerator() for details on mixed forest types).

vegLeadingProportion

Numeric between 0-1, determining the relative biomass threshold a species needs to pass to be considered "leading".

studyArea

A SpatialPolygons* object used as the principle study region, passed to reproducible::prepInputs().

dPath

Passed to speciesInStudyArea (which then passes to preProcess)

Value

Returns a named list with the same names as the arguments. These should likely be assigned to the sim object in the module following this function call.

Examples

## not run. usage example within module
# sppOuts <- sppHarmonize(sim$sppEquiv, sim$sppNameVector, P(sim)$sppEquivCol)
# sim$sppEquiv <- sppOuts$sppEquiv
# sim$sppNameVector <- sppOuts$sppNameVector
# P(sim)$sppEquivCol <- sppOuts$sppEquivCol