Check if all species in have trait values

Source: R/prepInputObjects.R

Check if all species in have trait values

checkSpeciesTraits(speciesLayers, species, sppColorVect)

Arguments

speciesLayers

A RasterStack or RasterLayer that should contain species cover data in the study area

species

a data.table with species traits such as longevity, shade tolerance, etc. Must have column speciesCode, with species names/IDs. The following is a list of default trait columns:

  • "species" same as "speciesCode" -- species ID name

  • "speciesCode"

  • "Area" -- inherited from LANDIS-II default table, the Canadian ecoregion from which traits where derived. Not used during the simulation

  • "firetolerance" -- modulerelative (to other species) fire tolerance

  • "growthcurve" and "mortalityshape" -- growth curve shape parameters.

  • "longevity" -- maximum species age

  • "postfireregen" -- post-fire regeneration strategy ("serotiny", "resprout" or "none")

  • "resproutprob" -- probability of resprouting

  • "resproutage_min" -- minimum age at which species is capable of resprouting

  • "resproutage_max" -- maximum age at which species is capable of resprouting

  • "seeddistance_eff" -- effective dispersal distance

  • "seeddistance_max" -- maximum dispersal distance

  • "shadetolerance" -- relative (to other species) shade tolerance

  • "sexualmature" -- age at sexual maturity Known optional parameters added/needed by some modules (the user may add others for their own modules):

  • "inflationFactor" -- Biomass_speciesParameters module: inflation factor for maxB

  • "growthCurveSource" -- Biomass_speciesParameters module: how "growthcurve" was estimated

  • "mANPPproportion" -- Biomass_speciesParameters module: multiplication factor to calculate maxANPP from maxB

  • "thermokarsttol" -- Biomass_disturbances module: proportion of biomass surviving after thermokarst (i.e. permafrost thaw). Applied equally across cohorts. Parameters inherited from LANDIS-II default table, but not used in LandR at the moment:

  • "leaflongevity"

  • "wooddecayrate"

  • "leafLignin"

  • "hardsoft" Please see the LANDIS-II Biomass Succession Extension v3.2.1 manual (Scheller and Miranda 2015) for further detail.

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).

Value

A list with the speciesLayers and sppColorVect

containing only the species that have trait values in species