checkSpeciesTraits: Check if all species in have trait values

In PredictiveEcology/LandR: Landscape Ecosystem Modelling in R

Check if all species in have trait values

Description

Check if all species in have trait values

Usage

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

PredictiveEcology/LandR documentation built on June 7, 2024, 4:16 p.m.