LandR: Landscape Ecosystem Modelling in R

speciesTableUpdate

R Documentation

Change species table of parameters/traits

Description

Changes longevity and shade tolerance values in the species table. Longevity values are changed to follow Burton & Cumming (1995) for the following species: Abies balsamea, Abies lasiocarpa, Betula papyrifera, Larix laricina, Larix occidentalis, Picea engelmannii, Picea glauca, Picea mariana, Pinus banksiana, Pinus contorta, Pinus resinosa, Pinus strobus, Populus balsamifera v. balsamifera, Populus tremuloides, Pseudotsuga menziesii var. glauca, Pseudotsuga menziesii, Thuja plicata, Tsuga heterophylla, Tsuga mertensiana x heterophylla, and only for the Boreal Shield West (BSW), Boreal Plains (BP) and Montane Cordillera (MC) speciesTable$Areas. Note that BSW and BP areas correspond more closely to the region considered in Table 2 of Burton & Cumming (1995), while MC will correspond to both tables.

Usage

speciesTableUpdate(species, speciesTable, sppEquiv, sppEquivCol)

Arguments

`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.
`speciesTable`	A species traits table, with at least the following columns: `speciesCode` an character representation of species; `Area` a character of geographical area within a species range for which trait values are relevant; `longevity` species longevity in years, `sexualmature` age in years at sexual maturity; `shadetolerance` numeric value between 1-5 of relative shade tolerance (with respect to other species); `seeddistance_eff` the "effective" seed dispersal distance; `seeddistance_max` a numeric with the maximum seed dispersal distance; `mortalityshape` and `growthcurve`: growth curve shape parameters. Other columns (e.g. fire-related traits) can also be included depending on LandR modules in use. Please see the LANDIS-II Biomass Succession Extension v3.2.1 manual (Scheller and Miranda 2015) for further detail.
`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")`.
`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".

Details

Of the above species, shade tolerance values are changed for Abies spp, Picea spp, and Tsuga spp. to reflect western boreal shade tolerances better.

When different longevity/shade tolerance trait values exist for a given species, the minimum value across Area's (BSW, BP, MC) is kept.

ATTENTION: if none of species in species are from BSW, BP or MC area this function will not change any values.

All other species/Area trait values follow Dominic Cyr and Yan Boulanger's trait values available at: (https://raw.githubusercontent.com/dcyr/LANDIS-II_IA_generalUseFiles/master/speciesTraits.csv).