doSerotiny: Activate serotiny after a (fire) disturbance
In PredictiveEcology/LandR: Landscape Ecosystem Modelling in R

doSerotiny

R Documentation

Activate serotiny after a (fire) disturbance

Description

Activate serotiny after a (fire) disturbance

Usage

doSerotiny(
  burnedPixelCohortData,
  postFirePixelCohortData,
  postFireRegenSummary = NULL,
  species,
  sufficientLight,
  speciesEcoregion,
  currentTime,
  treedFirePixelTableSinceLastDisp,
  calibrate = FALSE
)

Arguments

`burnedPixelCohortData`	An expanded `cohortData` `data.table` with pixel-level cohort information on burnt pixels and the following (optional) columns: `severity` - fire severity in that pixel calculated based on fire behaviour properties; `firetolerance` - species-level fire tolerance; `severityToleranceDif` - the difference between `severity` and `firetolerance`.
`postFirePixelCohortData`	an empty `cohortData`-like table with columns: `age`, `B`, `mortality`, `aNPPAct`, and `sumB` removed; and `pixelIndex` added.
`postFireRegenSummary`	a data.table summarizing for which species serotiny/resprouting were activated and in how many pixels, for each year. Only necessary if `calibrate = TRUE`.
`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.
`sufficientLight`	a `data.frame` (not `data.table`!) containing probability of establishment, given a site's light conditions (`X0`-`X5`) for each level of a species shade tolerance (`1`-`5`).
`speciesEcoregion`	A `data.table` with `species`-`ecoregion`-specific species trait values. Ecoregion refers to "ecolocation", a categorical variable grouping sites with similar biophysical characteristics. The table should have at least the following columns: `speciesCode` and `ecoregionGroup`, character representation of species and ecoregion groups respectively, `maxB` the maximum biomass for the species in a given 'ecoregion', `maxANPP` the maximum aboveground net primary productivity and `SEP` the species establishment probability. May contain columns `inflationFactor` (used to adjust `maxB`) and `mANPPproportion` (used to calculate `maxANPP`).
`currentTime`	integer. The current simulation time obtained with `time(sim)`
`treedFirePixelTableSinceLastDisp`	a vector of pixels that burnt and were forested in the previous time step.
`calibrate`	logical. Determines whether to output `postFirePixelCohortData`. Defaults to FALSE

Value

A list of objects: postFirePixelCohortData, a data.table with the cohorts that undergo serotiny; serotinyPixel, a vector of pixels where serotiny was activated; postFireRegenSummary, the updated postFireRegenSummary, if calibrate = TRUE.