Activate resprouting after a (fire) disturbance

Source: R/serotiny-resprouting.R

Activate resprouting after a (fire) disturbance

doResprouting(
  burnedPixelCohortData,
  postFirePixelCohortData,
  postFireRegenSummary = NULL,
  serotinyPixel,
  treedFirePixelTableSinceLastDisp,
  currentTime,
  species,
  sufficientLight,
  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.

serotinyPixel

a vector of pixels where serotiny was activated;

treedFirePixelTableSinceLastDisp

a vector of pixels that burnt and were forested in the previous time step.

currentTime

integer. The current simulation time obtained with time(sim)

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).

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.