determineInitialCohorts: Determine the initial conditions for a set of cohorts
In tilbud/rCTM: R-Cohort Marsh Equilibrium Model

View source: R/determineInitialCohorts.R

determineInitialCohorts

R Documentation

Determine the initial conditions for a set of cohorts

Description

Determine the initial conditions for a set of cohorts

Usage

determineInitialCohorts(
  initElv,
  meanSeaLevel,
  meanHighWater,
  meanHighHighWater = NA,
  meanHighHighWaterSpring = NA,
  suspendedSediment,
  nFloods = 705.79,
  floodTime.fn = floodTimeLinear,
  bMax,
  zVegMin,
  zVegMax,
  zVegPeak,
  plantElevationType,
  rootToShoot,
  rootTurnover,
  rootDepthMax,
  shape = "linear",
  abovegroundTurnover = NA,
  speciesCode = NA,
  omDecayRate,
  recalcitrantFrac,
  captureRate,
  omPackingDensity = 0.085,
  mineralPackingDensity = 1.99,
  rootPackingDensity = omPackingDensity,
  initialCohorts = NA,
  uplandCohorts = NA,
  supertidalCohorts = NA,
  supertidalSedimentInput = NA,
  ...
)

Arguments

`initElv`	a numeric, the initial elevation of the marsh at the start of the scenario
`meanSeaLevel`	a numeric, Mean Sea Level
`meanHighWater`	a numeric, Mean High Water level
`meanHighHighWater`	a numeric (optional), Mean Higher High Water level
`meanHighHighWaterSpring`	a numeric (optional), Mean Higher High Spring Tide Water level
`suspendedSediment`	a numeric, suspended sediment concentration of the water column
`nFloods`	a numeric, the number of tidal flooding events per year
`floodTime.fn`	a function, specify the method used to calculate flooding time per tidal cycle
`bMax`	a numeric or vector of numerics, maximum biomass
`zVegMin`	a numeric or vector of numerics, lower elevation of biomass limit
`zVegMax`	a numeric or vector of numerics, upper elevation of biomass limit
`zVegPeak`	a numeric or vector of numerics, (optional) elevation of peak biomass
`plantElevationType`	character, either "orthometric" or "dimensionless", specifying elevation reference of the vegetation growing elevations
`rootToShoot`	a numeric or vector of numerics, root to shoot ratio
`rootTurnover`	a numeric or vector of numerics, below ground biomass annual turnover rate
`rootDepthMax`	a numeric or vector of numerics, maximum (95%) rooting depth
`shape`	a character, "linear" or "exponential" describing the shape of the relationship between depth and root mass
`abovegroundTurnover`	(optional) a numeric or vector of numerics, aboveground biomass annual turnover rate
`speciesCode`	(optional) a character or vector of characters, species names or codes associated with biological inputs
`omDecayRate`	a numeric, annual fractional mass lost
`recalcitrantFrac`	a numeric, fraction of organic matter resistant to decay
`captureRate`	a numeric, the number of times a water column will clear per tidal cycle
`omPackingDensity`	a numeric, the bulk density of pure organic matter
`mineralPackingDensity`	a numeric, the bulk density of pure mineral matter
`rootPackingDensity`	a numeric, the bulk density of pure root matter
`initialCohorts`	a data frame, (optional) custom set of mass cohorts that will override any decision making this function does
`uplandCohorts`	a data frame, (optional) custom set of mass cohorts to be used if initial elevation is higher than both maximum tidal height and maximum wetland vegetation tolerance
`supertidalCohorts`	a data frame, (optional) custom set of mass cohorts to be used if initial elevation is higher than maximum tidal height, but not maximum wetland vegetation tolerance
`supertidalSedimentInput`	a numeric, (optional) grams per cm^2 per year, an optional parameter which will define annual suspended sediment delivery to a sediment column that is is higher than maximum tidal height, but not maximum wetland vegetation tolerance