runCohortMem: Run Marsh Equilibrium Model with Cohorts
In tilbud/rCTM: R-Cohort Marsh Equilibrium Model

runCohortMem

R Documentation

Run Marsh Equilibrium Model with Cohorts

Description

This function takes an initial elevation, average annual suspended sediment concentration and tidal properties, plant traits, and decay rates, then builds a scenario, and runs the marsh equilibrium model over that scenario tracking individual sediment mass cohorts including mineral, live root, slow decay organic mater pool and a fast organic matter pool.

Usage

runCohortMem(
  startYear,
  endYear = startYear + 99,
  relSeaLevelRiseInit,
  relSeaLevelRiseTotal,
  initElv,
  meanSeaLevel,
  meanSeaLevelDatum = meanSeaLevel[1],
  meanHighWaterDatum,
  meanHighHighWaterDatum = NA,
  meanHighHighWaterSpringDatum = NA,
  suspendedSediment,
  lunarNodalAmp,
  lunarNodalPhase = 2011.181,
  nFloods = 705.79,
  floodTime.fn = floodTimeLinear,
  bMax,
  zVegMin,
  zVegMax,
  zVegPeak,
  plantElevationType,
  rootToShoot,
  rootTurnover,
  abovegroundTurnover = NA,
  speciesCode = NA,
  rootDepthMax,
  shape = "linear",
  omDecayRate,
  recalcitrantFrac,
  captureRate,
  omToOcParams = list(B0 = 0, B1 = 0.48),
  omPackingDensity = 0.085,
  mineralPackingDensity = 1.99,
  rootPackingDensity = omPackingDensity,
  initialCohorts = NA,
  uplandCohorts = NA,
  supertidalCohorts = NA,
  supertidalSedimentInput = NA,
  ...
)

Arguments

`startYear`	an integer, year in form YYYY, the start year of the scenario
`endYear`	an integer, year in form YYYY, the end year of the scenario
`relSeaLevelRiseInit`	a numeric, initial rate of relative sea-level rise
`relSeaLevelRiseTotal`	a numeric, total relative sea-level rise over the course of the scenario
`initElv`	a numeric, the initial elevation of the marsh at the start of the scenario
`meanSeaLevel`	a numeric or a vector, Mean Sea Level at the start of the scenario, or a vector of Mean Sea Levels the same length as the number of years in a scenario
`meanSeaLevelDatum`	a numeric, Mean Sea level over the last datum period
`meanHighWaterDatum`	a numeric, Mean High Water level over the last datum period
`meanHighHighWaterDatum`	a numeric (optional), Mean Higher High Water level over the last datum period
`meanHighHighWaterSpringDatum`	a numeric (optional), Mean Higher High Spring Tide Water level over the last datum period
`suspendedSediment`	a numeric, suspended sediment concentration of the water column
`lunarNodalAmp`	a numeric, the amplitude of the 18-year lunar nodal cycle
`lunarNodalPhase`	a numeric, in decimal years (YYYY) the start year of the sine wave representing the lunar nodal cycle
`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`	(optional) a numeric, or vector of numerics, 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, belowground biomass annual turnover rate
`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
`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
`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
`omToOcParams`	a list, of numerics listed B0, B1 and optionally B3. These define a linear or parabolic relationship between organic matter and organic carbon
`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
`...`