runCohortMemTransect: Run Marsh Equilibrium Model with Cohorts Across an Elevation...
In tilbud/rCTM: R-Cohort Marsh Equilibrium Model

runCohortMemTransect

R Documentation

Run Marsh Equilibrium Model with Cohorts Across an Elevation Transect

Description

This function takes an elevation minimum, maximum, and intervals, uses them to simulate an elevation transect, then batch runs runCohortMem over it.

Usage

runCohortMemTransect(
  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,
  initElvMin = meanSeaLevel[1],
  initElvMax = max(meanHighWaterDatum, meanHighHighWaterDatum,
    meanHighHighWaterSpringDatum, na.rm = T) + relSeaLevelRiseTotal,
  elvIntervals = 4,
  ...
)

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
`initElvMin`	a numeric, the lowest initial elevation over which to batch run the model
`initElvMax`	a numeric, the highest initial elevation over which to batch run the model
`elvIntervals`	a numeric, the elevation intervals of the transect
`...`