addCohort: Add another cohort to the soil profile
In tilbud/rCTM: R-Cohort Marsh Equilibrium Model

addCohort

R Documentation

Add another cohort to the soil profile

Description

This function adds a new cohort to a soil profile. Cohorts are constructed as follows:

Cohorts are aged by timeStep increment.
Organic matter pools decay
If there are non-zero mineral inputs, they are added to the top of the soil profile as a new cohort.
The top and bottom of the cohort layer is recalculated.
A new root profile is constructed based on the cohort layers.

Usage

addCohort(
  massPools,
  rootTurnover,
  rootOmFrac,
  omDecayRate,
  packing,
  mineralInput = NA,
  mineralInput.fn = sedimentInputs,
  massLiveRoots.fn = massLiveRoots,
  calculateDepthOfNonRootVolume.fn = calculateDepthOfNonRootVolume,
  timeStep = 1,
  ...
)

Arguments

`massPools`	A data frame containing the following columns: age, fast_OM, slow_OM, mineral, layer_top, layer_bottom, root_mass. Each row of this data frame represents a single cohort. To increase runtime in simulations, the profile is buffered with NA's at the top of the data frame, see code comments for details.
`rootTurnover`	A numeric as the root turnover time in faction per year.
`rootOmFrac`	A list of numerics called fast and slow which is the allocation fraction between fast and slow organic matter pool respectively for dead roots.
`omDecayRate`	A list of numerics called fast and slow which is the decay rate for the fast and slow organic matter pool in fraction per year.
`packing`	A list of numerics with mineral and organic arguments representing their respective packing densities.
`mineralInput`	An optional value for mineral input in grams per year (numeric) if mineralInput.fn is not used
`mineralInput.fn`	A function that returns the mineral input in grams per year (numeric)
`massLiveRoots.fn`	A function that returns the mass of live roots for specified depth layers, must accept `layerBottom` and `layerTop` as arguments.
`calculateDepthOfNonRootVolume.fn`	A function that returns the depth of a specified volume of soil, must accept `nonRootVolume` as an argument.
`timeStep`	A numeric of the time step in years. Typically set to 1 year.
`...`	arguments to be passed to the specified functions