BiteBiomass Class

BiteBiomass

Description

Simple javascript based growth

If no growthFunction is provided, the growth of the cell is calculated in javascript using the onCalculate handler.

logistic growth functions

A logistic growth function (e.g. K / (1 + ( (K - M) / M))*exp(-r*t)) can be used to model the biomass growth of the agent (see growthFunction for variable description). This mode is active when a value for growthFunction is provided. The following steps are executed:

  • calculate initial host biomass (see hostBiomassTree or hostBiomassCell), and initial value for K
  • calcuate the annual growth r rate for the agent (growthRateFunction)
  • for growthIterations steps:
    • estimate the agent biomass (via growthFunction, and t=1/growthIterations)
    • calculate the amount of consumed biomass: delta_bm = consumtion * agent_biomass * t, with agent_biomass the average agent biomass before and after the step
    • update the host biomass, and calculate a new value for K ( K=remaining_host_biomass/consumption)
  • the algorithm stops, if either host or agent biomass is depleted (agentBiomass is set to 0 in this case).
  • the variable agentImpact is set to the sum of consumed biomass during the year.

Setup

  • hostTrees (expression)

    A filter expression to select those trees on the pixel which are considered as hosts.

  • hostBiomass (dynamic expression)

    A dynamic expression to calculate the host biomass. If hostBiomass is an expression, it is evaluated for each host tree (>4m) (see hostTrees), and consequently the total host biomass is the sum over all trees. If hostBiomass is a Javascript function the host biomass is the result of the function which is evaluated with the parameter cell.

Javascript can be used to access sapling biomass (and to combine trees and saplings):

   hostBiomass: function(cell) {
       cell.reloadSaplings(); // trees are loaded automatically
       cell.saplings.filter('species=fasy and height>0.5'); // only beech and >0.5
       var bm_saplings = cell.saplings.sum('nrep*foliagemass'); // foliage * number of represented stems per cohort
       // or: bm_saplings = cell.saplings.sum('nrep*foliagemass', 'species=fasy and height>0.5');
       var bm_trees = cell.trees.sum('foliagemass', 'species=fasy'); // foliage of all beech trees
       Bite.log(cell.info() + ": sap: " + bm_saplings + " tree: " + bm_trees); 
       return bm_saplings + bm_trees;
   }

  • mortality (dynamic expression)

    A dynamic expression, whose result is interpreted as the probability of mortality for the agent on the cell. The expression is evaluated within the cell context.

  • growthFunction (Expression)

    The main growth function used to calcuate the the amount of agent biomass on a cell as a function of host biomass and environmental conditions. The growth function has a number of pre-defined variables (case-sensitive!):

variable description
M current agent biomass on the cell
K current maximum agent biomass (carrying capacity), calculated as host_biomass / consumption
r The growth rate, result of the growthRateFunction
t the time step, set to 1/growthIterations

  • growthRateFunction (Expression)

    calculates the growth rate used in growthFunction; the growth rate can be dependent on any cell variables (e.g. climatic variables).

  • consumption (dynamic expression)

    consumption rate of the agent, defined as kg host biomass / units agent per year. It means, that an unit of agent consumes consumption kg of host biomass per year (e.g. a defoliater might consume x kg leaves / kg agent biomass per year). The property is a dynamic expression evaluated in the context of the current cell.

  • growthIterations (integer)

    The growth function

  • verbose (bool)

    if true detailed log output of the growth cylce is written to the console. ## Properties

no properties

Variables

  • hostBiomass

    hostBiomass is a measure of the relevant host biomass that can be consumed/occupied by an agent. The value is the result of the host biomass calculation (see hostBiomass dynamic expression). The value is set to 0 when a cell dies.

  • agentBiomass

    agentBiomass is the total biomass of the agent on a cell. The agentBiomass is set to 0 when a cell dies. The value of the variable is the result of the Javascript handler (onCalculate) or the result of the logistic growth.

  • agentImpact

    The agentImpact is a measure for the consumed host biomass during the year. Note that the type of impact (e.g., foliage, roots) can differ. The value is the set as the difference in host biomass before and after the logistic growth.

Events

  • onSetup(item)

    The onSetup event is triggered after the setup of the item.

item is the BiteBiomass object.

  • onCalculate(cell)

    The handler is responsible for calculating the new state of the agent biomass. The handler is called after the calcuation of the carrying capacity, and the the varible agentBiomas is set to the return value of the function. Is only used when no growthFunction is present.

  • onMortality(cell)

    The handler is invoked if the cell dies (i.e. only if the random choice based on the probability (see mortality) decides the death of the agent on the cell).