Add cohorts to cohortData and pixelGroupMap

This is a wrapper for addPixelGroup, initiateNewCohort and updates to pixelGroupMap via assignment to new pixelIndex values in newCohortData. By running these all together, there is less chance that they will diverge. There are some checks internally for consistency.

Calculate new values for B, add age, then rbindlist this with cohortData.

addCohorts(newCohortData, cohortData, pixelGroupMap, time,
  speciesEcoregion)

initiateNewCohort(newCohortData, cohortData, pixelGroupMap, time,
  speciesEcoregion)

Arguments

newCohortData	must be a complete cohortData object with entirely new pixelGroup values (i.e., already non-overlapping with cohortData. Columns it must have: pixelGroup, speciesCode, ecoregionGroup
cohortData	a data.table with columns: pixelGroup, ecoregionGroup, speciesCode, age, B, mortality, aNPPAct, and sumB.
pixelGroupMap	Raster layer with pixel values equal to a pixel group number that correspondsd exactly to pixelGroup column in cohortData
time	Current time e.g., time(sim). This is used to extract the correct parameters in speciesEcoregion table if there are different values over time
speciesEcoregion	A speciesEcoregion table.

Value

A list of length 2, cohortData and pixelGroupMap, with newCohortData inserted.

initiateNewCohort returns A data.table with a new, rbindlisted cohortData

Details

Does the following:

1. add new cohort data into cohortdata;

2. assign initial biomass and age for new cohort;

3. assign the new pixelgroup to the pixels that have new cohort;

4. update the pixelgroup map.