Takes a single data.table input, which has the following columns in addition to others that will be labelled with species name, and contain percent cover of each:

  • pixelIndex (integer)

  • age (integer)

  • logAge (numeric)

  • initialEcoregionCode (factor)

  • totalBiomass (integer)

  • lcc (integer)

  • rasterToMatch (integer)

  • speciesCode (factor)

  • cover (integer)

  • coverOrig (integer)

  • B (integer)

makeAndCleanInitialCohortData(
  inputDataTable,
  sppColumns,
  imputeBadAgeModel = quote(lme4::lmer(age ~ B * speciesCode + cover * speciesCode + (1
    | initialEcoregionCode))),
  minCoverThreshold,
  doAssertion = getOption("LandR.assertions", TRUE),
  doSubset = TRUE
)

Arguments

inputDataTable

A data.table with columns described above.

sppColumns

A vector of the names of the columns in inputDataTable that represent percent cover by species, rescaled to sum up to 100%.

imputeBadAgeModel

DESCRIPTION NEEDED

minCoverThreshold

DESCRIPTION NEEDED

doAssertion

A logical indicating whether some internal tests should be run to ensure the function is running correctly. Default: getOption("LandR.assertions", TRUE).

doSubset

Turns on/off subsetting. Defaults to TRUE.