makeAndCleanInitialCohortData: Generate initial 'cohortData' table

In PredictiveEcology/LandR: Landscape Ecosystem Modelling in R

Description

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)

Usage

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.

Author(s)

Eliot McIntire

PredictiveEcology/LandR documentation built on Jan. 24, 2021, 12:52 a.m.