makeAndCleanInitialCohortData: Generate initial 'cohortData' table
In PredictiveEcology/LandR: Landscape Ecosystem Modelling in R

makeAndCleanInitialCohortData

R Documentation

Generate initial `cohortData` table

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:

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`	statistical model used to impute ages in pixels with missing data or with cover == 0. If set to NULL no imputation will be attempted, and pixels with missing age are excluded.
`minCoverThreshold`	minimum total cover percentage necessary to consider the pixel vegetated, or a cohort present in a pixel.
`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`.

Details

pixelIndex (integer)
age (integer)
logAge (numeric)
initialEcoregionCode (factor)
totalBiomass (integer)
lcc (integer)
rasterToMatch (integer)
speciesCode (factor)
cover (integer)
coverOrig (integer)
B (integer)

Several data correction/imputation operations are also performed. Namely, age is imputed in pixels where age data is missing (but not cover) and where cover == 0 but age > 0, total biomass is zeroed if age == 0, and age is zeroed if biomass == 0.