assertions: Assertions
In PredictiveEcology/LandR: Landscape Ecosystem Modelling in R

Assert that ecoregionCodes that were replaced, were correctly identified.

This is the full pixelCohortData, not the collapsed one.

assert1(
  cohortData34to36,
  cohortData,
  rmZeroBiomassQuote,
  classesToReplace = 34:36,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assert2(
  cohortDataNo34to36,
  classesToReplace = 34:36,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertUniqueCohortData(
  cohortData,
  columns,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertERGs(
  ecoregionMap,
  cohortData,
  speciesEcoregion,
  minRelativeB,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertColumns(
  obj,
  colClasses,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertCohortData(
  cohortData,
  pixelGroupMap,
  sim,
  maxExpectedNumDiverge = 1,
  message = "",
  doAssertion = getOption("LandR.assertions", TRUE),
  verbose = getOption("LandR.verbose", TRUE),
  cohortDefinitionCols = c("pixelGroup", "age", "speciesCode")
)

assertPixelCohortData(
  pixelCohortData,
  pixelGroupMap,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertSpeciesPlotLabels(
  speciesNames,
  sppEquiv,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertFireToleranceDif(
  burnedPixelCohortData,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertSpeciesLayers(
  speciesLayers,
  thresh,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertRstLCChange(
  rstLCChange,
  rasterToMatch,
  doAssertion = getOption("LandR.assertions", TRUE)
)

`cohortData34to36`	A `cohortData` `data.table` with only the pixels what were LCC 34:36
`cohortData`	A `data.table` with columns: `pixelGroup`, `ecoregionGroup`, `speciesCode`, and optionally `age`, `B`, `mortality`, `aNPPAct`, and `sumB`.
`rmZeroBiomassQuote`	An expression to evaluate, in the form of `quote(B>0)`, used to select cohorts with biomass.
`classesToReplace`	Integer vector of classes that are are to be replaced, e.g., 34, 35, 36 on LCC2005, which are burned young, burned 10 year, and cities.
`doAssertion`	A logical indicating whether some internal tests should be run to ensure the function is running correctly. Default: `getOption("LandR.assertions", TRUE)`.
`cohortDataNo34to36`	A `cohortData` `data.table` with only the pixels what were LCC 34:36
`columns`	Vector of column names on which to test for unique `cohortData`
`ecoregionMap`	The `ecoregionMap`, a raster of all the unique groupings
`speciesEcoregion`	A `data.table` with `speciesEcoregion` values.
`minRelativeB`	TODO: add description
`obj`	A data.frame or data.table-like object
`colClasses`	A named vector of column classes, where the names are the column names
`pixelGroupMap`	A `RasterLayer` with pixel values equal to a pixel group number that corresponds exactly to `pixelGroup` column in `cohortData`.
`sim`	If the `simList` is included, then the `browser()` call will be more useful.
`maxExpectedNumDiverge`	A numeric, length 1, indicating by how many they can diverge. Default 1.
`message`	An optional message to print. This may help identify where this function was called.
`verbose`	Controls message output. Defaults to `getOption("LandR.verbose")`
`cohortDefinitionCols`	the columns in `cohortData` that define unique cohorts
`pixelCohortData`	The full `cohortData` `data.table`
`speciesNames`	A vector of species names for which the labels will be checked
`sppEquiv`	table with species name equivalencies between the kNN and final naming formats. See `data("sppEquivalencies_CA", "LandR")`. Only necessary if `mixedType == 2`. If not provided and `mixedType == 2`, will attempt to use `data("sppEquivalencies_CA", "LandR")`.
`burnedPixelCohortData`	An expanded `cohortData` `data.table` with pixel-level cohort information on burnt pixels and columns: `severity` - fire severity in that pixel calculated based on fire behaviour properties; `firetolerance` - species-level fire tolerance; `severityToleranceDif` - the difference between `severity` and `firetolerance`.
`speciesLayers`	A `RasterStack` or `RasterLayer` that should contain species cover data in the study area
`thresh`	the minimum number of pixels where the species must have `biomass > 0` to be considered present in the study area. Defaults to 1.
`rstLCChange`	a raster layer indicating pixels were land-use change occurred as 1s
`rasterToMatch`	A `RasterLayer` objects to use as the template for all subsequent raster operations (i.e., the one used throughout the simulation).