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

assert1

R Documentation

Assertions

Description

assert1: Assert that ecoregionCodes that were replaced, were correctly identified;

This is the full pixelCohortData, not the collapsed one.

Usage

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

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

assertSppMaxBMaxANPP(
  speciesEcoregion,
  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,
  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)
)

assertSpeciesEcoregionCohortDataMatch(
  cohortData,
  speciesEcoregion,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertPixelCohortDataValid(
  standCohortData,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertRepsAllCohortData(
  allCohortData,
  reps,
  years,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertStandAgeMapAttr(
  standAgeMap,
  doAssertion = getOption("LandR.assertions", TRUE)
)

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

assertSppVectors(
  sppEquiv = NULL,
  sppNameVector = NULL,
  sppColorVect = NULL,
  sppEquivCol = NULL,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertSpeciesTableRaw(
  speciesTableRaw,
  doAssertion = getOption("LandR.assertions", TRUE)
)

assertSpeciesTable(
  speciesTable,
  doAssertion = getOption("LandR.assertions", TRUE)
)

Arguments

`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
`speciesEcoregion`	A `data.table` with `species`-`ecoregion`-specific species trait values. Ecoregion refers to "ecolocation", a categorical variable grouping sites with similar biophysical characteristics. The table should have at least the following columns: `speciesCode` and `ecoregionGroup`, character representation of species and ecoregion groups respectively, `maxB` the maximum biomass for the species in a given 'ecoregion', `maxANPP` the maximum aboveground net primary productivity and `SEP` the species establishment probability. May contain columns `inflationFactor` (used to adjust `maxB`) and `mANPPproportion` (used to calculate `maxANPP`).
`columns`	Vector of column names on which to test for unique `cohortData`
`ecoregionMap`	The `ecoregionMap`, a raster of all the unique ecoregion groupings, which group together pixels of similar biophysical characteristics.
`minRelativeB`	a `data.frame` with the cut points to classify stand shadiness.
`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`.
`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`	an table with a column containing species names
`burnedPixelCohortData`	An expanded `cohortData` `data.table` with pixel-level cohort information on burnt pixels and the following (optional) 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).
`standCohortData`	A `data.table` with simulated and observed stand data for validation
`allCohortData`	A `data.table` with all simulated `cohortData` to use for validation
`reps`	repetition ids
`years`	years
`standAgeMap`	A `rasterLayer` of stand ages with attribute `"imputedPixID"`
`sppNameVector`	A character vector of species to use. These species must all be from one naming convention, i.e., from one column in the `sppEquiv`.
`sppColorVect`	A named vector of colours to use for plotting. The names must conform with species name convention used (see sppEquivalencies_CA for possible naming conventions) and should also contain a colour for 'Mixed', when a mixed forest type is supported (see `vegLeadingProportion` parameter in `vegTypeGenerator()` for details on mixed forest types).
`sppEquivCol`	the column name to use from `sppEquiv`.
`speciesTableRaw`	raw species traits `data.table` (see `getSpeciesTable()`)
`speciesTable`	species traits `data.table` (see `prepSpeciesTable()`)