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Landscape Habitat Output Extension

OutputLandscapeHabitat.Rd

Landscape Habitat Output Extension

References

LANDIS-II Output Landscape Habitat v2 Extension User Guide https://github.com/LANDIS-II-Foundation/Extension-Output-Landscape-Habitat/blob/master/docs/LANDIS-II%20Landscape%20Habitat%20Output%20v2%20User%20Guide.pdf

See also

Other Landscape Habitat Output helpers: insertLandscapeHabitatClimateVariables(), insertLandscapeHabitatDerivedLocalVariables(), insertLandscapeHabitatDistanceVariables(), insertLandscapeHabitatLocalVariables(), insertLandscapeHabitatNeighborhoodVariables(), insertLandscapeHabitatSpeciesModels()

Super class

LandisExtension -> OutputLandscapeHabitat

Active bindings

LocalVariables

(Optional) Named list of data.frames.

DerivedLocalVariables

(Optional) Named character vector.

NeighborhoodVariables

(Optional) data.frame.

ClimateVariables

(Optional) data.frame.

DistanceVariables

(Optional) data.frame.

SpeciesModels

Named list of data.frames with columns Parameter, Type, Value.

LocalVarMapFileNames

Character. Must contain the literal placeholders {local-var-name} and {timestep}.

NeighborVarMapFileNames

Character. Must contain the literal placeholders {neighbor-var-name} and {timestep}.

ClimateVarMapFileNames

Character. Must contain the literal placeholders {climate-var-name} and {timestep}.

DistanceVarMapFileNames

Character. Must contain the literal placeholders {distance-var-name} and {timestep}.

SpeciesMapFileNames

Character. Must contain the literal placeholders {species-name} and {timestep}.

SpeciesLogFileNames

Character. Must contain the literal placeholder {species-name}.

LogFile

Character.

output_files

Character vector of output files (relative paths from the scenario directory) that this extension is expected to produce at run time. Subclasses override this to return their extension-specific log files, event CSVs, etc. These paths are collected by scenario() and written to output_manifest.txt so tar_landis() can track them explicitly without relying on list.files() discovery.

Map files whose names depend on the timestep (e.g. BiomassC-10.tif) are NOT included here; they are discovered by tar_landis()'s output_dir scan instead.

Methods

Public methods

Inherited methods

OutputLandscapeHabitat$new()

Usage

OutputLandscapeHabitat$new(
  path,
  Timestep = NULL,
  LocalVariables = NULL,
  DerivedLocalVariables = NULL,
  NeighborhoodVariables = NULL,
  ClimateVariables = NULL,
  DistanceVariables = NULL,
  SpeciesModels = NULL,
  LocalVarMapFileNames = NULL,
  NeighborVarMapFileNames = NULL,
  ClimateVarMapFileNames = NULL,
  DistanceVarMapFileNames = NULL,
  SpeciesMapFileNames = NULL,
  SpeciesLogFileNames = NULL,
  LogFile = "output/landscape-habitat/landscape_habitat_log.csv"
)

Arguments

path

Character. Directory path.

Timestep

Integer. Years between updates.

LocalVariables

(Optional) Named list mapping reclass map names to data frames with columns ForestType, AgeRange, Species. Each row defines one forest-type/age/species rule.

DerivedLocalVariables

(Optional) Named character vector. Names are derived-variable names; values are arithmetic expressions referencing the local variables (e.g. "reclass2[LowlandCon] + reclass2[LowlandHdwd]").

NeighborhoodVariables

(Optional) data.frame with columns Name, LocalVar, NeighborRadius, Transform.

ClimateVariables

(Optional) data.frame with columns Name, Year, Months, Source, ClimateVar, Transform.

DistanceVariables

(Optional) data.frame with columns Name, LocalVar, Transform.

SpeciesModels

Named list. Each name is a species name; each value is a data.frame with columns Parameter, Type, Value describing the logistic-regression terms (use "intercept" for the intercept row).

LocalVarMapFileNames

(Optional) Character. Output template for local-variable maps; must contain the literal placeholders {local-var-name} and {timestep}.

NeighborVarMapFileNames

(Optional) Character. Output template for neighborhood maps; must contain the literal placeholders {neighbor-var-name} and {timestep}.

ClimateVarMapFileNames

(Optional) Character. Output template for climate maps; must contain the literal placeholders {climate-var-name} and {timestep}.

DistanceVarMapFileNames

(Optional) Character. Output template for distance maps; must contain the literal placeholders {distance-var-name} and {timestep}.

SpeciesMapFileNames

(Optional) Character. Output template for species-model maps; must contain the literal placeholders {species-name} and {timestep}.

SpeciesLogFileNames

(Optional) Character. Output template for species log files; must contain the literal placeholder {species-name}.

LogFile

Character. Relative file path for the main log.

OutputLandscapeHabitat$write()

Write extension inputs to disk

Usage

OutputLandscapeHabitat$write()

OutputLandscapeHabitat$clone()

The objects of this class are cloneable with this method.

Usage

OutputLandscapeHabitat$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.