Skip to contents

Climate BDA (Biological Disturbance Agent) Extension

ClimateBDA.Rd

Climate BDA (Biological Disturbance Agent) Extension

References

LANDIS-II Biological Disturbance Agent v5 Extension User Guide https://github.com/LANDIS-II-Foundation/Extension-Base-BDA/blob/master/docs/LANDIS-II%20Biological%20Disturbance%20Agent%20v5%20User%20Guide.pdf

See also

Other Climate BDA helpers: bdaAgent(), insertAgentHeader(), insertBDAInputFiles(), insertBDASpeciesParameters(), insertDispersal(), insertDisturbanceModifiers(), insertEcoregionModifiers(), insertIgnoredSpecies(), insertIntensityClasses(), insertNeighborhood(), insertOutbreakPattern(), writeAgentFile()

Super class

LandisExtension -> ClimateBDA

Active bindings

Agents

List of BDAAgent objects.

MapNames

Character. Output map filename pattern; must contain the literal {agentName} and {timestep} placeholders.

SRDMapNames

(Optional) Character. SRD output map filename pattern; must contain {agentName} and {timestep}.

NRDMapNames

(Optional) Character. NRD output map filename pattern; must contain {agentName} and {timestep}.

BDPMapNames

(Optional) Character. BDP output map filename pattern; must contain {agentName} and {timestep}.

LogFile

Character. Relative file path.

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

ClimateBDA$new()

Usage

ClimateBDA$new(
  path,
  Timestep = NULL,
  Agents = list(),
  MapNames = NULL,
  SRDMapNames = NULL,
  NRDMapNames = NULL,
  BDPMapNames = NULL,
  LogFile = "bda/bda-log.csv"
)

Arguments

path

Character. Directory path.

Timestep

Integer.

Agents

List of BDAAgent objects (see bdaAgent()).

MapNames

Character. Output map filename pattern; must contain the literal {agentName} and {timestep} placeholders.

SRDMapNames

(Optional) Character. SRD output map filename pattern; must contain the literal {agentName} and {timestep} placeholders.

NRDMapNames

(Optional) Character. NRD output map filename pattern; must contain the literal {agentName} and {timestep} placeholders.

BDPMapNames

(Optional) Character. BDP output map filename pattern; must contain the literal {agentName} and {timestep} placeholders.

LogFile

Character. Relative file path for the BDA CSV log.

ClimateBDA$add_agent()

Usage

ClimateBDA$add_agent(value)

Arguments

value

BDAAgent object to append to $Agents.

ClimateBDA$write()

Write extension inputs to disk

Usage

ClimateBDA$write()

ClimateBDA$clone()

The objects of this class are cloneable with this method.

Usage

ClimateBDA$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.