Epidemiological Disturbance Agents (EDA) Extension

Epidemiological Disturbance Agents (EDA) Extension

References

LANDIS-II Base EDA v3 Extension User Guide https://github.com/LANDIS-II-Foundation/Extension-Base-EDA/blob/master/docs/LANDIS-II%20Base%20EDA%20v3%20User%20Guide.pdf

See also

Other EDA helpers: edaAgent(), insertEDADisturbanceModifiers(), insertEDAIgnoredSpecies(), insertEDAInputFiles(), insertEDASpeciesParameters(), writeEDAAgentFile()

Super class

LandisExtension -> EDA

Active bindings

Agents

List of EDAAgent objects.

MapNames

Character. Output map filename pattern; must contain the literal {agentName} and {timestep} placeholders – LANDIS-II replaces them with the agent name and simulation year, e.g. "eda/{agentName}-{timestep}.tif".

MORTMapNames

(Optional) Character. Mortality output map filename pattern; must contain the literal {agentName} and {timestep} placeholders, e.g. "eda/{agentName}-MORT-{timestep}.tif".

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

• EDA$new()

• EDA$add_agent()

• EDA$write()

• EDA$clone()

Inherited methods

• LandisExtension$add_file()

---

EDA$new()

Usage

EDA$new(
  path,
  Timestep = NULL,
  Agents = list(),
  MapNames = NULL,
  MORTMapNames = NULL,
  LogFile = "eda/eda-log.csv"
)

Arguments

path

Character. Directory path.

Timestep

Integer. Years between updates.

Agents

List of EDAAgent objects (see edaAgent()).

MapNames

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

MORTMapNames

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

LogFile

Character. Relative file path for the EDA CSV log.

---

EDA$add_agent()

Usage

EDA$add_agent(value)

Arguments

value

EDAAgent object to append to $Agents.

---

EDA$write()

Write extension inputs to disk

Usage

EDA$write()

---

EDA$clone()

The objects of this class are cloneable with this method.

Usage

EDA$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.