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Root Rot Extension

RootRot.Rd

Root Rot Extension

LANDIS-II v8 compatibility

Root Rot has not yet been updated by the LANDIS-II developers for LANDIS-II v8; the most recent upstream release targets the v7 core only. This R6 class is provided to track the v1.0 schema and exercise the input-file generation, but $write()-produced files cannot currently be run through a LANDIS-II v8 console. Constructing a RootRot object emits a one-time warning() to remind users of this. The warning will be removed once a v8-compatible Root Rot release is available

References

LANDIS-II Root Rot v1.0 Extension User Guide https://github.com/LANDIS-II-Foundation/Extension-Root-Rot/blob/master/Docs/LANDIS-II%20Root%20Rot%20v1.0%20User%20Guide.pdf

See also

Other Root Rot helpers: insertRootRotSpeciesSusceptibility()

Super class

LandisExtension -> RootRot

Active bindings

Pathogen

(Optional) Character. Annotated alongside the header.

InputMap

(Optional) Character. Initial infection raster path.

SpeciesSusceptibility

data.frame with columns Species, Index1, Index2.

LethalTemp

Numeric <= 0 (°C). Minimum air temperature below which the pathogen cannot survive.

MinSoilTemp

Numeric (°C). Minimum soil temperature below which the pathogen cannot transition Uninfected -> Infected.

PhWet

Numeric. Pressure head (wet condition threshold).

PhDry

Numeric. Pressure head (dry condition threshold).

PhMax

Numeric. Pressure head (maximum threshold).

MinProbID

Numeric in [0, 1].

MaxProbDI

Numeric in [0, 1].

OutputMapName

Character. Infection-status output raster pattern; must contain {timestep}.

TOLDMapName

Character. Time-of-Last-Disease output raster pattern; must contain {timestep}.

LethalTempMapName

Character. Lethal-temperature output raster pattern; must contain {timestep}.

TotalBiomassRemovedMapName

Character. Total biomass-removed output pattern; must contain {timestep}.

SpeciesBiomassRemovedMapName

Character. Per-species biomass- removed output pattern; must contain {species} and {timestep}.

EventLog

(Optional) Character. Relative file path for the events CSV log; NULL disables.

SummaryLog

(Optional) Character. Relative file path for the summary CSV log; NULL disables.

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

RootRot$new()

Usage

RootRot$new(
  path,
  Timestep = NULL,
  Pathogen = NULL,
  InputMap = NULL,
  SpeciesSusceptibility = NULL,
  LethalTemp = NULL,
  MinSoilTemp = NULL,
  PhWet = NULL,
  PhDry = NULL,
  PhMax = NULL,
  MinProbID = NULL,
  MaxProbDI = NULL,
  OutputMapName = NULL,
  TOLDMapName = NULL,
  LethalTempMapName = NULL,
  TotalBiomassRemovedMapName = NULL,
  SpeciesBiomassRemovedMapName = NULL,
  EventLog = "rootrot/events.csv",
  SummaryLog = "rootrot/summary.csv"
)

Arguments

path

Character. Directory path.

Timestep

Integer. Years between updates.

Pathogen

(Optional) Character. Pathogen name to annotate alongside the LandisData header (e.g. "Phytophthora cinnamomi").

InputMap

(Optional) Character. Initial infection raster path. When omitted, the model assumes all cells begin Uninfected.

SpeciesSusceptibility

data.frame with columns Species, Index1 (initial susceptibility), Index2 (secondary susceptibility); both indices in [0, 1].

LethalTemp

Numeric <= 0 (°C). Minimum air temperature below which the pathogen cannot survive.

MinSoilTemp

Numeric (°C). Minimum soil temperature below which the pathogen cannot transition Uninfected → Infected.

PhWet, PhDry, PhMax

Numeric > 0 (m). Pressure-head thresholds: wet, dry, and extremely-dry conditions.

MinProbID, MaxProbDI

Numeric in [0, 1]. Min infection→diseased probability and max diseased→infected probability.

OutputMapName

(Optional) Character. Infection-status output raster pattern; must contain {timestep}.

TOLDMapName

(Optional) Character. Time-of-Last-Disease output raster pattern; must contain {timestep}.

LethalTempMapName

(Optional) Character. Lethal-temperature output raster pattern; must contain {timestep}.

TotalBiomassRemovedMapName

(Optional) Character. Total biomass- removed output raster pattern; must contain {timestep}.

SpeciesBiomassRemovedMapName

(Optional) Character. Per-species biomass-removed output raster pattern; must contain both {species} and {timestep}.

EventLog

(Optional) Character. Relative file path for the events CSV log; pass NULL to disable.

SummaryLog

(Optional) Character. Relative file path for the summary CSV log; pass NULL to disable.

RootRot$write()

Write extension inputs to disk

Usage

RootRot$write()

RootRot$clone()

The objects of this class are cloneable with this method.

Usage

RootRot$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.