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Biomass Browse Extension

BiomassBrowse.Rd

Biomass Browse Extension

LANDIS-II v8 compatibility

Biomass Browse has not yet been updated by the LANDIS-II developers for LANDIS-II v8; the most recent upstream release (v2.0, May 2022) targets the v7 core only. This R6 class tracks the v2.0 schema and exercises the input-file generation, but $write()-produced files cannot currently be run through a LANDIS-II v8 console. Constructing a BiomassBrowse object emits a one-time warning() to remind users of this. The warning will be removed once a v8-compatible Biomass Browse release is available.

References

LANDIS-II Browse Disturbance v2.0 Extension User Guide https://github.com/LANDIS-II-Foundation/Extension-Biomass-Browse/blob/master/docs/LANDIS-II%20Biomass%20Browse%20v2.0%20User%20Guide.pdf

See also

Other Biomass Browse helpers: insertBrowseDynamicPopulation(), insertBrowseSpeciesTable()

Super class

LandisExtension -> BiomassBrowse

Active bindings

SpeciesTable

data.frame with the six columns enumerated in .browseSpeciesTableCols.

ZoneMap

Character. Relative path to the population-zones raster.

BrowseMethod

Character. One of "Population", "BDI".

DefinedPopulationFile

Character. Relative path.

DynamicPopulation

List of dynamic-population parameters, or NULL. Required keys (all numeric): RMin, RMax, MortalityMin, MortalityMax, PredationMin, PredationMax, HarvestMin, HarvestMax.

ConsumptionRate

Integer.

ANPPForageProp

Numeric in [0, 1].

MinBrowsePropinReach

Numeric in [0, 1].

BrowseBiomassThreshold

Numeric in [0, 1].

BrowseBiomassThresholdMin

Numeric in [0, 1].

BrowseBiomassThresholdMax

Numeric in [0, 1].

EscapeBrowsePropLong

Numeric in [0, 1].

CalibrateMode

Character "ON"/"OFF".

GrowthReduction

Character "ON"/"OFF".

Mortality

Character "ON"/"OFF".

CountNonForageinSitePref

Character "TRUE"/"FALSE" (set from a logical).

UseInitBiomassAsForage

Character "TRUE"/"FALSE" (set from a logical).

ForageInReachMethod

One of "Ordered", "LinearEachCohort".

ForageQuantity

Integer (neighborhood radius).

SitePreference

Integer (neighborhood radius).

SitePrefMapNames

Character. Output filename pattern.

SiteForageMapNames

Character. Output filename pattern.

SiteHSIMapNames

Character. Output filename pattern.

SitePopulationMapNames

Character. Output filename pattern.

BiomassRemovedMapNames

Character. Output filename pattern.

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

BiomassBrowse$new()

Usage

BiomassBrowse$new(
  path,
  Timestep = 1L,
  SpeciesTable = NULL,
  ZoneMap = NULL,
  BrowseMethod = "Population",
  DefinedPopulationFile = NULL,
  DynamicPopulation = NULL,
  ConsumptionRate = NULL,
  ANPPForageProp = 0.66,
  MinBrowsePropinReach = NULL,
  BrowseBiomassThreshold = NULL,
  BrowseBiomassThresholdMin = NULL,
  BrowseBiomassThresholdMax = NULL,
  EscapeBrowsePropLong = NULL,
  CalibrateMode = NULL,
  GrowthReduction = NULL,
  Mortality = NULL,
  CountNonForageinSitePref = NULL,
  UseInitBiomassAsForage = NULL,
  ForageInReachMethod = NULL,
  ForageQuantity = NULL,
  SitePreference = NULL,
  SitePrefMapNames = NULL,
  SiteForageMapNames = NULL,
  SiteHSIMapNames = NULL,
  SitePopulationMapNames = NULL,
  BiomassRemovedMapNames = NULL,
  LogFile = "browse/browse-log.csv"
)

Arguments

path

Character. Directory path.

Timestep

Integer. Years between browse updates (typically 1; §4.2.1).

SpeciesTable

data.frame with six columns matching §4.2.2: Species (character), Preference, GrowthReductionThreshold, GrowthReductionMaximum, MortalityThreshold, MortalityMaximum (all numeric in [0, 1]).

ZoneMap

Character. Relative path to the population-zones raster (§4.2.3).

BrowseMethod

Character. One of "Population" or "BDI" (§4.2.4).

DefinedPopulationFile

Character. Relative path to the population / BDI definition file (§4.2.5).

DynamicPopulation

List of dynamic-population parameters (§4.2.6) when running in dynamic mode; pass NULL for static/defined population. Required keys (all numeric): RMin, RMax, MortalityMin, MortalityMax, PredationMin, PredationMax, HarvestMin, HarvestMax.

ConsumptionRate

Integer (kg/yr/individual; §4.2.7).

ANPPForageProp

Numeric in [0, 1]; proportion of ANPP that counts as forage (§4.2.8; default 0.66).

MinBrowsePropinReach

Numeric in [0, 1]; minimum proportion of browse within reach for a cohort to be browsed (§4.2.9).

BrowseBiomassThreshold

Numeric in [0, 1]; proportion of ecoregion max biomass at which cohorts begin to escape browse (§4.2.12).

BrowseBiomassThresholdMin, BrowseBiomassThresholdMax

(Optional) Numeric in [0, 1]; thresholds for the ForageInReachMethod = "LinearEachCohort" form (§4.2.10–4.2.11).

EscapeBrowsePropLong

Numeric in [0, 1]; proportion of longevity at which cohorts are considered escaped from browse (§4.2.13).

CalibrateMode

Character ("ON" / "OFF"); optional, default "OFF" (§4.2.14).

GrowthReduction

Character ("ON" / "OFF"); optional, default "ON" (§4.2.15).

Mortality

Character ("ON" / "OFF"); optional, default "ON" (§4.2.16).

CountNonForageinSitePref

Logical; optional, default FALSE (§4.2.17).

UseInitBiomassAsForage

Logical; optional, default FALSE (§4.2.18).

ForageInReachMethod

Character; one of "Ordered" or "LinearEachCohort"; optional, default "Ordered" (§4.2.19).

ForageQuantity

(Optional) Integer; HSI neighborhood radius for forage-quantity component (§4.2.20.1). Either this or SitePreference (or both) must be provided to compute HSI maps.

SitePreference

(Optional) Integer; HSI neighborhood radius for site-preference component (§4.2.20.2).

SitePrefMapNames, SiteForageMapNames, SiteHSIMapNames, SitePopulationMapNames, BiomassRemovedMapNames

(Optional) Character. Output filename patterns; each must contain {timestep} (§4.2.21).

LogFile

Character. Relative path to the events CSV log (§4.2.22).

BiomassBrowse$write()

Write extension inputs to disk

Usage

BiomassBrowse$write()

BiomassBrowse$clone()

The objects of this class are cloneable with this method.

Usage

BiomassBrowse$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.