Skip to contents

Biomass Succession Extension

BiomassSuccession.Rd

Biomass Succession Extension

References

LANDIS-II Biomass Succession v7 Extension User Guide https://github.com/LANDIS-II-Foundation/Extension-Biomass-Succession/blob/master/docs/LANDIS-II%20Biomass%20Succession%20v7%20User%20Guide.pdf

See also

Helpers that prepare inputs for this extension: prepMinRelativeBiomass(), prepEcoregionParameters(), prepSpeciesEcoregionDataFile(), prepFireReductionParameters(), prepHarvestReductionParameters(). Shared scenario inputs: prepClimateConfig(), prepInitialCommunities(), prepSpeciesData().

Other Biomass Succession helpers: insertEcoregionParameters(), insertFireReductionParameters(), insertHarvestReductionParameters(), insertMinRelativeBiomass(), insertSpeciesEcoregionDataFile(), insertSufficientLight(), prepEcoregionParameters(), prepFireReductionParameters(), prepHarvestReductionParameters(), prepMinRelativeBiomass(), prepSpeciesEcoregionDataFile()

Super class

LandisExtension -> BiomassSuccession

Active bindings

SeedingAlgorithm

Character. Dispersal algorithm to use. One of "WardSeedDispersal", "NoDispersal", "UniversalDispersal".

InitialCommunitiesFiles

Character. Relative file paths.

ClimateConfigFile

Character. Relative file path.

CalibrateMode

Logical, or character indicating "yes" or "no".

SpinupCohorts

Logical, or character indicating "yes" or "no". Optional (NULL = omit).

SpinupMortalityFraction

Real. Optional (NULL = omit).

MinRelativeBiomass

data.frame.

SufficientLight

data.frame.

SpeciesDataFile

Character. Relative file path.

EcoregionParameters

data.frame.

SpeciesEcoregionDataFile

Character. Relative file path.

FireReductionParameters

data.frame.

HarvestReductionParameters

data.frame.

Methods

Public methods

Inherited methods

BiomassSuccession$new()

Usage

BiomassSuccession$new(
  path = NULL,
  Timestep = 10L,
  SeedingAlgorithm = NULL,
  InitialCommunitiesFiles = NULL,
  ClimateConfigFile = NULL,
  CalibrateMode = NULL,
  SpinupCohorts = NULL,
  SpinupMortalityFraction = NULL,
  MinRelativeBiomass = NULL,
  SufficientLight = NULL,
  SpeciesDataFile = NULL,
  EcoregionParameters = NULL,
  SpeciesEcoregionDataFile = NULL,
  FireReductionParameters = NULL,
  HarvestReductionParameters = NULL
)

Arguments

path

Character. Directory path.

Timestep

Integer.

SeedingAlgorithm

Character. Dispersal algorithm to use. One of "WardSeedDispersal", "NoDispersal", "UniversalDispersal".

InitialCommunitiesFiles

Character. Relative file paths.

ClimateConfigFile

Character. Relative file path.

CalibrateMode

Logical, or character indicating "yes" or "no".

SpinupCohorts

Logical, or character indicating "yes" or "no".

SpinupMortalityFraction

Real.

MinRelativeBiomass

data.frame.

SufficientLight

data.frame.

SpeciesDataFile

Character. Relative file path.

EcoregionParameters

data.frame.

SpeciesEcoregionDataFile

Character. Relative file path.

FireReductionParameters

data.frame.

HarvestReductionParameters

data.frame.

BiomassSuccession$write()

Write extension inputs to disk

Usage

BiomassSuccession$write()

BiomassSuccession$clone()

The objects of this class are cloneable with this method.

Usage

BiomassSuccession$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.