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DGS (DAMM-McNiP, GIPL, SHAW) Succession Extension

DGSSuccession.Rd

R6 class representing the LANDIS-II DGS Succession (v2.0) extension's main input file. DGS integrates a NECN-style vegetation dynamics model with the DAMM-McNiP soil C/N model, the SHAW physically-based hydrology / energy balance model, and the GIPL deep-soil permafrost model.

The DGS extension must be run with Social Climate Fire (v4.01) and the Output Reclass extension (v4.0).

References

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

See also

Helpers that prepare inputs for this extension: prepDGSFireReductionParameters(). Shared scenario inputs: prepClimateConfig(), prepInitialCommunities(), prepSpeciesData().

Other DGS Succession helpers: defaultDGSDammMcNIPParameters(), insertDGSFireReductionParameters(), insertDGSHarvestReductionParameters(), prepDGSFireReductionParameters()

Super class

LandisExtension -> DGSSuccession

Active bindings

CalibrateMode

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

ClimateConfigFile

Character. Relative file path.

AtmosphericNSlope

Numeric.

AtmosphericNIntercept

Numeric.

InitialCommunities

Character. Relative file path.

InitialCommunitiesMap

Character. Relative file path.

Latitude

Numeric (degrees).

ShawGiplConfigFile

Character. Relative file path.

ShawGiplFiles

Character vector of relative file paths.

SoilMaps

Named list of relative file paths. Required keys: SoilDepthMapName, SoilDrainMapName, SoilBaseFlowMapName, SoilStormFlowMapName, SoilFieldCapacityMapName, SoilWiltingPointMapName, SoilPercentSandMapName, SoilPercentClayMapName, SoilBulkDensityMapName, SoilParticleDensityMapName, InitialSOC_PrimaryMapName, InitialSON_PrimaryMapName, InitialDeadWoodSurfaceMapName, InitialDeadCoarseRootsMapName.

InitialFineFuels

Numeric in [0, 1].

InitialMineralN

Numeric (g m-2).

DenitrificationRate

Numeric in [0, 1].

WaterDecayFunction

Character. One of "Linear" or "Ratio".

DammMcNIPParameters

Named list of numeric scalar parameters. Required keys: InitialMicrobialC, InitialMicrobialN, InitialEnzymeConc, ActEnergySOMDepoly, ActEnergyDOCUptake, ExpConstSOMDepoly, ExpConstDOCUptake, FractionSOMUnprotect, CNEnzymes, KmSOMDepoly, KmDOCUptake, EnzTurnRate, MicrobialTurnRate, CarbonUseEfficiency, PropEnzymeSOM, PropCEnzymeProduction, PropNEnzymeProduction, FractDeadMicrobialBiomassSOM, MMConstantO2, DiffConstantO2, DiffConstantSOMLiquid, FractionVolumeO2, DOCFraction, DONFraction, FractionLitterToDOC.

SeedingAlgorithm

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

ProbabilityEstablishAdjust

Numeric. Default 1.0.

SpeciesParameters

Character. Relative file path.

FireReductionParameters

data.frame.

HarvestReductionParameters

data.frame.

Methods

Public methods

Inherited methods

DGSSuccession$new()

Usage

DGSSuccession$new(
  path,
  Timestep = 1L,
  CalibrateMode = NULL,
  ClimateConfigFile = NULL,
  AtmosphericNSlope = NULL,
  AtmosphericNIntercept = NULL,
  InitialCommunities = NULL,
  InitialCommunitiesMap = NULL,
  Latitude = NULL,
  ShawGiplConfigFile = NULL,
  ShawGiplFiles = NULL,
  SoilMaps = NULL,
  InitialFineFuels = NULL,
  InitialMineralN = NULL,
  DenitrificationRate = NULL,
  WaterDecayFunction = NULL,
  DammMcNIPParameters = NULL,
  SeedingAlgorithm = NULL,
  ProbabilityEstablishAdjust = 1,
  SpeciesParameters = NULL,
  FireReductionParameters = NULL,
  HarvestReductionParameters = NULL
)

Arguments

path

Character. Directory path for the extension input files.

Timestep

Integer (years).

CalibrateMode

Logical, or character indicating "yes" or "no". When TRUE, an additional DGS-calibrate-log.csv is produced; intended for single-cell runs only.

ClimateConfigFile

Character. Relative file path to the climate library configuration file (see §2.4 of the user guide).

AtmosphericNSlope

Numeric. Slope for the linear N-deposition model (Total N = AtmosphericNSlope * precipitation + AtmosphericNIntercept). The user-guide prose refers to this as AtmosNslope, but the parser keyword is AtmosphericNSlope.

AtmosphericNIntercept

Numeric. Intercept for the linear N-deposition model. The user-guide prose calls this AtmosNinter, but the parser keyword is AtmosphericNIntercept.

InitialCommunities

Character. Relative file path to the initial communities text file (see §7 of the user guide).

InitialCommunitiesMap

Character. Relative file path to the initial communities raster.

Latitude

Numeric. Study-site latitude (degrees).

ShawGiplConfigFile

Character. Relative file path to the SHAW/GIPL configuration file that names the SHAW/GIPL input files (see §3 of the user guide).

ShawGiplFiles

(Optional) Character vector of additional SHAW/GIPL input files (e.g., ListThus, ShawGeneralInputs, ShawPlantTypes, ShawSoilTypes, GiplProperties, Unfrozen.txt) to register so the scenario can collect them.

SoilMaps

Named list of relative file paths for the required soil physical and initial soil C/N / dead-wood map inputs. Required keys: SoilDepthMapName, SoilDrainMapName, SoilBaseFlowMapName, SoilStormFlowMapName, SoilFieldCapacityMapName, SoilWiltingPointMapName, SoilPercentSandMapName, SoilPercentClayMapName, SoilBulkDensityMapName, SoilParticleDensityMapName, InitialSOC_PrimaryMapName, InitialSON_PrimaryMapName, InitialDeadWoodSurfaceMapName, InitialDeadCoarseRootsMapName.

InitialFineFuels

Numeric in [0, 1]. Fraction of initial dead wood allocated to fine fuels.

InitialMineralN

Numeric. Initial mineral N ($g/m^2$).

DenitrificationRate

Numeric in [0, 1]. Monthly fraction of mineral N lost through volatilization and denitrification.

WaterDecayFunction

Character. One of "Linear" or "Ratio".

DammMcNIPParameters

Named list of numeric scalar parameters for the DAMM-McNiP soil C/N block. Required keys (all must be supplied): InitialMicrobialC, InitialMicrobialN, InitialEnzymeConc, ActEnergySOMDepoly, ActEnergyDOCUptake, ExpConstSOMDepoly, ExpConstDOCUptake, FractionSOMUnprotect, CNEnzymes, KmSOMDepoly, KmDOCUptake, EnzTurnRate, MicrobialTurnRate, CarbonUseEfficiency, PropEnzymeSOM, PropCEnzymeProduction, PropNEnzymeProduction, FractDeadMicrobialBiomassSOM, MMConstantO2, DiffConstantO2, DiffConstantSOMLiquid, FractionVolumeO2, DOCFraction, DONFraction, FractionLitterToDOC.

SeedingAlgorithm

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

ProbabilityEstablishAdjust

Numeric. Multiplier applied to the probability of establishment. Default 1.0.

SpeciesParameters

Character. Relative file path to the species-parameters CSV (see §2.54 of the user guide).

FireReductionParameters

data.frame with columns FireSeverity, CoarseDebrisReduction, FineLitterReduction, CohortWoodReduction, CohortLeafReduction, OrganicHorizonReduction. Required even when no fire extension is used.

HarvestReductionParameters

(Optional) data.frame with columns PrescriptionName, DeadWoodReduction, DeadLitterReduction, SOMReduction, CohortWoodRemoval, CohortLeafRemoval. The SOMReduction column is required by the parser even though the user guide (§2.56) does not list it.

DGSSuccession$write()

Write extension inputs to disk

Usage

DGSSuccession$write()

DGSSuccession$clone()

The objects of this class are cloneable with this method.

Usage

DGSSuccession$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.