NECN Succession Extension

NECN Succession Extension

References

LANDIS-II Net Ecosystem CN Succession v8 Extension User Guide https://github.com/LANDIS-II-Foundation/Extension-NECN-Succession/blob/master/docs/LANDIS-II%20Net%20Ecosystem%20CN%20Succession%20v8%20User%20Guide.pdf

See also

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

Other NECN Succession helpers: insertNECNFireReductionParameters(), insertNECNHarvestReductionParameters(), prepNECNFireReductionParameters()

Super class

LandisExtension -> NECNSuccession

Active bindings

SeedingAlgorithm

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

InitialCommunitiesCSV

Character. Relative file path.

InitialCommunitiesMap

Character. Relative file path.

ClimateConfigFile

Character. Relative file path.

SoilMaps

Named list of relative file paths. Required keys: SoilDepthMapName, SoilDrainMapName, SoilBaseFlowMapName, SoilStormFlowMapName, SoilFieldCapacityMapName, SoilWiltingPointMapName, SoilPercentSandMapName, SoilPercentClayMapName, InitialSOM1CsurfMapName, InitialSOM1NsurfMapName, InitialSOM1CsoilMapName, InitialSOM1NsoilMapName, InitialSOM2CMapName, InitialSOM2NMapName, InitialSOM3CMapName, InitialSOM3NMapName, InitialDeadWoodSurfaceMapName, InitialDeadCoarseRootsMapName.

OptionalClimateMaps

Named list of relative file paths. Allowed keys: SlopeMapName, AspectMapName, NormalSWAMapName, NormalCWDMapName, NormalTempMapName.

CalibrateMode

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

SmokeModelOutputs

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

Write_SWA_Maps

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

Write_CWD_Maps

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

Write_Temperature_Maps

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

Write_Species_Drought_Maps

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

WaterDecayFunction

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

ProbabilityEstablishAdjust

Numeric.

InitialMineralN

Numeric (g m-2).

InitialFineFuels

Numeric in [0, 1].

AtmosphericNSlope

Numeric.

AtmosphericNIntercept

Numeric.

Latitude

Numeric (degrees).

DenitrificationRate

Numeric in [0, 1].

DecayRateSurf

Numeric in [0, 1].

DecayRateSOM1

Numeric in [0, 1].

DecayRateSOM2

Numeric in [0, 1].

DecayRateSOM3

Numeric in [0, 1].

GrassThresholdMultiplier

Numeric.

OutputMaps

Named list. See table 3 of the user guide. Allowed names: ANPPMapName, ANPPMapFrequency, ANEEMapName, ANEEMapFrequency, SoilCarbonMapName, SoilNitrogenMapName, TotalCMapName. *MapName values are file-name templates and must contain the literal {timestep} placeholder (user guide §2.29) – LANDIS-II replaces it with the simulation year, e.g. "NECN/ANPP-{timestep}.tif".

CreateInputCommunityMaps

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

VariableOverrides

Named list. Allowed names: Stormflow, WaterFactor1, WaterFactor2, AnaerobicFactor1, AnaerobicFactor2, AnaerobicFactor3.

SpeciesParameters

Character. Relative file path.

DroughtMortalityParameters

Character. Relative file path.

FireReductionParameters

data.frame.

HarvestReductionParameters

data.frame.

Methods

Public methods

• NECNSuccession$new()

• NECNSuccession$write()

• NECNSuccession$clone()

Inherited methods

• LandisExtension$add_file()

---

NECNSuccession$new()

Usage

NECNSuccession$new(
  path,
  Timestep = 10L,
  SeedingAlgorithm = NULL,
  InitialCommunitiesCSV = NULL,
  InitialCommunitiesMap = NULL,
  ClimateConfigFile = NULL,
  SoilMaps = NULL,
  OptionalClimateMaps = NULL,
  CalibrateMode = NULL,
  SmokeModelOutputs = NULL,
  Write_SWA_Maps = NULL,
  Write_CWD_Maps = NULL,
  Write_Temperature_Maps = NULL,
  Write_Species_Drought_Maps = NULL,
  WaterDecayFunction = NULL,
  ProbabilityEstablishAdjust = 1,
  InitialMineralN = NULL,
  InitialFineFuels = NULL,
  AtmosphericNSlope = NULL,
  AtmosphericNIntercept = NULL,
  Latitude = NULL,
  DenitrificationRate = NULL,
  DecayRateSurf = NULL,
  DecayRateSOM1 = NULL,
  DecayRateSOM2 = NULL,
  DecayRateSOM3 = NULL,
  GrassThresholdMultiplier = NULL,
  OutputMaps = NULL,
  CreateInputCommunityMaps = NULL,
  VariableOverrides = NULL,
  SpeciesParameters = NULL,
  DroughtMortalityParameters = NULL,
  FireReductionParameters = NULL,
  HarvestReductionParameters = NULL
)

Arguments

path

Character. Directory path.

Timestep

Integer.

SeedingAlgorithm

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

InitialCommunitiesCSV

Character. Relative file path to the initial communities CSV (see §4 of the user guide).

InitialCommunitiesMap

Character. Relative file path to the initial communities raster.

ClimateConfigFile

Character. Relative file path to the climate library configuration file.

SoilMaps

Named list of relative file paths for required soil physical and initial soil organic matter / dead wood map inputs. Keys must match the NECN keywords (Tables 1 and 2 of the user guide): SoilDepthMapName, SoilDrainMapName, SoilBaseFlowMapName, SoilStormFlowMapName, SoilFieldCapacityMapName, SoilWiltingPointMapName, SoilPercentSandMapName, SoilPercentClayMapName, InitialSOM1CsurfMapName, InitialSOM1NsurfMapName, InitialSOM1CsoilMapName, InitialSOM1NsoilMapName, InitialSOM2CMapName, InitialSOM2NMapName, InitialSOM3CMapName, InitialSOM3NMapName, InitialDeadWoodSurfaceMapName, InitialDeadCoarseRootsMapName.

OptionalClimateMaps

(Optional) Named list of relative file paths for any of SlopeMapName, AspectMapName, NormalSWAMapName, NormalCWDMapName, NormalTempMapName.

CalibrateMode

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

SmokeModelOutputs

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

Write_SWA_Maps

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

Write_CWD_Maps

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

Write_Temperature_Maps

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

Write_Species_Drought_Maps

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

WaterDecayFunction

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

ProbabilityEstablishAdjust

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

InitialMineralN

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

InitialFineFuels

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

AtmosphericNSlope

Numeric. Slope for linear N-deposition model.

AtmosphericNIntercept

Numeric. Intercept for linear N-deposition model.

Latitude

Numeric. Study-site latitude (degrees).

DenitrificationRate

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

DecayRateSurf

Numeric in [0, 1]. Max decay rate of SOM1-surface pool.

DecayRateSOM1

Numeric in [0, 1]. Max decay rate of SOM1-soil pool.

DecayRateSOM2

Numeric in [0, 1]. Max decay rate of SOM2 (slow) pool.

DecayRateSOM3

Numeric in [0, 1]. Max decay rate of SOM3 (passive) pool.

GrassThresholdMultiplier

(Optional) Numeric. Grass/tree competition multiplier; see user guide §2.28.

OutputMaps

(Optional) Named list of optional output-map keywords and values. See table 3 of the user guide. Allowed names: ANPPMapName, ANPPMapFrequency, ANEEMapName, ANEEMapFrequency, SoilCarbonMapName, SoilNitrogenMapName, TotalCMapName. *MapName values are file-name templates and must contain the literal {timestep} placeholder (user guide §2.29), e.g. "NECN/ANPP-{timestep}.tif".

CreateInputCommunityMaps

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

VariableOverrides

(Optional) Named list of numeric override values. Allowed names: Stormflow, WaterFactor1, WaterFactor2, AnaerobicFactor1, AnaerobicFactor2, AnaerobicFactor3.

SpeciesParameters

Character. Relative file path to the species-parameters CSV (see §2.32, Table 4, of the user guide).

DroughtMortalityParameters

(Optional) Character. Relative file path to the drought-mortality-parameters CSV (see §2.33, Table 5, of the user guide).

FireReductionParameters

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

HarvestReductionParameters

(Optional) data.frame with columns PrescriptionName, DeadWoodReduction, DeadLitterReduction, CohortWoodRemoval, CohortLeafRemoval.

---

NECNSuccession$write()

Write extension inputs to disk

Usage

NECNSuccession$write()

---

NECNSuccession$clone()

The objects of this class are cloneable with this method.

Usage

NECNSuccession$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.