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PnET-Succession Extension

PnETSuccession.Rd

Builds the LANDIS-II PnET-Succession v6.0 extension input file (compatible with LANDIS-II v8). The top-level PnET-Succession parameters are written via this class' $write() method; auxiliary inputs (PnET generic / species / ecoregion parameters, disturbance reductions, Saxton-and-Rawls soil parameters, climate, and PnET output sites) are written by the companion prep*() helpers.

References

LANDIS-II PnET-Succession v6.0 Extension User Guide https://github.com/LANDIS-II-Foundation/Extension-PnET-Succession/blob/master/deploy/docs/LANDIS-II%20PnET-Succession%20v6.0%20User%20Guide%20Jan21%202026.pdf

See also

Helpers that prepare inputs for this extension: prepPnETGenericParameters(), prepPnETSpeciesParameters(), prepPnETEcoregionParameters(), prepPnETDisturbanceReductions(), prepPnETClimateFile(), prepPNEToutputsites(). Shared scenario inputs: prepClimateConfig(), prepInitialCommunities().

Other PnET Succession helpers: defaultPnETDisturbanceReductions(), prepPNEToutputsites(), prepPnETClimateFile(), prepPnETDisturbanceReductions(), prepPnETEcoregionParameters(), prepPnETGenericParameters(), prepPnETSpeciesParameters()

Super class

LandisExtension -> PnETSuccession

Active bindings

StartYear

Integer. Climate year in which the simulation begins.

SeedingAlgorithm

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

Latitude

Numeric (optional). Degrees.

PNEToutputsites

Character (optional). Relative file path.

InitialCommunities

Character. Relative file path.

InitialCommunitiesMap

Character. Relative file path.

LitterMap

Character (optional). Relative file path.

WoodyDebrisMap

Character (optional). Relative file path.

PnETGenericParameters

Character (optional). Relative file path.

PnETSpeciesParameters

Character. Relative file path.

EcoregionParameters

Character. Relative file path.

DisturbanceReductions

Character (optional). Relative file path.

ClimateConfigFile

Character (optional). Relative file path.

SaxtonAndRawlsParameters

Character (optional). Relative file path.

CohortBinSize

Integer (optional). Must be >= Timestep.

Methods

Public methods

Inherited methods

PnETSuccession$new()

Usage

PnETSuccession$new(
  path = NULL,
  Timestep = 10L,
  StartYear = NULL,
  SeedingAlgorithm = NULL,
  Latitude = NULL,
  PNEToutputsites = NULL,
  InitialCommunities = NULL,
  InitialCommunitiesMap = NULL,
  LitterMap = NULL,
  WoodyDebrisMap = NULL,
  PnETGenericParameters = NULL,
  PnETSpeciesParameters = NULL,
  EcoregionParameters = NULL,
  DisturbanceReductions = NULL,
  ClimateConfigFile = NULL,
  SaxtonAndRawlsParameters = NULL,
  CohortBinSize = NULL
)

Arguments

path

Character. Directory path.

Timestep

Integer. Succession timestep in years (recommended <= 10).

StartYear

Integer. Climate year in which the simulation begins.

SeedingAlgorithm

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

Latitude

(Optional) Numeric. Global study-site latitude in degrees. Can alternatively be set per-ecoregion in the EcoregionParameters file.

PNEToutputsites

(Optional) Character. Relative file path to the PNEToutputsites input file (see §12 of the user guide).

InitialCommunities

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.

LitterMap

(Optional) Character. Relative file path to the initial leaf litter map ($g/m^2$).

WoodyDebrisMap

(Optional) Character. Relative file path to the initial dead woody debris map ($g/m^2$).

PnETGenericParameters

(Optional) Character. Relative file path to the PnET generic parameters file (§7).

PnETSpeciesParameters

Character. Relative file path to the PnET species parameters file (§8).

EcoregionParameters

Character. Relative file path to the PnET ecoregion parameters file (§9).

DisturbanceReductions

(Optional) Character. Relative file path to the disturbance reductions file (§10).

ClimateConfigFile

(Optional) Character. Relative file path to the LANDIS-II climate library configuration file. When omitted, the climate file(s) referenced from EcoregionParameters are used.

SaxtonAndRawlsParameters

(Optional) Character. Relative file path to an override Saxton-and-Rawls soil parameter file.

CohortBinSize

(Optional) Integer. Number of years represented by an age cohort; must be >= Timestep.

PnETSuccession$write()

Write extension inputs to disk

Usage

PnETSuccession$write()

PnETSuccession$clone()

The objects of this class are cloneable with this method.

Usage

PnETSuccession$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.