PnET Biomass Output Extension

Companion output extension to PnETSuccession; both share the same user guide. §11 of the v6.0 guide documents the LandisData "Output-PnET" input file format and the supported output keywords (e.g. Biomass, LeafAreaIndex, the Monthly* keywords, etc.); §11.5 covers the output-file-name templates and the {species} / {timestep} placeholders.

References

LANDIS-II PnET-Succession v6.0 Extension User Guide (§11 covers the Output-PnET input file) https://github.com/LANDIS-II-Foundation/Extension-Output-Biomass-PnET/blob/master/docs/LANDIS-II%20PnET-Succession%20v6.0%20User%20Guide%20Jan21%202026.pdf

See also

PnETSuccession (this extension's required succession backend; output fields here consume PnET-specific cohort state).

Other PnET Output helpers: defaultPnETOutputFiles()

Super class

LandisExtension -> OutputBiomassPnET

Active bindings

Species

Character vector of species codes, or "all" / "none".

Outputs

Named list mapping LANDIS-II output keywords to file patterns.

Methods

Public methods

• OutputBiomassPnET$new()

• OutputBiomassPnET$write()

• OutputBiomassPnET$clone()

Inherited methods

• LandisExtension$add_file()

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OutputBiomassPnET$new()

Usage

OutputBiomassPnET$new(path, Timestep = NULL, Species = "all", Outputs = NULL)

Arguments

path

Character. Directory path.

Timestep

Integer. Years between output snapshots.

Species

Character vector of species codes, or "all" / "none".

Outputs

Named list mapping LANDIS-II output keywords (any of Biomass, BelowgroundBiomass, WoodBiomass, FoliageBiomass, RootBiomass, WoodySenescence, FoliageSenescence, AgeDistribution, CohortsPerSpecies, CohortBalance, LeafAreaIndex, MonthlyAvgLAI, Water, MonthlyAvgWater, MonthlyEvap, MonthlyInterception, MonthlyActualTrans, MonthlyPotentialTrans, MonthlyPotentialEvap, MonthlyLeakage, MonthlyRunoff, MonthlyAET, AET, AETAvg, PET, AnnualPsn, MonthlyNetPsn, MonthlyGrossPsn, MonthlyFolResp, MonthlyMaintResp, NSC, WoodyDebris, Litter, SubCanopyPAR, Albedo, MonthlyActiveLayerDepth, MonthlyFrostDepth, MonthlyAvgSnowPack, EstablishmentTable, EstablishmentProbability, Establishment, MortalityTable, SiteMossDepth) to character file patterns. Each pattern may contain {timestep}, {species}, {month}, or {year} placeholders depending on the keyword. Use defaultPnETOutputFiles() for a sensible default set.

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OutputBiomassPnET$write()

Write extension inputs to disk

Usage

OutputBiomassPnET$write()

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OutputBiomassPnET$clone()

The objects of this class are cloneable with this method.

Usage

OutputBiomassPnET$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.