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Read Output.Biomass raster snapshots

read_biomass_output_rasters.Rd

General-purpose reader. Reads per-species biomass rasters written by the LANDIS-II Output Biomass v4 extension (Output.Biomass-v4) and returns per-cell, per-species total live biomass at the requested snapshot years.

Usage

read_biomass_output_rasters(
  dirs,
  times,
  species,
  live_map_pattern = "outputs/biomass/biomass-{species}-{timestep}.tif",
  run_name = NULL
)

Arguments

dirs

Character vector of replicate root directories (one per replicate), each containing output rasters at the path given by live_map_pattern.

times

Integer vector of snapshot years to extract.

species

Character vector of species names to include.

live_map_pattern

Character. File naming pattern for live-biomass rasters, using {species} and {timestep} as literal placeholders (same notation as the MapNames directive in the Output Biomass extension config file). Default: "outputs/biomass/biomass-{species}-{timestep}.tif".

run_name

Character. Scenario label attached as the scenario column. If NULL (default), derived from basename(dirname(dirs[1])).

Value

A data.table with columns scenario, replicate, Time, row, column, species, biomass where biomass is total live biomass in Mg C ha^-1. The ecoregion column present in read_biomass_c_snapshots() output is absent here (rasters do not carry ecoregion attribution per cell), but all downstream functions treat ecoregion as optional. This is the canonical format accepted by all downstream functions (leading_species(), community_label(), biomass_landscape_summary()).

Details

This reader works with any LANDIS-II succession extension (Biomass Succession, ForCS, NECN, etc.) as long as Output.Biomass is included in the scenario. Be aware that writing many raster outputs can slow down the simulation; for ForCS scenarios, read_biomass_c_snapshots() avoids this overhead by reading the per-cohort carbon log that ForCS writes unconditionally.

Raster values are assumed to be in g C m^-2 and are converted to Mg C ha^-1 (multiply by 0.01). This is correct for ForCS; for Biomass Succession the rasters store g dry biomass m^-2, so apply an appropriate carbon fraction before downstream use.

See also

read_biomass_c_snapshots() for the ForCS-specific fast path.

Other Vegetation transition helpers: biomass_landscape_summary(), community_label(), leading_species(), plot_species_biomass(), plot_transitions(), read_biomass_c_snapshots(), transition_data()