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Share of burned area that lost its dominant cohort

landis_overstory_mortality_share.Rd

The proportion of a replicate's burned cells in which the cohort holding the most biomass was killed. This is the model-side counterpart of a field burn-severity class defined by mortality of the structurally dominant vegetation, and unlike the extension's own severity classes – which are crown fraction burned – it is comparable with an observed mortality measure. In a forest that burns hot at ground level without crowning, the two disagree by construction.

Usage

landis_overstory_mortality_share(rep_dir)

Arguments

rep_dir

Character. Path to the replicate directory.

Value

A list with burned_cells, high_cells and share (NA when nothing burned), or NULL when the replicate holds no severity maps or is missing one of the files above.

Details

Everything needed is in the replicate directory, because a run is a copy of its scenario:

  • fire/severity-{t}.tif – the severity map per timestep. The Dynamic Fire encoding is 0 inactive, 1 active and unburned, 2 burned with no cohort damaged, and severity + 2 for a damaged cell, so a cell's severity class is its map value MINUS TWO.

  • initial-communities.csv / .tif – the cohorts on each cell.

  • species.txt – longevity, which the damage table's age thresholds are shares of.

  • DynamicFire_Spp_Table.csv – each species' fire tolerance.

  • dynamic-fire.txt – the FireDamageTable, mapping severity minus tolerance to the oldest cohort killed, as a percentage of longevity.

A cohort dies when severity is 5 (the extension kills everything at that severity, whatever the tolerance) or when its age is at or below that percentage of its species' longevity. Composition is read at time zero, so a cell that burns twice in one replicate is scored on its original cohorts; in a calibration run, where succession is frozen, only reburns are affected.

See also

Other Dynamic Fire calibration helpers: apply_calibrated_damage_age(), apply_calibrated_hi_prop(), apply_calibrated_ignprob(), apply_calibrated_num_fires(), bc_fuel_code_to_base(), build_calibration_scenario_template(), build_calibration_spinup_scenario(), calibrate_dynamic_fire(), calibration_par_names(), dedup_community_snapshot(), default_severity_prior_sturtevant2009(), loss_from_stats(), observed_fire_sizes(), parse_dynamic_fire_logs(), patch_fire_config(), run_calibration_spinup(), run_calibration_validation(), save_observed_fire_targets(), sim_landis(), sim_mock(), sim_r_reimpl()