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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,
  by_class = FALSE,
  engine_rule = FALSE
)

Arguments

rep_dir

Character. Path to the replicate directory.

by_class

Logical. Also return the burned cells counted by timestep, map code and severity class?

engine_rule

Logical. Make the damage table's age test in single precision, as the extension does, rather than in double precision? See fire_cohort_killed().

Value

A list with burned_cells, high_cells and share (NA when nothing burned), or NULL when the replicate holds no severity maps, is missing one of the files above, or has no cohort of a species with both a tolerance and a longevity. With by_class = TRUE the list also holds by_class, a tibble of integer columns timestep, MapCode, class and cells: the burned cells of the severity map of each timestep, by the cell's map code (NA where the initial-communities map has none) and severity class (0 for a cell burned with no cohort damaged), in that order. Its cells sum to burned_cells, and the cells of the rows in which fire_cohort_killed() kills the landis_dominant_cohorts() cohort of MapCode sum to high_cells.

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.

  • the core species file – longevity, which the damage table's age thresholds are shares of. Its name is read from scenario.txt's Species directive, since prepSpeciesData(type = "core") names it species-core.txt while the LANDIS-II examples use species.txt; the latter is the fallback when there is no directive to read.

  • the Dynamic Fire per-species table – each species' fire tolerance. Its name is read from dynamic-fire.txt's Species_CSV_File directive, since DynamicFire$new() names it dynamic-fire-species.csv while this package's own df_input() default and the LANDIS-II examples use DynamicFire_Spp_Table.csv; the latter is the fallback when there is no directive to read.

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

The dominant cohort of each map code is the one landis_dominant_cohorts() returns, and whether it died is decided by fire_cohort_killed(): it dies when severity is 5 (the extension kills everything at that severity, whatever the tolerance) or when its age is at or below the percentage of its species' longevity that the damage table gives for severity minus tolerance. A cell on a map code with no dominant cohort counts as burned but never as killed. 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.

When a species' GroundFireKill is set, high_cells is the expected number of cells that lose their dominant cohort (fire_cohort_mortality()), so it can be fractional, and the function stops unless Landis-log.txt shows the extension applied each value.

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(), bc_fuel_label_to_base(), build_calibration_scenario_template(), build_calibration_spinup_scenario(), calibrate_dynamic_fire(), calibration_par_names(), dedup_community_snapshot(), default_severity_prior_sturtevant2009(), fire_cohort_killed(), fire_cohort_mortality(), ground_fire_kill_par_names(), landis_dominant_cohorts(), 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()