Package index • landisutils

All functions

BiomassBrowse: Biomass Browse Extension
BiomassHarvest: Biomass Harvest Extension
BiomassSuccession: Biomass Succession Extension
ClimateBDA: Climate BDA (Biological Disturbance Agent) Extension
DGSSuccession: DGS (DAMM-McNiP, GIPL, SHAW) Succession Extension
DynamicFire: Dynamic Fire System Extension
DynamicFuels: Dynamic Fuel System Extension
EDA: Epidemiological Disturbance Agents (EDA) Extension
ForCS: Forest Carbon Succession (ForCS) Extension
ForestRoadsSimulation: Forest Roads Simulation Extension
Hurricane: Biomass Hurricane Extension
LandUsePlus: Land Use Plus Extension
LandisClimateConfig: LandisClimateConfig class
LandisExtension: LandisExtension class
LandisScenario: LandisScenario class
LinearWind: Linear Wind Disturbance Extension
MagicHarvest: Magic Harvest Extension
MapNames(): Create Map Names pattern for file outputs
NECNSuccession: NECN Succession Extension
OriginalFire: Original Fire Extension
OriginalWind: Original Wind Extension
OutputBiomass: Biomass Output Extension
OutputBiomassByAge: Biomass Output by Age Extension
OutputBiomassCommunity: Biomass Community Output Extension
OutputBiomassPnET: PnET Biomass Output Extension
OutputBiomassReclass: Biomass Reclassification Output Extension
OutputCohortStats: Cohort Statistics Extension
OutputLandscapeHabitat: Landscape Habitat Output Extension
OutputLocalHabitat: Local Habitat Suitability Output Extension
OutputMaxSpeciesAge: Max Species Age Extension
OutputWildlifeHabitat: Wildlife Habitat Output Extension
PnETSuccession: PnET-Succession Extension
RootRot: Root Rot Extension
SocialClimateFire: Social-Climate-Fire Extension
appendPercent(): Ensure percent symbol appended to table values
apply_calibrated_damage_age(): Scale a fire damage table's cohort ages by a calibrated multiplier
apply_calibrated_hi_prop(): Overwrite FireSizesTable Sp/Sum/Fall HiProp columns with calibrated values
apply_calibrated_ignprob(): Apply per-base-fuel-type IgnProb multipliers to a FuelTypeTable
apply_calibrated_num_fires(): Apply a calibrated ignition rate to a FireSizesTable
assemble_climate_library_file(): Assemble LANDIS-II Climate Library wide-format table from a BioSIM Arrow dataset
assemble_climate_library_file_monthly(): Assemble LANDIS-II Climate Library wide-format table from a monthly BioSIM Arrow dataset
assemble_climate_library_file_monthly_climr(): Assemble LANDIS-II Climate Library wide-format table from a climr Arrow dataset
assemble_climate_library_file_monthly_terraclim(): Assemble LANDIS-II Climate Library wide-format table from a TerraClim Arrow dataset
assemble_climate_library_file_scf(): Assemble Social-Climate-Fire-shaped daily climate CSV from a BioSIM Arrow dataset
bc_fuel_code_to_base(): Default fuel-code -> base-fuel-type mapping (BC FUEL_TYPE_CD factor levels)
bdaAgent(): Construct a Climate BDA agent
biomass_landscape_summary(): Landscape biomass summary by species
build_calibration_scenario_template(): Build the calibration scenario template directory
build_calibration_spinup_scenario(): Build a calibration spinup scenario directory
calibrate_dynamic_fire(): DEoptim driver for Dynamic Fire calibration
calibration_events(): Pool the per-replicate fire-event logs
calibration_par_names(): Canonical parameter names for the Dynamic Fire calibration vector
calibration_plot_palette(): Colour roles for the calibration diagnostic plots
climr_ensemble_8: bcgov-recommended eight-member climr GCM ensemble
cohortSelector(): Construct a cohort selector for a Land Use Plus change block
community_label(): Community label per cell at each snapshot
create_locations_df(): Build batched point-location table from a study area
dedup_community_snapshot(): Collapse duplicate communities in an Output Biomass Community snapshot
defaultDGSDammMcNIPParameters(): Default DGS Succession DAMM-McNiP scalar parameters
defaultFireDamageTable(): Create sample Fire Damage Table
defaultFuelCurveTable(): Create sample Fuel Curve Table
defaultFuelTypeTable(): Create default Fuel Type Table
defaultHurricaneMortalityCurve(): Default Hurricane wind-speed mortality curve
defaultLinearWindSeverities(): Default WindSeverities table for the Linear Wind extension
defaultPnETDisturbanceReductions(): Default PnET-Succession DisturbanceReductions table
defaultPnETOutputFiles(): Default Outputs list for the PnET Biomass Output extension
defaultWindSeverities(): Default WindSeverities table for the Original Wind extension
default_severity_prior_sturtevant2009(): Default severity-class prior (Sturtevant et al. 2009)
edaAgent(): Construct an EDA agent
elevationCostRange(): Construct an elevation cost-range entry
exitRoadType(): Construct an exit road type (where wood leaves the landscape)
extract_landscape_cohort_structures(): Extract distinct cohort structures from the initial communities
fps_output_files(): Files FPSM writes into its working directory
fps_pools(): Summarise FPSM output into annual carbon stocks and atmospheric emissions
fps_run_docker(): Run the Forest Product Sector Module in a Docker container
fps_stocks_by_pool(): Annual FPSM stocks broken out by pool
georef_landis_raster(): Attach CRS and extent from a template to a LANDIS-II raster
get_clim_daily(): Fetch a single year of daily BioSIM weather for one location batch
get_clim_monthly(): Fetch + cache one year of monthly BioSIM weather for one location batch (per-study-area store)
get_clim_monthly_climr(): Fetch one year of monthly climr weather and write Arrow CSV partitions
get_clim_monthly_terraclim(): Fetch a single year-variable of monthly TerraClim weather
get_elevation_rast(): Get an elevation raster for a study area
get_fwi_daily(): Fetch a single year of daily BioSIM Fire Weather Index for one location batch
growth_add_objective(): Rank fit statistics
growth_auto_window(): Derive one species' fitting window from where its references have support
growth_best_candidates(): Best candidate per species, or an explicit refusal
growth_bin_observations(): Condense a ground-plot cloud into an age-binned series
growth_calibration_design(): Build the calibration design table
growth_calibration_partition(): Partition a design into batches that fit in memory
growth_calibration_work_root(): Resolve a writable, Docker-bind-mountable run root for calibration runs
growth_climatic_distance(): Score each observation by climatic distance from a target
growth_climatic_weight(): Turn climatic distance into a calibration weight
growth_expand_over_pseudo_species(): Expand a per-species parameter table over pseudo-species
growth_factorial_ratio_grid(): Expand a shape-and-ratio sweep into absolute ForCS parameters
growth_fitting_windows(): Per-species fitting windows
growth_identifiability(): Is a swept parameter actually determined by the references?
growth_inflation_factor(): Recover the biomass_max a candidate implies
growth_mortality_onset_frac(): Fraction of longevity at which age-related mortality begins
growth_plot_palette(): Colours for the growth-calibration figures
growth_pseudo_species_name(): Name a pseudo-species
growth_reference_curves(): Build one species' reference curves on a common age grid
growth_reference_inflection(): Age at which a reference growth curve's increment peaks
growth_score_fit(): Score a simulated growth curve against its references
growth_scoring_for(): Look up one species' scoring controls, with defaults
growth_smooth_observations(): Smooth a ground-plot cloud for display
growth_structure_cell_curves(): Reduce structure-factorial curves to one trajectory per cell
growth_structure_cohort_table(): Tabulate the cohorts the structure factorial actually simulated
growth_structure_design(): Build a design crossing landscape cohort structures with a parameter sweep
growth_structure_summary(): Summarise structure-factorial trajectories by stand composition
growth_window_for(): Look up one species' fitting window
harvestPrescription(): Construct a Biomass Harvest prescription
host_cpu_info(): Host CPU and RAM identification (cross-platform)
insertANPPTimeSeries(): Specify ANPPTimeSeries for Forest Carbon Succession (ForCS) extension
insertAvailableLightBiomass(): Specify AvailableLightBiomass for Forest Carbon Succession (ForCS) extension
insertBuildUpIndex(): Specify Dynamic Fire Extension BuildUpIndex
insertClimateConfigFile(): Specify ClimateConfigFile
insertDOMPools(): Specify DOMPools for Forest Carbon Succession (ForCS) extension
insertDisturbanceConversionTable(): Specify Dynamic Fuel Extension's Disturbance Conversion Table
insertEcoSppDOMParameters(): Specify EcoSppDOMParameters for Forest Carbon Succession (ForCS) extension
insertEcoregionParameters(): Specify EcoregionParameters table
insertEcoregionTable(): Specify Dynamic Fuel Extension's Ecoregion Table
insertEcoregionsFiles(): Specify Ecoregions and EcoregionsMap Files
insertEstablishProbabilities(): Specify EstablishProbabilities for Forest Carbon Succession (ForCS) extension
insertSuccessionExtensions() insertDisturbanceExtensions() insertOtherExtensions(): Specify Scenario Extensions Tables
insertFile(): Specify an input file for an extension
insertFireReductionParameters(): Specify Biomass Succession Extension FireReductionParameters Table
insertFireRegionParametersTable(): Specify Fire Region Parameters Table
insertFireSizesTable(): Specify Fire Size Table
insertForCSMapControl(): Specify ForCSMapControl for Forest Carbon Succession (ForCS) extension
insertForCSProportions(): Specify ForCSProportions for Forest Carbon Succession (ForCS) extension
insertFuelCurveTable(): Specify Original Fire FuelCurveTable
insertFuelTypeTable(): Specify Dynamic Fire Extension FuelTypeTable
insertFuelTypesTable(): Specify Dynamic Fuel Extension's Fuel Types Table
insertGroundSlopeFile(): Specify Dynamic Fire Extension GroundSlopeFile
insertHarvestReductionParameters(): Specify Biomass Succession Extension HarvestReductionParameters Table
insertInitialCommunities(): Specify InitialCommunities and InitialCommunitiesMap Files
insertLandisData(): Write a LANDIS-II LandisData header block
insertLightEstablishmentTable(): Specify LightEstablishmentTable for Forest Carbon Succession (ForCS) extension
insertMaxBiomassTimeSeries(): Specify MaxBiomassTimeSeries for Forest Carbon Succession (ForCS) extension
insertMinRelativeBiomass(): Specify Biomass Succession Extension MinRelativeBiomass Table
insertOutputTables(): Specify OutputTables for Forest Carbon Succession (ForCS) extension
insertRandomNumberSeed(): Specify Scenario RandomNumberSeed
insertRootDynamics(): Specify RootDynamics for Forest Carbon Succession (ForCS) extension
insertSeasonTable(): Specify Dynamic Fire Extension's Season Table
insertSpeciesDataFile(): Specify Species Data File
insertSpeciesEcoregionDataFile(): Specify SpeciesEcoregionData File
insertSpeciesFuelCoefficients(): Specify Dynamic Fuel Extension's Species Fuel Coefficients
insertSpeciesParameters(): Specify SpeciesParameters for Forest Carbon Succession (ForCS) extension
insertSpinUp(): Specify SpinUp for Forest Carbon Succession (ForCS) extension
insertSufficientLight(): Specify Biomass Succession Extension SufficientLight Table
insertUphillSlopeAzimuthMap(): Specify Dynamic Fire Extension UphillSlopeAzimuthMap
insertValue(): Specify an input parameter value for an extension
insertWindCurveTable(): Specify Original Fire WindCurveTable
landCoverChange(): Construct a Land Cover Change for a landUseType()
landUseType(): Construct a Land Use type
landis_archive_rep(): Move a completed LANDIS-II replicate from scratch to its final location
landis_assert_version(): Require a specific LANDIS-II core generation before running anything
landis_datatype(): Pick a raster pixel type LANDIS-II can read
landis_find(): Find the LANDIS-II console for a local installation
landis_find_docker(): Find the LANDIS-II console path inside a Docker container
landis_image_info(): Read the LANDIS-II Docker image reference used for a run
landis_input_hash(): Input hash of one LANDIS-II replicate
landis_overstory_mortality_share(): Share of burned area that lost its dominant cohort
landis_pool_exec(): Execute a command in one of the warm-pool containers
landis_pool_restart_one(): Restart a single container in a warm Docker pool
landis_pool_start(): Start a warm Docker pool for LANDIS-II calibration
landis_pool_stop(): Stop and remove all containers in a warm Docker pool
landis_rep_is_current(): Is a LANDIS-II replicate already complete for these inputs?
landis_replicate(): Create replicate directories for a LANDIS-II scenario
landis_process() landis_run(): Run a LANDIS-II simulation from the R session
landis_run_docker(): Run a LANDIS-II simulation inside a Docker container
landis_run_local(): Run a LANDIS-II simulation locally (synchronous)
landis_target_version(): The LANDIS-II core generation this package targets
landis_version(): Report the version of a LANDIS-II console
leading_species(): Leading species per cell at each snapshot
loss_from_stats(): Compute the calibration loss from N replicate trial outputs
observed_fire_sizes(): Observed per-fire sizes: one per ignition point, upgraded to mapped area
open_forcs_log_summary_dataset(): Open the ForCS log_Summary Arrow dataset for one or more scenarios
open_fps_raw_out_dataset(): Open the FPSM raw-output Arrow dataset for one or more scenarios
parse_dynamic_fire_logs(): Parse a Dynamic Fire run's event and summary logs
parse_landis_log_versions(): Parse a LANDIS-II Landis-log.txt for version metadata
patch_fire_config(): Patch a dynamic-fire.txt in place with candidate calibration parameters
plot_calibration_area_by_fuel(): Plot observed against simulated area burned by base fuel type
plot_calibration_convergence(): Plot the DEoptim search trace
plot_calibration_fire_counts(): Plot observed against simulated annual fire counts
plot_calibration_fire_sizes(): Plot observed against simulated fire sizes
plot_calibration_loss(): Plot the weighted contribution of each objective component
plot_calibration_severity(): Plot observed against simulated burn-severity classes
plot_calibration_severity_by_size(): Plot simulated fire size against fire severity
plot_growth_calibration(): Plot a species' growth curve against its references
plot_growth_candidate(): Plot the current parameter set against a candidate, for review
plot_growth_factorial_sensitivity(): Plot factorial sensitivity of fit to each growth parameter
plot_growth_structures(): Plot mixtures against monocultures for one species
plot_species_biomass(): Plot species biomass over time (stacked area)
plot_species_growth_curves(): Plot fitted LANDIS-II growth curves against PSP observations
plot_transitions(): Plot vegetation transitions (Sankey / alluvial diagram)
prepClimateConfig(): Create ClimateConfigFile
prepClimateFile(): Prepare ForCSClimateFile for Forest Carbon Succession (ForCS) extension
prepDGSFireReductionParameters(): Prepare DGS Succession FireReductionParameters table
prepDisturbanceConversionTable(): Create Dynamic Fire Extension's Disturbance Conversion Table
prepDisturbanceMatrixFile(): Prepare DisturbanceMatrixFile for Forest Carbon Succession (ForCS) extension
prepDynamicEcoregionTable(): Prepare Dynamic Fire Extension DynamicEcoregionTable
prepDynamicWeatherTable(): Prepare Dynamic Fire Extension DynamicWeatherTable
prepEcoregionParameters(): Create Ecoregion Parameters Table
prepEcoregionsFiles(): Create Ecoregions and EcoregionsMap Files
prepFireReductionParameters(): Prepare Biomass Succession Extension FireReductionParameters Table
prepFireRegionParametersTable(): Prepare Original Fire Extension FireRegionParameters Table
prepFireSizesTable(): Prepare Dynamic Fire Extension FireSizes Table
prepFuelTypesTable(): Create Dynamic Fire Extension's Fuel Types Table
prepHarvestReductionParameters(): Prepare Biomass Succession Extension HarvestReductionParameters Table
prepInitialCommunities(): Create InitialCommunities and InitialCommunitiesMap Files
prepInitialFireRegionsMap(): Create Original Fire InitialFireRegionsMap
prepInitialWeatherDatabase(): Create Dynamic Fire Extension's Initial Weather Database
prepMinRelativeBiomass(): Prepare Biomass Succession Extension MinRelativeBiomass Table
prepNECNFireReductionParameters(): Prepare NECN Succession FireReductionParameters table
prepPNEToutputsites(): Prepare PnET-Succession PNEToutputsites input file
prepPnETClimateFile(): Prepare PnET-Succession Climate input file
prepPnETDisturbanceReductions(): Prepare PnET-Succession Disturbance Reductions file
prepPnETEcoregionParameters(): Prepare PnET-Succession Ecoregion Parameters file
prepPnETGenericParameters(): Prepare PnET-Succession Generic Parameters file
prepPnETSpeciesParameters(): Prepare PnET-Succession Species Parameters file
prepSnagFile(): Prepare SnagFile for Forest Carbon Succession (ForCS) extension
prepSpeciesData(): Species Data File
prepSpeciesEcoregionDataFile(): Create Species Ecoregion Data File
prepSuppression_CSV_File(): Prepare Suppression_CSV_File for Social-Climate-Fire extension
prepTopographyFile() prepGroundSlopeFile() prepUphillAzimuthMap(): Prepare topographical raster files
prepWindEventParametersTable(): Prepare Original Wind WindEventParametersTable
prep_daily_weather() prep_monthly_weather_biosim() prep_monthly_weather_climr() prep_monthly_weather(): Prepare Climate Data
proj_daymet: PROJ4 strings for climate data
proj_nrcan_lcc: PROJ4 strings for forest data
prov_landis_container(): LANDIS-II container image and digest (provenance)
prov_landis_versions(): LANDIS-II console and extension versions (provenance)
prov_run_resources(): LANDIS-II per-replicate resource use (provenance)
prov_stochasticity(): LANDIS-II stochasticity summary (provenance)
read_biomass_c_snapshots(): Read ForCS log_BiomassC snapshots
read_biomass_c_snapshots_for_scenario(): Open + collect a per-scenario biomass_snapshots Arrow dataset
read_biomass_output_rasters(): Read Output.Biomass raster snapshots
read_forcs_log_summary(): Read ForCS log_Summary.csv files for one scenario (all replicates)
read_fps_raw_out(): Read one or more FPSM FPS_raw_out.csv files
read_growth_scoring(): Read the per-species scoring controls
read_landis_raster(): Read a LANDIS-II output raster in the row order LANDIS-II wrote it
read_landis_resource_logs(): Read per-rep resource logs written by landis_run_docker() / landis_run_local()
read_landscape_cohort_structures(): Read a landscape cohort-structure table
repair_fwi_daily(): Repair and re-derive a table of BioSIM FWI_Daily records
repair_fwi_exponent(): Repair BioSIM's sign-dropped scientific-notation exponents
roadType(): Construct a non-exit road type
run_calibration_spinup(): Run the calibration spinup scenario (blocking)
run_calibration_validation(): Re-simulate at the calibrated parameter vector for goodness-of-fit plots
save_observed_fire_targets(): Save observed fire-regime targets (NFDB-derived) for calibration loss
scale_linetype_growth_reference(): Consistent linetype scale for reference curves
scenario(): Create LANDIS-II scenario files
sim_landis(): Run one DEoptim trial for a candidate parameter vector (blocking)
sim_mock(): Mock simulator backend for testing the calibration driver without LANDIS-II
sim_r_reimpl(): Standalone-R Dynamic Fire reimplementation (stub)
simplifyCohorts(): Simplify cohorts
suitabilityFile(): Construct a habitat-suitability file reference
tar_landis(): Create a targets target that runs one LANDIS-II replicate
test_ecoregionPolys: Test ecoregion polygons
transition_data(): Build a transition data frame for alluvial plots
validate_landis_scenario(): Validate a generated LANDIS-II scenario directory before running it
windSpeedVulnerability(): Construct a per-species wind-speed vulnerability curve
writeClimateData(): Write LANDIS-II Climate Input File to disk
write_biomass_c_snapshots_parquet(): Write one replicate's biomass_snapshots to a partitioned parquet
write_forcs_log_summary_parquet(): Write one replicate's ForCS log_Summary to a partitioned parquet
write_fps_raw_out_parquet(): Write one replicate's FPSM raw output to a partitioned parquet
write_growth_review_bundle(): Write a standalone calibration review bundle
write_landis_scenario_file(): Write a LANDIS-II scenario.txt file (lower-level helper)
yesno() truefalse(): Convert logical to a LANDIS-II yes/no or true/false token