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_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
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
calibrate_original_fire(): Calibrate Original Fire
calibration_par_names(): Canonical parameter names for the Dynamic Fire calibration vector
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
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)
get_clim_daily(): Fetch a single year of daily BioSIM weather for one location batch
get_clim_monthly(): Fetch a single year of monthly BioSIM weather for one location batch
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
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_find(): Find the LANDIS-II console for a local installation
landis_find_docker(): Find the LANDIS-II console path inside a Docker container
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_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)
leading_species(): Leading species per cell at each snapshot
loss_from_stats(): Compute the calibration loss from N replicate trial outputs
parse_dynamic_fire_logs(): Parse a Dynamic Fire run's event and summary logs
patch_fire_config(): Patch a dynamic-fire.txt in place with candidate calibration parameters
plot_species_biomass(): Plot species biomass over time (stacked area)
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
read_biomass_c_snapshots(): Read ForCS log_BiomassC snapshots
read_biomass_output_rasters(): Read Output.Biomass raster snapshots
read_landis_resource_logs(): Read per-rep resource logs written by landis_run_docker() / landis_run_local()
roadType(): Construct a non-exit road type
run_calibration_spinup(): Run the calibration spinup scenario (blocking)
save_observed_fire_targets(): Save observed fire-regime targets (NFDB-derived) for calibration loss
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
windSpeedVulnerability(): Construct a per-species wind-speed vulnerability curve
writeClimateData(): Write LANDIS-II Climate Input File to disk
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