landisutils

Tools and utilities for preparing data for and running LANDIS-II simulations, and post-processing their outputs.

1. prepare data in R and convert to LANDIS-II-compatible formats;
2. programmatically create and write LANDIS-II extension input files;
3. programmatically create and write LANDIS-II scenario and other simulation files;
4. extraction of data from output logs;
5. other post-processing tools;

Note

This package is a work in progress. Testing, feedback and help are greatly appreciated!

The following LANDIS-II extensions are currently supported:

LANDIS-II Succession Extension	landisutils class
Biomass Succession	BiomassSuccession
Forest Carbon Succession (ForCS)	ForCS
NECN Succession	coming soon
PnET Succession	coming soon
DGS Succession	coming soon

LANDIS-II Disturbance Extension	landisutils class
Original Fire	OriginalFire
Dynamic Biomass Fuels	DynamicFuels
Dynamic Fire System	DynamicFire
Social-Climate-Fire	SocialClimateFire
Linear Wind	coming soon
Original Wind	coming soon
Climate Biological Disturbance Agents	coming soon
Epidemiological Disturbance Agents	coming soon
Hurricanes	coming soon
Land Use Plus	coming soon
DGS Succession	coming soon

LANDIS-II Other Extension	landisutils class
Biomass Output	OutputBiomass
Biomass-by-Age Output	OutputBiomassByAge
Biomass Reclassification Output	coming soon
Cohort Statistics Output	OutputCohortStats
Landscape Habitat Output	coming soon
Local Habitat Suitability Output	coming soon
Maximum Species Age Output	OutputMaxSpeciesAge
PnET Output	coming soon

Installation

You can install the development version of landisutils like so:

remotes::install_github("FOR-CAST/landisutils")

Preparing data

Use prep*() functions to convert input data to LANDIS-II data formats or auxiliary config files.

## e.g., to prepare the initial communities .csv and raster files
init_comm_files <- prepInitialCommunities(cohortData, pixelGroupMap, tmp_pth)

Creating LANDIS-II input files

For any of the supported extensions, use new() method to create an object which can be used to produce configuration files. The configuration can be defined all at once, or built up in sequence, or modified to produce alternate configurations. If producing several configurations, be sure to update the path for each configuration to ensure they will not be overwritten.

## e.g., to prepare Biomass Succession inputs
ext_biomass_succession <- BiomassSuccession$new(
  path = tmp_pth,
  Timestep = 10,
  SeedingAlgorithm = "WardSeedDispersal",
  InitialCommunitiesFiles = init_comm_files,
  ClimateConfigFile = clim_file,
  CalibrateMode = NULL, ## optional
  SpinupCohorts = FALSE, ## optional; v7.1
  SpinupMortalityFraction = 0.05, ## v7.1
  MinRelativeBiomass = min_rel_b,
  SufficientLight = suff_light,
  SpeciesDataFile = spp_file,
  EcoregionParameters = erp_df,
  SpeciesEcoregionDataFile = spperd_file,
  FireReductionParameters = frp_df,
  HarvestReductionParameters = hrp_df
)

Once your configuration is ready to write to disk for use with LANDIS-II:

## show files associated with this configuration
ext_biomass_succession$files

## write the main extension configuration / input file
ext_biomass_succession$write()

Manual file creation (advanced use)

Use insert*() functions when generating LANDIS-II input text files manually.

insertInitialCommunities(init_comm_files)

Creating LANDIS-II scenario files

Use scenario() to construct scenario files:

## other extensions can be added to be run once created per above
scenario(
  cell_length = 250,
  duration = 200,
  extensions = list(
    succession = list(ext_biomass_succession),
    disturbance = list(),
    other = list()
  ),
  name = "my_scenario_a",
  path = file.path("path", "to", "project")
)

Working with simulation outputs

Coming soon!