landisutils
Tools and utilities for preparing data for and running LANDIS-II simulations, and post-processing their outputs.
- prepare data in R and convert to LANDIS-II-compatible formats;
- programmatically create and write LANDIS-II extension input files;
- programmatically create and write LANDIS-II scenario and other simulation files;
- extraction of data from output logs;
- other post-processing tools;
[!NOTE]
This package is a work in progress.
Testing, feedback and help are greatly appreciated!
The list of supported LANDIS-II extensions tracks the official v8 extension list.
Tables below are grouped by extension type and sorted alphabetically; use the file outline (top-right on github.com) to jump between sections.
Succession extensions
Disturbance extensions
Other extensions
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!
