run_alf_extraction: Run ALFRESCO data extraction
In leonawicz/alfresco: R Functions For ALFRESCO Wildfire Model

Description Usage Arguments Details Value See Also Examples

Extract data for different variables from ALFRESCO model outputs.

run_alf_extraction(domain = "akcan1km", type, loop_by = "rep",
  main_dir, out_dir, project, reps, years, cells, veg_labels,
  cru = FALSE, cru_id = "CRU 3.2", itervar = seq_along(years),
  mc.cores = 32, rmpi = TRUE)

`domain`	character, the ALFRESCO run spatial domain, either `"akcan1km"` or `"ak1km"`.
`type`	`"fsv"` or `"av"`. See details.
`loop_by`	`"rep"` or `"year"` (default).
`main_dir`	input directory.
`out_dir`	output directory. If missing, a default is provided by `alfdef()$alf_extract_dir`.
`project`	character, valid projects based on the domain. See details.
`reps`	integer vector, simulation replicates included in data extraction, e.g., `1:200`.
`years`	ALFRESCO model run years included in data extraction.
`cells`	data frame of raster grid cell indices appropriate to `domain`. See `get_domain_cells`.
`veg_labels`	vegetation labels appropriate to domain/vegetation input map for ALFRESCO runs. See `get_veg_labels`.
`cru`	logical, whether data extraction is for historical years (ALFRESCO runs based on CRU data) or projected years (GCM data).
`cru_id`	character, label for CRU data. Defaults to `"CRU 3.2"`.
`itervar`	integer vector, iterator, defaults to `1:length(years)`.
`mc.cores`	number of processors. See details.
`rmpi`	logical, use Rmpi. Defaults to `TRUE`.

The extracted data depends on type, which is "fsv" for fire size by vegetation class data or "av" for vegetation age and vegetation cover area data. A project refers to a collection of output directories pertaining to the set of climate models and emissions scenarios/RCPs that were used in project simulations. This function returns the full file path to each pertinent directory, given a valid domain and project. Valid projects for Alaska/western Canada include "IEM" and "FMO_Calibrated". For Alaska "statewide", it is "JFSP" and "CMIP5_SW". JFSP project names allow subproject/treatment run directories, e.g. "JFSP/tx1". mc.cores is used explicitly when rmpi = FALSE for parallel::mclapply instead of multi-node processing.

Extracted data are subsequently curated into estimated probability distribution tables by run_alf_extraction.

invisible, writes files.

alf_dist

# Not run; decontextualized example.
## Not run: run_alf_extraction(type = "fsv", main_dir = "Maps", project = "MyProject",
  reps = 1:200, years = 2014:2099, cells = cells, veg_labels = veg_labels)
## End(Not run)