Run the imurun fitting pipeline — run

The spreadsheet-first fitting entry point. Given a workbook or directory of inputs, it validates the observations, locations, target requests, and configuration; fits with imuGAP::sampling(); and outputs requested deliverables (results sheet in workbook, results CSV, and/or fit.rds).

Usage

run_fit(
  input,
  output_dir = NULL,
  dryrun = FALSE,
  result = c("xlsx"),
  overwrite = TRUE,
  ...
)

Arguments

input: character path to a .xlsx workbook or input directory, or a pre-loaded inputs list (from read_inputs()).
output_dir: character path to output directory. Defaults to the directory of input (for workbooks) or input itself (for directory inputs).
dryrun: logical; if TRUE, validates inputs without fitting the model and returns invisible(0L) on success. Default is FALSE.
result: character vector of requested outputs, e.g. c("xlsx") (default), c("rds"), c("csv"), or combinations/custom paths.
overwrite: logical; if TRUE (default), overwrites existing output files. If FALSE and a destination exists, prompts in interactive sessions or stops.
...: optional arguments passed to override configuration settings.

Value

Invisibly, an integer exit code (0L for success).

Examples

if (FALSE) { # \dontrun{
# Validate inputs only:
run_fit("imurun_example.xlsx", dryrun = TRUE)

# Fit and update spreadsheet with results:
run_fit("imurun_example.xlsx")

# Fit and save raw RDS object:
run_fit("imurun_example.xlsx", result = c("rds"))
} # }