Configuration class Encapsulates all configuration parameters for the package, with validation. The same object is used for all workflows, with workflow-specific validation methods.

Public fields

stics_exe: Path to STICS executable (required)
usms_workspace: Path to USMs workspace (required)
metadata_file: Path to metadata file (required if run_simulations = TRUE)
eval_workspace: Path to evaluation workspace (required)
output_dir: Path to output directory for export workflow (required for export)
run_simulations: Logical. Whether to run simulations or just prepare the workspace.
parallel: Logical. Whether to run workflow in parallel.
verbose: Integer. Verbosity level (0 = silent, 1 = info, 2 = debug).
cores: Integer or NA. Number of CPU cores to use for parallel processing (only if parallel = TRUE). NA means auto-detect.
percentage: Numeric. Percentage of simulations to consider for export and plots (between 0 and 100).
species: Character vector or NULL. If specified, only these species will be included in export and plots.
usms: Character vector or NULL. If specified, only these USMs will be included in export and plots.
var2exclude: Character vector or NULL. If specified, these variables will be excluded from export and plots.
sim_rds: Character or NULL. Path to an .rds file containing pre-computed simulation results. If supplied, bypasses the need to run simulations (see validate_eval()). Independent of obs_rds.
obs_rds: Character or NULL. Path to an .rds file containing observation data used as reference for evaluation, plots and balance closure. Independent of sim_rds — has no effect on required fields.
ref_sim_rds: Character or NULL. Path to an .rds file containing reference simulation results used for evaluation and plots. Required for evaluation.

Methods

Public methods

Configuration$new()
Configuration$validate_eval()
Configuration$validate_balance_closure()
Configuration$print()
Configuration$clone()

`Configuration$new()`

Create a Configuration object. Values are validated against a declarative schema.

Usage

Configuration$new(...)

Arguments

...: Named configuration fields. Must match names defined in config_schema$fields. Unspecified fields use their default values. Invalid or unknown fields will trigger validation errors.

`Configuration$validate_eval()`

Validate configuration for evaluation workflow. Note: if sim_rds is supplied, it bypasses the need to run simulations (see check_metadata_file). obs_rds is independent and has no effect on required fields. usms_workspace remains required for eval regardless of sim_rds/obs_rds.

Usage

Configuration$validate_eval()

`Configuration$validate_balance_closure()`

Validate configuration for balance closure test

Usage

Configuration$validate_balance_closure()

`Configuration$print()`

Print the configuration, with fields grouped by theme (paths, execution, filtering, ...) rather than as a flat list. Makes it much easier to eyeball the current state of a large Configuration.

Usage

Configuration$print(...)

Arguments

...: Ignored. For compatibility with R6 print() generic.

`Configuration$clone()`

The objects of this class are cloneable with this method.

Usage

Configuration$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.