//localhost:1313/runner/index.html Purpose Document CLI and YAML runner contracts for reproducible DSAMbayes runs. Audience Users operating DSAMbayes through scripts/dsambayes.R. Engineers maintaining runner config and artefact contracts. Pages Page Topic CLI Usage Commands, flags, exit codes, and error modes Config Schema YAML keys, defaults, and validation rules Output Artefacts Staged folder layout, file semantics, and precedence rules Hugo en-gb //localhost:1313/runner/cli-usage/index.html Mon, 01 Jan 0001 00:00:00 +0000 //localhost:1313/runner/cli-usage/index.html Purpose Define the supported command-line interface for scripts/dsambayes.R, including required flags, optional flags, and execution semantics. Prerequisites Before using the CLI: Complete Install and Setup. Run commands from repository root. Ensure DSAMbayes is installed and available in R_LIBS_USER. Entry point Rscript scripts/dsambayes.R <command> [flags] The script supports these commands: //localhost:1313/runner/config-schema/index.html Mon, 01 Jan 0001 00:00:00 +0000 //localhost:1313/runner/config-schema/index.html Purpose This page defines the YAML contract used by: scripts/dsambayes.R DSAMbayes::run_from_yaml() It documents defaults, allowed values, and cross-field constraints enforced by the runner. Schema processing order The runner processes config in this order: Parse YAML. Coerce YAML infinity tokens (.Inf, -.Inf). Apply defaults (resolve_config_defaults()). Resolve relative paths against the config file directory (resolve_config_paths()). Validate values and cross-field constraints (validate_config()). Validate formula safety unless security.allow_unsafe_formula: true. Root sections Key Default Notes schema_version 1 Must be 1. data object Input data path, format, date handling, dictionary metadata. model object Formula, model type, scaling, compile behaviour. cre object Correlated random effects settings (Mundlak). pooling object Pooled model map and grouping settings. transforms object Transform mode and sensitivity scenarios. priors object Default priors plus sparse overrides. boundaries object Parameter boundary overrides. time_components object Managed holiday feature generation. fit object MCMC or optimisation fit arguments. allocation object Post-fit budget optimisation settings. outputs object Run directory and artefact save flags. forecast object Reserved forecast stage toggle. diagnostics object Policy mode, identifiability, model selection, time-series selection. security object Formula safety bypass flag. Minimal valid config schema_version: 1 data: path: data/your_data.csv format: csv model: formula: y ~ x1 + x2 Expected outcome: this resolves with defaults for all omitted sections and passes schema validation if the file exists and formula variables exist in data. //localhost:1313/runner/output-artifacts/index.html Mon, 01 Jan 0001 00:00:00 +0000 //localhost:1313/runner/output-artifacts/index.html Purpose This page defines what the YAML runner writes, where files are written, and which config flags control each artefact. Related pages: CLI Usage Config Schema Run directory and layout semantics Run directory precedence: CLI --run-dir outputs.run_dir Timestamped folder under outputs.root_dir Layout behaviour: