How el-kizmi/wpp711 works
Batch cMSY++ is an R/Shiny application for multi-species stock assessment. The main user workflow imports catch and stock metadata, optionally derives an abundance index, validates stocks, configures MCMC parameters, runs CMSY++ jobs, and presents per-stock results and group summaries. The README documents a headless CLI as an alternate entry point, plus CPUE standardization and CSV exports. The graph follows the documented module flow; source excerpts were limited, so uncertain internal wiring is omitted.
Main entry points: mod_batch_cpue.R Abundance Index · mod_batch_validate.R Stock Validation · mod_batch_run.R Batch Execution · mod_batch_results.R Stock Results
Components 17
Wizard Workflow
- Import Data
R/mod_batch_import.R - Abundance Index
R/mod_batch_cpue.R - Stock Validation
R/mod_batch_validate.R - MCMC Parameters
R/mod_batch_params.R - Batch Execution
R/mod_batch_run.R
Analysis Runtime
- CPUE Standardization
R/cpue_helpers.R - Batch Helpers
R/batch_helpers.R - CMSY Job Runner
R/cmsy_runner.R - CMSY++ Engine
engine/CMSY++16.R
Results & Reporting
- Stock Results
R/mod_batch_results.R - Group Summary
R/mod_batch_summary.R
Other components
- Analyst
- Catch & Metadata CSV
- Raw CPUE Data
- CSV Exports
Connections 19
- Analyst → Shiny App: uses
- Analyst → Batch CLI: runs
- Catch & Metadata CSV → Import Data: uploads
- Shiny App → Import Data: hosts
- Import Data → Abundance Index: passes data
- Raw CPUE Data → Abundance Index: provides data
- Abundance Index → CPUE Standardization: standardizes
- Abundance Index → Stock Validation: passes index
- Stock Validation → Batch Helpers: validates with
- Stock Validation → MCMC Parameters: passes stocks
- MCMC Parameters → Batch Execution: sets options
- Batch Execution → CMSY Job Runner: dispatches jobs
- CMSY Job Runner → CMSY++ Engine: runs model
- Batch Execution → Stock Results: passes results
- Stock Results → Batch Helpers: classifies with
- Stock Results → Group Summary: passes metrics
- Group Summary → Batch Helpers: aggregates with
- Group Summary → CSV Exports: writes CSV
- Batch CLI → CMSY Job Runner: dispatches jobs