v1.5.3: Parallel processing, timers, OpenMP, facet labels, Rmd user guide

[Linbojun99]

Summary

Major update adding parallel processing, execution timing, and documentation improvements.

New Features

Parallel Processing (ncores parameter)

• run_acl(ncores): Parallel multi-start optimization via parLapply (socket cluster). Runs N independent optimizations from jittered starting points, keeps the best result. Purpose: robustness (avoid local optima), recommended ncores = 2–4.
• sim_acl(ncores): Parallel across simulation iterations via mclapply (Mac/Linux) or parLapply (Windows). Purpose: speed.
• retro_acl(ncores): Parallel across retrospective peels via mclapply/parLapply. Purpose: speed.

Execution Timers

• run_acl: Reports optimization time, sdreport time, and total time.
• sim_acl: Reports per-iteration time and total time with success count.
• retro_acl: Reports full model time, per-peel time, and total time breakdown.

OpenMP Support (ACL.cpp)

• Replaced Type nll = zero with parallel_accumulator<Type> nll(this) to enable TMB native OpenMP gradient parallelism.
• compile_acl.R: Auto-detects platform and compiles with OpenMP flags (-fopenmp). Falls back gracefully if OpenMP is unavailable.

Bug Fixes

Facet Label Improvements (7 plot functions)

• First/last length bins now display as open-ended: Length bin <7, Length bin >49 instead of 5-7, 49-51.
• Year facets now display as Year 1, Year 2 instead of 1, 2.
• Added shared helper function .acl_fix_len_labels() in acl_theme.R.
• Affected functions: plot_abundance, plot_biomass, plot_SSB, plot_CatL, plot_pla, plot_residuals.

Documentation

• Added ACL_User_Guide.Rmd: Full bilingual (EN/CN) user guide with all features documented.
• Updated example_1_simulation.R and example_2_YTF_real_data.R with core detection (Step 0) and ncores usage.
• Updated roxygen docs for run_acl, sim_acl, retro_acl with ncores parameter documentation.

Files Changed

• R/: run_acl.R, sim_acl.R, retro_acl.R, compile_acl.R, acl_theme.R, plot_abundance.R, plot_biomass.R, plot_SSB.R, plot_CatL.R, plot_pla.R, plot_residuals.R
• inst/extdata/ACL.cpp
• scr/example_1_simulation.R, scr/example_2_YTF_real_data.R
• ACL_User_Guide.Rmd (new)