[asgr]

Added functions to auto create Z inputs for relevant samplers (like AIES)

[Copilot]

🟡 Changes recommended

There are confirmed logic issues that can break runs (NA-unsafe if(any(...)) in Highlander and DEMC Z validation/diagnostics in Specs_help).

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR enhances the ergonomics and robustness of running LaplacesDemon algorithms by adding “auto-fill” helpers for Specs (especially ensemble / grid-based samplers) and by allowing Highlander() to seed starts and sampler inputs from a prior Lowlander() run to avoid out-of-bounds initialization failures.

Changes:

• Expanded Specs_help() to optionally use a Lowlander result (and Iterations/Thinning) to auto-generate algorithm-specific Specs, including Z for AIES/DEMC and grids for GG/AGG.
• Improved Lowlander() output validation (strict scalar return contract for likefunc) and added helper extractors (Lowlander_kept(), Lowlander_Z(), Lowlander_best()).
• Added Lowlander support in Highlander() (argument + seeding logic + parallel-dispatch safety) and updated documentation/vignette accordingly.

File summaries

File	Description
vignettes/LD-Algorithms.Rmd	Documents Specs_help() usage and Lowlander-based seeding patterns for restricted-likelihood models.
R/Specs_help.R	Implements Lowlander-seeded auto-generation/repair for Specs (notably AIES/DEMC Z, grids, and additional validation/warnings).
R/Lowlander.R	Makes Lowlander’s likefunc contract enforcement strict and preserves alignment by validating per-sample outputs before unlisting.
R/Lowlander_Z.R	Adds helper functions to extract kept samples and build Z/best start vectors from Lowlander results.
R/Highlander.R	Adds Lowlander argument, validates it early, seeds parm/lower/upper and (when defaulted) Specs, and adjusts multicore dispatch forwarding.
NAMESPACE	Adds imports for approx/rnorm used by the new helper logic.
man/Specs_help.Rd	Documents new Specs_help() arguments and Lowlander-seeding behavior.
man/Lowlander.Rd	Documents stricter likefunc return contract and new helper links.
man/Lowlander_helpers.Rd	Adds man page for the new Lowlander helper functions.
man/Highlander.Rd	Documents Highlander(Lowlander=...) behavior and interactions with Specs/LDargs.
DESCRIPTION	Adds testthat (suggested) and sets testthat edition config.
.github/workflows/main.yml	Adds testthat to CI dependencies.

Review details

Suppressed comments (1)

R/Specs_help.R:465

• The warning message concatenates ' x ', Npar, ' x '.... If Npar is NULL, paste0() returns character(0) and the warning becomes empty ("no message supplied"), which makes debugging much harder. The warning should render a placeholder when Npar is unknown.

        warning(paste0('DEMC: Z must be a 3-D array of dim ',
                       if (.sizeable) .z_rows(Iterations, Thinning) else 'floor(Iterations/Thinning)+1',
                       ' x ', Npar, ' x ', Nc, '. Set to NULL so LaplacesDemon ',
                       'regenerates it. Pass Iterations and Thinning to Specs_help ',
                       'to have the array built for you.'))

• Files reviewed: 12/12 changed files
• Comments generated: 3
• Review effort level: Lite

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[asgr]

@copilot Fix the code for all comments in this review thread.

When a review comment includes a suggested change, apply the suggestion exactly.

Do not make changes beyond what is described in the linked review thread.

[Copilot]

@copilot Fix the code for all comments in this review thread.

When a review comment includes a suggested change, apply the s...

Implemented the requested fixes from that review thread in commit fd8ab5b.