Robustness fixes + review report

[jimianelli]

No description provided.

[jimianelli]

@copilot resolve the merge conflicts in this pull request

[jimianelli]

@copilot resolve the merge conflicts in this pull request

[jimianelli]

@copilot resolve the merge conflicts in this pull request

[jimianelli]

@copilot resolve the merge conflicts in this pull request

[jimianelli]

@copilot resolve the merge conflicts in this pull request

[Copilot]

Pull request overview

Adds a Quarto-based review report to the repository and applies a set of small robustness/maintainability fixes to the jjmR R package code (file existence checks, safer option handling, and removal of eval(parse())).

Changes:

• Added reviews/ artifacts: the review source (.qmd), rendered HTML, and a patch file capturing the proposed fixes.
• Hardened model reading/execution paths (readJJM(), .getOutFile(), .runJJM()) and improved error handling for missing outputs.
• Simplified/safer internals: replaced eval(parse()) with do.call(), added column-count validation in get_index_fits(), and relaxed strict class checks with inherits().

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
reviews/jjmr_review.qmd	Adds the review report source document describing issues and recommended fixes.
reviews/jjmr_review.html	Adds rendered HTML version of the report.
reviews/jjmr_fixes.patch	Adds a patch file containing the proposed code changes for reference.
R/readJJMConfig.R	Fixes readJJMConfig.jjm.output() by adding the missing output argument.
R/readJJM.R	Adds explicit output-file existence checks and warning for missing .rep files.
R/jjmr-internal.R	Makes .getOutFile() tolerant of missing files and fixes .runJJM() adflags handling.
R/jjm.output-internal.R	Makes .combineModels() class checks robust via inherits().
R/get_index_fits.R	Adds validation to ensure expected index-fit column counts before renaming.
R/compareModels.R	Replaces eval(parse()) command assembly with do.call().

Comments suppressed due to low confidence (1)

R/readJJMConfig.R:44

• The new output argument in readJJMConfig.jjm.output() is later shadowed by output = .getJjmConfig(...) in the same function (and similarly in readJJMConfig.default). This makes the code harder to reason about and can lead to subtle bugs if output is referenced after the assignment. Rename the return variable (e.g., cfg/config) to avoid clobbering the output parameter.

readJJMConfig.jjm.output = function(model, path, input=NULL, output="results", ...) {
  
  ctl  = .getCtlFile(model=model, path=path) # path to ctl file
  dat  = .getDatFile(ctl=ctl, input=input) # path to dat file
  
  reps = .getRepFiles(model=model, output=output)

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