Fix discovered bugs

[rix133]

This pull request introduces several improvements and optimizations to the RDBEScore package, focusing on estimation object creation, memory management, and documentation. The main changes include more efficient handling of sub-sampling relationships, an option to exclude design variables for smaller objects, improved joining logic, and the addition of a GitHub Actions workflow for pkgdown site deployment.

Estimation object creation and memory management:

• Added an incDesignVariables parameter to createRDBESEstObject() to allow users to exclude design variables, reducing object size. Character columns are now converted to factors for further memory optimization. [1] [2] [3]
• Improved handling of sub-sampling relationships in the SA table by replacing recursive logic with a more efficient self-join and lookup table (prepareSubSampleLevelLookup), including warnings for missing or non-unique matches. [1] [2] [3]
• Added frequent calls to gc() (garbage collection) throughout the estimation object creation and joining functions to reduce memory usage during large data processing. [1] [2] [3] [4] [5] [6]

Joining logic and table handling:

• Improved join field selection for hierarchy 7 in procRDBESEstObjUppHier() and added comments about data.table vs. dplyr joins for future optimization. [1] [2]
• Updated logic for selecting VDid fields to avoid confusion when multiple fields are present.

Documentation and workflow:

• Added a GitHub Actions workflow (.github/workflows/pkgdown.yaml) for automated pkgdown site building and deployment to GitHub Pages.
• Updated .Rbuildignore to exclude pkgdown config and output files.
• Improved function documentation for clarity, including return value descriptions and parameter updates. [1] [2] [3]

Miscellaneous:

• Updated URLs in the DESCRIPTION file to include the pkgdown site.
• Optimized filtering logic in filterRDBESDataObject() to use data.table for efficiency.

[Copilot]

Pull Request Overview

This pull request standardizes vignette titles, improves cross-referencing between vignettes, fixes spelling errors, and removes obsolete test data directories. The changes focus primarily on documentation consistency and test data cleanup.

Key Changes:

• Standardized vignette titles with numeric prefixes (e.g., "01a", "02b") for better organization
• Added dynamic cross-referencing sections to all vignettes listing related documentation
• Fixed spelling errors ("prevenes" → "prevents")
• Removed two obsolete H7 test data directories (v1.19.18 and v1.19.26)
• Enhanced test coverage for validation rules, import functionality, and estimation object creation

Reviewed Changes

Copilot reviewed 88 out of 125 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
vignettes/*.Rmd (8 files)	Updated titles with numeric prefixes and added dynamic vignette cross-reference sections
tests/testthat/test-validateRDBESDataObject.R	Added tests for SL/IS validation rules
tests/testthat/test-importRDBESDataZIP.R	New test file for ZIP import functionality
tests/testthat/test-importRDBESDataCSV.R	New test file for CSV import functionality
tests/testthat/test-createRDBESEstObject.R	Added SSid assignments for parent-child relationships
tests/testthat/test-createRDBESDataObject.R	Updated tests to expect clear error messages for malformed data
tests/testthat/h7_v_1_19_26/* (11 files)	Removed obsolete H7 v1.19.26 test data directory
tests/testthat/h7_v_1_19_18/* (10 files)	Removed obsolete H7 v1.19.18 test data directory
man/upperTblData.Rd	Removed unnecessary blank line in examples section

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[Copilot]

The phrasing 'for sake of a simple example' should be 'for the sake of a simple example' to be grammatically correct.

Suggested change

	To demonstrate this we carry out a small alteration of the example data, removing the *Nephrops norvegicus* from the Species List. This creates a somewhat atypical situation: a haul where nothing was supposed to be looked for but still *Nephrops norvegicus* was registered. We use such situation here for sake of a simple example.
	To demonstrate this we carry out a small alteration of the example data, removing the *Nephrops norvegicus* from the Species List. This creates a somewhat atypical situation: a haul where nothing was supposed to be looked for but still *Nephrops norvegicus* was registered. We use such situation here for the sake of a simple example.