beerda · Copilot · Dec 19, 2025 · Dec 19, 2025 · Dec 19, 2025 · Dec 19, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,7 @@
 ^CRAN-SUBMISSION$
 ^.github$
 ^temp$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^index\.Rmd$
diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
@@ -0,0 +1,206 @@
+# Copilot Instructions for lfl
+
+## Project Overview
+
+`lfl` is an R package providing various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD), and forecasting time-series using fuzzy rule-based ensemble (FRBE). The package also contains basic fuzzy-related algebraic functions capable of handling missing values in different styles (Bochvar, Sobocinski, Kleene etc.), computation of Sugeno integrals and fuzzy transform.
+
+## Repository Structure
+
+- `R/` - R source code with roxygen2 documentation
+- `src/` - C++ source code using Rcpp (if any)
+- `tests/testthat/` - Unit tests using testthat framework (if any)
+- `man/` - Generated documentation (auto-generated, do not edit manually)
+- `vignettes/` - Package vignettes
+- `temp/vignette-src/` - Original LaTeX vignette source (for reference, do not modify)
+- `.github/workflows/` - CI/CD workflows for R CMD check, pkgdown
+
+## Development Setup
+
+### Prerequisites
+- R >= 3.6
+- C++ compiler (for Rcpp components)
+- Required R packages: Rcpp, devtools, roxygen2, testthat, knitr, rmarkdown
+
+### Building and Testing
+```r
+# Install dependencies
+devtools::install_deps(dependencies = TRUE)
+
+# Build documentation
+devtools::document()
+
+# Run R CMD check
+devtools::check()
+
+# Build package
+devtools::build()
+
+# Build pkgdown site
+pkgdown::build_site()
+```
+
+## Coding Standards
+
+### R Code
+
+1. **Documentation**: All exported functions must have complete roxygen2 documentation including:
+   - `@title` and description
+   - `@param` for all parameters
+   - `@return` for return values
+   - `@seealso` for references to related functions
+   - `@examples` with working examples
+   - `@export` for exported functions
+
+2. **Naming Conventions**:
+   - Functions: lowercase with dots (e.g., `algebra()`, `is.algebra()`)
+   - Internal functions: prefix with `.` (e.g., `.mustBeNumericScalar()`)
+   - Variables: camelCase or lowercase
+   - Use consistent naming patterns within the package
+
+3. **Error Handling**:
+   - Use internal validation functions (e.g., `.mustBe()`, `.mustBeNumericScalar()`)
+   - Provide clear error messages
+   - Validate input parameters at function entry
+
+4. **Style**:
+   - Use consistent indentation (4 spaces)
+   - Use `<-` for assignment
+   - Follow existing code style in the package
+   - Keep functions focused and modular
+
+### C++ Code (if applicable)
+
+1. **Standards**:
+   - Use Rcpp for R/C++ interface
+   - Follow C++ best practices
+   - Add comments for complex algorithms
+
+2. **Documentation**:
+   - Use Rcpp attributes for exported functions: `// [[Rcpp::export]]`
+   - Add roxygen2 documentation above exported functions
+   - Internal functions should have clear comments
+
+## Dependencies
+
+### R Package Dependencies
+- Runtime: Rcpp, foreach, forecast, plyr, tseries, e1071, tibble
+- Build/Link: Rcpp
+- Suggests: testthat, doMC, knitr, rmarkdown, R.rsp
+
+### Adding Dependencies
+- Add to appropriate field in DESCRIPTION (Imports, Suggests, LinkingTo)
+- Document why the dependency is needed
+- Keep dependencies minimal
+
+## Documentation
+
+- Use roxygen2 for all documentation
+- Run `devtools::document()` to regenerate man/*.Rd files
+- README.md is generated from README.Rmd - edit the .Rmd file only
+- Vignettes in `vignettes/*.Rmd`
+- Package website built with pkgdown at https://beerda.github.io/lfl/
+
+## Package Structure
+
+### Main Components
+
+1. **Fuzzy Algebras** (`algebra.R`, `algebraNA.R`):
+   - T-norms (Gödel, Goguen, Łukasiewicz)
+   - T-conorms, residua, bi-residua, negations
+   - Extensions for handling missing values
+
+2. **Fuzzy Sets** (`fsets.R`, `fcut.R`, `lcut.R`):
+   - Creation and manipulation of fuzzy sets
+   - Fuzzy partitioning of data
+   - Linguistic expressions
+
+3. **Linguistic Expressions** (`ctx.R`, `lingexpr.R`, `hedge.R`):
+   - Context definitions
+   - Evaluative linguistic expressions
+   - Linguistic hedges
+
+4. **Fuzzy Relations** (`compose.R`):
+   - Composition of fuzzy relations
+   - Various composition types
+
+5. **Association Rules** (`searchrules.R`, `farules.R`):
+   - Mining linguistic fuzzy association rules
+   - Rule manipulation and filtering
+
+6. **Perception-based Logical Deduction** (`pbld.R`, `fire.R`, `perceive.R`):
+   - PbLD inference method
+   - Rule firing and perception
+
+7. **Fuzzy Rule-Based Ensemble** (`frbe.R`, `frbemodel.R`):
+   - Time series forecasting
+   - Ensemble methods
+
+8. **Fuzzy Transform** (`ft.R`, `ftinv.R`):
+   - Fuzzy transform computation
+   - Inverse fuzzy transform
+
+9. **Sugeno Integral** (`sugeno.R`):
+   - Computation of Sugeno integrals
+
+## Common Tasks
+
+### Adding a New Function
+1. Create function in appropriate R/*.R file
+2. Add GPL-3 copyright header to the file if creating new file
+3. Add roxygen2 documentation
+4. Export if public function: `@export`
+5. Add tests if test infrastructure exists
+6. Run `devtools::document()` to update NAMESPACE and man/
+7. Run `devtools::check()`
+
+### Fixing a Bug
+1. Add a failing test that reproduces the bug (if test infrastructure exists)
+2. Fix the code
+3. Verify test passes
+4. Run `devtools::check()`
+
+### Adding a Vignette
+1. Create new .Rmd file in `vignettes/`
+2. Add appropriate YAML front matter
+3. Include vignette metadata for indexing
+4. Build with `devtools::build_vignettes()`
+
+## Best Practices
+
+1. **Never edit generated files**: NAMESPACE, man/*.Rd, RcppExports.cpp/R
+2. **Check the package**: Run `devtools::check()` before committing significant changes
+3. **Document as you code**: Add roxygen2 comments immediately
+4. **Follow existing patterns**: Study similar functions in the codebase before implementing new features
+5. **Maintain backward compatibility**: Deprecate functions properly before removal
+6. **Keep vignettes current**: Update vignettes when adding significant new features
+
+## CI/CD Workflows
+
+- **rhub**: Additional platform testing
+- **pkgdown**: Builds and deploys documentation site to GitHub Pages
+
+## Theoretical Background
+
+The package implements algorithms based on:
+- Fuzzy natural logic / linguistic fuzzy logic
+- Perception-based logical deduction (PbLD)
+- Fuzzy relational calculus
+- Linguistic fuzzy association rules
+- Fuzzy rule-based ensemble (FRBE)
+
+Key references:
+- Novák, V. (2008). A comprehensive theory of trichotomous evaluative linguistic expressions.
+- Štěpnička, M., & Burda, M. (2017). Towards a calculus of perceptions.
+- Burda, M., & Štěpnička, M. (2017). lfl: An R Package for Linguistic Fuzzy Logic.
+
+## Contributing
+
+Contributions should:
+- Follow the existing code style
+- Include appropriate documentation
+- Pass R CMD check without errors or warnings
+- Be compatible with R >= 3.6
+
+## License
+
+GPL-3: This package is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. See the GNU General Public License for details.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, devel]
+  pull_request:
+    branches: [main, master, devel]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          #- {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.gitignore b/.gitignore
@@ -30,3 +30,4 @@ config.status
 /autom4te.cache/
 .~*
 inst/doc
+docs/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -25,4 +25,4 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
 Language: en-US
-VignetteBuilder: R.rsp
+VignetteBuilder: knitr, R.rsp
diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,8 @@ knitr::opts_chunk$set(
 
 [![CRAN status](https://www.r-pkg.org/badges/version/lfl)](https://CRAN.R-project.org/package=lfl)
 [![codecov](https://codecov.io/gh/beerda/lfl/branch/master/graph/badge.svg)](https://app.codecov.io/gh/beerda/lfl)
-
+[![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/lfl)](https://cran.r-project.org/package=lfl)
+[![R-CMD-check](https://github.com/beerda/lfl/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/beerda/lfl/actions/workflows/R-CMD-check.yaml)
 
 # lfl
 
@@ -29,7 +30,9 @@ integrals and fuzzy transform.
 
 ## Documentation
 
-The complete documentation of the package is [available in this vignette](https://github.com/beerda/lfl/blob/master/vignettes/main.pdf).
+For complete documentation, please visit the [package website](https://beerda.github.io/lfl/).
+
+The original academic article describing the package is also [available as a vignette](https://github.com/beerda/lfl/blob/master/vignettes/main.pdf).
 
 
 ## Installation
-Original file line number
+Diff line change
@@ Expand Up / @@ -30,3 +30,4 @@ config.status @@
     /autom4te.cache/
     .~*
     inst/doc
+    docs/