docs: add documentation

.github/workflows/pkgdown.yaml

@@ -14,12 +14,6 @@ jobs:
   pkgdown:
     runs-on: ubuntu-latest
 
-    concurrency:  # restrict concurrency for non-PR jobs
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
     steps:
       - name: Checkout
         uses: actions/checkout@v5
@@ -58,3 +52,4 @@ jobs:
           branch: gh-pages
           folder: docs
 ...
+

_pkgdown.yml

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----
-url: https://AI-SDC.github.io/ACRO-R/
 template:
+  light-switch: true
   bootstrap: 5
-...
+  bslib:
+    primary: "#0051a5"
+
+navbar:
+  structure:
+    left: [home, reference, welcome, supports, installation, examples]
+    right: [search, github, lightswitch]
+  left:
+  - text: "Home"
+    href: index.html
+  - text: "Reference"
+    href: reference/index.html
+  - text: "Welcome to ACRO-R"
+    href: welcome.html
+  - text: "What ACRO-R Supports"
+    href: supports.html
+  - text: "Installation"
+    href: installation.html
+  - text: "Examples"
+    href: examples.html
+  right:
+  - icon: fab-github
+    href: https://github.com/AI-SDC/ACRO-R
+    aria-label: GitHub

examples.md

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+# Examples
+
+## Interactive Notebook
+
+For comprehensive examples and tutorials, see our interactive R notebook:
+
+[Example Notebook](articles/example-notebook.html)
+
+## Quick Start Examples
+
+### Basic Usage
+
+```r
+library("acro")
+
+# Initialize ACRO
+acro_init(suppress = TRUE)
+
+# Your analysis code here
+# ACRO will automatically check outputs for disclosure risks
+```
+
+### Creating Safe Tables
+
+```r
+# Example of creating a cross-tabulation with ACRO
+result <- acro_crosstab(data$variable1, data$variable2)
+
+# ACRO automatically applies disclosure control
+print(result)
+```
+
+### Finalizing Your Session
+
+```r
+# When you're done with your analysis
+acro_finalise()
+```
+
+For more detailed examples and use cases, please refer to the [Example Notebook](articles/example-notebook.html).

index.md

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+<img src="man/figures/SACRO_Logo_final.png" alt="Alt Text" width="20%">
+
+## AI-SDC Family Tools
+
+| **ACRO (Python)**                                                                                                                                                                                                                                                                                                               | **SACRO-ML**                                                                                                                                                                                                                                                                                              |
+| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **Statistical Disclosure Control for Python** <br />Tools for the Semi-Automatic Checking of Research Outputs. Drop-in replacements for common analysis commands with built-in privacy protection.<br />[Statistical Analysis](https://sacro-tools.org/ACRO/introduction.html){.btn .btn-acro .btn-sm} | **Machine Learning Privacy Tools** <br />Collection of tools and resources for managing the statistical disclosure control of trained machine learning models.<br />[Learn More](https://sacro-tools.org/SACRO-ML/introduction.html){.btn .btn-sacro-ml .btn-sm}                 |
+| **ACRO-R**                                                                                                                                                                                                                                                                                                                      | **SACRO-Viewer**                                                                                                                                                                                                                                                                                          |
+| **R Package Integration** <br />R-language interface for the Python ACRO library, providing familiar R syntax for statistical disclosure control.<br />[R Integration](reference/index.html){.btn .btn-acro-r .btn-sm}                                                     | **Graphical User Interface** <br />A graphical user interface for fast, secure and effective output checking, which can work in any TRE (Trusted Research Environment).<br />[View Docs](https://sacro-tools.org/SACRO-Viewer/introduction.html){.btn .btn-sacro-viewer .btn-sm} |
+
+## ACRO-R: Statistical Disclosure Control
+
+ACRO is a free and open source tool that supports the semi-automated checking of research outputs (SACRO) for privacy disclosure within secure data environments. SACRO is a framework that applies best-practice principles-based statistical disclosure control (SDC) techniques on-the-fly as researchers conduct their analysis. SACRO is designed to assist human checkers rather than seeking to replace them as with current automated rules-based approaches.
+
+## What is ACRO-R?
+
+ACRO implements a principles-based statistical disclosure control (SDC) methodology that:
+
+* Automatically identifies potentially disclosive outputs
+* Applies optional disclosure mitigation strategies
+* Reports reasons for applying SDC
+* Produces summary documents for output checkers
+
+## Core Features
+
+### Semi-Automated Disclosure Checking
+
+* **Drop-in replacements** for common Python analysis commands (pandas, statsmodels, etc.) with configurable disclosure checks
+* **Automated sensitivity tests** : frequency thresholds, dominance (p%, NK rules, etc.), residual degrees-of-freedom checks
+* **Optional mitigations** : suppression, rounding, and more to come
+* **Session management** : track, rename, comment, remove, add exceptions, and finalise reports
+* **Configurable risk parameters** via YAML files
+* **Generates auditable reports** in JSON or Excel
+
+### Design Principles
+
+* **Free and open source** under MIT (ACRO) / GPLv3 (SACRO Viewer)
+* **Easy to install** via PyPI, CRAN, or GitHub; cross-platform (Linux, macOS, Windows)
+* **Familiar APIs** - same function signatures as native commands: acro.crosstab mirrors pandas.crosstab, etc.
+* **Comprehensive coverage** - tables, regressions, histograms, survival plots, etc.
+* **Transparent & auditable** - clear reports, stored queries, designed for human-checkers
+* **Configurable & extensible** - organisation-defined disclosure rules, multi-language support
+* **Scalable** - lightweight, session-based, local execution
+
+## Getting Started
+
+| **Install**                                                                                                        | **Learn**                                                                                          | **Reference**                                                                                     |
+| ------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------- |
+| Get ACRO-R installed and configured in your environment<br />[Install Guide](articles/installation.html){.btn .btn-primary} | Explore tutorials and examples for common use cases<br />[Examples](articles/index.html){.btn .btn-primary} | Complete API documentation and function reference<br />[API Docs](reference/index.html){.btn .btn-primary} |

installation.md

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+# Installation Guide
+
+## Install from CRAN
+
+Install the **acro** package from CRAN as follows:
+
+```r
+install.packages("acro")
+```
+
+## Development Version
+
+To install the development version from GitHub:
+
+```r
+# Install devtools if you haven't already
+install.packages("devtools")
+
+# Install ACRO-R from GitHub
+devtools::install_github("AI-SDC/ACRO-R")
+```
+
+## Prerequisites
+
+ACRO-R requires:
+- R version 4.0 or higher
+- Python 3.8 or higher with the ACRO Python package installed
+
+## Python ACRO Installation
+
+The R package interfaces with the Python ACRO library. Install it using:
+
+```bash
+pip install acro
+```
+
+## Troubleshooting
+
+If you are having problems installing the package, please see the more detailed [installation guide](INSTALL.md) or check the [GitHub issues](https://github.com/AI-SDC/ACRO-R/issues).
+
+## Verification
+
+To verify your installation works correctly:
+
+```r
+library("acro")
+acro_init(suppress = TRUE)
+```
+
+If this runs without errors, your installation is successful!

pkgdown/extra.css

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+  border-color: #F66A0A;
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+
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pkgdown/extra.js

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