docs: reorganise documentation and simplify installation guide

README.md

@@ -40,8 +40,8 @@ If you are having problems installing the package, please see the more detailed
 Before using any function from the package, an acro object should be initialised using the following R code:
 
 ``` r
->>> library("acro")
->>> acro_init(suppress = TRUE)
+library("acro")
+acro_init(suppress = TRUE)
 ```
 
 ### Try Online with MyBinder

_pkgdown.yml

@@ -14,13 +14,13 @@ navbar:
   - text: "Reference"
     href: reference/index.html
   - text: "Welcome to ACRO-R"
-    href: welcome.html
+    href: articles/welcome.html
   - text: "What ACRO-R Supports"
-    href: supports.html
+    href: articles/supports.html
   - text: "Installation"
-    href: installation.html
+    href: articles/installation.html
   - text: "Examples"
-    href: examples.html
+    href: articles/examples.html
   right:
   - icon: fab-github
     href: https://github.com/AI-SDC/ACRO-R

inst/INSTALL.md

@@ -1,143 +1,42 @@
 # Installation Guides
 
-This document is intended to provide help installing and running acro-r in different settings.
+This document is intended to provide help installing and running acro-r.
 
-Keeping this comprehensive will require input from the community.
+## Prerequisites
 
-So please email sacro.contact@uwe.ac.uk, or [raise an issue on the GitHub repository](https://github.com/AI-SDC/ACRO-R/issues/new/choose) if:
- - you have a setting that is not covered, or
- - the steps outlined below do not work for you,
+- **Python 3.10+**: You must have Python installed on your system.
+- **R**: You need a working installation of R.
 
-**Please note**: most of the scenarios below assume that
-- you have a working version of Python 3 (version 3.9 or higher) on your system
-- you are able to access a terminal or command prompt to write and execute some commands.
+## Installation
 
----
+### Step 1: Install the R package
 
-## Step 1 create a python virtual environment and install the base python package *acro*
-**In every case** we recommend that you create what is called a 'python virtual environment' called **r-acro**.
-Virtual environments (*venv's*) are recommended best practice.
-This is because they isolate the impact of any changes you make in one venv - such as adding or updating a package- from the rest of your system.
+Install the **acro** package from CRAN:
 
-There are many tutorials available on the web if you get stuck.
-We do not endorse any particular site, but here are some examples:
-- [an overview with examples  for windows/linux/mac](https://python.land/virtual-environments/virtualenv)
-- [another that also contains instructions for VSCode and Pycharm](https://realpython.com/python-virtual-environments-a-primer/)
-
-**For individual users** we suggest that you do this in your home directory where you should have write permission.
-
-**To install site-wide** we assume you have access rights and know where your organisation's preferred locations are (for example, this might be ```/usr/local``` on a linux system).
-
-### Make a dedicated virtual environment
-You can make a new virtual environment  via:
-- the Anaconda GUI interface to the conda system
-- command line access - by opening a terminal or command prompt and entering the command:
- ```sh
-  conda create --n r-acro
-  ```
-if you have a version of conda installed or
- ```sh
-python -m venv ./r-acro
-```
-to use the native python *venv* package.
-
-### Change to that virtual environment and install acro
-Anaconda comes with its own GUI to makes this process easy.
-
-**On any system** using *conda* from the command line :
-```sh
-conda activate r-acro
-conda install conda-forge::acro
-
-#assuming this completes successfully you can now exit
-conda deactivate r-acro
-```
-
-**On Windows**from the command line with python's *pip* package manager:
-```sh
-# In cmd.exe
-r-acro\Scripts\activate.bat
-# In PowerShell
-r-acro\Scripts\Activate.ps1
-```
-followed by
-```sh
-python -m pip install acro
-#assuming this completes successfully you can now exit the virtual environment
-deactivate
-```
-
-**On linux/mac** using conda:
-
-```sh
-source r-acro/bin/activate
-#you should see the your command prompt change to show (r-acro)
-python -m pip install acro
-#assuming this completes successfully you can now exit the virtual environment
-deactivate
-```
----
-
-## Step 2 Install the R packages *reticulate* and *acro*
-
-The *reticulate* package is the industry-standard method for supporting communications between R and Python.
-It provides the `plumbing` between the R `front-end'
-
-These commands should work whether you are
-- working on a machine outside the TRE: in which case packages should install from a mirror of the CRAN service
-- working on a machine inside a TRE: in which case the administrator should have set up a local mirror of approved packages from CRAN
-
-**For individual users** without permission to make site-wide or machine-wide changes
-Open your preferred R interface - for  example, RStudio, and in a R window type
-```R
-install.packages*("reticulate")
+```r
 install.packages("acro")
 ```
 
-**For administrators wishing to install for all users site-wide** the commands are  the same but you will need to run them in *sudo* mode.
-
----
-
-## Step 3: Telling R and reticulate to use the new python virtual environment
-The final step of the process is to tell the R package reticulate which version of python to use.
-
-What we need to do is to set the value of a global variable ```RETICULATE_PYTHON```
-The [R documentation for doing this](https://rstudio.github.io/reticulate/articles/versions.html) is a little inconsistent here, but the following  options all seem to work.
+### Step 2: Initialize ACRO
 
-### Option 1- For individuals using RStudio
-If you follow the menu items from ```Tools->Project Options ->Python``` or ```Tools->Global Options->Python``` you can tell it to use the version of python from the virtual environment you create in step 1, either for a specific R project or for all your sessions as shown below
+The `acro` package interfaces with the Python `acro` library. The package provides a helper function to set up the necessary Python environment and dependencies automatically.
 
-![This is what it looks like: step0](./images/settingpython-rstudio-step0.png)
+Run the following in your R console:
 
-![This is what it looks like: step1](./images/settingpython-rstudio-step1.png)
-
-![This is what it looks like: step2](./images/settingpython-rstudio-step2.png)
-
-![This is what it looks like: step3](./images/settingpython-rstudio-step3.png)
-
-### Option 2 - Adding code to an individual project file
-    you add add one of the following lines at the start of your file
-   ```R
-   #Either
-    use_python("~/r-acro/bin/python")
-   #or
-   use_virtualenv("~/r-acro")
-   #or
-   use_condaenv("r-acro")
-   #finally followed by
-  library(reticulate)
-  library("acro)"
-   ```
-
-### Option 3 - Editing your personal R preferences
-In your home directory create (or edit) the file ```.Rprofile``` file, adding the lines
-
-```R
-Sys.setenv(RETICULATE_PYTHON=file.path(Sys.getenv("USERPROFILE"),"r-acro/bin/python"))
-Sys.setenv(RETICULATE_PYTHON_ENV=file.path(Sys.getenv("USERPROFILE"),"r-acro"))
+```r
+library("acro")
+acro_init()
 ```
 
+This command will:
+1. Check for a valid Python installation.
+2. Create a virtual environment named `r-acro`.
+3. Install the required Python `acro` package into this environment.
+
+Once initialized, you are ready to use ACRO-R!
 
+## Troubleshooting
 
-### Option 4- Making site-wide changes
- You can also edit the [site-wide Rprofile]() file to add these global environment variables, using replacing *~/r-acro* with the path to wherever you created the dedicated virtual environment.
+If you encounter issues during `acro_init()`:
+- Ensure Python 3.10+ is installed and added to your system PATH.
+- If you are on a restricted network, you may need to configure proxy settings for Python package installation.

inst/examples.md → vignettes/examples.Rmd

@@ -1,10 +1,14 @@
+---
+title: "Examples"
+---
+
 # Examples
 
 ## Interactive Notebook
 
 For comprehensive examples and tutorials, see our interactive R notebook:
 
-[Example Notebook](articles/example-notebook.html)
+[Example Notebook](example-notebook.html)
 
 ## Quick Start Examples
 
@@ -37,4 +41,4 @@ print(result)
 acro_finalise()
 ```
 
-For more detailed examples and use cases, please refer to the [Example Notebook](articles/example-notebook.html).
+For more detailed examples and use cases, please refer to the [Example Notebook](example-notebook.html).

inst/installation.md → vignettes/installation.Rmd

@@ -1,3 +1,7 @@
+---
+title: "Installation Guide"
+---
+
 # Installation Guide
 
 ## Install from CRAN
@@ -24,19 +28,22 @@ devtools::install_github("AI-SDC/ACRO-R")
 
 ACRO-R requires:
 - R version 4.0 or higher
-- Python 3.10+ or higher with the ACRO Python package installed
+- Python 3.10+ or higher
 
-## Python ACRO Installation
+## Initialization
 
-The R package interfaces with the Python ACRO library. Install it using:
+The package interfaces with the Python ACRO library. Use `acro_init()` to automatically handle the Python environment setup:
 
-```bash
-pip install acro
+```r
+library("acro")
+acro_init(suppress = TRUE)
 ```
 
+This will create a virtual environment and install the required Python packages if they are missing.
+
 ## 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).
+If you are having problems installing the package, please see the simplified steps above or check the [GitHub issues](https://github.com/AI-SDC/ACRO-R/issues).
 
 ## Verification