update webpages

.Rbuildignore

@@ -16,3 +16,4 @@ README.rst
 ^notebooks/
 man-roxygen
 ^\.github$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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: [devel]
+  pull_request:
+    branches: [devel]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+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@v3
+
+      - 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@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -16,3 +16,4 @@ vignettes/.build.timestamp
 doc
 vignettes/Bioconductor.sty
 vignettes/unsrturl.bst
+docs

DESCRIPTION

@@ -147,5 +147,5 @@ Suggests: agricolae,
  rappdirs
 VignetteBuilder: knitr
 biocViews: WorkflowStep, Metabolomics
-URL: https://github.com/computational-metabolomics/structToolbox
+URL: https://github.com/computational-metabolomics/structToolbox, https://computational-metabolomics.github.io/structToolbox/
 Roxygen: list(markdown = TRUE)

README.md

@@ -0,0 +1,44 @@
+# structToolbox
+
+An extensive set of data (pre-)processing and analysis methods and 
+tools for metabolomics and other omics, with a strong emphasis on statistics and 
+machine learning. 
+
+This toolbox allows the user to build extensive and 
+standardised workflows for data analysis. The methods and tools have been 
+implemented using class-based templates provided by the `struct` (<u>St</u>atistics 
+in <u>R</u> <u>U</u>sing <u>C</u>lass-based <u>T</u>emplates) package. 
+The toolbox includes pre-processing 
+methods (e.g. signal drift and batch correction, normalisation, missing value 
+imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, 
+Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and
+PLS, including cross-validation and permutation testing) as well as machine 
+learning methods (e.g. Support Vector Machines). The 
+STATistics Ontology (STATO) has been integrated and implemented to provide 
+standardised definitions for the different methods, inputs and outputs.
+
+## Installation
+
+To install this package:
+
+```
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("structToolbox")
+```
+
+To install the development version:
+
+```
+if (!require("remotes", quietly = TRUE))
+    install.packages("remotes")
+
+remotes::install_github("computational-metabolomics/structToolbox")
+```
+
+<!-- badges: start -->
+[![BioC version](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fbioconductor.org%2Fconfig.yaml&query=%24.release_version&label=Bioconductor)](http://www.bioconductor.org)
+[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/structToolbox.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/structToolbox)
+<!-- badges: end -->
+

_pkgdown.yml

@@ -0,0 +1,6 @@
+url: https://computational-metabolomics.github.io/structToolbox/
+template:
+  bootstrap: 5
+  bootswatch: flatly
+
+