fixing issue with documentation initial setup

run build

.Rbuildignore

@@ -3,8 +3,8 @@
 debug
 .Rcheck
 ..Rcheck
-^vignettes/PredomicsPlotting\.Rmd$
-^vignettes/vignette\.Rmd$
+^vignettes$
+^vignettes_disabled$
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$

.github/workflows/pkgdown.yaml

@@ -45,4 +45,4 @@ jobs:
         with:
           clean: false
           branch: gh-pages
-          folder: docs
+          folder: pkgdown

.gitignore

@@ -9,6 +9,5 @@ vignettes/*_cache
 #NAMESPACE
 Profiling_*
 *.yml
-man/
 debug
 pkgdown

docs/Authors.md

@@ -0,0 +1,14 @@
+# Authors
+
+Predomics was created by:
+
+-   **Edi Prifti**: Edi is the creator and maintainer of the `predomics` approach and package since 2015. He has proposed the genetic algorithm approaches (`TerGa1` and `TerGa2`), the concept of the Family of Best Models, numérous visuzalization tools and lots of other cool ideas.
+-   **Jean-Daniel Zucker**: Jean-Daniel has brought numerous founding ideas behind the method since 2015. He has also proposed the beam search heuristic (`TerBeam`) and has co-led the work.
+-   **Yann Chevaleyre**: Yann was involved in the initial developments and has worked on the concepts of balances and the mathematical optimization method (`TerDa`).
+-   **Blaise Hanczar**: Blaise was also involved in the initial developments and has contributed notably to the selection of the best models and other general ideas behind the framework.
+-   **Eugeni Belda**: Eugeni joined the project in 2019 and has brought his contribution in the interpretability of the signatures, notably applied to the human microbiome as well as their visualization. He has also extensively tested the package using a plethora of datasets.
+-   **Lucas Robin**: Lucas, joined the project in 2016 as part of a student project and has worked on the implementation of the `TerGa2` algorithm and has brought some code optimization elements.
+-   **Shasha Cui**: Shasha also joined the project as part of a student internship in 2017. Her work focused on the concepts of feature importance.
+-   **Magali Cousin Thorez**: Magali joined the project in 2019 during her a student internship. Her work focused on the simplification of the classification signatures and their exploration on the context of microbial ecosystems.
+-   **Youcef Sklab**: Youcef has co-led with Edi a couple student projects in collaboration with the ![Sup Galilée engineering school](https://www.sup-galilee.univ-paris13.fr) to build the R Shiny predomicsapp application.
+-   **Gaspar Roy**: Gaspar has worked on 2023 on on evolved version of the R shiny application ![predomicsapp](https://predomics.ummisco.ioit).

docs/Contact.md

@@ -0,0 +1,6 @@
+# Contact
+
+If you have any questions or feedback, please contact us at:
+
+-   Email: [contact\@predomics.com](mailto:[email protected]){.email}
+-   GitHub Issues: [Predomics Issues](https://github.com/predomics/predomicspkg/issues)

docs/Contributing.md

@@ -0,0 +1,9 @@
+# Contributing to Predomics
+
+We welcome contributions to the Predomics project! Here’s how you can help:
+
+1. **Reporting Bugs**: Open an issue in the [GitHub Issue Tracker](https://github.com/predomics/predomicspkg/issues).
+2. **Suggesting Enhancements**: Have a feature in mind? Let us know by opening an issue.
+3. **Contributing Code**: Fork the repository, make your changes, and submit a pull request.
+
+Please make sure to follow our [Code of Conduct](CODE_OF_CONDUCT.md) and read the [development guidelines](docs/Development.md) before contributing.

docs/FAQs.md

@@ -0,0 +1,9 @@
+# Frequently Asked Questions
+
+**Q1: How do I install Predomics?**
+
+A1: Please refer to the [Installation](Installation.md) guide.
+
+**Q2: Where can I find examples on how to use Predomics?**
+
+A2: Check out the [Usage](Usage.md) and [Features](Features.md) sections for examples and detailed information.

docs/Features.md

@@ -0,0 +1,9 @@
+# Features
+
+Predomics offers a wide array of features:
+
+1. **Feature 1**: Description of Feature 1.
+2. **Feature 2**: Description of Feature 2.
+3. **Feature 3**: Description of Feature 3.
+
+Explore each feature to make the most out of Predomics.

docs/Installation.md

@@ -0,0 +1,21 @@
+# Installation
+
+Follow these steps to install the Predomics package:
+
+1.  Install R from [CRAN](https://cran.r-project.org/).
+2.  Install the predomics package along with all its dependencies : 
+    `doSNOW`, `foreach`, `snow`, `doRNG`, `gtools`, `glmnet`, `pROC`, `viridis`, `kernlab`, `randomForest`,`effsize`
+
+```
+devtools::install_github("predomics/predomicspkg", dependencies = TRUE)
+
+## install dependencies
+# install.packages(c("doSNOW", "foreach", "snow", "doRNG", "gtools", "glmnet", "pROC", "viridis", "kernlab", "randomForest","effsize"))
+# if (!requireNamespace("BiocManager", quietly = TRUE))
+#     install.packages("BiocManager")
+# BiocManager::install("BioQC")
+# install.packages("testthat")
+# install.packages("roxygen2")
+```
+
+Once eveything is installed un the check ...

docs/Screenshots.md

@@ -0,0 +1,9 @@
+# Screenshots
+
+Here are some screenshots to give you an overview of Predomics:
+
+![Screenshot 1](path/to/screenshot1.png)
+Caption for Screenshot 1.
+
+![Screenshot 2](path/to/screenshot2.png)
+Caption for Screenshot 2.

docs/Technologies.md

@@ -0,0 +1,8 @@
+# Technologies Used
+
+Predomics is built with the following technologies:
+
+- R
+- Other Libraries
+
+We chose these technologies for their ...

docs/Usage.md

@@ -0,0 +1,10 @@
+# Usage
+
+Here's how you can get started with Predomics:
+
+```         
+R
+library(predomics)
+result <- mainFunction(data)
+print(result)
+```