Updated docs

.Rbuildignore

@@ -12,3 +12,6 @@
 ^docs$
 ^doc$
 ^Meta$
+^CODE_OF_CONDUCT\.md$
+^tools$
+^vignettes/*\.md$

.github/workflows/pkgdown.yaml

@@ -41,15 +41,16 @@ jobs:
         Rscript -e "install.packages(c('matrixStats', 'RcppProgress', 'rpca', 'BiocManager'), repo = 'https://cloud.r-project.org/')"
         Rscript -e "BiocManager::install('sparseMatrixStats', ask = FALSE, update = FALSE)"
         # Clone `diffusr` package
-        git clone https://github.com/randef1ned/diffusr.git
-        R CMD INSTALL diffusr
+        # git clone https://github.com/randef1ned/diffusr.git
+        # R CMD INSTALL diffusr
+        Rscript -e "remotes::install_github('randef1ned/diffusr', upgrade = 'always')"
       
-    - name: Update docs
-      run: devtools::document()
-      shell: Rscript {0}
-
     - name: Build site
-      run: pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)
+      run: |
+        devtools::document()
+        devtools::load_all()
+        pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        pkgdown::build_reference(topics = 'random_walk')
       shell: Rscript {0}
 
     - name: Deploy to GitHub pages 🚀

.gitignore

@@ -60,5 +60,7 @@ src/*.dll
 Rcpp.pro
 Rcpp.pro.user
 *.autosave
-/doc/
+/doc/*.R
+/doc/*.html
+/doc/*.Rmd
 /Meta/

CODE_OF_CONDUCT.md

@@ -0,0 +1,134 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+

DESCRIPTION

@@ -15,7 +15,6 @@ Description: One paragraph description of what the package does
 License: GPL (>= 2)
 URL: https://github.com/randef1ned/labyrinth
 BugReports: https://github.com/randef1ned/labyrinth/issues
-biocViews: limma
 Imports: 
     checkmate,
     Matrix,

NAMESPACE

@@ -29,9 +29,7 @@ importFrom(checkmate,assert_string)
 importFrom(checkmate,check_numeric)
 importFrom(checkmate,test_atomic_vector)
 importFrom(checkmate,test_matrix)
-importFrom(diffusr,assert_dgCMatrix)
 importFrom(diffusr,hub.correction)
-importFrom(diffusr,is.dgCMatrix)
 importFrom(diffusr,normalize.stochastic)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)

NEWS.md

@@ -1,54 +1,54 @@
-# labyrinth v0.2.3
+## labyrinth v0.2.3
 
 * Added `predict()` function
 * Added several data
 * Bug fix
 
-# labyrinth v0.2.2
+## labyrinth v0.2.2
 
 * Added multi-threaded capability
 * Added random walk
 * Bug fix
 
-# labyrinth v0.2.1
+## labyrinth v0.2.1
 
 * Performance improvement
 * Bug fix
 
-# labyrinth v0.2.0
+## labyrinth v0.2.0
 
 * Rewrote all codes
 * Dropped robust z score
 * Applied Eigen and MKL
 
-# labyrinth v0.1.1
+## labyrinth v0.1.1
 
 * Bug fix
 
-# labyrinth v0.1.0
+## labyrinth v0.1.0
 
 * Bug fix
 
-# labyrinth v0.0.5
+## labyrinth v0.0.5
 
 * Bug fix
 * Remove stopword file
 
-# labyrinth v0.0.4
+## labyrinth v0.0.4
 
 * Bug fix
 * Added stopword file
 
-# labyrinth v0.0.3
+## labyrinth v0.0.3
 
 * Bug fix
 
-# labyrinth v0.0.2
+## labyrinth v0.0.2
 
 * Added Windows support
 * Added C++ version of robust z score
 
-# labyrinth v0.0.1
+## labyrinth v0.0.1
 
 * Initial submission
 

R/random_walk.R

@@ -65,8 +65,7 @@
 #' @importFrom checkmate assert_number assert_int assert_logical assert_numeric
 #'                       assert test_matrix check_numeric test_atomic_vector
 #' @importFrom methods as
-#' @importFrom diffusr normalize.stochastic hub.correction is.dgCMatrix
-#'                     assert_dgCMatrix
+#' @importFrom diffusr normalize.stochastic hub.correction
 #' @importFrom Rcpp sourceCpp
 #'
 #' @examples

README.md

@@ -1,3 +1,114 @@
-I am currently rewriting this R package
+# Labyrinth
+
+[![Current devel version: 0.2.3](https://img.shields.io/badge/devel%20version-0.2.3-blue.svg)](https://github.com/randef1ned/labyrinth)
+[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![License: GPL v2](https://img.shields.io/badge/License-GPL_v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/09b138b2fa9242229f081cd180f6fc91)](https://app.codacy.com/gh/randef1ned/labyrinth/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+[![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg)](https://makeapullrequest.com)
+[![Last commit](https://img.shields.io/github/last-commit/randef1ned/labyrinth.svg)](https://github.com/randef1ned/labyrinth/commits/master)
+[![Code size](https://img.shields.io/github/languages/code-size/randef1ned/labyrinth.svg)](https://github.com/randef1ned/labyrinth)
+
+Labyrinth is a human-inspired computational framework for personalized drug prioritization.
+
+## Introduction
+
+`labyrinth` is a computational framework designed at drug prioritization at both the population and individual levels. It integrates multiple sources of prior medical knowledge, including:
+
+- Clinical trial information.
+- Co-occurrence networks from literature citations.
+- Drug-target interactions.
+- Drug-indication importance.
+- Disease-drug distance.
+
+`labyrinth` emphasizes the importance of aligning computational models with intuitive human reasoning. Thus, it employs a human-like knowledge retrieval methodology to identify potential drug candidates for various diseases. `labyrinth` aims to strike a balance between predictive accuracy and model interpretability, as demonstrated by its robust performance across diverse diseases, evaluated using ROC-AUC metrics.
+
+![A simple schema of the labyrinth](man/figures/intro.jpg)
+
+
+## A notice on operating system compatibility
+
+I developed and tested `labyrinth` on Fedora Linux version 38 and 39. While this package does not contain any operating system-specific code, it has not been tested on other operating systems. In theory, `labyrinth` should work on other Unix-like operating systems as long as the required dependencies are installed.
+
+We recommended these dependencies to be installed:
+
+- **R (≥ 4.3.0)**: We developed this R package using R version 4.3.3.
+- **Python**: Python is required for drawing plots in demos. It is recommended to have Python and `seaborn` installed, as the `reticulate` package will use the system's Python installation.
+- **OpenMP**: This package uses OpenMP for parallelization and multithreading if OpenMP exists. Having OpenMP installed can significantly improve performance.
+- **Intel oneAPI Math Kernel Library (oneMKL)**: This library can further enhance mathematical performance, especially on Intel processors. oneMKL is not required but highly recommended.
+
+If you encounter any issues while running this package on other operating system, please open an [issue](https://github.com/randef1ned/labyrinth/issues).
+
+
+## Before installation
+
+Before installation, we recommended you install Intel oneAPI Math Kernel Library (oneMKL) to optimize the computational performance of linear algebra.
+
+Windows users can download oneMKL from [Intel's website](https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-download.html) and install it in the default directory. The default directory is: `C:\Program Files (x86)\Intel\oneAPI`.
+
+Debian and Ubuntu users can download oneMKL using apt in the non-free repo:
+
+``` bash
+# Install oneMKL version 2020.4.304-4
+sudo apt install intel-mkl-full
+```
+
+Or using the Intel repo:
+
+``` bash
+# Set up the repository and signed the entry
+wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
+| gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+# Update the package list
+sudo apt update
+# Install the latest oneMKL (version 2024.1)
+sudo apt install intel-oneapi-mkl
+```
+
+Fedora users can download oneMKL by using dnf:
+
+``` bash
+# Create dnf repository file
+tee > /tmp/oneAPI.repo << EOF
+[oneAPI]
+name=Intel® oneAPI repository
+baseurl=https://yum.repos.intel.com/oneapi
+enabled=1
+gpgcheck=1
+repo_gpgcheck=1
+gpgkey=https://yum.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+EOF
+sudo mv /tmp/oneAPI.repo /etc/yum.repos.d
+# Install the latest oneMKL (version 2024.0)
+sudo dnf install intel-oneapi-mkl
+```
+
+
+## Installation
+
+Install `labyrinth` using:
+
+``` r
+install.packages(c('devtools', 'BiocManager'))
+remotes::install_github("randef1ned/labyrinth")
+```
+
+Or you can download the pre-built binary packages from [Releases](https://github.com/randef1ned/labyrinth/releases).
+
+
+## Usage
+
+Load the package using `library(labyrinth)`. We provide a vignette for the package that can be called using: `vignette("labyrinth")`. Alternatively, you can view the online version on [website](https://labyrinth.yinchun.su/articles/labyrinth) or [GitHub](doc/labyrinth_knit.md). Basically that is all you have to know.
+
+[This documentation](doc/training_knit.md) contains information about the contents and the necessary information for training the model used in this project. The `tools/` folder contains all the code and scripts required for constructing your own model, so that you can understand the technical details. Besides, you can refer to [this documentation](doc/preface_knit.md) for the background and inspirations behind the overall workflow of `labyrinth.
+
+
+## Changelog
 
 Changelog: [see this](NEWS.md)
+
+<!--
+## Star history
+
+[![Star History Chart](https://api.star-history.com/svg?repos=randef1ned/labyrinth&type=Date)](https://star-history.com/#randef1ned/labyrinth&Date)
+-->

_pkgdown.yml

@@ -0,0 +1,3 @@
+url: https://labyrinth.yinchun.su
+template:
+  bootstrap: 5

doc/labyrinth_knit.md

@@ -0,0 +1,5 @@
+- [Introduction](#introduction)
+
+## Introduction
+
+ab