diff --git a/.Rbuildignore b/.Rbuildignore index e4c56a9..5dd9949 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -3,3 +3,7 @@ ^LICENSE\.md$ ^workflow$ ^assets$ +^_pkgdown\.yml$ +^docs$ +^pkgdown$ +^\.github$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..3d3caf0 --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,57 @@ +# 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: [main] # Add your test branch name here + pull_request: + release: + types: [published] + workflow_dispatch: + +name: pkgdown + +permissions: read-all + +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@v4 + + - 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: Copy assets to docs + run: | + if [ -d "assets" ]; then + mkdir -p docs/assets + cp -r assets/* docs/assets/ + fi + shell: bash + + - name: Deploy to GitHub pages 🚀 + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@v4.5.0 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.gitignore b/.gitignore index 0a80a09..f611cb9 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ .DS_Store .quarto permAprox_0.0.1.9000.tar.gz +docs diff --git a/DESCRIPTION b/DESCRIPTION index bd5ed5a..0fa3979 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,40 +1,47 @@ Package: DGrowthR Title: Bacterial Growth Curve Analysis -Description: A Comprehensive Toolset for Modelling of Bacterial Growth Curves via Gaussian Processes, Differential Testing and Empirical p-value Adjustment. -Author: Medina Feldl [aut, cre], - Roberto Olayo Alarcon [aut] -Maintainer: Medina Feldl +Description: A Comprehensive Toolset for Modelling of Bacterial Growth + Curves via Gaussian Processes, Differential Testing and Empirical + p-value Adjustment. +Authors@R: c( + person("Medina", "Feldl", email = "mail@medinabajramovic.de", + role = c("aut", "cre")), + person("Roberto", "Olayo Alarcon", email = "roberto.olayo@lmu.de", + role = "aut") + ) +URL: https://bio-datascience.github.io/DGrowthR/, https://github.com/bio-datascience/DGrowthR/ +BugReports: https://github.com/bio-datascience/DGrowthR/issues Version: 1.0 License: GPL-3 + file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.3.1 Imports: - methods, - tidyselect, - magrittr, - fdapace, + dbscan, dplyr, - tibble, - tidyr, - pracma, - stringr, - laGP, - ggplot2, - tools, - foreach, - snow, doSNOW, + fdapace, + foreach, + ggplot2, jsonlite, - methods, - utils, - dbscan, - stats, - uwot, + laGP, + magrittr, mclust, + methods, mvtnorm, + pracma, + purrr, readr, - purrr + snow, + stats, + stringr, + tibble, + tidyr, + tidyselect, + tidyverse, + tools, + utils, + uwot Depends: R (>= 2.10) LazyData: true diff --git a/README.Rmd b/README.Rmd deleted file mode 100644 index f307b7a..0000000 --- a/README.Rmd +++ /dev/null @@ -1,71 +0,0 @@ ---- -title: 'DGrowthR: A comprehensive workflow for growth curve analysis' -date: "Compiled on `r format(Sys.time(), '%Y-%m-%d %H:%M:%S', tz = 'UTC')`" -output: github_document ---- - - - -```{r setup, include = FALSE} -knitr::opts_chunk$set( - collapse = TRUE, - comment = "#>", - fig.path = "man/figures/README-", - out.width = "100%" -) -``` - -![](assets/Logo-DGrowthR.png) - - -This repository hosts the `DGrowthR` R package and the workflow for the detailed analysis of publicly available datasets mentioned in our pre-print. This workflow is designed to showcase the application of the `DGrowthR` package to model complex, non-linear dynamics of bacterial growth using Gaussian Process Regression. - -![](assets/dgrowthr_panel.png) - - - - - -## Installation Guide - -To install the `DGrowthR` R package directly from this repository. First make sure you clone the repository and enter into the cloned folder. Then you can execute the following commands in R. - -1. Ensure that you have the `devtools` package installed. If not, you can install it using the following command - -```{r install.devtools, eval=FALSE} - -# Install devtools -install.packages("devtools") - -# Load the library -library(devtools) -``` - - -2. Use the `install` function to install the `DGrowthR` package: -```{r install.dgrowthr, eval=FALSE} - -install() - -``` - - -## How to use `DGrowthR`. - -An overview of the main functionalities of `DGrowthR` with concrete examples can be found in our [tutorial vignette](https://github.com/bio-datascience/DGrowthR/blob/main/vignettes/DGrowthR.Rmd) - - -## Analysis workflow. - -Additionally, you see our analysis of publicly available datasets from the [Brochado 2018](https://www.nature.com/articles/s41586-018-0278-9) and [Brenzinger 2024](https://www.nature.com/articles/s41564-023-01556-y) studies. - -All steps are in our [workflow](https://github.com/bio-datascience/DGrowthR/tree/main/workflow) folder - - - - - - - - - diff --git a/README.md b/README.md index ed72138..d9b5735 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,7 @@ -DGrowthR: A comprehensive workflow for growth curve analysis -================ -Compiled on 2025-03-21 18:53:56 - ![](assets/Logo-DGrowthR.png) +# DGrowthR: A comprehensive workflow for growth curve analysis + This repository hosts the `DGrowthR` R package and the workflow for the detailed analysis of publicly available datasets mentioned in our pre-print. This workflow is designed to showcase the application of the @@ -12,7 +10,8 @@ growth using Gaussian Process Regression. ![](assets/dgrowthr_panel.png) -**For more details, check out our [pre-print](https://www.biorxiv.org/content/10.1101/2025.03.25.645164v2):** +> [!TIP] +> For more details, check out our pre-print [Statistical end-to-end analysis of large-scale microbial growth data with DGrowthR](https://www.biorxiv.org/content/10.1101/2025.03.25.645164v2) on bioRxiv. ## Installation Guide @@ -23,8 +22,7 @@ Then you can execute the following commands in R. 1. Ensure that you have the `devtools` package installed. If not, you can install it using the following command -``` r - +```r # Install devtools install.packages("devtools") @@ -34,8 +32,7 @@ library(devtools) 2. Use the `install` function to install the `DGrowthR` package: -``` r - +```r install() ``` diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..515218f --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,16 @@ +url: https://bio-datascience.github.io/DGrowthR/ +template: + bootstrap: 5 + light-switch: true + +navbar: + structure: + left: [intro, reference, biods] + right: [search, github, lightswitch] + components: + biods: + text: "BioDS" + href: https://bio-datascience.github.io/ + target: "_blank" + aria-label: "Bio Data Science" + icon: fa-arrow-up-right-from-square