DILiS-lab · vmeomeo · Jun 20, 2026 · Jun 19, 2026 · Jun 19, 2026 · Jun 19, 2026
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,11 +1,14 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.Rhistory
-^\.gitignore
-LICENSE
-README.md
-^\.DS_Store
+^\.Rhistory$
+(^|/)\.Rhistory$
+^\.gitignore$
+^\.github$
+LICENSE$
+README.md$
+^\.DS_Store$
 ^\.git$
-cran_comments.md
+cran_comments.md$
 ^doc$
 ^Meta$
+^\.old$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} / R ${{ matrix.config.r }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest, r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
diff --git a/.gitignore b/.gitignore
@@ -9,6 +9,15 @@ source/
 /.Rproj.user/*
 LoopDetectR.Rproj
 
+.Rhistory
+.Rproj.user/
+*.Rproj
+.DS_Store
+doc/
+Meta/
+*.tar.gz
+*.Rcheck/
+
 
 # Compiled source #
 ###################
@@ -40,6 +49,10 @@ __pycache__
 *.sql
 *.sqlite
 
+# Backup #
+######################
+old/
+
 # OS generated files #
 ######################
 .DS_Store

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: LoopDetectR
 Type: Package
 Title: Comprehensive Feedback Loop Detection in ODE Models
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: c(person("Katharina", "Baum", email = "katharina.baum@hpi.de",
                   role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7256-0566")), 
            person("Sandra", "Krüger", role = c("ctb")))
@@ -15,5 +15,7 @@ Encoding: UTF-8
 LazyData: true
 Depends: 
     R (>= 4.0.0)
-RoxygenNote: 7.1.0
+RoxygenNote: 7.3.3
 VignetteBuilder: knitr
+URL: https://github.com/DILiS-lab/LoopDetectR, https://cran.r-project.org/package=LoopDetectR
+BugReports: https://github.com/DILiS-lab/LoopDetectR/issues
diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,7 @@
+# LoopDetectR 0.1.3
+
+* Updated installation instructions from GitLab to GitHub.
+* Added GitHub repository and issue tracker links to DESCRIPTION.
+* Cleaned repository metadata and normalized text-file formatting.
+* Removed local development history files from the repository.
+* Added GitHub Actions checks for package validation.
diff --git a/R/data.R b/R/data.R
@@ -20,7 +20,7 @@
 #' Division Cycle of Caulobacter crescentus Stalked Cells. Plos Comput Biol. 
 #' 2008;4(1):e9. The solutions were generated with MATLAB using the
 #' functions accompanying the above reference on 
-#' \url{http://mpf.biol.vt.edu/research/caulobacter/SWST/pp/}.
+#' \doi{10.1371/journal.pcbi.0040009}.
 #' 
 "li08_solution"
 
@@ -59,7 +59,7 @@
 #' Li S, Brazhnik P, Sobral B, Tyson JJ. A Quantitative Study of the 
 #' Division Cycle of Caulobacter crescentus Stalked Cells. Plos Comput Biol. 
 #' 2008;4(1):e9. The function corresponds to the MATLAB function modelwtin(t,y)
-#' as given on \url{http://mpf.biol.vt.edu/research/caulobacter/SWST/pp/}.
+#' as given on \doi{10.1371/journal.pcbi.0040009}.
 #' 
 #' @details
 #' The Caulobacter cell cycle model function will only give the solution as 

diff --git a/README.md b/README.md
@@ -1,5 +1,17 @@
 # LoopDetectR: An R package for comprehensive detection of feedback loops in ODE models
 
+<p align="center">
+  <a href="https://github.com/DILiS-lab/loopdetect">
+    <img src="https://img.shields.io/badge/Python-implementation-3776AB?style=for-the-badge&logo=python&logoColor=white" alt="Python implementation">
+  </a>
+  <a href="https://github.com/DILiS-lab/LoopDetectR">
+    <img src="https://img.shields.io/badge/R-implementation-276DC3?style=for-the-badge&logo=r&logoColor=white" alt="R implementation">
+  </a>
+  <a href="https://github.com/DILiS-lab/loopdetect_for_matlab">
+    <img src="https://img.shields.io/badge/MATLAB-implementation-orange?style=for-the-badge&logo=mathworks&logoColor=white" alt="MATLAB implementation">
+  </a>
+</p>
+
 ## Scope of the package
 This package can be used to detect feedback loops (cycles, circuits) 
 between species in ordinary differential equation (ODE) models. These are paths from one node to itself without 
@@ -21,13 +33,17 @@ LoopDetectR is on CRAN [link](https://cran.r-project.org/web/packages/LoopDetect
 	# Load package
 	library("LoopDetectR")
 
-You can also install the package from gitlab. Call the following 
-commands in an R session. 
+You can also install the development version from GitHub. Call the following 
+commands in an R session.
 
-	# Install from gitlab
-	remotes::install_gitlab(kabaum/LoopDetectR, build_manual = TRUE, build_vignettes = TRUE)
-	# Load package
-	library("LoopDetectR")
+	# install.packages("remotes")
+	remotes::install_github(
+		"DILiS-lab/LoopDetectR",
+		build_manual = TRUE,
+		build_vignettes = TRUE
+	)
+
+	library(LoopDetectR)
 
 ## Workflow and documentation
 
@@ -37,7 +53,6 @@ A detailed workflow document can be found in the *vignettes* folder and as CRAN
 
 within an R session with installed and loaded LoopDetectR to obtain details on the function `find_loops`. For an overview of the functions, download the [reference manual](https://cran.r-project.org/web/packages/LoopDetectR/LoopDetectR.pdf).
 
-
 ## Licensing
 All code is licensed under the GNU GPLv3, LoopDetectR, Copyright (C) 2020  Katharina Baum.
 
diff --git a/cran_comments.md b/cran_comments.md
@@ -1,25 +1,26 @@
-##Resubmission v. 0.1.2
-This is a resubmission to the initial package version 0.1.1.
+##LoopDetectR v. 0.1.3
 
-Introduced changes
-* suppress installation of all packages in the vignette (I had overlooked one, sorry for that)
-* checked all examples in the help files: they do not install any package
+## Changes
 
-## Test environments for version 0.1.2
-* local OS X install (R 4.0.2, R-devel 2020-07-01 r78761)
-* win-builder (4.0.2, R-devel 2020-07-11 r788124)
+This is a maintenance release.
 
+* Updated installation instructions from GitLab to GitHub.
+* Updated repository links to point to `DILiS-lab/LoopDetectR`.
+* Removed local development history files from the source repository.
+* Added GitHub Actions checks for R CMD check.
 
 ## R CMD check results
-There were no ERRORs or WARNINGs. 
 
-* checking CRAN incoming feasibility ... NOTE
-Maintainer: ‘Katharina Baum <katharina.baum@hpi.de>’
-
-New submission
-This is correct, it is (the resubmission of) a new submission.
+0 errors | 0 warnings | 0 notes
 
+## Test environments
 
+* GitHub Actions: macOS-latest, R release
+* GitHub Actions: Windows-latest, R release
+* GitHub Actions: Ubuntu-latest, R devel
+* GitHub Actions: Ubuntu-latest, R release
+* GitHub Actions: Ubuntu-latest, R oldrel-1
 
 ## Downstream dependencies
+
 There are currently no downstream dependencies for this package.
diff --git a/man/func_li08.Rd b/man/func_li08.Rd
diff --git a/man/li08_solution.Rd b/man/li08_solution.Rd
diff --git a/vignettes/.Rhistory b/vignettes/.Rhistory
diff --git a/vignettes/workflow_LoopDetectR.Rmd b/vignettes/workflow_LoopDetectR.Rmd
@@ -22,13 +22,16 @@ LoopDetectR is on CRAN and can be installed within R by
 install.packages("LoopDetectR")
 ```
 
-Alternatively, you can install the package from gitlab. Call the following 
+Alternatively, you can install the package from GitHub. Call the following 
 commands in an R session. 
 
 ```{r install_fromgit, message=FALSE, results='hide', eval=FALSE}
 # Install the package including the vignette and the manual
-remotes::install_gitlab("kabaum/LoopDetectR", build_manual=TRUE, 
-                        build_vignettes = TRUE)
+remotes::install_github(
+  "DILiS-lab/LoopDetectR",
+  build_manual = TRUE,
+  build_vignettes = TRUE
+)
 
 ```