Merging main into macros

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for RangeShifter
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/improve-existing-content.md

@@ -0,0 +1,10 @@
+---
+name: Improve existing content
+about: 'Make a suggestion to improve the R package '
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+

.github/workflows/r.yml

@@ -0,0 +1,50 @@
+name: Install Package
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  install:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        r: ['release']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.r }}
+          rtools-version: '44'
+
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
+        shell: bash
+
+      - name: Install pak (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          install.packages("pak", repos = "https://cran.r-project.org")
+        shell: Rscript {0}
+
+      - name: Install pak (macOS/Linux)
+        if: runner.os != 'Windows'
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/stable/")
+        shell: Rscript {0}
+
+      - name: Install RangeShiftR
+        run: |
+          pak::pak("RangeShifter/RangeShiftR-pkg/RangeShiftR@${{ github.head_ref || github.ref_name }}")
+        shell: Rscript {0}

.gitignore

@@ -81,4 +81,8 @@ vignettes/*.pdf
 *.utf8.md
 *.knit.md
 
+# Test Scripts
+/Model/
+TestScript.R
+
 

CONTRIBUTING.md

@@ -0,0 +1,97 @@
+# The RangeShifter platform - An eco-evolutionary modelling framework
+
+## How to contribute
+
+Thank you for your interest in contributing to the RangeShifter platform. 
+In this document we will give you guidance on how to contribute to the RangeShifter project regarding issues, bug fixing and adding new features. We distinguish between contributing to the RangeShifter core code and the different interfaces - in this case the R package.
+
+## Repo structure
+
+![Rangeshifter repo structure](RangeShiftR/man/figures/RS_repos.png)
+
+RangeShifter is distributed with three user interfaces, each living in their own repo:
+
+- the [RangeShifter GUI](https://github.com/RangeShifter/RangeShifter_GUI) (clickable Windows interface)*
+- RangeShifter [Batch Mode](https://github.com/RangeShifter/RangeShifter_batch) (command line interface)
+- the [RangeShiftR](https://github.com/RangeShifter/RangeShiftR-pkg) package (R interface)
+
+All three share the same source code for the core simulation (i.e., the actual model), which lives in its own repo (RScore). Each of the interfaces keeps a copy of this core code in a subfolder called RScore, kept in sync with the RScore repo via a git subtree (see [Git subtree usage section](https://github.com/RangeShifter/RScore?tab=readme-ov-file#usage-git-subtree). 
+
+⚠️ If you wish to propose a change to the core code of the simulation, please do so *in the [RScore](https://github.com/RangeShifter/RScore) repo*, rather than in the RScore folder of either interface.
+
+*The RangeShifter GUI is currently not maintained and only available with RangeShifter v2.0.
+
+## Roles
+
+#### Maintainers
+
+- [@JetteReeg](https://github.com/JetteReeg): RScore repo and lead in R package
+
+Maintainers are responsible for coordinating development efforts and ensuring that RangeShifter keeps building continuously.
+
+#### Developers
+
+Regular contributors and members of the [RangeShifter development team](https://github.com/orgs/RangeShifter/people), including maintainers.
+
+#### Contributors
+
+Anyone who whishes to make changes to RangeShifter's code, including regular developers.
+
+## Branching policy
+
+![](RangeShiftR/man/figures/branches.png)
+
+This policy applies to RScore and all three RangeShifter interfaces.
+RangeShifter uses the following branching structure:
+
+- `main` is the default branch, where the stable releases live. Because it contains the version of RangeShifter that users normally interact with, it must be stable and build at all times.
+Only maintainers should make changes to `main`, either directly for small changes (e.g. typo fixes), or by merging `develop` into `main` for any larger change.
+- `develop` is the development branch containing new features not yet made available to users.
+Contributors are welcome to make changes to `develop`, but because this is the version that every contributor uses as a reference, one should ensure that new changes do not break `develop`.
+If one happens to break `develop`, it should be their first priority to fix it.
+For this reason, we recommend working from feature branches instead.
+- Feature branches are created from `develop` by contributors to work on a new feature or other change, e.g. `cmake`, `mutualism`, etc. 
+Contributors can also create their own branch, e.g. `theo` or `jette` to experiment with the code or implement miscellaneous changes.
+Once a contributor deems their changes ready to be added to the development version, they should merge their changes from the feature branch into `develop`.
+Optionally, we encourage contributors to seek a review from one or more developers and or maintainers by opening a pull request to merge their branch into develop.
+
+### Contributing to RangeShifter core code
+
+Any changes regarding the RangeShifter core code should be done in [this](https://github.com/RangeShifter/RScore) repository and can afterwards be synced with all interfaces using the git subtree feature (see [Git subtree](https://github.com/RangeShifter/RScore/tree/main#usage-git-subtrees) section in the README).
+
+#### Bugs
+
+To report a bug, please [open an issue](https://github.com/RangeShifter/RangeShiftR-pkg/issues/new), using the Bug Report template. 
+Please do check if a related issue has already open on one of the other interfaces ([here](https://github.com/RangeShifter/RangeShifter_batch/issues) for the batch interface).
+To propose a bug fix (thank you!!), please create and work on your own branch or fork, from either `main` or `develop` (preferred), and open a pull request when your fix is ready to be merged into the original branch.
+
+
+
+### Contributing to the RangeShiftR package
+
+Please follow these guidelines for issues, bugs or new features related to the RangeShiftR-package. 
+
+#### Issues and bugs
+
+Issues should be used for reporting technical problems and bugs with the R package or suggest improvements e.g. in the documentation. 
+General and more conceptual questions regarding the application and settings of RangeShifter parameters should be asked in the [discussion forum](https://github.com/RangeShifter/RangeshiftR-tutorials/discussions) and answered by the broader RangeShifter community.
+
+#### Create a new issue
+
+If you encounter a technical problem, find a bug related to the RangeShiftR package or would like to suggest an improvement to the R package, please search if [a related issue already exists](https://github.com/RangeShifter/RangeShiftR-package-dev/issues). If you can't find a related issue, you can open a new issue using a relevant [issue form](https://github.com/RangeShifter/RangeShiftR-pkg/issues/new/choose). To propose a bug fix (thank you!!), please create and work on your own branch or fork, from either `main` or `develop` (preferred), and open a pull request when your fix is ready to be merged into the original branch.
+
+As a prerequisite for merging, please ensure that the R package is build correctly. GitHub Action will soon be used for ensuring a successfull build of the R package interface on all operating systems (i.e. R CMD CHECK needs to run without warnings).
+
+Maintainers will review the pull request, possibly request changes, and eventually integrate the bug fix into the RangeShiftR package. 
+
+### New feature
+
+Do you have an idea of a new feature in the RangeShiftR package that should be integrated and is of use for other RangeShiftR users? 
+Please get in touch with the RangeShifter development team directly (rangeshiftr@uni-potsdam.de) to discuss a collaboration.
+
+⚠️ We advise to contact the developer team as early as possible if you plan on implementing a new feature of the R package interface. This could prevent simultaneous development of the same feature and coordinate potential joint development.
+
+Alternatively, proceed as with the bug fix above: create your own branch _from `develop`_ and work from there, and submit a pull request when your new features are ready to join the core code. 
+We recommend that you update your branch regularly to new changes on `develop` (using `git merge develop`) to reduce the risk of merge conflicts or your version getting out-of-touch in the late stages of development.
+We also recommend that you work in small commits, as this makes the code easier to debug, and makes it easier for maintainers to understand your contributions when reviewing a pull request.
+

LICENSE

@@ -1,7 +1,7 @@
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
@@ -645,7 +645,7 @@ the "copyright" line and a pointer to where the full notice is found.
     GNU General Public License for more details.
 
     You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 Also add information on how to contact you by electronic and paper mail.
 
@@ -664,11 +664,11 @@ might be different; for a GUI interface, you would use an "about box".
   You should also get your employer (if you work as a programmer) or school,
 if any, to sign a "copyright disclaimer" for the program, if necessary.
 For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
+<https://www.gnu.org/licenses/>.
 
   The GNU General Public License does not permit incorporating your program
 into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.md

@@ -1,3 +1,69 @@
-# RangeshiftR
+# RangeShiftR <img src="RangeShiftR/man/figures/RSRlogo.png" align="right" height = 150/>
 
-R-package that provides interface to RangeShifter simulation software
+The RangeShiftR package implements the RangeShifter simulation platform for R.
+
+[RangeShifter](https://rangeshifter.github.io/)
+is a state-of-the-art eco-evolutionary modelling platform that is becoming 
+increasingly used worldwide for both theoretical and applied purposes
+[(Bocedi et al. 2014)](https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12162).
+
+RangeShifter is a spatially-explicit, individual-based simulation platform that 
+allows modelling species’ range dynamics, such as expansion and shifting, and 
+patch connectivity by linking complex local population dynamics and dispersal 
+behaviour, while also taking into account inter-individual variability and 
+evolutionary processes. RangeShifter is highly flexible in terms of the spatial 
+resolution and extent, and regarding the complexity of the considered ecological 
+processes. Due to its modular structure, the level of detail in demographic and 
+dispersal processes can be easily adapted to different research questions and 
+available data.
+
+
+## Installation
+
+RangeShiftR is only available from this github repository.
+(It may move to CRAN in the future.)
+
+RangeShiftR has to be built from source and requires the package `Rcpp` as
+well as a functional C++ compiler toolchain.
+
+```r
+# Install RangeShiftR from GitHub:
+pak::pak("RangeShifter/RangeShiftR-pkg/RangeShiftR@main")
+```
+
+## Usage and help
+
+Please refer to our [website](https://rangeshifter.github.io/) for more information about RangeShifter simulation 
+platform. RangeShifter is accompanied by extensive documentation. 
+
+For getting acquainted with the software, we recommend to first read the [manual](https://github.com/RangeShifter/RangeShifter-documentation-and-tutorial/blob/master/RangeShifter_v3.0_UserManual.pdf) to understand the conceptual underpinnings of RangeShifter.
+
+Analogous to the RangeShifter GUI and batchmode, we provide [tutorials](https://rangeshifter.github.io/RangeshiftR-tutorials/) to learn the different features of RangeshiftR using example applications from Bocedi et al. (2014, 2021) and Malchow et al. (2021). These cover some of the main features of RangeShifter, and help becoming familiar with the software.
+
+If you have any further question related to the general concepts and usage of RangeShifter, please browse earlier topics in the [forum pages](https://github.com/RangeShifter/RangeshiftR-tutorials/discussions) or add a new one. Often it is also helpful to review [published studies](https://rangeshifter.github.io/site/references/) using the RangeShifter modelling platform.
+
+For technical questions related to the RangeShiftR package interface and which cannot be answered with the documentation provided above, please browse the [issues section](https://github.com/RangeShifter/RangeShiftR-package-dev/issues) of this repository and open a new issues if required. We also offer *technical support* for the RangeShiftR package via mail (rangeshiftr@uni-potsdam.de) if you follow the guidelines of how to ask for help, e.g. guidelines given by [StackOverflow](https://stackoverflow.com/help/how-to-ask):
+
+## Contributing
+
+See [Contributing guidelines](https://github.com/RangeShifter/RangeShiftR-pkg/blob/main/CONTRIBUTING.md)
+
+## See also
+
+-    [Documentation and tutorials](https://github.com/RangeShifter/RangeShifter-documentation-and-tutorial)
+-    [RScore](https://github.com/RangeShifter/RScore), source for RangeShifter's core code
+-    [RangeShifter batch mode](https://github.com/RangeShifter/RangeShifter_batch), source for the batch mode interface
+
+## Maintainer
+
+- [@JetteReeg](https://github.com/JetteReeg)
+
+## References
+
+ - Bocedi G, Palmer SCF, Pe’er G, Heikkinen RK, Matsinos YG, Watts K, Travis JMJ (2014). 
+ *RangeShifter: A Platform for Modelling Spatial Eco-Evolutionary Dynamics and 
+ Species’ Responses to Environmental Changes.* Methods in Ecology and Evolution 5: 388–96. 
+
+ - Bocedi G, Palmer SCF, Malchow AK, Zurell D, Watts K, Travis JMJ (2021) RangeShifter 2.0: An extended and enhanced platform for modelling spatial eco-evolutionary dynamics and species’ responses to environmental changes. Ecography 44:1453-1462.
+
+ - Malchow AK, Bocedi G, Palmer SCF, Travis JMJ, Zurell D (2021) RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and species’ responses to environmental change. Ecography 4: 1443-1452.

RangeShiftR/DESCRIPTION

@@ -1,31 +1,38 @@
 Package: RangeShiftR
 Type: Package
 Title: An R package for individual-based simulation of spatial eco-evolutionary dynamics and species' responses to environmental changes
-Version: 1.0.4
+Version: 3.0.1
 Authors@R: c(
 	person("Anne-Kathleen", "Malchow", email = "rangeshiftr@uni-potsdam.de", role = c("aut", "cre")),
 	person("Greta", "Bocedi", role = c("aut")),
 	person("Stephen C.F.", "Palmer", role = c("aut")),
 	person("Justin M.J.", "Travis", role = c("aut")),
+	person("Jette", "Wolff", role= c("aut")),
+	person("Théo", "Pannetier", role=c("aut")),
+	person("Roslyn", "Henry", role=c("aut")),
 	person("Damaris", "Zurell", role = c("aut"))
 	)
-Date: 2021-08-04
+Date: 2026-04-22
 URL: https://rangeshifter.github.io/RangeshiftR-tutorials/
 Description: RangeShiftR provides individual-based simulations of spatial eco-evolutionary dynamics. It is based on the C++ software RangeShifter, making it flexible and fast. RangeShiftR models the processes of demography, dispersal and evolution in an inter-dependent way, offering substantial complexity in the corresponding modelling choices. It is entirely open-source and aims to facilitate the application of individual-based and mechanistic modelling to eco-evolutionary questions.
 License: GPL-3
 Depends: R (>= 3.6)
-SystemRequirements: C++11
+SystemRequirements: C++20
 Imports: 
     Rcpp (>= 1.0.0),
-    raster (>= 3.0.0),
     Rdpack (>= 0.7),
     methods,
-    rmarkdown
+    rmarkdown,
+    terra,
+    RcppArmadillo
 RdMacros: Rdpack
-LinkingTo: Rcpp
+LinkingTo: 
+    Rcpp,
+    RcppArmadillo
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.3
 Collate: 
+    'class_ManagementParams.R'
     'Rfunctions.R'
     'plotProbs.R'
     'class_InitialisationParams.R'