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: ''
+
+---
+
+

CONTRIBUTING.md

@@ -0,0 +1,93 @@
+# 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 (clickable Windows interface)*
+- RangeShifter Batch Mode (command line interface)
+- the RangeShiftR 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 being rewritten, and is not open source yet.
+
+## Roles
+
+#### Maintainers
+
+- [@JetteReeg](https://github.com/JetteReeg): RScore repo and lead in R package
+- [@TheoPannetier](https://github.com/TheoPannetier): RScore repo and lead in batch mode
+
+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 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 significant changes to `main`, normally by merging `develop` into `main` to make newly developed features and bug fixes available to users, and marking a release while doing so.
+- `develop` is the development branch containing new, in-development features. It is the reference branch for all developers. Contributors may make small changes and bug fixes directly to `develop` but should ensure that new changes do not break the build. If one happens to break `develop`, it should be their top priority to fix it as this will disrupt the work of all other contributors.
+  Larger changes should instead be developed on feature branches.
+- Larger changes should be first developed on feature (e.g. `cmake`, `mutualism`, etc.) or contributor (e.g., `theo`) branches. Contributors are welcome to experiment and break such branches at any time, as this will not impact users or other contributors.
+
+  When progress is deemed satisfactory, changes can be brought to `develop`. Please open a pull request on GitHub, and assign at least one maintainer as a reviewer. As a pre-requisite, RangeShifter must build on the branch before merging. Please enter a descriptive title and use the description field to describe what you have changed. 
+
+  In the meantime, we encourage contributors to work in small and frequent commits, and to merge `develop` into their branch often to update their branch with newest changes.
+
+If you need a reminder on the main git commands related to committing and branching, head to the [Git cheatsheet](https://github.com/RangeShifter/RScore/blob/main/git_cheatsheet.md).
+
+## Contributing to the RangeShifter core code
+
+Any changes (issues, bugs, features) regarding the actual 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?tab=readme-ov-file#usage-git-subtree) section in the README). 
+
+Please check the [contributing guidelines for the RScore code](https://github.com/RangeShifter/RScore/blob/main/CONTRIBUTING.md). 
+
+## 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-package-dev/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:
+devtools::install_github("RangeShifter/RangeShiftR-pkg", ref="main", subdir="RangeShiftR")
+```
+
+## 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://raw.githubusercontent.com/RangeShifter/RangeShifter-software-and-documentation/master/RangeShifter_v2.0_UserManual.pdf) to understand the conceptual underpinnings of RangeShifter.
+
+Analogous to the RangeShifter GUI, 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-package-dev/blob/main/CONTRIBUTING.md)
+
+## See also
+
+-    [Compiled software and documentation](https://github.com/RangeShifter/RangeShifter-software-and-documentation)
+-    [RScore](https://github.com/RangeShifter/RScore), source for RangeShifter's core code
+-    [RangeShifter batch mode](https://github.com/RangeShifter/RangeShifter_batch_dev), 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

@@ -1,30 +1,31 @@
 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: 1.1.2
 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("Damaris", "Zurell", role = c("aut"))
 	)
-Date: 2021-08-04
+Date: 2025-09-26
 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
 RdMacros: Rdpack
 LinkingTo: Rcpp
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.3
 Collate: 
     'Rfunctions.R'
     'plotProbs.R'

RangeShiftR/NAMESPACE

@@ -19,7 +19,6 @@ export(SMSpathLengths)
 export(Settlement)
 export(Simulation)
 export(StageStructure)
-export(createODD)
 export(getLocalisedEquilPop)
 export(plotAbundance)
 export(plotOccupancy)

RangeShiftR/R/RangeShiftR.R

@@ -51,8 +51,8 @@ NULL
 
 # Show start-up message upon loading the package
 .onAttach <- function(libname, pkgname) {
-    packageStartupMessage("RangeshiftR version 1.0.4 (10.05.2022)\n",
-                          "Copyright (C) 2020-2022 Anne-Kathleen Malchow, Greta Bocedi, Stephen C.F. Palmer, Justin M.J. Travis, Damaris Zurell\n\n",
+    packageStartupMessage("RangeshiftR version 1.1.2 (26.09.2025)\n",
+                          "Copyright (C) 2020-2025 Anne-Kathleen Malchow, Greta Bocedi, Stephen C.F. Palmer, Justin M.J. Travis, Jette Wolff, Damaris Zurell\n\n",
                           "This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.\n",
                           "You are welcome to redistribute it and/or modify it under certain conditions;\n",
                           "type 'RangeShiftR_license()' for details.\n")
@@ -69,8 +69,8 @@ NULL
 #' @export
 RangeShiftR_license <- function ()
 {
-    cat("\nRangeshiftR version 1.0.4 (10.05.2022)\n")
-    cat("Copyright (C) 2020-2022 Anne-Kathleen Malchow, Greta Bocedi, Stephen C.F. Palmer, Justin M.J. Travis, Damaris Zurell\n\n")
+    cat("\nRangeshiftR version 1.1.2 (26.09.2025)\n")
+    cat("Copyright (C) 2020-2024 Anne-Kathleen Malchow, Greta Bocedi, Stephen C.F. Palmer, Justin M.J. Travis, Jette Wolff, Damaris Zurell\n\n")
     cat("This program is free software: you can redistribute it and/or modify\n")
     cat("it under the terms of the GNU General Public License as published by\n")
     cat("the Free Software Foundation, either version 3 of the License, or\n")