r.pops.spread

This is a GRASS GIS module r.pops.spread for simulating spread of pests and pathogens. The module is a GRASS GIS interface to the PoPS (Pest or Pathogen Spread) model implemented in C++ library maintained in the PoPS Core repository.

The purpose of the r.pops.spread module is to provide easy way of running the model in GRASS GIS environment once you have calibrated the model for your purposes. You can obtain the calibration from a colleague or published work or you can calibrate the model manually (in GRASS GIS) or use the R interface to PoPS called rpops to do that.

Note: Earlier versions of this module were called r.spread.pest and r.spread.sod.

How to cite

If you use this software or code, please cite the following paper:

Jones, C., Jones, S., Petrasova, A., Petras, V., Gaydos, D., Skrip, M., Takeuchi, Y., Bigsby, K., and Meentemeyer, R., 2021. Iteratively forecasting biological invasions with PoPS and a little help from our friends. Frontiers in Ecology and the Environment DOI: 10.1002/fee.2357

In case you are using the automatic management feature in rpops or the steering version of r.pops.spread (from the branch steering), please cite also:

Petrasova, A., Gaydos, D.A., Petras, V., Jones, C.M., Mitasova, H. and Meentemeyer, R.K., 2020. Geospatial simulation steering for adaptive management. Environmental Modelling & Software 133: 104801. DOI: 10.1016/j.envsoft.2020.104801

In addition to citing the above paper, we also encourage you to reference, link, and/or acknowledge specific version of the software you are using, for example:

We have used r.pops.spread GRASS module version 1.0.2 from https://github.com/ncsu-landscape-dynamics/r.pops.spread DOI: 10.5281/zenodo.5160179.

You can find the DOI for the specific version you are using at Zenodo.

Download

Download and install

The latest release of the r.pops.spread module is available in GRASS GIS Addons repository and can be installed directly in GRASS GIS through graphical user interface or using the following command:

g.extension r.pops.spread

Alternatively, you can obtain latest source code here and install it from this repository (see below).

Source code download

Just use Git, but note that the PoPS Core library is in a submodule, so use --recursive when cloning, for example:

git clone --recursive git@github.com:ncsu-landscape-dynamics/r.pops.spread.git

If you have already cloned, you can obtain the submodules using:

git submodule update --init

Note that downloading as ZIP won't include the source code for the submodule, so downloading as ZIP is not useful for this repo.

Contributing

Please see the pops-core repository for contributing best practices and release policies. Other than that, just open pull requests against this repo.

Updating submodule to latest version

To update the submodule, i.e. update submodule's commit used in this repository, use:

git submodule update --remote

Note that this change is recorded in the repository. In other words, the latest commit of a submodule is part of this repository. The reason for this is that the code in this repository is linked to a particular commit in the submodule repository (rather than the latest version). Git works this way to avoid breaking things unexpectedly due to changes in the submodule repository.

Updating the code of the submodule

cd pops-core
git switch -c new-feature-branch
git add file.hpp
git commit -m "this and that change"
git push

Then create a PR. After the PR is merged, then update the submodule and commit:

cd ..
git submodule update --remote
git commit pops-core -m "update to latest pops commit"
git push

The files

The main.cpp file contains the main program to run. The model is in pops-core/include/pops-core directory.

To run the model

You can use Linux to run the model in the following way.

Open an terminal and install dependencies:

sudo apt-get install grass grass-dev

Download this repo using Git (see above):

git clone ...

Change the current directory to the model directory:

cd ...

Compile:

grass --tmp-location XY --exec g.extension module=r.pops.spread url=.

Run (assuming you checked how to create a GRASS GIS mapset with our data):

grass .../modeling/scenario1 --exec r.pops.spread ...

Authors and contributors

Authors

(alphabetical order)

Chris Jones
Margaret Lawrimore
Vaclav Petras
Anna Petrasova

Previous contributors