Table of Contents

• About the project
  • Built With
• Getting Started
  • Prerequisites
  • Installation
• Usage
• Roadmap
• Contributing
• License
• Contact
• Acknowledgements

About the project

XOffFieldSoil is a modular model that simulates processes at a landscape-scale and allows assessing potential effects of pesticide applications on off-field soil organisms. Its main features are:

• A modular structure that couples existing expert models like XDrift (spray-drift model based on Rautmann drift values) and RunOffPrzm (PRZM-based implementation of spatial run-off distribution) and that allows to flexibly replace or add further modules.
• A unified and consistent view on the environmental state of the simulated landscape that is shared among modules and available to risk-assessment.
• Data semantics that explicitly express values and their physical units at different spatial and temporal scales plus the ability of transient data transformations according to the requirements of used models.
• Computational scaling that allows to conduct Monte Carlo runs in different sizes of landscapes, ranging from small schematic setups to real-world landscapes.

Built with

XOffFieldSoil is composed of the following building blocks:

• The Landscape Model core that provides the base functionality for managing experiments and exchanging data in a landscape-scale context. See \model\core\README for further details.
• The AnalysisObserver that implements default assessments of simulations, including the output of maps, plots and tables. See \model\variant\AnalysisObserver\README for further details.
• RunOffPrzm, an PRZM-based implementation of spatial run-off distribution. See \model\variant\RunOffPrzm\README for further details.
• XDrift, a spray-drift model based on Rautmann drift values ( https://doi.org/10.1016/j.softx.2020.100610). See \model\variant\XSprayDrift\README for further details.
• An exemplary schematic landscape scenario consisting of a 100 m x 100 m habitat next to a 100 m x 100 m field. See \scenario\schematic-100x100\README for further details.
• Two R risk analysis scripts. See \model\variant\RiskAnalysis\README for further details.

Getting Started

XOffFieldSoil is portable and is tested to run on a range of hardware.

Prerequisites

XOffFieldSoil requires a 64-bit Windows to run.

Installation

From zipfile

If someone provides you with a zipped version of xOffFieldSoilRisk, simply extract the archive into a folder on your hard drive. Simulation data and temporary files will be written to a sub-folder of this folder, so a fast hard-drive with lots of available space is preferable.

From GitHub.com using Sourcetree

The newest stable version of xOffFieldSoilRisk can be found at GitHub.com. You can access the git repository with any git client, including command-line and graphical clients. The following is a step-by-step guide to retrieve a copy of xOffFieldSoilRisk using the graphical git client Sourcetree.

1. Download Sourcetree from the Atlassian website: https://www.sourcetreeapp.com/.
2. During setup of Sourcetree, you can skip the registration of a Bitbucket account. It is also not necessary to install the Mercurial tools. Under Preferences, provide your username and email address as they should appear in your commits to the git repository. When asked to load an SSH key, select "No".
3. After setting up, take the time to tweak some Sourcetree options under Tools > Options. Important options that are suggested to be changed are enabling of Perform submodule actions recursively in the Git tab and to make sure that an embedded git is used by pressing the Embedded button in the Git tab and confirming the download. The submodule recursive actions will make it easier to update the repository later on and the embedded git will make sure that you use a current git version that supports all necessary features.
4. After closing the Options dialog, switch to the Clone tab to finally clone the repository. Under Source Path / URL, type in the xOffFieldSoilRisk endpoint which is https://github.com/xlandscape/xOffFieldSoilRisk. After the input field looses focus, Sourcetree should indicate that This is a Git repository.
5. Under Destination Path, specify the folder on your computer where the repository should be cloned into. The Name field should be automatically filled out and equal the name of the folder where the repository is cloned into. The Local Folder is fixed to [Root]. Under Advanced Options, make sure that the Checkout branch is set to master to assure that you clone the latest stable version. Make sure that the option Recurse submodules is enabled to download the entire Landscape Model and not only part of its. Confirm everything by pressing the Clone button.
6. After cloning is finished, you can find your copy of the Landscape Model variant in the specified folder and can start using it.

Usage

1. Open the template.xrun in any text editor and modify the parameters for the simulation to your needs. The template.xrun contains in-line documentation to assist you in deciding for valid parameter values. Please check especially that the parameter <RunOffTempDir> points to an existing directory.
2. Save the modified template.xrun under a different name in the same directory, using a .xrun extension.
3. Drag and drop the saved parameterization file onto the __start__.bat.
4. Check the console window occasionally for successful conclusion of the simulation or for errors. Logfiles can be found under \run\<name-of-your-experiment>\log.
5. If the run was successful, you can find analysis results over the entire experiment under \run\<name-of-your-experiment>\analysis and for individual Monte Carlo runs under \run\<name-of-your-experiment>\mcs\<MC-identifier>\analysis.

Roadmap

XOffFieldSoil is under continuous development. Future versions will include further and updated models. Usage of ontologies for semantic description of data are planned.

Contributing

Contributions are welcome. Please contact the authors (see Contact).

License

XOffFieldSoil is distributed under the CC0 License. See the according LICENSE files for more information. WinPRZM that is used by the RunOffPrzm component is an established open access model widely used in regulatory science. Its precise license conditions are not known, and it is provided here with consent of the PRZM model development team of Waterborne Environmental Inc., Marty Williams, Amy Ritter, Gerco Hoogeweg, J Mark Cheplick as well as Gerald Reinken (Bayer AG).

Contact

Thorsten Schad - thorsten.schad@bayer.com Sascha Bub - sascha.bub@xlandscape.org

Acknowledgements

See READMEs of individual building blocks for acknowledgements of these parts. We thank the PRZM model development team of Waterborne Environmental Inc., Marty Williams, Amy Ritter, Gerco Hoogeweg, J Mark Cheplick as well as Gerald Reinken (Bayer AG) for its consent to distribute WinPRZM together with XOffFieldSoil.