VeMoMoTo - Vector Movement Modelling Tools

“Vector movement modelling tools” is a collection of python packages aiming to model the movement of invasive species or disease vectors through road networks.

  • The package hybrid_vector_model provides the core functionality for the model.

  • The package lopaths contains an algorithm to identify locally optimal routes in road networks. These routes are used in the hybrid vector model.

  • The package ci_rvm contains an algorithm to identify profile likelihood confidence intervals. The algorithm is in particular used to assess the hybrid vector model.

  • The package vemomoto_core provides helpful tools required by the other packages.

Warning

This documentation and also parts of the software packages are still under construction. The API is not yet complete, and working examples are still to be addedd. Furthermore, some variables and methods may be renamed in future versions without notice, so be cautious with using this early version of the software.

Installation

The packages are available on the Python package index and can be installed via pip. The project includes some C extensions, which need to be compiled before they can be used. For Python 3.7 on 64-bit Windows, precompiled packages are available. If working on a different platform, a compiler will be required. If you are working with Anaconda on 64-bit Linux, you may satisfy this requirement via running

conda install gxx_linux-64
conda install cmake

If working on a 32-bit machine, replace the 64 with a 32. The VeMoMoTo packages have not been tested on Mac OS yet, but replacing gxx_linux-64 with clangxx_osx-64 should work. See the Anaconda documentation for details.

To install all VeMoMoTo packages via pip, run

pip install vemomoto

Installation instructions for individual packages can be found on the corresponding subpages.

The optimizier for vector control included in this package depends on the commercial software MOSEK. If this software is not installed, a respective warning may be displayed upon import of the packages. For instructions on how to install MOSEK, and for the respective terms and conditions, refer to the MOSEK documentation. If working with Anaconda, you may use

conda install -c mosek mosek

Note

Some algorithms implemented in this package rely on share memory libraries that work on Unix systems only. If the vemomoto packages are to be applied to large sytems, it is strongly encouraged to execute the code on Linux, as some tasks are not implemented to run in parallel on Windows.

License and Referencing in Scientific Publications

This project is distributed under the the LGPL v3 license. Some of the packages are based on scientific publications. If you publish results obtained with the help of one of the packages in a scientific journal, please cite the corresponding papers. Links to the corresponding papers can be found on the respective subpages.

Bugs, Feature Requests, and Contributions

If you have found a bug or have a feature request, you may create a ticket on the project’s github page. You are also invited to fork and contribute to the project!

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