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FIELD_software

FIELD: High-Resolution, US-scale Digital Similar of Interacting Livestock, Wild Birds, and Human Ecosystems for Multi-host Epidemic Spread

Code and data organization

The code is organized in folers corresponding to the major modules as defined in the paper:

  1. Livestock ./livestock,
  2. Wild birds ./wildbirds,
  3. Human population ./population,

In addition, we have a folder for

  1. Processing data ./data,
  2. Verification and validation ./vnv,
  3. Risk assessment ./risk

We have separate README.md files in each folder describing.

Some of the code was written to be run on a Linux/Unix high-performance computing cluster with SLURM job scheduling (https://www.rc.virginia.edu/userinfo/rivanna/overview/). It makes heavy use of parallelism, with pipeline inputs and outputs spread out across many files. If a SLURM cluster is available, complete with anaconda (or a similar python installation) and gurobipy, the code may be run as intended with slight adjustments.

Assume all commands below are run within a work directory so that scripts are not accidentally overwritten or deleted.