plant_vector_viruses

Species interactions affect the spread of vector-borne plant pathogens independent of transmission mode

Jan Medlock <jan.medlock@oregonstate.edu>, Department of Biomedical Sciences, Oregon State University, OR, USA;
David W. Crowder, Department of Entomology, Washington State University, WA, USA;
Jing Li, Department of Mathematics, California State University Northridge, CA, USA;
Elizabeth T. Borer, Department of Ecology, Evolution, and Behavior, University of Minnesota, MN, USA;
Deborah L. Finke, Division of Plant Sciences, University of Missouri, MO, USA;
Rakefet Sharon, MIGAL-Galilee Research Institute, Northern Research & Development, Israel;
David Pattemore, The New Zealand Institute for Plant & Food Research Limited, Hamilton, NZ.

Copyright 2015–2019, Jan Medlock et al. All rights reserved. Released under the GNU AGPL 3.

This repository contains code used to simulate and analyze the effects species interactions on the spread of vector-borne plant pathogens.

Crowder DW, Li J, Borer ET, Finke DL, Sharon R, Pattemore D, Medlock J. 2019. Species interactions affect the spread of vector-borne plant pathogens independent of transmission mode. Ecology. e02782. doi:10.1002/ecy.2782.

The scripts and model code are written in Python3, using some third-party libraries. See Python3, NumPy & SciPy, matplotlib, pandas, Seaborn, joblib, and ad.

Files

• Core
  • odes.py defines the model as a system of differential equations and functions for building initial conditions and solving the model.
  • parameters.py defines two baseline parameter sets, one for a persistent pathogen and one for a non-persistent pathogen.
  • common.py has common definitions and functions used by the analysis and plotting scripts.
• Analysis & plotting scripts
  • solutions.py plots model solutions vs. time for the two basic parameter sets.
  • growth_rates.py analyzes & plots the pathogen intrinsic growth rate vs. initial vector population size.
  • sensitivity_1param.py analyzes & plots the sensitivity of the pathogen intrinsic growth rate to the parameters, 1 parameter at a time.
  • sensitivity_2params.py analyzes & plots the sensitivity of the pathogen intrinsic growth rate to the parameters, 2 parameters at a time.
  • sensitivity_pairs.py analyzes & plots the sensitivity of the pathogen intrinsic growth rate to the parameters, for pairs of parameters that are linked to each other.