This page provides additional information and tools related to the following paper:
Buddenhagen*, C. E., J. F. Hernandez Nopsa*, K. F. Andersen, J. Andrade-Piedra, G. A. Forbes, P. Kromann, S. Thomas-Sharma, P. Useche, and K. A. Garrett. 2017. Epidemic network analysis for mitigation of invasive pathogens in seed systems: Potato in Ecuador. Phytopathology 107: First Look: https://doi.org/10.1094/PHYTO-03-17-0108-FI.
Interactive interface for exploring epidemic behavior in the seed network
The following link goes to an interactive Shiny interface designed by Y. Xing, C. E. Buddenhagen, and K. A. Garrett, for exploring the potential for epidemic spread in the Ecuadorian potato seed system analyzed by Buddenhagen, Hernandez Nopsa et al (2017). Evaluating potential disease spread is the first step in evaluating the role of individual nodes for sampling or mitigating disease.
https://yanru-xing.shinyapps.io/INA_Conpapa
Selected R scripts
Code for analysis of key nodes in networks such as the CONPAPA seed system is available at
https://github.com/GarrettLab/INApreliminary
The above code is currently being updated
Illustration of application of exponential random graph models (ERGMs) is available through this [link] related to the following paper:
Garrett, K. A., R. I. Alcalá-Briseño, K. F. Andersen, C. E. Buddenhagen, R. A. Choudhury, J. C. Fulton, J. F. Hernandez Nopsa, R. Poudel, and Y. Xing. 2018. Network analysis: A systems framework to address grand challenges in plant pathology. Annual Review of Phytopathology 56: 559-580. [link]