INApreliminary

This is a preliminary version of the INA (impact network analysis) R package. For the current version, please see GarrettLab/INA

The following commands can be used to install and load the INApreliminary package in R

install.packages("devtools")

library(devtools)

devtools::install_github("GarrettLab/INApreliminary")

library(INApreliminary)

General references for impact network analysis

Garrett, K. A. 2021a. User guide to impact network analysis (INA). CGIAR Research Program on Roots, Tubers and Bananas (RTB). RTB User Guide. No. 2021-4. Lima, Peru. https://cgspace.cgiar.org/handle/10568/111326

Garrett, K. A. 2021b. Impact network analysis and the INA R package: Decision support for regional management interventions. Methods in Ecology and Evolution, in press. (Preprint version available at bioRxiv 2020.11.08.373621. https://www.biorxiv.org/content/10.1101/2020.11.08.373621v1)

Vignettes illustrating analyses in Garrett 2021b

Versions of these vignettes are also included in this depository as pdfs

V1. Identifying key sampling locations for smart surveillance using the smartsurv function. (Exp 1 in Garrett 2021b) Link: https://www.garrettlab.com/wp-content/uploads/2020/10/V1-smartsurv-function-Exp-1.pdf

V2. Smaller functions that can create system components for the INAscene function. Link: https://www.garrettlab.com/wp-content/uploads/2020/10/V2-components-of-INAscene-function.pdf 

V3. Evaluating the likelihood of project success in scenario analyses for regional management using the INAscene function. (Exp 2 in Garrett 2021b) Link: https://www.garrettlab.com/wp-content/uploads/2020/10/V3-INAscene-for-project-evaluation-Exp-2.pdf

V4. Evaluating potential adaptation plans for regional management under global change using the INAscene function. (Exp 3 in Garrett 2021b) Link: https://www.garrettlab.com/wp-content/uploads/2020/10/V4-INAscene-for-adaptation-planning-Exp-3.pdf

V5. How function speed scales with node number: V5 How function speed scales with node number. Link: https://www.garrettlab.com/wp-content/uploads/2020/10/V5-How-function-speed-scales-with-node-number.pdf

Examples of published applications

Andersen, K. F., C. E. Buddenhagen, P. Rachkara, R. Gibson, S. Kalule, D. Phillips, and K. A. Garrett. 2019. Modeling epidemics in seed systems and landscapes to guide management strategies: The case of sweetpotato in Northern Uganda. Phytopathology 109:1519-1532. Open access link: https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-03-18-0072-R

Andersen Onofre, K. F., G. A. Forbes, J. Andrade-Piedra, C. E. Buddenhagen, J. C. Fulton, M. Gatto, Z. Khidesheli, R. Mdivani, Y. Xing, K. A. Garrett. 2021. An integrated seed health strategy and phytosanitary risk assessment: potato in the Republic of Georgia. Agricultural Systems 191:103144. Open access link: https://www.sciencedirect.com/science/article/pii/S0308521X21000974

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 107:1209-1218. Open access link: https://apsjournals.apsnet.org/doi/10.1094/PHYTO-03-17-0108-FI