phytorisk

phytorisk is an R package developed to quantify the risk of invasion of the oomycete Phytophthora cinnamomi Rands (Pc hereafter). Pc is a pathogen that infects plant’s roots, and in many cases, kills the host. The dispersal of the pathogen depends on multiple factors, which are depicted in the next figure:

Potential mechanisms of dispersal of Pc

1. Movement of inoculum in the field due to diffusive root-to-root contact mec_rootcontact()

2. Inoculum movement to roots in water particles within soil mec_soilwater()

3. Dispersion of inoculum by domestic and wild animal movement mec_zoospread()

4. Inoculum spread in surface water mec_surfaceflow()

Installation

You can install the development version of phytorisk from GitHub with:

# install.packages("pak")
pak::pak("Cidree/phytorisk")

System requirements

phytorisk uses compiled code and requires Rtools on Windows. Download and install it from https://cran.r-project.org/bin/windows/Rtools/.

Non-CRAN dependencies

phytorisk depends on flowdem, which is not available on CRAN and must be installed manually beforehand:

pak::pak("KennethTM/flowdem")