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:
Movement of inoculum in the field due to diffusive root-to-root contact
mec_rootcontact()Inoculum movement to roots in water particles within soil
mec_soilwater()Dispersion of inoculum by domestic and wild animal movement
mec_zoospread()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")