viticolR

A mechanistic compartment model to assist in fungicide decision support for downy mildew (Plasmodia viticola) infections in grapevines. This model is translated and adapted from A mechanistic model simulating primary infections of downy mildew in grapevine by Vittorio Rossi, Tito Caffi, Simona Giosue and Riccardo Bugiani. This paper was first published in Ecological Modelling in 2008.

Getting started

Installing the package

Install the R package and dependency (epiphytoolR) from github using the following code

remotes::install_github("https://github.com/PaulMelloy/epiphytoolR")
remotes::install_github("https://github.com/PaulMelloy/viticolR")

Format weather data

The model only requires clean weather data formatted with epiphytoolR::format_weather() function. The package contains a clean dataset nt_weather which is already formatted using this method. See example code for how to format weather data from BOM sources, including m=imputing missing weather data.

Running the model

NT_DMod <- estimate_DM_PI(nt_weather)

Inspecting model output

Return a summary of the model

summary(NT_DMod)

Get a formatted table output of each state variable

get_PI_dates(NT_DMod)

Plot model progress

Plot weather data

plot_weather(NT_DMod)

Plot oospore cohort progress

ggplot2::ggplot() +
  geom_line_viticolR(v_mod)

Add a ribbon layer to show when sporangia have fully matured and dispersal is possible

ggplot2::ggplot() +
  geom_line_viticolR(NT_DMod)+
  geom_ribbon_viticolR(NT_DMod)+
  ggplot2::ylim()