summarise_trace: Summarise a trace_asco output nested list as a single...

In IhsanKhaliq/ascotraceR: Simulate the Spread of Ascochyta Blight in Chickpea

Summarise a trace_asco output nested list as a single data.frame object

Description

Creates a paddock-level summary data.table from the output of trace_asco() on a daily time-step where each row represents one day for the entire paddock.

Usage

summarise_trace(trace)

summarize_trace(trace)

Arguments

trace

a nested list output from trace_asco()

Value

A data.table summarising the model's output for a paddock on a daily time-step with the area under the disease progress curve (AUDPC) at the paddock level for the simulation's run with the following columns:

i_day:	Model iteration day (day)
new_gp:	New growing points on i_day (n)
susceptible_gp:	Susceptible growing points on i_day (n)
exposed_gp:	Exposed growing points on i_day (n)
i_date:	Calendar date corresponding to model's i_day
day:	Julian day or numeric day of year (day)
cdd:	Cumulative degree days (day)
cwh:	Cumulative wet hours (h)
cr:	Cumulative rainfall (mm)
gp_standard:	standard growing points assuming growth is not impeded by infection on i_day (n)
AUDPC:	Area under the disease progress curve (AUDPC) for the duration of the model's run.

See Also

trace_asco(), tidy_trace()

Examples

Newmarracarra <-
   read.csv(system.file("extdata",
            "1998_Newmarracarra_weather_table.csv", package = "ascotraceR"))
station_data <-
   system.file("extdata", "stat_dat.csv", package = "ascotraceR")

weather_dat <- format_weather(
   x = Newmarracarra,
   POSIXct_time = "Local.Time",
   temp = "mean_daily_temp",
   ws = "ws",
   wd_sd = "wd_sd",
   rain = "rain_mm",
   wd = "wd",
   station = "Location",
   time_zone = "Australia/Perth",
   lonlat_file = station_data)

traced <- trace_asco(
  weather = weather_dat,
  paddock_length = 100,
  paddock_width = 100,
  initial_infection = "1998-06-10",
  sowing_date = "1998-06-09",
  harvest_date = "1998-06-30",
  time_zone = "Australia/Perth",
  primary_infection_foci = "centre")

summarised <- summarise_trace(traced)



Newmarracarra <-
   read.csv(system.file("extdata",
            "1998_Newmarracarra_weather_table.csv", package = "ascotraceR"))
station_data <-
   system.file("extdata", "stat_dat.csv", package = "ascotraceR")

weather_dat <- format_weather(
   x = Newmarracarra,
   POSIXct_time = "Local.Time",
   temp = "mean_daily_temp",
   ws = "ws",
   wd_sd = "wd_sd",
   rain = "rain_mm",
   wd = "wd",
   station = "Location",
   time_zone = "Australia/Perth",
   lonlat_file = station_data)

traced <- trace_asco(
  weather = weather_dat,
  paddock_length = 100,
  paddock_width = 100,
  initial_infection = "1998-06-10",
  sowing_date = as.POSIXct("1998-06-09"),
  harvest_date = as.POSIXct("1998-06-09") + lubridate::ddays(100),
  time_zone = "Australia/Perth",
  primary_infection_foci = "centre")

summarised <- summarise_trace(traced)

IhsanKhaliq/ascotraceR documentation built on May 22, 2022, 11:37 a.m.