R/summarise_trace.R
summarise_trace.RdCreates 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.
summarise_trace(trace)
summarize_trace(trace)a nested list output from trace_asco()
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. |
if (FALSE) { # interactive()
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)
}
if (FALSE) { # interactive()
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)
}