APSIM-Wheat module
wheatPhenology(
sim,
stages = 6,
stageNames = "flow",
model = "APSIM",
met = NULL,
daily = FALSE,
...
)The path to sim file.
The stages of outputs
The stage names of outputs
The model of Phenology. APSIM for default method in APSIM, V1 and V2 change the minimum function to multiple. V2 extend photoperiod effect of flowering
The weather data with weaana class.
whether output daily stages
Other arguments
met <- system.file("extdata/weather.met", package = "APSIMWheatPhenology")
sim <- system.file("extdata/example.sim", package = "APSIMWheatPhenology")
# Flowering time using parameter in the sim file
df <- wheatPhenology(sim, stages = 6, stageNames = 'flow', model = 'APSIM',
met = met, daily = FALSE)
head(df)
#> Name Number Latitude Longitude year sow_doy flow_doy flow_das
#> 1 DEMO Weather Site 2 0000002 -25 130 1981 105 189 84
#> 2 DEMO Weather Site 2 0000002 -25 130 1982 105 197 92
#> 3 DEMO Weather Site 2 0000002 -25 130 1983 105 192 87
#> 4 DEMO Weather Site 2 0000002 -25 130 1984 106 190 84
#> 5 DEMO Weather Site 2 0000002 -25 130 1985 105 191 86
#> 6 DEMO Weather Site 2 0000002 -25 130 1986 105 182 77
# Models V1 or V2 can be used
df <- wheatPhenology(sim, stages = 6, stageNames = 'flow', model = 'V1',
met = met, daily = FALSE)
head(df)
#> Name Number Latitude Longitude year sow_doy flow_doy flow_das
#> 1 DEMO Weather Site 2 0000002 -25 130 1981 105 219 114
#> 2 DEMO Weather Site 2 0000002 -25 130 1982 105 227 122
#> 3 DEMO Weather Site 2 0000002 -25 130 1983 105 222 117
#> 4 DEMO Weather Site 2 0000002 -25 130 1984 106 222 116
#> 5 DEMO Weather Site 2 0000002 -25 130 1985 105 226 121
#> 6 DEMO Weather Site 2 0000002 -25 130 1986 105 213 108
# Weather can be passed as a weaana object
met_data <- weaana::readWeatherRecords(met)
df <- wheatPhenology(sim, stages = 6, stageNames = 'flow', model = 'APSIM',
met = met_data, daily = FALSE)
head(df)
#> Name Number Latitude Longitude year sow_doy flow_doy flow_das
#> 1 DEMO Weather Site 2 0000002 -25 130 1981 105 189 84
#> 2 DEMO Weather Site 2 0000002 -25 130 1982 105 197 92
#> 3 DEMO Weather Site 2 0000002 -25 130 1983 105 192 87
#> 4 DEMO Weather Site 2 0000002 -25 130 1984 106 190 84
#> 5 DEMO Weather Site 2 0000002 -25 130 1985 105 191 86
#> 6 DEMO Weather Site 2 0000002 -25 130 1986 105 182 77
# Multiple stages can be calculated
df <- wheatPhenology(sim, stages = c(5.74, 6), stageNames = c("head", 'flow'),
model = 'APSIM',
met = met_data, daily = FALSE)
#> Warning: photoperiod existed, overwriting.
#> Warning: tempcr existed, overwriting.
#> Warning: dlt_tt existed, overwriting.
#> Warning: dlt_cumvd existed, overwriting.
head(df)
#> Name Number Latitude Longitude year sow_doy head_doy head_das
#> 1 DEMO Weather Site 2 0000002 -25 130 1981 105 179 74
#> 2 DEMO Weather Site 2 0000002 -25 130 1982 105 186 81
#> 3 DEMO Weather Site 2 0000002 -25 130 1983 105 180 75
#> 4 DEMO Weather Site 2 0000002 -25 130 1984 106 178 72
#> 5 DEMO Weather Site 2 0000002 -25 130 1985 105 181 76
#> 6 DEMO Weather Site 2 0000002 -25 130 1986 105 171 66
#> flow_doy flow_das
#> 1 189 84
#> 2 197 92
#> 3 192 87
#> 4 190 84
#> 5 191 86
#> 6 182 77
# Daily output can be exported
df <- wheatPhenology(sim, stages = c(5.74, 6), stageNames = c("head", 'flow'),
model = 'APSIM',
met = met_data, daily = TRUE)
#> Warning: photoperiod existed, overwriting.
#> Warning: tempcr existed, overwriting.
#> Warning: dlt_tt existed, overwriting.
#> Warning: dlt_cumvd existed, overwriting.
head(df)
#> Name Number Latitude Longitude year sow_doy das stage
#> 1 DEMO Weather Site 2 0000002 -25 130 1981 105 1 1.999000
#> 2 DEMO Weather Site 2 0000002 -25 130 1981 105 2 2.000000
#> 3 DEMO Weather Site 2 0000002 -25 130 1981 105 3 2.369374
#> 4 DEMO Weather Site 2 0000002 -25 130 1981 105 4 2.532852
#> 5 DEMO Weather Site 2 0000002 -25 130 1981 105 5 2.724591
#> 6 DEMO Weather Site 2 0000002 -25 130 1981 105 6 2.906765
# Multiple simulations can be specified in a factor
# Any parameters related with plant can be used
factors <- expand.grid(list(vern_sens = seq(1, 5), photop_sens = seq(1, 5)))
df <- wheatPhenology(sim, stages = c(5.74, 6), stageNames = c("head", 'flow'),
model = 'APSIM',
met = met_data, daily = FALSE,
factors = factors)
#> Warning: photoperiod existed, overwriting.
#> Warning: tempcr existed, overwriting.
#> Warning: dlt_tt existed, overwriting.
#> Warning: dlt_cumvd existed, overwriting.
head(df)
#> Name Number Latitude Longitude vern_sens photop_sens year
#> 1 DEMO Weather Site 2 0000002 -25 130 1 1 1981
#> 2 DEMO Weather Site 2 0000002 -25 130 2 1 1981
#> 3 DEMO Weather Site 2 0000002 -25 130 3 1 1981
#> 4 DEMO Weather Site 2 0000002 -25 130 4 1 1981
#> 5 DEMO Weather Site 2 0000002 -25 130 5 1 1981
#> 6 DEMO Weather Site 2 0000002 -25 130 1 2 1981
#> sow_doy head_doy head_das flow_doy flow_das
#> 1 105 171 66 180 75
#> 2 105 191 86 202 97
#> 3 105 229 124 238 133
#> 4 105 264 159 271 166
#> 5 105 280 175 286 181
#> 6 105 171 66 180 75