WofostR, tutorial
R implementation of Wofost crop simulation model
See De Wit et al. (2019) for details.
Python version available at ajdewit/pcse as part of the Python Crop Simulation Environment (PCSE/WOFOST).
Installation
Install with:
devtools::install_github('lucabutikofer/WofostR',
build_opts = c("--no-resave-data", "--no-manual"),
build_vignettes = T)
Testing
After installation is complete you can test the program with test().This command uses the files published by De Wit et al. downloading a copy from the WofostR_testData repository to test either a specific routine (e.g. test(component = "leafdynamics")) or all available components if none is specified. Currently only “astro”, “leafdynamics” and “potentialproduction” are implemented. Many routines are not independent funtions like in PCSE/WOFOST but are hardcoded within function Wofost(), which is run in the “potentialproduction” and “waterlimitedproduction” tests. Passing the “potentialproduction” or “waterlimitedproduction” tests means also passing “assimilation”, “astro”, “leafdynamics”, “partitioning”, “phenology”, “respiration”, “rootdynamics” and “transpiration” (although transpiration is not actually used to copute potential production).
By default only three test sets are randomly chosen to perform tests on. This is done to speed up the process. To perform tests on all available sets call test(complete = TRUE).
test(component = 'phenology', complete = TRUE)
test()
Input files
Four types of input files are required to run the Wofost():
- CropObjects
- WeatherObjects
- SoilObjects
- ManagerObjects
These are S4 classes containing the variables required by function Wofost(). Crop objects can be generated by calling dwn.crop() or load.crop() to download crops from the web or to load them from a local repository respectively. dwn.crop() retrieves specific crop parameters from ajwdewit/WOFOST_crop_parameters by specifying the crop and variety names. A list of corp and varieties names can be printed with cropVarList.
load.crop() works in a similar way as dwn.crop() but reads .yaml files saved in the local directory crLocal.
cr <- dwn.crop(cropName = "sugarbeet",
variety = "Sugarbeet_601")
cr
#>
#> WofostR Crop Object:
#> >> Crop name: sugarbeet
#> >> Variety name: Sugarbeet_601
#> >> 92 crop parameters out of 92 are specified.
#>
str(cr, list.len = 3)
#> Formal class 'CropObject' [package "WofostR"] with 92 slots
#> ..@ CROPNAME : chr "sugarbeet"
#> ..@ VARNAME : chr "Sugarbeet_601"
#> ..@ CO2EFFTB : num [1:5, 1:2] 40 360 720 1000 2000 0 1 1.11 1.11 1.11
#> .. ..- attr(*, "dimnames")=List of 2
#> .. .. ..$ : NULL
#> .. .. ..$ : chr [1:2] "x" "y"
#> .. [list output truncated]
Weather objects must contain minimum and maximum temperature, radiation and latitude at daily time-steps starting from the day the model expected to start. An example weather object can be seen with randomWeather. WeatherObjects can be printed with the plot() function.
randomWeather
#>
#> WofostR Weather Object:
#>
#> >> From date: 2010-04-16
#> >> To date: 2010-12-31
#>
#> VARIABLES LENGTH
#> 1 @DAY 260
#> 2 @E0 260
#> 3 @ELEV 260
#> 4 @ES0 260
#> 5 @ET0 260
#> 6 @IRRAD 260
#> 7 @LAT 260
#> 8 @LON 260
#> 9 @RAIN 260
#> 10 @SNOWDEPTH 260
#> 11 @TEMP 260
#> 12 @TMAX 260
#> 13 @TMIN 260
#> 14 @VAP 260
#> 15 @WIND 260
str(randomWeather, list.len = 3)
#> Formal class 'WeatherObject' [package "WofostR"] with 15 slots
#> ..@ DAY : Date[1:260], format: "2010-04-16" ...
#> ..@ E0 : num [1:260] 0.292 0.307 0.303 0.345 0.332 0.295 0.288 0.333 0.369 0.439 ...
#> ..@ ELEV : num [1:260] 440 440 440 440 440 440 440 440 440 440 ...
#> .. [list output truncated]
plot(randomWeather, var = c('RAIN','TMIN'))
SoilObjects are used to compute water-limited production (Wofost(... , waterLimited = T)) and contain soil variables for a single location. An example weather object can be seen with randomSoil.
randomSoil
#>
#> WofostR Soil Object:
#> >> 14 soil parameters out of 14 are specified.
#>
str(randomSoil)
#> Formal class 'SoilObject' [package "WofostR"] with 14 slots
#> ..@ SMFCF : num 0.318
#> ..@ SM0 : num 0.415
#> ..@ SMW : num 0.151
#> ..@ CRAIRC: num 0.06
#> ..@ SOPE : num 10
#> ..@ KSUB : num 10
#> ..@ K0 : num 10
#> ..@ RDMSOL: num 60
#> ..@ IFUNRN: int 0
#> ..@ SSMAX : num 0
#> ..@ SSI : num 0
#> ..@ WAV : num 10
#> ..@ NOTINF: num 0
#> ..@ SMLIM : num 0.318
ManagerObjects are used to run a sequence of crops simulation in succession for the same location (e.g. a crop rotation or the same crop over multiple years). An example ManagerObject can be seen with exampleManager.
mo <- ManagerObject(
cropSequence = c(
'barley-Spring_barley_301',
'millet-Millet_VanHeemst_1988',
'maize-Grain_maize_201'),
sequenceStart = '2010/04/16',
sequenceFinish = '2012/01/01',
cropStartType = c('sowing', 'sowing', 'sowing'),
cropStartDate = c(NA, '2011/04/16', NA),
cropFinish = c('maturity','2011/05/16','maturity'),
spacing = c(0, NA, 10 )
)
mo
#>
#> WofostR Manager Object:
#> >> Starting sequence: 2010/04/16
#> >> Finishing sequence: 2012/01/01
#> >> Crop rotation:
#>
#> Crops Start_types Start_dates Finish
#> [1,] barley-Spring_barley_301 sowing <NA> maturity
#> [2,] millet-Millet_VanHeemst_1988 sowing 2011/04/16 2011/05/16
#> [3,] maize-Grain_maize_201 sowing <NA> maturity
#> Spacing
#> [1,] 0
#> [2,] <NA>
#> [3,] 10
Running Wofost
Wofost crop simulation model is run by functions Wofost(). Potential Production and Free Draining water-limited production are called by setting variable waterLimited to FALSE or TRUE respectively.
# Run Potential Production
outPP <- Wofost(crop = dwn.crop(), w = randomWeather)
# Run Water-Limited Production
outFD <- Wofost(crop = dwn.crop(), w = randomWeather, soil = randomSoil,
waterLimited = TRUE)
plot(outFD)
# Run crop rotation with ManagerObject
outMN <- Wofost(w = randomWeatherLong, manager = exampleManager)
plot(outMN, var = 'tagp')
Available Crops and Varieties
| crop | variety |
|---|---|
| barley | Spring_barley_301 |
| cassava | Cassava_VanHeemst_1988 |
| chickpea | Chickpea_VanHeemst_1988 |
| cotton | Cotton_VanHeemst_1988 |
| cowpea | Cowpea_VanHeemst_1988 |
| fababean | Faba_bean_801 |
| groundnut | Groundnut_VanHeemst_1988 |
| maize | Maize_VanHeemst_1988 |
| maize | Grain_maize_201 |
| maize | Grain_maize_202 |
| maize | Grain_maize_203 |
| maize | Grain_maize_204 |
| maize | Grain_maize_205 |
| millet | Millet_VanHeemst_1988 |
| mungbean | Mungbean_VanHeemst_1988 |
| pigeonpea | Pigeonpea_VanHeemst_1988 |
| potato | Potato_701 |
| potato | Potato_702 |
| potato | Potato_703 |
| potato | Potato_704 |
| rapeseed | Oilseed_rape_1001 |
| rapeseed | Oilseed_rape_1002 |
| rapeseed | Oilseed_rape_1003 |
| rapeseed | Oilseed_rape_1004 |
| rice | Rice_501 |
| rice | Rice_HYV_IR8 |
| rice | Rice_IR64616H_DS |
| rice | Rice_IR64616H_WS |
| rice | Rice_IR64 |
| rice | Rice_IR72 |
| rice | Rice_IR72_DS |
| rice | Rice_IR72_WS |
| rice | Rice_IR8A |
| sorghum | Sorghum_VanHeemst_1988 |
| soybean | Soybean_901 |
| soybean | Soybean_902 |
| soybean | Soybean_903 |
| soybean | Soybean_904 |
| soybean | Soybean_905 |
| soybean | Soybean_906 |
| soybean | Soybean_VanHeemst_1988 |
| sugarbeet | Sugarbeet_601 |
| sugarbeet | Sugarbeet_602 |
| sugarbeet | Sugarbeet_603 |
| sugarbeet | Sugarbeet_604 |
| sugarcane | Sugarcane_VanHeemst_1988 |
| sunflower | Sunflower_1101 |
| sweetpotato | Sweetpotato_VanHeemst_1988 |
| tobacco | Tobacco_VanHeemst_1988 |
| wheat | Winter_wheat_101 |
| wheat | Winter_wheat_102 |
| wheat | Winter_wheat_103 |
| wheat | Winter_wheat_104 |
| wheat | Winter_wheat_105 |
| wheat | Winter_wheat_106 |
| wheat | Winter_wheat_107 |