Modify apsimx file

Several functions are designed to modify the apsimx file, including * replace an existing model * remove an existing model * append a new model as sibling node * insert a new model as child

Read apsimx file

read_apsimx is used to read files with apsimx json format, i.e. *.apsimx for simulations and *.json for model under resource.

 library(rapsimng)
wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
 #wheat <- read_apsimx("inst/Wheat.json")

Modify existing model

The existing model can be replaced and removed. The example below shows to update the critical thermal and then remove it.

 # Find the ThermalTime model 
a <- search_path(wheat, '[Wheat].Phenology.ThermalTime')
a$node$Children[[1]]$X[[2]]
 #> [1] 26
 # Update the optimum temperature
a$node$Children[[1]]$X[[2]] <- 27
 # Replace with new value
wheat_new <- replace_model(wheat, a$path, a$node)
b <- search_path(wheat_new, '[Wheat].Phenology.ThermalTime')
 # The optimum temperature should be updated now
b$node$Children[[1]]$X[[2]]
 #> [1] 27
 
 # The ThermalTime model can also be removed
a <- search_path(wheat, '[Wheat].Phenology.ThermalTime')
wheat_new <- remove_model(wheat, a$path)
b <- search_path(wheat_new, '[Wheat].Phenology.ThermalTime')
 # The ThermalTime model should not be found now (i.e. Empty list)
b
 #> list()

Create new model

Function new_model is used to generate the required elements for a new model, e.g. createing a new cultivar Hartog

new_cultivar <- new_model("PMF.Cultivar", name = "Hartog")
new_cultivar
 #> $`$type`
 #> [1] "Models.PMF.Cultivar, Models"
 #> 
 #> $Name
 #> [1] "Hartog"
 #> 
 #> $Children
 #> list()
 #> 
 #> $IncludeInDocumentation
 #> [1] TRUE
 #> 
 #> $Enabled
 #> [1] TRUE
 #> 
 #> $ReadOnly
 #> [1] FALSE
 #> 
 #> $Alias
 #> list()
 #> 
 #> $Command
 #> list()

Then the Command can be updated to specify new parameter values.

new_cultivar$Command <- list(
 "[Phenology].MinimumLeafNumber.FixedValue = 6",
 "[Phenology].VrnSensitivity.FixedValue = 0")

Finally the new cultivar can be inserted into apsimx file.

 # Read the apsimx file
wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
 # Create a new Replacements
replacements <- new_model("Core.Replacements")
 # Insert the replacements into root folder
wheat_new <- insert_model(wheat, 1, replacements)
replacements_node <- search_path(wheat_new, ".Simulations.Replacements")
replacements_node$path
 #> [1] 1 3
 
 # Insert the new cultivar
wheat_new <- insert_model(wheat_new, replacements_node$path, new_cultivar)
 
 # Check the new cultivar
cultivar_node <- search_path(wheat_new,
 ".Simulations.Replacements.Hartog")
cultivar_node$path
 #> [1] 1 3 1
cultivar_node$node$Command
 #> [[1]]
 #> [1] "[Phenology].MinimumLeafNumber.FixedValue = 6"
 #> 
 #> [[2]]
 #> [1] "[Phenology].VrnSensitivity.FixedValue = 0"

Available models

A new model can be generated in R according to Models assemble in APSIM Next Generation. The rapsimng package stores a copy of Models.xml from APSIM Next Generation on 1st August, 2020.
The available models can be listed using function available_models.

 head(data.frame(model = available_models()))
 #> model
 #> 1 AgPasture.AGPBiomass
 #> 2 AgPasture.BiomassAndN
 #> 3 AgPasture.BiomassAndNLayered
 #> 4 AgPasture.TissuesHelper
 #> 5 AgPasture.SimpleGrazing
 #> 6 AgPasture.SimpleGrazing.GrazingRotationTypeEnum

Update cultivar parameter values

Function update_cultivar is a short way to update parameter values for cultivars.

wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
 # Update cultivars
df <- data.frame(name = rep("Hartog", 3),
 parameter = c("[Phenology].MinimumLeafNumber.FixedValue",
 "[Phenology].VrnSensitivity.FixedValue",
 "[Phenology].PpSensitivity.FixedValue"),
 value = c(9, 7, 3))
wheat_cultivar <- update_cultivar(wheat, df)
 # Check update cultivar paramters
hartog <- search_path(wheat_cultivar, "[Replacements].Hartog")
hartog$path
 #> NULL