Interface to use Simplace from R"
In simplace: Interface to Use the Modelling Framework 'SIMPLACE'

withSimplace <- FALSE
try({
  withSimplace <- !is.na(simplace::findFirstSimplaceInstallation())
})

Introduction

This package provides methods to interact with the modelling framework Simplace^[ Scientific Impact assessment and Modelling PLatform for Advanced Crop and Ecosystem management. See www.simplace.net for more information on Simplace]. Simplace is written in Java (and some parts in Scala) so one can access it from R via rJava. The purpose of this package is to simplify the interaction between R and Simplace, by providing functions to:

initialize and configure Simplace
load a simulation (solution and project)
parameterize the simulation
run whole simulation or run it stepwise
get simulation output and convert it to formats suitable for R

Installing the Simplace Framework

For installing Simplace, please consult the webpage www.simplace.net. A brief guide to install Simplace:

If you don't have installed Java, please install an appropriate version of the (JRE or JDK) from openjdk.java.net or adoptium.net (recommended).
Get Simplace from www.simplace.net
Install the simplace package in R:

install.packages('simplace')

Basic Usage

The usage of Simplace in R follows roughly this scheme:

init Simplace by providing the path to your simplace installation directory, your working directory and your outputs
open a Simplace project form a solution (and project) file
create a list of simulation parameters you want to change
create and run a Simulation
get the result from the simulation
convert the result to a R object (data.frame, list etc.)

Troubleshooting

Package rJava should be installed automatically with simplace. If not, install it manually:
install.packages('rJava')
Architecture of R and Java have to match. If you are using 64-bit Java, you have to use 64-bit R.
If you want to use the development version instead of the console mode, make sure that the projects simplace_core, simplace_modules and optionally simplace_run are in a common directory and set the installation dir to this directory.

Example

Run the simulation

library(simplace)
SimplaceInstallationDir <- findFirstSimplaceInstallation()

Solution <- paste(SimplaceInstallationDir,
        "simplace_run/simulation/gk/solution/complete/Complete.sol.xml",sep="")

simplace <- initSimplace(SimplaceInstallationDir)

openProject(simplace, Solution)

parameter <- list()
parameter$enddate <- "31-12-1992"

sid <- createSimulation(simplace,parameter)
runSimulations(simplace)

result <- getResult(simplace,"DIAGRAM_OUT", sid);

closeProject(simplace)

After specifying the directories and the solution, the framework is initialized and the project opened. The end date of the simulation is (re)set and the simulation is run. After the run the result is retrieved.

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Get the result and plot it

simdata <- resultToDataframe(result)

dates <- 300:730
weights <- simdata[dates,
    c("TOP_LINE_Roots","TOP_LINE_Leaves","TOP_LINE_Stems","TOP_LINE_StorageOrgans")]
matplot(dates,weights,type="l",xlab="Days",ylab="Weight [g/m2]",main="Simulated Biomass")
legend(300,800,legend=c("Roots","Leaves","Stems","Storage Organs"),lty=1:4,col=1:4)

The result is converted to a dataframe. Interesting variables are extracted and then plotted.

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Get arrays and plot them as contour plot

resultlistexp <- resultToList(result,expand=TRUE)
water <- resultlistexp$BOTTOM_ARRAY_VolumetricWaterContent
wmat <- do.call(rbind,water)
wmatpart <- wmat[dates,]
layers <- dim(wmatpart)[2]
filled.contour(dates,-(layers:1),wmatpart[,layers:1],
               xlab="Day", ylab="Layer", main="Water content in soil",
               color.palette = function(n){rgb((n:1)/n,(n:1)/n,1)})