setupNUCOM: make setupNUCOM

In NUCOMBog: NUtrient Cycling and COMpetition Model Undisturbed Open Bog Ecosystems in a Temperate to Sub-Boreal Climate

Description

Code to make the setup structure needed run the model.

The data used in the example is stored in the package and can be copied to a user specified location via the copytestdata function of this package.

Usage

setupNUCOM(mainDir, climate, environment, inival, start, end, type,
  numFolders = 1, parallel = F, separate = F, startval = 1)

Arguments

mainDir	Working directory
climate	climate input (monthly) format: year, month, air temperature, precipitation, potential evapotranspiration (tab seperated). The potential evapotranspiration needs to be calcluated by using the Penman open water evapotranspiration.
environment	environment input (yearly) format: year, atmospheric co2 values, nitrogen deposition
inival	initial values of biomass
start	year in which the simulation starts
end	year in which the simulation ends
type	Which output is needed? For more information see the help of the getData function.
numFolders	The amount of folders that needs to be created (in case of parallel computing)
parallel	Run the model on parallel cores? TRUE/FALSE, default is FALSE.
separate	Does the model needs to be run for all parameters seperate? Default is FALSE
startval	From which row does the output need to be loaded. Default is 1.

Value

A list with paths and filenames and parameter values which can be implemented in the runnucom and the runnucomParallel function.

Author(s)

JWM Pullens

Source

The executable and the source code of the model can downloaded from https://github.com/jeroenpullens/NUCOMBog.

Examples

## Not run: 
#Define complete file path in setup
for LINUX: ~/home/...../data/ ! pay attention to the last "/"
for Windows_ C://..//data// ! pay attention to the last "//"

##Single core setup:
test_setup_singlecore <- setupNUCOM(mainDir="/home/jeroen/NUCOMBog_data/",
                                     climate="ClimLVMhis.txt",
                                     environment="EnvLVMhis.txt",
                                     inival="inivalLVMhis.txt",
                                     start=1766,
                                     end=1999,
                                     type=c("NEE","WTD"),
                                     parallel=F)

## Multi core setup:
names<-c("CO2ref","gram_Beta","eric_MaxGr")

nparvector<-50
initialParameters <- matrix(runif(n=length(names)*nparvector,
                   min=c(300,0.1,40),
                   max=c(500,1,80)),
                   nrow=length(names))
initialParameters<-data.frame(names,initialParameters)
names(initialParameters)<-c("names",rep("values",nparvector))
initialParameters$names<-as.character(initialParameters$names)

test_setup <- setupNUCOM(mainDir="/home/jeroen/NUCOMBog_data/",
                          climate="ClimLVMhis.txt",
                          environment="EnvLVMhis.txt",
                          inival="inivalLVMhis.txt",
                          start=1766,
                          end=1999,
                          type=c("NEE","WTD"),
                          parallel=T,
                          numFolders=nparvector,
                          separate=F,
                          startval=1)


## End(Not run)

NUCOMBog documentation built on May 2, 2019, 11:01 a.m.