R Graphical Manual

Browse All

Last data update: 2014.03.03

R: make setupNUCOM

setupNUCOM

R Documentation

make setupNUCOM

Description

Code to make the setup structure needed run the model.

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 model can be sent upon request at jeroenpullens[at]gmail[dot]com

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)