Nothing
require(scaRabee)
if (.Platform$OS.type=="windows"){
end.of.folder <- ''
} else {
end.of.folder <- '/'
}
# User-prompt: define target directory
if (interactive()){
cat('\nExample 6 - Simulation of a model defined with ordinary differential equations at the \n')
cat('subject level\n\n')
repeat{
wd <- readline('Enter a path to store the demo files:\n>')
if (wd!=''){
if (substring(wd,nchar(wd),nchar(wd))!='/'){
wd <- paste(wd,end.of.folder,sep='')
}
if (!file.exists(wd)){
action <- readline(sprintf(paste('\nDirectory \'%s\' does not exist:\n',
' [c] Continue with current working directory: %s\n',
' [r] Retry\n',
' [a] Abort\n>',sep=''),wd,getwd()))
if (action == 'a') {
stop('Demo aborted',call.=FALSE)
} else if (action == 'c') {
wd <- getwd()
if (substring(wd,nchar(wd),nchar(wd))!='/'){
wd <- paste(wd,end.of.folder,sep='')
}
options(warn=-1)
nd <- try(file.create(paste(wd,'test.R',sep='')))
options(warn=0)
if (nd) { # User has permission on directory
file.remove(paste(wd,'test.R',sep=''))
break
}
cat('\nYou don\'t have permissions on this directory.\n')
}
} else {
if (substring(wd,nchar(wd),nchar(wd))!='/'){
wd <- paste(wd,end.of.folder,sep='')
}
options(warn=-1)
nd <- try(file.create(paste(wd,'test.R',sep='')))
options(warn=0)
if (nd) { # User has permission on directory
file.remove(paste(wd,'test.R',sep=''))
break
}
cat('\nYou don\'t have permissions on this directory.\n')
}
} else {
wd <- getwd()
if (substring(wd,nchar(wd),nchar(wd))!='/'){
wd <- paste(wd,end.of.folder,sep='')
}
options(warn=-1)
if (file.exists(wd))
nd <- try(file.create(paste(wd,'test.R',sep='')))
options(warn=0)
if (nd) { # User has permission on directory
file.remove(paste(wd,'test.R',sep=''))
break
}
cat('\nYou don\'t have permissions on this directory.\n')
}
}
} else {
return(NULL)
}
# Set files
old.wd <- getwd()
wd <- paste(wd,'/example6/',sep='')
ana.file <- paste(wd,'example6.R',sep='')
data.file <- paste(wd,'data.csv',sep='')
param.file <- paste(wd,'initials.csv',sep='')
model.file <- paste(wd,'model.txt',sep='')
# Copy files
data(example6.data,
example6.initials)
# Create main and model.definition directory
if (file.exists(wd)) {
stop(sprintf(paste('\nDirectory \'%s\' already exists.\nDemo aborted. ',
'Please retry using a different target directory.\n',sep=''),wd),
call.=FALSE)
}
scarabee.new(name='example6',
path=wd,
type='simulation',
method='subject',
template='explicit')
setwd(wd)
# Update the data file
write.table(example6.data,
file=data.file,
sep=',',
quote=FALSE,
row.names=FALSE,
append=FALSE)
# Update the parameter file
write.table(example6.initials,
file=param.file,
sep=',',
quote=FALSE,
row.names=FALSE,
col.names=FALSE,
append=TRUE)
# Update the model file
tmp <- c('$ANALYSIS example6',
'',
'$DERIVED',
' ke <- CL/V',
' kin <- kout*R0',
'$IC',
' init <- c(0,R0,R0)',
'',
'$SCALE',
' scale <- c(1,1,1)',
'',
'$ODE',
' inh <- 1 - Imax*(a1/V)/(IC50+(a1/V))',
' dadt <- rbind(-ke*a1, # CP',
' kin-kt*inh*a2, # P',
' kt*inh*a2 - kout*a3) # R',
'',
'$OUTPUT',
' y <- rbind(f[1,]/V,',
' f[2,],',
' f[3,])'
)
write(tmp,
file=model.file,
sep='\n',
append=FALSE)
# Run example 6
source(ana.file)
setwd(old.wd)
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