Nothing
require(scaRabee)
if (.Platform$OS.type=="windows"){
end.of.folder <- ''
} else {
end.of.folder <- '/'
}
# User-prompt: define target directory
if (interactive()){
cat('\nExample 1 - Simulation of a model defined with algebraic equations at the \n')
cat('population 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,'/example1/',sep='')
ana.file <- 'example1.R'
data.file <- 'data.csv'
param.file <- 'initials.csv'
model.file <- 'model.txt'
# Copy files
data(example1.data,
example1.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='example1',
path=wd,
type='simulation',
method='population',
template='explicit')
# Update the data file
write.table(example1.data,
file=data.file,
sep=',',
quote=FALSE,
row.names=FALSE,
append=FALSE)
# Update the parameter file
write.table(example1.initials,
file=param.file,
sep=',',
quote=FALSE,
row.names=FALSE,
col.names=FALSE,
append=TRUE)
# Update the model file
tmp <- c('$ANALYSIS example1',
'',
'$OUTPUT',
' ke <- cl/vc',
' flag <- ifelse((times-2)>0,1,0)',
'',
' Cp <- (DOSE[1]*500/vc)*((1/ke)*(1-flag*(1-exp(-ke*(times-2)))-exp(-ke*times)))',
' y <- rbind(log(Cp),',
' base*(1-imax*Cp/(ic50+Cp)))')
write(tmp,
file=model.file,
sep='\n',
append=FALSE)
# Run example 1
source(ana.file)
setwd(old.wd)
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