Greetings All,
I am looking to write a parametrized Rscript that will accept a variable
name(that also is the name of the flat file), transform the data into a data
frame and preform various modeling on the structure and save the output and
plot of the model. In this example i am using a rpart decision tree. The
only problem i am having is integrating the parameter into the internal
object name when tying to save it. Solving this one porblem will help me
start blasting though 100's of models and saving their output for later use.
I would call the script from command line as
Rscript file_name.R argument
for this example
Rscript rpart_code.R Kyphosis
#/bin/R
args <- commandArgs(TRUE) # Read the argument
require(rpart, quietly = TRUE)
#for this example lets use the kyphosis data in the rpart package
args <- "Kyphosis"
X<-paste(args," ~.", sep ="") # create model formula
call. X = "Kyphosis ~."
assign(paste("cart_",args, sep =""),rpart(X,
method="class",
data=kyphosis))
#NOW MY TROUBLE. I have an rpart object but cannot save it under a file name
that incorporates the parameter
#Here is the file name
file<-paste("cart_",args, sep ="")
#hard coding the rpart object works
save(cart_Kyphosis, file = file)
However when I try to use the main parameter to accomplish this i get an
error
save(paste("cart_",args, sep =""), file = file)
#I get
Error in save(paste("cart_", args, sep = ""), file = file) :
object 'paste("cart_", args, sep = "")' not found
#or
save(get(paste("cart_",args, sep ="")), file = file)
get(paste("cart_",args, sep ="")) # print the rpart object
#I have tried several variation even creating a text line and parsing it
paste("save(cart_", args, ", file=file)",sep="")
[1] "save(cart_Kyphosis, file=file)"
parse(text=paste("save(cart_", args, ",
file=file)",sep=""))
#or
as.expression(parse(text =paste("save(cart_", args, ",
file=file)",sep="") ))
expression(save(cart_Kyphosis, file=file))
attr(,"srcfile")
<text>
attr(,"wholeSrcref")
save(cart_Kyphosis, file=file)
#nothing works. Any thoughts?
#even this works but not the save
png(filename=paste("cart_",args,".png" sep ="") ,
height = 500, width = 500,
bg = "white")
plot(get(paste("cart_",args, sep ="")))
dev.off()
#or
print(get(paste("cart_",args, sep ="")))
Many Thanks,
John
[[alternative HTML version deleted]]
I have found the solution. i need to use eval() to execute my text parse
like
eval(parse(text =as.expression(paste("save(cart_", args, ",
file=file)",sep=""))))
I hope this helps someone else.
John
On Fri, Apr 22, 2011 at 3:42 PM, John Dennison
<dennison.john@gmail.com>wrote:
> Greetings All,
>
> I am looking to write a parametrized Rscript that will accept a variable
> name(that also is the name of the flat file), transform the data into a
data
> frame and preform various modeling on the structure and save the output and
> plot of the model. In this example i am using a rpart decision tree. The
> only problem i am having is integrating the parameter into the internal
> object name when tying to save it. Solving this one porblem will help me
> start blasting though 100's of models and saving their output for later
use.
>
>
>
> I would call the script from command line as
> Rscript file_name.R argument
>
> for this example
>
> Rscript rpart_code.R Kyphosis
>
> #/bin/R
> args <- commandArgs(TRUE) # Read the argument
>
> require(rpart, quietly = TRUE)
>
> #for this example lets use the kyphosis data in the rpart package
> args <- "Kyphosis"
>
> X<-paste(args," ~.", sep ="") # create model formula
call. X = "Kyphosis
> ~."
>
> assign(paste("cart_",args, sep =""),rpart(X,
method="class",
> data=kyphosis))
>
>
> #NOW MY TROUBLE. I have an rpart object but cannot save it under a file
> name that incorporates the parameter
> #Here is the file name
> file<-paste("cart_",args, sep ="")
>
> #hard coding the rpart object works
> save(cart_Kyphosis, file = file)
>
> However when I try to use the main parameter to accomplish this i get an
> error
>
> save(paste("cart_",args, sep =""), file = file)
>
> #I get
>
> Error in save(paste("cart_", args, sep = ""), file =
file) :
> object 'paste("cart_", args, sep = "")' not
found
>
>
> #or
> save(get(paste("cart_",args, sep ="")), file = file)
>
> get(paste("cart_",args, sep ="")) # print the rpart
object
>
> #I have tried several variation even creating a text line and parsing it
>
>
> paste("save(cart_", args, ",
file=file)",sep="")
>
> [1] "save(cart_Kyphosis, file=file)"
>
> parse(text=paste("save(cart_", args, ",
file=file)",sep=""))
>
> #or
>
> as.expression(parse(text =paste("save(cart_", args, ",
file=file)",sep="") ))
>
> expression(save(cart_Kyphosis, file=file))
> attr(,"srcfile")
> <text>
> attr(,"wholeSrcref")
> save(cart_Kyphosis, file=file)
>
> #nothing works. Any thoughts?
>
> #even this works but not the save
>
> png(filename=paste("cart_",args,".png" sep
="") , height = 500, width > 500, bg = "white")
> plot(get(paste("cart_",args, sep ="")))
> dev.off()
>
> #or
>
> print(get(paste("cart_",args, sep ="")))
>
>
> Many Thanks,
>
> John
>
>
>
>
[[alternative HTML version deleted]]
John -
When you have a character string, and you want the R object whose
name is contained in that character string, the easiest way to get
the object is to use the get() function. So
save(get(paste("cart_",args, sep ="")), file = file)
would probably do what you want.
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spector at stat.berkeley.edu
On Fri, 22 Apr 2011, John Dennison wrote:
> Greetings All,
>
> I am looking to write a parametrized Rscript that will accept a variable
> name(that also is the name of the flat file), transform the data into a
data
> frame and preform various modeling on the structure and save the output and
> plot of the model. In this example i am using a rpart decision tree. The
> only problem i am having is integrating the parameter into the internal
> object name when tying to save it. Solving this one porblem will help me
> start blasting though 100's of models and saving their output for later
use.
>
>
>
> I would call the script from command line as
> Rscript file_name.R argument
>
> for this example
>
> Rscript rpart_code.R Kyphosis
>
> #/bin/R
> args <- commandArgs(TRUE) # Read the argument
>
> require(rpart, quietly = TRUE)
>
> #for this example lets use the kyphosis data in the rpart package
> args <- "Kyphosis"
>
> X<-paste(args," ~.", sep ="") # create model formula
call. X = "Kyphosis ~."
>
> assign(paste("cart_",args, sep =""),rpart(X,
method="class",
> data=kyphosis))
>
>
> #NOW MY TROUBLE. I have an rpart object but cannot save it under a file
name
> that incorporates the parameter
> #Here is the file name
> file<-paste("cart_",args, sep ="")
>
> #hard coding the rpart object works
> save(cart_Kyphosis, file = file)
>
> However when I try to use the main parameter to accomplish this i get an
> error
>
> save(paste("cart_",args, sep =""), file = file)
>
> #I get
>
> Error in save(paste("cart_", args, sep = ""), file =
file) :
> object 'paste("cart_", args, sep = "")' not
found
>
>
> #or
> save(get(paste("cart_",args, sep ="")), file = file)
>
> get(paste("cart_",args, sep ="")) # print the rpart
object
>
> #I have tried several variation even creating a text line and parsing it
>
>
> paste("save(cart_", args, ",
file=file)",sep="")
>
> [1] "save(cart_Kyphosis, file=file)"
>
> parse(text=paste("save(cart_", args, ",
file=file)",sep=""))
>
> #or
>
> as.expression(parse(text =paste("save(cart_", args, ",
file=file)",sep="") ))
>
> expression(save(cart_Kyphosis, file=file))
> attr(,"srcfile")
> <text>
> attr(,"wholeSrcref")
> save(cart_Kyphosis, file=file)
>
> #nothing works. Any thoughts?
>
> #even this works but not the save
>
> png(filename=paste("cart_",args,".png" sep
="") , height = 500, width = 500,
> bg = "white")
> plot(get(paste("cart_",args, sep ="")))
> dev.off()
>
> #or
>
> print(get(paste("cart_",args, sep ="")))
>
>
> Many Thanks,
>
> John
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
On 4/22/2011 12:42 PM, John Dennison wrote:> Greetings All, > > I am looking to write a parametrized Rscript that will accept a variable > name(that also is the name of the flat file), transform the data into a data > frame and preform various modeling on the structure and save the output and > plot of the model. In this example i am using a rpart decision tree. The > only problem i am having is integrating the parameter into the internal > object name when tying to save it. Solving this one porblem will help me > start blasting though 100's of models and saving their output for later use. > > > > I would call the script from command line as > Rscript file_name.R argument > > for this example > > Rscript rpart_code.R Kyphosis > > #/bin/R > args<- commandArgs(TRUE) # Read the argument > > require(rpart, quietly = TRUE) > > #for this example lets use the kyphosis data in the rpart package > args<- "Kyphosis" > > X<-paste(args," ~.", sep ="") # create model formula call. X = "Kyphosis ~." > > assign(paste("cart_",args, sep =""),rpart(X, method="class", > data=kyphosis)) > > > #NOW MY TROUBLE. I have an rpart object but cannot save it under a file name > that incorporates the parameter > #Here is the file name > file<-paste("cart_",args, sep ="") > > #hard coding the rpart object works > save(cart_Kyphosis, file = file) > > However when I try to use the main parameter to accomplish this i get an > error > > save(paste("cart_",args, sep =""), file = file)How about save(list=paste("cart_",args, sep =""), file = file)> #I get > > Error in save(paste("cart_", args, sep = ""), file = file) : > object 'paste("cart_", args, sep = "")' not found > > > #or > save(get(paste("cart_",args, sep ="")), file = file) > > get(paste("cart_",args, sep ="")) # print the rpart object > > #I have tried several variation even creating a text line and parsing it > > > paste("save(cart_", args, ", file=file)",sep="") > > [1] "save(cart_Kyphosis, file=file)" > > parse(text=paste("save(cart_", args, ", file=file)",sep="")) > > #or > > as.expression(parse(text =paste("save(cart_", args, ", file=file)",sep="") )) > > expression(save(cart_Kyphosis, file=file)) > attr(,"srcfile") > <text> > attr(,"wholeSrcref") > save(cart_Kyphosis, file=file) > > #nothing works. Any thoughts? > > #even this works but not the save > > png(filename=paste("cart_",args,".png" sep ="") , height = 500, width = 500, > bg = "white") > plot(get(paste("cart_",args, sep =""))) > dev.off() > > #or > > print(get(paste("cart_",args, sep =""))) > > > Many Thanks, > > John > > [[alternative HTML version deleted]] >-- Brian S. Diggs, PhD Senior Research Associate, Department of Surgery Oregon Health & Science University