R help - Aug 2010 - Importing arguments for use by functions in a script

QUESTION:
Is there a way of passing arguments from an external file to a script so
that they can be used directly by functions within the script?

I have a series of interdependent functions. I wish to test the time for
processing various datasets.
I was initially doing something along the lines of the following (yes, I am
new to R):

rm(list= ls())
systime1<-system.time(source("seq_imp_fct.R"))
systime2<-system.time(source("pattern_fct.R"))
systime3<-system.time(source("AAdistribution_fct.R"))

# run function
systime101<-system.time(seqres<-seq_imp_fct("testprot.txt"))
systime102<-system.time(patres<-pattern_fct(pattern="SS{1,2}",sequences=seqres))
systime103<-system.time(AAres<-AAdistribution_fct(sequences=patres))


As my list is of functions is growing, I was attempting to write a script
that would allow me to semi-automate this.
I have created a table of function file names, variables to hold return
values, arguments

Function	Returns	Arguments
"seq_imp_fct.R"	seqres	"testprot.txt"
"pattern_fct.R"	patres	pattern="SS{1,2}",sequences=seqres
"AAdistribution_fct.R"	Aares	sequences=patres

which I am reading in:

funcs<-read.table("functions.txt",sep="\t",header=TRUE,colClasses
"character")
> funcs
                 Function   Returns                       Arguments
1           seq_imp_fct.r    seqres                     testprot.txt
2           pattern_fct.r    patres pattern=SS{1,2},sequences=seqres
3    AAdistribution_fct.r     Aares                 sequences=patres


#######################################################################
# source functions and get system times
#######################################################################

systimes<-data.frame()
nrows<-nrow(funcs)

i<-0
for(i in 1:nrows)
{
 
 func<-funcs[i,1]

 systime<-system.time(source(func))
 systimes[i,1]<-func
 systimes[i,2]<-"source"
 systimes[i,3]<-systime[1]
 systimes[i,4]<-systime[2]
 systimes[i,5]<-systime[3]
 
}

#######################################################################
# run functions and get system times
#######################################################################

ii<-i+1
iiend<-i*2
i<-0

for(ii in ii:iiend)
{
  i<-i+1
 
  func<-funcs[i,1]
  rets<-as.name(funcs[i,2])
  args<-funcs[i,3]
  
  # remove .R from function
  sfunc<-substring(func,1,((nchar(func))-2))
  
  # convert text string to an object
  ssfunc<-get(sfunc)

  # convert text string in rets to object pointer and run function
 
systemtime<-system.time(eval(call("<-",rets,call("<-",rets,(ssfunc(args))))))
  
  print(seqres)
 
  systimes[ii,1]<-func
  systimes[ii,2]<-"process"
  systimes[ii,3]<-systemtime[1]
  systimes[ii,4]<-systemtime[2]
  systimes[ii,5]<-systemtime[3]
 
} 


This works fine when doing the equivalent of:

systime101<-system.time(seqres<-seq_imp_fct("testprot.txt"))

But falls over when doing the "equivalent" of:
systime102<-system.time(patres<-pattern_fct(pattern="SS{1,2}",sequences=seqres))

Generating error:
Error in gregexpr(pattern, as.character(sequences[, 3]), perl = T) : 
argument "sequences" is missing, with no default
Timing stopped at: 0 0.01 0.02 

I don't want to have to customise the handling of arguments for each
function.
Is there a way around this?

-- 
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Sent from the R help mailing list archive at Nabble.com.

Hi,

Since no one has answered this, I will take a shot.  I doubt it would
really take more work to just put the functions in a script.  Sure you
would have to 'customize' each one, but since you are entering their
names, name of the desired output object, and arguments, simply
directly entering that into a script and then running the whole thing
with source() seems pretty comparable to me.  I guess my point with
all that is that you might reconsider problem and what your goal is.
Nevertheless, if you are determined that storing all of that in a text
file is what you want to do, perhaps this will help you get things to
work.  I imagine you could even wrap up all the steps below into a
function and then just apply() that function to your text file and
skip all the for loops.  Note the single quotes inside the character
strings.

resname <- "whatever"
funname <- "grep"
argname <- "pattern = 'h', x =
c('hi','bye')"
myfun <- paste(funname, "(", argname, ")", sep =
"")
system.time(assign(x = resname, value = eval(parse(text = myfun))))

Josh

On Sun, Aug 8, 2010 at 7:36 AM, EvansA <annaevans66 at hotmail.com>
wrote:
>
> QUESTION:
> Is there a way of passing arguments from an external file to a script so
> that they can be used directly by functions within the script?
>
> I have a series of interdependent functions. I wish to test the time for
> processing various datasets.
> I was initially doing something along the lines of the following (yes, I am
> new to R):
>
> rm(list= ls())
> systime1<-system.time(source("seq_imp_fct.R"))
> systime2<-system.time(source("pattern_fct.R"))
> systime3<-system.time(source("AAdistribution_fct.R"))
>
> # run function
>
systime101<-system.time(seqres<-seq_imp_fct("testprot.txt"))
>
systime102<-system.time(patres<-pattern_fct(pattern="SS{1,2}",sequences=seqres))
> systime103<-system.time(AAres<-AAdistribution_fct(sequences=patres))
>
>
> As my list is of functions is growing, I was attempting to write a script
> that would allow me to semi-automate this.
> I have created a table of function file names, variables to hold return
> values, arguments
>
> Function ? ? ? ?Returns Arguments
> "seq_imp_fct.R" seqres ?"testprot.txt"
> "pattern_fct.R" patres
?pattern="SS{1,2}",sequences=seqres
> "AAdistribution_fct.R" ?Aares ? sequences=patres
>
> which I am reading in:
>
>
funcs<-read.table("functions.txt",sep="\t",header=TRUE,colClasses
> "character")
>
>> funcs
> ? ? ? ? ? ? ? ? Function ? Returns ? ? ? ? ? ? ? ? ? ? ? Arguments
> 1 ? ? ? ? ? seq_imp_fct.r ? ?seqres ? ? ? ? ? ? ? ? ? ? testprot.txt
> 2 ? ? ? ? ? pattern_fct.r ? ?patres pattern=SS{1,2},sequences=seqres
> 3 ? ?AAdistribution_fct.r ? ? Aares ? ? ? ? ? ? ? ? sequences=patres
>
>
> #######################################################################
> # source functions and get system times
> #######################################################################
>
> systimes<-data.frame()
> nrows<-nrow(funcs)
>
> i<-0
> for(i in 1:nrows)
> {
>
> ?func<-funcs[i,1]
>
> ?systime<-system.time(source(func))
> ?systimes[i,1]<-func
> ?systimes[i,2]<-"source"
> ?systimes[i,3]<-systime[1]
> ?systimes[i,4]<-systime[2]
> ?systimes[i,5]<-systime[3]
>
> }
>
> #######################################################################
> # run functions and get system times
> #######################################################################
>
> ii<-i+1
> iiend<-i*2
> i<-0
>
> for(ii in ii:iiend)
> {
> ?i<-i+1
>
> ?func<-funcs[i,1]
> ?rets<-as.name(funcs[i,2])
> ?args<-funcs[i,3]
>
> ?# remove .R from function
> ?sfunc<-substring(func,1,((nchar(func))-2))
>
> ?# convert text string to an object
> ?ssfunc<-get(sfunc)
>
> ?# convert text string in rets to object pointer and run function
>
>
systemtime<-system.time(eval(call("<-",rets,call("<-",rets,(ssfunc(args))))))
>
> ?print(seqres)
>
> ?systimes[ii,1]<-func
> ?systimes[ii,2]<-"process"
> ?systimes[ii,3]<-systemtime[1]
> ?systimes[ii,4]<-systemtime[2]
> ?systimes[ii,5]<-systemtime[3]
>
> }
>
>
> This works fine when doing the equivalent of:
>
>
systime101<-system.time(seqres<-seq_imp_fct("testprot.txt"))
>
> But falls over when doing the "equivalent" of:
>
systime102<-system.time(patres<-pattern_fct(pattern="SS{1,2}",sequences=seqres))
>
> Generating error:
> Error in gregexpr(pattern, as.character(sequences[, 3]), perl = T) :
> argument "sequences" is missing, with no default
> Timing stopped at: 0 0.01 0.02
>
> I don't want to have to customise the handling of arguments for each
> function.
> Is there a way around this?
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/Importing-arguments-for-use-by-functions-in-a-script-tp2317758p2317758.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> 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.
>


-- 
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/

Thank you for your response.

Re: "I guess my point with all that is that you might reconsider problem
and
what your goal is"

You are quite right, I just got caught up with the not being able to do
something - and now see the error of my ways. 

But I am glad to see your solution.
-- 
View this message in context:
http://r.789695.n4.nabble.com/Importing-arguments-for-use-by-functions-in-a-script-tp2317758p2320383.html
Sent from the R help mailing list archive at Nabble.com.