[R] Importing arguments for use by functions in a script

[EvansA]

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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