Editing a .r file from within another .r file

Question

I am trying to make my current project reproducible, and so am creating a master document (eventually a .rmd file) that will be used to call and execute several other documents. This way myself and other investigators only need to open and run one file.

There are three layers to the current setup: master file, 2 read-in files, 2 databases. The master file calls the read-in files using source(), and the read-in files parse the .csv databases and apply labels.

The read-in files and the databases are generated automatically with the data management software I'm currently using (REDCap) each time I download the updated data.

However, the read-in files have a line of code that removes all of the objects in my environment. I would like to edit the read-in files directly from the master file so that I do not have to open the read-in files individually each time I run my report. Specifically, since all the read-in files are the same, I would like to remove line #2 in each.

I've tried searching Google, and tried file.edit(), but have been unable to find anything. Not even sure it is possible, but figured I would ask. Let me know if I can improve this question or if you need any additional code to answer it. Thanks!

Current relevant master code (edited for generality):

 source("read-in1")  
 source("read-in2")

Current relevant read-in file code (same in each file, except for the database name):

 #Clear existing data and graphics  
 rm(list=ls())  
 graphics.off()  
 #Load Hmisc library  
 library(Hmisc)  
 #Read Data  
 data=read.csv('database.csv')  
 #Setting Labels  

[read-in code truncated]

Additional details:
OS: Windows 7 Professional x86
R version: 3.1.3
R Studio version: 0.99.441

Answer 1

You could try this. It just calls some shell commands: (1) renames the file, then (2) copies all lines not containing rm(list=ls()) to a new file with the same name as the original file, then (3) removes the copy.

files_to_change <- c("read-in1.R", "read-in2.R")
for (f in files_to_change) {
    old <- paste0(f, ".old")
    system(paste("cmd.exe /c ren", f, old))
    system(paste("cmd.exe /c findstr /v rm(list=ls())", old, ">", f))
    system(paste("cmd.exe /c rm", old))
}

After calling this loop you should have

#Clear existing data and graphics  
graphics.off()  
#Load Hmisc library  
library(Hmisc)  
#Read Data  
data=read.csv('database.csv')  
#Setting Labels  

in your read-in*.R files. You could put this in a batch script

@echo off
ren "%~f1" "%~nx1.old"
findstr /v "rm(list=ls())" "%~f1.old" > "%~f1"
rm "%~nx1.old"

say, "example.bat", and call that in the same way using system.

Answer 2

You might try readLines() and something like the following (which was simplified greatly by a suggestion from @Hong Ooi below):

eval(parse(readLines("read-in1.R")[-2]))

My original solution which was much more pedantic:

f <- file("read-in1.R", open="r")
t <- readLines(f)
close(f)

for (l in t[-2]) { eval(parse(text=l)) }

The for() loop just parses and evaluates each line from the text file except for the second one (that's what the -2 index value does). If you're reading and writing longer files then the following will be much faster than the second option, however still less preferable than @Hong Ooi's:

f <- file("read-in1.R", open="r")
t <- readLines(f)
close(f)

f <- file("out.R", open="w")
o <- writeLines(t[-2], f)
close(f)
source("out.R")

Answer 3

Sorry I'm so late in noticing this question, but you may want to investigate getting access the the REDCap API and using either the redcapAPI package or the REDCapR package. Both of those packages will allow you to export the data from REDCap and directly into R without having to use the download scripts. redcapAPI will even apply all the formats and dates (REDCapR might do this now too. It was in the plan, but I haven't used it in a while).