Passing Parameters to an R Script via CMD or Batch - r

Question

Currently I have an R Script that takes 8 parameters that are hard-coded as the first 8 lines of my script.
I've made a Batch file to try and manually change the parameters on the fly, but it doesn't seem to be working the way I want it to.
Batch that currently runs the script (But doesnt actually change the parameters)
echo off
ECHO PRESS ENTER AT ANY INPUT TO ACCEPT the DEFAULT VALUE.
:: Setting of Variables
#Set /P RScript=Set path to R:_
#Set /P RProgram=Set path to RScript:_
#Set /P RStartDir=Set Start Directory:_
#Set /P Begin=Begin on which Loan?:_
#Set /P End=End on which Loan?:_
#Set /P OutputDir=Set Output Directory:_
#Set /P Deal=Set Deal input file (.txt):_
#Set /P OutputFile=Name Deal Output File:_
#Set /P AsOfDate=As of Date?:_
#Set /P ThirtyYrSpread=Thirty Year Mortgage Spread?:_
:: If Blank (enter), set variables/paths to Defaults (Listed Below)
if "%RScript%"=="" Set RScript=c:\program files\r\r-
3.4.3\bin\x64\rscript.exe
if "%RProgram%"=="" Set RProgram=C:\MortgageMatt\Cirt2014-
1\0.Mortgage Model.R
if "%RStartDir%"=="" Set RStartDir=C:\MortgageMatt\Cirt2014-1
if "%Begin%"=="" Set Begin=1
if "%End%"=="" Set End=2
if "%OutputDir%"=="" Set OutputDir=C:\MortgageMatt\Cirt2014-1
if "%Deal%"=="" Set Deal=Cirt 2014-1 Loan Level.txt
if "%OutputFile%"=="" Set OutputFile=Cirt 2014-1d
if "%AsOfDate%"=="" Set AsOfDate=62017
if "%ThirtyYrSpread%" == "" Set ThirtyYrSpread=135
echo "%RScript% %RProgram% %RStartDir% %Begin% %End% %OutputDir% %Deal%
%OutputFile% %AsOfDate% %ThirtyYrSpread%"
ECHO PLEASE CHECK IF THESE VALUES ARE CORRECT
pause
:: Command Prompt, /c Carries out command specified by string and then
terminates
cmd /c ""%RScript%" "%RProgram%" "%RStartDir%" "%Begin%" "%End%"
"%OutputDir%" "%Deal%" "%OutputFile%" "%AsOfDate%" "%ThirtyYrSpread%""
So because the parameters were actually hard coded into the R Script, this is what I've added to try to accommodate. Does this look okay? I think this is where I'm running into errors.
Added to R Script
args <- commandArgs(trailingOnly = TRUE)
if (length(args) == 0) {
if (!exists("dataDir")) { stop("variables dataDir not found") }
# Set dataDir variable when Running inside a R Session
args <- c(getwd(), 1, 2, ".", "Cirt 2014-1 Loan Level.txt", "Cirt 2014-
1", "62017", 175)
}
print(args)
# Input Values
Input.Directory <- paste(args[1]) ## getwd() , "/", "inputs", sep = "")
Begin.Sim <- args[2]
End.Sim <- args[3]
Output.Directory <- paste(args[1],"\\",args[4],sep = "") ##, "/", "outputs",
sep = "")
Pool.ID.File <- args[5] #"Cirt 2014-1 Loan Level.txt"
Pool.ID <- args[6] #"Cirt 2014-1"
asofdate <- args[7] #"62017"
Thirty.Yr.Mort.Spread <- args[8] # 175
When I try to run it in cmd using the .bat.. I get an error that says cannot change working directory. Anyone have any suggestions?
I sort-of understand where the error is but I'm struggling to fix it.
The path to my file with everything in it is
C:\MortgageMatt\Cirt2014-1
Edit:
I've also heard of something called R CMD Batch... should I look into that? I'm finding that it's an older technique.
What my code looked like before the Args/IF
# Input Values
Input.Directory <- "C:/Mortgage/Cirt 2014 - 1"
Output.Directory <- "C:/Mortgage/Cirt 2014 - 1"
Pool.ID.File <- "Cirt 2014-1 Loan Level.txt"
Pool.ID <- "Cirt 2014-1 NEW"
start<- 1
sims <- 2 # Number of Simulations
asofdate <- "62017"
Thirty.Yr.Mort.Spread <- 175

Answer 1

You can do all of this in R using one of these packages to parse command-line options:
docopt (my favourite)
optparse
argparse
getopt
or doing it manually -- not recommended.
You also do not want the older R CMD BATCH -- use Rscript (or littler, but littler does not work on Windows).
Code Example
#!/usr/bin/Rscript
suppressMessages(library(docopt))
doc <- "Usage: foo.R [-h] [-x] [--src REPODIR] [--out OUTDIR] [FILES...]
-s --src REPODIR source root directory [default: ~/git]
-o --out OUTDIR output directory [default: /tmp]
-h --help show this help text"
opt <- docopt(doc) # docopt parsing
print(opt)
Use with -h
You get a nice message, automatically, with not formatting need:
edd#rob:/tmp$ Rscript so50256138.R -h
Usage: foo.R [-h] [-x] [--src REPODIR] [--out OUTDIR] [FILES...]
-s --src REPODIR source root directory [default: ~/git]
-o --out OUTDIR output directory [default: /tmp]
-h --help show this help text
edd#rob:/tmp$
Use with argument
Note how one default argument is used, and the other from the command-line:
edd#rob:/tmp$ Rscript so50256138.R -s A
List of 9
$ --src : chr "A"
$ --out : chr "/tmp"
$ --help: logi FALSE
$ -x : logi FALSE
$ FILES : list()
$ src : chr "A"
$ out : chr "/tmp"
$ help : logi FALSE
$ x : logi FALSE
NULL
You can access them in opt by name or by option flag.
The docopt site has more; this is actually a portable specification and the CRAN package implements it for R.