[R] R & bash script

[(Ted Harding)]

On 18-Feb-05 Christian Schulz wrote:
> how is it possible to use more than one command when i'm
> didn't want use R CMD BATCH for specific reason?
> 
> $ echo "(x<-1:10)" | R --vanilla
> works
> 
> $ echo "(x<-1:10 ;y<-20:30 ;lm(y ~ x))" | R --vanilla
> works not.

Two things wrong with the above:

1. Use y<-21:30 with x<-1:10 otherwise "variable lengths differ"!

2. While (x<-1:10) returns the value of the assignment, i.e.
   [1]  1  2  3  4  5  6  7  8  9 10
   (which I suppose you wanted to see, as a check),
   even (x<-1:10 ;y<-20:30) is a syntax error in R, and
   (x<-1:10 ;y<-20:30 ;lm(y ~ x)) is an even bigger one!

You can emulate completely the typing in of commands by using
the "-e" option to echo, which allows you to use escape
sequences in the string, so that you can insert "\n" where
you would usually press Return. So:

echo -e "(x<-1:10) \n (y<-21:30) \n lm(y~x)" | R --vanilla

will work fine; and here the "(...)" cause R to print out
confirmation of the assignments "x<-1:10" and "y<-1:10"
which normally you perhaps wouldn't want, so the "production"
version of the above would be

echo -e "x<-1:10 \n y<-21:30 \n lm(y~x)" | R --vanilla

> Is it further possible using  bash variables like $i  from a loop
> in the bash echo call  i.e.
>   dm$x$i$k <- read.data("dmdata$x$i$k.dat",header=T)

Of course it is, as in

export LIM="10"
echo -e "x<-1:$LIM \n y<-21:30 \n lm(y~x)" | R --vanilla

but just make sure that you escape "$" when you need it
as part of an R syntax, e.g. when accessing named components
of a list. Thus:

echo -e "x<-1:$LIM \n y<-21:30 \n lm(y~x)\$fitted.values" | R --vanilla

Compare with what happens when you don't escape the "$", i.e.

echo -e "x<-1:$LIM \n y<-21:30 \n lm(y~x)$fitted.values" | R --vanilla

You need to take similar precautions for all shell metacharacters
which might occur in an R statement (see "man bash" for these).

Hoping this helps,
Ted.


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Date: 19-Feb-05                                       Time: 08:53:58
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