Generating R plots through Perl

First off, if you are working in perl you might want to be aware of  
ruby and the "r for ruby" project:
http://rubyforge.org/projects/r4ruby/

Hello,

$R->send(qq (xVal <- c(1,2,3,4,5,6)));
$R->send(qq (yVal <- c(3,5,2,6,1,5)));
$R->send(qq (pdf("C:/Test Environment/R/perlPlotTest.pdf")));
$R->send(qq (plot(xVal, yVal)));
$R->send(qq (graphics.off()));

I don't really know how to write this in perl, but could you perhaps  
put the last three lines all in one call to "$R->send", using dev.off 
() then? Don't know if it would make a difference, but that's the  
only thing I could think of. I'm guessing something like this:

$R->send(qq (pdf("C:/Test Environment/R/perlPlotTest.pdf"); plot 
(xVal, yVal); dev.off()));

As the code indicates, I am using R's pdf function to create a pdf  
file
containing the plot of xVal and yVal.  I am using the graphics.off()
function rather than the dev.off() function as I get an error  
message of
"<simpleError in dev.off(): cannot shut down device 1 (the null
device)>" when dev.off() is used.  Is there another way to generate  
and
save a plot using the bridge connection that I described?  If not,  
what
would be an efficient way of generating and saving plots from  
within my
Perl program?  Any help would be greatly appreciated.

Thank you,
Ryan

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

Hello,

I tried what you suggested (i.e. combine the separate plot creation
commands into one command from Perl to R), and it worked.  The syntax is
as follows:

$R->send(qq (xVal <- c(1,2,3,4,5,6)));
$R->send(qq (yVal <- c(3,5,2,6,1,5)));
$R->send(qq (c(pdf("C:/Test Environment/R/perlPlotTest.pdf"), plot(xVal,
yVal), dev.off())));

I appreciate your help with this, and I will look into ruby and the "r
for ruby" project for future use.

Thanks again,
Ryan


-----Original Message-----
From: Charilaos Skiadas [mailto:skiadas at hanover.edu] 
Sent: Thursday, March 01, 2007 6:15 PM
To: Huckstorf, Ryan
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Generating R plots through Perl

First off, if you are working in perl you might want to be aware of ruby
and the "r for ruby" project:
http://rubyforge.org/projects/r4ruby/

Hello,

$R->send(qq (xVal <- c(1,2,3,4,5,6))); $R->send(qq (yVal <- 
c(3,5,2,6,1,5))); $R->send(qq (pdf("C:/Test 
Environment/R/perlPlotTest.pdf")));
$R->send(qq (plot(xVal, yVal)));
$R->send(qq (graphics.off()));

I don't really know how to write this in perl, but could you perhaps put
the last three lines all in one call to "$R->send", using dev.off
() then? Don't know if it would make a difference, but that's the only
thing I could think of. I'm guessing something like this:

$R->send(qq (pdf("C:/Test Environment/R/perlPlotTest.pdf"); plot (xVal,
yVal); dev.off()));

As the code indicates, I am using R's pdf function to create a pdf 
file containing the plot of xVal and yVal.  I am using the 
graphics.off() function rather than the dev.off() function as I get an

error message of "<simpleError in dev.off(): cannot shut down device 1

(the null device)>" when dev.off() is used.  Is there another way to 
generate and save a plot using the bridge connection that I described?

If not, what would be an efficient way of generating and saving plots 
from within my Perl program?  Any help would be greatly appreciated.

Thank you,
Ryan

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

Dear list,

It's never happened to me before in such a simple exercise but is not going away and I've checked my data are good. I want a simple lm model with one response and one predictor, where N is about 4,200 * data set not exactly small. Both x and y are nice, continuous variables having NA filtered out with a call to na.omit. So I did

mod = lm( y ~ x, data=x1)

Then the error,

Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
        NA/NaN/Inf in foreign function call (arg 4)

I did a trace back and it turned out it's an error thrown by the Fortran subroutine that seems to be trying a QR decomposition,

traceback()
3: .Fortran("dqrls", qr = x, n = n, p = p, y = y, ny = ny, tol = as.double(tol), 
       coefficients = mat.or.vec(p, ny), residuals = y, effects = y, 
       rank = integer(1), pivot = 1:p, qraux = double(p), work = double(2 * 
           p), PACKAGE = "base")
2: lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...)
1: lm(log.p.sales ~ log.mktcap, data = x1)

My question is why would QR fail since the default in lm.fit is 'singular.ok' ? Furthermore, is there a way to get around presumably a singularity in my design matrix? 

Thanks in advance.

Horace W. Tso

Folks, apologize for such an obvious oversight on my part. The reason qr
fails is, one of the data points has value of -Inf (response is actually
the log of something, and I have a zero in the original set). That
explains the error message in call to dqrls. I should have taken the
mean of the response before proceeding and that would tell me right away
what's wrong. 

Thanks.

H.

"Horace Tso" <Horace.Tso at pgn.com> 3/6/2007 1:45:28 PM >>>

Dear list,

It's never happened to me before in such a simple exercise but is not
going away and I've checked my data are good. I want a simple lm model
with one response and one predictor, where N is about 4,200 * data set
not exactly small. Both x and y are nice, continuous variables having NA
filtered out with a call to na.omit. So I did

mod = lm( y ~ x, data=x1)

Then the error,

Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...)
: 
        NA/NaN/Inf in foreign function call (arg 4)

I did a trace back and it turned out it's an error thrown by the
Fortran subroutine that seems to be trying a QR decomposition,

traceback()
3: .Fortran("dqrls", qr = x, n = n, p = p, y = y, ny = ny, tol =
as.double(tol), 
       coefficients = mat.or.vec(p, ny), residuals = y, effects = y, 
       rank = integer(1), pivot = 1:p, qraux = double(p), work =
double(2 * 
           p), PACKAGE = "base")
2: lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...)
1: lm(log.p.sales ~ log.mktcap, data = x1)

My question is why would QR fail since the default in lm.fit is
'singular.ok' ? Furthermore, is there a way to get around presumably a
singularity in my design matrix? 

Thanks in advance.

Horace W. Tso

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