[R] How to capture console output in a numeric format

[Matt Shotwell]

Ravi, 

Consider using an environment (i.e. a 'reference' object) to store the
results, avoiding string manipulation, and the potential for loss of
precision:

fr <- function(x, env) {   ## Rosenbrock Banana function
    x1 <- x[1]
    x2 <- x[2]
    f <- 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
    if(exists('fout', env))
        fout <- rbind(get('fout', env), c(x1, x2, f))
    else
        fout <- c(x1=x1, x2=x2, f=f)
    assign('fout', fout, env)
    f   
}

out <- new.env()
ans <- optim(c(-1.2, 1), fr, env=out)
out$fout

Best,
Matt

> 
On Fri, 2011-06-24 at 15:10 +0000, Ravi Varadhan wrote:
> Thank you very much, Jim.  That works!  
> 
> I did know that I could process the character strings using regex, but was also wondering if there was a direct way to get this.  
> 
> Suppose, in the current example I would like to obtain a 3-column matrix that contains the parameters and the function value:
> 
> fr <- function(x) {   ## Rosenbrock Banana function
>     on.exit(print(cbind(x1, x2, f)))
>     x1 <- x[1]
>     x2 <- x[2]
>     f <- 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
>     f	
> }
> 
> fvals <- capture.output(ans <- optim(c(-1.2,1), fr))
> 
> Now, I need to tweak your solution to get the 3-column matrix.  It would be nice, if there was a more direct way to get the numerical output, perhaps a numeric option in capture.output().
> 
> Best,
> Ravi.
> 
> -------------------------------------------------------
> Ravi Varadhan, Ph.D.
> Assistant Professor,
> Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University
> 
> Ph. (410) 502-2619
> email: rvaradhan at jhmi.edu
> 
> -----Original Message-----
> From: jim holtman [mailto:jholtman at gmail.com] 
> Sent: Friday, June 24, 2011 10:48 AM
> To: Ravi Varadhan
> Cc: r-help at r-project.org
> Subject: Re: [R] How to capture console output in a numeric format
> 
> try this:
> 
> > fr <- function(x) {   ## Rosenbrock Banana function
> +    on.exit(print(f))
> +    x1 <- x[1]
> +    x2 <- x[2]
> +    f <- 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
> +    f
> + }
> >
> > fvals <- capture.output(ans <- optim(c(-1.2,1), fr))
> > # convert to numeric
> > fvals <- as.numeric(sub("^.* ", "", fvals))
> >
> > fvals
>   [1] 24.20000000000000  7.09529600000000 15.08000000000000  4.54169600000000
>   [5]  6.02921600000000  4.45625600000000  8.87993600000000  7.77785600000000
>   [9]  4.72812500000000  5.16790100000000  4.21000000000000  4.43767000000000
>  [13]  4.17898900000000  4.32602300000000  4.07081300000000  4.22148900000000
>  [17]  4.03981000000000  4.89635900000000  4.00937900000000  4.07713000000000
>  [21]  4.02079800000000  3.99360000000000  4.02458600000000  4.11762500000000
>  [25]  3.99311500000000  3.97608100000000  3.97108900000000  4.02390500000000
>  [29]  3.98080700000000  3.95257700000000  3.93217900000000  3.93534500000000
> 
> 
> On Fri, Jun 24, 2011 at 10:39 AM, Ravi Varadhan <rvaradhan at jhmi.edu> wrote:
> > Hi,
> >
> > I would like to know how to capture the console output from running an algorithm for further analysis.  I can capture this using capture.output() but that yields a character vector.  I would like to extract the actual numeric values.  Here is an example of what I am trying to do.
> >
> > fr <- function(x) {   ## Rosenbrock Banana function
> >    on.exit(print(f))
> >    x1 <- x[1]
> >    x2 <- x[2]
> >    f <- 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
> >    f
> > }
> >
> > fvals <- capture.output(ans <- optim(c(-1.2,1), fr))
> >
> > Now, `fvals' contains character elements, but I would like to obtain the actual numerical values.  How can I do this?
> >
> > Thanks very much for any suggestions.
> >
> > Best,
> > Ravi.
> >
> > -------------------------------------------------------
> > Ravi Varadhan, Ph.D.
> > Assistant Professor,
> > Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University
> >
> > Ph. (410) 502-2619
> > email: rvaradhan at jhmi.edu<mailto:rvaradhan at jhmi.edu>
> >
> >
> >        [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
> 
> 
> 

-- 
Matthew S. Shotwell
Assistant Professor, Department of Biostatistics
School of Medicine, Vanderbilt University
1161 21st Ave. S2323 MCN Office CC2102L
Nashville, TN 37232-2158