R help - Jun 2011 - How to capture console output in a numeric format

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@jhmi.edu<mailto:rvaradhan@jhmi.edu>


	[[alternative HTML version deleted]]

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.
>


-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?

One possibility involves applying a regular expression via gsub:

   as.numeric(gsub("^\\[1\\] ","",fvals))


On Friday 24 June 2011 14:39:31 Ravi Varadhan 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.

Try using dput(f) instead of print(f) and
use eval(parse(text=capture.output(...))).

I would tend to use something like
   OUTPUTS <- list()
   fr <- function(x) {
       on.exit(OUTPUTS[[length(OUTPUTS)+1]] <<- list(x=x,f=f))
       ... compute and return f
   }
so you don't have to use capture.output.
(You can use trace() to automate this sort
of thing.)

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com  
> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Ravi Varadhan
> Sent: Friday, June 24, 2011 7:40 AM
> To: r-help at r-project.org
> Subject: [R] How to capture console output in a numeric format
> 
> 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.
>

Here is one approach (different from capture.output) that I believe accomplishes
what you are trying to do:

frtop <- function(){

	out <- numeric(0)
	topenv <- environment()

	fr <- function(x) {   ## Rosenbrock Banana function
    		x1 <- x[1]
    		x2 <- x[2]
    		f <- 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
		topenv$out <- c(topenv$out, f)
    		f
	}

	ans <- optim(c(-1.2,1), fr)

	list(ans=ans, out=out)
}

out <- frtop()

Now out is a list with 2 components, the first is the return value from optim,
the second is a vector with all the f values from the evaluation of the fr
function.

The basic idea is to wrap everything in a toplevel function, so that it has its
own local environment, then define the out vector in the toplevel environment. 
We also have a link to that environment through the topenv variable.  Now fr is
defined inside of frtop so it can access that environment (lexical scoping) and
so when we assign to topenv$out it is doing the assignment in the environment of
frtop.  Then we just run optim which calls fr a bunch of times, then output a
list with the output and the values at each call.

Hope this helps,


-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Ravi Varadhan
Sent: Friday, June 24, 2011 8:40 AM
To: r-help at r-project.org
Subject: [R] How to capture console output in a numeric format

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.