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

[David Winsemius]

On Jun 24, 2011, at 11:27 AM, Matt Shotwell wrote:

> 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))

So _that's_ what a reference object is?

This seems to give the same results in this example. Am I committing  
any sins by sneaking around the get()?

     if(exists('fout', env))
        fout <- rbind(env[['fout']], c(x1, x2, f))  # seems more direct

Thinking I also might be able to avoid the later assign(), I tried  
these without success.

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))
        env[['fout']] <- rbind(env[['fout']], c(x1, x2, f))
    else
        fout <- c(x1=x1, x2=x2, f=f)

    f
}

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

  Is there no '[[<-' for environments? (Also tried '<<-' but I know  
that is sinful/ )

-- 
David.
>    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
>
> ______________________________________________
> 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.

David Winsemius, MD
West Hartford, CT