Re: [R] How to capture console output in a numeric format
Hmmm. Caution would seem more appropriate than fear.
My point was that if you want the results as numbers rather than characters,
it seems perverse to convert them to characters with print; you should use a
suitable mechanism to return them as numbers. If you're nervous of returning
values via the environment list and scoping rules it seems curious to accept
return via console output.
I used '-' as shorthand for a suitable mechanism. Depending on your
circumstances, '-' may not be OK- in this example it seems very clear
where it will find an existing definition of the variable being assigned.
Others in this thread have covered more robust approaches, but as long as
you're careful with environments and scoping it seems there are several ways
to do what you want.
Best regards,
Keith J
Ravi Varadhan rvarad...@jhmi.edu wrote in message
news:2f9ea67ef9ae1c48a147cb41be2e15c303e...@dom-eb-mail1.win.ad.jhu.edu...
I did think of this solution, Keith, but I am generally uncomfortable (may
be paranoid is a better word) with the use of `-'. Perhaps, my fear is
unjustified in this particular situation.
Thanks,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology School of Medicine Johns
Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Keith Jewell
Sent: Friday, June 24, 2011 11:49 AM
To: r-h...@stat.math.ethz.ch
Subject: Re: [R] How to capture console output in a numeric format
If you don't want the information as character, why are you printing it
rather than storing it in a matrix?
Why not something along the lines of this...
fr - function(x) { ## Rosenbrock Banana function
on.exit(aMatrix - rbind(aMatrix,(cbind(x1, x2, f
x1 - x[1]
x2 - x[2]
f - 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
f
}
aMatrix - NULL
ans - optim(c(-1.2,1), fr)
aMatrix
HTH
Keith J
-Original Message-
Ravi Varadhan rvarad...@jhmi.edu wrote in message
news:2f9ea67ef9ae1c48a147cb41be2e15c303e...@dom-eb-mail1.win.ad.jhu.edu...
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: rvarad...@jhmi.edu
__
R-help@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.
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] 24.20 7.095296 15.08 4.541696
[5] 6.029216 4.456256 8.879936 7.777856
[9] 4.728125 5.167901 4.21 4.437670
[13] 4.178989 4.326023 4.070813 4.221489
[17] 4.039810 4.896359 4.009379 4.077130
[21] 4.020798 3.993600 4.024586 4.117625
[25] 3.993115 3.976081 3.971089 4.023905
[29] 3.980807 3.952577 3.932179 3.935345
On Fri, Jun 24, 2011 at 10:39 AM, Ravi Varadhan rvarad...@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: rvarad...@jhmi.edumailto:rvarad...@jhmi.edu
[[alternative HTML version deleted]]
__
R-help@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?
__
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Re: [R] How to capture console output in a numeric format
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: rvarad...@jhmi.edumailto:rvarad...@jhmi.edu
[[alternative HTML version deleted]]
__
R-help@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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to capture console output in a numeric format
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: rvarad...@jhmi.edu
-Original Message-
From: jim holtman [mailto:jholt...@gmail.com]
Sent: Friday, June 24, 2011 10:48 AM
To: Ravi Varadhan
Cc: r-help@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] 24.20 7.095296 15.08 4.541696
[5] 6.029216 4.456256 8.879936 7.777856
[9] 4.728125 5.167901 4.21 4.437670
[13] 4.178989 4.326023 4.070813 4.221489
[17] 4.039810 4.896359 4.009379 4.077130
[21] 4.020798 3.993600 4.024586 4.117625
[25] 3.993115 3.976081 3.971089 4.023905
[29] 3.980807 3.952577 3.932179 3.935345
On Fri, Jun 24, 2011 at 10:39 AM, Ravi Varadhan rvarad...@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: rvarad...@jhmi.edumailto:rvarad...@jhmi.edu
[[alternative HTML version deleted]]
__
R-help@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?
__
R-help@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.
Re: [R] How to capture console output in a numeric format
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-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Ravi Varadhan
Sent: Friday, June 24, 2011 7:40 AM
To: r-help@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: rvarad...@jhmi.edumailto:rvarad...@jhmi.edu
[[alternative HTML version deleted]]
__
R-help@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.
__
R-help@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.
Re: [R] How to capture console output in a numeric format
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-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Ravi Varadhan
Sent: Friday, June 24, 2011 8:40 AM
To: r-help@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: rvarad...@jhmi.edumailto:rvarad...@jhmi.edu
[[alternative HTML version deleted]]
__
R-help@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.
__
R-help@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.
Re: [R] How to capture console output in a numeric format
On Jun 24, 2011, at 11:10 AM, 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()
Now, I need to tweak your solution to get the 3-column matrix.
I don't understand the 3 column matrix part of your request. Are
you asking for something that is not printed to the console? I only
get a sequence of single element vectors at my console when I execute:
ans - optim(c(-1.2,1), fr)
It would be nice, if there was a more direct way to get the
numerical output, perhaps a numeric option in capture.output().
But maybe Snow's answer is a complete solution.
Best,
Ravi.
--
David Winsemius, MD
West Hartford, CT
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to capture console output in a numeric format
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 +, 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: rvarad...@jhmi.edu
-Original Message-
From: jim holtman [mailto:jholt...@gmail.com]
Sent: Friday, June 24, 2011 10:48 AM
To: Ravi Varadhan
Cc: r-help@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] 24.20 7.095296 15.08 4.541696
[5] 6.029216 4.456256 8.879936 7.777856
[9] 4.728125 5.167901 4.21 4.437670
[13] 4.178989 4.326023 4.070813 4.221489
[17] 4.039810 4.896359 4.009379 4.077130
[21] 4.020798 3.993600 4.024586 4.117625
[25] 3.993115 3.976081 3.971089 4.023905
[29] 3.980807 3.952577 3.932179 3.935345
On Fri, Jun 24, 2011 at 10:39 AM, Ravi Varadhan rvarad...@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: rvarad...@jhmi.edumailto:rvarad...@jhmi.edu
[[alternative HTML version deleted]]
__
R-help@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
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to capture console output in a numeric format
If you don't want the information as character, why are you printing it
rather than storing it in a matrix?
Why not something along the lines of this...
fr - function(x) { ## Rosenbrock Banana function
on.exit(aMatrix - rbind(aMatrix,(cbind(x1, x2, f
x1 - x[1]
x2 - x[2]
f - 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
f
}
aMatrix - NULL
ans - optim(c(-1.2,1), fr)
aMatrix
HTH
Keith J
-Original Message-
Ravi Varadhan rvarad...@jhmi.edu wrote in message
news:2f9ea67ef9ae1c48a147cb41be2e15c303e...@dom-eb-mail1.win.ad.jhu.edu...
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: rvarad...@jhmi.edu
__
R-help@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.
Re: [R] How to capture console output in a numeric format
I did think of this solution, Keith, but I am generally uncomfortable (may be
paranoid is a better word) with the use of `-'. Perhaps, my fear is
unjustified in this particular situation.
Thanks,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins
University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Keith Jewell
Sent: Friday, June 24, 2011 11:49 AM
To: r-h...@stat.math.ethz.ch
Subject: Re: [R] How to capture console output in a numeric format
If you don't want the information as character, why are you printing it
rather than storing it in a matrix?
Why not something along the lines of this...
fr - function(x) { ## Rosenbrock Banana function
on.exit(aMatrix - rbind(aMatrix,(cbind(x1, x2, f
x1 - x[1]
x2 - x[2]
f - 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
f
}
aMatrix - NULL
ans - optim(c(-1.2,1), fr)
aMatrix
HTH
Keith J
-Original Message-
Ravi Varadhan rvarad...@jhmi.edu wrote in message
news:2f9ea67ef9ae1c48a147cb41be2e15c303e...@dom-eb-mail1.win.ad.jhu.edu...
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: rvarad...@jhmi.edu
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to capture console output in a numeric format
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 +, 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: rvarad...@jhmi.edu
-Original Message-
From: jim holtman [mailto:jholt...@gmail.com]
Sent: Friday, June 24, 2011 10:48 AM
To: Ravi Varadhan
Cc: r-help@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] 24.20 7.095296 15.08
4.541696
[5] 6.029216 4.456256 8.879936
7.777856
[9] 4.728125 5.167901 4.21
4.437670
[13] 4.178989 4.326023 4.070813
4.221489
[17] 4.039810 4.896359 4.009379
4.077130
[21] 4.020798 3.993600 4.024586
4.117625
[25] 3.993115 3.976081 3.971089
4.023905
[29] 3.980807 3.952577 3.932179
3.935345
On Fri, Jun 24, 2011 at 10:39 AM, Ravi Varadhan
rvarad...@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: rvarad...@jhmi.edumailto:rvarad...@jhmi.edu
[[alternative HTML version deleted]]
__
R-help@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
Re: [R] How to capture console output in a numeric format
On Fri, Jun 24, 2011 at 11:10 AM, Ravi Varadhan rvarad...@jhmi.edu 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().
This works in general assuming that we only wish to keep those output
lines having the same number of numerics as the most frequently output
length, i.e. 3 in your example above and 1 in the original example.
Also it does not require modification of the function to be optimized.
The first line extracts all numerics that have a decimal in them (so
that, for example, the 1 in [1] is not extracted). The next two lines
count how many numbers are in each extracted line and returns the most
frequently occurring non-zero length as n so that n is 3 here. The
final line extracts those lines and rbind's them. fvals is from your
post.
library(gsubfn)
fvals.numeric - strapply(fvals, [-0-9]+[.][0-9]*, as.numeric)
tab - table(sapply(fvals.numeric, length))
n - as.numeric(names(which.max(tab[names(tab) 0])))
do.call(rbind, Filter(function(x) length(x) == n, fvals.numeric))
If we knew in advance that we wanted only lines with 3 numbers and
that those three numbers are each prefaced by a space (both of which
are the case in your example) then we could simplify it to just this:
library(gsubfn)
fvals.numeric - strapply(fvals, [-0-9.]+, as.numeric)
do.call(rbind, fn$Filter(x ~ length(x) == 3, fvals.numeric))
There is more on strapply and fn$ at http://gsubfn.googlecode.com
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
__
R-help@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.
Re: [R] How to capture console output in a numeric format
On Fri, 2011-06-24 at 12:09 -0400, David Winsemius wrote:
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?
Well, environments have 'pass-by-reference' behavior. That is, when they
are passed to a function, modifications to the environment persist
outside the function call.
This is distinct from the Reference class (?methods::ReferenceClass).
But there are similar concepts. The methods of a reference class can
modify the class fields in a 'by-reference' fashion. However, the fields
need not be passed to a method.
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
'env$fout' works here too.
Thinking I also might be able to avoid the later assign(), I tried
these without success.
fr - function(x, env) { ## Rosenbrock Banana function
x1 - x[1]
x2 - x[2]
f - 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
if(exists('fout', env))
env[['fout']] - rbind(env[['fout']], c(x1, x2, f))
else
fout - c(x1=x1, x2=x2, f=f)
f
}
this would work with 'env$fout - c(x1=x1, x2=x2, f=f)' following the
'else'. Hence, David's version might look like this:
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
env$fout - c(x1=x1, x2=x2, f=f)
f
}
out - new.env()
ans - optim(c(-1.2, 1), fr, env=out)
out$fout
-Matt
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 +, 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: rvarad...@jhmi.edu
-Original Message-
From: jim holtman [mailto:jholt...@gmail.com]
Sent: Friday, June 24, 2011 10:48 AM
To: Ravi Varadhan
Cc: r-help@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] 24.20 7.095296 15.08
4.541696
[5] 6.029216 4.456256 8.879936
7.777856
[9] 4.728125 5.167901 4.21
4.437670
[13] 4.178989 4.326023 4.070813
4.221489
[17] 4.039810 4.896359 4.009379
4.077130
[21] 4.020798 3.993600 4.024586
4.117625
[25] 3.993115 3.976081 3.971089
4.023905
[29] 3.980807 3.952577 3.932179
3.935345
On Fri, Jun 24, 2011 at 10:39 AM, Ravi Varadhan
rvarad...@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
Re: [R] How to capture console output in a numeric format
On Fri, Jun 24, 2011 at 11:16 AM, William Dunlap wdun...@tibco.com wrote:
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.)
A variation of this is to use a proto object (or to use environments
directly at the expense of slightly more code). Below we keep all the
loose ends (i.e. aMatrix and fr) in p. Note that p$fr automatically
fills in the first argument of fr so that the version that ultimately
gets passed to optim only has one argument, x.
fr - function(p, x) { ## Rosenbrock Banana function
on.exit(p$aMatrix - rbind(p$aMatrix,cbind(x1, x2, f)))
x1 - x[1]
x2 - x[2]
f - 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
f
}
library(proto)
p - proto(fr = fr, aMatrix = NULL)
fvals - capture.output(ans - optim(c(-1.2,1), p$fr))
p$aMatrix
By the way, in my example using gsubfn another possibility might be to
assume that the last line of output defines the number of fields that
are to be used. That gives this which is intermediate in length
between the other two gsubfn solutions:
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))
library(gsubfn)
fvals.numeric - strapply(fvals, [-0-9]+[.][0-9]*, as.numeric)
n - length(tail(fvals.numeric, 1)[[1]])
do.call(rbind, Filter(function(x) length(x) == n, fvals.numeric))
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
