Re: [R] write output in a custom format
Perhaps I am missing the obvious, but can't you simply write a small
function that, given each particle object, returns a string with
the required output format (probably a couple of paste calls with
sep and collapse set), and then use sapply and this function on the
list of particles to create one long character vector, and simply
write that out in one go? If you wanted to avoid a loop, then that
means you have enough memory to store all the data, so you should
have enough memory for this character vector as well.
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
On Feb 15, 2008, at 7:57 AM, baptiste Auguié wrote:
Fair point! I guess I'll see how long it takes with a pure R
solution, and maybe then try some optimization if needed.
Thanks again,
baptiste
On 14 Feb 2008, at 21:27, jim holtman wrote:
There is nothing wrong with a loop for handling this case. Most of
your time is probably going to be spent writing out the files. If
you
don't want 'for' loops, you can use 'lapply', but I am not sure what
type of performance improvement you will see. You are having to
make decisions on each particle on how to write it. You can also use
awk/perl as you indicated, but you would have to write the data out
for those programs. You might take a test run and see. I would
guess
that by the time you format it for awk and then run awk, you could
have done the whole thing in R. But it is your choice and there are
plenty of tools to choose from.
On 2/14/08, baptiste Auguié [EMAIL PROTECTED] wrote:
Thanks for the input! It does work fine, however I'll have to do
another loop to repeat this whole process quite a few times (10^3,
10^4 particles maybe), so I was hoping for a solution without loop.
Maybe I could reshape all the values into a big array, dump it to a
file and replace some values using system(awk...). I just don't
really know how to format the data, having different number of
values
for some lines. Would that be a sensible thing to do?
thanks,
baptiste
On 14 Feb 2008, at 16:49, jim holtman wrote:
Here is a start. You basically have to interate through your
data and
use 'cat' to write it out:
particle - list(dose=c(1,100.0,0),pos=data.frame(x=c(0,1,0,1),y=c
(0,1,0,1)))
output - file(/tempxx.txt, w)
cat(particle$dose, \n, file=output, sep= )
for (i in 1:nrow(particle$pos)){
cat(particle$pos$x[i], particle$pos$y[i], \n, file=output,
sep= )
}
cat(#\n, file=output, sep= )
close(output)
Here is what the file looks like:
1 100 0
0 0
1 1
0 0
1 1
#
On 2/14/08, baptiste Auguié [EMAIL PROTECTED] wrote:
Hi,
I need to create a text file in the following format,
1 100.0 0
0 0
1 1
0 0
1 1
#
1 100.0 0
0 0
0 1
1 0
1 1
...
where # is part of the format and not a R comment.
Each block (delimited by #) consists of a first line with three
values, call it dose, and a list of (x,y) coordinates which are a
matrix or data.frame,
particle - list(dose=c(1,100.0,0),pos=data.frame(x=c
(0,1,0,1),y=c
(0,1,0,1)))
print(particle)
I'd like to establish a connection to a file and append to it a
particle block in the format above, or even write the whole
file at
once.
Because different lines have a different number of elements, I
couldn't get write.table to work in this case, and my attempts at
sink
(), dump(), writeLines(), writeChar() all turn into really dirty
solutions. I have this feeling I'm overlooking a simple solution.
Any help welcome,
baptiste
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto
__
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
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto
__
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
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
[R] write output in a custom format
Hi, I need to create a text file in the following format, 1 100.0 0 0 0 1 1 0 0 1 1 # 1 100.0 0 0 0 0 1 1 0 1 1 ... where # is part of the format and not a R comment. Each block (delimited by #) consists of a first line with three values, call it dose, and a list of (x,y) coordinates which are a matrix or data.frame, particle - list(dose=c(1,100.0,0),pos=data.frame(x=c(0,1,0,1),y=c (0,1,0,1))) print(particle) I'd like to establish a connection to a file and append to it a particle block in the format above, or even write the whole file at once. Because different lines have a different number of elements, I couldn't get write.table to work in this case, and my attempts at sink (), dump(), writeLines(), writeChar() all turn into really dirty solutions. I have this feeling I'm overlooking a simple solution. Any help welcome, baptiste _ Baptiste Auguié Physics Department University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag http://projects.ex.ac.uk/atto __ 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] write output in a custom format
Here is a start. You basically have to interate through your data and
use 'cat' to write it out:
particle - list(dose=c(1,100.0,0),pos=data.frame(x=c(0,1,0,1),y=c(0,1,0,1)))
output - file(/tempxx.txt, w)
cat(particle$dose, \n, file=output, sep= )
for (i in 1:nrow(particle$pos)){
cat(particle$pos$x[i], particle$pos$y[i], \n, file=output, sep= )
}
cat(#\n, file=output, sep= )
close(output)
Here is what the file looks like:
1 100 0
0 0
1 1
0 0
1 1
#
On 2/14/08, baptiste Auguié [EMAIL PROTECTED] wrote:
Hi,
I need to create a text file in the following format,
1 100.0 0
0 0
1 1
0 0
1 1
#
1 100.0 0
0 0
0 1
1 0
1 1
...
where # is part of the format and not a R comment.
Each block (delimited by #) consists of a first line with three
values, call it dose, and a list of (x,y) coordinates which are a
matrix or data.frame,
particle - list(dose=c(1,100.0,0),pos=data.frame(x=c(0,1,0,1),y=c
(0,1,0,1)))
print(particle)
I'd like to establish a connection to a file and append to it a
particle block in the format above, or even write the whole file at
once.
Because different lines have a different number of elements, I
couldn't get write.table to work in this case, and my attempts at sink
(), dump(), writeLines(), writeChar() all turn into really dirty
solutions. I have this feeling I'm overlooking a simple solution.
Any help welcome,
baptiste
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto
__
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
Cincinnati, OH
+1 513 646 9390
What is the problem 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] write output in a custom format
Thanks for the input! It does work fine, however I'll have to do
another loop to repeat this whole process quite a few times (10^3,
10^4 particles maybe), so I was hoping for a solution without loop.
Maybe I could reshape all the values into a big array, dump it to a
file and replace some values using system(awk...). I just don't
really know how to format the data, having different number of values
for some lines. Would that be a sensible thing to do?
thanks,
baptiste
On 14 Feb 2008, at 16:49, jim holtman wrote:
Here is a start. You basically have to interate through your data and
use 'cat' to write it out:
particle - list(dose=c(1,100.0,0),pos=data.frame(x=c(0,1,0,1),y=c
(0,1,0,1)))
output - file(/tempxx.txt, w)
cat(particle$dose, \n, file=output, sep= )
for (i in 1:nrow(particle$pos)){
cat(particle$pos$x[i], particle$pos$y[i], \n, file=output,
sep= )
}
cat(#\n, file=output, sep= )
close(output)
Here is what the file looks like:
1 100 0
0 0
1 1
0 0
1 1
#
On 2/14/08, baptiste Auguié [EMAIL PROTECTED] wrote:
Hi,
I need to create a text file in the following format,
1 100.0 0
0 0
1 1
0 0
1 1
#
1 100.0 0
0 0
0 1
1 0
1 1
...
where # is part of the format and not a R comment.
Each block (delimited by #) consists of a first line with three
values, call it dose, and a list of (x,y) coordinates which are a
matrix or data.frame,
particle - list(dose=c(1,100.0,0),pos=data.frame(x=c(0,1,0,1),y=c
(0,1,0,1)))
print(particle)
I'd like to establish a connection to a file and append to it a
particle block in the format above, or even write the whole file at
once.
Because different lines have a different number of elements, I
couldn't get write.table to work in this case, and my attempts at
sink
(), dump(), writeLines(), writeChar() all turn into really dirty
solutions. I have this feeling I'm overlooking a simple solution.
Any help welcome,
baptiste
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto
__
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
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto
__
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] write output in a custom format
There is nothing wrong with a loop for handling this case. Most of
your time is probably going to be spent writing out the files. If you
don't want 'for' loops, you can use 'lapply', but I am not sure what
type of performance improvement you will see. You are having to
make decisions on each particle on how to write it. You can also use
awk/perl as you indicated, but you would have to write the data out
for those programs. You might take a test run and see. I would guess
that by the time you format it for awk and then run awk, you could
have done the whole thing in R. But it is your choice and there are
plenty of tools to choose from.
On 2/14/08, baptiste Auguié [EMAIL PROTECTED] wrote:
Thanks for the input! It does work fine, however I'll have to do
another loop to repeat this whole process quite a few times (10^3,
10^4 particles maybe), so I was hoping for a solution without loop.
Maybe I could reshape all the values into a big array, dump it to a
file and replace some values using system(awk...). I just don't
really know how to format the data, having different number of values
for some lines. Would that be a sensible thing to do?
thanks,
baptiste
On 14 Feb 2008, at 16:49, jim holtman wrote:
Here is a start. You basically have to interate through your data and
use 'cat' to write it out:
particle - list(dose=c(1,100.0,0),pos=data.frame(x=c(0,1,0,1),y=c
(0,1,0,1)))
output - file(/tempxx.txt, w)
cat(particle$dose, \n, file=output, sep= )
for (i in 1:nrow(particle$pos)){
cat(particle$pos$x[i], particle$pos$y[i], \n, file=output,
sep= )
}
cat(#\n, file=output, sep= )
close(output)
Here is what the file looks like:
1 100 0
0 0
1 1
0 0
1 1
#
On 2/14/08, baptiste Auguié [EMAIL PROTECTED] wrote:
Hi,
I need to create a text file in the following format,
1 100.0 0
0 0
1 1
0 0
1 1
#
1 100.0 0
0 0
0 1
1 0
1 1
...
where # is part of the format and not a R comment.
Each block (delimited by #) consists of a first line with three
values, call it dose, and a list of (x,y) coordinates which are a
matrix or data.frame,
particle - list(dose=c(1,100.0,0),pos=data.frame(x=c(0,1,0,1),y=c
(0,1,0,1)))
print(particle)
I'd like to establish a connection to a file and append to it a
particle block in the format above, or even write the whole file at
once.
Because different lines have a different number of elements, I
couldn't get write.table to work in this case, and my attempts at
sink
(), dump(), writeLines(), writeChar() all turn into really dirty
solutions. I have this feeling I'm overlooking a simple solution.
Any help welcome,
baptiste
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto
__
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
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto
__
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
Cincinnati, OH
+1 513 646 9390
What is the problem 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.
