Re: [R] growing a list sequentially -- memory management
Thank you all for your answers. I think I have enough to keep going:
As pointed out it is probably not growing a list of objects each of size
6824 bytes that is the source of the problem per se (even if the list is not
pre-allocated), but rather a memory leak with the function fun within the
loop. I'm not providing the full example here because the code spans several
files.
Nonetheless the body of fun itself contains deeply nested lists, some which
are temporary and others which are part of the return value. So i'm now
trying to see what to do about these nested lists instead. About memory
leak: my assumption was that the memory needed for a temporary object (i.e.
defined within the body of a function) would be redeemed after the function
call, but perhaps i'm wrong about that (no automatic garbage collection)?
On Fri, Nov 14, 2008 at 6:37 AM, Patrick Burns [EMAIL PROTECTED]wrote:
The recommended technique is to create objects
as their final size and then subscript into them
with your data.
My intuition (which is often brutally wrong) tells
me that your case should not be overly traumatic.
So I'm suspicious that you are fragmenting memory
in other ways as well.
Patrick Burns
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
erwann rogard wrote:
hello,
i have something like:
out-list()
for(i in 1:n){
data-gen(...) #fixed size data
out[[i]]- fun(data)
}
object.size(out[[1]])
6824
In principle 1 GB should allow
n = 1024^3/6824 = 157347?
i have about 2GB are not taken by other processes. however, I can see the
memory shrinking quite rapidly on my system monitor and have to stop the
simulation after only n=300. why such a discrepancy? any remedy?
x86_64-pc-linux/RKWard/R2.8.0/ 4GB
thanks.
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[R] growing a list sequentially -- memory management
hello,
i have something like:
out-list()
for(i in 1:n){
data-gen(...) #fixed size data
out[[i]]- fun(data)
}
object.size(out[[1]])
6824
In principle 1 GB should allow
n = 1024^3/6824 = 157347?
i have about 2GB are not taken by other processes. however, I can see the
memory shrinking quite rapidly on my system monitor and have to stop the
simulation after only n=300. why such a discrepancy? any remedy?
x86_64-pc-linux/RKWard/R2.8.0/ 4GB
thanks.
[[alternative HTML version deleted]]
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[R] trellis: conditional statements within a panel function
hello,
what i'm trying to achieve is shown in the comment (# ...) below, which is
surely very wrong, but probably intuitively more meaningful that i can
provide in words.
xyplot(y~x2|x1+which,data=make.groups(
a=data.a,
b=data.b,
c=data.c
),
panel=function(...){
panel.abline(a=0,b=0)
panel.points(...)
# if(x1==0 which==a) panel.abline(...)
},
layout=c(2,3),
pch=20,
ylim=c(-10,10),
xlab=x2,
cex=0.5
)
thank!
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Re: [R] Arrays of Trellis plots
hi, xyplot(y~x2|x1+which,data= make.groups(dataframe1, dataframe2)) i'd like to replace the labels for dataframe1 and dataframe2 say with c(A,B). is there a way? thanks! On Mon, Oct 27, 2008 at 2:23 PM, Deepayan Sarkar [EMAIL PROTECTED]wrote: On 10/27/08, erwann rogard [EMAIL PROTECTED] wrote: hello, the example below does not work. (i know it's not supposed, but it makes it clear what i'm trying to achieve) par(mfrow=c(2,1)) xyplot(y~x2|x1,data=dataframe1,pch=20) xyplot(y~x2|x1,data=dataframe2,pch=20) i know i could probably merge the two datasets and do something like xyplot(y~x2|x1+dataset,data=merged) any other suggestion? xyplot(y~x2|x1+which,data=make.groups(dataframe1, dataframe2)) -Deepayan [[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] Arrays of Trellis plots
hello, the example below does not work. (i know it's not supposed, but it makes it clear what i'm trying to achieve) par(mfrow=c(2,1)) xyplot(y~x2|x1,data=dataframe1,pch=20) xyplot(y~x2|x1,data=dataframe2,pch=20) i know i could probably merge the two datasets and do something like xyplot(y~x2|x1+dataset,data=merged) any other suggestion? thanks. [[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.
Re: [R] Arrays of Trellis plots
Thank you all, I've got everything I need now.
On Mon, Oct 27, 2008 at 2:29 PM, [EMAIL PROTECTED] wrote:
the example below does not work. (i know it's not supposed, but it makes
it
clear what i'm trying to achieve)
par(mfrow=c(2,1))
xyplot(y~x2|x1,data=dataframe1,pch=20)
xyplot(y~x2|x1,data=dataframe2,pch=20)
i know i could probably merge the two datasets and do something like
xyplot(y~x2|x1+dataset,data=merged)
par is a base graphics command, and doesn't work with grid/lattice
graphics. While it is possible to merge grid and base graphics using for
example the gridBase package, I suspect what you want is to draw two
lattice plots on the same figure. For this, you need to read up on
viewports, and try an example like this:
pushViewport(viewport(layout=grid.layout(2,1)))
pushViewport(viewport(layout.pos.row=1))
topplot = xyplot(Sepal.Length ~ Petal.Length | Species, data = iris)
print(topplot, newpage=FALSE)
upViewport()
pushViewport(viewport(layout.pos.row=2))
bottomplot = xyplot(Sepal.Width ~ Petal.Width | Species, data = iris)
print(bottomplot, newpage=FALSE)
popViewport(2)
See also section 5.5 in Paul Murrell's book ('R Graphics').
Regards,
Richie.
Mathematical Sciences Unit
HSL
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[R] Extracting variables with a given prefix in the parent environment
hi,
get.vars.name.prefix-function(prefix){
result-list()
len-nchar(prefix)
var.names-ls(name=1,pattern=prefix) #name=1 probably wrong option
print(var.names)
for(i in 1:length(var.names)){
name-var.names[i]
field-substr(name,len+1,nchar(name))
result[[field]]-get(name)
}
result
}
for example
x.1-1
x.2-2
get.vars.name.prefix(x.) should return 1,2
this does not work if i call if from within another function:
g-function(){
x.1-1
x.2-2
get.vars.name.prefix(x.) # should return 1,2, nothing else
}
i would like the environment specified within ls(...) to be that of the body
of the function that calls get.vars.name.prefix. apparently name=1 is
probably not the right option.
thanks.
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Re: [R] Extracting variables with a given prefix in the parent environment
Thank you all for your answers.
On Mon, Oct 20, 2008 at 6:32 AM, Henrique Dallazuanna [EMAIL PROTECTED]wrote:
Try this:
Using 'envir' argument, in ls and get function:
get.vars.name.prefix-function(prefix, envir = parent.frame()){
result-list()
len-nchar(prefix)
var.names-ls(envir = envir,pattern=prefix)
print(var.names)
for(i in 1:length(var.names)){
name-var.names[i]
field-substr(name,len+1,nchar(name))
result[[field]]-get(name, envir = envir)
}
result
}
On Mon, Oct 20, 2008 at 4:06 AM, erwann rogard [EMAIL PROTECTED]wrote:
hi,
get.vars.name.prefix-function(prefix){
result-list()
len-nchar(prefix)
var.names-ls(name=1,pattern=prefix) #name=1 probably wrong option
print(var.names)
for(i in 1:length(var.names)){
name-var.names[i]
field-substr(name,len+1,nchar(name))
result[[field]]-get(name)
}
result
}
for example
x.1-1
x.2-2
get.vars.name.prefix(x.) should return 1,2
this does not work if i call if from within another function:
g-function(){
x.1-1
x.2-2
get.vars.name.prefix(x.) # should return 1,2, nothing else
}
i would like the environment specified within ls(...) to be that of the
body
of the function that calls get.vars.name.prefix. apparently name=1 is
probably not the right option.
thanks.
[[alternative HTML version deleted]]
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--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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[R] passing a list where names arguments are expected
hi,
say i have a function f and i'd like to to call it like this:
1) f(list(a=...,b=...))
but i can't do it, because f is defined as:
2) f-function(a=NULL,b=NULL){...}
is there a way that i can approximate 1), such as mapping list(a=,...b=...)
to list(a=,...b=...) and then replacing list by f, and then evaluating
the expression?
thanks.
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Re: [R] passing a list where names arguments are expected
Indeed, that's all I need. Thanks!
On Sun, Oct 19, 2008 at 11:09 PM, Kaom Te [EMAIL PROTECTED] wrote:
I believe you want
do.call(f, list(a =..., b=...))
?do.call
-Kaom
On Oct 19, 2008, at 7:55 PM, erwann rogard wrote:
hi,
say i have a function f and i'd like to to call it like this:
1) f(list(a=...,b=...))
but i can't do it, because f is defined as:
2) f-function(a=NULL,b=NULL){...}
is there a way that i can approximate 1), such as mapping
list(a=,...b=...)
to list(a=,...b=...) and then replacing list by f, and then
evaluating
the expression?
thanks.
[[alternative HTML version deleted]]
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Re: [R] R-code in Latex --- $ sign causes error
Haven't tried fancyvrb, but meanwhile this fixes it:
http://www.latex-community.org/viewtopic.php?f=4t=2783p=10955#p10955
On Sat, Oct 18, 2008 at 12:00 AM, Henrik Bengtsson [EMAIL PROTECTED]wrote:
Check out the 'fancyvrb' latex package - that is quite flexible and I
wouldn't be surprised if it can help you. Make sure to read the docs
(fancyvrb.pdf).
/H
On Fri, Oct 17, 2008 at 8:37 PM, erwann rogard [EMAIL PROTECTED]
wrote:
Thanks for clarifying. Yes, \$ works in latex, but not *within* the
lstlisting environment.
On Fri, Oct 17, 2008 at 11:32 PM, Gabor Grothendieck
[EMAIL PROTECTED] wrote:
Greg was referring to what to write in R character literals in order to
generate
a single \ in the output from R which in turn would be fed into latex or
Sweave
and then latex. Google this: special characters in latex
On Fri, Oct 17, 2008 at 11:23 PM, erwann rogard
[EMAIL PROTECTED]
wrote:
Thanks, but unfortunately
\begin{lstlisting}
\\$
\end{lstlisting}
and
\begin{lstlisting}
$
\end{lstlisting}
still generate the same error.
On Fri, Oct 17, 2008 at 9:38 PM, Greg Snow [EMAIL PROTECTED]
wrote:
The $ is special in TeX/LaTeX as a shortcut for beginning/ending
inline
math mode, so if you want an actual $ then you need to escape it so
that
the
TeX/LaTeX file has \$ in it. This means that in your R code that
generates
the file you may need \\$ or in some cases $.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of erwann rogard
Sent: Friday, October 17, 2008 5:18 PM
To: r-help@r-project.org
Subject: [R] R-code in Latex --- $ sign causes error
hi,
here's what i have:
\lstset{
basicstyle=\ttfamily,
keywordstyle=\bfseries,
showstringspaces=false,
columns = fullflexible,
mathescape = true,
language=R
}
\begin{lstlisting}
lst$val-val
\end{lstlisting}
./software.tex:16:Extra }, or forgotten \endgroup. lst$
the culprit here is the $ sign.
thanks.
ps:
i'm posting here rather than Latex is bec i guess an R user is more
likely 2
to have encountered this before, but if not ok, pls let me know.
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[R] R-code in Latex --- $ sign causes error
hi,
here's what i have:
\lstset{
basicstyle=\ttfamily,
keywordstyle=\bfseries,
showstringspaces=false,
columns = fullflexible,
mathescape = true,
language=R
}
\begin{lstlisting}
lst$val-val
\end{lstlisting}
./software.tex:16:Extra }, or forgotten \endgroup. lst$
the culprit here is the $ sign.
thanks.
ps:
i'm posting here rather than Latex is bec i guess an R user is more likely 2
to have encountered this before, but if not ok, pls let me know.
[[alternative HTML version deleted]]
__
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.
Re: [R] R-code in Latex --- $ sign causes error
Thanks, but unfortunately
\begin{lstlisting}
\\$
\end{lstlisting}
and
\begin{lstlisting}
$
\end{lstlisting}
still generate the same error.
On Fri, Oct 17, 2008 at 9:38 PM, Greg Snow [EMAIL PROTECTED] wrote:
The $ is special in TeX/LaTeX as a shortcut for beginning/ending inline
math mode, so if you want an actual $ then you need to escape it so that the
TeX/LaTeX file has \$ in it. This means that in your R code that generates
the file you may need \\$ or in some cases $.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of erwann rogard
Sent: Friday, October 17, 2008 5:18 PM
To: r-help@r-project.org
Subject: [R] R-code in Latex --- $ sign causes error
hi,
here's what i have:
\lstset{
basicstyle=\ttfamily,
keywordstyle=\bfseries,
showstringspaces=false,
columns = fullflexible,
mathescape = true,
language=R
}
\begin{lstlisting}
lst$val-val
\end{lstlisting}
./software.tex:16:Extra }, or forgotten \endgroup. lst$
the culprit here is the $ sign.
thanks.
ps:
i'm posting here rather than Latex is bec i guess an R user is more
likely 2
to have encountered this before, but if not ok, pls let me know.
[[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.
[[alternative HTML version deleted]]
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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.
Re: [R] R-code in Latex --- $ sign causes error
Thanks for clarifying. Yes, \$ works in latex, but not *within* the
lstlisting environment.
On Fri, Oct 17, 2008 at 11:32 PM, Gabor Grothendieck
[EMAIL PROTECTED] wrote:
Greg was referring to what to write in R character literals in order to
generate
a single \ in the output from R which in turn would be fed into latex or
Sweave
and then latex. Google this: special characters in latex
On Fri, Oct 17, 2008 at 11:23 PM, erwann rogard [EMAIL PROTECTED]
wrote:
Thanks, but unfortunately
\begin{lstlisting}
\\$
\end{lstlisting}
and
\begin{lstlisting}
$
\end{lstlisting}
still generate the same error.
On Fri, Oct 17, 2008 at 9:38 PM, Greg Snow [EMAIL PROTECTED] wrote:
The $ is special in TeX/LaTeX as a shortcut for beginning/ending inline
math mode, so if you want an actual $ then you need to escape it so that
the
TeX/LaTeX file has \$ in it. This means that in your R code that
generates
the file you may need \\$ or in some cases $.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of erwann rogard
Sent: Friday, October 17, 2008 5:18 PM
To: r-help@r-project.org
Subject: [R] R-code in Latex --- $ sign causes error
hi,
here's what i have:
\lstset{
basicstyle=\ttfamily,
keywordstyle=\bfseries,
showstringspaces=false,
columns = fullflexible,
mathescape = true,
language=R
}
\begin{lstlisting}
lst$val-val
\end{lstlisting}
./software.tex:16:Extra }, or forgotten \endgroup. lst$
the culprit here is the $ sign.
thanks.
ps:
i'm posting here rather than Latex is bec i guess an R user is more
likely 2
to have encountered this before, but if not ok, pls let me know.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-
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and provide commented, minimal, self-contained, reproducible code.
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[R] Trellis, conditioning on more than 2 variables,
hello, i need help with: data$f1-as.factor(data$f1) data$f2-as.factor(data$f2) s3-equal.count(data$s2,number=3) densityplot(~y| f1 + f2 + s3, data=mydata ) this produces 3 plots, *successively*, one for each value of s3. i was hoping it would produce one plot. is trellis limited to 2 conditional variables? if not, what are the appropriate commands? thanks! [[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.
