Re: [R] Thinning Lattice Plot
I see. I typically use a (one-sided) formula as the first argument to Ecdf, but didn't even think about that distinction in putting together this example. Thanks again for your help. - Elliot On Tue, Jul 31, 2012 at 12:46 PM, Deepayan Sarkar wrote: > On Tue, Jul 31, 2012 at 6:43 PM, Elliot Joel Bernstein > wrote: > > > Thanks everyone for your replies. I didn't know about the ecdfplot > function, > > so I'll start using that instead of Ecdf. Why is Ecdf not a lattice plot? > > The result certainly looks like other lattice plots, the arguments are > > similar to other lattice plots. In fact, internally it seems to just call > > the "histogram" function with a different prepanel and panel function. > Is it > > not considered a lattice plot only because it isn't part of the lattice > > package? > > Of course not. What you are saying is a valid description of the > Ecdf.formula() method, which definitely produces a lattice plot (or > trellis plot if you prefer). However, the example you gave, namely, > > x <- rnorm(1e6) > Ecdf(x) > > ends up calling Ecdf.default(), which is very much a traditional > graphics function. I should add that this is for Hmisc 3.9-2, and > don't know if the behaviour is different with other versions. > > Note that Ecdf() has more features than ecdfplot(), in particular it > allows weights. > > -Deepayan > -- Elliot Joel Bernstein, Ph.D. | Research Associate | FDO Partners, LLC 134 Mount Auburn Street | Cambridge, MA | 02138 Phone: (617) 503-4619 | Email: elliot.bernst...@fdopartners.com [[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] Thinning Lattice Plot
On Tue, Jul 31, 2012 at 6:43 PM, Elliot Joel Bernstein wrote: > Thanks everyone for your replies. I didn't know about the ecdfplot function, > so I'll start using that instead of Ecdf. Why is Ecdf not a lattice plot? > The result certainly looks like other lattice plots, the arguments are > similar to other lattice plots. In fact, internally it seems to just call > the "histogram" function with a different prepanel and panel function. Is it > not considered a lattice plot only because it isn't part of the lattice > package? Of course not. What you are saying is a valid description of the Ecdf.formula() method, which definitely produces a lattice plot (or trellis plot if you prefer). However, the example you gave, namely, x <- rnorm(1e6) Ecdf(x) ends up calling Ecdf.default(), which is very much a traditional graphics function. I should add that this is for Hmisc 3.9-2, and don't know if the behaviour is different with other versions. Note that Ecdf() has more features than ecdfplot(), in particular it allows weights. -Deepayan __ 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] Thinning Lattice Plot
Well, yes.
Terminology-wise, I guess one could say that it's a trellis plot in
the Hmisc package.
But I'd agree that this is nitpicking.
-- Bert
On Tue, Jul 31, 2012 at 6:13 AM, Elliot Joel Bernstein
wrote:
> Thanks everyone for your replies. I didn't know about the ecdfplot
> function, so I'll start using that instead of Ecdf. Why is Ecdf not a
> lattice plot? The result certainly looks like other lattice plots, the
> arguments are similar to other lattice plots. In fact, internally it seems
> to just call the "histogram" function with a different prepanel and panel
> function. Is it not considered a lattice plot only because it isn't part of
> the lattice package?
>
> Thanks.
>
> - Elliot
>
> On Tue, Jul 31, 2012 at 2:32 AM, Deepayan Sarkar
> wrote:
>
>> On Tue, Jul 31, 2012 at 2:43 AM, Elliot Joel Bernstein
>> wrote:
>> > Is there an easy way to "thin" a lattice plot? I often create plots from
>> > large data sets, and use the "pdf" command to save them to a file, but
>> the
>> > resulting files can be huge, because every point in the underlying
>> dataset
>> > is rendered in the plot, even though it isn't possible to see that much
>> > detail.
>> >
>> > For example:
>> >
>> > require(Hmisc)
>> > x <- rnorm(1e6)
>> >
>> > pdf("test.pdf")
>> > Ecdf(x)
>> > dev.off()
>>
>> (This is not a lattice plot, BTW.)
>>
>> > The resulting pdf files is 31MB.
>>
>> Hmm, for me it's 192K. Perhaps you have not bothered to update R recently.
>>
>> > Is there any easy way to get a smaller pdf
>> > file without having to manually prune the dataset?
>>
>> In general, as David noted, you need to do some sort of data
>> summarization; great if tools are available to that, otherwise
>> yourself. In this case, for example, it seems reasonable to do
>>
>> Ecdf(quantile(x, probs = ppoints(500, a=1)))
>>
>> If you don't like to do this yourself, ecdfplot() in latticeExtra will
>> allow
>>
>> library(latticeExtra)
>> ecdfplot(x, f.value = ppoints(500, a=1))
>>
>> -Deepayan
>>
>
>
>
> --
> Elliot Joel Bernstein, Ph.D. | Research Associate | FDO Partners, LLC
> 134 Mount Auburn Street | Cambridge, MA | 02138
> Phone: (617) 503-4619 | Email: elliot.bernst...@fdopartners.com
>
> [[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.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
__
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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] Thinning Lattice Plot
Thanks everyone for your replies. I didn't know about the ecdfplot
function, so I'll start using that instead of Ecdf. Why is Ecdf not a
lattice plot? The result certainly looks like other lattice plots, the
arguments are similar to other lattice plots. In fact, internally it seems
to just call the "histogram" function with a different prepanel and panel
function. Is it not considered a lattice plot only because it isn't part of
the lattice package?
Thanks.
- Elliot
On Tue, Jul 31, 2012 at 2:32 AM, Deepayan Sarkar
wrote:
> On Tue, Jul 31, 2012 at 2:43 AM, Elliot Joel Bernstein
> wrote:
> > Is there an easy way to "thin" a lattice plot? I often create plots from
> > large data sets, and use the "pdf" command to save them to a file, but
> the
> > resulting files can be huge, because every point in the underlying
> dataset
> > is rendered in the plot, even though it isn't possible to see that much
> > detail.
> >
> > For example:
> >
> > require(Hmisc)
> > x <- rnorm(1e6)
> >
> > pdf("test.pdf")
> > Ecdf(x)
> > dev.off()
>
> (This is not a lattice plot, BTW.)
>
> > The resulting pdf files is 31MB.
>
> Hmm, for me it's 192K. Perhaps you have not bothered to update R recently.
>
> > Is there any easy way to get a smaller pdf
> > file without having to manually prune the dataset?
>
> In general, as David noted, you need to do some sort of data
> summarization; great if tools are available to that, otherwise
> yourself. In this case, for example, it seems reasonable to do
>
> Ecdf(quantile(x, probs = ppoints(500, a=1)))
>
> If you don't like to do this yourself, ecdfplot() in latticeExtra will
> allow
>
> library(latticeExtra)
> ecdfplot(x, f.value = ppoints(500, a=1))
>
> -Deepayan
>
--
Elliot Joel Bernstein, Ph.D. | Research Associate | FDO Partners, LLC
134 Mount Auburn Street | Cambridge, MA | 02138
Phone: (617) 503-4619 | Email: elliot.bernst...@fdopartners.com
[[alternative HTML version deleted]]
__
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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] Thinning Lattice Plot
On Tue, Jul 31, 2012 at 2:43 AM, Elliot Joel Bernstein
wrote:
> Is there an easy way to "thin" a lattice plot? I often create plots from
> large data sets, and use the "pdf" command to save them to a file, but the
> resulting files can be huge, because every point in the underlying dataset
> is rendered in the plot, even though it isn't possible to see that much
> detail.
>
> For example:
>
> require(Hmisc)
> x <- rnorm(1e6)
>
> pdf("test.pdf")
> Ecdf(x)
> dev.off()
(This is not a lattice plot, BTW.)
> The resulting pdf files is 31MB.
Hmm, for me it's 192K. Perhaps you have not bothered to update R recently.
> Is there any easy way to get a smaller pdf
> file without having to manually prune the dataset?
In general, as David noted, you need to do some sort of data
summarization; great if tools are available to that, otherwise
yourself. In this case, for example, it seems reasonable to do
Ecdf(quantile(x, probs = ppoints(500, a=1)))
If you don't like to do this yourself, ecdfplot() in latticeExtra will allow
library(latticeExtra)
ecdfplot(x, f.value = ppoints(500, a=1))
-Deepayan
__
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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] Thinning Lattice Plot
You might also check ?pdf on your system. On Windows the default is for
compression. Your code creates a 186K file although it is slow to load
reflecting the overhead from decompressing the file.
--
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
> project.org] On Behalf Of David Winsemius
> Sent: Monday, July 30, 2012 5:47 PM
> To: Elliot Joel Bernstein
> Cc: r-help@r-project.org
> Subject: Re: [R] Thinning Lattice Plot
>
>
> On Jul 30, 2012, at 2:13 PM, Elliot Joel Bernstein wrote:
>
> > Is there an easy way to "thin" a lattice plot? I often create plots
> > from
> > large data sets, and use the "pdf" command to save them to a file,
> > but the
> > resulting files can be huge, because every point in the underlying
> > dataset
> > is rendered in the plot, even though it isn't possible to see that
> > much
> > detail.
> >
> > For example:
> >
> > require(Hmisc)
> > x <- rnorm(1e6)
> >
> > pdf("test.pdf")
> > Ecdf(x)
> > dev.off()
> >
> > The resulting pdf files is 31MB. Is there any easy way to get a
> > smaller pdf
> > file without having to manually prune the dataset?
>
> There are plotting routines that display the density of distributions.
> I use hexbin fairly frequently but that is for 2d plots. If you
> wanted the ECDF of a 1d vector, you could use cumsum() on the output
> of hist() or quantile() with suitable arguments to their parameters to
> control the degree of aggregation. Either of these yields an 8KB file
> on my machine.
>
> > pdf("test.pdf")
> > xyplot( cumsum(hist(x, plot=F)$intensities) ~ hist(x, plot=F)
> $breaks )
> > dev.off()
> quartz
> 2
>
> > pdf("test.pdf")
> > xyplot( (0:100)/100 ~ quantile(x, prob=(0:100)/100) )
> > dev.off()
> quartz
> 2
>
>
>
> >
> > Thanks.
> >
> > - Elliot
> >
> > --
> > Elliot Joel Bernstein, Ph.D. | Research Associate | FDO Partners, LLC
> > 134 Mount Auburn Street | Cambridge, MA | 02138
> > Phone: (617) 503-4619 | Email: elliot.bernst...@fdopartners.com
> >
>
> David Winsemius, MD
> Alameda, CA, USA
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Thinning Lattice Plot
On Jul 30, 2012, at 2:13 PM, Elliot Joel Bernstein wrote:
Is there an easy way to "thin" a lattice plot? I often create plots
from
large data sets, and use the "pdf" command to save them to a file,
but the
resulting files can be huge, because every point in the underlying
dataset
is rendered in the plot, even though it isn't possible to see that
much
detail.
For example:
require(Hmisc)
x <- rnorm(1e6)
pdf("test.pdf")
Ecdf(x)
dev.off()
The resulting pdf files is 31MB. Is there any easy way to get a
smaller pdf
file without having to manually prune the dataset?
There are plotting routines that display the density of distributions.
I use hexbin fairly frequently but that is for 2d plots. If you
wanted the ECDF of a 1d vector, you could use cumsum() on the output
of hist() or quantile() with suitable arguments to their parameters to
control the degree of aggregation. Either of these yields an 8KB file
on my machine.
> pdf("test.pdf")
> xyplot( cumsum(hist(x, plot=F)$intensities) ~ hist(x, plot=F)
$breaks )
> dev.off()
quartz
2
> pdf("test.pdf")
> xyplot( (0:100)/100 ~ quantile(x, prob=(0:100)/100) )
> dev.off()
quartz
2
Thanks.
- Elliot
--
Elliot Joel Bernstein, Ph.D. | Research Associate | FDO Partners, LLC
134 Mount Auburn Street | Cambridge, MA | 02138
Phone: (617) 503-4619 | Email: elliot.bernst...@fdopartners.com
David Winsemius, MD
Alameda, CA, USA
__
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.
[R] Thinning Lattice Plot
Is there an easy way to "thin" a lattice plot? I often create plots from
large data sets, and use the "pdf" command to save them to a file, but the
resulting files can be huge, because every point in the underlying dataset
is rendered in the plot, even though it isn't possible to see that much
detail.
For example:
require(Hmisc)
x <- rnorm(1e6)
pdf("test.pdf")
Ecdf(x)
dev.off()
The resulting pdf files is 31MB. Is there any easy way to get a smaller pdf
file without having to manually prune the dataset?
Thanks.
- Elliot
--
Elliot Joel Bernstein, Ph.D. | Research Associate | FDO Partners, LLC
134 Mount Auburn Street | Cambridge, MA | 02138
Phone: (617) 503-4619 | Email: elliot.bernst...@fdopartners.com
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
