Re: [R] Hardware for a new Workstation for best performance using R
I can speak to some of these issues. I don't know about how much benefit you can get from SMP for *single* instances of R, though. 1.) Multicore will be helpful, at least, if you are running several instances of R at once. So, for example, if you have people running two different models at the same time, the OS can use separate processors or cores for each instance. 2.) Yes, by all means you should use linux instead of windows. The graphics output is completely compatible with whatever applications you want to paste them into on Windows. Linux is cheaper, stabler, and better at using the system's resources. 3.) If you're doing big datasets, you certainly need a 64-bit processor, operating system, and R. Consider, perhaps, a dual-Athlon XP 64 machine with a big pile of RAM? Andy -- Andrew J Perrin - andrew_perrin (at) unc.edu - http://perrin.socsci.unc.edu Assistant Professor of Sociology; Book Review Editor, _Social Forces_ University of North Carolina - CB#3210, Chapel Hill, NC 27599-3210 USA New Book: http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/178592.ctl On Thu, 15 Mar 2007, Sascha Morach wrote: > Hi, > > we are looking for a new workstation for big datasets/applications (easily > up to 100'000 records and up to 300 Variables) using R. As an example: > Variable Selection for a multivariate regression using stepAIC. > > What is the best configuration for a workstation to reach a high performance > level for computing with R? > > Single core or multi core (is R together with nws package really able to use > advantage of multi core processors, any experience/benchmarks on that)? > > Shall we use Linux instead of Windows? If yes, how is the compatibility of > graphics computed on Linux if we like to use them after on windows? And what > are the advantages using Linux instead of Windows? > > What kind of workstations are you using (hardware and operating system) for > big data computations? And are you satisfied with it? > > I'm quite familiar with pc or server hardware. > > Thanks in advance > > Sascha Morach > > __ > R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part) > > 2.) Yes, by all means you should use linux instead of windows. The > graphics output is completely compatible with whatever applications you > want to paste them into on Windows. This turns out not to be the case. It is not trivial to produce good graphics off Windows for adding to Microsoft Office documents (regrettably an important case for many people). There has been much discussion of this on the R-sig-mac mailing list, for example, where PNG bitmaps (at sufficiently high resolution) seem to be the preferred method. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote: > On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part) > > > > 2.) Yes, by all means you should use linux instead of windows. The > > graphics output is completely compatible with whatever applications you > > want to paste them into on Windows. > > This turns out not to be the case. > > It is not trivial to produce good graphics off Windows for adding to > Microsoft Office documents (regrettably an important case for many > people). There has been much discussion of this on the R-sig-mac mailing > list, for example, where PNG bitmaps (at sufficiently high resolution) > seem to be the preferred method. On Windows one can produce metafile output directly from R. This is a Windows vector graphics format so it retains resolution under expansion and shrinkage and it also works well with Microsoft Office. This would likely give superior results (maximum resolution, more flexibility in post processing, easier to do, interfaces better with Office) to using and transferring graphics from another OS, particularly png which is only bit-mapped rather than vector-based. __ R-help@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
On Mon, 2007-03-19 at 11:43 -0400, Gabor Grothendieck wrote: > On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote: > > On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part) > > > > > > 2.) Yes, by all means you should use linux instead of windows. The > > > graphics output is completely compatible with whatever applications you > > > want to paste them into on Windows. > > > > This turns out not to be the case. > > > > It is not trivial to produce good graphics off Windows for adding to > > Microsoft Office documents (regrettably an important case for many > > people). There has been much discussion of this on the R-sig-mac mailing > > list, for example, where PNG bitmaps (at sufficiently high resolution) > > seem to be the preferred method. > > On Windows one can produce metafile output directly from R. This > is a Windows vector graphics format so it retains resolution under expansion > and shrinkage and it also works well with Microsoft Office. This > would likely give > superior results (maximum resolution, more flexibility in post processing, > easier to do, interfaces better with Office) to using and transferring > graphics > from another OS, particularly png which is only bit-mapped rather than > vector-based. Gabor, The problem is the the WMF/EMF formats are Windows specific, given the proprietary nature of the format. On non-Windows platforms (ie. Linux) which is what Thomas was referring to, there is the libEMF library, but experience indicates it is not a satisfactory method. Thus, as has been discussed on r-help extensively as well over the past several years, there is no real _cross-platform_ approach to getting 'simple' vector based graphics into Word or Powerpoint for use in 'normal' day to day operations, which typically means viewing on a screen. The alternative as Thomas noted, is typically to use a high-res PNG file, which ends up being quite large and if there are several, makes the .DOC or .PPT file quite large as well, and ultimately, impractical. Another approach is to use EPS images generated in R, enable the creation of lower-res bitmapped previews on import into Office, to enable basic visual review and placement, but to then print a hard copy or export to a PS file via a PS compatible printer/driver which will properly render the embedded EPS image. If required, one can convert the PS file to a PDF file, when then allows for subsequent display using a PDF viewer in full screen mode, if a presentation is the goal. Until such time as SVG becomes more of a standard on multiple platforms (even OO.org does not yet support it for import), creating vector based images for use in Windows apps, from non-Windows systems, will continue to be problematic. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
On 3/19/07, Marc Schwartz <[EMAIL PROTECTED]> wrote: > On Mon, 2007-03-19 at 11:43 -0400, Gabor Grothendieck wrote: > > On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote: > > > On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part) > > > > > > > > 2.) Yes, by all means you should use linux instead of windows. The > > > > graphics output is completely compatible with whatever applications you > > > > want to paste them into on Windows. > > > > > > This turns out not to be the case. > > > > > > It is not trivial to produce good graphics off Windows for adding to > > > Microsoft Office documents (regrettably an important case for many > > > people). There has been much discussion of this on the R-sig-mac mailing > > > list, for example, where PNG bitmaps (at sufficiently high resolution) > > > seem to be the preferred method. > > > > On Windows one can produce metafile output directly from R. This > > is a Windows vector graphics format so it retains resolution under expansion > > and shrinkage and it also works well with Microsoft Office. This > > would likely give > > superior results (maximum resolution, more flexibility in post processing, > > easier to do, interfaces better with Office) to using and transferring > > graphics > > from another OS, particularly png which is only bit-mapped rather than > > vector-based. > > Gabor, > > The problem is the the WMF/EMF formats are Windows specific, given the > proprietary nature of the format. > > On non-Windows platforms (ie. Linux) which is what Thomas was referring I don't think so. The statement being quoted was: Yes, by all means you should use linux instead of windows __ R-help@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
On Mon, 19 Mar 2007, Gabor Grothendieck wrote: > On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote: >> On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part) >>> >>> 2.) Yes, by all means you should use linux instead of windows. The >>> graphics output is completely compatible with whatever applications you >>> want to paste them into on Windows. >> >> This turns out not to be the case. >> >> It is not trivial to produce good graphics off Windows for adding to >> Microsoft Office documents (regrettably an important case for many >> people). There has been much discussion of this on the R-sig-mac mailing >> list, for example, where PNG bitmaps (at sufficiently high resolution) >> seem to be the preferred method. > > On Windows one can produce metafile output directly from R. Yes, indeed. However, this fact is of limited help when working on another operating system, which was the focus of the original question. -thomas __ R-help@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote: > On Mon, 19 Mar 2007, Gabor Grothendieck wrote: > > > On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote: > >> On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part) > >>> > >>> 2.) Yes, by all means you should use linux instead of windows. The > >>> graphics output is completely compatible with whatever applications you > >>> want to paste them into on Windows. > >> > >> This turns out not to be the case. > >> > >> It is not trivial to produce good graphics off Windows for adding to > >> Microsoft Office documents (regrettably an important case for many > >> people). There has been much discussion of this on the R-sig-mac mailing > >> list, for example, where PNG bitmaps (at sufficiently high resolution) > >> seem to be the preferred method. > > > > On Windows one can produce metafile output directly from R. > > Yes, indeed. However, this fact is of limited help when working on another > operating system, which was the focus of the original question. What was being discussed included: "Yes, by all means you should use linux instead of windows." and the subsequent discussion seemed to support that including the suggestion that producing graphics on linux is just as good as producing it on windows even if its intended to be transferred to Microsoft Office on Windows but in fact there are a number of advantages to doing it on Windows if you intend to use Microsoft Office there. __ R-help@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
Thomas Lumley wrote: > On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part) > >> 2.) Yes, by all means you should use linux instead of windows. The >> graphics output is completely compatible with whatever applications you >> want to paste them into on Windows. >> > > This turns out not to be the case. > > It is not trivial to produce good graphics off Windows for adding to > Microsoft Office documents (regrettably an important case for many > people). There has been much discussion of this on the R-sig-mac mailing > list, for example, where PNG bitmaps (at sufficiently high resolution) > seem to be the preferred method. > > -thomas > > One option for people who are paying for software anyways is to install Adobe Acrobat Writer software for generating PDF files from Word. This also allows you to include ouput from the pdf() device, and the end result comes out really nice. __ R-help@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
On Mon, 19 Mar 2007, Thomas Lumley wrote: >> On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote: >>> On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part) 2.) Yes, by all means you should use linux instead of windows. The graphics output is completely compatible with whatever applications you want to paste them into on Windows. >>> >>> This turns out not to be the case. >>> >>> It is not trivial to produce good graphics off Windows for adding to >>> Microsoft Office documents (regrettably an important case for many >>> people). There has been much discussion of this on the R-sig-mac mailing >>> list, for example, where PNG bitmaps (at sufficiently high resolution) >>> seem to be the preferred method. >> >> On Windows one can produce metafile output directly from R. > > Yes, indeed. However, this fact is of limited help when working on another > operating system, which was the focus of the original question. > > -thomas One solution which has not been covered here is to use both operating systems. For example, I need to present in Powerpoint, yet my work is done under Linux where I have substantially more RAM and CPU power. Typically, I'll run my analysis under Linux and then take advantage of the binary compatibility of the .RData file and move my final values from Linux to Windows via Samba; I may delete large intermediate results before the transfer to compendate for my lack of RAM under Windows. Some small scripts which may have been developed under Linux are used to create the plots which are placed in my Powerpoint presentations. By an large, the plots developed under Linux drop right into the Windows presentations, although there are occasional font size difficulties that require adjustments. Mark Dalphin -- Mark Dalphin Dept Comp Biol, M/S AW2/D3262 Amgen, Inc. 1201 Amgen Court W Seattle, WA 98119 __ R-help@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
For any kind of R plots that need to be inserted in office documents
either on Windows OR on Linux you will always achieve the best result by
using the postscript device, then converting *.ps to *.eps and inserting
*.eps into Office (OpenOffice as well). *.eps files contain previews for
you to edit the documents on screen, but the final output can be done
using Print to file using a Postscript driver and converting to PDF --
this will ensure all your R-graphics, but also ALL of your vector
illustrations, to be displayed in high quality vector manner.
In fact this is about the only way to put high quality plots into
presentations or word processing documents (ANY, MSOffice included). In
general it works easier on Linux because you will have all tools in the
repository and for free. On Windows you will probably end up using
Distiller, which costs quite a lot or FreePdfXP if it still exists and
works correctly.
There is only one place where Windows, or for that sake Mac, scores
better, and yet not ultimately: if you want to draw or design vector
illustrations then you have larger selection of tools on Windows (Corel,
Illustrator, Xara etc), on Mac - Illustrator and on Linux - InkScape
(recommnded) and Xara.
Now if you go this way, the workflow looks like:
> postscript("fig1.ps", width=5,height=5)
> plot(x~y)
> dev.off()
> q()
$ ps2eps --ignoreBB --gsbbox -r 300 -R + -f fig1.ps # 300dpi thumbnail
$ ooffice
- import eps file, you will see the same as usual hi-res preview
- Print, print to file, on request "Reduce Transparency" - YES
$ ps2pdf13 mydoc.ps
result: mydoc.pdf
For presentations simply use US Letter landscape instead of A4 for paper
size and printing (to file) and this will nicely fit into the screen
with minimal loss of space.
If the question is in the impossibility to do things on Linux: Windows
will not help you to do the above -- there are no tools. You may find
another solution, but for the quality of output the above is the best.
Other formats, like WMF, EMF, AI, CDR are either of no good use for
anything (the first 2) or are incompatible with Office (AI, CDR).
Moreover, using InkScape and RSvgDevice you can create SVG plots to
which you can add whatever illustrations you want just in the same
document because SVG is native for InkScape.
Oleg
PS. If you want to see examples of how such plots and illustrations look
like (created fully on Linux with the above workflow, drop me a line, I
will send a PDF).
Dalphin, Mark wrote:
> On Mon, 19 Mar 2007, Thomas Lumley wrote:
>>> On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote:
On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part)
> 2.) Yes, by all means you should use linux instead of windows. The
> graphics output is completely compatible with whatever applications you
> want to paste them into on Windows.
This turns out not to be the case.
It is not trivial to produce good graphics off Windows for adding to
Microsoft Office documents (regrettably an important case for many
people). There has been much discussion of this on the R-sig-mac
> mailing
list, for example, where PNG bitmaps (at sufficiently high resolution)
seem to be the preferred method.
>>> On Windows one can produce metafile output directly from R.
>> Yes, indeed. However, this fact is of limited help when working on another
>
>> operating system, which was the focus of the original question.
>>
>> -thomas
>
> One solution which has not been covered here is to use both operating
> systems. For example, I need to present in Powerpoint, yet my work is
> done under Linux where I have substantially more RAM and CPU
> power. Typically, I'll run my analysis under Linux and then take
> advantage of the binary compatibility of the .RData file and move my
> final values from Linux to Windows via Samba; I may delete large
> intermediate results before the transfer to compendate for my lack of
> RAM under Windows. Some small scripts which may have been developed
> under Linux are used to create the plots which are placed in my
> Powerpoint presentations. By an large, the plots developed under Linux
> drop right into the Windows presentations, although there are
> occasional font size difficulties that require adjustments.
>
> Mark Dalphin
>
> --
> Mark Dalphin
> Dept Comp Biol, M/S AW2/D3262
> Amgen, Inc.
> 1201 Amgen Court W
> Seattle, WA 98119
>
> __
> R-help@stat.math.ethz.ch 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.
--
Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www
Re: [R] Hardware for a new Workstation for best performance using R
I think there are a lot of misconceptions regarding what is possible on Windows.
On Windows you just right click the graphic in R and choose Copy as Metafile
which puts a vector graphic representation on the clipboard and then
ctrl-V in Word to copy it in. (Alternately save all your graphics as files
and then later insert them into Word.)
Once in Word you can even edit the elements of the graphic after the fact
such as changing the x and y axis labels right in Word, etc. Just right click
the graphic and choose Edit to get into the graphic editor. You don't need
any other software to do that. This is very easy, fast, flexible and gives
top resolution since its in a vector format.
(By the way, there are many free PDF generators on Windows. I use FreePDF
on my Windows machine but I normally don't need it with R since
I just do the above.)
On 3/19/07, Oleg Sklyar <[EMAIL PROTECTED]> wrote:
>
> For any kind of R plots that need to be inserted in office documents
> either on Windows OR on Linux you will always achieve the best result by
> using the postscript device, then converting *.ps to *.eps and inserting
> *.eps into Office (OpenOffice as well). *.eps files contain previews for
> you to edit the documents on screen, but the final output can be done
> using Print to file using a Postscript driver and converting to PDF --
> this will ensure all your R-graphics, but also ALL of your vector
> illustrations, to be displayed in high quality vector manner.
>
> In fact this is about the only way to put high quality plots into
> presentations or word processing documents (ANY, MSOffice included). In
> general it works easier on Linux because you will have all tools in the
> repository and for free. On Windows you will probably end up using
> Distiller, which costs quite a lot or FreePdfXP if it still exists and
> works correctly.
>
> There is only one place where Windows, or for that sake Mac, scores
> better, and yet not ultimately: if you want to draw or design vector
> illustrations then you have larger selection of tools on Windows (Corel,
> Illustrator, Xara etc), on Mac - Illustrator and on Linux - InkScape
> (recommnded) and Xara.
>
> Now if you go this way, the workflow looks like:
>
> > postscript("fig1.ps", width=5,height=5)
> > plot(x~y)
> > dev.off()
> > q()
> $ ps2eps --ignoreBB --gsbbox -r 300 -R + -f fig1.ps # 300dpi thumbnail
> $ ooffice
> - import eps file, you will see the same as usual hi-res preview
> - Print, print to file, on request "Reduce Transparency" - YES
> $ ps2pdf13 mydoc.ps
>
> result: mydoc.pdf
>
> For presentations simply use US Letter landscape instead of A4 for paper
> size and printing (to file) and this will nicely fit into the screen
> with minimal loss of space.
>
> If the question is in the impossibility to do things on Linux: Windows
> will not help you to do the above -- there are no tools. You may find
> another solution, but for the quality of output the above is the best.
> Other formats, like WMF, EMF, AI, CDR are either of no good use for
> anything (the first 2) or are incompatible with Office (AI, CDR).
>
> Moreover, using InkScape and RSvgDevice you can create SVG plots to
> which you can add whatever illustrations you want just in the same
> document because SVG is native for InkScape.
>
> Oleg
>
> PS. If you want to see examples of how such plots and illustrations look
> like (created fully on Linux with the above workflow, drop me a line, I
> will send a PDF).
>
> Dalphin, Mark wrote:
> > On Mon, 19 Mar 2007, Thomas Lumley wrote:
> >>> On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote:
> On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part)
> > 2.) Yes, by all means you should use linux instead of windows. The
> > graphics output is completely compatible with whatever applications you
> > want to paste them into on Windows.
> This turns out not to be the case.
>
> It is not trivial to produce good graphics off Windows for adding to
> Microsoft Office documents (regrettably an important case for many
> people). There has been much discussion of this on the R-sig-mac
> > mailing
> list, for example, where PNG bitmaps (at sufficiently high resolution)
> seem to be the preferred method.
> >>> On Windows one can produce metafile output directly from R.
> >> Yes, indeed. However, this fact is of limited help when working on another
> >
> >> operating system, which was the focus of the original question.
> >>
> >> -thomas
> >
> > One solution which has not been covered here is to use both operating
> > systems. For example, I need to present in Powerpoint, yet my work is
> > done under Linux where I have substantially more RAM and CPU
> > power. Typically, I'll run my analysis under Linux and then take
> > advantage of the binary compatibility of the .RData file and move my
> > final values from Linux to Windows via Samba; I may delete large
> > intermediate results before the transfer to compen
Re: [R] Hardware for a new Workstation for best performance using R
Along the lines you mention, check out: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/32297.html On 3/19/07, Dalphin, Mark <[EMAIL PROTECTED]> wrote: > On Mon, 19 Mar 2007, Thomas Lumley wrote: > >> On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote: > >>> On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part) > > 2.) Yes, by all means you should use linux instead of windows. The > graphics output is completely compatible with whatever applications you > want to paste them into on Windows. > >>> > >>> This turns out not to be the case. > >>> > >>> It is not trivial to produce good graphics off Windows for adding to > >>> Microsoft Office documents (regrettably an important case for many > >>> people). There has been much discussion of this on the R-sig-mac > mailing > >>> list, for example, where PNG bitmaps (at sufficiently high resolution) > >>> seem to be the preferred method. > >> > >> On Windows one can produce metafile output directly from R. > > > > Yes, indeed. However, this fact is of limited help when working on another > > > operating system, which was the focus of the original question. > > > > -thomas > > One solution which has not been covered here is to use both operating > systems. For example, I need to present in Powerpoint, yet my work is > done under Linux where I have substantially more RAM and CPU > power. Typically, I'll run my analysis under Linux and then take > advantage of the binary compatibility of the .RData file and move my > final values from Linux to Windows via Samba; I may delete large > intermediate results before the transfer to compendate for my lack of > RAM under Windows. Some small scripts which may have been developed > under Linux are used to create the plots which are placed in my > Powerpoint presentations. By an large, the plots developed under Linux > drop right into the Windows presentations, although there are > occasional font size difficulties that require adjustments. > > Mark Dalphin > > -- > Mark Dalphin > Dept Comp Biol, M/S AW2/D3262 > Amgen, Inc. > 1201 Amgen Court W > Seattle, WA 98119 > > __ > R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Hardware for a new Workstation for best performance using R
At the risk of beating a dead horse...
odfWeave can be used on Linux (or anywhere Open Office is available) to
create reports that can then be converted to Word, rtf, html, pdf etc.
In still in the process of getting Impress (OO's presentation
application) working, but I'll get there.
Max
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Oleg Sklyar
Sent: Monday, March 19, 2007 3:03 PM
To: Dalphin, Mark
Cc: Thomas Lumley; r-help@stat.math.ethz.ch
Subject: Re: [R] Hardware for a new Workstation for best performance
using R
For any kind of R plots that need to be inserted in office documents
either on Windows OR on Linux you will always achieve the best result by
using the postscript device, then converting *.ps to *.eps and inserting
*.eps into Office (OpenOffice as well). *.eps files contain previews for
you to edit the documents on screen, but the final output can be done
using Print to file using a Postscript driver and converting to PDF --
this will ensure all your R-graphics, but also ALL of your vector
illustrations, to be displayed in high quality vector manner.
In fact this is about the only way to put high quality plots into
presentations or word processing documents (ANY, MSOffice included). In
general it works easier on Linux because you will have all tools in the
repository and for free. On Windows you will probably end up using
Distiller, which costs quite a lot or FreePdfXP if it still exists and
works correctly.
There is only one place where Windows, or for that sake Mac, scores
better, and yet not ultimately: if you want to draw or design vector
illustrations then you have larger selection of tools on Windows (Corel,
Illustrator, Xara etc), on Mac - Illustrator and on Linux - InkScape
(recommnded) and Xara.
Now if you go this way, the workflow looks like:
> postscript("fig1.ps", width=5,height=5)
> plot(x~y)
> dev.off()
> q()
$ ps2eps --ignoreBB --gsbbox -r 300 -R + -f fig1.ps # 300dpi thumbnail
$ ooffice
- import eps file, you will see the same as usual hi-res preview
- Print, print to file, on request "Reduce Transparency" - YES
$ ps2pdf13 mydoc.ps
result: mydoc.pdf
For presentations simply use US Letter landscape instead of A4 for paper
size and printing (to file) and this will nicely fit into the screen
with minimal loss of space.
If the question is in the impossibility to do things on Linux: Windows
will not help you to do the above -- there are no tools. You may find
another solution, but for the quality of output the above is the best.
Other formats, like WMF, EMF, AI, CDR are either of no good use for
anything (the first 2) or are incompatible with Office (AI, CDR).
Moreover, using InkScape and RSvgDevice you can create SVG plots to
which you can add whatever illustrations you want just in the same
document because SVG is native for InkScape.
Oleg
PS. If you want to see examples of how such plots and illustrations look
like (created fully on Linux with the above workflow, drop me a line, I
will send a PDF).
Dalphin, Mark wrote:
> On Mon, 19 Mar 2007, Thomas Lumley wrote:
>>> On 3/19/07, Thomas Lumley <[EMAIL PROTECTED]> wrote:
>>>> On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part)
>>>>> 2.) Yes, by all means you should use linux instead of windows. The
>>>>> graphics output is completely compatible with whatever
applications you
>>>>> want to paste them into on Windows.
>>>> This turns out not to be the case.
>>>>
>>>> It is not trivial to produce good graphics off Windows for adding
to
>>>> Microsoft Office documents (regrettably an important case for many
>>>> people). There has been much discussion of this on the R-sig-mac
> mailing
>>>> list, for example, where PNG bitmaps (at sufficiently high
resolution)
>>>> seem to be the preferred method.
>>> On Windows one can produce metafile output directly from R.
>> Yes, indeed. However, this fact is of limited help when working on
another
>
>> operating system, which was the focus of the original question.
>>
>> -thomas
>
> One solution which has not been covered here is to use both operating
> systems. For example, I need to present in Powerpoint, yet my work is
> done under Linux where I have substantially more RAM and CPU
> power. Typically, I'll run my analysis under Linux and then take
> advantage of the binary compatibility of the .RData file and move my
> final values from Linux to Windows via Samba; I may delete large
> intermediate results before the transfer to compendate for my lack of
> RAM under Windows. Some small scripts which may have been developed
> under Linux are used to create the plots which are placed in my
> Powerpoint presentations
Re: [R] Hardware for a new Workstation for best performance using R
On Mon, 19-Mar-2007 at 07:23PM +0100, Peter Dalgaard wrote:
|> Thomas Lumley wrote:
|> > On Thu, 15 Mar 2007, Andrew Perrin wrote: (in part)
|> >
|> >> 2.) Yes, by all means you should use linux instead of windows. The
|> >> graphics output is completely compatible with whatever applications you
|> >> want to paste them into on Windows.
|> >>
|> >
|> > This turns out not to be the case.
|> >
|> > It is not trivial to produce good graphics off Windows for adding to
|> > Microsoft Office documents (regrettably an important case for many
|> > people). There has been much discussion of this on the R-sig-mac mailing
|> > list, for example, where PNG bitmaps (at sufficiently high resolution)
|> > seem to be the preferred method.
|> >
|> >-thomas
|> >
|> >
|> One option for people who are paying for software anyways is to install
|> Adobe Acrobat Writer software for generating PDF files from Word. This
|> also allows you to include ouput from the pdf() device, and the end
|> result comes out really nice.
I've been told that there are also free PDF writers, so it's not
necessary to spend money on Adobe Acrobat Writer. One example is
http://www.cutepdf.com/
I personally find that PNGs are fine provided I know what final size
is needed. PNGs certainly don't have the flexibility that Gabor
mentions but they are usually as small as any other format.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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