R newbie example code question

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R newbie example code question

mark leeds-4
Sometimes I print out a package
and read about it and there
are sometimes nice examples
that I would like to run myself.
 
Is there a way to bring them
into R from the package or
are they only meant to be typed
in manually ? If manual is the
only way, that's fine. I was
just checking whether there was
a quicker way. Thanks.
 
                           Mark


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Re: R newbie example code question

Uwe Ligges
Mark Leeds wrote:

> Sometimes I print out a package
> and read about it and there
> are sometimes nice examples
> that I would like to run myself.
>  
> Is there a way to bring them
> into R from the package or
> are they only meant to be typed
> in manually ? If manual is the
> only way, that's fine. I was
> just checking whether there was
> a quicker way. Thanks.

See (you won't believe it): ?example

Uwe Ligges




>                            Mark
>
>
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Re: R newbie example code question

mark leeds-4
In reply to this post by mark leeds-4
wow. example() was exactly what
I wanted.  you all have made all these
incredible facilities
for a new person.  thanks.

                mark


-----Original Message-----
From: Uwe Ligges [mailto:[hidden email]]
Sent: Monday, January 09, 2006 1:30 PM
To: Mark Leeds
Cc: R-Stat Help
Subject: Re: [R] R newbie example code question

Mark Leeds wrote:

> Sometimes I print out a package
> and read about it and there
> are sometimes nice examples
> that I would like to run myself.
>  
> Is there a way to bring them
> into R from the package or
> are they only meant to be typed
> in manually ? If manual is the
> only way, that's fine. I was
> just checking whether there was
> a quicker way. Thanks.

See (you won't believe it): ?example

Uwe Ligges




>                            Mark
>
>
> **********************************************************************
> This email and any files transmitted with it are
confidentia...{{dropped}}
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
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http://www.R-project.org/posting-guide.html



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Re: R newbie example code question

John Sorkin
In reply to this post by mark leeds-4
Mark,
I am not user where you find your reading material, but if it is online, perhaps you can copy and paste it into an R session.
John

John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC and
University of Maryland School of Medicine Claude Pepper OAIC

University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524

410-605-7119
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>>> "Mark Leeds" <[hidden email]> 1/9/2006 1:20 PM >>>
Sometimes I print out a package
and read about it and there
are sometimes nice examples
that I would like to run myself.
 
Is there a way to bring them
into R from the package or
are they only meant to be typed
in manually ? If manual is the
only way, that's fine. I was
just checking whether there was
a quicker way. Thanks.
 
                           Mark


**********************************************************************
This email and any files transmitted with it are confidentia...{{dropped}}

______________________________________________
[hidden email] mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: R newbie example code question

Ted.Harding
In reply to this post by mark leeds-4

On 09-Jan-06 Mark Leeds wrote:

> Sometimes I print out a package
> and read about it and there
> are sometimes nice examples
> that I would like to run myself.
>  
> Is there a way to bring them
> into R from the package or
> are they only meant to be typed
> in manually ? If manual is the
> only way, that's fine. I was
> just checking whether there was
> a quicker way. Thanks.
>  
>                            Mark
>
>
> **********************************************************************
> This email and any files transmitted with it are
> confidentia...{{dropped}}
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html

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Re: R newbie example code question

Ted.Harding
On 10-Jan-06 Ted Harding wrote:

>
> On 09-Jan-06 Mark Leeds wrote:
>> Sometimes I print out a package
>> and read about it and there
>> are sometimes nice examples
>> that I would like to run myself.
>>  
>> Is there a way to bring them
>> into R from the package or
>> are they only meant to be typed
>> in manually ? If manual is the
>> only way, that's fine. I was
>> just checking whether there was
>> a quicker way. Thanks.
>>  
>>                            Mark

Apologies for sending a NULL response!
My machine froze as I was working how to write the
response, and on re-boot it seems to have sent the
message all by itself!

Best wishes,
Ted.

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Re: R newbie example code question

Ted.Harding
In reply to this post by mark leeds-4
On 09-Jan-06 Mark Leeds wrote:

> Sometimes I print out a package
> and read about it and there
> are sometimes nice examples
> that I would like to run myself.
>  
> Is there a way to bring them
> into R from the package or
> are they only meant to be typed
> in manually ? If manual is the
> only way, that's fine. I was
> just checking whether there was
> a quicker way. Thanks.
>  
>                            Mark

I had the same issue many moons ago, and for the
same reasons! It was discussed in a fairly extended,
and interesting, thread from 24-27 May 2003 -- go to
the R-help archives for that month, by thread, and
find the thread

  [R] help output paged in separate window

The solution I finally opted for, and still use,
is based (in a Linux environment) on including
the following code in your .Rprofile file:


.xthelp <- function() {
    tdir <- tempdir()
    pgr <- paste(tdir, "/pgr", sep="")
    con <- file(pgr, "w")
    cat("#! /bin/bash\n", file=con)
    cat("export HLPFIL=`mktemp ", tdir, "/R_hlp.XXXXXX`\n",
         sep="", file=con)
    cat("cat > $HLPFIL\nxterm -e less $HLPFIL &\n", file=con)
    close(con)
    system(paste("chmod 755 ", pgr, sep=""))
    options(pager=pgr)
}
.xthelp()
rm(.xthelp)


(and it's also specific to the 'bash' shell because
of the "#! /bin/bash\n", but you should be able to
change this appropriately). The above was posted by
Roger Bivand on 27 May.

When you start an R session, this code is executed as
part of sourcing your .Rprofile, and it has the effect that
any output from R which would be paged is stored in a
temporary  file which is then read by 'less' in a
separate X window which is detached from your R session
(i.e. your command interface will not hang while it is
being displayed). You can close the X window displaying
the 'less' output by closing 'less' (e.g. type "q"), or
you can leave it open and any new paged output will go
into a new window -- so you can for instance do

?glm
?family
?binomial

and you will have three mutually relevant help windows
open at once between which you can cross-reference.

As to extracting the code for examples, this is easy
in X windows since you just use your mouse: left-button
drag to hghlight a block of text, middle-button click
to paste the block into another window (of course the
mouse must be over the correct window!)

So you can use the mouse to copy code from the "help"
pages to the command window.

As I say, this is a Linux-oriented solution, and I don't
know what details would be required for anything similar
in a Windows environment.

It is also worth reading the various contributions to
the above thread, since several suggestions were made.

Hoping this helps,
Ted.

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Re: R newbie example code question

McGehee, Robert
In reply to this post by mark leeds-4
Hello,
Why not just copy and paste the examples from the help pages? No need to
type anything.

However, if you'd like to run the entire help section for a function,
check out the example function, i.e.:
> example(plot)

Robert

-----Original Message-----
From: Mark Leeds [mailto:[hidden email]]
Sent: Monday, January 09, 2006 1:20 PM
To: R-Stat Help
Subject: [R] R newbie example code question

Sometimes I print out a package
and read about it and there
are sometimes nice examples
that I would like to run myself.
 
Is there a way to bring them
into R from the package or
are they only meant to be typed
in manually ? If manual is the
only way, that's fine. I was
just checking whether there was
a quicker way. Thanks.
 
                           Mark


**********************************************************************
This email and any files transmitted with it are
confidentia...{{dropped}}

______________________________________________
[hidden email] mailing list
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http://www.R-project.org/posting-guide.html

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Re: R newbie example code question

Martin Maechler
>>>>> "RobMcG" == McGehee, Robert <[hidden email]>
>>>>>     on Tue, 10 Jan 2006 10:55:47 -0500 writes:

    RobMcG> Hello,
    RobMcG> Why not just copy and paste the examples from the help pages? No need to
    RobMcG> type anything.

    RobMcG> However, if you'd like to run the entire help section for a function,
    RobMcG> check out the example function, i.e.:

    >> example(plot)

    RobMcG> Robert

Hmm, since this thread seems to perpetuate ..
let me take the opportunity to explain how enormously nicely (:-)
this is achieved in ESS (Emacs Speaks Statistics):

1) ?plot opens a separate emacs buffer with the help page.
2)       and emacs gains a separate "ESS-help" menu.

3) From that menu you can learn that you can very quickly move
   around in the help buffer using "n"(ext) and "p"(revious) or
   skip to a section via  "s <letter>."
   Now the most used keystroke in ESS help buffers I use is
   "s e" := "[S]kip to the [E]xamples section".

4) Inside the examples section, 'l' (single lowercase "L" for [L]ine)
   sends single lines to the running *R* process, or 'r' sends a
   whole [R]egion (that you typically have marked with the mouse).


Since it seems that there are ESS users who don't know about
this feature, I'm also CCing this to ESS-help.

(and yes, I could go on: You can also send code from the
 examples when *editing* the *.Rd  (R help) files ...)

Martin Maechler, ETH Zurich


   > -----Original Message-----
   > From: Mark Leeds [mailto:[hidden email]]
   > Sent: Monday, January 09, 2006 1:20 PM
   > To: R-Stat Help
   > Subject: [R] R newbie example code question

   > Sometimes I print out a package
   > and read about it and there
   > are sometimes nice examples
   > that I would like to run myself.
 
   > Is there a way to bring them
   > into R from the package or
   > are they only meant to be typed
   > in manually ? If manual is the
   > only way, that's fine. I was
   > just checking whether there was
   > a quicker way. Thanks.
 
   > Mark

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Re: R newbie example code question

Gabor Grothendieck
In reply to this post by Uwe Ligges
You can also get access to the code chunks in vignettes
as shown here:

   http://tolstoy.newcastle.edu.au/~rking/R/help/05/12/17822.html

On 1/9/06, Uwe Ligges <[hidden email]> wrote:

> Mark Leeds wrote:
>
> > Sometimes I print out a package
> > and read about it and there
> > are sometimes nice examples
> > that I would like to run myself.
> >
> > Is there a way to bring them
> > into R from the package or
> > are they only meant to be typed
> > in manually ? If manual is the
> > only way, that's fine. I was
> > just checking whether there was
> > a quicker way. Thanks.
>
> See (you won't believe it): ?example
>
> Uwe Ligges
>
>
>
>
> >                            Mark
> >
> >
> > **********************************************************************
> > This email and any files transmitted with it are confidentia...{{dropped}}
> >
> > ______________________________________________
> > [hidden email] mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

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Re: R newbie example code question

Michael Friendly
In reply to this post by Ted.Harding
Ted:

Your .xthelp is extremely useful, help on Linux being otherwise
quite awkward to use since a pager in the same window make it hard
to cut/paste examples --- where 'more' or 'less' really means
'instead of' :-)

Suggestion: include -title

      cat("cat > $HLPFIL\nxterm -title 'R-help' -e less $HLPFIL &\n",
file=con)

<hint>It would be nice if this solution made it into the R-FAQ or R-Admin
manual.</hint>
Failing that, it is a good example of something that would
work well in a wiki.  But, thankfully, you included the subject line
from the original thread to make it searchable in the news archives.


(Ted Harding) wrote:


>   [R] help output paged in separate window
>
> The solution I finally opted for, and still use,
> is based (in a Linux environment) on including
> the following code in your .Rprofile file:
>
>
> .xthelp <- function() {
>     tdir <- tempdir()
>     pgr <- paste(tdir, "/pgr", sep="")
>     con <- file(pgr, "w")
>     cat("#! /bin/bash\n", file=con)
>     cat("export HLPFIL=`mktemp ", tdir, "/R_hlp.XXXXXX`\n",
>          sep="", file=con)
>     cat("cat > $HLPFIL\nxterm -e less $HLPFIL &\n", file=con)
>     close(con)
>     system(paste("chmod 755 ", pgr, sep=""))
>     options(pager=pgr)
> }
> .xthelp()
> rm(.xthelp)
>
>
> (and it's also specific to the 'bash' shell because
> of the "#! /bin/bash\n", but you should be able to
> change this appropriately). The above was posted by
> Roger Bivand on 27 May.
>
> When you start an R session, this code is executed as
> part of sourcing your .Rprofile, and it has the effect that
> any output from R which would be paged is stored in a
> temporary  file which is then read by 'less' in a
> separate X window which is detached from your R session
> (i.e. your command interface will not hang while it is
> being displayed). You can close the X window displaying
> the 'less' output by closing 'less' (e.g. type "q"), or
> you can leave it open and any new paged output will go
> into a new window -- so you can for instance do
>
> ?glm
> ?family
> ?binomial
>
> and you will have three mutually relevant help windows
> open at once between which you can cross-reference.
>
> As to extracting the code for examples, this is easy
> in X windows since you just use your mouse: left-button
> drag to hghlight a block of text, middle-button click
> to paste the block into another window (of course the
> mouse must be over the correct window!)
>
> So you can use the mouse to copy code from the "help"
> pages to the command window.
>
> As I say, this is a Linux-oriented solution, and I don't
> know what details would be required for anything similar
> in a Windows environment.
>
> It is also worth reading the various contributions to
> the above thread, since several suggestions were made.
>
> Hoping this helps,
> Ted.
>
> --------------------------------------------------------------------
> E-Mail: (Ted Harding) <[hidden email]>
> Fax-to-email: +44 (0)870 094 0861
> Date: 10-Jan-06                                       Time: 13:30:35
> ------------------------------ XFMail ------------------------------
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

--
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA

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Re: R newbie example code question

Ted.Harding
On 13-Jan-06 Michael Friendly wrote:
> Ted:
>
> Your .xthelp is extremely useful, help on Linux being otherwise
> quite awkward to use since a pager in the same window make it hard
> to cut/paste examples --- where 'more' or 'less' really means
> 'instead of' :-)

Glad you found it useful. I find it indispensable!
For the record: this is not my code but Roger Bivand's,
it being the one out of several suggestions on that thread
which I decided to adopt. I still admire the neat way he
wrapped it all up.

One of the beautiful features is that *anything* which would
be paged comes up in the separate window, so for instance
you could execute in R

  page(glm)

and you can then scan up and down, and cut&paste chunks if
you want, etc., and in several different windows for different
things at once (or even the same thing several times over if
you want to see different parts at the same time). Great for
playing with variants.

> Suggestion: include -title
>
> cat("cat > $HLPFIL\nxterm -title 'R-help' -e less $HLPFIL &\n",
> file=con)
>
> <hint>It would be nice if this solution made it into the R-FAQ
> or R-Admin manual.</hint> Failing that, it is a good example of
> something that would work well in a wiki.  But, thankfully, you
> included the subject line from the original thread to make it
> searchable in the news archives.

A good <hint>! In fact a good place for it (or for a URL to it)
could be the help file for "help" and friends. In the circumstances,
this is where I would have looked first.</hint>

Best wishes,
Ted.

> (Ted Harding) wrote:
>
>
>>   [R] help output paged in separate window
>>
>> The solution I finally opted for, and still use,
>> is based (in a Linux environment) on including
>> the following code in your .Rprofile file:
>>
>>
>> .xthelp <- function() {
>>     tdir <- tempdir()
>>     pgr <- paste(tdir, "/pgr", sep="")
>>     con <- file(pgr, "w")
>>     cat("#! /bin/bash\n", file=con)
>>     cat("export HLPFIL=`mktemp ", tdir, "/R_hlp.XXXXXX`\n",
>>          sep="", file=con)
>>     cat("cat > $HLPFIL\nxterm -e less $HLPFIL &\n", file=con)
>>     close(con)
>>     system(paste("chmod 755 ", pgr, sep=""))
>>     options(pager=pgr)
>> }
>> .xthelp()
>> rm(.xthelp)
>>
>>
>> (and it's also specific to the 'bash' shell because
>> of the "#! /bin/bash\n", but you should be able to
>> change this appropriately). The above was posted by
>> Roger Bivand on 27 May.
>>
>> When you start an R session, this code is executed as
>> part of sourcing your .Rprofile, and it has the effect that
>> any output from R which would be paged is stored in a
>> temporary  file which is then read by 'less' in a
>> separate X window which is detached from your R session
>> (i.e. your command interface will not hang while it is
>> being displayed). You can close the X window displaying
>> the 'less' output by closing 'less' (e.g. type "q"), or
>> you can leave it open and any new paged output will go
>> into a new window -- so you can for instance do
>>
>> ?glm
>> ?family
>> ?binomial
>>
>> and you will have three mutually relevant help windows
>> open at once between which you can cross-reference.
>>
>> As to extracting the code for examples, this is easy
>> in X windows since you just use your mouse: left-button
>> drag to hghlight a block of text, middle-button click
>> to paste the block into another window (of course the
>> mouse must be over the correct window!)
>>
>> So you can use the mouse to copy code from the "help"
>> pages to the command window.
>>
>> As I say, this is a Linux-oriented solution, and I don't
>> know what details would be required for anything similar
>> in a Windows environment.
>>
>> It is also worth reading the various contributions to
>> the above thread, since several suggestions were made.
>>
>> Hoping this helps,
>> Ted.
>>
>> --------------------------------------------------------------------
>> E-Mail: (Ted Harding) <[hidden email]>
>> Fax-to-email: +44 (0)870 094 0861
>> Date: 10-Jan-06                                       Time: 13:30:35
>> ------------------------------ XFMail ------------------------------
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide!
>> http://www.R-project.org/posting-guide.html
>>
>
> --
> Michael Friendly     Email: friendly AT yorku DOT ca
> Professor, Psychology Dept.
> York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
> 4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
> Toronto, ONT  M3J 1P3 CANADA

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Re: R newbie example code question

dusadrian
In reply to this post by Ted.Harding
 <Ted.Harding <at> nessie.mcc.ac.uk> writes:

> [...]
> The solution I finally opted for, and still use,
> is based (in a Linux environment) on including
> the following code in your .Rprofile file:
>
> .xthelp <- function() {
>     tdir <- tempdir()
>     pgr <- paste(tdir, "/pgr", sep="")
>     con <- file(pgr, "w")
>     cat("#! /bin/bash\n", file=con)
>     cat("export HLPFIL=`mktemp ", tdir, "/R_hlp.XXXXXX`\n",
>          sep="", file=con)
>     cat("cat > $HLPFIL\nxterm -e less $HLPFIL &\n", file=con)
>     close(con)
>     system(paste("chmod 755 ", pgr, sep=""))
>     options(pager=pgr)
> }
> .xthelp()
> rm(.xthelp)
>
> (and it's also specific to the 'bash' shell because
> of the "#! /bin/bash\n", but you should be able to
> change this appropriately). The above was posted by
> Roger Bivand on 27 May.
> [...]

I also like the function, it's beautiful. I wonder if anyone could help me with
the correct syntax for my bash shell (I assume this is the problem) because I
get this error:

Error in rm(.xthelp) : cannot remove variables from base namespace

when starting R and when installing a new package.
Thank you,
Adrian

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Re: R newbie example code question

Adrian Dusa-2
In reply to this post by Ted.Harding
On Friday 13 January 2006 17:45, Ted Harding wrote:

> On 13-Jan-06 Michael Friendly wrote:
> > Ted:
> >
> > Your .xthelp is extremely useful, help on Linux being otherwise
> > quite awkward to use since a pager in the same window make it hard
> > to cut/paste examples --- where 'more' or 'less' really means
> > 'instead of' :-)
>
> Glad you found it useful. I find it indispensable!
> For the record: this is not my code but Roger Bivand's,
> it being the one out of several suggestions on that thread
> which I decided to adopt. I still admire the neat way he
> wrapped it all up.
> [...snip...]

I also like the function very much, but I get an annoying error when starting
R or when installing a new package:

Error in rm(.xthelp) : cannot remove variables from base namespace

I assume it has something to do with my bash shell, but I have no idea what to
do. I run I inside Kubuntu 5.10 Breezy (compiled from source).

> R.Version()
$platform
[1] "i686-pc-linux-gnu"
$arch
[1] "i686"
$os
[1] "linux-gnu"
$system
[1] "i686, linux-gnu"
$status
[1] ""
$major
[1] "2"
$minor
[1] "2.1"
$year
[1] "2005"
$month
[1] "12"
$day
[1] "20"
$"svn rev"
[1] "36812"
$language
[1] "R"

Thank you,
Adrian

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