R help - Mar 2010 - How good is R at making publication quality tables?

Hello Everyone,
 
I have just started learning R and am in the process of figuring out what it can
and can't do. I must say I am very impressed with R so far and am amazed
that something this good can actually be free.
 
Recently, I finished reading R for SAS and SPSS Users and have begun reading SAS
and R and Data Manipulation with R. Based on what I've read in these books
and elsewhere, I get the impression that R is very good at drawing high quality
graphs but maybe not so good at creating nice looking tables of the sort I'm
used to getting through SAS ODS.
 
Am I right or wrong about this? If I am wrong, can anyone show me some examples
of how R can be used to create really nice looking tables? I often make tables
of adverse events in clinical trials that have n(%) values in the cells. I'd
love to see an example that does a nice job of making that sort of table but
would be happy to see any examples that someone might be willing to send to me.
 
Thanks,
 
Paul
 


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	[[alternative HTML version deleted]]

Please look at the latex function in the Hmisc package.
The default display is very good.  And there are many optional
arguments that give you very fine control over the appearance of
the table.

Rich

	[[alternative HTML version deleted]]

Paul Miller wrote:
> Hello Everyone,
> 
> I have just started learning R and am in the process of figuring out
> what it can and can't do. I must say I am very impressed with R so
> far and am amazed that something this good can actually be free.
> 
> Recently, I finished reading R for SAS and SPSS Users and have begun
> reading SAS and R and Data Manipulation with R. Based on what I've
> read in these books and elsewhere, I get the impression that R is
> very good at drawing high quality graphs but maybe not so good at
> creating nice looking tables of the sort I'm used to getting through
> SAS ODS.
You're really only limited by your imagination here.  I have written 
several custom table functions to output LaTeX, but you can output 
whatever you like (HTML, plain-text, org-mode files...), you're in 
complete control with R.

I can second the Hmisc package though.  I often use a combination of 
summary.formula and the latex function to output really nice looking 
tables that get put into a long PDF report for a study.

I can say that both of these functions, summary.formula and latex, in 
Hmisc have a LOT of arguments, and almost every time I said "I wish it 
looked a little different", there was an option to control it.

Specifically, I found the options:

exclude1, long, longtable, combine, test,

do be very useful.  I often make tables by some treatment group, so all 
these are using method = "reverse" to accomplish that.

And if you don't like the output, latex.summary.formula.reverse is a 
good function to make your own version of, to output exactly what you 
want.  I have a local copy that augments the tables that contain 
unadjusted p-values with adjusted p-values from a model.

But apart from Hmisc, just realize that with R you have a nice 
programming language to produce any type of output you want, you're not 
limited to what someone else gave you.

--Erik

Hi Paul,
For instructions and examples using the Hmisc latex() function you
might want to take a look at
http://lib.stat.cmu.edu/S/Harrell/doc/summary.pdf.

-Best,
Ista

On Wed, Mar 17, 2010 at 10:51 AM, Paul Miller <pjmiller_57 at yahoo.com>
wrote:
> Hello Everyone,
>
> I have just started learning R and am in the process of figuring out what
it can and can't do. I must say I am very impressed with R so far and am
amazed that something this good can actually be free.
>
> Recently, I finished reading R for SAS and SPSS Users and have begun
reading SAS and R and Data Manipulation with R. Based on what I've read in
these books and elsewhere, I get the impression that R is very good at drawing
high quality graphs but maybe not so good at creating nice looking tables of the
sort I'm used to getting through SAS ODS.
>
> Am I right or wrong about this? If I am wrong, can anyone show me some
examples of how R can be used to create really nice looking tables? I often make
tables of adverse events in clinical trials?that have n(%) values in the cells.
I'd love to see an example that does a nice job of making that sort of table
but would be happy to see any examples that someone might be willing to send to
me.
>
> Thanks,
>
> Paul
>
>
>
> ? ? ?__________________________________________________________________
> Looking for the perfect gift? Give the gift of Flickr!
>
>
> ? ? ? ?[[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-help at 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.
>
>


-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org

On Wed, Mar 17, 2010 at 2:51 PM, Paul Miller <pjmiller_57 at yahoo.com>
wrote:
> Am I right or wrong about this? If I am wrong, can anyone show me some
examples of how R can be used to create really nice looking tables? I often make
tables of adverse events in clinical trials?that have n(%) values in the cells.
I'd love to see an example that does a nice job of making that sort of table
but would be happy to see any examples that someone might be willing to send to
me.
>
To complement all said up to now, see this documentation [1]. For
clinical trials you might also want to check rreport [2]. There was
also a recent thread [3] on the topic.
Liviu

[1]
http://cran.r-project.org/web/packages/RcmdrPlugin.Export/RcmdrPlugin.Export.pdf
[2] http://biostat.mc.vanderbilt.edu/wiki/Main/Rreport
[3] [R] Use of R in clinical trials

If you are working in Windows and want Word output,
it might be worthwhile to have a look at SWord
available from the download section on rcom.univie.ac.at.

Warning: the program is free for noncommercial use,
but NOT licensed under GPL or LGPL.


On 3/17/2010 3:51 PM, Paul Miller wrote:
> Hello Everyone,
>  
> I have just started learning R and am in the process of figuring out what
it can and can't do. I must say I am very impressed with R so far and am
amazed that something this good can actually be free.
>  
> Recently, I finished reading R for SAS and SPSS Users and have begun
reading SAS and R and Data Manipulation with R. Based on what I've read in
these books and elsewhere, I get the impression that R is very good at drawing
high quality graphs but maybe not so good at creating nice looking tables of the
sort I'm used to getting through SAS ODS.
>  
> Am I right or wrong about this? If I am wrong, can anyone show me some
examples of how R can be used to create really nice looking tables? I often make
tables of adverse events in clinical trials that have n(%) values in the cells.
I'd love to see an example that does a nice job of making that sort of table
but would be happy to see any examples that someone might be willing to send to
me.
>  
> Thanks,
>  
> Paul
>  
> 
> 
>       __________________________________________________________________
> Looking for the perfect gift? Give the gift of Flickr! 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
> 
> ______________________________________________
> R-help at 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.
-- 
Erich Neuwirth, University of Vienna
Faculty of Computer Science
Computer Supported Didactics Working Group
Visit our SunSITE at http://sunsite.univie.ac.at
Phone: +43-1-4277-39464 Fax: +43-1-4277-39459

Hi Paul,

Sorry I didn't get to that subject in the first edition of R for SAS and
SPSS Users. Several of the options people have mentioned will be in the second
edition, although that's about a year off. I did get them added to R for
Stata Users, due out in early April.

Cheers,
Bob

>-----Original Message-----
>From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org]
>On Behalf Of Paul Miller
>Sent: Wednesday, March 17, 2010 10:51 AM
>To: r-help at r-project.org
>Subject: [R] How good is R at making publication quality tables?
>
>Hello Everyone,
>
>I have just started learning R and am in the process of figuring out
>what it can and can't do. I must say I am very impressed with R so far
>and am amazed that something this good can actually be free.
>
>Recently, I finished reading R for SAS and SPSS Users and have begun
>reading SAS and R and Data Manipulation with R. Based on what I've read
>in these books and elsewhere, I get the impression that R is very good
>at drawing high quality graphs but maybe not so good at creating nice
>looking tables of the sort I'm used to getting through SAS ODS.
>
>Am I right or wrong about this? If I am wrong, can anyone show me some
>examples of how R can be used to create really nice looking tables? I
>often make tables of adverse events in clinical trials?that have n(%)
>values in the cells. I'd love to see an example that does a nice job of
>making that sort of table but would be happy to see any examples that
>someone might be willing to send to me.
>
>Thanks,
>
>Paul
>
>
>
>      __________________________________________________________________
>Looking for the perfect gift? Give the gift of Flickr!
>
>
>	[[alternative HTML version deleted]]

Hi Paul & al,

R-PLUS 3.3 has R publication quality tables with SAS ODS look & feel
and yes you can get  R-PLUS 3.3 Nano trial and keep it free for life.

youtube.com/rplus33 shows you a quick R-PLUS 3.3 demo and you can
request a longer
video by sending us an email.

Download Rplus 3.3 at  http://www.xlsolutions-corp.com/rplustrial.asp   
and send
an email to   rplus at experience-rplus.com  for the trial key.

Regards 

Sue Turner 
Senior Account Manager 
XLSolutions Corporation 
North American Division 
1700 7th Ave 
Suite 2100 
Seattle, WA 98101 
Phone:  206-686-1578 
Email: sue at xlsolutions-corp.com 
web: www.xlsolutions-corp.com/rcourses 




--- On Wed, 3/17/10, Frank E Harrell Jr <f.harrell at vanderbilt.edu>
wrote:
> From: Frank E Harrell Jr <f.harrell at vanderbilt.edu>
> Subject: Re: [R] How good is R at making publication quality tables?
> To: "Ista Zahn" <istazahn at gmail.com>
> Cc: r-help at r-project.org, "Paul Miller" <pjmiller_57 at
yahoo.com>
> Date: Wednesday, March 17, 2010, 12:44 PM
> Hi Ista,
> 
> Our material on statlib is far out of date.  Please
> refer to the primary 
> source at http://biostat.mc.vanderbilt.edu/StatReport
> 
> Thanks
> Frank
> 
> 
> Ista Zahn wrote:
> > Hi Paul,
> > For instructions and examples using the Hmisc latex()
> function you
> > might want to take a look at
> > http://lib.stat.cmu.edu/S/Harrell/doc/summary.pdf.
> > 
> > -Best,
> > Ista
> > 
> > On Wed, Mar 17, 2010 at 10:51 AM, Paul Miller <pjmiller_57 at
yahoo.com>
> wrote:
> >> Hello Everyone,
> >>
> >> I have just started learning R and am in the
> process of figuring out what it can and can't do. I must say
> I am very impressed with R so far and am amazed that
> something this good can actually be free.
> >>
> >> Recently, I finished reading R for SAS and SPSS
> Users and have begun reading SAS and R and Data Manipulation
> with R. Based on what I've read in these books and
> elsewhere, I get the impression that R is very good at
> drawing high quality graphs but maybe not so good at
> creating nice looking tables of the sort I'm used to getting
> through SAS ODS.
> >>
> >> Am I right or wrong about this? If I am wrong, can
> anyone show me some examples of how R can be used to create
> really nice looking tables? I often make tables of adverse
> events in clinical trials that have n(%) values in the
> cells. I'd love to see an example that does a nice job of
> making that sort of table but would be happy to see any
> examples that someone might be willing to send to me.
> >>
> >> Thanks,
> >>
> >> Paul
> >>
> >>
> >>
> >>     
> __________________________________________________________________
> >> Looking for the perfect gift? Give the gift of
> Flickr!
> >>
> >>
> >>        [[alternative HTML
> version deleted]]
> >>
> >>
> 
> 
> -- 
> Frank E Harrell Jr   Professor and
> Chairman        School of Medicine
>                
>       Department of
> Biostatistics   Vanderbilt University
> 
> ______________________________________________
> R-help at 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.
>

Hi Paul & al,

R-PLUS 3.3 has R publication quality tables with SAS ODS look & feel
and yes you can get  R-PLUS 3.3 Nano trial and keep it free for life.

youtube.com/rplus33 shows you a quick R-PLUS 3.3 demo and you can
request a longer
video by sending us an email.

Download Rplus 3.3 at  http://www.xlsolutions-corp.com/rplustrial.asp   
and send
an email to   rplus at experience-rplus.com  for the trial key.

Regards 

Sue Turner 
Senior Account Manager 
XLSolutions Corporation 
North American Division 
1700 7th Ave 
Suite 2100 
Seattle, WA 98101 
Phone:                206-686-1578         206-686-1578 
Email: sue at xlsolutions-corp.com 
web: www.xlsolutions-corp.com/rcourses 




--- On Wed, 3/17/10, Frank E Harrell Jr <f.harrell at vanderbilt.edu>
wrote:
> From: Frank E Harrell Jr <f.harrell at vanderbilt.edu>
> Subject: Re: [R] How good is R at making publication quality tables?
> To: "Ista Zahn" <istazahn at gmail.com>
> Cc: r-help at r-project.org, "Paul Miller" <pjmiller_57 at
yahoo.com>
> Date: Wednesday, March 17, 2010, 12:44 PM
> Hi Ista,
> 
> Our material on statlib is far out of date.  Please
> refer to the primary 
> source at http://biostat.mc.vanderbilt.edu/StatReport
> 
> Thanks
> Frank
> 
> 
> Ista Zahn wrote:
> > Hi Paul,
> > For instructions and examples using the Hmisc latex()
> function you
> > might want to take a look at
> > http://lib.stat.cmu.edu/S/Harrell/doc/summary.pdf.
> > 
> > -Best,
> > Ista
> > 
> > On Wed, Mar 17, 2010 at 10:51 AM, Paul Miller <pjmiller_57 at
yahoo.com>
> wrote:
> >> Hello Everyone,
> >>
> >> I have just started learning R and am in the
> process of figuring out what it can and can't do. I must say
> I am very impressed with R so far and am amazed that
> something this good can actually be free.
> >>
> >> Recently, I finished reading R for SAS and SPSS
> Users and have begun reading SAS and R and Data Manipulation
> with R. Based on what I've read in these books and
> elsewhere, I get the impression that R is very good at
> drawing high quality graphs but maybe not so good at
> creating nice looking tables of the sort I'm used to getting
> through SAS ODS.
> >>
> >> Am I right or wrong about this? If I am wrong, can
> anyone show me some examples of how R can be used to create
> really nice looking tables? I often make tables of adverse
> events in clinical trials that have n(%) values in the
> cells. I'd love to see an example that does a nice job of
> making that sort of table but would be happy to see any
> examples that someone might be willing to send to me.
> >>
> >> Thanks,
> >>
> >> Paul
> >>
> >>
> >>
> >>     
> __________________________________________________________________
> >> Looking for the perfect gift? Give the gift of
> Flickr!
> >>
> >>
> >>        [[alternative HTML
> version deleted]]
> >>
> >>
> 
> 
> -- 
> Frank E Harrell Jr   Professor and
> Chairman        School of Medicine
>                
>       Department of
> Biostatistics   Vanderbilt University
> 
> ______________________________________________
> R-help at 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.

On 03/18/2010 01:51 AM, Paul Miller wrote:
> Hello Everyone,
>
> I have just started learning R and am in the process of figuring out what
it can and can't do. I must say I am very impressed with R so far and am
amazed that something this good can actually be free.
>
> Recently, I finished reading R for SAS and SPSS Users and have begun
reading SAS and R and Data Manipulation with R. Based on what I've read in
these books and elsewhere, I get the impression that R is very good at drawing
high quality graphs but maybe not so good at creating nice looking tables of the
sort I'm used to getting through SAS ODS.
>
> Am I right or wrong about this? If I am wrong, can anyone show me some
examples of how R can be used to create really nice looking tables? I often make
tables of adverse events in clinical trials that have n(%) values in the cells.
I'd love to see an example that does a nice job of making that sort of table
but would be happy to see any examples that someone might be willing to send to
me.
>
Hi Paul,
While the latex option provides more flexibility in formatting, I use 
HTML listings from the prettyR package as the first step. For those who 
do not know that an HTML browser is needed to display them, modern OSs 
are smart enough to figure this out for them. All of the word processing 
packages that I use can directly import HTML documents, and the result 
has been good enough for any application so far. To see if this would be 
suitable, run the example for the delim.table function in the prettyR 
package, then open the "testglm.html" file with your favorite word 
processor.

Jim

Hello Everyone,
 
At last count, I had 14 responses to my question. Thanks very much to everyone
who replied, for helping me to understand that R is in fact capable of making
publication quality tables and is very flexible in rendering these outputs.
I'm still working my way through some of the basics of the program, but when
it comes time to learn how to make tables I'll certainly know where to look
for the necessary resources and information.
 
Thanks again,
 
Paul
 
 
 


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Jim Lemon <jim at bitwrit.com.au> [Wed, Mar 17, 2010 at 11:43:21PM CET]:


[...]
> All
> of the word processing packages that I use can directly import HTML
> documents, and the result has been good enough for any application
> so far. 
I have only MS Word as work and failed to import HTML so far (sometimes
succeeded with Copy/Paste). Could you give a hint if and how this can be 
accomplished?


-- 
Johannes H?sing               There is something fascinating about science. 
                              One gets such wholesale returns of conjecture 
mailto:johannes at huesing.name  from such a trifling investment of fact.
http://derwisch.wikidot.com         (Mark Twain, "Life on the
Mississippi")