A time series text with a title that seems designed to hide its
wide scope is:

Forecasting with Exponential Smoothing
The State Space Approach
Hyndman, R.J., Koehler, A.B., Ord, J.K., Snyder, R.D.
Springer 2009.

This book is actually an excellent overview of time series theory,
ARIMA as well as state space.  It is of course, in part, a manual
for the forecast and other packages in what has been the
forecasting bundle.  It does of course talk about forecasting
with exponential smoothing!

John Maindonald             email: john.maindonald@anu.edu.au
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.


On 16/06/2009, at 2:51 AM, r-help-request@r-project.org wrote:

> From: "Gerard M. Keogh" <GMKeogh@justice.ie>
> Date: 15 June 2009 8:10:34 PM
> To: Antonio Olinto <aolinto_r@bignet.com.br>
> Cc: r-help@r-project.org, r-help-bounces@r-project.org
> Subject: Re: [R] books on Time series
>
>
> Antonio,
>
> You basically need the cross-correlation function in R which is very  
> easy
> to use - just look up the examples in ?ccf.
> So, if any of the books you mention deal with it - you'll be ok.
>
> If you know about ARIMA models (or know someone who does in a maths/ 
> stats
> dept) and stuff like that then you can use "transfer functions" to  
> model
> the dynmaic relationships - I think ARIMA in R should allow you to  
> do that
> using an "x" input function.
>
> My own personal favourite TS book is which is a bit mathematical (i.e.
> easier than the "old testament" bible - TSA by Brockwell and Davis)  
> is:
>   Time Series Analyis: Univariate and Multivariate Methods, by W. S.  
> Wei,
>   1990.
> older, but still top notch in my opinion.
>
> Hope this helps!
>
> Gerard
>
>
>
>
>             Antonio Olinto
>             <aolinto_r@bignet
>             .com 
> .br>                                                   To
>             Sent by:                  r-help@r-project.org
>             r-help- 
> bounces@r-                                          cc
>             project.org
>                                                                    
> Subject
>                                       [R] books on Time series
>             15/06/2009 02:30
>
>
>
>
>
>
>
>
>
> Dear list fellows,
>
> I want to study time series and use R to analyse time series of  
> fishing
> data from several species (landings and cpue) investigating the
> correlation between them and with environmental factors (water
> temperature, wind, etc.).
>
> Searching at Amazon I found three books with examples in R:
>
> Time Series Analysis: With Applications in R by Jonathan D. Cryer and
> Jonathan D. Cryer
>
> Time Series Analysis and Its Applications: With R Examples by Robert  
> H.
> Shumway and Robert H. Shumway
>
> Introductory Time Series with R (Use R) by Paul S.P. Cowpertwait and
> Andrew V. Metcalfe
>
> I would like to receive any suggestion of which is most appropriate  
> for
> a non-statistician (I am a biologist). Reading only the index I could
> not evaluate it.
>
> Thanks in advance,
>
> Antonio Olinto
>
> Marine Fisheries Center
> Sao Paulo Fisheries Institute
> Brazil
>
> ______________________________________________
> 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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>
>
>
>
>
>
>
>
> From: ilenia fronza <ilenia.fronza@gmail.com>
> Date: 15 June 2009 8:39:09 PM
> To: r-help@r-project.org
> Subject: [R] Markov chains
>
>
> Hi,
> is there a package to apply Markov chains (order > 1) ?
>
> thanks in advance
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Philippe Grosjean <phgrosjean@sciviews.org>
> Date: 15 June 2009 8:41:40 PM
> To: baptiste auguie <baptiste.auguie@gmail.com>
> Cc: r-help@stat.math.ethz.ch
> Subject: Re: [R] a proposal regarding documentation
>
>
> baptiste auguie wrote:
>> I knew I had seen this in action! But as you mention, most pages  
>> only display ~~RDOC~~ at the moment.
>> I second the idea of using the wiki for such collaborative work. If  
>> the current (r-devel) version of all help pages could be  
>> automatically copied to the wiki, users would have a convenient way  
>> to propose changes. The coloured diff, user identification, and RSS  
>> feed make for a very user-friendly alternative to svn access  
>> (unthinkable anyway for non-R core members).
>
> Well, the help page itself is read-only, but you can use all this in  
> the Wiki discussion section.
>
> PhG
>
>> Best,
>> baptiste
>> Philippe Grosjean wrote:
>>> Ironically, this function is present since the beginning, although  
>>> a little buggy. If you try this in R on a computer that is  
>>> connected to the Internet:
>>>
>>> wikihelp <- function(topic)
>>>  browseURL(paste("http://wiki.r-project.org/rwiki/rhelp.php?id=",
>>>    topic, sep = ""))
>>> wikihelp("barplot")
>>>
>>> You got the help page of ?barplot in wiki format (with a few  
>>> presentation bugs, but everything is there, basically)... plus a  
>>> Wiki discussion section where people can add more material, links,  
>>> etc.
>>>
>>> The help page is not physically contained in the wiki page, but it  
>>> is a file stored elsewhere on the R Wiki server, and that is  
>>> supposed to be updated regularly (but it is not the case for the  
>>> moment). In the wiki page you see, there is only a ~~RDOC~~ marker  
>>> indicating where to include the help page.
>>>
>>> I have a problem with the R Wiki cache: until someone adds  
>>> comments to such a page, the content is not refreshed, but you  
>>> just see ~~RDOC~~.
>>>
>>> Try, for instance:
>>>
>>> wikihelp("chisq.test")
>>>
>>> If the engine thinks 'topic' is ambiguous, it displays a list of  
>>> possibilities (i.e., our wikihelp() function is somehow a mix of  
>>> help() and of apropos()). For instance:
>>>
>>> wikihelp("help")
>>>
>>>
>>> This should not be ambiguous, but it is considered as it currently  
>>> by rhelp.php (a minor bug probably easy to correct).
>>>
>>> Finally, all wiki pages are spelled with lowercase. It is the same  
>>> for help pages. So,
>>>
>>> wikihelp("RSiteSearch")
>>> wikihelp("rsitesearch")
>>>
>>> lead to the same rdoc:utils:rsitesearch wiki page. I have no  
>>> solutions for that!
>>>
>>> So, to conclude, most of the required mechanism is already  
>>> installed on R Wiki. It  just needs a little bit of debugging and  
>>> fine-tuning to become completely operational. A little help here  
>>> would be very appreciated!
>>>
>>> ... and, of course, a refined version of the wikihelp() function  
>>> must be made widely available to "reveal" this function. One could  
>>> even consider to write a pager that displays local help page and  
>>> warns if there are comments on this topic posted on the wiki... or  
>>> that link to a personal wiki engine where everybody could add its  
>>> own comments to the help pages, with full-text search ability!
>>>
>>> Best,
>>>
>>> Philippe Grosjean
>>>
>>> ..............................................<°}))><........
>>> ) ) ) ) )
>>> ( ( ( ( (    Prof. Philippe Grosjean
>>> ) ) ) ) )
>>> ( ( ( ( (    Numerical Ecology of Aquatic Systems
>>> ) ) ) ) )   Mons-Hainaut University, Belgium
>>> ( ( ( ( (
>>> ..............................................................
>>
>
>
>
>
>
>
>
>
>
> From: Jim Lemon <jim@bitwrit.com.au>
> Date: 15 June 2009 9:01:29 PM
> To: r-help@stat.math.ethz.ch
> Subject: Re: [R] a proposal regarding documentation
>
>
> I was studiously ignoring this thread (I have way too much to do  
> already) but Gabor's suggestion reminded me that I have often found  
> the PHP/MySQL online help pages very ... well, helpful. I can't  
> recall the number of times I have scrolled down when I didn't quite  
> get it, and found a comment that got it for me. I find it a really  
> good system.
>
> Jim
>
>
>
>
>
>
>
>
>
> From: John Sorkin <jsorkin@grecc.umaryland.edu>
> Date: 15 June 2009 9:06:00 PM
> To: Gabor Grothendieck <ggrothendieck@gmail.com>, Philippe Grosjean <phgrosjean@sciviews.org 
> >
> Cc: r-help@stat.math.ethz.ch, Patrick Burns <pburns@pburns.seanet.com>
> Subject: Re: [R] a proposal regarding documentation
>
>
> R 2.8.1, Firefox 3.0.11, windows XP
> Philippe,
> I suspect there are more substantial problems with the link to the  
> WIKI
> then you thought. When I tried your code I got a page that contained
> nothing more than (excluding the nice graphic header and the index on
> the left-hand page):
>
> Trace: » barplot
> == Rwiki file not found! ==
>
> There is a helpful discussion of adding labels to barplots here:
> https://stat.ethz.ch/pipermail/r-help/2002-October/025879.html
>
>
> This WIKI page is not at all useful,it does not as you suggested it
> does not contain  the help page of ?barplot in wiki format as you
> suggested int would!
> John
>
>
> John David Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> 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
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>
>>>> Philippe Grosjean <phgrosjean@sciviews.org> 6/15/2009 4:42 AM >>>
> Ironically, this function is present since the beginning, although a
> little buggy. If you try this in R on a computer that is connected to
> the Internet:
>
> wikihelp <- function(topic)
>   browseURL(paste("http://wiki.r-project.org/rwiki/rhelp.php?id=",
>     topic, sep = ""))
> wikihelp("barplot")
>
> You got the help page of ?barplot in wiki format (with a few
> presentation bugs, but everything is there, basically)... plus a Wiki
> discussion section where people can add more material, links, etc.
>
> The help page is not physically contained in the wiki page, but it  
> is a
>
> file stored elsewhere on the R Wiki server, and that is supposed to be
>
> updated regularly (but it is not the case for the moment). In the wiki
>
> page you see, there is only a ~~RDOC~~ marker indicating where to
> include the help page.
>
> I have a problem with the R Wiki cache: until someone adds comments to
>
> such a page, the content is not refreshed, but you just see ~~RDOC~~.
>
> Try, for instance:
>
> wikihelp("chisq.test")
>
> If the engine thinks 'topic' is ambiguous, it displays a list of
> possibilities (i.e., our wikihelp() function is somehow a mix of  
> help()
>
> and of apropos()). For instance:
>
> wikihelp("help")
>
>
> This should not be ambiguous, but it is considered as it currently by
> rhelp.php (a minor bug probably easy to correct).
>
> Finally, all wiki pages are spelled with lowercase. It is the same for
>
> help pages. So,
>
> wikihelp("RSiteSearch")
> wikihelp("rsitesearch")
>
> lead to the same rdoc:utils:rsitesearch wiki page. I have no solutions
>
> for that!
>
> So, to conclude, most of the required mechanism is already installed  
> on
>
> R Wiki. It  just needs a little bit of debugging and fine-tuning to
> become completely operational. A little help here would be very
> appreciated!
>
> ... and, of course, a refined version of the wikihelp() function must
> be
> made widely available to "reveal" this function. One could even
> consider
> to write a pager that displays local help page and warns if there are
> comments on this topic posted on the wiki... or that link to a  
> personal
>
> wiki engine where everybody could add its own comments to the help
> pages, with full-text search ability!
>
> Best,
>
> Philippe Grosjean
>
> ..............................................<°}))><........
>  ) ) ) ) )
> ( ( ( ( (    Prof. Philippe Grosjean
>  ) ) ) ) )
> ( ( ( ( (    Numerical Ecology of Aquatic Systems
>  ) ) ) ) )   Mons-Hainaut University, Belgium
> ( ( ( ( (
> ..............................................................
>
> Gabor Grothendieck wrote:
>> In PHP and also in MySQL the manual has a wiki capability
>> so that users can add notes at the end of each page, e.g.
>>
>> http://www.php.net/manual/en/functions.variable-functions.php
>>
>> http://dev.mysql.com/doc/refman/4.1/en/update.html
>>
>> That would combine documentation and wiki into one. Here it would
>> involve copying the R help pages into the wiki in a readonly mode
> with the
>> writeable wiki portion at the end of each such page.  It would also
> be
>> necessary to be able to update the help pages in the wiki when new
> versions
>> became available.
>>
>> No explicit email group or coordination would be needed.  It would
> also address
>> the organization problem as they could be organized as they are now,
> i.e. into
>> packages: base, stats, utils, ...
>>
>> It would require the development of a program to initially copy the
> help pages
>> and to update them while keeping the notes in place whenever a new
> version
>> of R came out.
>>
>> On Sun, Jun 14, 2009 at 5:35 PM, Peter
>> Flom<peterflomconsulting@mindspring.com> wrote:
>>> I certainly don't have anything against the WIKI, but I think that
> the documentation
>>> is where the action is, especially for newbies.  It's the  natural
> first step
>>> when you want to learn about a function or when you  get an error
> message you
>>> don't understand.
>>>
>>> Peter
>>>
>>> Peter L. Flom, PhD
>>> Statistical Consultant
>>> www DOT peterflomconsulting DOT com
>>>
>>> ______________________________________________
>>> 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.
>>>
>>
>>
>
> Confidentiality Statement:
> This email message, including any attachments, is for th...{{dropped: 
> 6}}
>
>
>
>
>
>
>
>
>
> From: poleteiep34 <poleteiep34@hotmail.com>
> Date: 15 June 2009 9:09:55 PM
> To: r-help@r-project.org
> Subject: [R] NA as a result of using GLM
> Reply-To: poleteiep34@hotmail.com
>
>
> Hi all!
> Maybe someone could help me with the following. I know this hasn't  
> directly to do with ecology but I'm also using glm.
>
> I have a list of 16 genes and 10 samples. The samples are of two  
> types, 4 Ctrl and 6 Diseased. If,
>
> labelInd<-as.factor(c(rep("0",4),rep("1",6)))
> genes.glm<-glm(labelInd ~ ., family=binomial, data=mat)
>
>
> beeing "mat" the 10x16 matrix (without NAs), I got 17 values, first  
> the intercept, 9 numerical values and "NA" for the last 7 genes.  
> Does anybody you know why this is happening or how I can model using  
> the 16 genes?
>
> I hope anyone could help me with this!
> Many thanks in advance,
>
> Paul
>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Philippe Grosjean <phgrosjean@sciviews.org>
> Date: 15 June 2009 9:17:11 PM
> To: John Sorkin <jsorkin@grecc.umaryland.edu>
> Cc: r-help@stat.math.ethz.ch, Patrick Burns <pburns@pburns.seanet.com>
> Subject: Re: [R] a proposal regarding documentation
>
>
> John Sorkin wrote:
>> R 2.8.1, Firefox 3.0.11, windows XP Philippe,
>> I suspect there are more substantial problems with the link to the  
>> WIKI
>> then you thought. When I tried your code I got a page that contained
>> nothing more than (excluding the nice graphic header and the index on
>> the left-hand page):
>> Trace: » barplot
>> == Rwiki file not found! ==
>> There is a helpful discussion of adding labels to barplots here:
>> https://stat.ethz.ch/pipermail/r-help/2002-October/025879.html   
>> This WIKI page is not at all useful,it does not as you suggested it
>> does not contain  the help page of ?barplot in wiki format as you
>> suggested int would!
>> John
>
> Still the problem with the cache. I refreshed the page, and now it  
> appears as it should.
> Best,
>
> PhG
>
>> John David Sorkin M.D., Ph.D.
>> Chief, Biostatistics and Informatics
>> 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
>> (Phone) 410-605-7119
>> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>>>>> Philippe Grosjean <phgrosjean@sciviews.org> 6/15/2009 4:42 AM >>>
>> Ironically, this function is present since the beginning, although  
>> a little buggy. If you try this in R on a computer that is  
>> connected to the Internet:
>> wikihelp <- function(topic)
>>   browseURL(paste("http://wiki.r-project.org/rwiki/rhelp.php?id=",
>>     topic, sep = ""))
>> wikihelp("barplot")
>> You got the help page of ?barplot in wiki format (with a few  
>> presentation bugs, but everything is there, basically)... plus a  
>> Wiki discussion section where people can add more material, links,  
>> etc.
>> The help page is not physically contained in the wiki page, but it  
>> is a
>> file stored elsewhere on the R Wiki server, and that is supposed to  
>> be
>> updated regularly (but it is not the case for the moment). In the  
>> wiki
>> page you see, there is only a ~~RDOC~~ marker indicating where to  
>> include the help page.
>> I have a problem with the R Wiki cache: until someone adds comments  
>> to
>> such a page, the content is not refreshed, but you just see ~~RDOC~~.
>> Try, for instance:
>> wikihelp("chisq.test")
>> If the engine thinks 'topic' is ambiguous, it displays a list of  
>> possibilities (i.e., our wikihelp() function is somehow a mix of  
>> help()
>> and of apropos()). For instance:
>> wikihelp("help")
>> This should not be ambiguous, but it is considered as it currently  
>> by rhelp.php (a minor bug probably easy to correct).
>> Finally, all wiki pages are spelled with lowercase. It is the same  
>> for
>> help pages. So,
>> wikihelp("RSiteSearch")
>> wikihelp("rsitesearch")
>> lead to the same rdoc:utils:rsitesearch wiki page. I have no  
>> solutions
>> for that!
>> So, to conclude, most of the required mechanism is already  
>> installed on
>> R Wiki. It  just needs a little bit of debugging and fine-tuning to  
>> become completely operational. A little help here would be very
>> appreciated!
>> ... and, of course, a refined version of the wikihelp() function must
>> be made widely available to "reveal" this function. One could even
>> consider to write a pager that displays local help page and warns  
>> if there are comments on this topic posted on the wiki... or that  
>> link to a personal
>> wiki engine where everybody could add its own comments to the help  
>> pages, with full-text search ability!
>> Best,
>> Philippe Grosjean
>> ..............................................<°}))><........
>>  ) ) ) ) )
>> ( ( ( ( (    Prof. Philippe Grosjean
>>  ) ) ) ) )
>> ( ( ( ( (    Numerical Ecology of Aquatic Systems
>>  ) ) ) ) )   Mons-Hainaut University, Belgium
>> ( ( ( ( (
>> ..............................................................
>> Gabor Grothendieck wrote:
>>> In PHP and also in MySQL the manual has a wiki capability
>>> so that users can add notes at the end of each page, e.g.
>>>
>>> http://www.php.net/manual/en/functions.variable-functions.php
>>> http://dev.mysql.com/doc/refman/4.1/en/update.html
>>> That would combine documentation and wiki into one. Here it would
>>> involve copying the R help pages into the wiki in a readonly mode
>> with the
>>> writeable wiki portion at the end of each such page.  It would also
>> be
>>> necessary to be able to update the help pages in the wiki when new
>> versions
>>> became available.
>>>
>>> No explicit email group or coordination would be needed.  It would
>> also address
>>> the organization problem as they could be organized as they are now,
>> i.e. into
>>> packages: base, stats, utils, ...
>>>
>>> It would require the development of a program to initially copy the
>> help pages
>>> and to update them while keeping the notes in place whenever a new
>> version
>>> of R came out.
>>>
>>> On Sun, Jun 14, 2009 at 5:35 PM, Peter
>>> Flom<peterflomconsulting@mindspring.com> wrote:
>>>> I certainly don't have anything against the WIKI, but I think that
>> the documentation
>>>> is where the action is, especially for newbies.  It's the  natural
>> first step
>>>> when you want to learn about a function or when you  get an error
>> message you
>>>> don't understand.
>>>>
>>>> Peter
>>>>
>>>> Peter L. Flom, PhD
>>>> Statistical Consultant
>>>> www DOT peterflomconsulting DOT com
>>>>
>>>> ______________________________________________
>>>> 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.
>>>>
>>>
>> Confidentiality Statement:
>> This email message, including any attachments, is for th... 
>> {{dropped:6}}
>> ______________________________________________
>> 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.
>
>
>
>
>
>
>
>
>
> From: Jim Lemon <jim@bitwrit.com.au>
> Date: 15 June 2009 9:27:21 PM
> To: Fernando Marmolejo Ramos <fernando.marmolejoramos@adelaide.edu.au>
> Cc: r-help@r-project.org
> Subject: Re: [R] simulating Likert-type data
>
>
> Fernando Marmolejo Ramos wrote:
>> Dear R members
>>
>> Could someone indicate me how to simulate Likert-type data using  
>> the GAMLSS
>> library and how to fit that data?
>>
>> Let’s say, 50 random numbers in a variable that goes from -4 to +4  
>> in steps of
>> 1 (i.e., -4, -3, -2, -1, 0, 1, 2, 3, 4) with a mean of 2 and SD of  
>> 0.15 and
>> belonging to a normal distribution?
>>
>>
> Hi Fernando,
> You can get something like a truncated normal (in the sense of, "If  
> I squint my eyes right down, it looks kind of normal") sample with:
>
> sample(-4:4,50,TRUE,prob=c(pnorm(-4:2,)pnorm(c(3,4), 
> 2,lower.tail=FALSE))
>
> but it will not pass any of the usual tests for normal distribution.
>
> Jim
>
>
>
>
>
>
>
>
>
> From: Philippe Grosjean <phgrosjean@sciviews.org>
> Date: 15 June 2009 9:36:45 PM
> To: John Sorkin <jsorkin@grecc.umaryland.edu>
> Cc: r-help@stat.math.ethz.ch, Patrick Burns <pburns@pburns.seanet.com>
> Subject: Re: [R] a proposal regarding documentation
>
>
> Sorry, after a second request, I got the ==Rwiki file not found!==  
> again. Obviously, I have to solve this bug first!
>
> PhG
>
> Philippe Grosjean wrote:
>> John Sorkin wrote:
>>> R 2.8.1, Firefox 3.0.11, windows XP Philippe,
>>> I suspect there are more substantial problems with the link to the  
>>> WIKI
>>> then you thought. When I tried your code I got a page that contained
>>> nothing more than (excluding the nice graphic header and the index  
>>> on
>>> the left-hand page):
>>>
>>> Trace: » barplot
>>> == Rwiki file not found! ==
>>>
>>> There is a helpful discussion of adding labels to barplots here:
>>> https://stat.ethz.ch/pipermail/r-help/2002-October/025879.html
>>> This WIKI page is not at all useful,it does not as you suggested it
>>> does not contain  the help page of ?barplot in wiki format as you
>>> suggested int would!
>>> John
>> Still the problem with the cache. I refreshed the page, and now it  
>> appears as it should.
>> Best,
>> PhG
>>>
>>> John David Sorkin M.D., Ph.D.
>>> Chief, Biostatistics and Informatics
>>> 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
>>> (Phone) 410-605-7119
>>> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>>>
>>>>>> Philippe Grosjean <phgrosjean@sciviews.org> 6/15/2009 4:42 AM >>>
>>> Ironically, this function is present since the beginning, although  
>>> a little buggy. If you try this in R on a computer that is  
>>> connected to the Internet:
>>>
>>> wikihelp <- function(topic)
>>>   browseURL(paste("http://wiki.r-project.org/rwiki/rhelp.php?id=",
>>>     topic, sep = ""))
>>> wikihelp("barplot")
>>>
>>> You got the help page of ?barplot in wiki format (with a few  
>>> presentation bugs, but everything is there, basically)... plus a  
>>> Wiki discussion section where people can add more material, links,  
>>> etc.
>>>
>>> The help page is not physically contained in the wiki page, but it  
>>> is a
>>>
>>> file stored elsewhere on the R Wiki server, and that is supposed  
>>> to be
>>>
>>> updated regularly (but it is not the case for the moment). In the  
>>> wiki
>>>
>>> page you see, there is only a ~~RDOC~~ marker indicating where to  
>>> include the help page.
>>>
>>> I have a problem with the R Wiki cache: until someone adds  
>>> comments to
>>>
>>> such a page, the content is not refreshed, but you just see  
>>> ~~RDOC~~.
>>>
>>> Try, for instance:
>>>
>>> wikihelp("chisq.test")
>>>
>>> If the engine thinks 'topic' is ambiguous, it displays a list of  
>>> possibilities (i.e., our wikihelp() function is somehow a mix of  
>>> help()
>>>
>>> and of apropos()). For instance:
>>>
>>> wikihelp("help")
>>>
>>>
>>> This should not be ambiguous, but it is considered as it currently  
>>> by rhelp.php (a minor bug probably easy to correct).
>>>
>>> Finally, all wiki pages are spelled with lowercase. It is the same  
>>> for
>>>
>>> help pages. So,
>>>
>>> wikihelp("RSiteSearch")
>>> wikihelp("rsitesearch")
>>>
>>> lead to the same rdoc:utils:rsitesearch wiki page. I have no  
>>> solutions
>>>
>>> for that!
>>>
>>> So, to conclude, most of the required mechanism is already  
>>> installed on
>>>
>>> R Wiki. It  just needs a little bit of debugging and fine-tuning  
>>> to become completely operational. A little help here would be very
>>> appreciated!
>>>
>>> ... and, of course, a refined version of the wikihelp() function  
>>> must
>>> be made widely available to "reveal" this function. One could even
>>> consider to write a pager that displays local help page and warns  
>>> if there are comments on this topic posted on the wiki... or that  
>>> link to a personal
>>>
>>> wiki engine where everybody could add its own comments to the help  
>>> pages, with full-text search ability!
>>>
>>> Best,
>>>
>>> Philippe Grosjean
>>>
>>> ..............................................<°}))><........
>>>  ) ) ) ) )
>>> ( ( ( ( (    Prof. Philippe Grosjean
>>>  ) ) ) ) )
>>> ( ( ( ( (    Numerical Ecology of Aquatic Systems
>>>  ) ) ) ) )   Mons-Hainaut University, Belgium
>>> ( ( ( ( (
>>> ..............................................................
>>>
>>> Gabor Grothendieck wrote:
>>>> In PHP and also in MySQL the manual has a wiki capability
>>>> so that users can add notes at the end of each page, e.g.
>>>>
>>>> http://www.php.net/manual/en/functions.variable-functions.php
>>>> http://dev.mysql.com/doc/refman/4.1/en/update.html
>>>> That would combine documentation and wiki into one. Here it would
>>>> involve copying the R help pages into the wiki in a readonly mode
>>> with the
>>>> writeable wiki portion at the end of each such page.  It would also
>>> be
>>>> necessary to be able to update the help pages in the wiki when new
>>> versions
>>>> became available.
>>>>
>>>> No explicit email group or coordination would be needed.  It would
>>> also address
>>>> the organization problem as they could be organized as they are  
>>>> now,
>>> i.e. into
>>>> packages: base, stats, utils, ...
>>>>
>>>> It would require the development of a program to initially copy the
>>> help pages
>>>> and to update them while keeping the notes in place whenever a new
>>> version
>>>> of R came out.
>>>>
>>>> On Sun, Jun 14, 2009 at 5:35 PM, Peter
>>>> Flom<peterflomconsulting@mindspring.com> wrote:
>>>>> I certainly don't have anything against the WIKI, but I think that
>>> the documentation
>>>>> is where the action is, especially for newbies.  It's the  natural
>>> first step
>>>>> when you want to learn about a function or when you  get an error
>>> message you
>>>>> don't understand.
>>>>>
>>>>> Peter
>>>>>
>>>>> Peter L. Flom, PhD
>>>>> Statistical Consultant
>>>>> www DOT peterflomconsulting DOT com
>>>>>
>>>>> ______________________________________________
>>>>> 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.
>>>>>
>>>>
>>>
>>> Confidentiality Statement:
>>> This email message, including any attachments, is for th... 
>>> {{dropped:6}}
>>>
>>> ______________________________________________
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>> ______________________________________________
>> R-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.
>
>
>
>
>
>
>
>
>
> From: Jim Lemon <jim@bitwrit.com.au>
> Date: 15 June 2009 9:47:27 PM
> To: Fernando Marmolejo Ramos <fernando.marmolejoramos@adelaide.edu.au>
> Cc: r-help@r-project.org
> Subject: Re: [R] simulating Likert-type data
>
>
> Oops, sorry. Sloppy translation from the R window
>>
>> sample(-4:4,50,TRUE,prob=c(pnorm(-4:2,2,0.15)pnorm(c(3,4), 
>> 2,0.15,lower.tail=FALSE))
>
> Jim
>
>
>
>
>
>
>
>
>
> From: Henrique Dallazuanna <wwwhsd@gmail.com>
> Date: 15 June 2009 10:11:01 PM
> To: Philippe Grosjean <phgrosjean@sciviews.org>
> Cc: r-help@stat.math.ethz.ch, John Sorkin  
> <jsorkin@grecc.umaryland.edu>, Patrick Burns  
> <pburns@pburns.seanet.com>
> Subject: Re: [R] a proposal regarding documentation
>
>
> On Mon, Jun 15, 2009 at 5:42 AM, Philippe Grosjean
> <phgrosjean@sciviews.org>wrote:
>
>> Ironically, this function is present since the beginning, although  
>> a little
>> buggy. If you try this in R on a computer that is connected to the  
>> Internet:
>>
>> wikihelp <- function(topic)
>> browseURL(paste("http://wiki.r-project.org/rwiki/rhelp.php?id=",
>>   topic, sep = ""))
>> wikihelp("barplot")
>>
>> You got the help page of ?barplot in wiki format (with a few  
>> presentation
>> bugs, but everything is there, basically)... plus a Wiki discussion  
>> section
>> where people can add more material, links, etc.
>>
>> The help page is not physically contained in the wiki page, but it  
>> is a
>> file stored elsewhere on the R Wiki server, and that is supposed to  
>> be
>> updated regularly (but it is not the case for the moment). In the  
>> wiki page
>> you see, there is only a ~~RDOC~~ marker indicating where to  
>> include the
>> help page.
>>
>> I have a problem with the R Wiki cache: until someone adds comments  
>> to such
>> a page, the content is not refreshed, but you just see ~~RDOC~~.
>>
>
> You can add the ~~NOCACHE~~ string at the page for refresh the cache  
> every
> time that someone open it.
>
>
>>
>> Try, for instance:
>>
>> wikihelp("chisq.test")
>>
>> If the engine thinks 'topic' is ambiguous, it displays a list of
>> possibilities (i.e., our wikihelp() function is somehow a mix of  
>> help() and
>> of apropos()). For instance:
>>
>> wikihelp("help")
>>
>>
>> This should not be ambiguous, but it is considered as it currently by
>> rhelp.php (a minor bug probably easy to correct).
>>
>> Finally, all wiki pages are spelled with lowercase. It is the same  
>> for help
>> pages. So,
>>
>> wikihelp("RSiteSearch")
>> wikihelp("rsitesearch")
>>
>> lead to the same rdoc:utils:rsitesearch wiki page. I have no  
>> solutions for
>> that!
>>
>> So, to conclude, most of the required mechanism is already  
>> installed on R
>> Wiki. It  just needs a little bit of debugging and fine-tuning to  
>> become
>> completely operational. A little help here would be very appreciated!
>>
>> ... and, of course, a refined version of the wikihelp() function  
>> must be
>> made widely available to "reveal" this function. One could even  
>> consider to
>> write a pager that displays local help page and warns if there are  
>> comments
>> on this topic posted on the wiki... or that link to a personal wiki  
>> engine
>> where everybody could add its own comments to the help pages, with  
>> full-text
>> search ability!
>>
>> Best,
>>
>> Philippe Grosjean
>>
>> ..............................................<°}))><........
>> ) ) ) ) )
>> ( ( ( ( (    Prof. Philippe Grosjean
>> ) ) ) ) )
>> ( ( ( ( (    Numerical Ecology of Aquatic Systems
>> ) ) ) ) )   Mons-Hainaut University, Belgium
>> ( ( ( ( (
>> ..............................................................
>>
>>
>> Gabor Grothendieck wrote:
>>
>>> In PHP and also in MySQL the manual has a wiki capability
>>> so that users can add notes at the end of each page, e.g.
>>>
>>> http://www.php.net/manual/en/functions.variable-functions.php
>>>
>>> http://dev.mysql.com/doc/refman/4.1/en/update.html
>>>
>>> That would combine documentation and wiki into one. Here it would
>>> involve copying the R help pages into the wiki in a readonly mode  
>>> with the
>>> writeable wiki portion at the end of each such page.  It would  
>>> also be
>>> necessary to be able to update the help pages in the wiki when new
>>> versions
>>> became available.
>>>
>>> No explicit email group or coordination would be needed.  It would  
>>> also
>>> address
>>> the organization problem as they could be organized as they are  
>>> now, i.e.
>>> into
>>> packages: base, stats, utils, ...
>>>
>>> It would require the development of a program to initially copy  
>>> the help
>>> pages
>>> and to update them while keeping the notes in place whenever a new  
>>> version
>>> of R came out.
>>>
>>> On Sun, Jun 14, 2009 at 5:35 PM, Peter
>>> Flom<peterflomconsulting@mindspring.com> wrote:
>>>
>>>> I certainly don't have anything against the WIKI, but I think  
>>>> that the
>>>> documentation
>>>> is where the action is, especially for newbies.  It's the   
>>>> natural first
>>>> step
>>>> when you want to learn about a function or when you  get an error  
>>>> message
>>>> you
>>>> don't understand.
>>>>
>>>> Peter
>>>>
>>>> Peter L. Flom, PhD
>>>> Statistical Consultant
>>>> www DOT peterflomconsulting DOT com
>>>>
>>>> ______________________________________________
>>>> R-help@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>>
>>>
>>>
>> ______________________________________________
>> R-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.
>>
>
>
>
> -- 
> Henrique Dallazuanna
> Curitiba-Paraná-Brasil
> 25° 25' 40" S 49° 16' 22" O
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Bessy <piglet630@hotmail.com>
> Date: 15 June 2009 10:18:08 PM
> To: r-help@r-project.org
> Subject: [R] Schoenfeld Residuals with tied data
>
>
>
> Dear all,
>
> I am struggling with calculation of Schoenfeld residuals of my Cox Ph
> models.
>
> Based on the formula as attached, I calculated the Schoenfeld  
> residuals for
> both non tied and tied data, respectively.
>
> And then I validated my results with R using the same data sets.  
> However, I
> found that my results for non-tied data was ok but the results for  
> tied data
> were different from R's.
>
> How does R calculate the Schoenfeld Residuals for tied data? Could  
> someone
> give me some hints, please?
>
> Thank you so much.
>
> Bessy http://www.nabble.com/file/p24033333/Schoenfeld%2BResiduals.doc
> Schoenfeld+Residuals.doc
> -- 
> View this message in context: http://www.nabble.com/Schoenfeld-Residuals-with-tied-data-tp24033333p24033333.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
>
>
>
>
>
>
> From: Julien Gagneur <julien.gagneur@embl.de>
> Date: 15 June 2009 11:01:20 PM
> To: r-help@r-project.org
> Subject: [R] multcomp: contrasts for count data
>
>
> Hi,
>
> I would like to derive p-values for pair-wise comparison (Tukey's) of
> effects when the response is a count.
>
> I am trying a test case where y ~ Po( lambda(x) ). x has three
> levels : A, B and C with lambda(x) = 10, 20 and 20 respectively.
> Hence, p-values for the contrast C - B should distribute uniformally.
>
> I have implemented this test case as below but do not get uniform
> distribution of those p-values, rather high values (close to 1). Is my
> code correct? The problem could be due to the normal approximation but
> I have also tried with larger sample sizes (n=1e4) and still get it.
>
> Is there an issue in using multcomp for count data? My final real case
> will be with quasipoisson data.
>
> Thanks for your help,
>
> Julien
>
>
>
> seed(0)
> pvals = t(
>         sapply(
>         1:100,
>         function(i){
>             x = factor(sample( c("A", "B", "C"), 1000, replace=TRUE ))
>             means  = c(A=10, B=20, C=20)
>             y = rpois(length(x), lambda=means[x])
>             fit = glm(y ~ x , family=poisson() )
>             summary( glht(fit, linfct = mcp(x = "Tukey") ) )$test
> $pvalues
>         }
> )
> )
>
> hist(pvals[,3], breaks=30)
>
>
>
>> Julien Gagneur
>> Computational Scientist
>> Steinmetz lab
>> Tel: +49-(0)6221-387-8114
>> Fax: +49-(0)6221-387-8518
>> Email: julien.gagneur@embl.de
>>
>> Room V205
>> EMBL
>> Meyerhofstrasse 1
>> D-69117 Heidelberg
>> Germany
>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Cecilia Carmo <cecilia.carmo@ua.pt>
> Date: 15 June 2009 11:26:09 PM
> To: r-help@r-project.org
> Subject: [R] how to obtain lm statistics for multiple subsets
>
>
> Hi everyone, my data is in a dataframe similar to this but with more  
> firms, more industries, more years and variables that correspond to  
> financial information:
>
>> firm<-c(rep(1,4),rep(2,4),rep(3,4),rep(4,4))
>> year<-c(rep(2000:2003,4))
>> industry<-c(rep(10,4),rep(20,4),rep(10,4),rep(30,4))
>> X1<-c(10,14,18,16,20,45,23,54,24,67,98,58,76,34,23,89)
>> X2<-c(11,46,89,36,72,78,55,44,22,78,53,25,12,45,87,23)
>> Y<-c(12,45,32,69,87,54,33,22,89,66,35,23,15,54,67,87)
>> data<-data.frame(firm, industry,year,Y,X1,X2)
>> data
>> firm industry year  Y X1 X2
> 1       10 2000 12 10 11
> 1       10 2001 45 14 46
> 1       10 2002 32 18 89
> 1       10 2003 69 16 36
> 2       20 2000 87 20 72
> 2       20 2001 54 45 78
> 2       20 2002 33 23 55
> 2       20 2003 22 54 44
> 3       10 2000 89 24 22
> 3       10 2001 66 67 78
> 3       10 2002 35 98 53
> 3       10 2003 23 58 25
> 4       30 2000 15 76 12
> 4       30 2001 54 34 45
> 4       30 2002 67 23 87
> 4       30 2003 87 89 23
>
> I need to obtain the coefficients and the statistics by year and by  
> industry, for the lm function:
> ff<-Y~b1 + b2.X1 + b3.X3
>
> So what I’ve done was: subset the dataframe by year, so I have 3  
> dataframes corresponding to the 3 years (dataframe2000,  
> dataframe2001, … ) and then I applied a function that I’ve found  
> in R-help mails:
> coef2000<- 
> as 
> .data 
> .frame 
> (t(sapply(split(dataframe2000,dataframe2000$industry),function(x) 
> {coef(lm(ff,data=x))})))
>
> I need help in two ways:
> First: I’d like to have in the dataframe of the coefficients more  
> statistics information that helps me to understand the significance  
> of the coefficients; and
> Second: Is that possible to obtain this output for all years at once?
> Thanks in advance,
> Cecília Carmo (Universidade de Aveiro – Portugal)
>
>
>
>
>
>
>
>
>
> From: Gabor Grothendieck <ggrothendieck@gmail.com>
> Date: 15 June 2009 11:34:05 PM
> To: Cecilia Carmo <cecilia.carmo@ua.pt>
> Cc: r-help@r-project.org
> Subject: Re: [R] how to obtain lm statistics for multiple subsets
>
>
> Check out:
> http://tolstoy.newcastle.edu.au/R/e2/help/07/05/17714.html
>
> On Mon, Jun 15, 2009 at 9:26 AM, Cecilia Carmo<cecilia.carmo@ua.pt>  
> wrote:
>> Hi everyone, my data is in a dataframe similar to this but with  
>> more firms,
>> more industries, more years and variables that correspond to  
>> financial
>> information:
>>
>>> firm<-c(rep(1,4),rep(2,4),rep(3,4),rep(4,4))
>>> year<-c(rep(2000:2003,4))
>>> industry<-c(rep(10,4),rep(20,4),rep(10,4),rep(30,4))
>>> X1<-c(10,14,18,16,20,45,23,54,24,67,98,58,76,34,23,89)
>>> X2<-c(11,46,89,36,72,78,55,44,22,78,53,25,12,45,87,23)
>>> Y<-c(12,45,32,69,87,54,33,22,89,66,35,23,15,54,67,87)
>>> data<-data.frame(firm, industry,year,Y,X1,X2)
>>> data
>>> firm industry year  Y X1 X2
>>
>>  1       10 2000 12 10 11
>> 1       10 2001 45 14 46
>> 1       10 2002 32 18 89
>> 1       10 2003 69 16 36
>> 2       20 2000 87 20 72
>> 2       20 2001 54 45 78
>> 2       20 2002 33 23 55
>> 2       20 2003 22 54 44
>> 3       10 2000 89 24 22
>> 3       10 2001 66 67 78
>>  3       10 2002 35 98 53
>> 3       10 2003 23 58 25
>> 4       30 2000 15 76 12
>> 4       30 2001 54 34 45
>> 4       30 2002 67 23 87
>> 4       30 2003 87 89 23
>>
>> I need to obtain the coefficients and the statistics by year and by
>> industry, for the lm function:
>> ff<-Y~b1 + b2.X1 + b3.X3
>>
>> So what I’ve done was: subset the dataframe by year, so I have 3  
>> dataframes
>> corresponding to the 3 years (dataframe2000, dataframe2001, … )  
>> and then I
>> applied a function that I’ve found in R-help mails:
>> coef2000<- 
>> as 
>> .data 
>> .frame 
>> (t(sapply(split(dataframe2000,dataframe2000$industry),function(x) 
>> {coef(lm(ff,data=x))})))
>>
>> I need help in two ways:
>> First: I’d like to have in the dataframe of the coefficients more  
>> statistics
>> information that helps me to understand the significance of the
>> coefficients; and
>> Second: Is that possible to obtain this output for all years at once?
>> Thanks in advance,
>> Cecília Carmo (Universidade de Aveiro – Portugal)
>>
>> ______________________________________________
>> 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.
>>
>
>
>
>
>
>
>
>
>
> From: Marc Schwartz <marc_schwartz@me.com>
> Date: 15 June 2009 11:43:36 PM
> To: Frank Harrell <f.harrell@vanderbilt.edu>
> Cc: Leisch Friedrich <Friedrich.Leisch@stat.uni-muenchen.de>, R list  
> <r-help@stat.math.ethz.ch>
> Subject: Re: [R] Centering graphics by default in Sweave
>
>
> Frank and Fritz,
>
> In follow up to Frank's post yesterday, I am including proposed  
> patches for Sweave.R and RweaveLatex.Rd. The patches are against the  
> current SVN main trunk.
>
> The patches include a new Sweave option called 'center.fig', which  
> defaults to FALSE to preserve existing behavior. When this option is  
> set to TRUE, the \includegraphics command will be wrapped with a  
> \centerline command. This will allow for space preserving centering,  
> whether in a 'figure' environment or not, as compared to using  
> \begin{center}...\end{center}.
>
> Frank, this option can be set on a per chunk basis:
>
>  <<fig=TRUE,center.fig=TRUE>>=
>
> or globally:
>
>  \SweaveOpts{center.fig=TRUE}
>
>
> I am also attaching an example .Rnw file and the associated PDF so  
> that you can see the resultant behavior under differing circumstances.
>
> Regards,
>
> Marc
>
>
>
> <SweavePatch.txt><RweaveLatexPatch.txt><test.pdf>
>
>
>
>
>
>
>
>
> From: kpal <kpalamartchouk@gmail.com>
> Date: 15 June 2009 11:45:09 PM
> To: r-help@r-project.org
> Subject: [R] Linear Models: Explanatory variables with uncertainties
>
>
> One of the assumptions, on which the (General) Linear Modelling is
> based is that the response variable is measured with some
> uncertainties (or weighted), but the explanatory variables are fixed.
> Is it possible to extend the model by assigning the weights to the
> explanatory variables as well? Is there a package for doing such a
> model fit?
>
> Thanks
>
>
>
>
>
>
>
>
>
> From: John Sorkin <jsorkin@grecc.umaryland.edu>
> Date: 15 June 2009 11:55:29 PM
> To: Philippe Grosjean <phgrosjean@sciviews.org>
> Cc: r-help@stat.math.ethz.ch, Patrick Burns <pburns@pburns.seanet.com>
> Subject: Re: [R] a proposal regarding documentation
>
>
> Below I have pasted an example from the R WIKI  (which is a copy of a
> man page), that illustrates a typical problem with the help system. A
> naive reader who wants to know something about the tcltk package will
> know little more after reading the page than before he, or she, looked
> at the page. Questions that might arise in the mind of the reader  
> would
> include, what is the package used for, is it important for me to know
> about tcltk if I am to use R, is there an example of the use of tcltk
> that I can see, do I need tcltk to use R, what is the DISPLAY  
> variable,
> etc. Further explanation in the WIKI would help, but so would a more
> comprehensive man page. I don't mean to impugn the people who gave  
> their
> time to develop the tcltk-package, its man page or the WIKI; their  
> work
> is greatly appreciated. I simply took the man page as an example of
> documentation that may not be as well done is the code written to
> perform the functions described by the man page. As a long time  
> software
> engineer, I know from personal experience that documentation is often
> not given as much attention as it deserves.
>
> MATERIAL BELOW IS TAKEN FROM THE WIKI:
>
> tcltk-package (tcltk)
>
> Tcl/Tk Interface
>
> Description
>
> Interface and language bindings to Tcl/Tk GUI elements.
> Details
>
> This package provides access to the platform-independent Tcl scripting
> language and Tk GUI elements. See TkWidgets for a list of supported
> widgets, TkWidgetcmds for commands to work with them, and references  
> in
> those files for more.
>
> The Tcl/Tk documentation is in the system man pages.
>
> For a complete list of functions, use ls(“package:tcltk”).
>
> Note that Tk will not be initialized if there is no DISPLAY variable
> set, but Tcl can still be used. This is most useful to allow the  
> loading
> of a package which depends on [rp>TclTk] in a session that does not
> actually use it (e.g. during installation).
>
>
> John
>
>
>
>
>
>
>
>
>
>
>
>
>
> John David Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> 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
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>
>>>> Philippe Grosjean <phgrosjean@sciviews.org> 6/15/2009 7:36 AM >>>
> Sorry, after a second request, I got the ==Rwiki file not found!==
> again. Obviously, I have to solve this bug first!
>
> PhG
>
> Philippe Grosjean wrote:
>> John Sorkin wrote:
>>> R 2.8.1, Firefox 3.0.11, windows XP Philippe,
>>> I suspect there are more substantial problems with the link to the
> WIKI
>>> then you thought. When I tried your code I got a page that
> contained
>>> nothing more than (excluding the nice graphic header and the index
> on
>>> the left-hand page):
>>>
>>> Trace: » barplot
>>> == Rwiki file not found! ==
>>>
>>> There is a helpful discussion of adding labels to barplots here:
>>> https://stat.ethz.ch/pipermail/r-help/2002-October/025879.html
>>>
>>> This WIKI page is not at all useful,it does not as you suggested it
>>> does not contain  the help page of ?barplot in wiki format as you
>>> suggested int would!
>>> John
>>
>> Still the problem with the cache. I refreshed the page, and now it
>> appears as it should.
>> Best,
>>
>> PhG
>>
>>>
>>> John David Sorkin M.D., Ph.D.
>>> Chief, Biostatistics and Informatics
>>> 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
>>> (Phone) 410-605-7119
>>> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>>>
>>>>>> Philippe Grosjean <phgrosjean@sciviews.org> 6/15/2009 4:42 AM
>>>>
>>> Ironically, this function is present since the beginning, although a
>
>>> little buggy. If you try this in R on a computer that is connected
> to
>>> the Internet:
>>>
>>> wikihelp <- function(topic)
>>>   browseURL(paste("http://wiki.r-project.org/rwiki/rhelp.php?id=",
>>>     topic, sep = ""))
>>> wikihelp("barplot")
>>>
>>> You got the help page of ?barplot in wiki format (with a few
>>> presentation bugs, but everything is there, basically)... plus a
> Wiki
>>> discussion section where people can add more material, links, etc.
>>>
>>> The help page is not physically contained in the wiki page, but it
> is a
>>>
>>> file stored elsewhere on the R Wiki server, and that is supposed to
> be
>>>
>>> updated regularly (but it is not the case for the moment). In the
> wiki
>>>
>>> page you see, there is only a ~~RDOC~~ marker indicating where to
>>> include the help page.
>>>
>>> I have a problem with the R Wiki cache: until someone adds comments
> to
>>>
>>> such a page, the content is not refreshed, but you just see
> ~~RDOC~~.
>>>
>>> Try, for instance:
>>>
>>> wikihelp("chisq.test")
>>>
>>> If the engine thinks 'topic' is ambiguous, it displays a list of
>>> possibilities (i.e., our wikihelp() function is somehow a mix of
> help()
>>>
>>> and of apropos()). For instance:
>>>
>>> wikihelp("help")
>>>
>>>
>>> This should not be ambiguous, but it is considered as it currently
> by
>>> rhelp.php (a minor bug probably easy to correct).
>>>
>>> Finally, all wiki pages are spelled with lowercase. It is the same
> for
>>>
>>> help pages. So,
>>>
>>> wikihelp("RSiteSearch")
>>> wikihelp("rsitesearch")
>>>
>>> lead to the same rdoc:utils:rsitesearch wiki page. I have no
> solutions
>>>
>>> for that!
>>>
>>> So, to conclude, most of the required mechanism is already installed
> on
>>>
>>> R Wiki. It  just needs a little bit of debugging and fine-tuning to
>
>>> become completely operational. A little help here would be very
>>> appreciated!
>>>
>>> ... and, of course, a refined version of the wikihelp() function
> must
>>> be made widely available to "reveal" this function. One could even
>>> consider to write a pager that displays local help page and warns if
>
>>> there are comments on this topic posted on the wiki... or that link
> to
>>> a personal
>>>
>>> wiki engine where everybody could add its own comments to the help
>>> pages, with full-text search ability!
>>>
>>> Best,
>>>
>>> Philippe Grosjean
>>>
>>> ..............................................<°}))><........
>>>  ) ) ) ) )
>>> ( ( ( ( (    Prof. Philippe Grosjean
>>>  ) ) ) ) )
>>> ( ( ( ( (    Numerical Ecology of Aquatic Systems
>>>  ) ) ) ) )   Mons-Hainaut University, Belgium
>>> ( ( ( ( (
>>> ..............................................................
>>>
>>> Gabor Grothendieck wrote:
>>>> In PHP and also in MySQL the manual has a wiki capability
>>>> so that users can add notes at the end of each page, e.g.
>>>>
>>>> http://www.php.net/manual/en/functions.variable-functions.php
>>>> http://dev.mysql.com/doc/refman/4.1/en/update.html
>>>> That would combine documentation and wiki into one. Here it would
>>>> involve copying the R help pages into the wiki in a readonly mode
>>> with the
>>>> writeable wiki portion at the end of each such page.  It would
> also
>>> be
>>>> necessary to be able to update the help pages in the wiki when new
>>> versions
>>>> became available.
>>>>
>>>> No explicit email group or coordination would be needed.  It would
>>> also address
>>>> the organization problem as they could be organized as they are
> now,
>>> i.e. into
>>>> packages: base, stats, utils, ...
>>>>
>>>> It would require the development of a program to initially copy
> the
>>> help pages
>>>> and to update them while keeping the notes in place whenever a new
>>> version
>>>> of R came out.
>>>>
>>>> On Sun, Jun 14, 2009 at 5:35 PM, Peter
>>>> Flom<peterflomconsulting@mindspring.com> wrote:
>>>>> I certainly don't have anything against the WIKI, but I think
> that
>>> the documentation
>>>>> is where the action is, especially for newbies.  It's the
> natural
>>> first step
>>>>> when you want to learn about a function or when you  get an error
>>> message you
>>>>> don't understand.
>>>>>
>>>>> Peter
>>>>>
>>>>> Peter L. Flom, PhD
>>>>> Statistical Consultant
>>>>> www DOT peterflomconsulting DOT com
>>>>>
>>>>> ______________________________________________
>>>>> 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.
>>>>>
>>>>
>>>
>>> Confidentiality Statement:
>>> This email message, including any attachments, is for
> th...{{dropped:6}}
>>>
>>> ______________________________________________
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>> ______________________________________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-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.
>
> Confidentiality Statement:
> This email message, including any attachments, is for th...{{dropped: 
> 6}}
>
>
>
>
>
>
>
>
>
> From: deanj2k <dl120@le.ac.uk>
> Date: 15 June 2009 9:23:46 PM
> To: r-help@r-project.org
> Subject: [R] axis on a non-uniform scale
>
>
>
> hi everyone, just wondering how i might go about plotting a graph  
> (say using
> the plot() function) where my x axis is plotting points which have
> Log(values) but i want my x axis to display values in exponentiated  
> form
>
> ie. my log values (also scale of the x axis)     x axis displays
>        -1                                                  exp(-1) =  
> 0.36
>         0                                                  exp(0) = 1
>         1                                                  exp(1) =  
> 2.72
>         2                                                  exp(2) =  
> 7.39
> ...etc
>
>
> -- 
> View this message in context: http://www.nabble.com/axis-on-a-non-uniform-scale-tp24032916p24032916.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
>
>
>
>
>
>
> From: David Barron <dnbarron@googlemail.com>
> Date: 15 June 2009 9:42:26 PM
> To: poleteiep34@hotmail.com
> Cc: r-help@r-project.org
> Subject: Re: [R] NA as a result of using GLM
>
>
> Because you have 16 variables but only 10 observations.
>
> David
>
> On Mon, Jun 15, 2009 at 12:09, poleteiep34 <poleteiep34@hotmail.com>  
> wrote:
>
>> Hi all!
>> Maybe someone could help me with the following. I know this hasn't  
>> directly
>> to do with ecology but I'm also using glm.
>>
>> I have a list of 16 genes and 10 samples. The samples are of two  
>> types, 4
>> Ctrl and 6 Diseased. If,
>>
>> labelInd<-as.factor(c(rep("0",4),rep("1",6)))
>> genes.glm<-glm(labelInd ~ ., family=binomial, data=mat)
>>
>>
>> beeing "mat" the 10x16 matrix (without NAs), I got 17 values, first  
>> the
>> intercept, 9 numerical values and "NA" for the last 7 genes. Does  
>> anybody
>> you know why this is happening or how I can model using the 16 genes?
>>
>> I hope anyone could help me with this!
>> Many thanks in advance,
>>
>> Paul
>>
>>
>>       [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: eitan lavi <lavi.eitan@gmail.com>
> Date: 15 June 2009 6:47:53 PM
> To: r-help@r-project.org
> Subject: [R] non-english text mining with tm package
>
>
> Hello,
>
> I'm having issues working with the tm package on non-english  
> languages.
>
> are there any extensions that enable the package to work with Hebrew  
> (and
> other non-roman letter languages for that matter) ?
>
> (e.g. although I can construct a Corpus that shows the hebrew  
> documents
> alright,
> I cannot create a term-document matrix (it does not identify any of  
> the
> hebrew words, so
> it thinks there are 0 terms inside the corpus)).
>
> Thanks
>
> eitan
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Bessy <piglet630@hotmail.com>
> Date: 15 June 2009 9:56:57 PM
> To: r-help@r-project.org
> Subject: [R] Schoenfeld Residuals with tied data
>
>
>
> Dear all,
>
> I am struggling with calculation of Schoenfeld residuals of my Cox Ph
> models.
>
> Based on the formula as attached, I calculated the Schoenfeld  
> residuals for
> both non tied and tied data, respectively.
>
> And then I validated my results with R using the same data sets.  
> However, I
> found that my results for non-tied data was ok but the results for  
> tied data
> were different from R's.
>
> How does R calculate the Schoenfeld Residuals for tied data? Could  
> someone
> give me some hints, please?
>
> Thank you so much.
>
> Bessy http://www.nabble.com/file/p24033333/Schoenfeld%2BResiduals.doc
> Schoenfeld+Residuals.doc
> -- 
> View this message in context: http://www.nabble.com/Schoenfeld-Residuals-with-tied-data-tp24033333p24033333.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
>
>
>
>
>
>
> From: Grześ <gregorio99@gmail.com>
> Date: 15 June 2009 11:29:32 PM
> To: r-help@r-project.org
> Subject: Re: [R] if + is.na
>
>
>
> Thank you very much ;)
>
> Jeremiah Rounds wrote:
>>
>>
>> Your error message is because "if" wants a single value and you are  
>> giving
>> it a vector.
>>
>>
>>
>> Typically you want to use functions "all" or any" to correct this  
>> error
>> message (look them up ?all ?any) and eg if(any(is.na(...)))   But  
>> in this
>> case to accomplish the task you're after I don't even think you  
>> want to
>> use an if.  I am not going to give you precise code because I  
>> wasn't able
>> to decipher exactly what you were trying to do but something like:
>>
>>
>>
>> b[is.na(a)] = 43
>>
>>
>>
>> might be helpful.  This line would put a 43 in b in the corresponding
>> entry that was na in a.
>>
>>
>>
>> Good luck!.
>>
>>
>>
>>
>>
>>> Date: Sun, 14 Jun 2009 12:48:58 -0700
>>> From: gregorio99@gmail.com
>>> To: r-help@r-project.org
>>> Subject: [R] if + is.na
>>>
>>>
>>> Hello!
>>> I wont to use a function is.na()
>>>
>>> I have two vectors:
>>>> a=c(1,NA,3,3,3)
>>>> b=c(0,0,0,0,0)
>>> and when I use is.na function it's ok:
>>>> is.na(a)
>>> [1] FALSE TRUE FALSE FALSE FALSE
>>>
>>> but I would create sth like this:
>>>
>>> for i in 1:length(a){
>>> if (wsp[i] == is.na(a)) {b=43}
>>> }
>>> or like this
>>>
>>> if(is.na(a)) b=3 else a
>>> [1] 1 NA 3 3 3
>>>
>>> but I always get an error:
>>> the condition has length > 1 and only the first element will be used
>>>
>>> Could you help me how I may avoid this problem and use function  
>>> is.na
>>> inside
>>> function if - else
>>> Please
>>>
>>>
>>> -- 
>>> View this message in context:
>>> http://www.nabble.com/if-%2B-is.na-tp24025136p24025136.html
>>> Sent from the R help mailing list archive at Nabble.com.
>>>
>>> ______________________________________________
>>> 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.
>>
>> _________________________________________________________________
>> Lauren found her dream laptop. Find the PC thats right for you.
>>
>> 	[[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.
>>
>>
>
> -- 
> View this message in context: http://www.nabble.com/if-%2B-is.na-tp24025136p24034678.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
>
>
>
>
>
>
> From: Paul Christoph Schröder <pschrode@alumni.unav.es>
> Date: 15 June 2009 8:54:04 PM
> To: r-help@r-project.org
> Subject: [R] NA as a result of using GLM
> Reply-To: pschrode@alumni.unav.es
>
>
> Hi all!
> Maybe someone could help me with the following. I know this hasn't  
> directly to do with ecology but I'm also using glm.
>
> I have a list of 16 genes and 10 samples. The samples are of two  
> types, 4 Ctrl and 6 Diseased. If,
>
> labelInd<-as.factor(c(rep("0",4),rep("1",6)))
> genes.glm<-glm(labelInd ~ ., family=binomial, data=mat)
>
>
> beeing "mat" the 10x16 matrix (without NAs), I got 17 values, first  
> the intercept, 9 numerical values and "NA" for the last 7 genes.  
> Does anybody you know why this is happening or how I can model using  
> the 16 genes?
>
> I hope anyone could help me with this!
> Many thanks in advance,
>
> Paul
>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: suparna mitra <suparna.mitra@googlemail.com>
> Date: 15 June 2009 7:57:00 PM
> To: r-help@r-project.org
> Subject: [R] How to build phylogenetic tree by R program from  
> distance any distance matrix
>
>
> Hello R users,
>  Can any one please help me to find a way to  build phylogenetic  
> tree by R
> program from any distance matrix.
> Suppose I have a data like :
> MATRIX
> [1] '1'    0.0
> [2] '2'    0.071 0.0
> [3] '3'    0.036 0.286 0.0
> [4] '4'    0.429 0.75 0.714 0.0
> [5] '5'   0.679 0.179 0.214 0.536 0.0
> [6] '6'   0.893 0.929 0.964 0.464 0.357 0.0
> [7] '7'   0.643 0.571 0.5 0.607 0.821 0.786 0.0
> [8] '8'   0.857 0.393 0.107 0.321 0.25 0.0 0.143 0.0
>
> Or as a vector I have the lower triangle like:
>> dist.mat
> [1] 0.071 0.036 0.286 0.429 0.750 0.714 0.679 0.179 0.214 0.536  
> 0.893 0.929
> 0.964 0.464 0.357 0.643 0.571 0.500 0.607 0.821 0.786 0.857 0.393  
> 0.107
> 0.321 0.250 0.000 0.143
>
> It will be really helpful if anyone can help me to get a tree  
> (between these
> 8 species) from this vector values. The matrix above I created by  
> hand to
> use as a nexus distance matrix data for other methods. So it is  
> better if I
> can use this distance matrix vector (dist.mat) directly.
> I couldn't find any package for phylogenetic tree from distance any  
> distance
> matrix in R.
> Thank you very much.
> With best regard,
> Suparna
> ----------------------------
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: "Sven Knüppel" <sven.knueppel@gmx.de>
> Date: 15 June 2009 7:40:39 PM
> To: r-help@r-project.org
> Subject: [R] coxph and robust variance estimation
>
>
>
> Hello,
>
> I would like to compare two different models in the framework of Cox  
> proportional hazards regression models.
>
> On Rsitesearch and google I don't find a clear answer to my question.
>
> My R-Code (R version 2.9.0)
>
> coxph.fit0 <- coxph(y ~ z2_ + cluster(as.factor(keys))+  
> strata(stratvar_),
>    method="breslow" ,robust=T  )
>
> coxph.fit1 <- coxph(y ~ z_ + cluster(as.factor(keys))+  
> strata(stratvar_),
>  method="breslow" ,robust=T  )  # marker and covariates
>
> # Analysis of Devaince table
> coxph.aov <- anova(coxph.fit0 , coxph.fit1, test="Chisq")
>
> In the single models coxph.fit0 and coxph.fit1 I can use a robust  
> variance estimation.
> It seems that the function anova don't use a robust estimation for  
> the analysis of deviance.
>
> My question is, how can I use robust estimation for the analysis of  
> deviance?
>
> With kind regards,
>
> Sven Knüppel
> -- 
> GMX FreeDSL Komplettanschluss mit DSL 6.000 Flatrate und  
> Telefonanschluss
> für nur 17,95 Euro/mtl.!* http://portal.gmx.net/de/go/dsl02
>
>
>
>
>
>
>
>
>
> From: Tony Breyal <tony.breyal@googlemail.com>
> Date: 15 June 2009 10:13:40 PM
> To: r-help@r-project.org
> Subject: Re: [R] 'Errors' with Ubuntu
>
>
> Hi Len,
>
> I have only just installed Ubuntu 9.04 the other day on my PC (1 HDD,
> partitioned with Windows Vista Premium) and experienced the Error 22.
> This would stop me from booting into either Windows or Ubuntu and just
> be a blank screen with the error message, no way to move forward.
>
> I am completely new to Linux, but one suggestion in the Ubuntu help
> forum was to reinstall Ubuntu from the Live CD. I did this (changing
> the BIOS to boot from the DVD drive first) and it corrected the GRUB
> error and I am now able to boot into either Operating System. I did
> not experience the other error numbers you mentioned so am not sure if
> this will help in your situation.
>
> My next challenge is working out how to install R on Ubuntu (will try
> this weekend)!
>
> HTH,
> Tony Breyal
>
>
>
> On 13 June, 01:18, Len Vir <len...@gmail.com> wrote:
>> Good Day To You All,
>>
>> I have installed Ubuntu 9.04 on a Laptop running Vista Business.
>>
>> When I try to start my little machine,
>> GRUB keeps telling me there is an error:
>>
>> Either: Error 25, Error 21, or  Error 5.
>> Once in a while, it is 'Error 22'.
>>
>> And then there is no way to go any further:
>> End of the line. The 'Error' crashes me into being nothing.
>>
>> Why do I get these 'Error Messages'
>> when I try to boot up my Laptop ?
>>
>> I have tried to boot up in many
>> different 'dimensions':
>> With or without the mouse connected,
>> with or without my external hard-drive connected,
>> with or without my girlfriend being in the bath tub or not,
>> etc.
>> and all the other permutations that R would allow me to do...
>> if I had access to it.
>>
>> Any and all cues would be greatly appreciated,
>>
>> Many Thanks,
>>
>> Len
>>
>>   len...@gmail.com <joseph.j.gazai...@gmail.com>
>>
>> p.s. Ubuntu 9.04 is giving me problems
>>        I never had with Ubuntu 8.04
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/ 
>> listinfo/r-help
>> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>
>
>
>
>
>
>
> From: Paul Hiemstra <p.hiemstra@geo.uu.nl>
> Date: 16 June 2009 12:16:53 AM
> To: ilenia fronza <ilenia.fronza@gmail.com>
> Cc: r-help@r-project.org
> Subject: Re: [R] Markov chains
>
>
> ilenia fronza wrote:
>> Hi,
>> is there a package to apply Markov chains (order > 1) ?
>>
>> thanks in advance
>>
>> 	[[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.
>>
> RSiteSearch("markov chain")
>
> -- 
> Drs. Paul Hiemstra
> Department of Physical Geography
> Faculty of Geosciences
> University of Utrecht
> Heidelberglaan 2
> P.O. Box 80.115
> 3508 TC Utrecht
> Phone:  +3130 274 3113 Mon-Tue
> Phone:  +3130 253 5773 Wed-Fri
> http://intamap.geo.uu.nl/~paul
>
>
>
>
>
>
>
>
>
> From: ltracy <lareet@hotmail.com>
> Date: 16 June 2009 12:19:59 AM
> To: r-help@r-project.org
> Subject: [R] how to interpret coefficients for a natural spline  
> smooth	function in a GLM
>
>
>
> Hello-
>
> I am trying to model infections counts over 120 months using a GLM  
> in R.
> The model is simple really including a factor variable for year (10  
> yrs in
> total) and another variable consisting of a natural spline function  
> for time
> in months.
>
> My code for the GLM is as follows:
> model1<-glm(ALL_COUNT~factor(FY)+ns(1:120, 10), offset=log(TOTAL_PTS),
> family=poisson, data=TS1)
>
> The summary output pertaining to the smooth function consists of 10
> coefficients for each df in the model.  Here are the coefficients:
>
> ns(1:120, 10)1  -0.72438    0.32773  -2.210 0.027084 *
> ns(1:120, 10)2  -1.19097    0.37492  -3.177 0.001490 **
> ns(1:120, 10)3  -1.40250    0.42366  -3.310 0.000931 ***
> ns(1:120, 10)4  -0.82722    0.47459  -1.743 0.081334 .
> ns(1:120, 10)5  -0.46139    0.49657  -0.929 0.352812
> ns(1:120, 10)6  -0.44892    0.51909  -0.865 0.387137
> ns(1:120, 10)7  -0.53060    0.54783  -0.969 0.332778
> ns(1:120, 10)8  -0.25699    0.55582  -0.462 0.643814
> ns(1:120, 10)9  -0.74091    0.63899  -1.160 0.246249
> ns(1:120, 10)10  0.41142    0.56317   0.731 0.465054
>
> What is still unclear to me is what these 10 coefficients from the  
> natural
> spline represent.
>
> Thanks in advace-
>
>
>
>
> -- 
> View this message in context: http://www.nabble.com/how-to-interpret-coefficients-for-a-natural-spline-smooth-function-in-a-GLM-tp24035485p24035485.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
>
>
>
>
>
>
> From: Michael <comtech.usa@gmail.com>
> Date: 16 June 2009 12:35:25 AM
> To: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
> Cc: r-help <R-help@stat.math.ethz.ch>
> Subject: Re: [R] lack of memory for logistic regression in R?
>
>
> Yet what's the benefit of using Design Package?
>
> Thanks!
>
> On Sun, Jun 14, 2009 at 8:04 PM, Frank E Harrell
> Jr<f.harrell@vanderbilt.edu> wrote:
>> Also it would be useful to compare glm with the lrm function in the  
>> Design
>> package, for speed and memory use.
>>
>> Frank
>>
>>
>> David Winsemius wrote:
>>>
>>> On Jun 14, 2009, at 9:06 PM, Michael wrote:
>>>
>>>> Hi all,
>>>>
>>>> I am getting the following error message:
>>>>
>>>>> mymodel = glm(response ~ . , family=binomial, data=C);
>>>>
>>>> Error: cannot allocate vector of size 734.2 Mb
>>>> In addition: Warning messages:
>>>> 1: In array(0, c(n, n), list(levs, levs)) :
>>>>  Reached total allocation of 1535Mb: see help(memory.size)
>>>> 2: In array(0, c(n, n), list(levs, levs)) :
>>>>  Reached total allocation of 1535Mb: see help(memory.size)
>>>> 3: In array(0, c(n, n), list(levs, levs)) :
>>>>  Reached total allocation of 1535Mb: see help(memory.size)
>>>> 4: In array(0, c(n, n), list(levs, levs)) :
>>>>  Reached total allocation of 1535Mb: see help(memory.size)
>>>>
>>>> -----------
>>>>
>>>> The data frame is 60000 x 20,
>>>>
>>>> is it too large for R?
>>>>
>>>> What shall I do? Will close all other softwares/applications  
>>>> help? My
>>>> PC is Vista with 4GB memory. Thank you.
>>>
>>> It's certainly not too large for R. Have you looked at the R  
>>> Windows FAQ
>>> on the topic?
>>>
>>>
>>> http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021
>>>
>>> ... and perhaps:
>>>
>>> http://finzi.psych.upenn.edu/Rhelp08/2008-August/171649.html
>>>
>>>
>>> David Winsemius, MD
>>> Heritage Laboratories
>>> West Hartford, CT
>>>
>>> ______________________________________________
>>> 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.
>>>
>>
>>
>> --
>> Frank E Harrell Jr   Professor and Chair           School of Medicine
>>                     Department of Biostatistics   Vanderbilt  
>> University
>>
>
>
>
>
>
>
>
>
>
> From: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
> Date: 16 June 2009 12:41:48 AM
> To: Michael <comtech.usa@gmail.com>
> Cc: r-help <R-help@stat.math.ethz.ch>
> Subject: Re: [R] lack of memory for logistic regression in R?
>
>
> Michael wrote:
>> Yet what's the benefit of using Design Package?
>> Thanks!
>
> For logistic models the code is streamlined.  You get automatic  
> tests of most interesting hypotheses (e.g., tests of linearity) and  
> easy to make graphics including nomograms.  There's also several  
> model validation functions.  LaTeX and other methods can print  
> fitted models in an easier to interpret fashion when restricted  
> cubic splines and interactions are present.  Getting odds ratios for  
> sensible changes of X, when X is nonlinear, is easy.
>
> Frank
>
>> On Sun, Jun 14, 2009 at 8:04 PM, Frank E Harrell
>> Jr<f.harrell@vanderbilt.edu> wrote:
>>> Also it would be useful to compare glm with the lrm function in  
>>> the Design
>>> package, for speed and memory use.
>>>
>>> Frank
>>>
>>>
>>> David Winsemius wrote:
>>>> On Jun 14, 2009, at 9:06 PM, Michael wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I am getting the following error message:
>>>>>
>>>>>> mymodel = glm(response ~ . , family=binomial, data=C);
>>>>> Error: cannot allocate vector of size 734.2 Mb
>>>>> In addition: Warning messages:
>>>>> 1: In array(0, c(n, n), list(levs, levs)) :
>>>>> Reached total allocation of 1535Mb: see help(memory.size)
>>>>> 2: In array(0, c(n, n), list(levs, levs)) :
>>>>> Reached total allocation of 1535Mb: see help(memory.size)
>>>>> 3: In array(0, c(n, n), list(levs, levs)) :
>>>>> Reached total allocation of 1535Mb: see help(memory.size)
>>>>> 4: In array(0, c(n, n), list(levs, levs)) :
>>>>> Reached total allocation of 1535Mb: see help(memory.size)
>>>>>
>>>>> -----------
>>>>>
>>>>> The data frame is 60000 x 20,
>>>>>
>>>>> is it too large for R?
>>>>>
>>>>> What shall I do? Will close all other softwares/applications  
>>>>> help? My
>>>>> PC is Vista with 4GB memory. Thank you.
>>>> It's certainly not too large for R. Have you looked at the R  
>>>> Windows FAQ
>>>> on the topic?
>>>>
>>>>
>>>> http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021
>>>>
>>>> ... and perhaps:
>>>>
>>>> http://finzi.psych.upenn.edu/Rhelp08/2008-August/171649.html
>>>>
>>>>
>>>> David Winsemius, MD
>>>> Heritage Laboratories
>>>> West Hartford, CT
>>>>
>
>
>
>
>
>
>
>
>
> From: Peter Dalgaard <P.Dalgaard@biostat.ku.dk>
> Date: 16 June 2009 12:38:14 AM
> To: r-announce@r-project.org
> Subject: [R] R 2.9.1 Scheduled for June 26, 2009
>
>
> This is to announce that we plan to release R version 2.9.1 on Friday,
> June 26, 2009.
>
> Release procedures start Tuesday, June 16.
>
> Those directly involved should review the generic schedule at
> http://developer.r-project.org/release-checklist.html
>
> The source tarballs will be made available daily (barring build
> troubles) and the tarballs can be picked up at
>
> http://cran.r-project.org/src/base-prerelease/
>
> a little later.
>
> Binary builds are expected to appear starting Friday June 19 at the  
> latest.
>
>    For the Core Team
>    Peter Dalgaard
>
>
> -- 
>   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
>  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
> (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45)  
> 35327918
> ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)              FAX: (+45)  
> 35327907
>
> _______________________________________________
> R-announce@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-announce
>
>
>
>
>
>
>
> From: vito muggeo <vmuggeo@dssm.unipa.it>
> Date: 16 June 2009 12:48:58 AM
> To: kpal <kpalamartchouk@gmail.com>
> Cc: r-help@r-project.org
> Subject: Re: [R] Linear Models: Explanatory variables with  
> uncertainties
>
>
> Probably you are looking for EIV (errors-in-variables) or ME  
> (measurement errors) models.
>
> "simex" is a possible package which needs to know the error variance..
> Also RSiteSearch() may be helpful..
>
> hope this helps,
> vito
>
>
> kpal ha scritto:
>> One of the assumptions, on which the (General) Linear Modelling is
>> based is that the response variable is measured with some
>> uncertainties (or weighted), but the explanatory variables are fixed.
>> Is it possible to extend the model by assigning the weights to the
>> explanatory variables as well? Is there a package for doing such a
>> model fit?
>> Thanks
>> ______________________________________________
>> 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.
>
> -- 
> ====================================
> Vito M.R. Muggeo
> Dip.to Sc Statist e Matem `Vianelli'
> Università di Palermo
> viale delle Scienze, edificio 13
> 90128 Palermo - ITALY
> tel: 091 6626240
> fax: 091 485726/485612
> http://dssm.unipa.it/vmuggeo
>
>
>
>
>
>
>
>
>
> From: Marc Schwartz <marc_schwartz@me.com>
> Date: 16 June 2009 12:57:34 AM
> To: pschrode@alumni.unav.es
> Cc: r-help@r-project.org
> Subject: Re: [R] NA as a result of using GLM
>
>
> On Jun 15, 2009, at 5:54 AM, Paul Christoph Schröder wrote:
>
>> Hi all!
>> Maybe someone could help me with the following. I know this hasn't  
>> directly to do with ecology but I'm also using glm.
>>
>> I have a list of 16 genes and 10 samples. The samples are of two  
>> types, 4 Ctrl and 6 Diseased. If,
>>
>> labelInd<-as.factor(c(rep("0",4),rep("1",6)))
>> genes.glm<-glm(labelInd ~ ., family=binomial, data=mat)
>>
>>
>> beeing "mat" the 10x16 matrix (without NAs), I got 17 values, first  
>> the intercept, 9 numerical values and "NA" for the last 7 genes.  
>> Does anybody you know why this is happening or how I can model  
>> using the 16 genes?
>>
>> I hope anyone could help me with this!
>> Many thanks in advance,
>>
>> Paul
>
> More than likely, the 7 genes for which you are getting NA's are  
> collinear to other genes. Thus you get NA's. If you switched the  
> order of the 7 genes for which you are getting NAs so that they come  
> first in the formula, you would get NAs for others.
>
> If you use:
>
>  summary(genes.glm)
>
> you will likely see a warning message about singularities in the  
> coefficient table header line. Something like:
>
>  Coefficients: (7 not defined because of singularities)
>
> I would use cor(mat) to take a look at the correlation matrix for  
> your data so that you can review this in more detail.
>
> BTW, with only 10 observations, you are significantly overfitting  
> the model by using so many covariates. You typically need at least  
> 10 to 20 'events' for each covariate degree of freedom in a logistic  
> regression model. With only 6 diseased (events) you really don't  
> even have enough data to support one covariate. The study, presuming  
> an 'a priori' design, is way underpowered for what you are  
> attempting to do.
>
> HTH,
>
> Marc Schwartz
>
>
>
>
>
>
>
>
>
> From: David Hunter <dhunter@stat.psu.edu>
> Date: 16 June 2009 1:12:54 AM
> To: r-help@r-project.org
> Subject: Re: [R] Fitting Mixture of Non-Central Student's t  
> Distributions
>
>
> Hi Susanne.  The mixtools package does not do this automatically and  
> I would be surprised if there were any package that does.  However,  
> it's not in principle too difficult to write code to implement an EM  
> algorithm to search for a maximum likelihood estimator in a finite  
> mixture model.   Check out a reference on finite mixture models that  
> discusses EM algorithms (e.g., Section 2.2 of http://www.stat.psu.edu/~dhunter/papers/mixtools.pdf 
>  although there are undoubtedly better references out there for this  
> purpose).
>
> In the case of components that are assumed to be noncentral Student  
> t distributions, you may have a bit of trouble since if I remember  
> correctly, it is not easy to do MLE even for the non-mixture case  
> here.  That said, in general, writing an EM algorithm for the finite- 
> mixture-model case is not much more difficult computationally than  
> writing code for MLE in the non-mixture case.  This means that you  
> could try expanding your search to include other packages that might  
> do MLE for the (non-mixture) case of noncentral t distributions.  If  
> such a package exists, then it shouldn't be too hard to write your  
> own mixture-model EM wrapper.
>
> Hope this helps.  Good luck!
> Dave
>
>
>
> David Hunter
> Associate professor
> Department of Statistics
> Penn State University
> Phone:  (814) 863-0979
> Fax:  (814) 863-7114
> www.stat.psu.edu/~dhunter
>
>
>
> On Jun 13, 2009, at 7:54 AM, Balzer Susanne wrote:
>
>> Dear all,
>>
>> I am attempting to model some one-dimensional data using a mixture  
>> model
>> of non-central Student's t distributions. However, I haven't been  
>> able
>> to find any R package that provides this functionality.
>> Could there be a way to "manipulate" the EM algorithms from the  
>> mixdist
>> or mixtools package to fit the model, or do you have any other
>> suggestions?
>>
>> If anyone could help me out, I would be extremely grateful.
>>
>> Kind regards,
>>
>> Susanne Balzer
>>
>>
>>
>> ****************************
>> Susanne Balzer
>> PhD Student
>> Institute of Marine Research
>> N-5073 Bergen, Norway
>> Phone: +47 55 23 69 45
>> susanne.balzer@imr.no
>> www.imr.no
>>
>> ______________________________________________
>> 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.
>
>
>
>
>
>
>
>
>
> From: poleteiep34 <poleteiep34@hotmail.com>
> Date: 16 June 2009 1:24:51 AM
> To: Marc Schwartz <marc_schwartz@me.com>
> Cc: r-help@r-project.org
> Subject: Re: [R] NA as a result of using GLM
> Reply-To: poleteiep34@hotmail.com
>
>
> Thanks Marc, as you said, this is a priori design. I'm trying to get
> more events.
> But for now, I'll have to try to get rid of the collinear genes. Is
> there any other method than using cor? Any method to state which genes
> behave in the same  manner?
> Paul
>
> Marc Schwartz escribió:
>> On Jun 15, 2009, at 5:54 AM, Paul Christoph Schröder wrote:
>>
>>> Hi all!
>>> Maybe someone could help me with the following. I know this hasn't
>>> directly to do with ecology but I'm also using glm.
>>>
>>> I have a list of 16 genes and 10 samples. The samples are of two
>>> types, 4 Ctrl and 6 Diseased. If,
>>>
>>> labelInd<-as.factor(c(rep("0",4),rep("1",6)))
>>> genes.glm<-glm(labelInd ~ ., family=binomial, data=mat)
>>>
>>>
>>> beeing "mat" the 10x16 matrix (without NAs), I got 17 values, first
>>> the intercept, 9 numerical values and "NA" for the last 7 genes.  
>>> Does
>>> anybody you know why this is happening or how I can model using the
>>> 16 genes?
>>>
>>> I hope anyone could help me with this!
>>> Many thanks in advance,
>>>
>>> Paul
>>
>> More than likely, the 7 genes for which you are getting NA's are
>> collinear to other genes. Thus you get NA's. If you switched the  
>> order
>> of the 7 genes for which you are getting NAs so that they come first
>> in the formula, you would get NAs for others.
>>
>> If you use:
>>
>>  summary(genes.glm)
>>
>> you will likely see a warning message about singularities in the
>> coefficient table header line. Something like:
>>
>>  Coefficients: (7 not defined because of singularities)
>>
>> I would use cor(mat) to take a look at the correlation matrix for  
>> your
>> data so that you can review this in more detail.
>>
>> BTW, with only 10 observations, you are significantly overfitting the
>> model by using so many covariates. You typically need at least 10 to
>> 20 'events' for each covariate degree of freedom in a logistic
>> regression model. With only 6 diseased (events) you really don't even
>> have enough data to support one covariate. The study, presuming an 'a
>> priori' design, is way underpowered for what you are attempting to  
>> do.
>>
>> HTH,
>>
>> Marc Schwartz
>>
>>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Kenny Larsen <k.larsen@sheffield.ac.uk>
> Date: 16 June 2009 1:50:31 AM
> To: r-help@r-project.org
> Subject: [R] Assigning Data a name from within another variable?
>
>
>
> Hi All,
>
> I have hunted high and low and tried dozens of things but have yet to
> achieve the result I require. Below is my code (taken mostly from  
> another
> thread on here) thus far:
>
> files<-list.files()
> files<-files[grep('.wm4', files)]
> labels<-gsub('.wm4', '',files)
>
> for(i in 1:length(files)){
> X<-read.table(files[i])
> <My problem is here!>
>
> What I am trying to do now is assign the first item in labels in  
> place of X
> so the table name will effectively be whatever is written in  
> labels[1]. The
> files simply consist of two columns of real numbers. I have tried  
> several
> things, such like replacing X with labels[1], but this simply writes  
> the
> data in one long column to the first place of labels(which makes  
> sense). How
> do I extract what is in labels[1] and set it as the table name?
>
> As always any help is greatly appreciated.
>
> Kenny Larsen
> -- 
> View this message in context: http://www.nabble.com/Assigning-Data-a-name-from-within-another-variable--tp24037279p24037279.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
>
>
>
>
>
>
> From: "Zhang,Yanwei" <Yanwei.Zhang@cna.com>
> Date: 16 June 2009 1:58:15 AM
> To: r-help@r-project.org
> Subject: [R] Create R object
>
>
> Dear R users,
>
> I have two simple questions here, and hope someone can help me on  
> this. Thanks in advance.
>
> 1.
> I have a list object lst=list(a1=matrix(rnorm(4),2,2),  
> a2=matrix(rnorm(4),2,2),a3=matrix(rnorm(4),2,2)). Here I only use  
> three elements for illustration, and in fact the length of lst, n,  
> is unknown in advance. I want to define an object for each element  
> of this lst, and the objects have names like "object1",  
> "object2",...,"objectn". I could use a loop like the following:
> for (i in 1:length(lst)){
> 	assign(paste("object",i,sep=""),lst[[i]])
> }
>
> I wonder if there's a way to avoid this loop?
>
>
> 2.
> I want to validate whether all of the "object"s have the same  
> dimension, that is, whether dim(object1)[1]==dim(object2) 
> [1]==dim(object3)[1]& dim(object1)[2]==dim(object2)[2]==dim(object3) 
> [2]  is true. How can I do that easily since the length of lst is  
> not fixed?
>
> Thanks.
>
> Wayne (Yanwei) Zhang
> Ttatistical *esearch
>> CNA
>>
>>
>>
>
> E-MAIL CONFIDENTIALITY NOTICE:  The contents of this e-mail message  
> and any attachments are intended solely for the
> addressee(s) and may contain confidential and/or legally privileged  
> information. If you are not the
> intended recipient of this message or if this message has been  
> addressed to you in error, please
> immediately alert the sender by reply e-mail and then delete this  
> message and any attachments. If you
> are not the intended recipient, you are notified that any use,  
> dissemination, distribution, copying, or
> storage of this message or any attachment is strictly prohibited.
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Julien Gagneur <julien.gagneur@embl.de>
> Date: 16 June 2009 1:58:56 AM
> To: r-help@r-project.org
> Subject: Re: [R] multcomp: contrasts for count data
>
>
> Peter Westfall has answered me giving useful links. Here is the
> exchange:
>
>
> thanks for your quick answer and the refs. My misconception was that i
> treated the p-values as if they were non adjusted p-values.
> Discreteness was a minor problem. The p-values look much more uniform
> once I test only for the contrast of interest and not all the pair-
> wise ones.
>
> summary( glht(fit, linfct = mcp( x=c(0, -1, 1)) ) )$test$pvalues
>
> instead of:
>
> summary( glht(fit, linfct = mcp(x = "Tukey") ) )$test$pvalues
>
> Julien
>
>
>
>
> On Jun 15, 2009, at 16:21 , Westfall, Peter wrote:
>
> P-values are uniform only when the distribution is continuous.  See
>
> Westfall, P.H. and Troendle, J.F. (2008).  Multiple Testing with
> Minimal Assumptions, Biometrical Journal 50, 745-755.
>
> Westfall, P.H., and Soper, K.A. (2001). "Using priors to improve
> multiple animal carcinogenicity tests<http://pubs.amstat.org/doi/pdfplus/10.1198/016214501753208852
>> ", Journal of the American Statistical Association 96, 827-834.
>
> Westfall, P.H. and Wolfinger, R.D.(1997). "Multiple Tests with
> Discrete Distributions<http://www.jstor.org/stable/2684683>," The
> American Statistician 51, 3-8.
>
> for the finite sample case.
>
> For the asymptotic case with Poisson etc, see
>
> Hothorn, T., Bretz, F., and Westfall, P. (2008).  Simultaneous
> Inference in General Parametric Models, Biometrical Journal 50(3),  
> 346
> 363.
>
>
> Good luck,
>
> Peter
>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Mike Prager <mike.prager@noaa.gov>
> Date: 16 June 2009 2:05:19 AM
> To: r-help@stat.math.ethz.ch
> Subject: Re: [R] replacing zeros by NAs
>
>
> Often, data are computed in real (not integer) numbers, and in
> such cases, comparison to zero is not as good as using a
> tolerance level. Modifying slightly the suggestions of others, I
> would use something like this:
>
> my.tol <- 1e-50
> x <- c(1.4, 2.97, 1.0e-100, pi, 0.2, 5.1, 6.8, 0.0)
> print(x)
> is.na(x) <- abs(x) < my.tol
> print(x)
>
>
> -- 
> Mike Prager, NOAA, Beaufort, NC
> * Opinions expressed are personal and not represented otherwise.
> * Any use of tradenames does not constitute a NOAA endorsement.
>
>
>
>
>
>
>
>
>
> From: jim holtman <jholtman@gmail.com>
> Date: 16 June 2009 2:13:55 AM
> To: "Zhang,Yanwei" <Yanwei.Zhang@cna.com>
> Cc: r-help@r-project.org
> Subject: Re: [R] Create R object
>
>
> Here is the answer for the second part:
>
>> lst=list(a1=matrix(rnorm(4),2,2),
> a2=matrix(rnorm(4),2,2),a3=matrix(rnorm(4),2,2))
>> l.dim <- sapply(lst, dim)
>> l.dim
>     a1 a2 a3
> [1,]  2  2  2
> [2,]  2  2  2
>> all(l.dim[1,1] == l.dim[1,]) && all(l.dim[2,1] == l.dim[2,])
> [1] TRUE
>>
> For the first part, why don't you just leave it a list and access  
> the list
> elements by names?  If you want to create new objects, the 'for' is  
> fine.
>
> On Mon, Jun 15, 2009 at 11:58 AM, Zhang,Yanwei  
> <Yanwei.Zhang@cna.com> wrote:
>
>> Dear R users,
>>
>> I have two simple questions here, and hope someone can help me on  
>> this.
>> Thanks in advance.
>>
>> 1.
>> I have a list object lst=list(a1=matrix(rnorm(4),2,2),
>> a2=matrix(rnorm(4),2,2),a3=matrix(rnorm(4),2,2)). Here I only use  
>> three
>> elements for illustration, and in fact the length of lst, n, is  
>> unknown in
>> advance. I want to define an object for each element of this lst,  
>> and the
>> objects have names like "object1", "object2",...,"objectn". I could  
>> use a
>> loop like the following:
>> for (i in 1:length(lst)){
>>       assign(paste("object",i,sep=""),lst[[i]])
>> }
>>
>> I wonder if there's a way to avoid this loop?
>>
>>
>> 2.
>> I want to validate whether all of the "object"s have the same  
>> dimension,
>> that is, whether dim(object1)[1]==dim(object2)[1]==dim(object3)[1]&
>> dim(object1)[2]==dim(object2)[2]==dim(object3)[2]  is true. How can  
>> I do
>> that easily since the length of lst is not fixed?
>>
>> Thanks.
>>
>> Wayne (Yanwei) Zhang
>> Ttatistical *esearch
>>> CNA
>>>
>>>
>>>
>>
>> E-MAIL CONFIDENTIALITY NOTICE:  The contents of this e-mail message  
>> and any
>> attachments are intended solely for the
>> addressee(s) and may contain confidential and/or legally privileged
>> information. If you are not the
>> intended recipient of this message or if this message has been  
>> addressed to
>> you in error, please
>> immediately alert the sender by reply e-mail and then delete this  
>> message
>> and any attachments. If you
>> are not the intended recipient, you are notified that any use,
>> dissemination, distribution, copying, or
>> storage of this message or any attachment is strictly prohibited.
>>
>>       [[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<http://www.r-project.org/posting-guide.html 
>> >
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> -- 
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem that you are trying to solve?
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: David Winsemius <dwinsemius@comcast.net>
> Date: 16 June 2009 2:17:49 AM
> To: ltracy <lareet@hotmail.com>
> Cc: r-help@r-project.org
> Subject: Re: [R] how to interpret coefficients for a natural spline  
> smooth function in a GLM
>
>
> Plot the predictions; you can almost never interpret the  
> coefficients of a spline fit individually. They are not really  
> independent or separately interpretable.
>
> Is this homework?
> -- 
> David
> On Jun 15, 2009, at 10:19 AM, ltracy wrote:
>
>>
>> Hello-
>>
>> I am trying to model infections counts over 120 months using a GLM  
>> in R.
>> The model is simple really including a factor variable for year (10  
>> yrs in
>> total) and another variable consisting of a natural spline function  
>> for time
>> in months.
>>
>> My code for the GLM is as follows:
>> model1<-glm(ALL_COUNT~factor(FY)+ns(1:120, 10),  
>> offset=log(TOTAL_PTS),
>> family=poisson, data=TS1)
>>
>> The summary output pertaining to the smooth function consists of 10
>> coefficients for each df in the model.  Here are the coefficients:
>>
>> ns(1:120, 10)1  -0.72438    0.32773  -2.210 0.027084 *
>> ns(1:120, 10)2  -1.19097    0.37492  -3.177 0.001490 **
>> ns(1:120, 10)3  -1.40250    0.42366  -3.310 0.000931 ***
>> ns(1:120, 10)4  -0.82722    0.47459  -1.743 0.081334 .
>> ns(1:120, 10)5  -0.46139    0.49657  -0.929 0.352812
>> ns(1:120, 10)6  -0.44892    0.51909  -0.865 0.387137
>> ns(1:120, 10)7  -0.53060    0.54783  -0.969 0.332778
>> ns(1:120, 10)8  -0.25699    0.55582  -0.462 0.643814
>> ns(1:120, 10)9  -0.74091    0.63899  -1.160 0.246249
>> ns(1:120, 10)10  0.41142    0.56317   0.731 0.465054
>>
>> What is still unclear to me is what these 10 coefficients from the  
>> natural
>> spline represent.
>>
>> Thanks in advace-
>>
>>
>>
>>
>> -- 
>> View this message in context: http://www.nabble.com/how-to-interpret-coefficients-for-a-natural-spline-smooth-function-in-a-GLM-tp24035485p24035485.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> 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.
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
>
>
>
>
>
>
>
>
> From: Hadley Wickham <hadley@rice.edu>
> Date: 16 June 2009 2:19:38 AM
> To: r-help <R-help@r-project.org>
> Subject: [R] [OT] VBA to save excel as csv
>
>
> Hi all,
>
> This is a little off-topic, but it is on the general topic of getting
> data in R.  I'm looking for a excel macro / vba script that will
> export all spreadsheets in a directory (with one file per tab) into
> csv.  Does anyone have anything like this?
>
> Thanks,
>
> Hadley
>
> -- 
> http://had.co.nz/
>
>
>
>
>
>
>
>
>
> From: jim holtman <jholtman@gmail.com>
> Date: 16 June 2009 2:22:20 AM
> To: Kenny Larsen <k.larsen@sheffield.ac.uk>
> Cc: r-help@r-project.org
> Subject: Re: [R] Assigning Data a name from within another variable?
>
>
> Use a 'list' to read in the data and access it:
>
> files<-list.files()
> files<-files[grep('.wm4', files)]
> labels<-gsub('.wm4', '',files)
>
> myInput <- lapply(files, read.table)
> # if you want to get rid of .wm4
> names(myInput) <- sub(".wm4$", "", names(myInput))
>
> On Mon, Jun 15, 2009 at 11:50 AM, Kenny Larsen <k.larsen@sheffield.ac.uk 
> >wrote:
>
>>
>> Hi All,
>>
>> I have hunted high and low and tried dozens of things but have yet to
>> achieve the result I require. Below is my code (taken mostly from  
>> another
>> thread on here) thus far:
>>
>> files<-list.files()
>> files<-files[grep('.wm4', files)]
>> labels<-gsub('.wm4', '',files)
>>
>> for(i in 1:length(files)){
>> X<-read.table(files[i])
>> <My problem is here!>
>>
>> What I am trying to do now is assign the first item in labels in  
>> place of X
>> so the table name will effectively be whatever is written in  
>> labels[1]. The
>> files simply consist of two columns of real numbers. I have tried  
>> several
>> things, such like replacing X with labels[1], but this simply  
>> writes the
>> data in one long column to the first place of labels(which makes  
>> sense).
>> How
>> do I extract what is in labels[1] and set it as the table name?
>>
>> As always any help is greatly appreciated.
>>
>> Kenny Larsen
>> --
>> View this message in context:
>> http://www.nabble.com/Assigning-Data-a-name-from-within-another-variable--tp24037279p24037279.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> 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<http://www.r-project.org/posting-guide.html 
>> >
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> -- 
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem that you are trying to solve?
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: "Zhang,Yanwei" <Yanwei.Zhang@cna.com>
> Date: 16 June 2009 2:25:31 AM
> To: jim holtman <jholtman@gmail.com>
> Cc: r-help@r-project.org
> Subject: Re: [R] Create R object
>
>
> Thanks a lot Jim.
>
> I just switched back to R from SAS, so I might carry over the old  
> style of creating tons of SAS macro variables...
>
> Another related question is :
> Suppose each element in my lst now is a numeric character:
> lst=list(a1=rnorm(4), a2=rnorm(4),a3=rnorm(4))
>
> Still the number of elements is not fixed.
> I'm trying to run a system of equations (actually just separate  
> regressions) like the following:
>
> fit1= lm(lst[[1]]~lst[[2]]+lst[[3]])
> fit2= lm(lst[[2]]~lst[[1]]+lst[[3]])
> fit3= lm(lst[[3]]~lst[[1]]+lst[[2]])
>
> Is there any easy way to do the above for a list of non-fixed length?
>
> Thanks a lot.
>
>
> Wayne (Yanwei) Zhang
> Ttatistical Áesearch
> CNA
>
>
>
>
> ________________________________
>
> 	From: jim holtman [mailto:jholtman@gmail.com]
> 	Sent: Monday, June 15, 2009 11:14 AM
> 	To: Zhang,Yanwei
> 	Cc: r-help@r-project.org
> 	Subject: Re: [R] Create R object
> 	
> 	
> 	Here is the answer for the second part:
> 	
> 	> lst=list(a1=matrix(rnorm(4),2,2), a2=matrix(rnorm(4), 
> 2,2),a3=matrix(rnorm(4),2,2))
> 	> l.dim <- sapply(lst, dim)
> 	> l.dim
> 	     a1 a2 a3
> 	[1,]  2  2  2
> 	[2,]  2  2  2
> 	> all(l.dim[1,1] == l.dim[1,]) && all(l.dim[2,1] == l.dim[2,])
> 	[1] TRUE
> 	>
> 	
> 	For the first part, why don't you just leave it a list and access  
> the list elements by names?  If you want to create new objects, the  
> 'for' is fine.
> 	
> 	
> 	On Mon, Jun 15, 2009 at 11:58 AM, Zhang,Yanwei  
> <Yanwei.Zhang@cna.com> wrote:
> 	
>
> 		Dear R users,
> 		
> 		I have two simple questions here, and hope someone can help me on  
> this. Thanks in advance.
> 		
> 		1.
> 		I have a list object lst=list(a1=matrix(rnorm(4),2,2),  
> a2=matrix(rnorm(4),2,2),a3=matrix(rnorm(4),2,2)). Here I only use  
> three elements for illustration, and in fact the length of lst, n,  
> is unknown in advance. I want to define an object for each element  
> of this lst, and the objects have names like "object1",  
> "object2",...,"objectn". I could use a loop like the following:
> 		for (i in 1:length(lst)){
> 		       assign(paste("object",i,sep=""),lst[[i]])
> 		}
> 		
> 		I wonder if there's a way to avoid this loop?
> 		
> 		
> 		2.
> 		I want to validate whether all of the "object"s have the same  
> dimension, that is, whether dim(object1)[1]==dim(object2) 
> [1]==dim(object3)[1]& dim(object1)[2]==dim(object2)[2]==dim(object3) 
> [2]  is true. How can I do that easily since the length of lst is  
> not fixed?
> 		
> 		Thanks.
> 		
> 		Wayne (Yanwei) Zhang
> 		Ttatistical *esearch
> 		> CNA
> 		>
> 		>
> 		>
> 		
> 		E-MAIL CONFIDENTIALITY NOTICE:  The contents of this e-mail  
> message and any attachments are intended solely for the
> 		addressee(s) and may contain confidential and/or legally  
> privileged information. If you are not the
> 		intended recipient of this message or if this message has been  
> addressed to you in error, please
> 		immediately alert the sender by reply e-mail and then delete this  
> message and any attachments. If you
> 		are not the intended recipient, you are notified that any use,  
> dissemination, distribution, copying, or
> 		storage of this message or any attachment is strictly prohibited.
> 		
> 		       [[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.
> 		
>
>
>
>
> 	--
> 	Jim Holtman
> 	Cincinnati, OH
> 	+1 513 646 9390
> 	
> 	What is the problem that you are trying to solve?
> 	
>
>
> E-MAIL CONFIDENTIALITY NOTICE:  The contents of this e-mail message  
> and any attachments are intended solely for the
> addressee(s) and may contain confidential and/or legally privileged  
> information. If you are not the
> intended recipient of this message or if this message has been  
> addressed to you in error, please
> immediately alert the sender by reply e-mail and then delete this  
> message and any attachments. If you
> are not the intended recipient, you are notified that any use,  
> dissemination, distribution, copying, or
> storage of this message or any attachment is strictly prohibited.
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Greg Snow <Greg.Snow@imail.org>
> Date: 16 June 2009 2:29:28 AM
> To: Payam Minoofar <payam.minoofar@meissner.com>, "r-help@r-project.org 
> " <r-help@r-project.org>
> Subject: Re: [R] Referencing data frames
>
>
> Generally when someone asks a question like this, they are trying to  
> program in a different language using R rather than taking advantage  
> of the power of R itself.  If you give us more information on what  
> you are trying to accomplish, then we may be able to give better  
> advice on how to accomplish your final goal using the power of R.
>
> -- 
> Gregory (Greg) L. Snow Ph.D.
> Statistical Data Center
> Intermountain Healthcare
> greg.snow@imail.org
> 801.408.8111
>
>> -----Original Message-----
>> From: r-help-bounces@r-project.org [mailto:r-help-bounces@r-
>> project.org] On Behalf Of Payam Minoofar
>> Sent: Friday, June 12, 2009 4:00 PM
>> To: r-help@r-project.org
>> Subject: [R] Referencing data frames
>>
>> Hi,
>>
>> How do I use the string content of a string variable to reference a
>> data frame of the same name? I want to do the typical tasks of 1)
>> building a name with a string variable and using the string  
>> variable to
>> create a data frame (or any object) whose name is the string value of
>> the variable and 2) pass on a string to a function as a parameter,  
>> and
>> then use that string to refer to an existing data frame.
>>
>> Thanks in advance.
>>
>> Payam
>> --
>> Payam Minoofar, Ph.D.
>> Scientist
>> Meissner Filtration Products
>> 4181 Calle Tesoro
>> Camarillo, CA 93012
>> USA
>> +1 805 388 9911
>> +1 805 388 5948 fax
>> Payam.minoofar@meissner.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.
>
>
>
>
>
>
>
>
>
> From: Marc Schwartz <marc_schwartz@me.com>
> Date: 16 June 2009 2:31:10 AM
> To: pschrode@alumni.unav.es
> Cc: r-help@r-project.org
> Subject: Re: [R] NA as a result of using GLM
>
>
> On Jun 15, 2009, at 10:13 AM, Paul Christoph Schröder wrote:
>
>> Thanks Marc, as you said, this is a priori design. I'm trying to get
>> more events.
>> But for now, I'll have to try to get rid of the collinear genes. Is
>> there any other method than using cor? Any method to state which
>> genes behave in the same  manner?
>> Paul
>
> Gene analysis is not in my area of expertise, so there may be other
> methods that make more sense here. I would defer to others with the
> appropriate expertise in the domain.  The BioConductor list would also
> be a good resource for you. More information at:
>
>   http://www.bioconductor.org/
>
> In terms of simply assessing correlation, there would be some
> graphical alternatives to reviewing a numeric correlation matrix.
>
> One would be to use pairs() to create a graphical visualization of the
> correlation matrix. See ?pairs and:
>
>   http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=137
>
> another would be to use the parallel lattice graphics function  
> splom():
>
>   http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=50
>
>
> Yet another would be to use correlation matrix ellipses with the
> plotcorr() function in the 'ellipse' CRAN package:
>
>   http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=149
>
>
> Each of the above are going to get you to the same basic place that a
> standard correlation matrix will get you to, which is to assess which
> genes seem to move in the same direction as others. That is, which
> gene pairs have a correlation of ~1.
>
> The problem that you have now is that you have so few observations,
> that it is conceivable that the correlation observed at this point is
> spurious and specific to this dataset. In other words, it may not be
> observed (or not to the same extent) if you had a much larger dataset.
> Thus, I would be cautious about trying to explain any behavior at this
> point.
>
> Remember, that with only 6 events, you cannot really create a viable
> LR model with even a single gene, using traditional approaches. So to
> simply eliminate the 7 collinear genes, in theory leaving you with 9
> genes as covariates in the model, is not going to be very helpful.
> Your model estimates are not going to be stable.
>
> As part of your model building and experimental design strategy, I
> would refer you to Frank's book "Regression Modeling Strategies". More
> information here:
>
>   http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/RmS
>
> Certainly, when you get substantially more data, there would be other
> data reduction techniques that could come into play here and Frank's
> book covers them.
>
> HTH,
>
> Marc
>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
>
>
>
>
>
> From: Michael <comtech.usa@gmail.com>
> Date: 16 June 2009 2:32:15 AM
> To: r-help <R-help@stat.math.ethz.ch>
> Subject: [R] hands-on book on multivariate statistics and data- 
> mining with R?
>
>
> Hi all,
>
> I am looking for pointers to good hands-on books on multivariate
> statistics and data-mining with R? So that I could learn while doing
> experiments...
>
> Thanks a lot!
>
>
>
>
>
>
>
>
>
> From: baptiste auguie <ba208@exeter.ac.uk>
> Date: 16 June 2009 2:34:31 AM
> To: Kenny Larsen <k.larsen@sheffield.ac.uk>
> Cc: r-help <r-help@r-project.org>
> Subject: Re: [R] Assigning Data a name from within another variable?
>
>
> Kenny Larsen wrote:
>> Hi All,
>>
>> I have hunted high and low and tried dozens of things but have yet to
>> achieve the result I require. Below is my code (taken mostly from  
>> another
>> thread on here) thus far:
>>
>> files<-list.files()
>> files<-files[grep('.wm4', files)]
>> labels<-gsub('.wm4', '',files)
>>
>> for(i in 1:length(files)){
>> X<-read.table(files[i])
>> <My problem is here!>
>>
>> What I am trying to do now is assign the first item in labels in  
>> place of X
>> so the table name will effectively be whatever is written in  
>> labels[1]. The
>> files simply consist of two columns of real numbers. I have tried  
>> several
>> things, such like replacing X with labels[1], but this simply  
>> writes the
>> data in one long column to the first place of labels(which makes  
>> sense). How
>> do I extract what is in labels[1] and set it as the table name?
>>
>> As always any help is greatly appreciated.
>>
>> Kenny Larsen
>>
> Hi,
>
> have you checked the r wiki,
>
> http://wiki.r-project.org/rwiki/doku.php?id=guides:assigning-variable-names
>
> this page is a really a work in progress, feel free to add comments.
>
> HTH,
>
> baptiste
>
>
>
>
>
>
>
>
>
> From: Payam Minoofar <payam.minoofar@meissner.com>
> Date: 16 June 2009 2:38:50 AM
> To: Greg Snow <Greg.Snow@imail.org>, "r-help@r-project.org" <r-help@r-project.org 
> >
> Subject: Re: [R] Referencing data frames
>
>
> You are, indeed, correct. I'm still used to the IGOR Pro programming  
> language (for which I even wrote an introductory manual, http://payam.minoofar.com/igor/)
>
> The feedback I've gotten has been fantastic, and I know how I'm  
> going to proceed from this point forward.
>
> Nevertheless, I'll solicit more feedback while I have willing "ears".
>
> I would like to have a function acquire an object by reference, and  
> within the function create new objects based on the original object  
> and then use the name of the original object as the base for the  
> names of the newly created objects.
>
> It seems to me that the optimal way of doing this is to have the  
> function acquire the name of the object as a string, and then use  
> get() to access the object, and then to use the same string to do  
> the name formation of the new objects.
>
> IGOR Pro has a built-in function that returns the name of an object  
> as a string, and I was wondering if R has a similar facility.
>
> Yes, I'm definitely getting used to the R language, but I've made  
> tremendous progress thanks to the list , and the power of R is  
> abundantly clear to me, as is the abstruseness of the language. :)
>
> Payam
>
>
> On 6/15/09 9:29 AM, "Greg Snow" <Greg.Snow@imail.org> wrote:
>
> Generally when someone asks a question like this, they are trying to  
> program in a different language using R rather than taking advantage  
> of the power of R itself.  If you give us more information on what  
> you are trying to accomplish, then we may be able to give better  
> advice on how to accomplish your final goal using the power of R.
>
> --
> Gregory (Greg) L. Snow Ph.D.
> Statistical Data Center
> Intermountain Healthcare
> greg.snow@imail.org
> 801.408.8111
>
>> -----Original Message-----
>> From: r-help-bounces@r-project.org [mailto:r-help-bounces@r-
>> project.org] On Behalf Of Payam Minoofar
>> Sent: Friday, June 12, 2009 4:00 PM
>> To: r-help@r-project.org
>> Subject: [R] Referencing data frames
>>
>> Hi,
>>
>> How do I use the string content of a string variable to reference a
>> data frame of the same name? I want to do the typical tasks of 1)
>> building a name with a string variable and using the string  
>> variable to
>> create a data frame (or any object) whose name is the string value of
>> the variable and 2) pass on a string to a function as a parameter,  
>> and
>> then use that string to refer to an existing data frame.
>>
>> Thanks in advance.
>>
>> Payam
>> --
>> Payam Minoofar, Ph.D.
>> Scientist
>> Meissner Filtration Products
>> 4181 Calle Tesoro
>> Camarillo, CA 93012
>> USA
>> +1 805 388 9911
>> +1 805 388 5948 fax
>> Payam.minoofar@meissner.com
>>
>>
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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.
>
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>
> From: Ryan van Laar <ryanvanlaar@gmail.com>
> Date: 16 June 2009 2:47:22 AM
> To: r-help@r-project.org
> Subject: [R] heatmap.2 questions
>
>
> I'm using this code to create a heatmap of expression data and  
> indicate a
> specific column of data, post clustering:
>
> #Generate heatmap:
> heatmapChipDx <- heatmap.2(L3data_med2,  
> dendrogram="column",trace="none",
> col=redgreen(64), colsep=seps, sepcolor="yellow", sepwidth = 0.1,
> margin=c(5,5), scale="row", key=FALSE)
>
> I have two problems that I'm hoping i can get some pointers on:
>
> 1. The column I want to indicate with a yellow line is column #1 in  
> the
> matrix, pre-clustering. How can I determine its position post- 
> clustering, so
> I can instruct the heatmap code to move the yellow 'sep' line to this
> position?
>
> 2. The intensity of the colours is very dull and I cannot figure out  
> how to
> increase the contrast (a la Treeview). I have attached two images  
> (not sure
> if this is allowed), one being the image as it comes out from the code
> above, and the other ("...copy.png") being how I would actuallt like  
> it to
> look. I adjusted the levels in photoshop to get this second image.
>
> The data is log2 scale gene expression data (single channel), and  
> scaled
> with this command:
>
> L3data_med<- scale(t(L3dataonly), center = TRUE)
>> L3data_med2<-t(L3data_med)
>>
>
> ...to median (mean?) centre the rows, prior to clustering.
>
> Thanks in advance,
>
> Ryan
> <heatmap.png><heatmap copy.png>
>
>
>
> _______________________________________________
> 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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