Re: [R] time function behavior for ts class objects
Try not reducing options(digit=)! I get (with the default value 7) time(xts) Jan Feb Mar Apr May Jun Jul Aug 1973 1973.000 1973.083 1973.167 1973.250 1973.333 1973.417 1973.500 1973.583 1974 1974.000 1974.083 1974.167 1974.250 1974.333 1974.417 1974.500 1974.583 Sep Oct Nov Dec 1973 1973.667 1973.750 1973.833 1973.917 1974 1974.667 1974.750 1974.833 1974.917 That is the 'correct linear sequence' in years, the units selected by 'frequency = 12'. It seems you printed it rounded to 4 digits (without telling us, so maybe you had forgotten that you had altered the setting). Please do not confuse the printed representation of an object with its value -- this is especially important if you choose to reduce the default printing precision so much. On Sat, 13 Jun 2009, Ron Burns wrote: Hi all- I am trying to use the time function for ts class objects and do not understand the return value. I want to use it to set up a time trend in arima fits. It does not seem to return a correct linear sequence that matches the underlying time series. I am running: R version 2.8.1 (2008-12-22). For example: R ## create a time series R x - rnorm(24) R (xts - ts(x,start=c(1973),frequency=12)) Jan Feb Mar Apr May Jun Jul Aug 1973 -0.09220 0.29838 -0.48667 -1.08046 -0.65665 -0.11695 0.3 0.00769 1974 1.23304 0.04211 0.88410 1.08454 -0.38852 0.05231 0.50548 -0.71105 Sep Oct Nov Dec 1973 -0.17923 -1.29722 -1.04519 -0.90785 1974 1.28810 0.43334 -0.71618 0.26681 R plot(xts) The plot of xts starts at 1973.0 as expected (as given by the plot x-axis first tick). R ## check what time returns R (time.ts - time(xts)) Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 1973 1973 1973 1973 1973 1973 1973 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1975 1975 1975 1975 1975 I would have expected the 1973 row to contain 1973 for all months and not to have a jump after Jun 1973 to Jul 1974. That is I would expect something like: R ## const my own time specific to this xts R y - c(rep(1973,12),rep(1974,12)) R (tsp(y) - attr(hasTsp(xts),tsp)) [1] 1973 1975 12 R (my.time.ts - as.ts(y)) Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 I certainly don't think R expects me to construct this myself! So I must be missing something, doing something wrong, or there is bug somewhere. Looking a bit further, I tried adding an offset in the time() call: R time(xts,offset=-6) Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 1973 1972 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 which is close (i.e. Jan 1972) still not what I expect. However time(xts,offset=(-6+.1)) Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1973 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 1974 does it. This behavior is not clear from the help pages (to me at least!) and also (to me at least!) represents buggy behavior. It is even less clear now to me how to properly set up the time trends for an arima fit? Does arma expect the results from time() without an offset, or what I think it should be? Thanks in advance for your consideration and help. Best regards, Ron -- R. R. Burns Physicist (Retired) Oceanside, CA -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 'Errors' with Ubuntu
Hi, As Uwe said, this is not really the place to get support for Ubuntu. They have excellent forums. But the problem seems to be that GRUB was not correctly installed. Run an ubuntu live cd and reinstall GRUB from that. The command might be grub-install, but i'm not sure cheers, Paul Len Vir schreef: 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-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] a proposal regarding documentation
Proposal That a new mailing list be established that pertains exclusively to R documentation. The purpose of the list would be to discuss weak sections of the documentation and establish fixes for those weak spots. Pro If it works, there would be better documentation. It would be an excellent opportunity for newish and/or less technical people to contribute to R. In some respects such people would be much more valuable to the process than very experienced people. It could take some pressure off of R-core. Con It needs at least one person (and probably more) with a strong commitment to make it work. The proposed changes would need to be installed, and activity would need to be encouraged and focused. Background A couple weeks ago I sent a message suggesting that people with issues about the documentation should send a message about it. I left the exact details vague for two reasons: 1) I wasn't sure what the preferred details are. 2) I realized that if people actually followed the suggestion and sent messages about documentation, R-core would be overwhelmed and not especially happy. Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of The R Inferno and A Guide for the Unwilling S User) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a proposal regarding documentation
Patrick Burns pbu...@pburns.seanet.com wrote Proposal That a new mailing list be established that pertains exclusively to R documentation. The purpose of the list would be to discuss weak sections of the documentation and establish fixes for those weak spots. Pro If it works, there would be better documentation. It would be an excellent opportunity for newish and/or less technical people to contribute to R. In some respects such people would be much more valuable to the process than very experienced people. It could take some pressure off of R-core. Con It needs at least one person (and probably more) with a strong commitment to make it work. The proposed changes would need to be installed, and activity would need to be encouraged and focused. Background A couple weeks ago I sent a message suggesting that people with issues about the documentation should send a message about it. I left the exact details vague for two reasons: 1) I wasn't sure what the preferred details are. 2) I realized that if people actually followed the suggestion and sent messages about documentation, R-core would be overwhelmed and not especially happy. I think this is an excellent idea. I would be glad to be one of the newish or less technical people. 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.
Re: [R] a proposal regarding documentation
Issues
(1) Will people use the new listserver?
(2) Will developers respond to postings
Question
(1) Are there any guidelines for creating documentation? If not should they be
developed? It seems to me that every help page should include (a) examples, and
when approprate (b) a reference to an article relevant to the help page's
content.
Thoughts
The pages should explain a concept using as little jargon as possible and
should try not to be circular, i.e. do not define something using the defined
term in its own definition.
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)
Peter Flom peterflomconsult...@mindspring.com 6/14/2009 7:05 AM
Patrick Burns pbu...@pburns.seanet.com wrote
Proposal
That a new mailing list be established
that pertains exclusively to R documentation.
The purpose of the list would be to discuss
weak sections of the documentation and
establish fixes for those weak spots.
Pro
If it works, there would be better documentation.
It would be an excellent opportunity for newish
and/or less technical people to contribute to R.
In some respects such people would be much more
valuable to the process than very experienced
people.
It could take some pressure off of R-core.
Con
It needs at least one person (and probably more)
with a strong commitment to make it work. The
proposed changes would need to be installed, and
activity would need to be encouraged and focused.
Background
A couple weeks ago I sent a message suggesting that
people with issues about the documentation should
send a message about it. I left the exact details
vague for two reasons:
1) I wasn't sure what the preferred details are.
2) I realized that if people actually followed
the suggestion and sent messages about documentation,
R-core would be overwhelmed and not especially happy.
I think this is an excellent idea.
I would be glad to be one of the newish or less technical people.
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.
Re: [R] a proposal regarding documentation
I have a package StreamMetabolism. I believe that documentation is
the toughest part. I find it to be straight foward, but then I wrote
the package. Lets try one? I don't m
ind helping.
Stephen Sefick
On Sun, Jun 14, 2009 at 7:23 AM, John Sorkinjsor...@grecc.umaryland.edu wrote:
Issues
(1) Will people use the new listserver?
(2) Will developers respond to postings
Question
(1) Are there any guidelines for creating documentation? If not should they
be developed? It seems to me that every help page should include (a)
examples, and when approprate (b) a reference to an article relevant to the
help page's content.
Thoughts
The pages should explain a concept using as little jargon as possible and
should try not to be circular, i.e. do not define something using the defined
term in its own definition.
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)
Peter Flom peterflomconsult...@mindspring.com 6/14/2009 7:05 AM
Patrick Burns pbu...@pburns.seanet.com wrote
Proposal
That a new mailing list be established
that pertains exclusively to R documentation.
The purpose of the list would be to discuss
weak sections of the documentation and
establish fixes for those weak spots.
Pro
If it works, there would be better documentation.
It would be an excellent opportunity for newish
and/or less technical people to contribute to R.
In some respects such people would be much more
valuable to the process than very experienced
people.
It could take some pressure off of R-core.
Con
It needs at least one person (and probably more)
with a strong commitment to make it work. The
proposed changes would need to be installed, and
activity would need to be encouraged and focused.
Background
A couple weeks ago I sent a message suggesting that
people with issues about the documentation should
send a message about it. I left the exact details
vague for two reasons:
1) I wasn't sure what the preferred details are.
2) I realized that if people actually followed
the suggestion and sent messages about documentation,
R-core would be overwhelmed and not especially happy.
I think this is an excellent idea.
I would be glad to be one of the newish or less technical people.
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 ...{{dropped:22}}
__
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] boxplot size
Hey everybody, I am trying to generate multiple boxplots on one page by using the layout () function. This works really well but the plots are always badly proportioned (3 times wider than high) and much too small to be easily readable. I have tried reducing margins to allow for bigger plots, but that hasn't had the desired effect. Does anybody know how if there is a size function in layout, or if I can at least determine boxplot size separately for each plot? Thank you! -- View this message in context: http://www.nabble.com/boxplot-size-tp24020781p24020781.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.
Re: [R] Gtk objects disappears
It woks fine. Thanks very much. Olivier -- Olivier G. Nuñez Email: onu...@iberstat.es Tel : +34 663 03 69 09 Web: http://www.iberstat.es El 14/06/2009, a las 4:30, Michael Lawrence escribió: I would recommend just running gtkMain(), so that GTK+ blocks R. Then you need your GUI to call gtkMainQuit() when it's time to kill R. On Fri, Jun 12, 2009 at 6:59 AM, Olivier Nuñez onu...@iberstat.es wrote: Dear John, I have a question. When I run a RGtk code in my terminal (without using the R GUI) R --vanilla EOF source(myRGtkcode.R) EOF the GTK objects do not remain on the screen. Until now, I bypass this problem using the following commands: require(tcltk) tkmessageBox(Press to exit) But it is not really satisfactory and the tcltk Box cannot be minimized (at least in Mac OSX). Any idea? Best regards. Olivier -- Olivier G. Nuñez Email: onu...@iberstat.es Tel : +34 663 03 69 09 Web: http://www.iberstat.es [[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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem in installation of Rgraphviz package
Hi,there, I could install Rgraphviz in R version 2.6. I could not install this in R version 2.7 or 2.8. Please try in version2.6. ram basnet wrote: Dear R users, I am not so used to this R software. I have to use the package Rgraphviz but found some problem in the installation process. I download this package and store in R library but i am not getting this package in R installation list. I made review in google search net and use the following command: ### source(http://bioconductor.org/biocLite.R;) biocLite(Rgraphviz) set.seed(123) V - letters[1:10] M - 1:4 g1 - randomGraph(V, M, 0.2) library(graph) library(grid) library(Rgraphviz) ### I got following Error message: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.0/library/Rgraphviz/libs/Rgraphviz.dll': LoadLibrary failure: The specified module could not be found. Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' Error: package/namespace load failed for 'Rgraphviz' ' May be some of users can recognize this problem and request for solutions. Thanks in advance. Sincerely, Ram Kumar Basnet Graduate student, Wageningen University, The Netherlands. [[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/Problem-in-installation-of-%22Rgraphviz%22-package-tp20196715p24019809.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.
Re: [R] boxplot size
Have you actually looked at the help page for layout()? -- David Winsemius On Jun 14, 2009, at 7:35 AM, luscinia wrote: Hey everybody, I am trying to generate multiple boxplots on one page by using the layout () function. This works really well but the plots are always badly proportioned (3 times wider than high) and much too small to be easily readable. I have tried reducing margins to allow for bigger plots, but that hasn't had the desired effect. Does anybody know how if there is a size function in layout, or if I can at least determine boxplot size separately for each plot?- -- 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.
Re: [R] a proposal regarding documentation
I neglected to say that I don't have the time to be one of the drivers for the proposed list. Pat Patrick Burns wrote: Proposal That a new mailing list be established that pertains exclusively to R documentation. The purpose of the list would be to discuss weak sections of the documentation and establish fixes for those weak spots. Pro If it works, there would be better documentation. It would be an excellent opportunity for newish and/or less technical people to contribute to R. In some respects such people would be much more valuable to the process than very experienced people. It could take some pressure off of R-core. Con It needs at least one person (and probably more) with a strong commitment to make it work. The proposed changes would need to be installed, and activity would need to be encouraged and focused. Background A couple weeks ago I sent a message suggesting that people with issues about the documentation should send a message about it. I left the exact details vague for two reasons: 1) I wasn't sure what the preferred details are. 2) I realized that if people actually followed the suggestion and sent messages about documentation, R-core would be overwhelmed and not especially happy. Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of The R Inferno and A Guide for the Unwilling S User) __ 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.
Re: [R] a proposal regarding documentation
I had only envisioned the scope of the
list to be the packages that R-core are
responsible for.
Expanding to contributed packages would
expand both potential usefulness and
certain complexity exponentially.
Pat
stephen sefick wrote:
I have a package StreamMetabolism. I believe that documentation is
the toughest part. I find it to be straight foward, but then I wrote
the package. Lets try one? I don't m
ind helping.
Stephen Sefick
On Sun, Jun 14, 2009 at 7:23 AM, John Sorkinjsor...@grecc.umaryland.edu wrote:
Issues
(1) Will people use the new listserver?
(2) Will developers respond to postings
Question
(1) Are there any guidelines for creating documentation? If not should they be
developed? It seems to me that every help page should include (a) examples, and
when approprate (b) a reference to an article relevant to the help page's
content.
Thoughts
The pages should explain a concept using as little jargon as possible and
should try not to be circular, i.e. do not define something using the defined
term in its own definition.
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)
Peter Flom peterflomconsult...@mindspring.com 6/14/2009 7:05 AM
Patrick Burns pbu...@pburns.seanet.com wrote
Proposal
That a new mailing list be established
that pertains exclusively to R documentation.
The purpose of the list would be to discuss
weak sections of the documentation and
establish fixes for those weak spots.
Pro
If it works, there would be better documentation.
It would be an excellent opportunity for newish
and/or less technical people to contribute to R.
In some respects such people would be much more
valuable to the process than very experienced
people.
It could take some pressure off of R-core.
Con
It needs at least one person (and probably more)
with a strong commitment to make it work. The
proposed changes would need to be installed, and
activity would need to be encouraged and focused.
Background
A couple weeks ago I sent a message suggesting that
people with issues about the documentation should
send a message about it. I left the exact details
vague for two reasons:
1) I wasn't sure what the preferred details are.
2) I realized that if people actually followed
the suggestion and sent messages about documentation,
R-core would be overwhelmed and not especially happy.
I think this is an excellent idea.
I would be glad to be one of the newish or less technical people.
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 ...{{dropped:22}}
__
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.
Re: [R] a proposal regarding documentation
That make sense to just do the R-core documentation. I was suggesting
using my package because I understand it and could have a dialog about
the design choices for the documentation, which would also improve the
package itself. I am starting my PhD program tomorrow and will
probably not have enough time to be in charge of this, but I wouldn't
mind helping.
Stephen Sefick
On Sun, Jun 14, 2009 at 12:30 PM, Patrick Burnspbu...@pburns.seanet.com wrote:
I had only envisioned the scope of the
list to be the packages that R-core are
responsible for.
Expanding to contributed packages would
expand both potential usefulness and
certain complexity exponentially.
Pat
stephen sefick wrote:
I have a package StreamMetabolism. I believe that documentation is
the toughest part. I find it to be straight foward, but then I wrote
the package. Lets try one? I don't m
ind helping.
Stephen Sefick
On Sun, Jun 14, 2009 at 7:23 AM, John Sorkinjsor...@grecc.umaryland.edu
wrote:
Issues
(1) Will people use the new listserver?
(2) Will developers respond to postings
Question
(1) Are there any guidelines for creating documentation? If not should
they be developed? It seems to me that every help page should include (a)
examples, and when approprate (b) a reference to an article relevant to the
help page's content.
Thoughts
The pages should explain a concept using as little jargon as possible and
should try not to be circular, i.e. do not define something using the
defined term in its own definition.
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)
Peter Flom peterflomconsult...@mindspring.com 6/14/2009 7:05 AM
Patrick Burns pbu...@pburns.seanet.com wrote
Proposal
That a new mailing list be established
that pertains exclusively to R documentation.
The purpose of the list would be to discuss
weak sections of the documentation and
establish fixes for those weak spots.
Pro
If it works, there would be better documentation.
It would be an excellent opportunity for newish
and/or less technical people to contribute to R.
In some respects such people would be much more
valuable to the process than very experienced
people.
It could take some pressure off of R-core.
Con
It needs at least one person (and probably more)
with a strong commitment to make it work. The
proposed changes would need to be installed, and
activity would need to be encouraged and focused.
Background
A couple weeks ago I sent a message suggesting that
people with issues about the documentation should
send a message about it. I left the exact details
vague for two reasons:
1) I wasn't sure what the preferred details are.
2) I realized that if people actually followed
the suggestion and sent messages about documentation,
R-core would be overwhelmed and not especially happy.
I think this is an excellent idea.
I would be glad to be one of the newish or less technical people.
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 ...{{dropped:22}}
__
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.
--
Stephen Sefick
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.
-K. Mullis
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] a proposal regarding documentation
The documentation for the nlme package was improved a few years ago by an informal process of this nature. When I first started following r-help, I answered many questions suggesting in part the the person read some portion of Pinheiro and Bates (2000). At that time, none of the help pages mentioned Pinheiro and Bates, because they were completed before the book and had not been updated. Eventually, I volunteered to add that to some of the help pages. Doug agreed. In the process, I also expanded some of the examples and modified the text in places where I thought I could make it more easily understood. One obvious way to do this would be to provide write access to the main R subversion repository. However, that likely would not be acceptable to the R-core team unless it were limited to a very few individuals they already knew and trusted, and those individuals could process suggestions from others. As mentioned, there would need to be additional ground rules. For example, an inappropriate example might cause R CMD check to fail on some platforms but not others. This could expose problems with the core code, which perhaps should be fixed but not necessarily in the time frame desired by this new documentation improvement team. For a second example, Brian Ripley once rejected a suggested change to a help page because it referred to a package outside the core R code. A less threatening alternative might be to direct this energy into improving the R Wiki. I have contributed to other Wiki projects, and I've found them to be quite useful and dynamic. The current R Wiki has not so far lived up to its potential. However, I believe that is just a matter of building a critical mass of R Wiki contributors. Many questions on R help could best be answers by first cheking and perhaps improving the R Wiki and then directing the questioner to the Wiki. I plan to do that sometime, but not yet. Hope this helps. Spencer Graves stephen sefick wrote: That make sense to just do the R-core documentation. I was suggesting using my package because I understand it and could have a dialog about the design choices for the documentation, which would also improve the package itself. I am starting my PhD program tomorrow and will probably not have enough time to be in charge of this, but I wouldn't mind helping. Stephen Sefick On Sun, Jun 14, 2009 at 12:30 PM, Patrick Burnspbu...@pburns.seanet.com wrote: I had only envisioned the scope of the list to be the packages that R-core are responsible for. Expanding to contributed packages would expand both potential usefulness and certain complexity exponentially. Pat stephen sefick wrote: I have a package StreamMetabolism. I believe that documentation is the toughest part. I find it to be straight foward, but then I wrote the package. Lets try one? I don't m ind helping. Stephen Sefick On Sun, Jun 14, 2009 at 7:23 AM, John Sorkinjsor...@grecc.umaryland.edu wrote: Issues (1) Will people use the new listserver? (2) Will developers respond to postings Question (1) Are there any guidelines for creating documentation? If not should they be developed? It seems to me that every help page should include (a) examples, and when approprate (b) a reference to an article relevant to the help page's content. Thoughts The pages should explain a concept using as little jargon as possible and should try not to be circular, i.e. do not define something using the defined term in its own definition. 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) Peter Flom peterflomconsult...@mindspring.com 6/14/2009 7:05 AM Patrick Burns pbu...@pburns.seanet.com wrote Proposal That a new mailing list be established that pertains exclusively to R documentation. The purpose of the list would be to discuss weak sections of the documentation and establish fixes for those weak spots. Pro If it works, there would be better documentation. It would be an excellent opportunity for newish and/or less technical people to contribute to R. In some respects such people would be much more valuable to the process than very experienced people. It could take some pressure off of R-core. Con It needs at least one person (and probably more) with a strong commitment to make it work. The proposed changes would need to be installed, and activity would need to be encouraged and focused. Background A couple weeks ago I sent a message suggesting that people with issues about the documentation should send a message about it. I left the exact details vague for two reasons: 1) I wasn't sure what the preferred details
Re: [R] a proposal regarding documentation
Perhaps help pages should have links to relevant portions of the WIKI. 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) spencerg spencer.gra...@prodsyse.com 6/14/2009 1:53 PM The documentation for the nlme package was improved a few years ago by an informal process of this nature. When I first started following r-help, I answered many questions suggesting in part the the person read some portion of Pinheiro and Bates (2000). At that time, none of the help pages mentioned Pinheiro and Bates, because they were completed before the book and had not been updated. Eventually, I volunteered to add that to some of the help pages. Doug agreed. In the process, I also expanded some of the examples and modified the text in places where I thought I could make it more easily understood. One obvious way to do this would be to provide write access to the main R subversion repository. However, that likely would not be acceptable to the R-core team unless it were limited to a very few individuals they already knew and trusted, and those individuals could process suggestions from others. As mentioned, there would need to be additional ground rules. For example, an inappropriate example might cause R CMD check to fail on some platforms but not others. This could expose problems with the core code, which perhaps should be fixed but not necessarily in the time frame desired by this new documentation improvement team. For a second example, Brian Ripley once rejected a suggested change to a help page because it referred to a package outside the core R code. A less threatening alternative might be to direct this energy into improving the R Wiki. I have contributed to other Wiki projects, and I've found them to be quite useful and dynamic. The current R Wiki has not so far lived up to its potential. However, I believe that is just a matter of building a critical mass of R Wiki contributors. Many questions on R help could best be answers by first cheking and perhaps improving the R Wiki and then directing the questioner to the Wiki. I plan to do that sometime, but not yet. Hope this helps. Spencer Graves stephen sefick wrote: That make sense to just do the R-core documentation. I was suggesting using my package because I understand it and could have a dialog about the design choices for the documentation, which would also improve the package itself. I am starting my PhD program tomorrow and will probably not have enough time to be in charge of this, but I wouldn't mind helping. Stephen Sefick On Sun, Jun 14, 2009 at 12:30 PM, Patrick Burnspbu...@pburns.seanet.com wrote: I had only envisioned the scope of the list to be the packages that R-core are responsible for. Expanding to contributed packages would expand both potential usefulness and certain complexity exponentially. Pat stephen sefick wrote: I have a package StreamMetabolism. I believe that documentation is the toughest part. I find it to be straight foward, but then I wrote the package. Lets try one? I don't m ind helping. Stephen Sefick On Sun, Jun 14, 2009 at 7:23 AM, John Sorkinjsor...@grecc.umaryland.edu wrote: Issues (1) Will people use the new listserver? (2) Will developers respond to postings Question (1) Are there any guidelines for creating documentation? If not should they be developed? It seems to me that every help page should include (a) examples, and when approprate (b) a reference to an article relevant to the help page's content. Thoughts The pages should explain a concept using as little jargon as possible and should try not to be circular, i.e. do not define something using the defined term in its own definition. 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) Peter Flom peterflomconsult...@mindspring.com 6/14/2009 7:05 AM Patrick Burns pbu...@pburns.seanet.com wrote Proposal That a new mailing list be established that pertains exclusively to R documentation. The purpose of the list would be to discuss weak sections of the documentation and establish fixes for those weak spots. Pro If it works, there would be better documentation. It would be an excellent opportunity for newish and/or less technical people to contribute to R. In some respects such people would be much more valuable to the process
[R] Centering graphics by default in Sweave
Is there an elegant way to get Sweave to center graphics by default?
I'd like to use \centerline{\includegraphics{}} etc. to save some
vertical space that \begin{center} ... \end{center} uses, and I'd like
to avoid centering with each fig=T=
Thanks
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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Re: [R] a proposal regarding documentation
Maybe once the list is going, people who are willing
to submit their packages to such scrutiny and critique
could join in?
Peter
-Original Message-
From: Patrick Burns pbu...@pburns.seanet.com
Sent: Jun 14, 2009 12:30 PM
To: stephen sefick ssef...@gmail.com
Cc: r-h...@stat.math.ethz.ch, John Sorkin jsor...@grecc.umaryland.edu
Subject: Re: [R] a proposal regarding documentation
I had only envisioned the scope of the
list to be the packages that R-core are
responsible for.
Expanding to contributed packages would
expand both potential usefulness and
certain complexity exponentially.
Pat
stephen sefick wrote:
I have a package StreamMetabolism. I believe that documentation is
the toughest part. I find it to be straight foward, but then I wrote
the package. Lets try one? I don't m
ind helping.
Stephen Sefick
On Sun, Jun 14, 2009 at 7:23 AM, John Sorkinjsor...@grecc.umaryland.edu
wrote:
Issues
(1) Will people use the new listserver?
(2) Will developers respond to postings
Question
(1) Are there any guidelines for creating documentation? If not should they
be developed? It seems to me that every help page should include (a)
examples, and when approprate (b) a reference to an article relevant to the
help page's content.
Thoughts
The pages should explain a concept using as little jargon as possible and
should try not to be circular, i.e. do not define something using the
defined term in its own definition.
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)
Peter Flom peterflomconsult...@mindspring.com 6/14/2009 7:05 AM
Patrick Burns pbu...@pburns.seanet.com wrote
Proposal
That a new mailing list be established
that pertains exclusively to R documentation.
The purpose of the list would be to discuss
weak sections of the documentation and
establish fixes for those weak spots.
Pro
If it works, there would be better documentation.
It would be an excellent opportunity for newish
and/or less technical people to contribute to R.
In some respects such people would be much more
valuable to the process than very experienced
people.
It could take some pressure off of R-core.
Con
It needs at least one person (and probably more)
with a strong commitment to make it work. The
proposed changes would need to be installed, and
activity would need to be encouraged and focused.
Background
A couple weeks ago I sent a message suggesting that
people with issues about the documentation should
send a message about it. I left the exact details
vague for two reasons:
1) I wasn't sure what the preferred details are.
2) I realized that if people actually followed
the suggestion and sent messages about documentation,
R-core would be overwhelmed and not especially happy.
I think this is an excellent idea.
I would be glad to be one of the newish or less technical people.
Peter
Peter L. Flom, PhD
Statistical Consultant
www DOT peterflomconsulting DOT com
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Peter L. Flom, PhD
Statistical Consultant
www DOT peterflomconsulting DOT com
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[R] learning about panel functions in lattice
Hi All,
I am trying to understand panel functions. Let's use this example.
library(lattice)
time-c(rep(1:10,5))
y -time+rnorm(50,5,2)
group-c(rep('A',30),rep('B',20))
subject-c(rep('a',10),rep('b',10),rep('c',10),rep('d',10),rep('e',10))
myData -data.frame(subject,group,time,y)
head(myData)
Plot 1
xyplot(y ~ time | group, data = myData, groups = subject,
panel = panel.superpose,
panel.groups = function(...)
panel.loess(...)
)
Plot 2
xyplot(y ~ time | group, data = myData, groups = subject,
panel = function(...) {
panel = panel.superpose(...)
panel.groups = function(...)
panel.loess(...)
})
Why does Plot 2 not produce the loess curves? Why are points not
plotted on Plot 1?
Plot 3
xyplot(y ~ time | group, data = myData, groups = subject,
panel = function(...) {
panel.superpose(...)
panel.superpose(panel.groups = panel.loess, ...)
})
What is the effect of writing panel.superpose twice? What is it about
this call that makes the data points
appear on the graph?
Thanks,
Juliet
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Re: [R] learning about panel functions in lattice
2009/6/14 Juliet Hannah juliet.han...@gmail.com:
Hi All,
I am trying to understand panel functions. Let's use this example.
library(lattice)
time-c(rep(1:10,5))
y -time+rnorm(50,5,2)
group-c(rep('A',30),rep('B',20))
subject-c(rep('a',10),rep('b',10),rep('c',10),rep('d',10),rep('e',10))
myData -data.frame(subject,group,time,y)
head(myData)
Plot 1
xyplot(y ~ time | group, data = myData, groups = subject,
panel = panel.superpose,
panel.groups = function(...)
panel.loess(...)
)
Plot 2
xyplot(y ~ time | group, data = myData, groups = subject,
panel = function(...) {
panel = panel.superpose(...)
panel.groups = function(...)
panel.loess(...)
})
Why does Plot 2 not produce the loess curves? Why are points not
plotted on Plot 1?
The above creates a function called panel.groups within the anonymous
panel function but that is meaningless. In particular, its not even
accessible outside of the anonymous function and is never called
within the anonymous function so its never called at all.
Plot 3
xyplot(y ~ time | group, data = myData, groups = subject,
panel = function(...) {
panel.superpose(...)
panel.superpose(panel.groups = panel.loess, ...)
})
What is the effect of writing panel.superpose twice? What is it about
this call that makes the data points
appear on the graph?
The first superpose draws the points and the second draws the
loess curve. Try instrumenting it with browser() calls (resulting
in a pause) and also adding a col attribute and it will become clearer:
xyplot(y ~ time | group, data = myData, groups = subject,
panel = function(...) {
browser()
panel.superpose(..., col = purple)
browser()
panel.superpose(panel.groups = panel.loess, col = green, ...)
browser()
}
)
Thanks,
Juliet
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[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.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] if + is.na
Grześ wrote:
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
Use ifelse instead of if
--
View this message in context:
http://www.nabble.com/if-%2B-is.na-tp24025136p24025414.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] if + is.na
On 15/06/2009, at 7:48 AM, Grześ wrote:
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
?ifelse
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Re: [R] External signal in ODE written in C (using deSolve and approx1?)
Glenn Woodart wrote: Dear Thomas Thank you for your excellent help. I agree method 3 would be the best one, and this is the one I have been trying to get working (like you described). So far my skills with pointers, what is returned etc in pure C code is limited, so my attempts have failed so far. That's why I use R for most cases, even if it is somewhat slower than C -- is simply much more comfortable. If it is possible to get a working example in the vignette it would be great. Yes, this will surely come ..., but for the moment, see the ad-hoc example on: http://www.simecol.de/models/c_ode_signal.zip You will see that in addition to linear interpolation one needs a method to transfer the data of the signal to the C side. There are several possibilities and I'm not yet sure which one will eventually find its way to the package. Note also that the code is a quick hack without any warranty. Again, thank you for your brilliant work on implementing solvers for differential equations in R. Best wishes Glenn Thanks for giving feedback. Thomas Petzoldt __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-help] how to install own R withour root?
Or you could do what I suggested below. I had assumed you had a
~/bin/ directory and knew how to make a symbolic link. If that
assumption is incorrect, let us know and we can tell you how to do
it.
As Bill suggests, removing the present old version would be
preferable, but I can understand you could be in a position of having
to depend on an unreachable administrator, so that might not be
possible.
best
Patrick
On Sat, 13-Jun-2009 at 03:43PM +1000, bill.venab...@csiro.au wrote:
| You need to adjust your PATH environment variable so that the
/path_of_my_home/R/bin comes ahead of the system R/bin directory. (Or you can
simply remove the system R/bin and substitute your own R/bin.
|
| W.
|
| From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf
Of Daofeng Li [lid...@gmail.com]
| Sent: 13 June 2009 15:28
| To: Paul Hiemstra
| Cc: r-help@r-project.org
| Subject: Re: [R] [R-help] how to install own R withour root?
|
| Hi,
|
| i had intstalled R in my home directory
| and i can run the new install R from /path_of_my_home/R/bin/R
| but when i type R, it runs the system installed older R 2.4
| can i just type an R command and it runs my new installed R?
|
| Thanks!
|
| On Tue, Jun 9, 2009 at 4:00 PM, Paul Hiemstra p.hiems...@geo.uu.nl wrote:
|
| Hi,
|
| In addition. You can also install everything just in your home drive. Using
| the configure script you can change the installation path of all R related
| stuff:
|
| ./configure --prefix=/home/bla/progsandlibs
|
| The binaries end up in ~/progsandlibs/bin, and the libraries in
| ~/progsandlibs/bin. If you use this consistently with all the programs you
| install using ./configure and add progsandlibs to you $PATH, you can
install
| all the software in your home drive with no difference in functionality.
|
| cheers,
| Paul
|
|
| Patrick Connolly wrote:
|
| On Tue, 09-Jun-2009 at 11:50AM +0800, Daofeng Li wrote:
|
| | Dear list members,
| | | i am currently want to install Rpy2 in a linux box which has R 2.4.0
| | installed
| | RPy requries R 2.7.0 or above
| | but i have no root previlleges
| | so my question is how to install R 2.7.0 on my own directory?
|
| You might as well install R-2.9.0 while you're at it.
|
| | and replace the system installed R 2.4.0 when i input R command from
| the
| | bash Shell?
|
| You can download the R-2.9.0.tar.gz to a directory you have access to.
| I'll call it ~/Rhome/
|
| uncompress the file with tar xvzf R-2.9.0.tar.gz
| and then move to the R-2.9.0 subdirectory that will be created.
|
| In that directory, you'll find a file called INSTALL which will give
| you very simple clear directions. Don't try to make a site-wide
| installation which isn't appropriate in your case.
|
| The executable will be at ~/Rhome/R-2.9.0/bin/R
|
| Assuming you have a ~/bin directory, I find the simplest thing is to
| make a link in that directory to the executable.
|
| Now the part that might be slightly tricky. If you can't get someone
| with root access to remove the R-2.4.0 installation, it's simple
| enough to prevent it clashing with your newer version. Make the name
| of the link in ~/bin/ something slightly different from R, such as RR
| or whatever you fancy. You then start R with that name.
|
| HTH
|
|
|
|
|
|
|
| --
| 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
|
|
|
|
| --
| Daofeng Li,PhD Candidate
| China Agricultural University
|
| [[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.
|
| __
| 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.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) . Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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[R] estimate the reliability of a scale with dichotomous items
hi, How can I compute a reliability score of a scale consisting only of dichotomous items? thanks for any help! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a proposal regarding documentation
John Sorkin wrote: Perhaps help pages should have links to relevant portions of the WIKI. 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) spencerg spencer.gra...@prodsyse.com 6/14/2009 1:53 PM The documentation for the nlme package was improved a few years ago by an informal process of this nature. When I first started following r-help, I answered many questions suggesting in part the the person read some portion of Pinheiro and Bates (2000). At that time, none of the help pages mentioned Pinheiro and Bates, because they were completed before the book and had not been updated. Eventually, I volunteered to add that to some of the help pages. Doug agreed. In the process, I also expanded some of the examples and modified the text in places where I thought I could make it more easily understood. One obvious way to do this would be to provide write access to the main R subversion repository. However, that likely would not be acceptable to the R-core team unless it were limited to a very few individuals they already knew and trusted, and those individuals could process suggestions from others. As mentioned, there would need to be additional ground rules. For example, an inappropriate example might cause R CMD check to fail on some platforms but not others. This could expose problems with the core code, which perhaps should be fixed but not necessarily in the time frame desired by this new documentation improvement team. For a second example, Brian Ripley once rejected a suggested change to a help page because it referred to a package outside the core R code. A less threatening alternative might be to direct this energy into improving the R Wiki. I have contributed to other Wiki projects, and I've found them to be quite useful and dynamic. The current R Wiki has not so far lived up to its potential. However, I believe that is just a matter of building a critical mass of R Wiki contributors. Many questions on R help could best be answers by first cheking and perhaps improving the R Wiki and then directing the questioner to the Wiki. I plan to do that sometime, but not yet. Hope this helps. Spencer Graves I agree. The R Wiki probably needs these steps: 1) To reorganize its general structure in order to find more easily relevant pages, 2) To rework the engine, and in particular the main page template to make it easier and more intuitive for R users, 3) ... most importantly: to move it to a faster server, so that it will be more responsive, and 4) To build a RWiki package with functions to ease access of the wiki pages (direct search in the wiki, retrieve code in R from a given wiki page, etc.). I have started something in this direction, but currently lack time to finalize it. Finally, the most important aspect is to get a group of volunteers to move and reformat nice discussions from R-Help/R-Devel/R-SIG-whatever into refined wiki pages... and with a referee mechanism to double/triple check content on the wiki. This happens erratically and certainly lacks proof-checking and feedback to the corresponding mailing list. Beside this, I am completely open to suggestions. Interested people could contact me directly. We could certainly arrange a dinner in Rennes at User!2009 to discuss evolution of the R Wiki, in particular, targeting collaborative writing of *good quality* documentation. Best, Philippe Grosjean [...] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a proposal regarding documentation
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.
Re: [R] estimate the reliability of a scale with dichotomous items
At 11:02 PM +0200 6/14/09, Martin Batholdy wrote: hi, How can I compute a reliability score of a scale consisting only of dichotomous items? RSiteSearch(cronbach's alpha) suggests the ltm, psych, psy, psycho, epicalc, packages (among others). There are a number of ways of estimating reliability, alpha is the most common (and perhaps overused). Other ways include MacDonald's omega_h and omega_t as well as the six estimates of Guttman. I tend to use the various functions found in psych, but then again, I am probably biased. Bill thanks for any help! __ 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. -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Attend ISSID/ARP:2009 http://issid.org/issid.2009/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a proposal regarding documentation
I agree that the documentation is a primary source, made now more accessible with the availability of the RSiteSearch package that allows more structures searches of the help pages in contributed packages than previously available. On the other hand, it can sometimes be difficult to get the attention and support of someone who can make necessary improvements to the help pages. Moreover, the R Wiki should be the primary place for comparing similar capabilities in different packages. For example, a function named gam appears in two different packages, with similar functionality but subtle incompatibilities. The R Wiki provides a forum for an open-ended debate about which is best for which purpose. The Wiki model has proven its worth by allowing anyone to write anything they feel moved to write (in the language of their choice). If something is disputed, there are referees to lock particular Wiki pages, after which point the dispute can continue but without burdening the casual reader with the details. The success of Wikipedia shows a context in which anarchy is almost uniformly superior to prior censorship. The current task views provide a very limited overview of contributed capabilities but the way those are currently managed make them entirely too static and unsuited to this kind of thing. I plan eventually to start contributing to the R Wiki, making comparisons of similar capabilities in different packages and inviting the package maintainers to correct or expand on anything I write. However, I have other tasks I need to complete before I can start working on that. Best Wishes, Spencer Graves Peter Flom 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.
[R] How to fix my nested conditional IF ELSE code?
Hi, I've been struggling most of the morning with an IF ELSE problem, and I wonder if someone might be able to sort me out. Here's what I need to do (dummy example, my data are more complicated): If type = A or B or C and status = a then count = 1 and status = b then count = 2 and status = c then count = 3 Else if type = D or E or F and status = a then count = 9 and status = b then count = 8 and status = c then count = 7 End Seems simple when I write it like that, but the R code is escaping me. Thanks! Mark Na [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a proposal regarding documentation
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 Flompeterflomconsult...@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.
Re: [R] How to fix my nested conditional IF ELSE code?
On 6/14/2009 6:18 PM, Mark Na wrote:
Hi,
I've been struggling most of the morning with an IF ELSE problem, and I
wonder if someone might be able to sort me out.
Here's what I need to do (dummy example, my data are more complicated):
If type = A or B or C
and status = a then count = 1
and status = b then count = 2
and status = c then count = 3
Else if type = D or E or F
and status = a then count = 9
and status = b then count = 8
and status = c then count = 7
End
Seems simple when I write it like that, but the R code is escaping me.
mydf - data.frame(type = sample(LETTERS[1:6], 40, replace=TRUE),
status = sample(letters[1:3], 40, replace=TRUE))
mydf$count - with(mydf,
ifelse(type %in% c('A','B','C') status == 'a', 1,
ifelse(type %in% c('A','B','C') status == 'b', 2,
ifelse(type %in% c('A','B','C') status == 'c', 3,
ifelse(type %in% c('D','E','F') status == 'a', 9,
ifelse(type %in% c('D','E','F') status == 'b', 8,
ifelse(type %in% c('D','E','F') status == 'c', 7,
NA)))
mydf
type status count
1 C c 3
2 F b 8
3 B b 2
4 A a 1
5 C b 2
6 D c 7
7 C a 1
8 E c 7
9 F a 9
10E b 8
11F a 9
12D a 9
13A c 3
14B b 2
15D b 8
16C c 3
17E c 7
18A c 3
19B a 1
20E a 9
21E b 8
22E a 9
23C b 2
24A b 2
25F b 8
26D a 9
27B c 3
28E b 8
29E c 7
30F b 8
31B a 1
32F c 7
33F b 8
34E c 7
35C b 2
36C a 1
37F b 8
38D c 7
39F a 9
40D b 8
Thanks!
Mark Na
[[alternative HTML version deleted]]
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Re: [R] a proposal regarding documentation
On 14-Jun-09 22:23:24, 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. That is an interesting and potentially very fruitful idea. I'd like to propose a quasi-readonly mode in which wiki users could interpolate the comments at chosen points within the original text of a help-page (but without any alteration of the original), with the interpolation clearly marked by some kind of highlighting (e.g. change of font or colour). In that way, a user reading through the original help-page on the wiki would encounter, in context and in timely fashion, comments by other users who had themselves met difficulties at that point and who (hopefully) have provided more detailed guidance and/or links to other parts of the documentation which illuminate or fill-in what was not obvious in the first place. With, preferably, the option to back up to where they were before, if they are led to some other help page. Ted. 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 Flompeterflomconsult...@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. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 14-Jun-09 Time: 23:41:39 -- XFMail -- __ 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] Leave One Out Cross Validation
Hi All, I have been trying to get this LOO-Cross Validation method to work on R for the past 3 weeks but have had no luck. I am hoping someone would kindly help me. Essentially I want to code the LOO-Cross Validation for the 'Local Constant' and 'Local Linear' constant estimators. I want to find optimal h, bandwidth. Thank you very much! -M -- View this message in context: http://www.nabble.com/Leave-One-Out-Cross-Validation-tp24025738p24025738.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.
Re: [R] a proposal regarding documentation
On Sun, Jun 14, 2009 at 6:41 PM, Ted Hardingted.hard...@manchester.ac.uk wrote: That is an interesting and potentially very fruitful idea. I'd like to propose a quasi-readonly mode in which wiki users could interpolate the comments at chosen points within the original text of a help-page (but without any alteration of the original), with the interpolation clearly marked by some kind of highlighting (e.g. change of font or colour). Potentially, many comments could disrupt the flow of the help page. I think it might be better to only have links to the comments which themselves are located below and even that might be too disruptive. Also, from an implementation viewpoint this would seem to add a significant complication particularly when updating the help pages with new versions of the help pages so I think it might be better to just follow the formats of PHP and MySQL and keep it simple. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a proposal regarding documentation
Well, suppose I wanted to suggest changes to some documentation, or write an alternate help file for some function. Where would I put it? Let's say I type, in R, ?median. Now suppose I have suggestions. If I look at http://wiki.r-project.org/rwiki/doku.php?id=idx=rdoc:base I don't see the median listed. Should I add one? OK, I do see mean listed, but the page http://wiki.r-project.org/rwiki/doku.php?id=rdoc:base:mean is blank. Should I edit it? Should it include the original documentation? My proposed changes? Or what? - Let's say I figure all that out. Now, someone else disagrees with my documentation and changes it, perhaps making it confusing (in my view). Is this a good way to proceed? 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] Comparative evaluation studies of R packages and functions. Was: Re: a proposal regarding documentation
Hi Spencer, You have brought up an important topic. I agree with you that a comparative evaluation of R packages providing similar capabilities is a worthwhile task. Your example of gam is a very good one. Let me give you a couple of other examples of comparative evaluation that I am working on: (1) optimization - John Nash and I are currently doing this for basic optimization packages. By basic optimization, I am referring to the optimization of smooth functions, with box-constarints or no constraints, (2) smoothing or non-parametric regression. I am currently comparing some smoothers for their ability to accurately estimate functions and their first 2 derivatives from discretely sampled data (in terms of mean integrated squared error). Comparative studies, if conducted rigorously and objectively by independent folks not associated with packages, are likely to be very useful to R users. The new R Journal would be a natural avenue to disseminate the results of comparative studies. I can think of some criteria for comparing packages or functions (in different packages) that are meant for essentially similar tasks (e.g. the 2 gam functions): 1. Ease of use and misuse 2. Documenation and examples 3. Transparency of coding (this would give more weight to all-R functions and packages as opposed to C/Fortran interfaces) 4. Theoretical foundation 5. Performance on simulated examples designed to highlight potential trouble spots 6. Actual performance on real problems. 7. Identification of niche areas for each package, i.e. things that no other package can do or do as well. Best, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: spencerg spencer.gra...@prodsyse.com Date: Sunday, June 14, 2009 6:08 pm Subject: Re: [R] a proposal regarding documentation To: Peter Flom peterflomconsult...@mindspring.com Cc: r-h...@stat.math.ethz.ch, Philippe Grosjean phgrosj...@sciviews.org, John Sorkin jsor...@grecc.umaryland.edu, Patrick Burns pbu...@pburns.seanet.com I agree that the documentation is a primary source, made now more accessible with the availability of the RSiteSearch package that allows more structures searches of the help pages in contributed packages than previously available. On the other hand, it can sometimes be difficult to get the attention and support of someone who can make necessary improvements to the help pages. Moreover, the R Wiki should be the primary place for comparing similar capabilities in different packages. For example, a function named gam appears in two different packages, with similar functionality but subtle incompatibilities. The R Wiki provides a forum for an open-ended debate about which is best for which purpose. The Wiki model has proven its worth by allowing anyone to write anything they feel moved to write (in the language of their choice). If something is disputed, there are referees to lock particular Wiki pages, after which point the dispute can continue but without burdening the casual reader with the details. The success of Wikipedia shows a context in which anarchy is almost uniformly superior to prior censorship. The current task views provide a very limited overview of contributed capabilities but the way those are currently managed make them entirely too static and unsuited to this kind of thing. I plan eventually to start contributing to the R Wiki, making comparisons of similar capabilities in different packages and inviting the package maintainers to correct or expand on anything I write. However, I have other tasks I need to complete before I can start working on that. Best Wishes, Spencer Graves Peter Flom 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 PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list PLEASE do read the posting guide 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
[R] Identifying clusters of size n
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Is there a library which is capable of identifying distinct clusters of size n from a series of XY coordinates? Failing this, I'd like to be able to to something like: Using a sliding window of size n along the x-axis I'd like to determine the distance between the center of the points in the window and the closest point outside the window. I could then use a distance cutoff to help define my clusters of size n. However, how can I calculate this distance? Cheers, Nathan - -- - Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAko1ikEACgkQ9gTv6QYzVL4sUACdGOMLYGaQ0Wkq+ywKD7k+w/kZ WkkAoKPA9RLFNc3nJOX5hR2qPJXfAZ8d =ATd3 -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to fix my nested conditional IF ELSE code?
On Jun 14, 2009, at 6:33 PM, Chuck Cleland wrote:
On 6/14/2009 6:18 PM, Mark Na wrote:
Here's what I need to do (dummy example, my data are more
complicated):
If type = A or B or C
and status = a then count = 1
and status = b then count = 2
and status = c then count = 3
Else if type = D or E or F
and status = a then count = 9
and status = b then count = 8
and status = c then count = 7
End
Seems simple when I write it like that, but the R code is escaping
me.
mydf - data.frame(type = sample(LETTERS[1:6], 40, replace=TRUE),
status = sample(letters[1:3], 40, replace=TRUE))
mydf$count - with(mydf,
ifelse(type %in% c('A','B','C') status == 'a', 1,
ifelse(type %in% c('A','B','C') status == 'b', 2,
ifelse(type %in% c('A','B','C') status == 'c', 3,
ifelse(type %in% c('D','E','F') status == 'a', 9,
ifelse(type %in% c('D','E','F') status == 'b', 8,
ifelse(type %in% c('D','E','F') status == 'c', 7,
NA)))
Or more compactly and perhaps easier to maintain since you are
approaching the nesting limits of ifelse and the OP said he had a more
complex operation to perform:
library(car)
mydf$count - with(mydf, ifelse( type %in% c('A','B','C'),
recode( status, 'a'=1; 'b'=2; 'c'=3 ,
FALSE),
ifelse( type %in% c('D','E','F') ,
recode( status, 'a'=9; 'b'=8;
'c'=7 , FALSE),
NA) ) )
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Centering graphics by default in Sweave
On Jun 14, 2009, at 2:28 PM, Frank E Harrell Jr wrote:
Is there an elegant way to get Sweave to center graphics by default?
I'd like to use \centerline{\includegraphics{}} etc. to save some
vertical space that \begin{center} ... \end{center} uses, and I'd
like to avoid centering with each fig=T=
Frank,
My comments below are based upon the presumption that you are using a
'figure' environment for your plots.
As far as I know, there is no Sweave option for this, however,
reviewing the code for the handling of the 'include' option, it looks
like (at first glance) that it might not be too difficult to add one.
The 'includegraphics' statement is output as part of the handling of
the 'include' option code. It would take more time to be sure that I
am not missing something.
However, there is an alternative, which is to define a new environment
using the \newenvironment command and have it encapsulate the normal
'figure' environment along with a \centering command. \centering will
accomplish the same thing as using \centerline, which is to save some
vertical space after the figure environment if otherwise using the
'center' environment. BTW, this extra vertical space occurs because
the 'center' environment is built on top of the 'list' environment,
which introduces different paragraph spacing.
To that end, below is some example .Rnw code for a document including
the specification of a new environment called 'centerfig', which can
then be used in the same way you would call the regular 'figure'
environment. The definition consists of two lines. The first is what
is used at the beginning of the environment and the second is used at
the end. In this case, the first line calls the figure environment
with the addition of \centering. The second line simply ends the
figure environment. Think of the two lines as macro substitutions.
I have included a copy of a PDF file that contains the result of this
code. Note that the first and third pages are essentially the same,
while the second has extra space after the figure when
\begin{center}...\end{center} is used.
This would be one way of altering the default behavior of the figure
environment, so that it is centered by default. Now just use:
\begin{centerfig}
...
\end{centerfig}
instead of:
\begin{figure}
\begin{center}
...
\end{center}
\end{figure}
HTH,
Marc Schwartz
\documentclass[10pt]{article}
\usepackage{graphicx}
\begin{document}
\setlength{\parindent}{0pt}
\setlength{\parskip}{0pt}
%% Here is the new environment called centerfig
\newenvironment{centerfig}
{\begin{figure}[htp]\centering}
{\end{figure}}
Here is some text before the figure
\begin{centerfig}
fig=TRUE=
x - seq(0, 5, 0.1)
y - x^3
par(mar = c(2, 3, 0, 0))
plot(x, y, ann = FALSE, type = l, las = 1)
@
\caption{Using ``centerfig''}
\end{centerfig}
Here is some text after the figure
\clearpage
Here is some text before the figure
\begin{figure}[htp]
\begin{center}
fig=TRUE=
x - seq(0, 5, 0.1)
y - x^3
par(mar = c(2, 3, 0, 0))
plot(x, y, ann = FALSE, type = l, las = 1)
@
\caption{Using ``figure'' with $\backslash$begin\{center\}...$
\backslash$end\{center\}}
\end{center}
\end{figure}
Here is some text after the figure
\clearpage
Here is some text before the figure
\begin{figure}[htp]
\begin{Schunk}
\begin{Sinput}
x - seq(0, 5, 0.1)
y - x^3
par(mar = c(2, 3, 0, 0))
plot(x, y, ann = FALSE, type = l, las = 1)
\end{Sinput}
\end{Schunk}
%% Use same graphic file as the first
\centerline{\includegraphics{test-001}}
\caption{Using ``figure'' with $\backslash$centerline}
\end{figure}
Here is some text after the figure
\end{document}
test.pdf
Description: Adobe PDF document
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Re: [R] How to fix my nested conditional IF ELSE code?
Note that TRUE and FALSE become 1 and 0 when used in arithmetic formulae so: result - with(DF, (type %in% c(A, B, C)) * (1 * (status == a) + 2 * (status == b) + 3 * (status == c)) + (type %in% c(D, E, F)) * (9 * (status == a) + 8 * (status == b) + 7 * (status == c))) If none of the conditions hold for row i then result[i] will be 0. On Sun, Jun 14, 2009 at 6:18 PM, Mark Namtb...@gmail.com wrote: Hi, I've been struggling most of the morning with an IF ELSE problem, and I wonder if someone might be able to sort me out. Here's what I need to do (dummy example, my data are more complicated): If type = A or B or C and status = a then count = 1 and status = b then count = 2 and status = c then count = 3 Else if type = D or E or F and status = a then count = 9 and status = b then count = 8 and status = c then count = 7 End Seems simple when I write it like that, but the R code is escaping me. Thanks! Mark Na [[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. __ 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] lack of memory for logistic regression in R?
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 6 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] FBI Homicide data?
Hi, Mario:
The following suggest to me that these data may not be available
in any contributed R package:
library(RSiteSearch)
fbi - RSiteSearch.function('FBI Homicide')
hits(fbi) # 0
hom - RSiteSearch.function('Homicide')
hits(hom) # 4
HTML(hom)
The 4 items exposed via the last line here seemed to be different
data sets from the one you described. This searched all the help pages
for contributed packages. I also searched for FBI with comparable
results. If it exists in a contributed package, it is not easy to find.
Have you tried writing to someone at the Institute for
Visualization and Perception Research at U Mass-Lowell?
Hope this helps.
Spencer
Mario Valle wrote:
Dear all,
do you know if it's available and where the FBI Homicide dataset?
It has at least the following columns: victim age, homicide age.
A scatterplot of this data is visible here:
http://www.uml.edu/gallery/main.php?g2_itemId=6016
Thanks for your help!
mario
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and provide commented, minimal, self-contained, reproducible code.
[R] books on Time series
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.
Re: [R] FBI Homicide data?
That graphic was created as part of a Ph D thesis in the mid 1990's. I
sent the OP off-list a link to that work and the FBI webpage that
describes access to such data.
--
David
On Jun 14, 2009, at 9:11 PM, spencerg wrote:
Hi, Mario:
The following suggest to me that these data may not be available
in any contributed R package:
library(RSiteSearch)
fbi - RSiteSearch.function('FBI Homicide')
hits(fbi) # 0
hom - RSiteSearch.function('Homicide')
hits(hom) # 4
HTML(hom)
The 4 items exposed via the last line here seemed to be
different data sets from the one you described. This searched all
the help pages for contributed packages. I also searched for FBI
with comparable results. If it exists in a contributed package, it
is not easy to find.
Have you tried writing to someone at the Institute for
Visualization and Perception Research at U Mass-Lowell?
Hope this helps. Spencer
Mario Valle wrote:
Dear all,
do you know if it's available and where the FBI Homicide dataset?
It has at least the following columns: victim age, homicide age.
A scatterplot of this data is visible here:
http://www.uml.edu/gallery/main.php?g2_itemId=6016
Thanks for your help!
mario
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] lack of memory for logistic regression in R?
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 6 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.
Re: [R] Identifying clusters of size n
On Sun, Jun 14, 2009 at 4:39 PM, Nathan S. Watson-Haighnathan.watson-ha...@csiro.au wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Is there a library which is capable of identifying distinct clusters of size n from a series of XY coordinates? Failing this, I'd like to be able to to something like: Using a sliding window of size n along the x-axis I'd like to determine the distance between the center of the points in the window and the closest point outside the window. I could then use a distance cutoff to help define my clusters of size n. However, how can I calculate this distance? Cheers, Nathan Here is a start, using PAM clustering: http://casoilresource.lawr.ucdavis.edu/drupal/node/340 cheers, Dylan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] if + is.na
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: gregori...@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.
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and provide commented, minimal, self-contained, reproducible code.
_
Lauren found her dream laptop. Find the PC thats right for you.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Identifying clusters of size n
On Sun, Jun 14, 2009 at 7:26 PM, Nathan S. Watson-Haighnathan.watson-ha...@csiro.au wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dylan Beaudette wrote: On Sun, Jun 14, 2009 at 4:39 PM, Nathan S. Watson-Haighnathan.watson-ha...@csiro.au wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Is there a library which is capable of identifying distinct clusters of size n from a series of XY coordinates? Failing this, I'd like to be able to to something like: Using a sliding window of size n along the x-axis I'd like to determine the distance between the center of the points in the window and the closest point outside the window. I could then use a distance cutoff to help define my clusters of size n. However, how can I calculate this distance? Cheers, Nathan Here is a start, using PAM clustering: http://casoilresource.lawr.ucdavis.edu/drupal/node/340 cheers, Dylan Hi, Thanks, that looks interesting. However I need a clustering algorithm which has the following properties: 1) The ability to define clusters of size n 2) No need to specify a priory how many clusters there will be 3) The ability to omit data from any cluster. I don't think this package can do this. Time to do some reading on the various clustering algorithms, their assumptions, and their overall behaviour. Although I am not an expert, many of the constraints you are trying to impose on the clustering will require some kind of programming / decision on your end. It may help to re-formulate the problem into some kind of raster-operation, in which case GRASS GIS might be of interest to you. I suspect for something like this I'll have to define, a priory, how tight points within a cluster should be using some measure. Hmm... In this case you may need to use a model-based / or density-based approach. See mclust and spatstat packages. (???) Cheers, Dylan Any thoughts? Nathan - -- - Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAko1sWMACgkQ9gTv6QYzVL7grwCZAQh72v33vPNJJgEFJEhfyNc3 718AnA3k7wvvLEZ4NS1enW3Xp5WhO+qJ =1gyG -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Centering graphics by default in Sweave
Thanks very much Marc for the very useful ideas.
I do hope there will be an even more concise way to do this. At present
I'm not using figure environments in Sweave as in stat reports I don't
usually need floats.
I tried re-defining \includegraphics to include \centerline but got into
infinite recursion as expected. It would be nice if LaTeX had an easy
way to \renewcommand that allowed use of the existing definition of the
command.
Frank
Marc Schwartz wrote:
On Jun 14, 2009, at 2:28 PM, Frank E Harrell Jr wrote:
Is there an elegant way to get Sweave to center graphics by default?
I'd like to use \centerline{\includegraphics{}} etc. to save some
vertical space that \begin{center} ... \end{center} uses, and I'd like
to avoid centering with each fig=T=
Frank,
My comments below are based upon the presumption that you are using a
'figure' environment for your plots.
As far as I know, there is no Sweave option for this, however, reviewing
the code for the handling of the 'include' option, it looks like (at
first glance) that it might not be too difficult to add one. The
'includegraphics' statement is output as part of the handling of the
'include' option code. It would take more time to be sure that I am not
missing something.
However, there is an alternative, which is to define a new environment
using the \newenvironment command and have it encapsulate the normal
'figure' environment along with a \centering command. \centering will
accomplish the same thing as using \centerline, which is to save some
vertical space after the figure environment if otherwise using the
'center' environment. BTW, this extra vertical space occurs because the
'center' environment is built on top of the 'list' environment, which
introduces different paragraph spacing.
To that end, below is some example .Rnw code for a document including
the specification of a new environment called 'centerfig', which can
then be used in the same way you would call the regular 'figure'
environment. The definition consists of two lines. The first is what is
used at the beginning of the environment and the second is used at the
end. In this case, the first line calls the figure environment with the
addition of \centering. The second line simply ends the figure
environment. Think of the two lines as macro substitutions.
I have included a copy of a PDF file that contains the result of this
code. Note that the first and third pages are essentially the same,
while the second has extra space after the figure when
\begin{center}...\end{center} is used.
This would be one way of altering the default behavior of the figure
environment, so that it is centered by default. Now just use:
\begin{centerfig}
...
\end{centerfig}
instead of:
\begin{figure}
\begin{center}
...
\end{center}
\end{figure}
HTH,
Marc Schwartz
\documentclass[10pt]{article}
\usepackage{graphicx}
\begin{document}
\setlength{\parindent}{0pt}
\setlength{\parskip}{0pt}
%% Here is the new environment called centerfig
\newenvironment{centerfig}
{\begin{figure}[htp]\centering}
{\end{figure}}
Here is some text before the figure
\begin{centerfig}
fig=TRUE=
x - seq(0, 5, 0.1)
y - x^3
par(mar = c(2, 3, 0, 0))
plot(x, y, ann = FALSE, type = l, las = 1)
@
\caption{Using ``centerfig''}
\end{centerfig}
Here is some text after the figure
\clearpage
Here is some text before the figure
\begin{figure}[htp]
\begin{center}
fig=TRUE=
x - seq(0, 5, 0.1)
y - x^3
par(mar = c(2, 3, 0, 0))
plot(x, y, ann = FALSE, type = l, las = 1)
@
\caption{Using ``figure'' with
$\backslash$begin\{center\}...$\backslash$end\{center\}}
\end{center}
\end{figure}
Here is some text after the figure
\clearpage
Here is some text before the figure
\begin{figure}[htp]
\begin{Schunk}
\begin{Sinput}
x - seq(0, 5, 0.1)
y - x^3
par(mar = c(2, 3, 0, 0))
plot(x, y, ann = FALSE, type = l, las = 1)
\end{Sinput}
\end{Schunk}
%% Use same graphic file as the first
\centerline{\includegraphics{test-001}}
\caption{Using ``figure'' with $\backslash$centerline}
\end{figure}
Here is some text after the figure
\end{document}
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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Re: [R] lack of memory for logistic regression in R?
I have to use logistic regression... On Sun, Jun 14, 2009 at 8:04 PM, Frank E Harrell Jrf.harr...@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 6 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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to fix my nested conditional IF ELSE code?
Thanks Gabor, this is quite clever and it's nice to see another way of doing it (without ifelse). Mark On Sun, Jun 14, 2009 at 6:51 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Note that TRUE and FALSE become 1 and 0 when used in arithmetic formulae so: result - with(DF, (type %in% c(A, B, C)) * (1 * (status == a) + 2 * (status == b) + 3 * (status == c)) + (type %in% c(D, E, F)) * (9 * (status == a) + 8 * (status == b) + 7 * (status == c))) If none of the conditions hold for row i then result[i] will be 0. On Sun, Jun 14, 2009 at 6:18 PM, Mark Namtb...@gmail.com wrote: Hi, I've been struggling most of the morning with an IF ELSE problem, and I wonder if someone might be able to sort me out. Here's what I need to do (dummy example, my data are more complicated): If type = A or B or C and status = a then count = 1 and status = b then count = 2 and status = c then count = 3 Else if type = D or E or F and status = a then count = 9 and status = b then count = 8 and status = c then count = 7 End Seems simple when I write it like that, but the R code is escaping me. Thanks! Mark Na [[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]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lack of memory for logistic regression in R?
Michael wrote: I have to use logistic regression... Good. That's what lrm is dedicated to. Frank On Sun, Jun 14, 2009 at 8:04 PM, Frank E Harrell Jrf.harr...@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 6 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 -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] Sweave template
Dear Group, I have made significant improvements to our Sweave template, have made the template self-contained (i.e., you can run it yourself and it will find the datasets it needs), and have included the output pdf file. This is at http://biostat.mc.vanderbilt.edu/SweaveTemplate . You will see in the pdf file the enhancements in how R code is pretty-printed, and I have added an example where some R function output is suppressed from the listing that Sweave typesets. The new template also suggests how to auto-document the computing environment at the end of the report, and how to properly reference R and add-on packages. Figures are centered (but not as nicely as Marc Schwartz' approach) and better defaults are used for axis label and tick mark label positioning. Thanks to Romain Francois for providing the trick of suppressing parts of R output (replacing it with ...) and Peter Ruckdeschel for his excellent SweaveListingUtils package. Suggestions for further improvements are welcomed. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Identifying clusters of size n
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dylan Beaudette wrote: On Sun, Jun 14, 2009 at 4:39 PM, Nathan S. Watson-Haighnathan.watson-ha...@csiro.au wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Is there a library which is capable of identifying distinct clusters of size n from a series of XY coordinates? Failing this, I'd like to be able to to something like: Using a sliding window of size n along the x-axis I'd like to determine the distance between the center of the points in the window and the closest point outside the window. I could then use a distance cutoff to help define my clusters of size n. However, how can I calculate this distance? Cheers, Nathan Here is a start, using PAM clustering: http://casoilresource.lawr.ucdavis.edu/drupal/node/340 cheers, Dylan Thanks, that looks interesting. However I need a clustering algorithm which has the following properties: 1) The ability to define clusters of size n 2) No need to specify a priory how many clusters there will be 3) The ability to omit data from any cluster. I don't think this package can do this. I suspect for something like this I'll have to define, a priory, how tight points within a cluster should be using some measure. Any thoughts? Nathan - -- - Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAko1sWMACgkQ9gTv6QYzVL7grwCZAQh72v33vPNJJgEFJEhfyNc3 718AnA3k7wvvLEZ4NS1enW3Xp5WhO+qJ =1gyG -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Identifying clusters of size n
Hey Nathan, You might like the DBSCAN algorithm. http://en.wikipedia.org/wiki/DBSCAN There's an implementation in the 'fpc' package. http://cran.r-project.org/web/packages/fpc/index.html -Mose On Sun, Jun 14, 2009 at 7:36 PM, Dylan Beaudettedylan.beaude...@gmail.com wrote: On Sun, Jun 14, 2009 at 7:26 PM, Nathan S. Watson-Haighnathan.watson-ha...@csiro.au wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dylan Beaudette wrote: On Sun, Jun 14, 2009 at 4:39 PM, Nathan S. Watson-Haighnathan.watson-ha...@csiro.au wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Is there a library which is capable of identifying distinct clusters of size n from a series of XY coordinates? Failing this, I'd like to be able to to something like: Using a sliding window of size n along the x-axis I'd like to determine the distance between the center of the points in the window and the closest point outside the window. I could then use a distance cutoff to help define my clusters of size n. However, how can I calculate this distance? Cheers, Nathan Here is a start, using PAM clustering: http://casoilresource.lawr.ucdavis.edu/drupal/node/340 cheers, Dylan Hi, Thanks, that looks interesting. However I need a clustering algorithm which has the following properties: 1) The ability to define clusters of size n 2) No need to specify a priory how many clusters there will be 3) The ability to omit data from any cluster. I don't think this package can do this. Time to do some reading on the various clustering algorithms, their assumptions, and their overall behaviour. Although I am not an expert, many of the constraints you are trying to impose on the clustering will require some kind of programming / decision on your end. It may help to re-formulate the problem into some kind of raster-operation, in which case GRASS GIS might be of interest to you. I suspect for something like this I'll have to define, a priory, how tight points within a cluster should be using some measure. Hmm... In this case you may need to use a model-based / or density-based approach. See mclust and spatstat packages. (???) Cheers, Dylan Any thoughts? Nathan - -- - Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAko1sWMACgkQ9gTv6QYzVL7grwCZAQh72v33vPNJJgEFJEhfyNc3 718AnA3k7wvvLEZ4NS1enW3Xp5WhO+qJ =1gyG -END PGP SIGNATURE- __ 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.
