Re: [R] new book on (Perl and) R for computational biology
It looks like the correct link is: http://www.crcpress.com/product/isbn/9781420069730 On Fri, May 8, 2009 at 6:49 PM, Gabriel Valiente valie...@lsi.upc.edu wrote: There is a new book on (Perl and) R for computational biology, G. Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R. Taylor Francis/CRC Press (2009) http://www.crcpress.com/product/isbn/9781420063677 I hope it will be of much use to R developers and users. Gabriel __ 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] clear screen?
I'm not sure how to put it in a function (or if this helps), but
Ctrl+L will clear the R Console in Windows.
Cheers,
Dan Viar
On Sun, May 3, 2009 at 6:58 PM, Charles Annis, P.E.
charles.an...@statisticalengineering.com wrote:
Thank you Gabor. I'm sorry I forgot whom to acknowledge as the author.
My (limited) understanding is that rcom with rscproxy essentially give the R
session the ability to look like a server, and that this scares some who are
concerned with security issues. I don't want any more capability than
necessary and thus wanted something less potent to clear the console.
Thanks for the insight.
Charles Annis, P.E.
charles.an...@statisticalengineering.com
phone: 561-352-9699
eFax: 614-455-3265
http://www.StatisticalEngineering.com
-Original Message-
From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com]
Sent: Sunday, May 03, 2009 7:31 PM
To: charles.an...@statisticalengineering.com
Cc: r-help@r-project.org
Subject: Re: [R] clear screen?
You got it from my post here:
http://tolstoy.newcastle.edu.au/R/help/06/02/21556.html
Don't know why rcom's dependencies are a consideration
but RDCOMClient can also handle this:
cls - function () {
require(RDCOMClient)
wsh - COMCreate(Wscript.Shell)
wsh$SendKeys(\f)
invisible(wsh)
}
cls()
On Sun, May 3, 2009 at 6:50 PM, Charles Annis, P.E.
charles.an...@statisticalengineering.com wrote:
I’ve been using this routine for several years. I’m sorry, I don’t
remember
where I got it. It works as it should, viz. it blanks the R console. But
it requires package rcom and now that requires rscproxy.
cls -
function ()
{
require(rcom)
wsh - comCreateObject(Wscript.Shell)
comInvoke(wsh, SendKeys, \f)
invisible(wsh)
}
cls()
Loading required package: rcom
Loading required package: rscproxy
This seems like overkill to me just to blank the R console, especially
since
I am trying to diminish the number of necessary packages to support my
home-brew package.
So, is there an easier way to blank the R console in Windows?
sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] splines tcltk stats graphics grDevices utils datasets
methods base
other attached packages:
[1] rcom_2.1-1 rscproxy_1.2-0 survival_2.35-3
RColorBrewer_1.0-2 RODBC_1.2-5 myhomebrew
loaded via a namespace (and not attached):
[1] tools_2.8.1
Charles Annis, P.E.
charles.an...@statisticalengineering.com
phone: 561-352-9699
eFax: 614-455-3265
http://www.StatisticalEngineering.com
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Re: [R] SAS Institute to invest upto $20 m with R Project
And a happy April Fools day to you to... On Wed, Apr 1, 2009 at 5:44 AM, Ajay ohri ohri2...@gmail.com wrote: A SAS spokesperson has confirmed to this blog that they have invested in the R –Core project to help build next generation algorithms . Details are sketchy but indications of some shift on cloud hosted SAS ,called SaaS are emerging.Also includes some details on Jim Davis ,SVP SAS marketing's statement on BI and Anne Milley having a new assignment within SAS Institute. Read more here - http://www.decisionstats.com/2009/04/sas-institute-invests-in-r-project/ __ 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] Programming objects in R
The third chapter of the book R Programming for Bioinformatics by Robert Gentleman is on object-oriented programming in R. Dan Viar Chesapeake, VA On Tue, Mar 31, 2009 at 6:15 AM, Patrick Burns pbu...@pburns.seanet.com wrote: I think that 'Software for Data Analysis' by John Chambers should certainly be on the reading list. 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) Tom Backer Johnsen wrote: I am planning a project where an object-oriented approach would be appropriate, and for a number of reasons I would prefer using either Python or R. My problem at the moment is to find out how to do OO programming in R. Are there any introductory texts anywhere ? Tom __ 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] permutations in R
Try this:
# Taken from combinations(gtools)
# library(gregmisc)
# Function permutations
fn_perm_list -
+ function (n, r, v = 1:n)
+ {
+if (r == 1)
+ matrix(v, n, 1)
+else if (n == 1)
+ matrix(v, 1, r)
+else {
+ X - NULL
+ for (i in 1:n) X - rbind(X, cbind(v[i], fn_perm_list(n -
+1, r - 1, v[-i])))
+X
+}
+ }
fn_perm_list(3,3)
[,1] [,2] [,3]
[1,]123
[2,]132
[3,]213
[4,]231
[5,]312
[6,]321
Note that the you can use library gregmisc without using this
function, but I thought it might be instructive for you to see how
this is done.
Here's how you would normally do this:
library(gregmisc)
permutations(3,3)
[,1] [,2] [,3]
[1,]123
[2,]132
[3,]213
[4,]231
[5,]312
[6,]321
Cheers,
Dan Viar
On Fri, Mar 13, 2009 at 8:06 PM, onyourmark william...@gmail.com wrote:
Hi. Does anyone know of a function which will take as input a number n (or a
let of n letters) and will give out, one at a time, the permutations of n
(or of those n letters) as a vector?
So that I can use the permutations one at a time. And such that it will
exhaust all the permutations with no repeats.
For example if n is 3, I would want a function which I could use in a loop
and the first time I use it in the loop it may give the vector
123
and then the next time in the loop it may give
132
and so on so that after 6 iterations through the loop I would get all 6
permutations of 123.
Thank you.
--
View this message in context:
http://www.nabble.com/permutations-in-R-tp22507989p22507989.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] R editor that will work with Rcmdr
Thanks for posting this. I've never used Eclipse before but this document inspired me to give it a try. Unfortunately, it's a little out of date, but I think that I finally got it to work. In case anyone else would like to try this, I put a PDF of my notes online at: http://www.gofsharp.com/R/Setting_up_Eclipse_with_R.pdf Thanks again, Dan Viar Chesapeake, VA On Fri, Mar 6, 2009 at 11:43 AM, Ledon Wong, Alain (Portfolio Analytics) alain_ledonw...@ml.com wrote: Hi, I also use R under Eclipse/StatET. I found the following doc really useful: http://www.splusbook.com/Rintro/R_Eclipse_StatET.pdf Regards Alain 212-449-4894 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of John Fox Sent: Friday, March 06, 2009 10:31 AM To: 'Michael Bibo' Cc: r-h...@stat.math.ethz.ch Subject: Re: [R] R editor that will work with Rcmdr Dear Michael, For what it's worth, I develop the Rcmdr under Eclipse, and it works fine with Eclipse -- both under Windows and under Mac OS X. Of the IDEs that I've used with R, I'm most impressed with Eclipse/StatET, but configuration is non-trivial and documentation is sparse. I have a little experience with the Rcmdr under Emacs (as opposed to XEmacs) on Windows, and that too seems to work. Regards, John -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Bibo Sent: March-06-09 5:20 AM To: r-h...@stat.math.ethz.ch Subject: Re: [R] R editor that will work with Rcmdr John Sorkin jsorkin at grecc.umaryland.edu writes: R 2.8.1 Windows XP Fedora Linux. I would like a suggestion for an editor that will help format my R code that can be used with Rcmdr. Is there anything I need to know about running or installing an editor when using Rcmdr? I run R on both Windows and Linux (Fedora). Thank you, John Hi John, From my experience, while (X)Emacs + ESS or JGR work with Rcmdr under Linux, there can be problems using either of these in conjunction with Rcmdr under Windows. From John Fox's own 'An Introduction to ESS + XEmacs for Windows Users of R': The Rcmdr package does not run reliably under XEmacs/ESS for Windows. On Windows XP at least, this still seems to be the case - for me it always ends up crashing R. Under Windows, Tinn-R and Notepad++ with NppToR (http://sourceforge.net/projects/npptor/) work fine alongside Rcmdr, but both of them are Windows only. Other IDEs such as Eclipse I haven't tested. Hope this is helpful, Michael Bibo Queensland Health __ 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. -- This message w/attachments (message) may be privileged, confidential or proprietary, and if you are not an intended recipient, please notify the sender, do not use or share it and delete it. Unless specifically indicated, this message is not an offer to sell or a solicitation of any investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Merrill Lynch. Subject to applicable law, Merrill Lynch may monitor, review and retain e-communications (EC) traveling through its networks/systems. The laws of the country of each sender/recipient may impact the handling of EC, and EC may be archived, supervised and produced in countries other than the country in which you are located. This message cannot be guaranteed to be secure or error-free. References to Merrill Lynch are references to any company in the Merrill Lynch Co., Inc. group of companies, which are wholly-owned by Bank of America Corporation. Secu! rities and Insurance Products: * Are Not FDIC Insured * Are Not Bank Guaranteed * May Lose Value * Are Not a Bank Deposit * Are Not a Condition to Any Banking Service or Activity * Are Not Insured by Any Federal Government Agency. Attachments that are part of this E-communication may have additional important disclosures and disclaimers, which you should read. This message is subject to terms available at the following link: http://www.ml.com/e-communications_terms/. By messaging with Merrill Lynch you consent to the foregoing. -- __ R-help@r-project.org mailing
Re: [R] matrix transpose
Here's one way that seems to work:
a - matrix(1:30,5,6)
# Create a target for the transpose
b - matrix(1:(nrow(a)*ncol(a)),ncol(a),nrow(a))
# populate b with the transpose of a
for (i in 1:ncol(a)) { b[i,1:(nrow(a))] - a[1:(nrow(a)),i]}
# Check: Did it work?
all.equal(b,t(a))
I'm sure there's a more R-like way of doing this...
Cheers,
Dan Viar
Chesapeake, VA
On Sun, Feb 15, 2009 at 3:05 PM, Rolf Turner r.tur...@auckland.ac.nz wrote:
On 16/02/2009, at 8:36 AM, Roger wrote:
This is supposed to be an easy operation, but R 2.8.1 on Mac OS X gives me
a
lot trouble. the t() function simply does not work properly. What I mean
is
it works sometimes but does not work at the most of the time, even with
the
same matrix.
this is an example taken from R help
a - matrix(1:30, 5,6)
t(a)
Error in t(a) : unused argument(s) (1:30)
It just gives this error. If I restart my Mac (Yeah, have to restart the
OS), then there are chances t() works, but sometimes it still does not
work.
Can anyone give me another way to compute the transpose in R?
No. That's the only way. :-)
(1) I have no problem doing your example (on Mac OS X).
(2) The error is weird in that you passed the argument ``1:30'' to matrix()
not to t(). Something is corrupted in your system. What happens when
you just type ``a'' (rather than t(a)) after creating a? What happens
when you type ``t'' (no parentheses) and ``matrix'' (no parentheses)?
(3) Possibly you have a workspace that is corrupted in some way. Try
starting
R with the --no-restore-data flag and see what happens. Or move .RData
to (say) ``save.RData'' before you start R, and see what happens.
(4) Good luck!
cheers,
Rolf Turner
##
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Re: [R] How do I get my IT department to bless R?
Many thanks to everyone that posted replies to this thread. I used some of the ideas from this thread and other sources to put together a case for R and I just received formal approval from our IT department today. In case this can be useful to anyone in the future, here's a summary of what was submitted (by the way, I love the slides found at http://www.matthewckeller.com/Lecture1.ppt, the Harry Potter stuff is brilliant): Thanks again to everyone! Dan Viar Chesapeake, VA - (head of IT name removed), Based on our conversation yesterday, below is some documentation that might be useful in trying to evaluate the risk that R might pose. I also contacted one of the company's that is trying to be a Red Hat for R and his response is included below. The salient points: · R is the de-facto standard for statistical computing and (for example) appears in peer reviewed journals of Statistics · R is a quality open-source product, not some small piece of freeware developed by an individual oFor example there are currently over 19 individuals responsible for the maintaining the source (see: http://www.r-project.org/contributors.html). These individuals are arguably some of the most talented in the field of Statistical Computing. · R is licensed under the GPL (e.g. see http://www.groklaw.net/article.php?story=2008081313212422) · R requires no more support from IT than a similar stat package (e.g. SAS). In other words, we may want to put R on our desktops (it doesn't write to the registry) or have it installed on a server like Bugsy but R would not generate calls to the help desk (unlike something like Excel). · Anecdotal evidence suggest that the technical support offered by the R community (through forums, email lists, etc…) is comparable if not better than that provided by commercial products. For instance, we have been evaluating various commercial packages (SAS, SPSS, S-Plus) and so far have had better responses to getting technical questions answers on the R-help list than through the help desks of company's trying to sell us their software. As another example, last night I posted How do I get my IT department to 'bless' R and so far I have received 12 replies. · R benefits from external innovation that makes it able to have quick reaction time to new statistical ideas. It is not uncommon for a cutting edge statistical technique to appear first in R and then make its way into a commercial package. R was recently featured in the NY Times: http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html According to the article Companies as diverse as Google, Pfizer, Merck, Bank of America, the InterContinental Hotels Group and Shell use it. I recently came across the following links that show that some commercial products like SAS and SPSS are providing functionality so that their programs can call R (as a selling point). Here's a link to some SAS marketing: http://support.sas.com/rnd/app/studio/Rinterface2.html From that site: R is a leading language for developing new statistical methods, said Bob Rodriguez, Senior Director of Statistical Development at SAS. Our new PhD developers learned R in their graduate programs and are quite versed in it. It's open source software, and many add-on packages for R have emerged, providing statisticians with convenient access to new research. Many new statistical methods are first programmed in R. While SAS is committed to providing the new statistical methodologies that the marketplace demands and will deliver new work more quickly with a recent decoupling of the analytical product releases from Base SAS, a commercial software vendor can only put out new work so fast. And never as fast as a professor and a grad student writing an academic implementation of brand-new methodology. This sounds like a pretty strong endorsement for R, from one of its commercial competitors. I also found the following link which is a Power Point presentation explaining why we would be interested in R (nice if you like Harry Potter). It does a good job of show casing the differences between SAS, SPSS, and R. http://www.matthewckeller.com/Lecture1.ppt Let me know if there is something formally that I need to do (forms to fill out, process, etc…). Thanks, Dan R: Regulatory Compliance and Validation Issues A Guidance Document for the Use of R in Regulated Clinical Trial Environments http://www.r-project.org/doc/R-FDA.pdf R installation and administration manual http://cran.r-project.org/doc/manuals/R-admin.pdf http://www.r-project.org/ http://www.revolution-computing.com/ From Colin Magee [co...@revolution-computing.com]: Hi Dan - Well, we'd love to talk to your Head of IT/ Manager about this.
[R] How do I get my IT department to bless R?
I currently use R at work under the radar, but there's a chance I could loose that access. I'd like to get our company to feel comfortable with open source and R in particular. Does anyone have any experience with their company's IT department and management that they would be willing to share? How does one get an all Microsoft shop on board with allowing users to user R? I know about the recent NY Times article and recent news. I'm afraid I may need some case studies or examples of what other companies have done. Any help would be greatly appreciated. Thanks Dan Viar Chesapeake, VA __ 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] Stat textbook recommendations?
You might want to check out the following: http://www.stochas.org/ http://www1.appstate.edu/~arnholta/PASWR/index.htm http://turtle.gis.umn.edu/pmwiki/pmwiki.php/StatisticsandDatawithR/HomePage http://www.janehorgan.com/ I own all of these books and like them. The book by Dr. Jan Horgan: Probability with R: An Introduction with Computer Science Applications is nice in that it's quick and right to the point. Don't let the title fool you, there's plenty of information applicable to all fields. The book by Dr. Kenneth Baclawski: Introduction to Probability with R is has more theory than the previous book and also has lots of worked problems. The other two books are general prob/stat books, I find they're both extremely well written with the Arnholt book with a little more theory. All of these books start from first principles (no required stat background, just some math) but I suspect that all of these may be a good next step to bridge the gaps that you mention. In addition, I think that owners of PASWR and SADWR may be able to get a solution manual from the author (if you're working on your own and not taking a class). Cheers, Dan Viar Chesapeake, VA On Fri, Jan 23, 2009 at 11:57 AM, Monte Milanuk memila...@gmail.com wrote: Hello, I'm looking for a textbook that can explain some of the math behind the intro-to-intermediate stuff like ANOVA, multiple regression, non- parametric tests, etc. A little background: I took an intro stats course last year and would like to further my education. Being as that was the highest (and only) stats class the local community college offers, it looks like I'm on my own from here. I've been working through some of the online 'stats with R' tutorials as well as Dalgaard's ISWR. Where I'm running into problems is the transition from Bluman's 'A Brief Introduction to Elementary Statistics' (covers up through paired t- tests, chi-squared/goodness-of-fit, simple linear regression correlation, and just barely mentions ANOVA) with a TI-83+, to even books like ISWR... when they start getting into the things like one and two-way ANOVA, multiple regression, model selection, survival, etc. I start feeling like I have one hand tied behind my back - I just don't have enough theoretical exposure to really understand what techniques I would use when, relative to my own projects outside the book. Several of the 'intro to stats using R' books and pdf tutorials mention that they are not really meant as a standalone statistics text book, but in addition to a traditional stats textbook (Verzani mentions Kitchen's book specifically). So I guess what I'm looking for is any other recommendations on intro or intermediate textbooks that deal primarily with the math/theory behind the processes. If they were oriented towards R that's be great, but otherwise I guess I'd be most interested in something relatively platform-agnostic - I've seen some books that were slanted heavily towards a particular software package (Minitab) that I cannot afford or justify for personal use. TIA, Monte [[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.
