Re: [R] Three most useful R package
On Wed, 3 Mar 2010 11:52:48 -0700 Greg Snow greg.s...@imail.org wrote: I also want a package that when people misuse certain functions/techniques it will cause a small door on the side of their monitor/computer to open and a mechanical hand will come out and slap them upside the head. But that package will not be useful until the hardware support is available. Such a package but without the hardware support would certainly be useful. (For LaTeX we have the 'nag' package, with a similar functionality.) -- Karl Ove Hufthammer __ 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] Newb question re. read.table...
On Thu, 4 Mar 2010 11:34:49 +1300 Rolf Turner r.tur...@auckland.ac.nz wrote: There are various ways to access components of a data frame: * plot(con$rel,con$len) * plot(con[[rel]],con[[len]]) * plot(con[,rel],con[,len]) * with(con, plot(rel,len)) And: plot(len~rel, data=con) -- Karl Ove Hufthammer __ 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] Three most useful R package
On Wed, 3 Mar 2010 11:52:48 -0700 Greg Snow greg.s...@imail.org wrote: I also want a package that when people misuse certain functions/techniques it will cause a small door on the side of their monitor/computer to open and a mechanical hand will come out and slap them upside the head. But that package will not be useful until the hardware support is available. Hi Greg, Had not my grandfather and a workmate, over 60 years ago, worked out a way to do something that no one else had been able to do by running a machine in a way that it was not supposed to be run, I might agree with you. Jim __ 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] two questions for R beginners
To me, as a biologist recycled to biostats, I have always worked with Excel and then SPSS and moving to R was difficult (and still is, since I am still learning). Being a self-taught person, I learn R looking for examples in Google, which many times takes me to Rwiki or other. I sometimes post questions and most of the answers were helpful, but I have found that sometimes the answers have been too short or didn´t give enough hints as to how to follow, and that has stopped me from asking again in order not to annoy experts. I have not answered too many questions from newbies but I have tried to explain as much as I could. Sometimes I find it better not to answer rather than just answering a short vague answer. Please, examples, examples, examples! I found most difficult the different data types, since I understand excel as a data frame with columns and rows, and that´s it. Then as someone has already commented, the class, mode and str functions helped a lot. But I think that to me, examples are the way to let people learn. From that, I moved to use loops, and am still nervous when people suggest ussing *apply functions, I can´t get down to use them!. I find loops more logical, and can´t see the way of moving them to *apply. Finally, I am not a Linux expert , and I cannot get round to install and organise a proper R directory and keep updated. I have once tried to use a package that needed the development R version and was only prepared for Linux R, but couldn´t keep the R-devel versions updated. Some more step-by-step would help sometimes. Thanks for a great tool! Date: Tue, 2 Mar 2010 12:44:23 -0600 From: keo.orms...@gmail.com To: landronim...@gmail.com CC: r-help@r-project.org; pbu...@pburns.seanet.com Subject: Re: [R] two questions for R beginners Liviu Andronic escribió: On Mon, Mar 1, 2010 at 11:49 PM, Liviu Andronic landronim...@gmail.com wrote: On 3/1/10, Keo Ormsby keo.orms...@gmail.com wrote: Perhaps my biggest problem was that I couldn't (and still haven't) seen *absolute beginners* documents. there was once a link posted on r-sig-teaching that would probably fit your needs, but I cannot find it now. OK, I found it. Below is an excerpt of that r-sig-teaching e-mail. Liviu On Thu, Jul 2, 2009 at 2:19 PM, Robert W. Hayden hay...@mv.mv.com wrote: I think such a website would be a real asset. It would be most useful if it either were restricted to intro. stats. OR organized so that materials for real beginners were easy to extract from all the materials for programmers and Ph.D. statisticians. As a relative beginner myself, I find the usual resources useless. In self defense, I created materials for my own beginning students: http://courses.statistics.com/software/R/Rhome.htm Hi Liviu, This is indeed the best site for introduction I have seen. Although it still assumes some things that at first might seem unintuitive to the absolute beginner I talk about. For instance, in the first page, it shows that you can do sqrt(x), where x can be a vector, and return a vector of the square roots of each number. Although this is high school matrix algebra, most users expect that the input to square root function to be a single number, not a matrix, as in Excel or a calculator. Other concepts that are not explicitly introduced are R workspace, the use of arguments in functions (with or without the =), etc. Others are things like diff(range(rainfall)) , where you have the output of one function used as the input to another, all in the same command line. All these things seem very basic, but can be difficult if you are trying to learn on your own with no prior experience in programming. I hope I am not sounding too difficult and contrarian, I am just trying to share my experience with starting with R, and in trying to convey this learning to my colleagues and students. In the end, I did find everything I needed to learn, and now I feel at ease with R, and I believe that almost anybody that can use Excel or something like it, could learn R. Thank you for the information, Best wishes, Keo. __ 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. _ Hotmail: Free, trusted and rich email service. [[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] Subset using partial values
Thanks very much David and Henrique for your help. It has made my life much simpler. -- View this message in context: http://n4.nabble.com/Subset-using-partial-values-tp1576614p1577792.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.
[R] IMPORTANT! How work constrOptim? Why error in this routine???
I have to calculate the value of a set of parameter that minimize a function
(scarti) with constrains. I know that scarti is
right.
Then, why I have error??? I don't understand!!! Help, thanks, it's very
important!!!
This is the routine:
-
#Stima su tassi swap del modello CIR
swap=c(1.311,1.878,2.248,2.556,2.81,3.031,3.216,3.3525,3.491,3.583,3.786,3.963,4.062,4.022,3.944)
scadswap=c(1,2,3,4,5,6,7,8,9,10,12,15,20,25,30)
swapint=approx(scadswap,swap,xout=1:30,method=linear)$y
flussi=mat.or.vec(nr=30,nc=30)
for (k in 1:30){
flussi[k,]=c(rep(swapint[k],k-1),100+swapint[k],rep(0,30-k))
}
A=rbind(flussi)
PMerc=rep(100,30)
scarti=function(r,d,fi,ni){
vs=mat.or.vec(nr=30,nc=1)
for (s in 1:30){
a=(d*exp(fi*s)/(fi*(exp(d*s)-1)+d))^(ni)
b=((exp(d*s)-1)/(fi*(exp(d*s)-1)+d))
vs[s]=a*exp(-r*b)
}
PMod=A%*%vs
return(sum((PMerc-PMod)^2))
}
parCIR=constrOptim(c(0.0088,0.3339,0.3092,1.7530),scarti,NULL,ui=rbind(c(1,0,0,0),c(0,1,-1,0),c(0,1,0,0),c(0,0,0,1)),ci=c(0,0,0,1))$par
---
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Re: [R] adonis(), design
inclusion of repeated measures of course should gain power, but here I guess one would have to restrict permutations and that's what may reduce power drastically if sample size is small, at least that's how I understood it. I have also dug out a thread where someone asked for random factors in adonis() and that's quite the same topic, I think. Gavin answered that function permuted.Index2() would serve - but still I don't know how to do it practically.. There is one of my postings in the r forge vegan forum that handles the same problem with sampling design for beta.disper() and if it turns out that in both cases the key is permuted.Index2() this thread may be redundant. Greetings, Kay -- View this message in context: http://n4.nabble.com/adonis-design-tp1568989p1577801.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] IMPORTANT! How work constrOptim? Why error in this routine???
The objective function, scarti, needs a vector as input and not 4 separate
arguments.
constrOptim will call
pp- c(0.0088,0.3339,0.3092,1.7530)
scarti(pp)
which produces the error
hth, Ingmar
On Thu, Mar 4, 2010 at 10:27 AM, barbara.r...@uniroma1.it wrote:
I have to calculate the value of a set of parameter that minimize a
function (scarti) with constrains. I know that scarti is
right.
Then, why I have error??? I don't understand!!! Help, thanks, it's very
important!!!
This is the routine:
-
#Stima su tassi swap del modello CIR
swap=c(1.311,1.878,2.248,2.556,2.81,3.031,3.216,3.3525,3.491,3.583,3.786,3.963,4.062,4.022,3.944)
scadswap=c(1,2,3,4,5,6,7,8,9,10,12,15,20,25,30)
swapint=approx(scadswap,swap,xout=1:30,method=linear)$y
flussi=mat.or.vec(nr=30,nc=30)
for (k in 1:30){
flussi[k,]=c(rep(swapint[k],k-1),100+swapint[k],rep(0,30-k))
}
A=rbind(flussi)
PMerc=rep(100,30)
scarti=function(r,d,fi,ni){
vs=mat.or.vec(nr=30,nc=1)
for (s in 1:30){
a=(d*exp(fi*s)/(fi*(exp(d*s)-1)+d))^(ni)
b=((exp(d*s)-1)/(fi*(exp(d*s)-1)+d))
vs[s]=a*exp(-r*b)
}
PMod=A%*%vs
return(sum((PMerc-PMod)^2))
}
parCIR=constrOptim(c(0.0088,0.3339,0.3092,1.7530),scarti,NULL,ui=rbind(c(1,0,0,0),c(0,1,-1,0),c(0,1,0,0),c(0,0,0,1)),ci=c(0,0,0,1))$par
---
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[R] precision issue?
Hi R Gurus, I am trying to figure out what is going on here. a - 68.08 b - a-1.55 a-b [1] 1.55 a-b == 1.55 [1] FALSE round(a-b,2) == 1.55 [1] TRUE round(a-b,15) == 1.55 [1] FALSE Why should (a - b) == 1.55 fail when in fact b has been defined to be a - 1.55? Is this a precision issue? How do i correct this? Alex _ Hotmail: Free, trusted and rich email service. [[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] running R from Notepad++ in Windows 7
gReetings Running R 2.10.1 with Notepad++ and NpptoR.exe, when I submit a script to run :- 1. On my work XP machine , it runs fine in an already-open Rgui window 2. On my home Windows 7 machine, it ignores the existing Rgui window and fires up a fresh one, which doesn't use the same .RData, so it fails. Anyone else hit this and, ideally, solved it ... ? cheers Bob Robert Kinley b...@lilly.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to create a SVG plot
Hi！ I want to know how to create a SVG plot with R. savePlot() can't make it . waiting for your answer. thank you . -- View this message in context: http://n4.nabble.com/How-to-create-a-SVG-plot-tp1577685p1577685.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] How to create a SVG plot
library(cairoDevice) Cairo_svg() On 04-Mar-10 8:13, Lesong Tsai wrote: Hi！ I want to know how to create a SVG plot with R. savePlot() can't make it . waiting for your answer. thank you . -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ 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] only actual variable names in all.names()
dear all, When I use all.vars(), I am interest in extracting only the variable names.. Here a simple example all.vars(as.formula(y~poly(x,k)+z)) returns [1] y x k z and I would like to obtain y x z Where is the trick? many thanks vito -- Vito M.R. Muggeo Dip.to Sc Statist e Matem `Vianelli' Università di Palermo viale delle Scienze, edificio 13 90128 Palermo - ITALY tel: 091 23895240 fax: 091 485726/485612 http://dssm.unipa.it/vmuggeo __ 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] [R-pkgs] KmL 1.1.1
‘kml’ is an implementation of k-means for longitudinal data (or trajectories). This algorithm is able to deal with missing value and provides an easy way to re roll the algorithm several times, varying the starting conditions and/or the number of clusters looked for. KmL 1.1.1 addition: - 7 imputations methods for longitudinal data - Calculus of three qualities criterion (CalinskiHarabatz, RayTuri, DaviesBouldin) - Implementation of the Frechet distance between two trajectories - Calculus of the Frechet path - Optimization of the function 'dist' for trajectories - Possibility to use three different ways to define the starting conditions - Correction of minor bugs Christophe Genolini ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] Odp: precision issue?
Hi r-help-boun...@r-project.org napsal dne 04.03.2010 10:36:43: Hi R Gurus, I am trying to figure out what is going on here. a - 68.08 b - a-1.55 a-b [1] 1.55 a-b == 1.55 [1] FALSE round(a-b,2) == 1.55 [1] TRUE round(a-b,15) == 1.55 [1] FALSE Why should (a - b) == 1.55 fail when in fact b has been defined to be a - 1. 55? Is this a precision issue? How do i correct this? In real world those definitions of b are the same but not in computer world. See FAQ 7.31 Use either rounding or all.equal. all.equal(a-b, 1.55) [1] TRUE To all, this is quite common question and it is documented in FAQs. However there is no such issue in Excel or some other spreadsheet programs, therefore maybe a confusion from novices. I wonder if there could be some type of global option which will get rid of these users mistakes or misunderstandings by setting some threshold option for equality testing by use ==. Regards Petr Alex _ Hotmail: Free, trusted and rich email service. [[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] precision issue?
Alexander Nervedi wrote: I am trying to figure out what is going on here. a - 68.08 b - a-1.55 a-b [1] 1.55 a-b == 1.55 [1] FALSE round(a-b,2) == 1.55 [1] TRUE round(a-b,15) == 1.55 [1] FALSE Why should (a - b) == 1.55 fail when in fact b has been defined to be a - 1.55? Is this a precision issue? How do i correct this? Read th R FAQ. See 7.31 Why doesn't R think these numbers are equal? Berend -- View this message in context: http://n4.nabble.com/precision-issue-tp1577815p1577903.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] Emacs for R
Thank you Uwe, Peter and David ! 2010/3/2 David Cross d.cr...@tcu.edu There exist a number of resources on the web for ESS, which one can find easily with a Google search on Emacs Speaks Statistics. Three articles that did not turn up in my search just now are: A. J. Rossini et al. Emacs Speaks Statistics ..., Unpublished, 2001, University of Washington (ross...@u.washington.edu) A. J. Rossini et al. Emacs Speaks Statistics ..., Journal of Computational and Graphical Statistics, 2004, 13(1), 247-261. R. M. Heidberger. Emacs Speaks Statistics ..., DSC 2001 Proceedings of the 2nd International Workshop on Distributed Statistical Computing, March 15-17, Vienna, Austria Cheers David Cross d.cr...@tcu.edu www.davidcross.us On Mar 1, 2010, at 10:41 AM, Gustave Lefou wrote: Dear all, From the recent discussion, I have wondered where I could find some quick step documentation on Emacs for R (especially on Windows). All I have found is that 80 pages pdf http://ess.r-project.org/ess.pdf Maybe I am asking for too much ? Best, Gustave [[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.htmlhttp://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] counting the number of ones in a vector
On Thu, 2010-03-04 at 00:03 +0100, Randall Wrong wrote: Thanks to all of you ! (Benjamin Nutter, Henrique Dallazuanna, Tobias Verbeke, Jorge Ivan Velez, David Reinke and Gavin Simpson) x - c(1, 1, 1, NA, NA, 2, 1, NA) table(x)[1] 1 4 Why do I get two numbers ? It is a printing a named vector. The 1 is the group of factor level, the 4 is the count, try: unname(table(x)[1]) and str(table(x)[1]) etc to see what is going on. HTH G Thanks, Randall 2010/2/26 Nutter, Benjamin nutt...@ccf.org But if x has any missing values: x - c(1, 1, 1, NA, NA, 2, 1, NA) sum( x == 1) [1] NA sum(x==1, na.rm=TRUE) [1] 4 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Henrique Dallazuanna Sent: Friday, February 26, 2010 9:47 AM To: Randall Wrong Cc: r-help@r-project.org Subject: Re: [R] counting the number of ones in a vector Try: sum(x == 1) On Fri, Feb 26, 2010 at 11:40 AM, Randall Wrong randall.wr...@gmail.com wrote: Dear R users, I want to count the number of ones in a vector x. That's what I did : length( x[x==1] ) Is that a good solution ? Thank you very much, Randall [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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. === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] logistic regression by group?
Hi, first, you should always provide some repeatable code for us to have a look at, that shows what you have tried so far. That being said, you can use the subset= option in glm to subdivide your data and run separate models like that, e.g. fit.1-glm(y~x1+x2, data=yourdat, family=binomial, subset=group==1) fit.2-glm(y~x1+x2, data=yourdat, family=binomial, subset=group==2) where group is your grouping variable. Which should give you that kind of stratified model. Hope this helps, Corey - Corey Sparks, PhD Assistant Professor Department of Demography and Organization Studies University of Texas at San Antonio 501 West Durango Blvd Monterey Building 2.270C San Antonio, TX 78207 210-458-3166 corey.sparks 'at' utsa.edu https://rowdyspace.utsa.edu/users/ozd504/www/index.htm -- View this message in context: http://n4.nabble.com/logistic-regression-by-group-tp1577655p1577971.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] Odp: precision issue?
On 04-Mar-10 10:50:56, Petr PIKAL wrote:
Hi
r-help-boun...@r-project.org napsal dne 04.03.2010 10:36:43:
Hi R Gurus,
I am trying to figure out what is going on here.
a - 68.08
b - a-1.55
a-b
[1] 1.55
a-b == 1.55
[1] FALSE
round(a-b,2) == 1.55
[1] TRUE
round(a-b,15) == 1.55
[1] FALSE
Why should (a - b) == 1.55 fail when in fact b has been defined
to be a - 1.55? Is this a precision issue? How do i correct this?
In real world those definitions of b are the same but not in computer
world. See FAQ 7.31
Use either rounding or all.equal.
all.equal(a-b, 1.55)
[1] TRUE
To all, this is quite common question and it is documented in FAQs.
programs, therefore maybe a confusion from novices.
I wonder if there could be some type of global option which will
get rid of these users mistakes or misunderstandings by setting
some threshold option for equality testing by use ==.
Regards
Petr
Alex
Interesting suggestion, but in my view it would probably give
rise to more problems than it would avoid!
The fundamental issue is that many inexperienced users are not
aware that once 68.08 has got inside the computer (as used by
R and other programs which do fixed-length binary arithmetic)
it is no longer 68.08 (though 1.55 is still 1.55).
Since == tests for equality of stored binary representations,
it is inevitable that it will often return FALSE when the user
would logically expect TRUE (as in Alex's query above). When
a naive users encounters this, and is led to raise a query on
the list, a successful reply will have the effect that yet one
more user has learned something. This is useful.
As the help page ?Comparison (also accessible from ?== etc.)
states:
Do not use '==' and '!=' for tests, such as in 'if' expressions,
where you must get a single 'TRUE' or 'FALSE'. Unless you are
absolutely sure that nothing unusual can happen, you should use
the 'identical' function instead.
For numerical and complex values, remember '==' and '!=' do not
allow for the finite representation of fractions, nor for rounding
error. Using 'all.equal' with 'identical' is almost always
preferable. See the examples.
It can on occasion be useful to be able to test for exact equality
of internal binary representations. Also, what is really going on
when == appears to fail can be ascertained by evaluating the
within-computer difference between allegedly equivalent expressions.
Thus, for instance:
a - 68.08
b - a-1.55
a-b == 1.55
# [1] FALSE
(a-b) - 1.55
# [1] -2.88658e-15
all.equal((a-b), 1.55)
# [1] TRUE
I think that introducing a default tolerance option to ==,
thus making it masquerade as all.equal(), would both suppress
the capability of == to test exact equality of internal
representations, and contribute to persistence of misconceptions
by naive users. At least the current situation contributes to
removing the latter.
The result of the latter could well be that a complicated
program goes astray because a deep-lying use of == gives
the equal within tolerance result rather than the not
exactly equal result, leading to some really difficult
queries to the list!
Of course, the use of all.equal((a-b), 1.55) is a lot longer
than the use of (a-b) == 1.55, and there is an understandable
argument for something as snappy as == for testing approximate
equality. But I think that subverting == is the wrong way to
go about it. Leave == alone and, according to taste, introduce
a new operator (which the user can define for himself anyway),
say %==%:
%==% - function(x,y){ all.equal(x,y) }
(a-b) %==% 1.55
# [1] TRUE
Or perhaps
%==% - function(x,y){ identical(all.equal(x,y),True) }
as in the Example in ?Comparison. Then you have a snappy shorthand,
and it operates exactly as all.equal() does and with the same
tolerance, and it won't break anything else as a result of
subverting ==.
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 04-Mar-10 Time: 12:35:08
-- XFMail --
__
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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.
[R] Rows classification problem
Dear all, I have a table like this: a - read.csv(test.csv, header = TRUE, sep = ;) a UTM pUrbpUrb_class 1 NF188520,160307 NA 2 NF188651,965649 NA 3 NF189326,009581 NA 4 NF1894 3,141484 NA 5 NF189564,296826 NA 6 NF189614,174068 NA 7 NF189740,985589 NA 8 NF189834,054325 NA 9 NF189920,657632 NA 10NF198254,712737 NA 11NF198356,016067 NA 12NF1984 5,977961 NA What I wanted to do is to obtain classified values for pUrb_class in relation to pUrb as if: pUrb 20 --- pUrb_class = 1 pUrb 20-40 --- pUrb_class = 2 pUrb 40-60 --- pUrb_class = 3 Can anyone help me? Thanks in advance, Carlos __ 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] Histogram color
In a histogram , is it possible to have different colors? Example. I generated x - rnorm(100) hist(x) I want the histogram to have different colors based on the following condition mean(x)+sd(x) with red color and mean(x) - sd(x) with red color as well. The middle one with blue color. Is it possible to do that in R? Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] End of line marker?
On Mar 3, 2010, at 2:22 PM, jonas garcia wrote: Dear R users, I am trying to read a huge file in R. For some reason, only a part of the file is read. When I further investigated, I found that in one of my non-numeric columns, there is one odd character responsible for this, which I reproduce bellow: In case you cannot see it, it looks like a right arrow, but it is not the one you get from microsoft word in menu insert symbol. I think my dat file is broken and that funny character is an EOL marker that makes R not read the rest of the file. I am sure the character is there by chance but I fear that it might be present in some other big files I have to work with as well. So, is there any clever way to remove this inconvenient character in R avoiding having to edit the file in notepad and remove it manually? Code I am using: read.csv(new3.dat, header=F) Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'new3.dat' I think you should identify the offending line by using the count.fields function and fix it with an editor. -- David I am working with R 2.10.1 in windows XP. Thanks in advance Jonas [[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. 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] Odp: precision issue?
On 04/03/2010 7:35 AM, (Ted Harding) wrote:
On 04-Mar-10 10:50:56, Petr PIKAL wrote:
Hi
r-help-boun...@r-project.org napsal dne 04.03.2010 10:36:43:
Hi R Gurus,
I am trying to figure out what is going on here.
a - 68.08
b - a-1.55
a-b
[1] 1.55
a-b == 1.55
[1] FALSE
round(a-b,2) == 1.55
[1] TRUE
round(a-b,15) == 1.55
[1] FALSE
Why should (a - b) == 1.55 fail when in fact b has been defined
to be a - 1.55? Is this a precision issue? How do i correct this?
In real world those definitions of b are the same but not in computer
world. See FAQ 7.31
Use either rounding or all.equal.
all.equal(a-b, 1.55)
[1] TRUE
To all, this is quite common question and it is documented in FAQs.
programs, therefore maybe a confusion from novices.
I wonder if there could be some type of global option which will
get rid of these users mistakes or misunderstandings by setting
some threshold option for equality testing by use ==.
Regards
Petr
Alex
Interesting suggestion, but in my view it would probably give
rise to more problems than it would avoid!
The fundamental issue is that many inexperienced users are not
aware that once 68.08 has got inside the computer (as used by
R and other programs which do fixed-length binary arithmetic)
it is no longer 68.08 (though 1.55 is still 1.55).
I think most of what you write above and below is true, but your
parenthetical remark is not. 1.55 can't be represented exactly in the
double precision floating point format used in R. It doesn't have a
terminating binary expansion, so it will be rounded to a binary
fraction. I believe you can see the binary expansion using this code:
x - 1.55
for (i in 1:70) {
cat(floor(x))
if (i == 1) cat(.)
x - 2*(x - floor(x))
}
which gives
1.10001100110011001100110011001100110011001100110011010
Notice how it becomes a repeating expansion, with 0011 repeated 12
times, but then it finishes with 010, because we've run
out of bits.
So 1.55 is actually stored as a number which is ever so slightly bigger.
Duncan Murdoch
Since == tests for equality of stored binary representations,
it is inevitable that it will often return FALSE when the user
would logically expect TRUE (as in Alex's query above). When
a naive users encounters this, and is led to raise a query on
the list, a successful reply will have the effect that yet one
more user has learned something. This is useful.
As the help page ?Comparison (also accessible from ?== etc.)
states:
Do not use '==' and '!=' for tests, such as in 'if' expressions,
where you must get a single 'TRUE' or 'FALSE'. Unless you are
absolutely sure that nothing unusual can happen, you should use
the 'identical' function instead.
For numerical and complex values, remember '==' and '!=' do not
allow for the finite representation of fractions, nor for rounding
error. Using 'all.equal' with 'identical' is almost always
preferable. See the examples.
It can on occasion be useful to be able to test for exact equality
of internal binary representations. Also, what is really going on
when == appears to fail can be ascertained by evaluating the
within-computer difference between allegedly equivalent expressions.
Thus, for instance:
a - 68.08
b - a-1.55
a-b == 1.55
# [1] FALSE
(a-b) - 1.55
# [1] -2.88658e-15
all.equal((a-b), 1.55)
# [1] TRUE
I think that introducing a default tolerance option to ==,
thus making it masquerade as all.equal(), would both suppress
the capability of == to test exact equality of internal
representations, and contribute to persistence of misconceptions
by naive users. At least the current situation contributes to
removing the latter.
The result of the latter could well be that a complicated
program goes astray because a deep-lying use of == gives
the equal within tolerance result rather than the not
exactly equal result, leading to some really difficult
queries to the list!
Of course, the use of all.equal((a-b), 1.55) is a lot longer
than the use of (a-b) == 1.55, and there is an understandable
argument for something as snappy as == for testing approximate
equality. But I think that subverting == is the wrong way to
go about it. Leave == alone and, according to taste, introduce
a new operator (which the user can define for himself anyway),
say %==%:
%==% - function(x,y){ all.equal(x,y) }
(a-b) %==% 1.55
# [1] TRUE
Or perhaps
%==% - function(x,y){ identical(all.equal(x,y),True) }
as in the Example in ?Comparison. Then you have a snappy shorthand,
and it operates exactly as all.equal() does and with the same
tolerance, and it won't break anything else as a result of
subverting ==.
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 04-Mar-10 Time: 12:35:08
--
Re: [R] Odp: precision issue?
On Mar 4, 2010, at 4:50 AM, Petr PIKAL wrote: Hi r-help-boun...@r-project.org napsal dne 04.03.2010 10:36:43: Hi R Gurus, I am trying to figure out what is going on here. a - 68.08 b - a-1.55 a-b [1] 1.55 a-b == 1.55 [1] FALSE round(a-b,2) == 1.55 [1] TRUE round(a-b,15) == 1.55 [1] FALSE Why should (a - b) == 1.55 fail when in fact b has been defined to be a - 1. 55? Is this a precision issue? How do i correct this? In real world those definitions of b are the same but not in computer world. See FAQ 7.31 Use either rounding or all.equal. all.equal(a-b, 1.55) [1] TRUE To all, this is quite common question and it is documented in FAQs. However there is no such issue in Excel or some other spreadsheet programs, therefore maybe a confusion from novices. snip Actually, there are floating point issues in Excel. Search the archives using Excel rounding and you will see discussions dating back to circa 2003 on this, which also reference the differences in OO.org's Calc and Gnumeric's handling of floats. Also: http://support.microsoft.com/default.aspx?scid=kb;[LN];214118 http://support.microsoft.com/default.aspx?scid=kb;EN-US;78113 HTH, Marc Schwartz __ 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] Odp: precision issue?
OK, I understand. Your suggestion is far better then mine. Maybe it could
be incorporated in base R and mentioned on help page for logical operators
as one of standard way for testing equality of fractional numbers.
Regards
Petr
r-help-boun...@r-project.org napsal dne 04.03.2010 13:35:11:
On 04-Mar-10 10:50:56, Petr PIKAL wrote:
Hi
r-help-boun...@r-project.org napsal dne 04.03.2010 10:36:43:
Hi R Gurus,
I am trying to figure out what is going on here.
a - 68.08
b - a-1.55
a-b
[1] 1.55
a-b == 1.55
[1] FALSE
round(a-b,2) == 1.55
[1] TRUE
round(a-b,15) == 1.55
[1] FALSE
Why should (a - b) == 1.55 fail when in fact b has been defined
to be a - 1.55? Is this a precision issue? How do i correct this?
In real world those definitions of b are the same but not in computer
world. See FAQ 7.31
Use either rounding or all.equal.
all.equal(a-b, 1.55)
[1] TRUE
To all, this is quite common question and it is documented in FAQs.
programs, therefore maybe a confusion from novices.
I wonder if there could be some type of global option which will
get rid of these users mistakes or misunderstandings by setting
some threshold option for equality testing by use ==.
Regards
Petr
Alex
Interesting suggestion, but in my view it would probably give
rise to more problems than it would avoid!
The fundamental issue is that many inexperienced users are not
aware that once 68.08 has got inside the computer (as used by
R and other programs which do fixed-length binary arithmetic)
it is no longer 68.08 (though 1.55 is still 1.55).
Since == tests for equality of stored binary representations,
it is inevitable that it will often return FALSE when the user
would logically expect TRUE (as in Alex's query above). When
a naive users encounters this, and is led to raise a query on
the list, a successful reply will have the effect that yet one
more user has learned something. This is useful.
As the help page ?Comparison (also accessible from ?== etc.)
states:
Do not use '==' and '!=' for tests, such as in 'if' expressions,
where you must get a single 'TRUE' or 'FALSE'. Unless you are
absolutely sure that nothing unusual can happen, you should use
the 'identical' function instead.
For numerical and complex values, remember '==' and '!=' do not
allow for the finite representation of fractions, nor for rounding
error. Using 'all.equal' with 'identical' is almost always
preferable. See the examples.
It can on occasion be useful to be able to test for exact equality
of internal binary representations. Also, what is really going on
when == appears to fail can be ascertained by evaluating the
within-computer difference between allegedly equivalent expressions.
Thus, for instance:
a - 68.08
b - a-1.55
a-b == 1.55
# [1] FALSE
(a-b) - 1.55
# [1] -2.88658e-15
all.equal((a-b), 1.55)
# [1] TRUE
I think that introducing a default tolerance option to ==,
thus making it masquerade as all.equal(), would both suppress
the capability of == to test exact equality of internal
representations, and contribute to persistence of misconceptions
by naive users. At least the current situation contributes to
removing the latter.
The result of the latter could well be that a complicated
program goes astray because a deep-lying use of == gives
the equal within tolerance result rather than the not
exactly equal result, leading to some really difficult
queries to the list!
Of course, the use of all.equal((a-b), 1.55) is a lot longer
than the use of (a-b) == 1.55, and there is an understandable
argument for something as snappy as == for testing approximate
equality. But I think that subverting == is the wrong way to
go about it. Leave == alone and, according to taste, introduce
a new operator (which the user can define for himself anyway),
say %==%:
%==% - function(x,y){ all.equal(x,y) }
(a-b) %==% 1.55
# [1] TRUE
Or perhaps
%==% - function(x,y){ identical(all.equal(x,y),True) }
as in the Example in ?Comparison. Then you have a snappy shorthand,
and it operates exactly as all.equal() does and with the same
tolerance, and it won't break anything else as a result of
subverting ==.
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 04-Mar-10 Time: 12:35:08
-- 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-help@r-project.org mailing list
Re: [R] only actual variable names in all.names()
Try this: all.vars(substitute(y ~ poly(x, k) + z, list(k = NA))) Or if you don't want substitute the var k: gsub(.*\\((.*),.*, \\1, rownames(attr(terms(y ~ poly(x, k) + z), 'factors'))) On Thu, Mar 4, 2010 at 6:57 AM, Vito Muggeo (UniPa) vito.mug...@unipa.it wrote: dear all, When I use all.vars(), I am interest in extracting only the variable names.. Here a simple example all.vars(as.formula(y~poly(x,k)+z)) returns [1] y x k z and I would like to obtain y x z Where is the trick? many thanks vito -- Vito M.R. Muggeo Dip.to Sc Statist e Matem `Vianelli' Università di Palermo viale delle Scienze, edificio 13 90128 Palermo - ITALY tel: 091 23895240 fax: 091 485726/485612 http://dssm.unipa.it/vmuggeo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] Type-I v/s Type-III Sum-Of-Squares in ANOVA
John Fox j...@mcmaster.ca 02/03/2010 02:19
There's also a serious question about whether one would
be interested in main effects defined as averages over the level of
the
other factor when interactions are present.
My personal take on this particular chestnut is that I often want to
ask something about the relative size of the effects. If the so-called
main effect(s) is/are very much larger than the interactions, one may
be able to make generalisations which have practical use. If the effects
are much of a size, there's nothing much to be gained by asking about
main effects.
Mind you, that's probably a crit of significance testing as the be-all
and end-all, rather than a problem with type I-III. Asking 'how big is
it?' is a step beyond 'is it there?'.
Steve E
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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.
[R] Rows classification problem
Dear all, I have a table like this: a - read.csv(test.csv, header = TRUE, sep = ;) a UTM pUrbpUrb_class 1 NF188520,160307 NA 2 NF188651,965649 NA 3 NF189326,009581 NA 4 NF1894 3,141484 NA 5 NF189564,296826 NA 6 NF189614,174068 NA 7 NF189740,985589 NA 8 NF189834,054325 NA 9 NF189920,657632 NA 10NF198254,712737 NA 11NF198356,016067 NA 12NF1984 5,977961 NA What I wanted to do is to obtain classified values for pUrb_class in relation to pUrb as if: pUrb 20 --- pUrb_class = 1 pUrb 20-40 --- pUrb_class = 2 pUrb 40-60 --- pUrb_class = 3 Can anyone help me? Thanks in advance, Carlos __ 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] Histogram color
On Mar 4, 2010, at 7:41 AM, Ashta wrote: In a histogram , is it possible to have different colors? Example. I generated x - rnorm(100) hist(x) I want the histogram to have different colors based on the following condition mean(x)+sd(x) with red color and mean(x) - sd(x) with red color as well. The middle one with blue color. bkrs - hist(x); hist(x, col= ifelse(bkrs$mids 0-1,red, ifelse(bkrs $mids 0+1, blue, black ) ) ) This has the side effect of first plotting a histogram with bars that have default fill but then gathers the values in an object bkrs that is used to assign colors based on midpoints. Following your lead, I used the default values for mean and SD, so filling them in is left as an an exercise for the poster. Is it possible to do that in R? Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rows classification problem
Try this: a$pUrb_class - cut(a$pUrb, c(-Inf, 20, 40, 60, Inf), labels = 1:4) On Thu, Mar 4, 2010 at 11:11 AM, Carlos Guerra carlosguerra@gmail.com wrote: Dear all, I have a table like this: a - read.csv(test.csv, header = TRUE, sep = ;) a UTM pUrb pUrb_class 1 NF1885 20,160307 NA 2 NF1886 51,965649 NA 3 NF1893 26,009581 NA 4 NF1894 3,141484 NA 5 NF1895 64,296826 NA 6 NF1896 14,174068 NA 7 NF1897 40,985589 NA 8 NF1898 34,054325 NA 9 NF1899 20,657632 NA 10 NF1982 54,712737 NA 11 NF1983 56,016067 NA 12 NF1984 5,977961 NA What I wanted to do is to obtain classified values for pUrb_class in relation to pUrb as if: pUrb 20 --- pUrb_class = 1 pUrb 20-40 --- pUrb_class = 2 pUrb 40-60 --- pUrb_class = 3 Can anyone help me? Thanks in advance, Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] Rows classification problem
Hi Carlos, Take a look at ?cut, ?ifelse and ?transform for some ideas. Also, the function recode in car might help. HTH, Jorge On Thu, Mar 4, 2010 at 7:35 AM, Carlos Guerra wrote: Dear all, I have a table like this: a - read.csv(test.csv, header = TRUE, sep = ;) a UTM pUrbpUrb_class 1 NF188520,160307 NA 2 NF188651,965649 NA 3 NF189326,009581 NA 4 NF1894 3,141484 NA 5 NF189564,296826 NA 6 NF189614,174068 NA 7 NF189740,985589 NA 8 NF189834,054325 NA 9 NF189920,657632 NA 10NF198254,712737 NA 11NF198356,016067 NA 12NF1984 5,977961 NA What I wanted to do is to obtain classified values for pUrb_class in relation to pUrb as if: pUrb 20 --- pUrb_class = 1 pUrb 20-40 --- pUrb_class = 2 pUrb 40-60 --- pUrb_class = 3 Can anyone help me? Thanks in advance, Carlos __ 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] nu-SVM crashes in e1071
For the records: this was a bug in e1071 (which is already fixed new version on CRAN). Best David Steve Lianoglou wrote: Hi, On Wed, Mar 3, 2010 at 4:08 AM, Häring, Tim (LWF) tim.haer...@lwf.bayern.de wrote: (...) While you're sending your bug report to David, perhaps you can try the SVM from kernlab. It relies on code from libsvm, too, but ... you never know. It can't hurt to try. Hi Steve, thanks for that hint. I tried ksvm()-function bet get an error message: model - ksvm(soil_unit~., train, type=nu-svc) Using automatic sigma estimation (sigest) for RBF or laplace kernel Error in votematrix[i, ret 0] - votematrix[i, ret 0] + 1 : NAs are not allowed in subscripted assignments But there are no NAs in my dataset. I checked it with summary(is.na(train)) All the same, it seems there might be something funky with your data? Not sure how to help debug further. If you like you send an *.rda file of your soil_unit data offline and I can try, but otherwise I guess you're on your own? What if you remove some of the columns of your matrix? Will this eventually work? -steve -- Priv.-Doz. Dr. David Meyer Department of Information Systems and Operations WU Wirtschaftsuniversität Wien Vienna University of Economics and Business Augasse 2-6, 1090 Vienna, Austria Tel: +43-1-313-36-4393 Fax: +43-1-313-36-90-4393 HP: http://ec.wu.ac.at/~meyer __ 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
Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of datadir i have to mention the character string of the directory of these .cel files. I don't know how to give the path for all these files. i set the path as given below, rna.data-exprs(justRMA(filenames=file.names, celfile.path=*D:/MONO1.CEL D:/MONO2.CEL D:/MONO3.CEL D:/MACRO1.CEL D:/MACRO2.CEL D:/MACRO3.CEL*,sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) it shows this error, Error: unexpected string constant in rna.data-exprs(justRMA(filenames=file.names, celfile.path=D:/MONO1 D:/MONO2 could u please help me in this case. Thanks in advance. with regards, S.Mahalakshmi [[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] Please help me how to make input files in Extremes Toolkit model
Dear sir/madam My name is Quan, I am a PhD student in Korea. my major is Hydrological in Water Resources Engineering. I am interested in Extremes Toolkit model and I known you from information in internet. I installed successfully this model but I didn't know how to make the type of files input for this model such as: Flood.dat; Ozone4H.dat; Flood.R; HEAT.R. (free download these files of example and show in attachment files) I want to learn the way make these files from sample files. http://www.isse.ucar.edu/extremevalues/evtk.html but i can not download those files because this link was errored. Please help me how to get this file and to make files input, if you have some sample files, please send to me to learn and make them. thank you so much for your help me and hope to see your infomation as soon as possible. Mr. Ngo Quan __ 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] cluster with mahalanobis distance
Model-based clustering, e.g. using package mclust will do what you want: it uses normal densities to calculate similarities of objects to clusters, which is a monotone transformation of Mahalanobis distance (basically what's inside the exp() of the multivariate Gaussian density). If you believe that Mahalanobis distance is the right one for your data, then believing in a multivariate Gaussian model isn't too far-fetched ... Best, Fritz On Wed, 3 Mar 2010 16:55:19 -0800 (PST), Phil Spector (PS) wrote: Albyn - That's a very important fact that I overlooked in my original response. Thanks for pointing it out. - Phil On Wed, 3 Mar 2010, Albyn Jones wrote: Note: this procedure assumes that all clusters have the same covariance matrix. albyn On Wed, Mar 03, 2010 at 01:23:37PM -0800, Phil Spector wrote: The manhattan distance and the Mahalanobis distances are quite different. One of the main differences is that a covariance matrix is necessary to calculate the Mahalanobis distance, so it's not easily accomodated by dist. There is a function in base R which does calculate the Mahalanobis distance -- mahalanobis(). So if you pass a distance matrix calculated by mahalanobis() to the clustering function, you'll get what you want. - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Wed, 3 Mar 2010, Tal Galili wrote: when you create the distance function to put into the hclust, use: dist(x, method = manhattan) Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Wed, Mar 3, 2010 at 9:14 PM, naama nw...@technion.ac.il wrote: How can I perform cluster analysis using the mahalanobis distance instead of the euclidean distance? thank you Naama Wolf -- View this message in context: http://n4.nabble.com/cluster-with-mahalanobis-distance-tp1577038p1577038.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. [[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-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] What is assign attribute?
I am sorry I still don't understand. In the example you give the 'assign' vecotr is a vector of length 6 and there are indeed 6 columns in the data frame. But the formula only has two variables namely 'Month' and 'Wind'. Where do the values if the 'assign' vector come from? I see '0 1 1 1 1 2'. What is '1' an index to? '2'? Maybe I am get confused with what the term 'factors' does to the formula. Thanks agiain for your help. Kevin Peter Dalgaard p.dalga...@biostat.ku.dk wrote: rkevinbur...@charter.net wrote: I am just curious. Every once and a while I see an attribute attached to an object called assign. What meaning does this have? For example: dist ~ speed, data=cars forms a matrix like: num [1:50, 1:2] 1 1 1 1 1 1 1 1 1 1 ... - attr(*, dimnames)=List of 2 ..$ : chr [1:50] 1 2 3 4 ... ..$ : chr [1:2] (Intercept) speed - attr(*, assign)= int [1:2] 0 1 The dimnames attribute is fairly self-explanatory. I just am not sure what the assign attribute means. It has to do with the mapping between terms of the formula and columns of the design matrix: str(model.matrix(Ozone~factor(Month)+Wind,data=airquality)) num [1:116, 1:6] 1 1 1 1 1 1 1 1 1 1 ... - attr(*, dimnames)=List of 2 ..$ : chr [1:116] 1 2 3 4 ... ..$ : chr [1:6] (Intercept) factor(Month)6 factor(Month)7 factor(Month)8 ... - attr(*, assign)= int [1:6] 0 1 1 1 1 2 - attr(*, contrasts)=List of 1 ..$ factor(Month): chr contr.treatment I.e. columns 2:5 belong to the first non-intercept term, factor(Month). (Notice that it is implicitly assumed that you have the corresponding terms() output to hand, likewise for the contrasts attribute.) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ 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] help
Dear Mahalakshmi, the simplest way to do this and to avoid your error is to open R directtly for the folder in which there are your .CEL files and then: data-ReadAffy() #read all the .CEL files in the working director data.rma-rma(data) #in order to use rma on your .CEL files hope helps 2010/3/4 mahalakshmi sivamani mahasiva1...@gmail.com: Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of datadir i have to mention the character string of the directory of these .cel files. I don't know how to give the path for all these files. i set the path as given below, rna.data-exprs(justRMA(filenames=file.names, celfile.path=*D:/MONO1.CEL D:/MONO2.CEL D:/MONO3.CEL D:/MACRO1.CEL D:/MACRO2.CEL D:/MACRO3.CEL*,sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) it shows this error, Error: unexpected string constant in rna.data-exprs(justRMA(filenames=file.names, celfile.path=D:/MONO1 D:/MONO2 could u please help me in this case. Thanks in advance. with regards, S.Mahalakshmi [[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. -- - Dr. Alberto Goldoni Bologna, Italy __ 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] filtering signals per day
ok this is simpler thank for helping guys :) - Anna Lippel -- View this message in context: http://n4.nabble.com/filtering-signals-per-day-tp1577044p1578176.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.
[R] sum of list elements
Dear list, I have some difficulty in manipulating list elements. More specifically, I am performing svm regression and have a list of lists, called pred.svm. The elements of the second list are 3D arrays. Thus I have pred.svm[[i]][[j]], with 1=i=5 and 1=j=20. I want to take the sum of the elements a specific array dimension across all j, for one i. Mathematically speaking, I want to calculate *W* as: *W = pred.svm[[i]][[1]][1,2,5] + pred.svm[[i]][[2]][1,2,5]+ pred.svm[[i]][[3]][1,2,5]+...+ pred.svm[[i]][[20]][1,2,5]* I have tried to apply the *lapply() *function but it seems that its arguments can only be vector elements of a list...Do I need to convert the array data to vector data? Any advice would be very welcome! Thanks a lot, Eleni [[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] Passing rq models to Fstats
I have seen literature on using a combination of the 'strucchange' and 'segmented' packages to find and fit piecewise linear models. I have been trying to apply the same methods to quantile regression from the quantreg package, but am having issues using a rq object where the function assumes a lm. Has anyone had this issue? -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly [[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] Type-I v/s Type-III Sum-Of-Squares in ANOVA
On Thu, Mar 4, 2010 at 9:03 AM, S Ellison s.elli...@lgc.co.uk wrote:
John Fox j...@mcmaster.ca 02/03/2010 02:19
There's also a serious question about whether one would
be interested in main effects defined as averages over the level of
the
other factor when interactions are present.
My personal take on this particular chestnut is that I often want to
ask something about the relative size of the effects. If the so-called
main effect(s) is/are very much larger than the interactions, one may
be able to make generalisations which have practical use.
Sure. But if there is an interaction, main effect generalizations are
going to be less precise than generalizations based on simple effects.
I agree that there are some situations in which it makes sense to
ignore a small but significant interaction, but I think this should be
a rare exception to the rule don't interpret main effects in the
presence of an interaction.
-Ista
If the effects
are much of a size, there's nothing much to be gained by asking about
main effects.
Mind you, that's probably a crit of significance testing as the be-all
and end-all, rather than a problem with type I-III. Asking 'how big is
it?' is a step beyond 'is it there?'.
Steve E
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Re: [R] sum of list elements
do these lists contain 3D arrays of the same dimensions? If yes, then
you could use
Reduce(+, pred.svm[[i]])[1,2,5]
otherwise a for-loop will also be clear and efficient, e.g.,
W - pred.svm[[i]][[1]][1,2,5]
for (j in 2:20) {
W - W + pred.svm[[i]][[j]][1,2,5]
}
I hope it helps.
Best,
Dimitris
On 3/4/2010 4:02 PM, Eleni Christodoulou wrote:
Dear list,
I have some difficulty in manipulating list elements. More specifically, I
am performing svm regression and have a list of lists, called pred.svm. The
elements of the second list are 3D arrays. Thus I have pred.svm[[i]][[j]],
with 1=i=5 and 1=j=20.
I want to take the sum of the elements a specific array dimension across all
j, for one i. Mathematically speaking, I want to calculate *W* as:
*W = pred.svm[[i]][[1]][1,2,5] + pred.svm[[i]][[2]][1,2,5]+
pred.svm[[i]][[3]][1,2,5]+...+ pred.svm[[i]][[20]][1,2,5]*
I have tried to apply the *lapply() *function but it seems that its
arguments can only be vector elements of a list...Do I need to convert the
array data to vector data?
Any advice would be very welcome!
Thanks a lot,
Eleni
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--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
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[R] mysqlWriteTable . error in your SQL syntax?
Hi,
Can somebody advice on weird mysqlWriteTable bug.
mysqlWriteTable(conn, 'comparison',design2, row.names = F, overwrite=T)
Error in mysqlExecStatement(conn, statement, ...) :
RS-DBI driver: (could not run statement: You have an error in your SQL syntax;
check the manual that corresponds to your MySQL server version for the right
syntax to use near 'condition text,
treatment text,
condition2 text,
conditionNum double,
impo' at line 12)
[1] FALSE
Warning message:
In mysqlWriteTable(conn, comparison, design2, row.names = F, overwrite = T) :
could not create table: aborting mysqlWriteTable
The problem seems to be in double qoutes:
syntax to use near 'condition text,
I have tracked down it to the problem with specific column in my frame
If condition clumn is exluded, it works fine
mysqlWriteTable(conn, 'comparison',design2[,-10], row.names = F, overwrite=T)
[1] TRUE
class(design2[,10])
[1] character
packageDescription('RMySQL')
Package: RMySQL
Version: 0.7-4
Date: 2009-04-07
Title: R interface to the MySQL database
Author: David A. James and Saikat DebRoy
Maintainer: Jeffrey Horner jeff.hor...@vanderbilt.edu
Description: Database interface and MySQL driver for R. This version
complies with the database interface definition as implemented
in the package DBI 0.2-2.
LazyLoad: true
Depends: R (= 2.8.0), methods, DBI (= 0.2-2), utils
License: GPL-2
URL: http://biostat.mc.vanderbilt.edu/RMySQL
Collate: S4R.R zzz.R MySQLSupport.R dbObjectId.R MySQL.R
Packaged: Tue Apr 7 15:19:44 2009; hornerj
Repository: CRAN
Date/Publication: 2009-04-14 17:26:56
Built: R 2.10.1; x86_64-unknown-linux-gnu; 2010-01-16 19:42:24 UTC;
unix
Vladimir Morozov
Sr. Computational Biologist
ALS Therapy Development Institute
215 First Street, Cambridge MA, 02142
Phone: 617-441-7242
www.als.nethttp://www.als.net/
Want to help stop ALS? Become an ALS Ambassador and take action. Learn more
online at www.als.net/ambassadorhttp://www.als.net/ambassador
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[R] ifthen() question
Hi All,
I am using a specialized aggregation function to reduce a dataset with
multiple rows per id down to 1 row per id. My function work perfect when
there are 1 id but alters the 'var.g' in undesirable ways when this
condition is not met, Therefore, I have been trying ifthen() statements to
keep the original value when length of unique id == 1 but I cannot get it to
work. e.g.:
#function to aggregate effect sizes:
aggs - function(g, n.1, n.2, cor = .50) {
n.1 - mean(n.1)
n.2 - mean(n.2)
N_ES - length(g)
corr.mat - matrix (rep(cor, N_ES^2), nrow=N_ES)
diag(corr.mat) - 1
g1g2 - cbind(g) %*% g
PSI - (8*corr.mat + g1g2*corr.mat^2)/(2*(n.1+n.2))
PSI.inv - solve(PSI)
a - rowSums(PSI.inv)/sum(PSI.inv)
var.g - 1/sum(PSI.inv)
g - sum(g*a)
out-cbind(g,var.g, n.1, n.2)
return(out)
}
# automating this procedure for all rows of df. This format works perfect
when there is 1 id per row only:
agg_g - function(id, g, n.1, n.2, cor = .50) {
st - unique(id)
out - data.frame(id=rep(NA,length(st)))
for(i in 1:length(st)) {
out$id[i] - st[i]
out$g[i] - aggs(g=g[id==st[i]], n.1= n.1[id==st[i]],
n.2 = n.2[id==st[i]], cor)[1]
out$var.g[i] - aggs(g=g[id==st[i]], n.1= n.1[id==st[i]],
n.2 = n.2[id==st[i]], cor)[2]
out$n.1[i] - round(mean(n.1[id==st[i]]),0)
out$n.2[i] - round(mean(n.2[id==st[i]]),0)
}
return(out)
}
# The attempted solution using ifthen() and minor changes to function but
it's not working properly:
agg_g - function(df,var.g, id, g, n.1, n.2, cor = .50) {
df$var.g - var.g
st - unique(id)
out - data.frame(id=rep(NA,length(st)))
for(i in 1:length(st)) {
out$id[i] - st[i]
out$g[i] - aggs(g=g[id==st[i]], n.1= n.1[id==st[i]],
n.2 = n.2[id==st[i]], cor)[1]
out$var.g[i]-ifelse(length(st[i])==1, df$var.g[id==st[i]],
aggs(g=g[id==st[i]],
n.1= n.1[id==st[i]],
n.2 = n.2[id==st[i]], cor)[2])
out$n.1[i] - round(mean(n.1[id==st[i]]),0)
out$n.2[i] - round(mean(n.2[id==st[i]]),0)
}
return(out)
}
# sample data:
id-c(1, rep(1:19))
n.1-c(10,20,13,22,28,12,12,36,19,12,36,75,33,121,37,14,40,16,14,20)
n.2 - c(11,22,10,20,25,12,12,36,19,11,34,75,33,120,37,14,40,16,10,21)
g - c(.68,.56,.23,.64,.49,-.04,1.49,1.33,.58,1.18,-.11,1.27,.26,.40,.49,
.51,.40,.34,.42,1.16)
var.g -
c(.08,.06,.03,.04,.09,.04,.009,.033,.0058,.018,.011,.027,.026,.0040,
.049,.0051,.040,.034,.0042,.016)
df-data.frame(id, n.1,n.2, g, var.g)
Any help is much appreciated,
AC
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Re: [R] Three most useful R package
Hi all, 1) I mostly use the base packages. But if I should decide for three others, it would be - plyr: I've just started to use it in some specific cases, but it seems really powerful and practical - doBy is also quite good but I use only one function from it (summaryBy). For now I have what I need, but it might prove useful later - xlsReadWrite: it's fast and good. 2) I've serach a lot recently to read/write xls files. As you can guess, I've ended up using xlsReadWrite which is really intuitive to use. The problem is that you cannot append (neither append lines on the same sheet nor append other sheets on the same files). RODBC can append sheets on a file, but it is not as flexible. Since I often want to export results from tests that are stored as lists of differing size (different number of columns AND rows), I'm still stuck with write.csv(). So I would like to have the both appending options (i.e. line + sheets) in a package as easy to use as xlsReadWrite. Basically xlsReadWritePro, but for free (am I asking too much?). Thanks for asking! Regards, Ivan On 2 March 2010 21:13, Ralf Bralf.bie...@gmail.com wrote: Hi R-fans, I would like put out a question to all R users on this list and hope it will create some feedback and discussion. 1) What are your 3 most useful R package? and 2) What R package do you still miss and why do you think it would make a useful addition? Pulling answers together for these questions will serve as a guide for new users and help people who just want to get a hint where to look first. Happy replying! Best, Ralf __ 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] Analogue to SPSS regression commands ENTER and REMOVE in R?
I am not sure if this question has been asked before - but is there a procedure in R (in lm or glm?) that is equivalent to ENTER and REMOVE regression commands in SPSS? Thanks a lot! -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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] Type-I v/s Type-III Sum-Of-Squares in ANOVA
Hello, Since I initiated this discussion some days ago, I discovered a paper that may be of interest: ANOVA for unbalanced data: Use Type II instead of Type III sums of squares by ØYVIND LANGSRUD Statistics and Computing 13: 163–167, 2003 Ravi Kulkarni -- View this message in context: http://n4.nabble.com/Type-I-v-s-Type-III-Sum-Of-Squares-in-ANOVA-tp1573657p1578273.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] sum of list elements
Thank you Dimitris!
I have 3D arrays of the same dimensions, so Reduce worked...
Best,
Eleni
On Thu, Mar 4, 2010 at 5:13 PM, Dimitris Rizopoulos
d.rizopou...@erasmusmc.nl wrote:
do these lists contain 3D arrays of the same dimensions? If yes, then you
could use
Reduce(+, pred.svm[[i]])[1,2,5]
otherwise a for-loop will also be clear and efficient, e.g.,
W - pred.svm[[i]][[1]][1,2,5]
for (j in 2:20) {
W - W + pred.svm[[i]][[j]][1,2,5]
}
I hope it helps.
Best,
Dimitris
On 3/4/2010 4:02 PM, Eleni Christodoulou wrote:
Dear list,
I have some difficulty in manipulating list elements. More specifically, I
am performing svm regression and have a list of lists, called pred.svm.
The
elements of the second list are 3D arrays. Thus I have pred.svm[[i]][[j]],
with 1=i=5 and 1=j=20.
I want to take the sum of the elements a specific array dimension across
all
j, for one i. Mathematically speaking, I want to calculate *W* as:
*W = pred.svm[[i]][[1]][1,2,5] + pred.svm[[i]][[2]][1,2,5]+
pred.svm[[i]][[3]][1,2,5]+...+ pred.svm[[i]][[20]][1,2,5]*
I have tried to apply the *lapply() *function but it seems that its
arguments can only be vector elements of a list...Do I need to convert the
array data to vector data?
Any advice would be very welcome!
Thanks a lot,
Eleni
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Dimitris Rizopoulos
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Erasmus University Medical Center
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Re: [R] mysqlWriteTable . error in your SQL syntax?
I have partialy figured out the problem condition might be some intrenal
MySQL function/variable and can't be use as column name directly.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Vladimir Morozov
Sent: Thursday, March 04, 2010 10:25 AM
To: 'r-help@r-project.org'
Subject: [R] mysqlWriteTable . error in your SQL syntax?
Hi,
Can somebody advice on weird mysqlWriteTable bug.
mysqlWriteTable(conn, 'comparison',design2, row.names = F,
overwrite=T)
Error in mysqlExecStatement(conn, statement, ...) :
RS-DBI driver: (could not run statement: You have an error in your SQL syntax;
check the manual that corresponds to your MySQL server version for the right
syntax to use near 'condition text,
treatment text,
condition2 text,
conditionNum double,
impo' at line 12)
[1] FALSE
Warning message:
In mysqlWriteTable(conn, comparison, design2, row.names = F, overwrite = T) :
could not create table: aborting mysqlWriteTable
The problem seems to be in double qoutes:
syntax to use near 'condition text,
I have tracked down it to the problem with specific column in my frame
If condition clumn is exluded, it works fine
mysqlWriteTable(conn, 'comparison',design2[,-10], row.names = F,
overwrite=T)
[1] TRUE
class(design2[,10])
[1] character
packageDescription('RMySQL')
Package: RMySQL
Version: 0.7-4
Date: 2009-04-07
Title: R interface to the MySQL database
Author: David A. James and Saikat DebRoy
Maintainer: Jeffrey Horner jeff.hor...@vanderbilt.edu
Description: Database interface and MySQL driver for R. This version
complies with the database interface definition as implemented
in the package DBI 0.2-2.
LazyLoad: true
Depends: R (= 2.8.0), methods, DBI (= 0.2-2), utils
License: GPL-2
URL: http://biostat.mc.vanderbilt.edu/RMySQL
Collate: S4R.R zzz.R MySQLSupport.R dbObjectId.R MySQL.R
Packaged: Tue Apr 7 15:19:44 2009; hornerj
Repository: CRAN
Date/Publication: 2009-04-14 17:26:56
Built: R 2.10.1; x86_64-unknown-linux-gnu; 2010-01-16 19:42:24 UTC;
unix
Vladimir Morozov
Sr. Computational Biologist
ALS Therapy Development Institute
215 First Street, Cambridge MA, 02142
Phone: 617-441-7242
www.als.nethttp://www.als.net/
Want to help stop ALS? Become an ALS Ambassador and take action. Learn more
online at www.als.net/ambassadorhttp://www.als.net/ambassador
***
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Re: [R] Three most useful R package
Hi Matthew, Sorry that I've read your email a bit too late and answered to the thread before. You're right about Crantastic, it's a really good thing, and I actually voted for the packages I really use (even though a little). It was suggested to me by a r-helper some time ago. I was also surprised to see that there are some 19 users (and it increased recently, didn't it?) of plyr (which is from the replies obviously one of the most used packages). Looks like few people vote on Crantastic and I find it sad. When I'm now looking for a package I go directly there and can find all the basic information on all packages, though sometimes the general aim of the package is not clearly stated. Of course, the real potential would be revealed only if all users vote for, comment on and write reviews on packages. Crantastic rules! Thanks for pointing it out! Ivan PS: I'm gonna write some comments on a package or 2! Le 3/3/2010 18:48, Matthew Dowle a écrit : Dieter, One way to check if a package is active, is by looking on r-forge. If you are referring to data.table you would have found it is actually very active at the moment and is far from abandoned. What you may be referring to is a warning, not an error, with v1.2 on R2.10+. That was fixed many moons ago. The r-forge version is where its at. Rather than commenting in public about a warning on a package, and making a conclusion about its abandonment, and doing this without copying the maintainer, perhaps you could have contacted the maintainer to let him know you had found a problem. That would have been a more community spirited action to take. Doing that at the time you found out would have been helpful too rather than saving it up for now. Or you can always check the svn logs yourself, as the r-forge guys even made that trivial to do. All, Can we please now stop this thread ? The crantastic people worked hard to provide a better solution. If the community refuses to use crantastic, thats up to the community, but to start now filling up r-help with votes on packages when so much effort was put in to a much much better solution ages ago? Its as quick to put your votes into crantastic as it is to write to r-help. What your problem, folks, with crantastic? The second reply mentioned crantastic but you all chose to ignore it, it seems. If you want to vote, use crantastic. If you don't want to vote, don't vote. But using r-help to vote ?! The better solution is right there: http://crantastic.org/ Matthew Dieter Mennedieter.me...@menne-biomed.de wrote in message news:1267626882999-1576618.p...@n4.nabble.com... Rob Forler wrote: And data.table because it does aggregation about 50x times faster than plyr (which I used to use a lot). This is correct, from the error message its spits out one has to conclude that is was abandoned at R-version 2.4.x Dieter -- View this message in context: http://n4.nabble.com/Three-most-useful-R-package-tp1575671p1576618.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. __ 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] Date conversion problem
Hi All, I have a character data.frame that contains character columns and date columns. I've manage to convert some of my character columns to a date format using as.Date(x, format=%m/%d/%y). An example of one of my dates is PROCHIDtDeath icdcucd date_admission1 date_admission_2 CAO0004563 NANA 2005-09-01 NA CAO0073505 NANA 1998-03-05 NA CAO0079987 NANA 2002-04-14 NA CAO0182089 NANA 2007-06-10 11/06/07 CAO0194809 17/02/2005 I64 2004-09-04 14/02/05 CAO0204000 NANA 1999-05-31 NA CAO027 NANA 1999-07-29 NA CAO0330844 29/11/2001 I64NA NA CAO0395045 NANA 2007-02-13 14/02/07 CAO0507333 NANA 2005-10-08 NA I have converted date_admission1 from a character to a date. I used the same script to convert DtDeath but it returns the dates in this format: NA NA NA NA 0017-02-20 [6] NA NA 0029-11-20 NA NA [11] NA NA 0013-10-20 NA NA [16] NA 0007-12-20 NA NA NA [21] NA NA NA NA NA [26] NA NA NA NA NA [31] NA NA NA NA NA [36] NA NA NA NA NA [41] NA NA NA NA NA [46] NA 0029-01-20 0018-05-20 NA NA [51] NA NA NA NA NA [56] NA 0013-07-20 NA NA NA [61] NA 0026-07-20 NA NA NA [66] 0029-04-20 NA NA NA 0012-12-20 [71] NA NA NA NA NA [76] NA NA NA NA NA [81] NA NA 0022-01-20 NA 0029-05-20 [86] NA NA NA NA 0022-02-20 [91] NA I've tried as.Date(as.character(DtDeath, %d/%m/%y) just in case and have used different versions of the format (%m/%d/%Y, and the reverse)but still get the incorrect format. I'm not sure what the problem is? Thanks, natalie -- View this message in context: http://n4.nabble.com/Date-conversion-problem-tp1578296p1578296.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] Analogue to SPSS regression commands ENTER and REMOVE in R?
I bet you stirred the pot here because you arre asking about stepwise procedures. Look at step, or stepAIC in the MASS library. \Mike On Thu, 4 Mar 2010 07:47:34 -0800 Dimitri Liakhovitski ld7...@gmail.com wrote: I am not sure if this question has been asked before - but is there a procedure in R (in lm or glm?) that is equivalent to ENTER and REMOVE regression commands in SPSS? Thanks a lot! __ 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] fisher.test gives p1
The purpose of this email is to (1) report an example where fisher.test returns p 1 (2) ask if there is a reliable way to avoid p1 with fisher.test. If one has designed one's code to return an error when it finds a nonsensical probability, of course a value of p1 can cause havoc. Example: junk-data.frame(score=c(rep(0,14), rep(1,29), rep(2, 16))) junk-rbind(junk, junk) junk$group-c(rep(DOG, nrow(junk)/2), rep(kitty, nrow(junk)/2)) table(junk$score, junk$group) DOG kitty 0 1414 1 2929 2 1616 dput(fisher.test(junk$score, junk$group)$p.value) 1.12 dput(fisher.test(junk$score, junk$group, simulate.p.value=TRUE)$p.value) 1 In this particular case, specifying a simulated p value solved the problem. But is there a reliable way to avoid p1 in general? sessionInfo() R version 2.10.1 (2009-12-14) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.1 Thanks for any insight Jacob A. Wegelin Assistant Professor Department of Biostatistics Virginia Commonwealth University 730 East Broad Street Room 3006 P. O. Box 980032 Richmond VA 23298-0032 U.S.A. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Analogue to SPSS regression commands ENTER and REMOVE in R?
Hi Dimitri, It works a bit differently: ## The SPSS way: compute dum1 = 0. compute dum2 = 0. if(grp = b) dum1 = 1. if(grp = c) dum2 = 1. exe. regression /var = y x1 x2 z1 z2 grp /des = def /sta = def zpp cha tol f /dep = y /met = enter x1 x2 /met = enter z1 z2 /met = enter dum1 dum2. ## The R way: contrasts(Dat$grp) - contr.treatment(n=3, base=1) m.x - lm(y ~ x1 + x2, data=Dat) m.xz - update(m.x, . ~ . + z1 + z2) m.xzg - update(m.xz, . ~ . + grp) anova(m.x, m.xz, m.xzg) Hope it helps, Ista On Thu, Mar 4, 2010 at 10:47 AM, Dimitri Liakhovitski ld7...@gmail.com wrote: I am not sure if this question has been asked before - but is there a procedure in R (in lm or glm?) that is equivalent to ENTER and REMOVE regression commands in SPSS? Thanks a lot! -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ 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] Analogue to SPSS regression commands ENTER and REMOVE in R?
Hi Michael, I don't think Dimitry was asking for stepwise procedures, but rather how to add sets of variables to a model, for example to see if set B predicts over and above some standard set A. -Ista On Thu, Mar 4, 2010 at 11:14 AM, Michael Conklin michael.conk...@markettools.com wrote: I bet you stirred the pot here because you arre asking about stepwise procedures. Look at step, or stepAIC in the MASS library. \Mike On Thu, 4 Mar 2010 07:47:34 -0800 Dimitri Liakhovitski ld7...@gmail.com wrote: I am not sure if this question has been asked before - but is there a procedure in R (in lm or glm?) that is equivalent to ENTER and REMOVE regression commands in SPSS? Thanks a lot! __ 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. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ 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] Analogue to SPSS regression commands ENTER and REMOVE in R?
Oops, forgot the example data used in previous post: set.seed(133) Dat - data.frame(y=rnorm(10), x1=rnorm(10), x2=rnorm(10), z1=rnorm(10), z2=rnorm(10), grp = factor(c(rep(a, 3), rep(b, 4), rep(c, 3))) ) On Thu, Mar 4, 2010 at 11:14 AM, Ista Zahn istaz...@gmail.com wrote: Hi Dimitri, It works a bit differently: ## The SPSS way: compute dum1 = 0. compute dum2 = 0. if(grp = b) dum1 = 1. if(grp = c) dum2 = 1. exe. regression /var = y x1 x2 z1 z2 grp /des = def /sta = def zpp cha tol f /dep = y /met = enter x1 x2 /met = enter z1 z2 /met = enter dum1 dum2. ## The R way: contrasts(Dat$grp) - contr.treatment(n=3, base=1) m.x - lm(y ~ x1 + x2, data=Dat) m.xz - update(m.x, . ~ . + z1 + z2) m.xzg - update(m.xz, . ~ . + grp) anova(m.x, m.xz, m.xzg) Hope it helps, Ista On Thu, Mar 4, 2010 at 10:47 AM, Dimitri Liakhovitski ld7...@gmail.com wrote: I am not sure if this question has been asked before - but is there a procedure in R (in lm or glm?) that is equivalent to ENTER and REMOVE regression commands in SPSS? Thanks a lot! -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ 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] Analogue to SPSS regression commands ENTER and REMOVE in R?
On Mar 4, 2010, at 10:47 AM, Dimitri Liakhovitski wrote: I am not sure if this question has been asked before - but is there a procedure in R (in lm or glm?) that is equivalent to ENTER and REMOVE regression commands in SPSS? Thanks a lot! I haven't used SPSS for 25 years (excluding a brief session where I talked an inexperienced SPSS user through creating a multi-way table of mortality ratios a couple of years ago) but my memory is that those operations drop or add terms to a model formula and produced voluminous paper output as a result. Looking at the lm function help page, I guessed that I might find more information at the anova.lm help page and sure enough, there at the bottom of the page was drop1. My vague memory that there was a matching add1 was rewarded with confirmation when I followed the drop1 link. I generally just make another call to lm(). -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com -- 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] Please help me how to make input files in Extremes Toolkit model
On Mar 4, 2010, at 5:47 AM, Huyen Quan wrote: Dear sir/madam My name is Quan, I am a PhD student in Korea. my major is Hydrological in Water Resources Engineering. I am interested in Extremes Toolkit model and I known you from information in internet. I installed successfully this model but I didn't know how to make the type of files input for this model such as: Flood.dat; Ozone4H.dat; Flood.R; HEAT.R. (free download these files of example and show in attachment files) No files were attached. Did you read the Posting Guide section that describes what sorts of files can be sent through the r-help server? I want to learn the way make these files from sample files. http://www.isse.ucar.edu/extremevalues/evtk.html but i can not download those files because this link was errored. Sorry to hear of your difficulties, but don't you think this is an issue to be resolved by your local administrator? That link works perfectly well for me. Please help me how to get this file and to make files input, if you have some sample files, please send to me to learn and make them. thank you so much for your help me and hope to see your infomation as soon as possible. Mr. Ngo Quan 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.
[R] Unsigned Posts; Was Setting graphical parameters
Folks: Rolf's (appropriate, in my view) response below seems symptomatic of an increasing tendency of posters to hide their identities with pseudonyms and fake headers. While some of this may be due to identity paranoia (which I think is overblown for this list), I suspect that a good chunk of it is lazy students trying to beat the system by having us do their homework. The etiquette of this list has traditionally been, like the software, open: we sign our names. I would urge helpeRs to adhere to this etiquette and ignore unsigned posts. Contrary views welcome, either via public or private responses. -- Bert Bert Gunter Genentech Nonclinical Statistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Rolf Turner Sent: Wednesday, March 03, 2010 6:42 PM To: Pitmaster Cc: r-help@r-project.org Subject: Re: [R] Setting graphical parameters Do your own expletive deleted homework! It looks pretty trivial; what's your problem? cheers, Rolf Turner On 4/03/2010, at 2:39 PM, Pitmaster wrote: Hi guys... I have problem with this excersise... Consider the pressure data frame again. (a) Plot pressure against temperature, and use the following command to pass a curve through these data: curve((0.168 + 0.007*x)(20/3), from=0, to=400, add=TRUE) (b) Now, apply the power transformation y3/20 to the pressure data values. Plot these transformed values against temperature. Is a linear or nonlinear relationship evident now? Use the abline() function to pass a straight line through the points. (You need an intercept and slope for this see the previous part of this question to obtain appropriate values.) (c) Add a suitable title to the graph. (d) Re-do the above plots, but use the mfrow() function to display them in a 2 × 1 layout on the graphics page. Repeat once again using a 1 × 2 layout. DATA: pressure temperature pressure 10 0.0002 2 20 0.0012 3 40 0.0060 4 60 0.0300 5 80 0.0900 6 100 0.2700 7 120 0.7500 8 140 1.8500 9 160 4.2000 10 180 8.8000 11 200 17.3000 12 220 32.1000 13 240 57. 14 260 96. 15 280 157. 16 300 247. 17 320 376. 18 340 558. 19 360 806. Can anyone know the solution ? ## Attention: This e-mail message is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This e-mail has been scanned and cleared by MailMarshal www.marshalsoftware.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] Analogue to SPSS regression commands ENTER and REMOVE in R?
Yes, I was indeed asking about stepwise procedures! On Thu, Mar 4, 2010 at 11:29 AM, David Winsemius dwinsem...@comcast.net wrote: On Mar 4, 2010, at 10:47 AM, Dimitri Liakhovitski wrote: I am not sure if this question has been asked before - but is there a procedure in R (in lm or glm?) that is equivalent to ENTER and REMOVE regression commands in SPSS? Thanks a lot! I haven't used SPSS for 25 years (excluding a brief session where I talked an inexperienced SPSS user through creating a multi-way table of mortality ratios a couple of years ago) but my memory is that those operations drop or add terms to a model formula and produced voluminous paper output as a result. Looking at the lm function help page, I guessed that I might find more information at the anova.lm help page and sure enough, there at the bottom of the page was drop1. My vague memory that there was a matching add1 was rewarded with confirmation when I followed the drop1 link. I generally just make another call to lm(). -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com -- David Winsemius, MD Heritage Laboratories West Hartford, CT -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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] Analogue to SPSS regression commands ENTER and REMOVE in R?
Yes, David is absolutely right - that's it! On Thu, Mar 4, 2010 at 12:21 PM, Dimitri Liakhovitski ld7...@gmail.com wrote: Yes, I was indeed asking about stepwise procedures! On Thu, Mar 4, 2010 at 11:29 AM, David Winsemius dwinsem...@comcast.net wrote: On Mar 4, 2010, at 10:47 AM, Dimitri Liakhovitski wrote: I am not sure if this question has been asked before - but is there a procedure in R (in lm or glm?) that is equivalent to ENTER and REMOVE regression commands in SPSS? Thanks a lot! I haven't used SPSS for 25 years (excluding a brief session where I talked an inexperienced SPSS user through creating a multi-way table of mortality ratios a couple of years ago) but my memory is that those operations drop or add terms to a model formula and produced voluminous paper output as a result. Looking at the lm function help page, I guessed that I might find more information at the anova.lm help page and sure enough, there at the bottom of the page was drop1. My vague memory that there was a matching add1 was rewarded with confirmation when I followed the drop1 link. I generally just make another call to lm(). -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com -- David Winsemius, MD Heritage Laboratories West Hartford, CT -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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] ascending permutation within treatment
Hi R-users, I have a question related to permutations in R. I started learning something about the permutation/randomization tests using Edgington and Onghena (2007) and i tried replicating some of the examples in the book (i have seen also the packages from R that concern permutation ), but at some point i got stuck. If i have 3 treatments, 7 subjects in an experiment, and a 2 of them take treatment A, 2 take treatment B and 3 take treatment C then there are 7!/2!2!3! =210 ways in which they can be assigned. So how can i create sequences in R that are of the form A BC 1 2 | 3 4 | 5 6 7 1 2 | 3 5 | 4 6 7 1 2 | 3 6 | 4 5 7 1 2 | 3 7 | 4 5 6 1 2 | 4 5 | 3 6 7 . 6 7 | 3 4 | 1 2 5 6 7 | 3 5 | 1 2 4 6 7 | 4 5 | 1 2 3 The list is generated taking into account that in each treatment the sequence is always ascending, and so this way it can be avoided listing 7!=5040, but only 7!/2!2!3! =210 sequences will be listed. Can anyone please, offer some guidance, or some advice on how to generate this permutations with this constraint that the order within the treatment is ascending. My hope is that using only this relevant set can greatly improve the time needed for the computation, when i have a larger sample. I have seen also the recommendations to sample a lot of permutations, and i have no problem in doing that, everything goes smoothly and fast, but i want also to be able to do this. Thank you very much and have a great day ahead! Eugen Pircalabelu (0032)471 842 140 (0040)727 839 293 __ 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] fisher.test gives p1
Jacob Wegelin jacobwege...@fastmail.fm on Thu, 4 Mar 2010 11:15:51 -0500 (EST) writes: The purpose of this email is to (1) report an example where fisher.test returns p 1 (2) ask if there is a reliable way to avoid p1 with fisher.test. If one has designed one's code to return an error when it finds a nonsensical probability, of course a value of p1 can cause havoc. Example: junk-data.frame(score=c(rep(0,14), rep(1,29), rep(2, 16))) junk-rbind(junk, junk) junk$group-c(rep(DOG, nrow(junk)/2), rep(kitty, nrow(junk)/2)) table(junk$score, junk$group) DOG kitty 0 14 14 1 29 29 2 16 16 dput(fisher.test(junk$score, junk$group)$p.value) 1.12 dput(fisher.test(junk$score, junk$group, simulate.p.value=TRUE)$p.value) 1 In this particular case, specifying a simulated p value solved the problem. But is there a reliable way to avoid p1 in general? Yes, using the very latest version of R-devel (svn revision = 51204) :-) Of course, the above is just the result of rounding error propagation in an extreme case. I've now simply replaced PVAL by max(0, min(1, PVAL)) in the one place it seems sensible. Martin Maechler, ETH Zurich sessionInfo() R version 2.10.1 (2009-12-14) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.1 Thanks for any insight Jacob A. Wegelin Assistant Professor Department of Biostatistics Virginia Commonwealth University 730 East Broad Street Room 3006 P. O. Box 980032 Richmond VA 23298-0032 U.S.A. __ 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] Unrealistic dispersion parameter for quasibinomial
Ben Bolker wrote : The dispersion parameter depends on the Pearson residuals, not the deviance residuals (i.e., scaled by expected variance). I haven't checked into this in great detail, but the Pearson residual of your first data set is huge, probably because the fitted value is tiny (and hence the expected variance is tiny) and the observed value is 0.2. dfr - df.residual(model2) deviance(model2)/dfr d2 - sum(residuals(model2,pearson)^2) (disp2 - d2/dfr) fitted(model2) residuals(model2,pearson) Sorry to dig that one from one year ago, but it seems it is still interesting (at least to me). From summary.glm, it looks like the deviance is obtained by the working type deviance, which gave close results to pearson type (when working residuals are multiplied by the weights). I couldn't find a lot of information on the working type. How is it computed (from ?glm, I know that these are «the residuals in the final iteration of the IWLS fit») ? sum(model2$weights * residuals(model2, type=working)^2) sum(residuals(model2, type=pearson)^2) Maybe I'm wrong, but could someone clarify that (which type is used and what difference it makes) ? Thank you in advance, Etienne __ 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] End of line marker?
On Mar 4, 2010, at 12:50 PM, jonas garcia wrote: Thank you so much for your reply. I can identify the characters very easily in a couple of files. The reason I am worried is that I have thousands of files to read in. The files were produced in a very old MS-DOS software that records information on oceanographic data and geographic position during a survey. My main goal is read all these files into R for further analysis. Most of the files are cleared of these EOL markers but some are not. I only noticed the problem by chance when I was looking and comparing one of them. I wonder if I can solve this problem using R, without having to go for text editors separately. I could not see the character you pasted, so maybe others were similarly in the dark or under water as might be a more appropriate analogy here. Can you look at the character with a hex- editor or translate it to a character code so that better minds than mine might be able to comment on what sort of weirdness might have been introduced and how it could be scanned? -- David. Help on this would be much appreciated. Thanks again J On 3/4/10, David Winsemius dwinsem...@comcast.net wrote: On Mar 3, 2010, at 2:22 PM, jonas garcia wrote: Dear R users, I am trying to read a huge file in R. For some reason, only a part of the file is read. When I further investigated, I found that in one of my non-numeric columns, there is one odd character responsible for this, which I reproduce bellow: In case you cannot see it, it looks like a right arrow, but it is not the one you get from microsoft word in menu insert symbol. I think my dat file is broken and that funny character is an EOL marker that makes R not read the rest of the file. I am sure the character is there by chance but I fear that it might be present in some other big files I have to work with as well. So, is there any clever way to remove this inconvenient character in R avoiding having to edit the file in notepad and remove it manually? Code I am using: read.csv(new3.dat, header=F) Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'new3.dat' I think you should identify the offending line by using the count.fields function and fix it with an editor. -- David I am working with R 2.10.1 in windows XP. Thanks in advance Jonas [[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. David Winsemius, MD Heritage Laboratories West Hartford, CT David Winsemius, MD Heritage Laboratories West Hartford, CT [[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] Modified R/S statistic
Hi R users, Does anyone know if Lo's modified R/S statistic is implemented in R? Thank you very much, Alexandra Almeida -- Alexandra R M de Almeida [[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] two questions for R beginners
Patrick, 1. Implicit intercepts. Implicit intercepts are not too bad for the main model, but they creep in occasionally in strange places where they might not be expected. For example, in some of the variance structures specified in lme, (~x) automatically expands to (~1+x). Venables said in the Exegeses paper: For teaching purposes it would be useful to have a switch that required users to include the intercept term in formulae if it is needed. This would deï¬nitely help more students than it would hinder. In other words it should be possible to override the automatic intercept term. 2. Working with colors. There are a number of functions in R for working with colors and since colors can be specified by palette number, name, hexadecimal string, values between 0 and 1, or values between 0 and 256, things can be confusing. One problem is that not all functions accept the same type of arguments or produce the same type of return values. For example, the awkward need of t and conversion to [0,255] in adding alpha levels to a color: rgb(t(col2rgb(c(navy,maroon))),alpha=120,max=255) 3. Factors. R tries to convert everything that it possibly can into a factor. Except, occasionally, it doesn't try. Further, after sub-setting data so that some factor levels have no data, too many functions fail. I shouldn't need to use drop.levels from gdata package all over the place to keep automated scripts running smoothly. Let's not forget: R as.numeric(factor(c(NA,0,1))) [1] NA 1 2 4. is.list(list(1)[1]) [1] TRUE is.matrix(matrix(1)[1,]) [1] FALSE Ouch. Ouch. Ouch. 5. Most useful: apropos and Rseek. Best, Kevin On Thu, Feb 25, 2010 at 11:31 AM, Patrick Burns pbu...@pburns.seanet.comwrote: * What were your biggest misconceptions or stumbling blocks to getting up and running with R? * What documents helped you the most in this initial phase? I especially want to hear from people who are lazy and impatient. Feel free to write to me off-list. Definitely write off-list if you are just confirming what has been said on-list. -- Patrick Burns pbu...@pburns.seanet.com 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. -- Kevin Wright [[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] Screen settings for point of view in lattice and misc3d
If I remember correctly, the order in which you specify x, y, and z matters for wireframe, so you may want to try rotating by x first, then z. You may also find the rotate.wireframe function in the TeachingDemos package (make sure that you have also loaded the tcltk package) useful in finding the rotation, it lets you adjust the rotation by using sliders to see the effect, or the tkexamp function in the same package could be used for a different interface. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Waichler, Scott R Sent: Wednesday, March 03, 2010 2:22 PM To: r-h...@stat.math.ethz.ch Subject: [R] Screen settings for point of view in lattice and misc3d I'm making some 3D plots with contour3d from misc3d and wireframe from lattice. I want to view them from below; i.e. the negative z-axis. I can't figure out how to do so. I would like my point of view looking up from below, with the z, y, and x axes positive going away. Can anyone tell me the correct settings for screen to achieve this? Here is what I've found so far: screen=list(z=-40, x=-60, y=0), # looking down and away in negative x direction screen=list(z=40, x=60, y=0), # domain turned upside down, looking up and away in neg. x direction screen=list(z=-40, x=60, y=0), # domain turned upside down, looking up and away in pos. x direction screen=list(z=40, x=-60, y=0), # looking down and away in positive x direction Scott Waichler Pacific Northwest National Laboratory P.O. Box 999, Richland, WA 99352 scott.waich...@pnl.gov 509-372-4423, 509-341-4051 (cell) __ 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] counting the number of ones in a vector
I got tired of writing length(which()) so I define a useful function which I source in my .Rprofile: count - function( x ) length(which(x)) Then: count( x == 1 ) -- View this message in context: http://n4.nabble.com/counting-the-number-of-ones-in-a-vector-tp1570700p1578549.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.
[R] estimagint MLE of covariance matrix subject to constraints
Hi there, I need a MLE of a covariance matrix under the constraint that particular elements of the inverse covariance matrix are zero. I can't find any function/package that'd do that. Any suggestions? Jason [[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] End of line marker?
Thank you so much for your reply. I can identify the characters very easily in a couple of files. The reason I am worried is that I have thousands of files to read in. The files were produced in a very old MS-DOS software that records information on oceanographic data and geographic position during a survey. My main goal is read all these files into R for further analysis. Most of the files are cleared of these EOL markers but some are not. I only noticed the problem by chance when I was looking and comparing one of them. I wonder if I can solve this problem using R, without having to go for text editors separately. Help on this would be much appreciated. Thanks again J On 3/4/10, David Winsemius dwinsem...@comcast.net wrote: On Mar 3, 2010, at 2:22 PM, jonas garcia wrote: Dear R users, I am trying to read a huge file in R. For some reason, only a part of the file is read. When I further investigated, I found that in one of my non-numeric columns, there is one odd character responsible for this, which I reproduce bellow: In case you cannot see it, it looks like a right arrow, but it is not the one you get from microsoft word in menu insert symbol. I think my dat file is broken and that funny character is an EOL marker that makes R not read the rest of the file. I am sure the character is there by chance but I fear that it might be present in some other big files I have to work with as well. So, is there any clever way to remove this inconvenient character in R avoiding having to edit the file in notepad and remove it manually? Code I am using: read.csv(new3.dat, header=F) Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'new3.dat' I think you should identify the offending line by using the count.fields function and fix it with an editor. -- David I am working with R 2.10.1 in windows XP. Thanks in advance Jonas [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT [[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] Removing colon from numerical data
Basic question, looked through the forum and documentation but didnt see a solution. So consider O-c(1:20) D-c(1:,2:,3:,4:,5:,6:,7:,8:,9:,10:,11:,12:,13:,14:,15:,16:, 17:,18:,19:,20:) Time-c(51:70) AveTT-data.frame(O,D,Time) I would like to remove the colon from the D column's data. This is how the data is being given to me and its too big to put into excel to remove the colons. I tried the below but neither returns what i want. AveTT$D-as.numeric(AveTT$D) AveTT$D-substr(AveTT$D,1,nchar(AveTT$D)-1) so i want O D Time 1 1 1: 51 2 2 2: 52 3 3 3: 53 4 4 4: 54 5 5 5: 55 6 6 6: 56 7 7 7: 57 8 8 8: 58 9 9 9: 59 10 10 10: 60 to become O D Time 1 1 1 51 2 2 2 52 3 3 3 53 4 4 4 54 5 5 5 55 6 6 6 56 7 7 7 57 8 8 8 58 9 9 9 59 10 10 10 60 while maintaining the data's integrity. Thanks JR -- View this message in context: http://n4.nabble.com/Removing-colon-from-numerical-data-tp1578397p1578397.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.
[R] Plot help
Is there an easy way to do two things: I have a dataframe with headers and 18 columns I want to plot all the columns on same y axis plot(df) does this. BUT 1. There is no legend, the legend function seems pedantic - surely there must be an easy way to just pick up my headers? 2. How do I vary the colours. By default they repeat quite frequently and I have lots of red lines etc. Moon -- View this message in context: http://n4.nabble.com/Plot-help-tp1578510p1578510.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] Removing colon from numerical data
On Mar 4, 2010, at 12:12 PM, LCOG1 wrote: Basic question, looked through the forum and documentation but didnt see a solution. So consider O-c(1:20) D- c (1 :,2 :,3 :,4 :,5:,6:,7:,8:,9:,10:,11:,12:,13:,14:,15:,16:, 17:,18:,19:,20:) Time-c(51:70) AveTT-data.frame(O,D,Time) AveTT$D - gsub(:, , AveTT$D) I would like to remove the colon from the D column's data. This is how the data is being given to me and its too big to put into excel to remove the colons. I tried the below but neither returns what i want. AveTT$D-as.numeric(AveTT$D) AveTT$D-substr(AveTT$D,1,nchar(AveTT$D)-1) so i want O D Time 1 1 1: 51 2 2 2: 52 3 3 3: 53 4 4 4: 54 5 5 5: 55 6 6 6: 56 7 7 7: 57 8 8 8: 58 9 9 9: 59 10 10 10: 60 to become O D Time 1 1 1 51 2 2 2 52 3 3 3 53 4 4 4 54 5 5 5 55 6 6 6 56 7 7 7 57 8 8 8 58 9 9 9 59 10 10 10 60 while maintaining the data's integrity. Thanks JR -- View this message in context: http://n4.nabble.com/Removing-colon-from-numerical-data-tp1578397p1578397.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing colon from numerical data
Try this: D - as.numeric(gsub([[:punct:]], , D)) On Thu, Mar 4, 2010 at 2:12 PM, LCOG1 jr...@lcog.org wrote: Basic question, looked through the forum and documentation but didnt see a solution. So consider O-c(1:20) D-c(1:,2:,3:,4:,5:,6:,7:,8:,9:,10:,11:,12:,13:,14:,15:,16:, 17:,18:,19:,20:) Time-c(51:70) AveTT-data.frame(O,D,Time) I would like to remove the colon from the D column's data. This is how the data is being given to me and its too big to put into excel to remove the colons. I tried the below but neither returns what i want. AveTT$D-as.numeric(AveTT$D) AveTT$D-substr(AveTT$D,1,nchar(AveTT$D)-1) so i want O D Time 1 1 1: 51 2 2 2: 52 3 3 3: 53 4 4 4: 54 5 5 5: 55 6 6 6: 56 7 7 7: 57 8 8 8: 58 9 9 9: 59 10 10 10: 60 to become O D Time 1 1 1 51 2 2 2 52 3 3 3 53 4 4 4 54 5 5 5 55 6 6 6 56 7 7 7 57 8 8 8 58 9 9 9 59 10 10 10 60 while maintaining the data's integrity. Thanks JR -- View this message in context: http://n4.nabble.com/Removing-colon-from-numerical-data-tp1578397p1578397.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] counting the number of ones in a vector
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of sjaffe Sent: Thursday, March 04, 2010 10:59 AM To: r-help@r-project.org Subject: Re: [R] counting the number of ones in a vector I got tired of writing length(which()) so I define a useful function which I source in my .Rprofile: count - function( x ) length(which(x)) Then: count( x == 1 ) How about sum(x==1) ? No need to write a new function, and it is even 2 characters less to type. Hope this is helpful, Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 __ 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] Is it possible to recursively update a function?
Here is the test code.
foo-function(x) exp(-x)
for (i in 1:5)
{
foo-function(x) foo(x)*x
foo(2)
}
The error is evalution nested too deeply. I tried Recall() but it
didn't work either. Thanks a lot for your input.
__
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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] logistic regression by group?
Corey, Thanks for the quick reply. I cant give any sample code as I don't know how to code this in R. That's why I tried to pass along some pseudo code. I'm looking for the best beta that maximize likelihood over all the groups. So, while your suggestion is close, it isn't quite what I need. I've seen the formula written as: L = product( exp(xb) / sum(exp(xb)) ) Where sum(exp(xb)) represents the sum of all the items in the group. Does that make sense? -N On 3/4/10 4:04 AM, Corey Sparks wrote: Hi, first, you should always provide some repeatable code for us to have a look at, that shows what you have tried so far. That being said, you can use the subset= option in glm to subdivide your data and run separate models like that, e.g. fit.1-glm(y~x1+x2, data=yourdat, family=binomial, subset=group==1) fit.2-glm(y~x1+x2, data=yourdat, family=binomial, subset=group==2) where group is your grouping variable. Which should give you that kind of stratified model. Hope this helps, Corey - Corey Sparks, PhD Assistant Professor Department of Demography and Organization Studies University of Texas at San Antonio 501 West Durango Blvd Monterey Building 2.270C San Antonio, TX 78207 210-458-3166 corey.sparks 'at' utsa.edu https://rowdyspace.utsa.edu/users/ozd504/www/index.htm __ 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] fisher.test gives p1
On Thu, 2010-03-04 at 11:15 -0500, Jacob Wegelin wrote: The purpose of this email is to (1) report an example where fisher.test returns p 1 (2) ask if there is a reliable way to avoid p1 with fisher.test. If one has designed one's code to return an error when it finds a nonsensical probability, of course a value of p1 can cause havoc. Example: junk-data.frame(score=c(rep(0,14), rep(1,29), rep(2, 16))) junk-rbind(junk, junk) junk$group-c(rep(DOG, nrow(junk)/2), rep(kitty, nrow(junk)/2)) table(junk$score, junk$group) DOG kitty 0 1414 1 2929 2 1616 dput(fisher.test(junk$score, junk$group)$p.value) 1.12 Hi jacob, I think this is cover in R FAQ 7.31, but look this command all.equal(dput(fisher.test(matrix(c(14,14,29,29,16,16),byrow=T,ncol=2))$p.value),1) 1.12 [1] TRUE P.S R FAQ 7.31 - http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f -- Bernardo Rangel Tura, M.D,MPH,Ph.D National Institute of Cardiology 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] Is it possible to recursively update a function?
What exactly are you trying to do? 'foo' calls 'foo' calls 'foo'
How did you expect it to stop the recursive calls?
On Thu, Mar 4, 2010 at 2:08 PM, Seeker zhongm...@gmail.com wrote:
Here is the test code.
foo-function(x) exp(-x)
for (i in 1:5)
{
foo-function(x) foo(x)*x
foo(2)
}
The error is evalution nested too deeply. I tried Recall() but it
didn't work either. Thanks a lot for your input.
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] Is it possible to recursively update a function?
On 04.03.2010 20:08, Seeker wrote:
Here is the test code.
foo-function(x) exp(-x)
for (i in 1:5)
{
foo-function(x) foo(x)*x
foo(2)
Hmmm, wenn do you think does the evaluation stop? Your recursion has an
infinity depth.
If you cannot get the recursion right (and even if you can): Try to get
around without recursion, it is in most cases a bad idea in R: You are
wasting memory and it is rather slow compared to iterative approaches.
Uwe Ligges
}
The error is evalution nested too deeply. I tried Recall() but it
didn't work either. Thanks a lot for your input.
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Re: [R] Odp: precision issue?
On 04-Mar-10 13:35:42, Duncan Murdoch wrote:
On 04/03/2010 7:35 AM, (Ted Harding) wrote:
On 04-Mar-10 10:50:56, Petr PIKAL wrote:
Hi
r-help-boun...@r-project.org napsal dne 04.03.2010 10:36:43:
Hi R Gurus,
I am trying to figure out what is going on here.
a - 68.08
b - a-1.55
a-b
[1] 1.55
a-b == 1.55
[1] FALSE
round(a-b,2) == 1.55
[1] TRUE
round(a-b,15) == 1.55
[1] FALSE
Why should (a - b) == 1.55 fail when in fact b has been defined
to be a - 1.55? Is this a precision issue? How do i correct this?
In real world those definitions of b are the same but not in
computer
world. See FAQ 7.31
Use either rounding or all.equal.
all.equal(a-b, 1.55)
[1] TRUE
To all, this is quite common question and it is documented in FAQs.
programs, therefore maybe a confusion from novices.
I wonder if there could be some type of global option which will
get rid of these users mistakes or misunderstandings by setting
some threshold option for equality testing by use ==.
Regards
Petr
Alex
Interesting suggestion, but in my view it would probably give
rise to more problems than it would avoid!
The fundamental issue is that many inexperienced users are not
aware that once 68.08 has got inside the computer (as used by
R and other programs which do fixed-length binary arithmetic)
it is no longer 68.08 (though 1.55 is still 1.55).
I think most of what you write above and below is true, but your
parenthetical remark is not. 1.55 can't be represented exactly in the
double precision floating point format used in R. It doesn't have a
terminating binary expansion, so it will be rounded to a binary
fraction. I believe you can see the binary expansion using this code:
x - 1.55
for (i in 1:70) {
cat(floor(x))
if (i == 1) cat(.)
x - 2*(x - floor(x))
}
which gives
1.10001100110011001100110011001100110011001100110011010
Notice how it becomes a repeating expansion, with 0011 repeated 12
times, but then it finishes with 010, because we've run
out of bits.
So 1.55 is actually stored as a number which is ever so slightly
bigger.
Duncan Murdoch
Of course you are quite right! My parenthetical remark was
an oversight and a blunder -- not so much a typo as a braino,
due to crossing wires between dividing by 2 (1.5 = 1 + 1/2)
and dividing by 10 ( 1.55 != 1 + 1/2 + (1/2)/2) )!
However, your detailed explanation will certainly be useful
to some. And your method of producing the binary expansion
is very neat indeed.
[the rest of my stuff snipped]
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 04-Mar-10 Time: 20:11:39
-- XFMail --
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Re: [R] Histogram color
Here is another approach:
x - rnorm(100)
tmp - hist(x, plot=FALSE)
plot(tmp, col='blue')
tu - par('usr')
par(xpd=FALSE)
clip( tu[1], mean(x) - sd(x), tu[3], tu[4] )
plot(tmp, col='red', add=TRUE)
clip( mean(x) + sd(x), tu[2], tu[3], tu[4] )
plot(tmp, col='red', add=TRUE)
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Ashta
Sent: Thursday, March 04, 2010 5:42 AM
To: R help
Subject: [R] Histogram color
In a histogram , is it possible to have different colors?
Example. I generated
x - rnorm(100)
hist(x)
I want the histogram to have different colors based on the following
condition
mean(x)+sd(x) with red color and mean(x) - sd(x) with red color as
well. The middle one with blue color.
Is it possible to do that in R?
Thanks
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Re: [R] Three most useful R package
Well, the HeadSlap package would of course require the esp package so that it could tell the difference between someone doing something clever and someone doing something because everyone else does. For example, user 1 calls the pie function, HeadSlap using esp finds out that user 1 will also be creating a bar chart and dot plot of same data to use in a presentation comparing the types of plots and showing why you should not use pie charts. HeadSlap allows pie chart to be created. User 2 calls the pie function because they think pie charts are pretty and have never learned better, HeadSlap first issues a warning/error with references to Cleveland and others. Further attempts to use pie by same user for same reason result in activating the hardware. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Jim Lemon Sent: Thursday, March 04, 2010 1:49 AM To: r-h...@stat.math.ethz.ch Subject: Re: [R] Three most useful R package On Wed, 3 Mar 2010 11:52:48 -0700 Greg Snow greg.s...@imail.org wrote: I also want a package that when people misuse certain functions/techniques it will cause a small door on the side of their monitor/computer to open and a mechanical hand will come out and slap them upside the head. But that package will not be useful until the hardware support is available. Hi Greg, Had not my grandfather and a workmate, over 60 years ago, worked out a way to do something that no one else had been able to do by running a machine in a way that it was not supposed to be run, I might agree with you. Jim __ 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] fisher.test gives p1
On 04-Mar-10 19:27:16, Bernardo Rangel Tura wrote: On Thu, 2010-03-04 at 11:15 -0500, Jacob Wegelin wrote: The purpose of this email is to (1) report an example where fisher.test returns p 1 (2) ask if there is a reliable way to avoid p1 with fisher.test. If one has designed one's code to return an error when it finds a nonsensical probability, of course a value of p1 can cause havoc. Example: junk-data.frame(score=c(rep(0,14), rep(1,29), rep(2, 16))) junk-rbind(junk, junk) junk$group-c(rep(DOG, nrow(junk)/2), rep(kitty, nrow(junk)/2)) table(junk$score, junk$group) DOG kitty 0 1414 1 2929 2 1616 dput(fisher.test(junk$score, junk$group)$p.value) 1.12 Hi jacob, I think this is cover in R FAQ 7.31, but look this command all.equal(dput(fisher.test(matrix(c(14,14,29,29,16,16),byrow=T,ncol=2))$ p.value),1) 1.12 [1] TRUE P.S R FAQ 7.31 - http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-the se-numbers-are-equal_003f -- Bernardo Rangel Tura, M.D,MPH,Ph.D National Institute of Cardiology Brazil This is yet another example where the advice (in my posting in the precision thread), that if an anomaly occurs it is is useful to check the magnitude of the anomaly, applies. Then: a - 68.08 ; b - a-1.55 ; a-b == 1.55 # [1] FALSE (a-b) - 1.55 # [1] -2.88658e-15 Here (as Jakob found for himself): p = 1.12 Or, more precisely (using Jakob's data): fisher.test(junk$score, junk$group)$p.value -1 # [1] 5.728751e-14 (which is not quite the same, but makes the same point). The presence of a discrepancy of the order of 1e-14 or 1e-15 (or smaller) is always a strong clue that errors due to the accumulation of imprecise binary representations may have occurred. Martin's replacement with max(0, min(1, PVAL)) will remove such anomalies (which still will not guarantee that a result of 0.9974 is exact, but that is probably not important; what is important is that it does not break the logic of probability. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 04-Mar-10 Time: 20:33:03 -- 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] Hi
How Can I write this this matlab code in R:
options=optimset('TolFun',1e-9,'TolX',1e-9,'MaxIter',1e8,'MaxFunEvals',1e8);
c=c/2;
[alpha, delta, epsilon, nofcup] = ustrs(set_date,mat_date);
y = fminsearch('pbond',.15,options,p,c,nofcup,delta/epsilon);
y = 200*y;
Note
pbond is a function in Matlab I already wrote in R
ustrs is a function in Matlab I already convert into r
Thank you
HI
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Re: [R] Hi
I would help, but I don't know matlab.
Stephen
On Thu, Mar 4, 2010 at 2:50 PM, hussain abu-saaq hussain...@hotmail.com wrote:
How Can I write this this matlab code in R:
options=optimset('TolFun',1e-9,'TolX',1e-9,'MaxIter',1e8,'MaxFunEvals',1e8);
c=c/2;
[alpha, delta, epsilon, nofcup] = ustrs(set_date,mat_date);
y = fminsearch('pbond',.15,options,p,c,nofcup,delta/epsilon);
y = 200*y;
Note
pbond is a function in Matlab I already wrote in R
ustrs is a function in Matlab I already convert into r
Thank you
HI
[[alternative HTML version deleted]]
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--
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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Re: [R] End of line marker?
Have you considered reading the file in a binary/raw, finding the offending character and replacing it with a blank (or whatever and then writing the file back out). You can then probably process it using read.table.; On Thu, Mar 4, 2010 at 12:50 PM, jonas garcia garcia.jona...@googlemail.com wrote: Thank you so much for your reply. I can identify the characters very easily in a couple of files. The reason I am worried is that I have thousands of files to read in. The files were produced in a very old MS-DOS software that records information on oceanographic data and geographic position during a survey. My main goal is read all these files into R for further analysis. Most of the files are cleared of these EOL markers but some are not. I only noticed the problem by chance when I was looking and comparing one of them. I wonder if I can solve this problem using R, without having to go for text editors separately. Help on this would be much appreciated. Thanks again J On 3/4/10, David Winsemius dwinsem...@comcast.net wrote: On Mar 3, 2010, at 2:22 PM, jonas garcia wrote: Dear R users, I am trying to read a huge file in R. For some reason, only a part of the file is read. When I further investigated, I found that in one of my non-numeric columns, there is one odd character responsible for this, which I reproduce bellow: In case you cannot see it, it looks like a right arrow, but it is not the one you get from microsoft word in menu insert symbol. I think my dat file is broken and that funny character is an EOL marker that makes R not read the rest of the file. I am sure the character is there by chance but I fear that it might be present in some other big files I have to work with as well. So, is there any clever way to remove this inconvenient character in R avoiding having to edit the file in notepad and remove it manually? Code I am using: read.csv(new3.dat, header=F) Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'new3.dat' I think you should identify the offending line by using the count.fields function and fix it with an editor. -- David I am working with R 2.10.1 in windows XP. Thanks in advance Jonas [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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] Equation for model generated by auto.arima
I would like to know how to use the coefficients generated by the ARIMA model to predict future values. What formula should be used with the coeffcients to determine the future values. Thanks -- View this message in context: http://n4.nabble.com/Equation-for-model-generated-by-auto-arima-tp1578756p1578756.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] Is it possible to recursively update a function?
I need to update posterior dist function upon the coming results and
find the posterior mean each time.
On Mar 4, 1:31 pm, jim holtman jholt...@gmail.com wrote:
What exactly are you trying to do? 'foo' calls 'foo' calls 'foo'
How did you expect it to stop the recursive calls?
On Thu, Mar 4, 2010 at 2:08 PM, Seeker zhongm...@gmail.com wrote:
Here is the test code.
foo-function(x) exp(-x)
for (i in 1:5)
{
foo-function(x) foo(x)*x
foo(2)
}
The error is evalution nested too deeply. I tried Recall() but it
didn't work either. Thanks a lot for your input.
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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[R] partial differentiation of a dynamic expression
Hello,
It is possible to use 'deriv' when the expression itself is dynamic? I have
data where the conditional mean is time-varying (like a GARCH(1,1) model) as
mu_{t} = omega1 + alpha1*N_{t-1} + beta1*mu_{t-1}.
The parameter vector is c(omega1, alpha1, beta1) and N_t is the
observation at each time.
I want two things:
1. the derivative of mu_t with respect to each parameter. So for example, the
first derivative with respect to omega1 is 1 + beta1* d mu_{t-1}/ d omega1.
2. Once I have the expression in 1, I want its first partial derivative.
Ultimately, I want to find the root of an estimating function using
Newton-Raphson, where
param - param - solve(mat)%*% param,
and where param is an estimating function which has first partial derivatives
in it and 'mat' is a matrix which involves the first partial derivatives of
elements in 'param'.
Thanks,
Melody
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Re: [R] Equation for model generated by auto.arima
Hi, the help page for arima() suggests looking at predict.Arima(), so take a look at ?predict.Arima(). You will probably not use the coefficients, but just feed it the output from arima(). And take a look at auto.arima() in the forecast package. HTH Stephan testuser schrieb: I would like to know how to use the coefficients generated by the ARIMA model to predict future values. What formula should be used with the coeffcients to determine the future values. Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] missing date and time intervals in data frame
I posted a similar question, but feel it needs a bit more elaboration. I have a data frame (read from a csv file) that may have missing rows. Each day has 7 time intervals associated with it, with a range from 17:00 hrs to 18:00 hrs in 10 minute bins. What I am looking for is a script that will run through the data frame and insert NAin the Volume column for any dates that are missing a time interval. For example: DateTime Camera Volume 57 2009-10-09 5:00:00 PM MANBRIN_RIVER_NB210 58 2009-10-09 5:10:00 PM MANBRIN_RIVER_NB207 59 2009-10-09 5:20:00 PM MANBRIN_RIVER_NB250 60 2009-10-09 5:30:00 PM MANBRIN_RIVER_NB193 61 2009-10-09 5:40:00 PM MANBRIN_RIVER_NB205 62 2009-10-09 6:00:00 PM MANBRIN_RIVER_NB185 Note that between row 61 and row 62, there is a missing time interval (5:50 PM). I want the data frame to look like this: Date Time Camera Volume 57 2009-10-09 5:00:00 PM MANBRIN_RIVER_NB210 58 2009-10-09 5:10:00 PM MANBRIN_RIVER_NB207 59 2009-10-09 5:20:00 PM MANBRIN_RIVER_NB250 60 2009-10-09 5:30:00 PM MANBRIN_RIVER_NB193 61 2009-10-09 5:40:00 PM MANBRIN_RIVER_NB205 *62 2009-10-09 5:50:00 PM MANBRIN_RIVER_NB NA* 62 2009-10-09 6:00:00 PM MANBRIN_RIVER_NB185 Thanks in advance, Kindra [[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] missing date and time intervals in data frame
On Mar 4, 2010, at 4:45 PM, Kindra Martinenko wrote: I posted a similar question, but feel it needs a bit more elaboration. I have a data frame (read from a csv file) that may have missing rows. Each day has 7 time intervals associated with it, with a range from 17:00 hrs to 18:00 hrs in 10 minute bins. What I am looking for is a script that will run through the data frame and insert NAin the Volume column for any dates that are missing a time interval. For example: DateTime Camera Volume 57 2009-10-09 5:00:00 PM MANBRIN_RIVER_NB210 58 2009-10-09 5:10:00 PM MANBRIN_RIVER_NB207 59 2009-10-09 5:20:00 PM MANBRIN_RIVER_NB250 60 2009-10-09 5:30:00 PM MANBRIN_RIVER_NB193 61 2009-10-09 5:40:00 PM MANBRIN_RIVER_NB205 62 2009-10-09 6:00:00 PM MANBRIN_RIVER_NB185 Here is one method of generating a series of time points at 10 minute intervals: as.POSIXlt(5:00:00 PM, format=%I:%M:%s %p ) + (1:20)*60*10 [1] 2010-03-04 05:10:00 EST 2010-03-04 05:20:00 EST 2010-03-04 05:30:00 EST [4] 2010-03-04 05:40:00 EST 2010-03-04 05:50:00 EST 2010-03-04 06:00:00 EST [7] 2010-03-04 06:10:00 EST 2010-03-04 06:20:00 EST 2010-03-04 06:30:00 EST [10] 2010-03-04 06:40:00 EST 2010-03-04 06:50:00 EST 2010-03-04 07:00:00 EST [13] 2010-03-04 07:10:00 EST 2010-03-04 07:20:00 EST 2010-03-04 07:30:00 EST [16] 2010-03-04 07:40:00 EST 2010-03-04 07:50:00 EST 2010-03-04 08:00:00 EST [19] 2010-03-04 08:10:00 EST 2010-03-04 08:20:00 EST Applying that to the solution you referenced should finish the job. -- David. Note that between row 61 and row 62, there is a missing time interval (5:50 PM). I want the data frame to look like this: Date Time Camera Volume 57 2009-10-09 5:00:00 PM MANBRIN_RIVER_NB210 58 2009-10-09 5:10:00 PM MANBRIN_RIVER_NB207 59 2009-10-09 5:20:00 PM MANBRIN_RIVER_NB250 60 2009-10-09 5:30:00 PM MANBRIN_RIVER_NB193 61 2009-10-09 5:40:00 PM MANBRIN_RIVER_NB205 *62 2009-10-09 5:50:00 PM MANBRIN_RIVER_NB NA* 62 2009-10-09 6:00:00 PM MANBRIN_RIVER_NB185 Thanks in advance, Kindra [[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. 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] help
On 03/04/2010 10:30 PM, mahalakshmi sivamani wrote: Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of datadir i have to mention the character string of the directory of these .cel files. I don't know how to give the path for all these files. i set the path as given below, rna.data-exprs(justRMA(filenames=file.names, celfile.path=*D:/MONO1.CEL D:/MONO2.CEL D:/MONO3.CEL D:/MACRO1.CEL D:/MACRO2.CEL D:/MACRO3.CEL*,sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) it shows this error, Error: unexpected string constant in rna.data-exprs(justRMA(filenames=file.names, celfile.path=D:/MONO1 D:/MONO2 Hi Mahalakshmi, If you want to pass more than one string as an argument, you must pass them as a character vector. celfile.path=c(D:/MONO1.CEL,D:/MONO2.CEL,D:/MONO3.CEL, D:/MACRO1.CEL,D:/MACRO2.CEL,D:/MACRO3.CEL) Although this is not guaranteed to make your function work correctly. Jim __ 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] Running script with double-click
Hi, I need to be able to run an R script by double-clicking the file name in Windows. I've tried associating the .r extension with the different R .exe's in /bin but none seems to work. Some open R then close right away, and Rgui.exe gives the message ARGUMENT /my/file.r __ignored__ before opening a new, blank session. I've tried Google and looking in the R for Windows FAQ but didn't see anything. Thanks. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Hi
a quick google of fminsearch in R
resulted in this
http://www.google.com/search?q=fminsearch+in+Rie=utf-8oe=utf-8aq=trls=org.mozilla:en-US:officialclient=firefox-a
take a look. there appears to be a function called optim that you can look
at
http://sekhon.berkeley.edu/stats/html/optim.html
before you ask a question on r-help I would highly suggest doing at least a
small amount of googling.
On Thu, Mar 4, 2010 at 3:01 PM, stephen sefick ssef...@gmail.com wrote:
I would help, but I don't know matlab.
Stephen
On Thu, Mar 4, 2010 at 2:50 PM, hussain abu-saaq hussain...@hotmail.com
wrote:
How Can I write this this matlab code in R:
options=optimset('TolFun',1e-9,'TolX',1e-9,'MaxIter',1e8,'MaxFunEvals',1e8);
c=c/2;
[alpha, delta, epsilon, nofcup] = ustrs(set_date,mat_date);
y = fminsearch('pbond',.15,options,p,c,nofcup,delta/epsilon);
y = 200*y;
Note
pbond is a function in Matlab I already wrote in R
ustrs is a function in Matlab I already convert into r
Thank you
HI
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--
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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Re: [R] Unsigned Posts; Was Setting graphical parameters
On 03/05/2010 04:11 AM, Bert Gunter wrote: Folks: Rolf's (appropriate, in my view) response below seems symptomatic of an increasing tendency of posters to hide their identities with pseudonyms and fake headers. While some of this may be due to identity paranoia (which I think is overblown for this list), I suspect that a good chunk of it is lazy students trying to beat the system by having us do their homework. The etiquette of this list has traditionally been, like the software, open: we sign our names. I would urge helpeRs to adhere to this etiquette and ignore unsigned posts. Contrary views welcome, either via public or private responses. Hi Bert (and anyone else who wishes to read this), I had a working hypothesis about this, but decided to check the data before replying. Looking at the ten most recent obvious pseudonyms, all were from free email accounts like gmail or yahoo. A few of these included all or part of the name of the user anyway. As such accounts tend to be used for lots of things, the users may well be concerned about identification, even if everyone on the R help list is of the highest moral standing. I think Rolf's guess about the provenance of the request was based upon the carefully copied format, which Blind Freddie could see was homework (and the requester actually admitted it!). Personally, I never answer requests that have the due date for the assignment at the bottom. Jim __ 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] Running script with double-click
Tena koe Matt I tend to create a .bat file with one line: R\R-Current\bin\R CMD BATCH yourScript.R where you replace R\R-Current\bin\R with the path to your R, and the .bat file is in the same folder as yourScript.R. There may be better ways, and doubtless someone will enlighten us both if there are. HTH Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Matt Asher Sent: Friday, 5 March 2010 12:43 p.m. To: r-help@r-project.org Subject: [R] Running script with double-click Hi, I need to be able to run an R script by double-clicking the file name in Windows. I've tried associating the .r extension with the different R .exe's in /bin but none seems to work. Some open R then close right away, and Rgui.exe gives the message ARGUMENT /my/file.r __ignored__ before opening a new, blank session. I've tried Google and looking in the R for Windows FAQ but didn't see anything. Thanks. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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.
