[R] The function predict

2008-02-11 Thread Carla Rebelo
Good Morning! May you help me? I need to understand the function predict. I need to understand the algorithm implemented, the calculations associated. Where can I find this information? Thank You! __ R-help@r-project.org mailing list

[R] tree() producing NA's

2008-02-11 Thread Amnon Melzer
Hi Hoping someone can help me (a newbie). I am trying to construct a tree using tree() in package tree. One of the fields is a factor field (owner), with many levels. In the resulting tree, I see many NA's (see below), yet in the actual data there are none. rr200.tr - tree(backprof ~

[R] Dendrogram for agglomerative hierarchical clustering result

2008-02-11 Thread noorpiilur
Hey group, I have a problem of drawing dendrogram as the result of my program written in C. My algorithm is a approximation algorithm for single linkage method. AS a result I will get the following data: [Average distance] [cluster A] [cluster B] For example: 42.593141 1 26

[R] image quality

2008-02-11 Thread John Lande
dear all, I am writing a sweave documentation for my analysis, and I am plotting huge scatter plot data for microarray. unlucly this take a lot of resource to my pc because of the quality of the image which is to high (I see the PC get stuck for each single spot). how can I overcome this problem?

[R] Conditional rows

2008-02-11 Thread Ng Stanley
Hi, Given a simple example, test - matrix(c(0.1, 0.2, 0.1, 0.2, 0.1, 0.1, 0.3, 0.1, 0.1), 3, 3) How to generate row indexes for which their corresponding row values are less than or equal to 0.2 ? For this example, row 2 and 3 are the correct ones. Thanks [[alternative HTML version

Re: [R] how to generate a column based on other columns in a data frame

2008-02-11 Thread Henrique Dallazuanna
Try this: x2 - merge(x, cbind(unique(x), Site=sprintf(S%d, seq_len(nrow(unique(x), by=c(X, Y)) x2[order(x2$site)] On 11/02/2008, Weidong Gu [EMAIL PROTECTED] wrote: HI, I am working on a data set with multiple collections of mosquitoes at sampling sites. Each row represents a

[R] gcc 4.3 any known issues?

2008-02-11 Thread Stefan Grosse
Hi, Fedora is for Fedora 9 switching to gcc 4.3. Before I test it (rawhide) I want to be sure that R is running. So my question is whether there have been issues compiling R + packages using 4.3? Stefan __ R-help@r-project.org mailing list

Re: [R] Tinn-R not working well with latest R

2008-02-11 Thread John C Frain
Pending the solution of the problem I use tinn-R as follows. 1) I make none of the recommended additions to the Rprofile.site file 2) I start tinn-R from the desktop and then load an r-file from my working directory. 3) I then start R from the R| start preferred Rgui | menu in Tinn-R. This has

Re: [R] Subsetting a data.frame degenerates at one column?

2008-02-11 Thread Allen S. Rout
jim holtman [EMAIL PROTECTED] writes: try: input[,targets, drop=FALSE] see: ?[ for an explanation. Thanks, you who responded; this was exactly helpful, and a good reference to the part of the FM I was missing. To unpack (and demonstrate some comprehension gained.. ;) the subsetting

Re: [R] Tinn-R not working well with latest R

2008-02-11 Thread John C Frain
Corinna Thanks for the suggestion. I can not duplicate the error myself. I generally have a code segment open in Tinn-R and have sent it to R and wish to rerun it with some changes but when I try to make the changes they are transferred to the line above one character per line. This has

[R] WG: Tinn-R not working well with latest R

2008-02-11 Thread Schmitt, Corinna
I am in R command window and just make Crt+V. Corinna -Ursprüngliche Nachricht- Von: Farrel Buchinsky [mailto:[EMAIL PROTECTED] Gesendet: Mo 11.02.2008 21:16 An: Schmitt, Corinna Betreff: Re: Tinn-R not working well with latest R I can easily get R to open without an error. I

Re: [R] Histogram in Lattice with 3 factors

2008-02-11 Thread Deepayan Sarkar
On 2/11/08, willem vervoort [EMAIL PROTECTED] wrote: Dear R-help list, I am trying to construct a lattice histogram using 3 factors. My dataframe looks like this: (simulating a waterbalance over groundwater with different salinities) s days modelECEC_max 0.4 1A

[R] Histogram in Lattice with 3 factors

2008-02-11 Thread willem vervoort
Dear R-help list, I am trying to construct a lattice histogram using 3 factors. My dataframe looks like this: (simulating a waterbalance over groundwater with different salinities) s days modelECEC_max 0.4 1A 10 9 0.42 2A 10 9 0.44 3

Re: [R] [OT] good reference for mixed models and EM algorithm

2008-02-11 Thread Murray Jorgensen
Erin, as well as P B can I recommend McCullogh CE, Searle SR (2000), Generalized, Linear, and Mixed Models, Wiley I also found Data analysis using regression and multilevel/hierarchical models by Andrew Gelman and Jennifer Hill. Cambridge ; New York : Cambridge University Press, 2007.

Re: [R] R on Mac PRO does anyone have experience with R on such a platform ?

2008-02-11 Thread Charilaos Skiadas
JiHO, in case you are not following TextMate's mailing list, you might want to check out Hans-Jorg Bibiko's work on Rdaemon: http://article.gmane.org/gmane.editors.textmate.general/24195/ It provides a lot of the terminal functionality within a TextMate window, uses X11 for the plots, and

Re: [R] barplot or maybe related?

2008-02-11 Thread Manuel Morales
On Mon, 2008-02-11 at 09:31 -0800, questions? wrote: I have two distributions, represented by heights of several intervals. e.g. the distribution is partitioned into 10 segments, I have numbers(freq or counts) associated with each region in the format as: 0.2 0.3 0.1 0.1 . 0.01

Re: [R] Logistic regression with repeated measures

2008-02-11 Thread Dieter Menne
Steven Vamosi smvamosi at gmail.com writes: In a nutshell, the experiment involved presenting females from two groups (treatment, control) with an opportunity to mate with a virgin male every 6 hours for 48 hours. Every female was presented this opportunity at every time step (i.e., whether

Re: [R] gcc 4.3 any known issues?

2008-02-11 Thread Peter Dalgaard
Stefan Grosse wrote: Hi, Fedora is for Fedora 9 switching to gcc 4.3. Before I test it (rawhide) I want to be sure that R is running. So my question is whether there have been issues compiling R + packages using 4.3? I suspect that not many have tried. There is an R-2.6.2 RPM in

Re: [R] R on Mac PRO does anyone have experience with R on such a platform ?

2008-02-11 Thread jiho
On 2008-February-11 , at 19:14 , Roger Day wrote: My experience with R.app on a MACbook has been mostly very positive. I like the interface much better than that of Windows-- with two exceptions. a) I use stepping thru code with control-R. It's not as convenient on Mac- the code you

[R] Interpretation of log odds

2008-02-11 Thread Schmitt, Corinna
Hallo, fit12-lmFit(qrg[,1:2]) t12-toptable(fit12,adjust=fdr,number=15000,genelist=qrg$genes[,1]) t12 ID logFC t P.Value adj.P.ValB 1560orf6.2714 -5,95911144 -7,5045373620,0616459272630

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread Stas Kolenikov
On 2/11/08, Paul Gilbert [EMAIL PROTECTED] wrote: Stas Kolenikov wrote: ... Training researchers of tomorrow might be great, but ifyour students get on the market in the end of the semester, they won't have the luxury of waiting until R becomes THE package of choice. Not being a

[R] Viable Approach to Parallel R?

2008-02-11 Thread Lewis, Daniel (IS Consultant)
All, We are researching approaches to parallel R with the end goal of running R in a distributed manner on a Linux cluster. We expect of course to do some work decomposing our problems to be task-parallel or data-parallel, but wouldn't mind getting an initial boost working with embarrassingly

[R] Logistic regression with repeated measures

2008-02-11 Thread Steven Vamosi
Hello R list, I am hoping to conduct a logistic regression with repeated measures, and would love an actual code run through for such an analysis. I found only one related post on this list, but a full answer was never provided. I understand that the routine lmer (or lmer2) in the lme4 package is

[R] barplot or maybe related?

2008-02-11 Thread questions?
I have two distributions, represented by heights of several intervals. e.g. the distribution is partitioned into 10 segments, I have numbers(freq or counts) associated with each region in the format as: 0.2 0.3 0.1 0.1 . 0.01 0.02 I want to plot the two distributions side by side in

Re: [R] Loading Data to R

2008-02-11 Thread Gregory Warnes
On Microsoft Windows systems, it may be more convenient to install and use the XLSReadWRite packge. For non-windows systems, the gdata package provides this function, but requires perl to be present. -Greg (Maintainer of gdata) On Feb 9, 2008, at 1:09PM , Henrique Dallazuanna wrote: You

[R] Hastie - Tibshirani - Friedman pg 141 nnet question

2008-02-11 Thread G Ilhamto
Dear helper, I am working with a nnet using large data set (23K) and have some questions. I have a binary response (occurrence non-occurrence of event) with 8 predictors. (1) How can I reproduce plot in Hastie et al. (page 141), i.e. natural cubic splines of tensor product? (2) How does nnet

Re: [R] Dendrogram for agglomerative hierarchical clustering result

2008-02-11 Thread noorpiilur
Thank you for your reply Wolfgang I've seen these examples but my problem is that I don't know how to make the input data out of my given data. According to the example below hclust is making the clustering and will result in hclust object hc. In my case the clustering is already done and I need

[R] Difference between P.Value and adj.P.Value

2008-02-11 Thread Schmitt, Corinna
Hallo, fit12-lmFit(qrg[,1:2]) t12-toptable(fit12,adjust=fdr,number=25,genelist=qrg$genes[,1]) t12 ID logFC t P.Value adj.P.ValB 522PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965 1555 CD44_WIZ -6.569622 -8.227938 6.510169e-05 0.01212520

Re: [R] Length problem

2008-02-11 Thread Benilton Carvalho
if data was your data.frame, data[4:length(data)] was also a data.frame. but, c(data[4:length(data)] ) coerces it to a list. therefore coppie is a list. coppie[1] is also a list of length 1... compare that to: coppie[[1]] b On Feb 11, 2008, at 10:38 AM, milton ruser wrote: Ciao Paolo,

Re: [R] Length problem

2008-02-11 Thread jim holtman
You were asking for the length of the first element of the vector coppie, which is of course 1. Did you mean to say lgngth(coppie)? length(data[,4]) is asking how many elements in that column, which seems to be 5. also your statement coppie - c(data[4:length(data)]) seems strange. What did

Re: [R] Length problem

2008-02-11 Thread Paolo Grillo
Ciao Milthinho Here it is data yy mm dd C.531C.542 C.558C.565 1 2003 1 1 0.9941125 1.412338 0.8996750 2.258200 2 2003 1 2 1.7931375 2.786900NA 3.108725 3 2003 1 3NA 3.657775 1.7269750 2.541938 4 2003 1 4 1.0840625 1.766925

Re: [R] R programming style

2008-02-11 Thread Roland Rau
Hi, I think using Emacs+ESS [1,2] is always a good starting point for a clear layout with consistent and meaningful indentation. I don't know how other people think about it, but in my opinion, Elements of Programming Style by Kernighan and Plauger is still an interesting read -- although

[R] Odp: question_encoding

2008-02-11 Thread Petr PIKAL
Hi Is it only a question of PDF export or are the glyphs distorted in plot window too? If it is in plot window try to look into etc folder to Rdevga file. If it is during export from plot window to PDF then try to produce PDF file with pdf() plot(1,1, type=n) text(1,1, Ě Š Ť Č Ř Ň Á Í É

Re: [R] grep etc.

2008-02-11 Thread John Kane
I don't understand exactly what you are asking you can change v from 'insd-otsd' 'sppr-unsp' to 'insd--otsd', 'sppr--unsp' with sub(-, --,v) However do you want to change the entire assignment statement? --- Michael Kubovy [EMAIL PROTECTED] wrote: Dear R-helpers, How do I transform v -

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread bartjoosen
You can use a GUI to teach R, so the programming-style is gone. But using the command line aproach, it forces you to think about your analysis. In an GUI, it's easy to point and click, without knowing what you are doing. With the command line, you know where you start, and from there you go to

[R] Power law, lognormal end exponenntial statistical testing in one sample population

2008-02-11 Thread ΠΑΝΤΟΠΟΥΛΟΣ ΓΕΩΡΓΙΟ Σ
Hello, My name is George Pantopoulos, i am a phd student in the Dept. of Geology, University of Patras, Greece. I am studying the statistical behaviour of bed thickness datasets taken from outcrops. Until now, 4 statistical distributions seems to fit my datasets: power law, lognormal, lognormal

Re: [R] Conditional rows

2008-02-11 Thread Gabor Csardi
Because you need test = 0.2 | test 0.3 See ?| Gabor On Mon, Feb 11, 2008 at 09:12:57PM +0800, Stanley Ng wrote: That works beautfully. Why using test=0.2 || test 0.3 gives error ? -Original Message- From: Gabor Csardi [mailto:[EMAIL PROTECTED] Sent: Monday, February 11, 2008

Re: [R] RGTK2 and glade on Windows - GUI newbie

2008-02-11 Thread Liviu Andronic
On 2/11/08, Anja Kraft [EMAIL PROTECTED] wrote: I'd like to write a GUI (first choice with GTK+). There is also pmg [1] that uses GTK+. And, albeit more specific, playwith [2]. Also, creating a GUI under R issues were discussed previously, specifically this reference [3] may give you useful

[R] [R-pkgs] Release 3.2.0 of randomSurvivalForest is now availablle

2008-02-11 Thread Udaya B. Kogalur
Dear useRs: Release 3.2.0 of the CRAN package randomSurvivalForest is now available. -- Release 3.2.0 represents a significant upgrade in the functionality of the product. Key changes are as follows: o

Re: [R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]

2008-02-11 Thread Prof Brian Ripley
On Tue, 12 Feb 2008, [EMAIL PROTECTED] wrote: Thanks to all for your kind suggestions. After some discussion with our IT staff, I was told the UNIX system we have is Solaris and installation of R is very time consuming because Given that this software is not standard, and given the amount of

Re: [R] gcc 4.3 any known issues?

2008-02-11 Thread Prof Brian Ripley
On Mon, 11 Feb 2008, Peter Dalgaard wrote: Stefan Grosse wrote: Hi, Fedora is for Fedora 9 switching to gcc 4.3. Before I test it (rawhide) I want to be sure that R is running. So my question is whether there have been issues compiling R + packages using 4.3? I suspect that not many

Re: [R] WG: Tinn-R not working well with latest R

2008-02-11 Thread Gabor Grothendieck
Or try source(clipboard) On Feb 11, 2008 3:30 PM, Schmitt, Corinna [EMAIL PROTECTED] wrote: I am in R command window and just make Crt+V. Corinna -Ursprüngliche Nachricht- Von: Farrel Buchinsky [mailto:[EMAIL PROTECTED] Gesendet: Mo 11.02.2008 21:16 An: Schmitt, Corinna

Re: [R] image quality

2008-02-11 Thread Henrik Bengtsson
Have a look at the smoothScatter() function in the 'geneplotter' (Bioconductor) package. That might be sufficient for you. Alternatively, generate a bitmap (e.g. PNG) image plot instead (at least pdflatex can import those as is). /Henrik On Feb 11, 2008 2:18 AM, John Lande [EMAIL PROTECTED]

Re: [R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]

2008-02-11 Thread Don MacQueen
At 10:27 AM +1100 2/12/08, [EMAIL PROTECTED] wrote: Thanks to all for your kind suggestions. After some discussion with our IT staff, I was told the UNIX system we have is Solaris and installation of R is very time consuming because Given that this software is not standard, and given the amount

Re: [R] R programming style

2008-02-11 Thread Roland Rau
Hi, Earl F. Glynn wrote: Instead of using 1 or 2 in an apply, I'll write something like this trying for some sort of mnemonic apply(x, BY.ROW-1, sum) or apply(z, BY.COL-2, mean) It think it makes sense to use those magic numbers in the given case. Please let me give you several

Re: [R] overdispersion + GAM

2008-02-11 Thread Ravi Varadhan
No. Binomial data can indeed be overdispersed. See McCullagh Nelder (1989, section 4.5). Accounting for over(under)dispersion in binomial and Poisson distributions is, in fact, one of the original impetus for GEE type developments. See also a nice paper by Liang McCullagh (Biometrics 1993,

Re: [R] image quality

2008-02-11 Thread Philippe Glaziou
On 2/11/08, John Lande [EMAIL PROTECTED] wrote: I am writing a sweave documentation for my analysis, and I am plotting huge scatter plot data for microarray. unlucly this take a lot of resource to my pc because of the quality of the image which is to high (I see the PC get stuck for each

Re: [R] R programming style

2008-02-11 Thread Earl F. Glynn
David Scott [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] Can anyone provide further pointers to good style? While not written for R specifically, the book Code Complete: A Practical Handbook of Software Construction (2nd Edition) discusses a number of good concepts for writing

[R] How to fit discrete distribution to data in R having non standard shape?

2008-02-11 Thread Aswad Gurjar
Hello, I have 421 readings of time and no of requests coming at perticular time.Basically I have data with interval of one minute and corresponding no of requests arriving per minute.It is discrete in nature.I am collecting data from 9AM to 4PM.But some of readings are coming as 0.When I plotted

Re: [R] controlling the edge linewidth in Rgraphviz

2008-02-11 Thread Gabor Grothendieck
Check out: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/111006.html On Feb 11, 2008 9:56 PM, Adrian Dragulescu [EMAIL PROTECTED] wrote: Hello, I would like to have different linewidths for the edges of my graph. I read the documentation but could not find how to control this. On the

[R] controlling the edge linewidth in Rgraphviz

2008-02-11 Thread Adrian Dragulescu
Hello, I would like to have different linewidths for the edges of my graph. I read the documentation but could not find how to control this. On the Graphviz help page I've seen that there is something called penwidth but I could not find it in the R edge attributes. Thanks a lot for any help.

Re: [R] R on Mac PRO does anyone have experience with R on such a platform ?

2008-02-11 Thread Roger Day
My experience with R.app on a MACbook has been mostly very positive. I like the interface much better than that of Windows-- with two exceptions. a) I use stepping thru code with control-R. It's not as convenient on Mac- the code you want to run has to be actually selected; not good enough

Re: [R] User defined split function in rpart

2008-02-11 Thread R Help
I had a similar problem, trying to use lme within a custom rpart function. I got around it by passing the dataframe I needed through the parms option in rpart, and then using the parms option in evaluation, init and split as a dataset. It's not the most elegant solution, but it will work. Have

Re: [R] mistake during subscription

2008-02-11 Thread Ted Harding
On 11-Feb-08 16:34:36, Anna Meissner wrote: Dear R-helper, I made a mistake during my subscription, and think that I turned off from the mailing list. I confirm that I want to join the mailing list and wish to post some emails. Cheers, Anna Meissner Anna, If you [re-]visit the

Re: [R] how to generate a column based on other columns in a data frame

2008-02-11 Thread Gabor Grothendieck
Assuming this data frame: DF - data.frame(X = c(36.435, 36.435, 36.435, 35.329, 35.329, 36.431, 36.431, 35.421, 35.421, 35.421), Y = c(30.118, 30.118, 30.118, 29.657, 29.657, 30.111, 30.111, 29.797, 29.797, 29.797)) # Try this: DF$site - as.numeric(factor(interaction(DF$X, DF$Y))) If X and Y can

Re: [R] Length problem

2008-02-11 Thread milton ruser
Ciao Paulo, my.data-read.table(stdin(),head=T,sep=,) yy,mm,dd,C.531,C.542,C.558,C.565 2003,1,1,0.9941125,1.412338,0.8996750,2.258200 2003,1,2,1.7931375,2.786900,NA,3.108725 2003,1,3,NA,3.657775,1.7269750,2.541938 2003,1,4,1.0840625,1.766925,1.2313375,2.321300

[R] mistake during subscription

2008-02-11 Thread Anna Meissner
Dear R-helper, I made a mistake during my subscription, and think that I turned off from the mailing list. I confirm that I want to join the mailing list and wish to post some emails. Cheers, Anna Meissner [[alternative HTML version deleted]]

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread David Whiting
On Mon, Feb 11, 2008 at 07:37:04AM -0800, Neil Shephard wrote: Arin Basu-3 wrote: Comment 2: Finally, on a minor point, why is R the statistical software being used? SPSS is probably more widely available in the workplace – certainly in areas of social policy etc. (Prof NB)

[R] how to generate a column based on other columns in a data frame

2008-02-11 Thread Weidong Gu
HI, I am working on a data set with multiple collections of mosquitoes at sampling sites. Each row represents a collection of individual samples with coordinates for each collection. ... X, Y,... 1 36.435 30.118 2 36.435 30.118 3 36.435 30.118 4 35.329 29.657 5 35.329 29.657 6

Re: [R] Difference between P.Value and adj.P.Value

2008-02-11 Thread john seers (IFR)
Hi Corinna The p.adjusted value is the the p-value adjusted for Multiple Comparisons. Enter ?p.adjust to get more of an explanation. Regards JS --- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Schmitt, Corinna Sent: 11 February 2008 16:02 To:

[R] ROracle for windows

2008-02-11 Thread Daniel Ito
.. Somebody can help me to connect Oracle data base with R ? i`m just a user of this software and i don`t know about this especial thinks! sorry about my english... att -- Atenciosamente Daniel Ito Estatística UNICAMP EPR - CPFL [[alternative HTML version deleted]]

Re: [R] Length problem

2008-02-11 Thread milton ruser
Ciao Paolo, How about you show some row of your data? How many columns have your data.frame? One? By the way data is not a so good name for your data frame. We will be very happy to help you Kindly, Miltinho Brasile On 2/11/08, Paolo Grillo [EMAIL PROTECTED] wrote: Hi all I have this

[R] overdispersion + GAM

2008-02-11 Thread anna banana
Hi, there are a lot of messages dealing with overdispersion, but I couldn't find anything about how to test for overdispersion. I applied a GAM with binomial distribution on my presence/absence data, and would like to check for overdispersion. Does anyone know the command? Many thanks, Anna --

[R] Length problem

2008-02-11 Thread Paolo Grillo
Hi all I have this problem: In my database .dta, called data I have five rows data-read.dta(C:\\2_CO_mmobile_ALL_Rid.dta) # From this database I wuold like to create another coppie-c(data[4:length(data)]) but I find this # Length of original data length(data[,4])

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread Bernard Leemon
Hi Arin, Others have commented wisely an your first issue. As for your 2nd issue, I had my own concerns about using R in undergraduate teaching because I had always used a point-and-click program for that level. I should not have worried. The current generation has been typing on their

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread Stas Kolenikov
I've been teaching an intro stats class to engineering students (who are better in calculus and math than med students, I would imagine), and use of R has never been received very warmly. I might not be teaching it right, but their (quite valid, from their standpoint) concerns were that they would

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread Longinus
I will also evaluate what did the students used before in the introductory statistics class and how proficient they have become in using it. If they only barely touched it, I will use my class as a chance to further refine their familiarity with the software they saw before. Tool is tool, I

Re: [R] R programming style

2008-02-11 Thread Bernard Leemon
I just got a copy of A First Course in Statistical Programming with R by W. John Braun and Duncan J. Murdoch. Cambridge. at amazon: http://www.amazon.com/First-Course-Statistical-Programming-R/dp/0521694248/ first couple of chapters are base R that most everyone would know before wanting to

[R] Lower Confidence Bound

2008-02-11 Thread Feifei
Hi, I'm doing analysis of microarray data with affylmGUI package, and to make a comparison by using affylmGUI and dChip ( http://biosun1.harvard.edu/complab/dchip/ another tool to analyse microarrays). I'm trying to use the same criteria as many as I can, but there's a 90% lower confidence bound

Re: [R] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]

2008-02-11 Thread Jin.Li
Thanks to all for your kind suggestions. After some discussion with our IT staff, I was told the UNIX system we have is Solaris and installation of R is very time consuming because Given that this software is not standard, and given the amount of time required to compile the software (and

Re: [R] Conditional rows

2008-02-11 Thread Stanley Ng
That works beautfully. Why using test=0.2 || test 0.3 gives error ? -Original Message- From: Gabor Csardi [mailto:[EMAIL PROTECTED] Sent: Monday, February 11, 2008 18:27 To: Ng Stanley Cc: r-help Subject: Re: [R] Conditional rows which(apply(test=0.2, 1, all)) See ?which, ?all, and

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread John Fox
Dear Arin, -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] project.org] On Behalf Of Arin Basu Sent: February-10-08 10:41 PM To: r-help@r-project.org Subject: [R] Using R in a university course: dealing with proposal comments Hi All, I am scheduled to

Re: [R] RGTK2 and glade on Windows - GUI newbie

2008-02-11 Thread Felix Andrews
Yes, a GUI based on GTK+ (with or without Glade) will work on Windows XP. If what you want to do is relatively straightforward (say, without any fancy formatting, or advanced event handling) then you should consider gWidgets. Look at the vignette in the gWidgets package. If you do decide to go

[R] PDF with computationally expensive normalizing constant

2008-02-11 Thread Robin Hankin
Hi I am writing some functionality for a multivariate PDF. One problem is that evaluating the normalizing constant (NC) is massively computationally intensive [one recent example took 4 hours and bigger examples would take much much longer] and it would be good allow for this in the design of

Re: [R] Dendrogram for agglomerative hierarchical clustering result

2008-02-11 Thread Wolfgang Huber
Hi Risto, You could try example(dendrogram) best wishes Wolfgang noorpiilur scripsit: Hey group, I have a problem of drawing dendrogram as the result of my program written in C. My algorithm is a approximation algorithm for single linkage method. AS a result I will get the

Re: [R] local variance estimation using gam or locfit

2008-02-11 Thread Takatsugu Kobayashi
Hi, I appreciate if any one could give me clues about the following problem. I have a map data, x, y, z, and d, where (x,y) is the coordinate of a point and d is a distance from the urban center (0,0), and z is population density. Then I would like to calculate local standard deviations of

Re: [R] Help with write.csv

2008-02-11 Thread Richard . Cotton
I am new to R. I am using the impute package with data contained in csv file. I have followed the example in the impute package as follows: mydata = read.csv(sample_impute.csv, header = TRUE) mydata.expr - mydata[-1,-(1:2)] mydata.imputed - impute.knn(as.matrix(mydata.expr)) The

[R] svm: is this right?

2008-02-11 Thread Weiwei Shi
Hi, I have a question on using svm{e1071} for a classification task: No matter how I split the data into training and test, I always end with a perfect accuracy in training but sensitivity = 0 for test. One example is like this 1 2 1 209 0 2 0 67 pred1 1 2 1 47 0 2

Re: [R] learning S4

2008-02-11 Thread Robin Hankin
Christophe you might find the Brobdingnag package on CRAN helpful here. I wrote the package partly to teach myself S4; it includes a vignette that builds the various S4 components from scratch, in a step-by-step annotated cookbook. HTH rksh On 8 Feb 2008, at 15:30, [EMAIL PROTECTED]

Re: [R] Tinn-R not working well with latest R

2008-02-11 Thread Farrel Buchinsky
I can easily get R to open without an error. I simply removed the Tinn-R related lines from the Rprofile.site file C:\Program Files\R-2.6.2\etc\Rprofile.site but then when I try to manually load the svIDE library by entering library(svIDE) from the command line, I get a similar error. So when

Re: [R] R programming style

2008-02-11 Thread Scillieri, John
I second that, Code Complete is a great book! For anyone interested in improving their code no matter what language, (it has a C++/Java-type focus but is definitely applicable to R), it would definitely be a good place to start. I've read some negative reviews claiming that everything he writes

Re: [R] Viable Approach to Parallel R?

2008-02-11 Thread Scillieri, John
We've also had substantial success with the Condor project [http://www.cs.wisc.edu/condor/], not just with R, but as a generic computation grid. John -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Lewis, Daniel (IS Consultant) Sent: Monday, February

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread Neil Shephard
Neil Shephard wrote: (Most) of this problem isn't negated when using R. Start a new job and use the (excellent, extensible, and free) software that you've been using for years. Apologies for the double negative, that should have read (Most) of this problem _is_ negated when using R.

Re: [R] how to generate a column based on other columns in a data frame

2008-02-11 Thread Peter Dalgaard
Henrique Dallazuanna wrote: Try this: x2 - merge(x, cbind(unique(x), Site=sprintf(S%d, seq_len(nrow(unique(x), by=c(X, Y)) x2[order(x2$site)] That was (close to) my first thought as well. But what about site - with(x, interaction(X,Y, drop=TRUE)) levels(site) - paste(S,

Re: [R] [OT] good reference for mixed models and EM algorithm

2008-02-11 Thread Ravi Varadhan
Hi Doug Ted, The multivariate Aitken accelerator suggested by Ted is numerically ill-conditioned. I have written a globally-convergent, general-purpose EM accelerator that works well. It is quite simple to implement for any EM-type algorithm (e.g. ECM, ECME which are all monotone in

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread Paul Gilbert
Stas Kolenikov wrote: ... Training researchers of tomorrow might be great, but ifyour students get on the market in the end of the semester, they won't have the luxury of waiting until R becomes THE package of choice. Not being a teacher, I usually follow these discussions with a bit of

Re: [R] [OT] good reference for mixed models and EM algorithm

2008-02-11 Thread Ted Harding
On 11-Feb-08 15:07:37, Douglas Bates wrote: [...] Except that Doug Bates doesn't use the EM algorithm for fitting mixed models any more. The lme4 package previously had an option for starting with EM (actually ECME, which is a variant of EM) iterations but I have since removed it. For large

Re: [R] Length problem

2008-02-11 Thread Henrique Dallazuanna
I think that coppie is a list, so length(coppie[[1]]) On 11/02/2008, Paolo Grillo [EMAIL PROTECTED] wrote: Hi all I have this problem: In my database .dta, called data I have five rows data-read.dta(C:\\2_CO_mmobile_ALL_Rid.dta) # From this database I wuold like to create

Re: [R] genetics package not working

2008-02-11 Thread Farrel Buchinsky
Finally I found something that provides lower level examples. I was looking around the genetics package. I came across write.pop.file(genetics) and there I found the format of 'pedigree' files is documented at http://www.sph.umich.edu/csg/abecasis/GOLD/docs/pedigree.html That reference lays out

Re: [R] [OT] good reference for mixed models and EM algorithm

2008-02-11 Thread Douglas Bates
On Feb 10, 2008 2:32 PM, Spencer Graves [EMAIL PROTECTED] wrote: Hi, Erin: Have you looked at Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer)? As far as I know, Doug Bates has been the leading innovator in this area for the past 20 years. Pinheiro was

Re: [R] building packages for Linux vs. Windows

2008-02-11 Thread Paul Gilbert
Erin Hodgess wrote: Hi R People: I sure that this is a really easy question, but here goes: I'm trying to build a package that will run on both Linux and Windows. However, there are several commands in a section that will be different in Linux than they are in Windows. Erin Several

[R] Tinn-R not working well with latest R

2008-02-11 Thread Schmitt, Corinna
Hallo, I had the same problems before. I think the best solution is that you just copy the needed codepart out of Tinn-R with Ctr+C. Then open R directly from your desktop NOT from Tinn-R. Than paste in the command. you can still make changes in the command when you have not pressed enter

[R] nlme special case of corARMA?

2008-02-11 Thread Reid Landes
Dear All: I am trying to fit a special case of a 2-banded Toeplitz correlation structure. A 2-banded Toeplitz has ones on the diagonal, a correlation, RHO1, on the first off-diagonal, and a correlation, RHO2, on the second off-diagonal, with zeros on all subsequent off-diagonals. After reading

Re: [R] Using R in a university course: dealing with proposal comments

2008-02-11 Thread Neil Shephard
Arin Basu-3 wrote: Comment 2: Finally, on a minor point, why is R the statistical software being used? SPSS is probably more widely available in the workplace – certainly in areas of social policy etc. (Prof NB) What struck me in the above is the probably. How probable is it,

[R] Gini index of frequencies in a data frame

2008-02-11 Thread m. teodosiu
Dear All, I wish to calculate the Gini index (ineq from same package) and some other indices for the diameter distribution of each plot (df dgtot). dgtot: IDPlotDiameter(cm) 14 34.0 24 23.0 34 38.0 ... 51 5 16.0 52 5 8.0 53 5 9.0 ... 5301

Re: [R] tree() producing NA's

2008-02-11 Thread Prof Brian Ripley
Take a look at the levels of 'owner'. On Mon, 11 Feb 2008, Amnon Melzer wrote: Hi Hoping someone can help me (a newbie). I am trying to construct a tree using tree() in package tree. One of the fields is a factor field (owner), with many levels. In the resulting tree, I see many NA's

[R] Any one is porting or has ported prtools (http://www.prtools.org/) to R ?

2008-02-11 Thread Kwang Loong Stanley Ng
Hi, Any one is porting or has ported prtools (http://www.prtools.org/) to R ? Thanks Stanley __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] scatterplot in CAR

2008-02-11 Thread John Fox
Dear Aimin, -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] project.org] On Behalf Of Aimin Yan Sent: February-11-08 7:22 AM To: r-help@r-project.org Subject: [R] scatterplot in CAR I am trying to use scatterplot function in CAR like the following:

[R] scatterplot in CAR

2008-02-11 Thread Aimin Yan
I am trying to use scatterplot function in CAR like the following: scatterplot(X~Y) I want to label X points and Y ponits using the different color. Any idea for this? Aimin __ R-help@r-project.org mailing list

Re: [R] The function predict

2008-02-11 Thread Dieter Menne
Carla Rebelo crebelo at liaad.up.pt writes: May you help me? I need to understand the function predict. I need to understand the algorithm implemented, the calculations associated. Where can I find this information? In the documentation: predict is a generic function for predictions from

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