Re: [R] Help with rgl

2009-02-18 Thread Wacek Kusnierczyk
roger koenker wrote: Why I love R [Number 6]: Chinese extend a helping hand to Russians who happen to be in Brazil about a package written in Germany. Trotsky would be proud -- and amazed! ... and it's so . r specific! vQ __

Re: [R] Added system Info:--Segmentation Fault occured while connecting to the database

2009-02-18 Thread Prof Brian Ripley
Your R is ancient, and the R posting guide asked you to update before posting. This is a problem in a contributed DBMS package, so the posting guide asked you to contact the maintainer and the R-sig-db list would be the appropriate list to use. But please ensure you are using a current

[R] Remove top-K elements in Vector

2009-02-18 Thread Gundala Viswanath
Hi all, Suppose I hve this vector: x [1] 3 4 7 17 22 12 15 12 3 3 1 1 How can I remove the top-3 element. Yielding only: [1] 17 22 12 15 12 3 3 1 1 - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list

[R] which test-statistic to use for quasibinomial GLMs?

2009-02-18 Thread Thomas Mang
Hi, I have fitted quasibinomial GLM [glm(y ~ ..., family = quasibinomial)] to a binary response variable; quasibinomial, because there were clear signs of underdispersion in a 'simple' binomial GLM, and so the dispersion is a free parameter in the model. My question is now: In a

Re: [R] Remove top-K elements in Vector

2009-02-18 Thread Dimitris Rizopoulos
try this: x[-(1:3)] # or tail(x, -3) Best, Dimitris Gundala Viswanath wrote: Hi all, Suppose I hve this vector: x [1] 3 4 7 17 22 12 15 12 3 3 1 1 How can I remove the top-3 element. Yielding only: [1] 17 22 12 15 12 3 3 1 1 - Gundala Viswanath Jakarta - Indonesia

Re: [R] Remove top-K elements in Vector

2009-02-18 Thread ONKELINX, Thierry
Have a look at ?tail tail(x, -3) should do the trick. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg

[R] R as a web scraping tool using RCurl

2009-02-18 Thread Harsh
Hi List, I am trying to leverage my knowledge of R in trying to use it for tasks that may not make R the best choice for these tasks. I wish to automate a web scraping task, which requires a multi-step procedure: 1) log in to a website 2) Go to a particular page 3) From the drop down menu, click

Re: [R] R as a web scraping tool using RCurl

2009-02-18 Thread Ajay ohri
Try Firefox and an add in called I Macros from www.iopus.com as an simpler alternative read some stuff here http://www.decisionstats.com/2009/01/web-crawling-automation/ regards, Ajay On Wed, Feb 18, 2009 at 2:06 PM, Harsh singhal...@gmail.com wrote: Hi List, I am trying to leverage my

[R] Barplot with Sorted X-Axis

2009-02-18 Thread Gundala Viswanath
Hi, I have a binned data that looks like this. (8.048,18.05] (-21.95,-11.95] (-31.95,-21.95] (18.05,28.05] (-41.95,-31.95] 81 76 18 18 12 (-132,-122] (-122,-112] (-112,-102] (-162,-152] (-102,-91.95]

[R] Color Function

2009-02-18 Thread enrico.fosco...@libero.it
Good Morning to Everybody, I am searching a function which could define a vector of colors from a vector of gray, from white to black (not from black to white as the function gray()). I have to use it in the function image(), parameter col. Thank You very much, Enrico Foscolo

Re: [R] Percentiles/Quantiles with Weighting

2009-02-18 Thread Thomas Lumley
On Tue, 17 Feb 2009, Brigid Mooney wrote: Thanks for pointing me to the quantreg package as a resource. I was hoping to ask be able to address one quick follow-up question... I get slightly different variants between using the rq funciton with formula = mydata ~ 1 as I would if I ran the same

Re: [R] Help with rgl

2009-02-18 Thread Uwe Ligges
Yihui Xie wrote: Chinese extend a helping hand to Russians who happen to be in Brazil about a package written in Germany, which gladdened an American. Trotsky would be even more proud -- and amazed!! :-) Please note that rgl is maintained by a Canadian and two others (O. Nenadić and W.

Re: [R] Color Function

2009-02-18 Thread Uwe Ligges
enrico.fosco...@libero.it wrote: Good Morning to Everybody, I am searching a function which could define a vector of colors from a vector of gray, from white to black (not from black to white as the function gray()). rev(gray()) Uwe Ligges I have to use it in the function image(),

Re: [R] Possible Cause of Segmentation Fault

2009-02-18 Thread Uwe Ligges
Moumita Das wrote: Hi All, If you have already finished reading my previous emails regarding segmentation fault , please have a look at this .I think this may help you to diagnose the reason for the segmentation fault and help me,because i don't understand much. Rather than running the

Re: [R] matrix output

2009-02-18 Thread Jim Lemon
phoebe kong wrote: Hi friends, I have questions about printing a pretty big size matrix. As you could see from below, the matrix wasn't showed in R at full size (11X11), but it was cut partly into three smaller matrices (11X4,11X4,11X3). I'm wondering if there is a way to show the whole matrix

Re: [R] Barplot with Sorted X-Axis

2009-02-18 Thread Jim Lemon
Gundala Viswanath wrote: Hi, I have a binned data that looks like this. (8.048,18.05] (-21.95,-11.95] (-31.95,-21.95] (18.05,28.05] (-41.95,-31.95] 81 76 18 18 12 (-132,-122] (-122,-112] (-112,-102]

Re: [R] Python and R

2009-02-18 Thread Gabor Grothendieck
On Tue, Feb 17, 2009 at 6:59 PM, Esmail Bonakdarian esmail...@gmail.com wrote: Well, I have a program written in R which already takes quite a while to run. I was just wondering if I were to rewrite most of the logic in Python - the main thing I use in R are its regression facilities - if it

[R] distance betwenn axis and axis annotation

2009-02-18 Thread Luis Ridao Cruz
R-help, How can I specify the distance between the axis and axis annotation? Thanks in advance __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] distance betwenn axis and axis annotation

2009-02-18 Thread Dimitris Rizopoulos
have a look at ?par() and specifically parameter 'mgp', e.g., compare par(mfrow = c(1, 2)) plot(1, 1) plot(1, 1, mgp = c(2.5, 0.5, 0)) I hope it helps. Best, Dimitris Luis Ridao Cruz wrote: R-help, How can I specify the distance between the axis and axis annotation? Thanks in advance

Re: [R] distance betwenn axis and axis annotation

2009-02-18 Thread Duncan Murdoch
Luis Ridao Cruz wrote: R-help, How can I specify the distance between the axis and axis annotation? I don't think you can do this directly, but you can do it using mtext. For example: x - 1:10 y - rnorm(10) plot(x,y, axes=F) box() at - pretty(x) min - par(usr)[1] max - par(usr)[2] at

Re: [R] Python and R

2009-02-18 Thread Barry Rowlingson
2009/2/17 Esmail Bonakdarian esmail...@gmail.com: Well, I have a program written in R which already takes quite a while to run. I was just wondering if I were to rewrite most of the logic in Python - the main thing I use in R are its regression facilities - if it would speed things up. I

Re: [R] Subset Regression Package

2009-02-18 Thread Pedro Silva
-- Message: 72 Date: Tue, 17 Feb 2009 22:05:46 퍍 (UTC) From: Hans W. Borchers hwborch...@gmail.com Subject: Re: [R] Subset Regression Package To: r-h...@stat.math.ethz.ch Message-ID: loom.20090217t215556-...@post.gmane.org Content-Type: text/plain; charset=us-ascii

Re: [R] Python and R

2009-02-18 Thread Esmail Bonakdarian
Gabor Grothendieck wrote: See ?Rprof for profiling your R code. If lm is the culprit, rewriting your lm calls using lm.fit might help. Yes, based on my informal benchmarking, lm is the main bottleneck, the rest of the code consists mostly of vector manipulations and control structures. I

[R] bitmap .tif in colors

2009-02-18 Thread Lauri Nikkinen
Hello, How to produce .tif graphic in colors using bitmap function? e.g this produces figure in grayscale bitmap(file=volc.tif, type = tifflzw, res = 300) image(t(volcano)[ncol(volcano):1,]) dev.off() I'm using Windows XP and ghostscript. R.Version() $platform [1] i386-pc-mingw32 $arch [1]

Re: [R] Python and R

2009-02-18 Thread Gabor Grothendieck
On Wed, Feb 18, 2009 at 7:27 AM, Esmail Bonakdarian esmail...@gmail.com wrote: Gabor Grothendieck wrote: See ?Rprof for profiling your R code. If lm is the culprit, rewriting your lm calls using lm.fit might help. Yes, based on my informal benchmarking, lm is the main bottleneck, the rest

Re: [R] bitmap .tif in colors

2009-02-18 Thread Uwe Ligges
Lauri Nikkinen wrote: Hello, How to produce .tif graphic in colors using bitmap function? e.g this produces figure in grayscale bitmap(file=volc.tif, type = tifflzw, res = 300) image(t(volcano)[ncol(volcano):1,]) dev.off() Why not upgrade R and use the tiff() device? Uwe Ligges I'm

Re: [R] cumsum vs. sum

2009-02-18 Thread Martin Maechler
GaGr == Gabor Grothendieck ggrothendi...@gmail.com on Tue, 17 Feb 2009 20:53:18 -0500 writes: GaGr Check out sum.exact and cumsum.exact in the caTools package. library(caTools) GaGr Loading required package: bitops x - 1/(12:14) sum(x) - cumsum(x)[3] GaGr [1]

[R] alpha shape function

2009-02-18 Thread Pedroso MOACIR
Hi all, I want to approximate te shape of an area defined by a set of points. The convex hull is not good enough, but I think that an alpha shape would be fine. I did an RSiteSearch(), google search, RSeek.org search, looked at the CRAN Views, but was unable do find a function in R that

Re: [R] using stepAIC with negative binomial regression - e rror message help

2009-02-18 Thread Ben Bolker
t c mudiver1200 at yahoo.com writes: Dear List, I am having problems running stepAIC with a negative binomial regression model.  I am working with data on manta ray abundance, using 20 predictor variables.  [snip] The model I ran was: glm.nb.fullglm.nb(mantas~site+year+

[R] Counting/processing a character vector

2009-02-18 Thread Gavin Simpson
Dear List, I have a data set stored in the following format: head(dat, n = 10) id sppcode abundance 1 10307 1000 1 2 10307 16220602 2 3 10307 2000 5 4 10307 2011 2 5 10307 2400 1 6 10307 402183 7 10307 40210102

Re: [R] distance betwenn axis and axis annotation

2009-02-18 Thread Duncan Murdoch
On 18/02/2009 7:50 AM, Mark Difford wrote: Duncan Murdoch wrote: I don't think you can do this directly, but you can do it using mtext. This is not correct. It was correct at the time I wrote it. Of course things have changed now that you and Dimitris have been so helpful: now I *do*

[R] Training nnet in two ways, trying to understand the performance difference - with (i hope!) commented, minimal, self-contained, reproducible code

2009-02-18 Thread Tony Breyal
Dear all, Objective: I am trying to learn about neural networks. I want to see if i can train an artificial neural network model to discriminate between spam and nonspam emails. Problem: I created my own model (example 1 below) and got an error of about 7.7%. I created the same model using the

Re: [R] alpha shape function

2009-02-18 Thread roger koenker
As it happens, I have also been looking into this. I began by considering Ken Clarkson's hull: http://www.netlib.org/voronoi/hull.html but eventually discovered that its alpha shapes don't seem to treat holes in regions, only simply connected regions. (I would be happy to hear to the

Re: [R] Normal cdf modified function

2009-02-18 Thread dwinsemius
I would think this could be approached by segmenting the probability volume using identities such as these: P(Y1 Z1, Y2 Z2, Y3 Z3, Y4 Z4) + P(Y1 Z1, Y2 Z2, Y3 Z3, Y4 Z4) = P(Y1 Z1, Y2 Z2, Y3 Z3, Y4 Inf) and P(Y1 Z1, Y2 Z2, Y3 Z3, Y4 Inf) + P(Y1 Z1, Y2 Z2, Y3 Z3, Y4 Inf)

Re: [R] Plotting Binned Data

2009-02-18 Thread Ben Bolker
Gundala Viswanath wrote: Dear all, I have a binned data that looks like this: dat (-1,9] (9,19] (19,29] (29,39] (39,49] (49,59] (59,69] (69,79] 10063374 79 1643443 (79,89] (89,99] 62 I tried to plot a

Re: [R] Python and R

2009-02-18 Thread Kenn Konstabel
lm does lots of computations, some of which you may never need. If speed really matters, you might want to compute only those things you will really use. If you only need coefficients, then using %*%, solve and crossprod will be remarkably faster than lm # repeating someone else's example #

Re: [R] Cross classified or Multiple membership or Hierarchical (3level ) logistic models using Umacs

2009-02-18 Thread Doran, Harold
If the data are cross-classified, then hwy would you want a hierarchical linear model? You might try the lmer function for this instead. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Luwis Tapiwa Diya Sent: Tuesday, February

Re: [R] Python and R

2009-02-18 Thread Doran, Harold
lm(y ~ x-1) solve(crossprod(x), t(x))%*%y# probably this can be done more efficiently You could do crossprod(x,y) instead of t(x))%*%y __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] Counting/processing a character vector

2009-02-18 Thread Gavin Simpson
Apologies, Jim Holtman has pointed out a couple of problems/queries with my original email that I would like to make clear. Firstly, I introduced a typo when trying to be helpful. In my email below, I had incorrectly typed out one of the species codes I would count: 1000 16220602 2011

Re: [R] distance betwenn axis and axis annotation

2009-02-18 Thread Mark Difford
Duncan Murdoch wrote: There's no real difficulty there: axis takes an mgp arg as well. Thanks for that. A good bit of practical advice, which I hadn't yet clicked on. I won't comment on the thinking thing;) Regards, Mark. Duncan Murdoch-2 wrote: On 18/02/2009 7:50 AM, Mark Difford wrote:

Re: [R] Subset Regression Package

2009-02-18 Thread Alex Roy
Thank you very much for your help Alex On Wed, Feb 18, 2009 at 1:26 PM, Pedro Silva psi...@porto.ucp.pt wrote: -- Message: 72 Date: Tue, 17 Feb 2009 22:05:46 퍍 (UTC) From: Hans W. Borchers hwborch...@gmail.com Subject: Re: [R] Subset Regression Package To:

Re: [R] bitmap .tif in colors

2009-02-18 Thread Lauri Nikkinen
Thanks. I upgraded to R 2.8.1 and tried tiff(filename = volc.tif, width=600, height=400, compression = none, bg = white, res = 300) image(t(volcano)[ncol(volcano):1,]) dev.off() but this produces error Error in plot.new() : figure margins too large How this should be modified to produce a

Re: [R] Help with rgl

2009-02-18 Thread Iuri Gavronski
The funniest part is that we are close to carnival in Brazil... vacation time... more than 30C... and I am the one to try to get back to the track... Any clue on how to rotate the object? Examples? Also, still on the same object. If I change zoom, position, etc. with the mouse, where to query

Re: [R] Normal cdf modified function

2009-02-18 Thread Giovanni Petris
Let Y be a normal multivariate function. For example, let Y have 4 dimensions. I want to calculate P(Y1 Z1, Y2 Z2, Y3 Z3, Y4 Z4). There are R functions to do the calculation if all the inequalities are of the type (the cdf). But is there an R function where the The cdf, and some

Re: [R] bitmap .tif in colors

2009-02-18 Thread Uwe Ligges
Lauri Nikkinen wrote: Thanks. I upgraded to R 2.8.1 and tried tiff(filename = volc.tif, width=600, height=400, compression = none, bg = white, res = 300) image(t(volcano)[ncol(volcano):1,]) dev.off() but this produces error Error in plot.new() : figure margins too large How this should be

Re: [R] Help with rgl

2009-02-18 Thread Duncan Murdoch
On 18/02/2009 10:00 AM, Iuri Gavronski wrote: The funniest part is that we are close to carnival in Brazil... vacation time... more than 30C... and I am the one to try to get back to the track... Any clue on how to rotate the object? Examples? example(spin3d) Also, still on the same

Re: [R] bitmap .tif in colors

2009-02-18 Thread Prof Brian Ripley
On Wed, 18 Feb 2009, Lauri Nikkinen wrote: Thanks. I upgraded to R 2.8.1 and tried tiff(filename = volc.tif, width=600, height=400, compression = none, bg = white, res = 300) image(t(volcano)[ncol(volcano):1,]) dev.off() but this produces error Error in plot.new() : figure margins too large

Re: [R] Barplot with Sorted X-Axis

2009-02-18 Thread Gundala Viswanath
Hi Jim, or sorting the columns of the above table if that is what you are using to plot. How do you do that? Yes I am using that data exactly for the plotting. - GV. Jim __ R-help@r-project.org mailing list

Re: [R] bitmap .tif in colors

2009-02-18 Thread Lauri Nikkinen
Thanks Prof Ripley, now I understood. tiff(filename = volc.tif, width=600, height=400, compression = none, bg = white, res = 300, pointsize=3) par(mar=c(3,3,2,2), cex=1) image(t(volcano)[ncol(volcano):1,], xaxt=n, yaxt=n) axis(1, at=seq(0, 1, 0.1), cex.axis=0.8, tick=T) axis(2, at=seq(0, 1, 0.1),

Re: [R] alpha shape function

2009-02-18 Thread Yihui Xie
Hi, If the convex hull for *all* the data points is not ideal enough, is it feasible to break the data into small subsets using clustering methods such as kmeans() and compute the convex hull for each cluster? Finally we are able to know the borders of all clusters using chull(); I don't know how

Re: [R] Chromatogram deconvolution and peak matching

2009-02-18 Thread Michael Lawrence
Just to be sure you're aware, there are packages for chromatograpy and mass spec data in Bioconductor. Like xcms. Don't think any will directly address your problem, but they might be useful. Michael On Tue, Feb 17, 2009 at 5:44 AM, bartjoosen bartjoo...@hotmail.com wrote: Hi, I'm trying to

Re: [R] cumsum vs. sum

2009-02-18 Thread Martin Maechler
SM == Stavros Macrakis macra...@alum.mit.edu on Wed, 18 Feb 2009 10:00:40 -0500 writes: SM Nice! Glad to hear it. It sounds as though it is still possible for SM cumsum(x)[length(x)] to not be exactly equal to sum, though? Well, possible, probably yes, platform-dependently;

[R] multidimensional scaling with long form data

2009-02-18 Thread Kirsten Beyer
I have a dissimilarity dataset with the form: 1 1 dissimilarity value 1 2 ... 1 3 1 4 2 2 2 3 2 4 ... I would like to do nonmetric multidimensional scaling with this data, but I am having trouble using this format. I would like to either find a function that accepts this format or find

[R] March ** R ** course in New York City *** by XLSolutions Corp

2009-02-18 Thread s...@xlsolutions-corp.com
XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce our*** R/Splus Fundamentals and Programming Techniques and R Advanced Programming***courses at USA locations for March - April 2009. * New York City ** March 19-20, 2009 R/Splus Fundamentals and

Re: [R] cumsum vs. sum

2009-02-18 Thread Stavros Macrakis
Hmm. Why not use the same method to guarantee the same result? Or at least document the possibility that cumsum(x)[length(x)] != sum(x)... that seems like an easy trap to fall into. -s On Wed, Feb 18, 2009 at 11:39 AM, Martin Maechler maech...@stat.math.ethz.ch wrote: SM == Stavros

Re: [R] Barplot with Sorted X-Axis

2009-02-18 Thread Greg Snow
Can you show us the code used to get the data? The usual methods that I can think of would have sorted the columns correctly for you. The fact that this is not the case indicates that you are using a different method, or doing something that looses the information along the way. If you show

Re: [R] Counting/processing a character vector

2009-02-18 Thread Gavin Simpson
To answer my own post, and for the archives (hopefully not that anyone has to repeat what I had to do ;-), after much hair-pulling , frowning at the screen and general dumb headedness the following slab of R code achieves the results I wanted. It isn't elegant but does a job. msr - function(x) {

Re: [R] How to create sequence of constant time interval

2009-02-18 Thread Gabor Grothendieck
For version 2.3-30 of chron which just appeared on CRAN this can be simplified to: library(chron) tt - times(0:47/48) tt chron(1/1/09, tt) # no rep needed On Mon, Feb 16, 2009 at 6:04 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Try this (and see R News 4/1 for more). library(chron)

Re: [R] cumsum vs. sum

2009-02-18 Thread Duncan Murdoch
On 18/02/2009 12:41 PM, Stavros Macrakis wrote: Hmm. Why not use the same method to guarantee the same result? Or at least document the possibility that cumsum(x)[length(x)] != sum(x)... that seems like an easy trap to fall into. Assuming equality of floating point numbers computed by two

[R] Help on warning message from Neg. Binomial error during glm

2009-02-18 Thread Mahua Ghara
I am using glm.nb, a ~b*c ( b is categorical and c is continuous). when I run this model I get the warning message: Warning messages: 1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace : iteration limit reached 2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit,

[R] R code compiled, assembled or interpreted?

2009-02-18 Thread francogrex
Hi all, do you know if an R program is compiled to machine language when executed? And also is there any way to disassemble an R code/program: to see how it is generating the machine instructions for the processor? Thanks -- View this message in context:

[R] swich off printed info

2009-02-18 Thread robin
Dear R users, I use function kqr from package kernlab a large number of time and every time it is used it prints an info message which slows the process. Please note that it is not a warning message or an error message and that there is no info option in the function that could be set to

Re: [R] Training nnet in two ways, trying to understand the performance difference - with (i hope!) commented, minimal, self-contained, reproducible code

2009-02-18 Thread Tony Breyal
hmm, further investigation shows that two different fits are used. Why did nnet decide to use different fits when the data is basically the same (2 factors in nn1 and binary in nn2)? # uses an entropy fit (maximum conditional likelihood) nn1 a 57-3-1 network with 178 weights inputs: make

[R] auto.arima in forecasting package

2009-02-18 Thread emj83
I am using auto.arima to find the best arima model but am a little confused by the output. I want to choose the best model using the BIC criteria. This is my code (straightforward where a is the data)

[R] No results show up when running Rmdr

2009-02-18 Thread Andrew
Hi all, When running Rmdr using the demo data file using the following commands: data(mdrdata) cvk-10 nbr=2 res-rmdr(mdrdata,10,2, randomize=TRUE) I could not find the statistical results, but like this: [1] 1 Cross Validation 1 Wed Feb 18 09:05:23 2009 The best set of loci is 13 17 Cross

Re: [R] multidimensional scaling with long form data

2009-02-18 Thread Marcelino de la Cruz
This is my approach: If cosa is your data.frame . e.g. cosa i1 i2 dis [1,] 1 1 0.00 [2,] 1 2 0.93 [3,] 1 3 0.80 [4,] 1 4 1.00 [5,] 2 2 0.00 [6,] 2 3 0.02 [7,] 2 4 0.22 [8,] 3 3 0.00 [9,] 3 4 0.95 [10,] 4 4 0.00 # first crate a square matrix of

[R] C# / R interface problem

2009-02-18 Thread jonboyGaTech
This is my situation: I have a significant amount of data, and need to send it in pieces to R. I need R to return certain parameters for further use. I am sending files from C# (that are being queried from a database) into R. Currently I am trying to use the R(D)-Com package to figure out how to

Re: [R] R code compiled, assembled or interpreted?

2009-02-18 Thread Uwe Ligges
francogrex wrote: Hi all, do you know if an R program If R program means pure R code, than now, R is an interpreted language. For more information on the interpreter, you might want to start reading the manual R Internals. Uwe Ligges is compiled to machine language when executed? And

[R] Constraint in nls with factor in model?

2009-02-18 Thread Manuel Morales
Hi all, I'm trying to fit a model using the shorthand coeff[factor] instead of coding dummy variables. Is there a way to keep this notation when specifying constraints? See example below: x = runif(200) b0 = c(rep(0,100),runif(100)) b1 = 1 fac - as.factor(rep(c(0,1), each=100)) y =

[R] Running out of memory when importing SPSS files

2009-02-18 Thread dobomode
Hello R-help, I am trying to import a large dataset from SPSS into R. The SPSS file is in .SAV format and is about 1GB in size. I use read.spss to import the file and get an error saying that I have run out of memory. I am on a MAC OS X 10.5 system with 4GB of RAM. Monitoring the R process tells

[R] lineplot in ggplot2 with different colour and linetype

2009-02-18 Thread Harsh
Hi list, I would like to use ggplot2 in creating a line plot with 4 lines (groups), 2 of which I want in colour and the remaining two as dotted lines. ### R code ### library(ggplot2) ### create data vals - rnorm(400) div- c(rep(A,100),rep(B,100),rep(C,100),rep(D,100)) n- rep(1:100,4) df-

Re: [R] cumsum vs. sum

2009-02-18 Thread Berwin A Turlach
G'day all, On Wed, 18 Feb 2009 12:41:27 -0500 Stavros Macrakis macra...@alum.mit.edu wrote: Hmm. Why not use the same method to guarantee the same result? Hmm, I did not look at the source code but, potentially, sum() could use some tricks to reduce rounding errors further that would not be

[R] Age as time-scale in a cox model-How to calculate x-time risk?

2009-02-18 Thread Eleni Rapsomaniki
Dear R users, My question is more methodology related rather than specific to R usage. Using time on study as time in a cox model, eg: library(Design) stanf.cph1=cph(Surv(time, status) ~ t5+id+age, data=stanford2, surv=T) #In this case the 1000-day survival probability would be:

Re: [R] cumsum vs. sum

2009-02-18 Thread Stavros Macrakis
Duncan, Berwin, Martin, Thanks for your thoughtful explanations, which make perfect sense. May I simply suggest that the non-identity between last(cumsum) and sum might be worth mentioning in the cumsum doc page? -s __

[R] Creating several txt outputs

2009-02-18 Thread diego Diego
Dear R experts: I have a list (a very long one) and I need to create successively txt outputs (on diferent files ideally) for the data of each component of the list. How can I do this? Thanks in advance!! [[alternative HTML version deleted]]

Re: [R] lineplot in ggplot2 with different colour and linetype

2009-02-18 Thread Domenico Vistocco
Harsh wrote: Hi list, I would like to use ggplot2 in creating a line plot with 4 lines (groups), 2 of which I want in colour and the remaining two as dotted lines. ### R code ### library(ggplot2) ### create data vals - rnorm(400) div- c(rep(A,100),rep(B,100),rep(C,100),rep(D,100)) n-

Re: [R] How to connect R and WinBUGS/OpenBUGS/LinBUGS in Linux in Feb. 2009

2009-02-18 Thread chaogai
Hi, For me running winbugs through wine just works. Even when I do not specify any directories. The example they give in the bugs helpfile was my starting point. Setup is suse 11.1, latest Wine, R, R2WinBUGS winbugs. I assume you first tried without specifying directories? The directories

[R] RcolorBrewer

2009-02-18 Thread Alina Sheyman
I've downloaded the RcolorBrewer package, but when I try to run mypalette-brewer.pal(7,Greens) (or any other command with brewer.pal) I get the following error message - Error: could not find function brewer.pal Does anyone know why that's happening? Is there smth else I need to download?

Re: [R] Creating several txt outputs

2009-02-18 Thread Domenico Vistocco
diego Diego wrote: Dear R experts: I have a list (a very long one) and I need to create successively txt outputs (on diferent files ideally) for the data of each component of the list. How can I do this? Maybe this could help you: list2Files - list(1:3, letters[1:10], matrix(1:15, 5, 3))

Re: [R] RcolorBrewer

2009-02-18 Thread Domenico Vistocco
Alina Sheyman wrote: I've downloaded the RcolorBrewer package, but when I try to run mypalette-brewer.pal(7,Greens) (or any other command with brewer.pal) I get the following error message - Error: could not find function brewer.pal Does anyone know why that's happening? Is there smth else I

Re: [R] RcolorBrewer

2009-02-18 Thread Alina Sheyman
I figured it out thanks On Wed, Feb 18, 2009 at 3:50 PM, Domenico Vistocco visto...@unicas.itwrote: Alina Sheyman wrote: I've downloaded the RcolorBrewer package, but when I try to run mypalette-brewer.pal(7,Greens) (or any other command with brewer.pal) I get the following error message

[R] understanding how R determines numbers and characters when creating a data frame

2009-02-18 Thread Alan Smith
Hello R Users and Developers, I have a basic question about how R works. Over the past few years I have struggled when I try to generate a new data frame that I believe should contain numeric data in some columns and character data in others only to find everything converted to character data.

[R] [package-car:Anova] extracting residuals from Anova for Type II/III Repeated Measures ?

2009-02-18 Thread Tal Galili
Hello dear R members. I have been learning the Anova syntax in order to perform an SS type III Anova with repeated measures designs (thank you Prof. John Fox!) And another question came up: where/what are the (between/within) residuals for my model? Play code: phase -

Re: [R] Adding greek letters to plot title

2009-02-18 Thread Domenico Vistocco
gina patel wrote: I would like to add the greek letter mu to replace u in my title shown below. main=R=[0.001uM]:A=[750uM] i tried using main=expression(R=[0.001~mu~M]:A=[750~mu~M]) plot(1:3, main=expression(paste(R=[0.001~,mu,~M]:A=[750~,mu,~M]))) Ciao, domenico but this is not working at

Re: [R] How to connect R and WinBUGS/OpenBUGS/LinBUGS in Linux in Feb. 2009

2009-02-18 Thread Tobias Verbeke
Uwe Ligges wrote: Hi all, I've managed to get JAGS working on my Ubuntu Hardy Linux with a 32-bit computer and AMD processors using R 2.8.1. JAGS is great. I've read that JAGS is the fastest, but that hasn't been my experience. At any rate, I have more experience with WinBUGS under Windows

[R] Re place Values within vector using Translation vector

2009-02-18 Thread Christian Langkamp
Dear everyone I would like to change values in vectors doing a translation. i.e. I have a start vector giving me the levels in one vector (numbers 1 to x - rating) and then I have a second vector giving me the values to be allocated (loss probabilities), but the number of potential rating

Re: [R] understanding how R determines numbers and characters when creating a data frame

2009-02-18 Thread Greg Snow
The culprit is the cbind function. When given 2 vectors (not already something else), cbind will create a matrix, not a data frame. A matrix can only have 1 type, so the numbers get converted to character. In your first example you never do create a data frame, you just build a matrix (try

[R] color maps with counts

2009-02-18 Thread Alina Sheyman
I have yet another question concerning maps. This time I want to create a colored map of number of students by state. Can this be done using palettes in Rcolor brewer, is there some other way? I've been looking through R archives, but am still really at a loss here, so all help will be much

Re: [R] Re place Values within vector using Translation vector

2009-02-18 Thread Duncan Murdoch
On 18/02/2009 4:24 PM, Christian Langkamp wrote: Dear everyone I would like to change values in vectors doing a translation. i.e. I have a start vector giving me the levels in one vector (numbers 1 to x - rating) and then I have a second vector giving me the values to be allocated (loss

Re: [R] understanding how R determines numbers and characters when creating a data frame

2009-02-18 Thread Domenico Vistocco
Alan Smith wrote: Hello R Users and Developers, I have a basic question about how R works. Over the past few years I have struggled when I try to generate a new data frame that I believe should contain numeric data in some columns and character data in others only to find everything converted

Re: [R] Re place Values within vector using Translation vector

2009-02-18 Thread Greg Snow
The call to replace is replacing the 1st 3 elements of a (your indexes in Trans_CR) with the values and leaving the 4-6 elements alone. For what you want, try: A - Trans_Prob_values[ match(a, Trans_CR) ] Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain

[R] How to verify R is running with multi-threads

2009-02-18 Thread Jong
Hi all, I've compiled R (version 2.8.1) from the source code with --with- blas= option in order to use external multi-threaded blas package. However, it's very hard to verify that compilation is correct and R is using multi-threads correctly or not. Which command or operation in R will run with

[R] interaction.plot - gridlines and formatting legend title...

2009-02-18 Thread Dimitri Liakhovitski
Thank you for providing advice on this graphics question. I am building an interaction.plot. d=data.frame(xx=c(3,3,2,2,1,1),yy=c(4,3,4,3,4,3),zz=c(5.1,4.2,4.4,3.5,3.3,-1.1,-1.3) d[[1]]-as.factor(d[[1]]) d[[2]]-as.factor(d[[2]]) print(d) interaction.plot(d$xx, d$yy, d$zz, type=b,

Re: [R] Unadulterated plot

2009-02-18 Thread James Nicolson
Hi, Thanks for your help. I have looked at the beginners documentation and while there are options to configure various aspects of the plot none of them seem to have the desired effect. I have managed to ensure that the plot fills the space vertically with no margins, no axes etc (using

Re: [R] [package-car:Anova] extracting residuals from Anova for Type II/III Repeated Measures ?

2009-02-18 Thread John Fox
Dear Tal, I suppose that the between residuals would be obtained, for your example, by residuals(mod.ok). I'm not sure what the within residuals are. You could apply the transformation for each within-subject effect to the matrix of residuals to get residuals for that effect -- is that what you

[R] ggplot2 Y axis labels

2009-02-18 Thread Felipe Carrillo
Hi all: Using the example below, is there a way to add Y axis titles to each graphic instead of sharing the same title? library(ggplot2) RT = matrix(c(814, 500, 424, 394, 967, 574, 472, 446),4,2) colnames(RT) = c('repetition','alternation') rownames(RT) = c('7-yrs','11-yrs','15-yrs','21-yrs')

Re: [R] Running out of memory when importing SPSS files

2009-02-18 Thread Uwe Ligges
dobomode wrote: Hello R-help, I am trying to import a large dataset from SPSS into R. The SPSS file is in .SAV format and is about 1GB in size. I use read.spss to import the file and get an error saying that I have run out of memory. I am on a MAC OS X 10.5 system with 4GB of RAM. Monitoring

[R] indicator or deviation contrasts in log-linear modelling

2009-02-18 Thread maiya
I am fairly new to log-linear modelling, so as opposed to trying to fit modells, I am still trying to figure out how it actually works - hence I am looking at the interpretation of parameters. Now it seems most people skip this part and go directly to measuring model fit, so I am finding very few

Re: [R] Unadulterated plot

2009-02-18 Thread Patrizio Frederic
James, you're probably interested in image function rather than in filled.contour. Type ?image to see the syntax. Cheers, Patrizio 2009/2/18 James Nicolson jlnicol...@gmail.com: Hi, Thanks for your help. I have looked at the beginners documentation and while there are options to configure

Re: [R] Adding greek letters to plot title

2009-02-18 Thread Gabor Grothendieck
Try this (or replace selected occurrences of * with ~ to get spaces instead of juxtaposition): plot(1:3, main = ~ R=[ * 0.001 * mu * Mu * ]:A=[ * 750 * mu * Mu * ]) On Wed, Feb 18, 2009 at 3:56 PM, gina patel ginapatel1...@yahoo.com wrote: I would like to add the greek letter mu to replace u in

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