Re: [R] Quadratic Programming

2008-02-15 Thread Berwin A Turlach
G'day Jorge, On Fri, 15 Feb 2008 17:51:16 -0500 "Jorge Aseff" <[EMAIL PROTECTED]> wrote: > I am using solve.QP (from quadprog) to solve a standard quadratic > programming problem: min_w -0.5*w'Qw st ... I would like solve.QP to > do two things: 1) to start the optimization from a user-supplied >

Re: [R] History of R

2008-02-15 Thread Kathy Gerber
Thanks to all who responded so thoughtfully. I would like to summarize briefly the observations and opinions so far with some of my own interpretations and thoughts. John Fox is working on a much deeper history scheduled for August, and his three factors are a good starting point. John Fox w

Re: [R] History of R

2008-02-15 Thread John Fox
Dear Kathy, As Achim has mentioned, I've been doing interviews with members of the R Core team and with some other people central to the R Project. Although I haven't entirely organized and finished reflecting on this material, the following factors come immediately to mind: (1) Doug has already

[R] copying Quartz graphics windows on MAC

2008-02-15 Thread Rossi, Peter E.
I have R 2.6.2 installed on a Mac Probook with the lastest version of Leopoard (including recent graphics update). When I use either command-C or the Edit menu to "copy" the contents of an active quartz graphics window, the contents of the window disappears (much like "cut"). Has anyone had

Re: [R] Quadratic Programming

2008-02-15 Thread markleeds
>From: Jorge Aseff <[EMAIL PROTECTED]> >Date: 2008/02/15 Fri PM 04:51:16 CST >To: r-help@r-project.org >Subject: [R] Quadratic Programming Adrian Trapletti has a function in his tseries package ( the name of the function escapes me ) that uses the solve.QP solver to model some kind of quadratic p

[R] Quadratic Programming

2008-02-15 Thread Jorge Aseff
Hi, I am using solve.QP (from quadprog) to solve a standard quadratic programming problem: min_w -0.5*w'Qw st ... I would like solve.QP to do two things: 1) to start the optimization from a user-supplied initial condition; i.e., from a vector w_0 that satisfies the constraints, and 2) to return th

Re: [R] Extract from matrix

2008-02-15 Thread John Kane
?which Does something like this help? which(aa==29) aa[ -which(aa==29)] --- _Fede_ <[EMAIL PROTECTED]> wrote: > > Hi all. > > I have certain problem with the extraction of data > from matrices. I know how > extract elements from a matrix, but what I would > like to do is to extract a > concr

Re: [R] History of R

2008-02-15 Thread Achim Zeileis
For those of you who want to learn more about the history of the R project: There will be an invited lecture by John Fox and Kurt Hornik at this year's useR! conference in Dortmund in August (...unfortunately a bit too late for Kathy) about "The Past, Present, and Future of the R Project" see ht

[R] anyone know how to plot histograma and line in the same graph

2008-02-15 Thread Xin
Dear: I have two series data, which are: p1-obs p1-exp 13 13 20 23.296 22 18.139 19 14.972 10 12.576 16 10.658 8 9.0794 4 7.7625 3 6.6536 5 5.7141 7 4.9146 4 4.2321 0 3.648 4 3.1471 4

Re: [R] History of R

2008-02-15 Thread John Sorkin
Kathy. A suggestion. As you gather your information about the history, I suggest you put fingers to keyboard and write down the history. You could start with the material Douglas just sent to you. Perhaps we can convince the R folks to place the history on the CRAN website - perhaps in WIKI form

Re: [R] History of R

2008-02-15 Thread Douglas Bates
On Fri, Feb 15, 2008 at 3:23 PM, Douglas Bates <[EMAIL PROTECTED]> wrote: > On Fri, Feb 15, 2008 at 1:53 PM, Kathy Gerber <[EMAIL PROTECTED]> wrote: > > Earlier today I sent a question to Frank Harrell as an R developer with > > whom I am most familiar. He suggested also that I put my questions

Re: [R] History of R

2008-02-15 Thread Douglas Bates
On Fri, Feb 15, 2008 at 1:53 PM, Kathy Gerber <[EMAIL PROTECTED]> wrote: > Earlier today I sent a question to Frank Harrell as an R developer with > whom I am most familiar. He suggested also that I put my questions to > the list for additional responses. Next month I'll be giving a talk on >

Re: [R] ggplot2 used in a function - variable scope/environment

2008-02-15 Thread hadley wickham
Hi Martin, Two comments: * ggplot always requires the data to be plotted to be stored in a data.frame, not the environment - this makes it possible to (e.g.) save self contained plot objects - but that isn't the problem here, the problem is setting up the appropriate mapping * aes_string make

Re: [R] lmList, tapply() and lm()

2008-02-15 Thread Jonathan Baron
Here is an example I just did. I _LOVE_ lmList(). It is such a great convenience compared to the following. But right now it doesn't work for "family=binomial", so I had to do it differently. This is not your example, but it should give you an idea. The [[5]] was because I was interested only

[R] Data Mining Competition 2008

2008-02-15 Thread Xiaogang Su
Dear Colleagues, please help distribute the following announcement of a data mining competition. Thanks, -XG = Data Mining Competition 2008 = Website: http://dms.stat.ucf.edu/competition08/home.htm Department of Statistics & Actuarial Sc

[R] ggplot2 used in a function - variable scope/environment

2008-02-15 Thread Martin Rittner
Hi everybody! I'm trying to use ggplot2 to return a plot from a function (so I can add something or alter it then). Unfortunately, if I add a mapping to a layer in the function, the variable *name* is stored in the layer, rather than the variable's *value* - so that after the function returns

Re: [R] wire.frame tick labels from matrix

2008-02-15 Thread Deepayan Sarkar
On 2/15/08, Sundar Dorai-Raj <[EMAIL PROTECTED]> wrote: > > > Marlin Keith Cox said the following on 2/15/2008 11:39 AM: > > > Dear R Users, close to the end of this I used wireframe to create a 3D plot > > from a matrix. The x and y axis tick labels (1-6) for each were created > > from the mat

Re: [R] Transfer Crosstable to Word-Document

2008-02-15 Thread Don MacQueen
I usually use the write.table() function (with tab as the delimiter) to write to a text file, then copy/paste into Word, then use Word's convert text to table command. Obviously, if one needs to do this for many, many, tables, the amount of manual manipulation is excessive. That's when produ

Re: [R] LMER

2008-02-15 Thread Douglas Bates
On Fri, Feb 15, 2008 at 8:59 AM, Daniel Malter <[EMAIL PROTECTED]> wrote: > Thanks for your replies. My real problem is that, for my real data, I get > basically the same results from r2 and r3 (so to speak), but the coefficient > estimates and significance levels for r1 are very different from t

[R] History of R

2008-02-15 Thread Kathy Gerber
Earlier today I sent a question to Frank Harrell as an R developer with whom I am most familiar. He suggested also that I put my questions to the list for additional responses. Next month I'll be giving a talk on R as an example of high quality open source software. I think there is much to

Re: [R] wire.frame tick labels from matrix

2008-02-15 Thread Sundar Dorai-Raj
Marlin Keith Cox said the following on 2/15/2008 11:39 AM: > Dear R Users, close to the end of this I used wireframe to create a 3D plot > from a matrix. The x and y axis tick labels (1-6) for each were created > from the matrix being a 6X6 matrix. I need the axis tick labels to be the > row and

Re: [R] Clustering with ordinal data

2008-02-15 Thread Gavin Simpson
On Fri, 2008-02-15 at 10:45 -0800, Tim Smith wrote: > Hi, > > Is there any clustering package in R that can cluster with ordinal data? > > thanks! daisy() in recommended package 'cluster' can generate dissimilarities for ordinal data using Gower's general (dis)similarity coefficient for mixed da

Re: [R] Cholmod error `matrix not positive definite'

2008-02-15 Thread Douglas Bates
On Thu, Feb 14, 2008 at 3:14 PM, Douglas Bates <[EMAIL PROTECTED]> wrote: > Could you tell us which version of the lme4 package you are using? > You can just send the output produced by > > sessionInfo() > > If you can make your data available so we can test it then please do > so. If the data

[R] wire.frame tick labels from matrix

2008-02-15 Thread Marlin Keith Cox
Dear R Users, close to the end of this I used wireframe to create a 3D plot from a matrix. The x and y axis tick labels (1-6) for each were created from the matrix being a 6X6 matrix. I need the axis tick labels to be the row and column headings which you can see in the output (mat.x). I have tri

[R] predict.lm with matrix as newdata

2008-02-15 Thread Marlin Keith Cox
Z is a matrix and when I run the following line, it creates a prediction estimate using each column, how can I get it an estimate for each individual number. I have tried changing Z to a data.frame, but this does not do it either. model.lm<-lm(w~x) pred.est <- predict.lm(model.lm, data.frame(x=Z

[R] How to estimate weekly Variance

2008-02-15 Thread Felipe Carrillo
Dear All: Using the Excel formula below I am able to estimate daily variance(Daily VarPD)for PD,but I can't figure out how to estimate the Weekly variance for PD. Any hints? Daily VarPD = (PD * (1 - TD))/TD + VarTD * ((PD*(1-TD)+ PD^2*TD))/TD^3 WK TDVARTD PD Daily Var

Re: [R] Conditional Autoregressive (CAR) model simulation

2008-02-15 Thread Henrique Dallazuanna
See spautolm function in spdep package On 15/02/2008, Dae-Jin Lee <[EMAIL PROTECTED]> wrote: > Hi all ! > > I would like to simulate spatial lattice/areal data with a conditional > autoregressive (CAR) structure, for a given neighbouring matrix and for a > autocorrelation "rho". > > Is there a

[R] Conditional Autoregressive (CAR) model simulation

2008-02-15 Thread Dae-Jin Lee
Hi all ! I would like to simulate spatial lattice/areal data with a conditional autoregressive (CAR) structure, for a given neighbouring matrix and for a autocorrelation "rho". Is there any package or function in R to perform it ? I found the function "CARsimu" in the hdeco library, but this is

Re: [R] No response for help

2008-02-15 Thread Gabor Grothendieck
You will have better luck in soliciting responses if you follow the line at the bottom of every r-help message and post minimal reproducible code. Also read the posting guide. On Fri, Feb 15, 2008 at 8:29 AM, G Ilhamto <[EMAIL PROTECTED]> wrote: > Dear R admin, > > I sent so many emails but none

[R] Clustering with ordinal data

2008-02-15 Thread Tim Smith
Hi, Is there any clustering package in R that can cluster with ordinal data? thanks! Be a better friend, newshound, and [[alternative HTML version deleted]]

Re: [R] No response for help

2008-02-15 Thread Ted Harding
On 15-Feb-08 13:29:06, G Ilhamto wrote: > Dear R admin, > > I sent so many emails but none was posted. > What happened? > > Thanks > Ilham Are you subscribed to r-help? If not, you will not receive copies of any mails sent out by the list (though if a non-subscriber mails to the list, the mail w

Re: [R] Error 'singular gradient' in nonlinear model fitting

2008-02-15 Thread Gabor Grothendieck
Try fitting regressing log(WEIGHT) against log(TOTAL) using lm and then transform the results into starting values for nls (or possibly that is sufficient and you don't need the nls results). On Fri, Feb 15, 2008 at 12:41 PM, HongSheng Liao <[EMAIL PROTECTED]> wrote: > > w.age.female.2004 <- nls(W

Re: [R] Error 'singular gradient' in nonlinear model fitting

2008-02-15 Thread Peter Dalgaard
HongSheng Liao wrote: > w.age.female.2004 <- nls(WEIGHT ~ (alpha*TOTAL^beta)/454, > start=list(alpha=1, beta=3), > data=spottedseatrout2004.female.data) > > I am trying to fit above model to length-weight data of a fish species > (spotted seatrout) by

Re: [R] Error 'singular gradient' in nonlinear model fitting

2008-02-15 Thread Ravi Varadhan
Try a different set of starting values for alpha & beta. Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University

[R] Error 'singular gradient' in nonlinear model fitting

2008-02-15 Thread HongSheng Liao
w.age.female.2004 <- nls(WEIGHT ~ (alpha*TOTAL^beta)/454, start=list(alpha=1, beta=3), data=spottedseatrout2004.female.data) I am trying to fit above model to length-weight data of a fish species (spotted seatrout) by year (1999-2006). The converge

Re: [R] Transfer Crosstable to Word-Document

2008-02-15 Thread Gabor Grothendieck
In that case you shouldn't be using CrossTable in the first place. Suggest you look into the functions mentioned under See Also in ?CrossTable or look at the source of CrossTable and modify it for your purposes. On Fri, Feb 15, 2008 at 11:52 AM, <[EMAIL PROTECTED]> wrote: > > Thank you Gabor, >

Re: [R] Extract from matrix

2008-02-15 Thread Henrique Dallazuanna
Try also: mat[mat==29] <- NA On 15/02/2008, _Fede_ <[EMAIL PROTECTED]> wrote: > > Hi all. > > I have certain problem with the extraction of data from matrices. I know how > extract elements from a matrix, but what I would like to do is to extract a > concrete number, not an element. For examp

Re: [R] Extract from matrix

2008-02-15 Thread J. Arturo Coral Alamo
Look this can help you: mtz<-matrix(1:20,4,5) > mtz [,1] [,2] [,3] [,4] [,5] [1,]159 13 17 [2,]26 10 14 18 [3,]37 11 15 19 [4,]48 12 16 20 > mtz[2,3] [1] 10 > mtz [,1] [,2] [,3] [,4] [,5] [1,]159 13 17 [2,]2

Re: [R] Transfer Crosstable to Word-Document

2008-02-15 Thread Marc Schwartz
Udo, CrossTable() knows nothing about the proprietary formats of Word tables. The output is designed for the R console, using a fixed width (monospace) font. The cell boundaries are drawn using standard ASCII characters. There are no plans at present to modify the format of the output to supp

Re: [R] lmList, tapply() and lm()

2008-02-15 Thread Chuck Cleland
On 2/15/2008 11:00 AM, Marc Belisle wrote: > Howdee, > > *** I know that the lmList() function exists, yet I don't want to use it. > *** > > Would anyone be kind enough to tell how I can apply the function lm() to > each level of a given factor so to obtain the intercept and slope for each > fact

Re: [R] Extract from matrix

2008-02-15 Thread Gavin Simpson
On Fri, 2008-02-15 at 08:10 -0800, _Fede_ wrote: > Hi all. > > I have certain problem with the extraction of data from matrices. I know how > extract elements from a matrix, but what I would like to do is to extract a > concrete number, not an element. For example if I have this matrix X: > >

[R] Error in my R program

2008-02-15 Thread HongSheng Liao
w.age.female.2004 <- nls(WEIGHT ~ (alpha*TOTAL^beta)/454, start=list(alpha=1, beta=3), data=spottedseatrout2004.female.data) I am trying to fit above model to length-weight data of a fish species (spotted seatrout) by year (1999-2006). The converg

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

2008-02-15 Thread Michael Lawrence
That would be a good idea. I'm finishing up a much more comprehensive guide that will become available soon. Thanks for the suggestion, Michael 2008/2/14 Felix Andrews <[EMAIL PROTECTED]>: > I just discovered a good introduction to the RGtk2 package: > RShowDoc("overview2", package="RGtk2") > >

[R] Behaviour of integrate (was 'Poisson-lognormal probability calcul ations')

2008-02-15 Thread k . jewell
Hi again, Adding further information to my own query, this function gets to the core of the problem, which I think lies in the behaviour of 'integrate'. - function (x, meanlog = 0, sdlog = 1, ...) { require(stats) integrand <- function(t, x, meanlog, sdl

Re: [R] Transfer Crosstable to Word-Document

2008-02-15 Thread ukoenig
Thank you Gabor, but with 1. or 2. I don´t get a table, which can be changed and formatted using the WORD table functions (like changing column width and formatting text in rows). The result of 1. ist an bitmap and the result of 2. an ASCII-Table A rich formatted (*.rtf) table/object would be be

Re: [R] OT: installing the XML package - xmlOutputBufferCreateBuffer problem

2008-02-15 Thread Prof Brian Ripley
You need a later version of libxml2 (or at least, a different one as possibly an older one would also work). I met this on Windows -- 2.6.23 is old (more than 2 years), and I believe 2.6.28, 2.6.30 and 2.6.31 work. The Omegahat lists have been defunct for a while, AFAIK. I'd have used R-devel

[R] Extract from matrix

2008-02-15 Thread _Fede_
Hi all. I have certain problem with the extraction of data from matrices. I know how extract elements from a matrix, but what I would like to do is to extract a concrete number, not an element. For example if I have this matrix X: [,1] [,2] [,3] [,4] [1,]3 13 23 33 [2,]9 19

Re: [R] Transfer Crosstable to Word-Document

2008-02-15 Thread Gabor Grothendieck
Here are 2 ways: 1. Display it on the screen and hit the PrintScreen button. Then paste that into Word and use Word's image editor to crop it and expand or shrink it appropriately. 2. Run this in R: capture.output(CrossTable(...whatever...), file = "clipboard") Paste the clipboard into Word and

Re: [R] help on loop function

2008-02-15 Thread markleeds
>From: mohamed nur anisah <[EMAIL PROTECTED]> >Date: 2008/02/15 Fri AM 07:13:15 CST >To: r-help@r-project.org >Subject: [R] help on loop function a similar ( if not identical ? ) question was asked a few days ago and the answer is at the link below. http://article.gmane.org/gmane.comp.lang.r.gen

Re: [R] lineplot.CI problem

2008-02-15 Thread hadley wickham
On Fri, Feb 15, 2008 at 8:18 AM, Dieter Vanderelst <[EMAIL PROTECTED]> wrote: > Hi List, > > I have a problem plotting data using the lineplot.CI command in the sciplot > package. > > I want to plot the data of 2 experimental cases using different lines > (traces). Time is on the X-axis. The tr

[R] lmList, tapply() and lm()

2008-02-15 Thread Marc Belisle
Howdee, *** I know that the lmList() function exists, yet I don't want to use it. *** Would anyone be kind enough to tell how I can apply the function lm() to each level of a given factor so to obtain the intercept and slope for each factor level within a matrix? For instance, suppose a datafram

[R] Transfer Crosstable to Word-Document (2. attempt)

2008-02-15 Thread ukoenig
# Dear list, # I am an R-beginner and # spent the last days looking for a method to insert tables produced # with R into a word document. I thought about SPPS: copy a table from # an SPO-file and paste it into a word document # (if needed do some formatting with that table). # Annother idea was, t

Re: [R] contingency table

2008-02-15 Thread John Kane
Have a look at length(iris$Species) length(prev) --- Carla Rebelo <[EMAIL PROTECTED]> wrote: > Hello! > > May you help me? I'm trying to do a contingency > table using this > > > data(iris) > > library(rpart) > > modelo <- rpart(Species ~., iris) > > prev <- predict(modelo, iris) > > Final

Re: [R] Help, Statistics Question. Testing for equality of frequncies of an event

2008-02-15 Thread David Winsemius
<[EMAIL PROTECTED]> wrote in news:[EMAIL PROTECTED] orld.com: > Hi All, > > I have a basic statistics question you might be able to help. > > I have some data collected within a single population (say of > chronic illness) over a period of time (number under observation is > constant, say 100 s

Re: [R] lineplot.CI problem

2008-02-15 Thread Manuel Morales
On Fri, 2008-02-15 at 15:18 +0100, Dieter Vanderelst wrote: > Hi List, > > I have a problem plotting data using the lineplot.CI command in the sciplot > package. > > I want to plot the data of 2 experimental cases using different lines > (traces). Time is on the X-axis. The tricky thing is that

[R] Transfer Crosstable to Word-Document

2008-02-15 Thread ukoenig
# Dear list, # I am an R-beginner and # spent the last days looking for a method to insert tables produced # with R into a word document. I thought about SPPS: copy a table from # an SPO-file and paste it into a word document # (if needed do some formatting with that table). # Annother idea was, t

Re: [R] Question: about loading a new package

2008-02-15 Thread John Kane
Place the command library(newpackage) in your Rprofile is one way. --- Stefano Sofia <[EMAIL PROTECTED]> wrote: > I am using R Version 2.3.1 (2006-06-01) in Linux > with Ubuntu 7.4. > > I installed a new package with > > R CMD INSTALL -l /usr/lib/R/library > newpackage.tar.gz > > Each time I

[R] OT: installing the XML package - xmlOutputBufferCreateBuffer problem

2008-02-15 Thread Benilton Carvalho
Hi, first of, my apologies for the possibly off-topic message regarding a problem when installing the XML package (I meant to post at omegahat- help, but I get 404 at http://www.omegahat.org/mailman/listinfo) When installing the XML package using: install.packages("XML") everything seems

Re: [R] lmer in package of lme4

2008-02-15 Thread Ben Bolker
WANG newcastle.ac.uk> writes: > I use lmer to extract model in your package of lme4. It seems works > well. But the problem is when I use anova/summary the extracted model, > no p-value is shown at all. In previous version(nlme), I mainly use > p-value to judge which term is significant or not, a

Re: [R] lmer in package of lme4

2008-02-15 Thread jebyrnes
Rather than go over all of this again, see here http://wiki.r-project.org/rwiki/doku.php?id=guides:lmer-tests -- View this message in context: http://www.nabble.com/lmer-in-package-of-lme4-tp15501802p15502440.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] anyone know how to plot histograma and line in the same graph

2008-02-15 Thread Henrique Dallazuanna
Try this: hist(x[,1], ylim=c(0,max(x[,2]))) lines(x[,2], col="blue", lty=2) On 15/02/2008, Xin <[EMAIL PROTECTED]> wrote: > Dear: > >I have two series data, which are: > p1-obs p1-exp > 13 13 > 20 23.296 > 22 18.139 > 19 14.972 > 10 12.576 > 16 10.65

Re: [R] Controling width of boxes in boxplots

2008-02-15 Thread John Kane
Have a look at boxwex in boxplot. Something like boxplot(y,add=TRUE,at=118, boxwex=3) may give you what you want. --- Marcin Kozak <[EMAIL PROTECTED]> wrote: > Hi, > > I want to add boxplots to a scatterplot: > > plot(x,y, xlim=c(80,120),ylim=c(80,120)) > boxplot(y,add=TRUE,at=118) > boxplot(x,

Re: [R] LMER

2008-02-15 Thread Daniel Malter
Thanks for your replies. My real problem is that, for my real data, I get basically the same results from r2 and r3 (so to speak), but the coefficient estimates and significance levels for r1 are very different from those of r2 and r3. And therefore, I do not know which of the results to trust and

Re: [R] function similar to str_replace() in php.

2008-02-15 Thread Gabor Csardi
I don't know php very well, but perhaps you need ?sub Gabor On Fri, Feb 15, 2008 at 03:54:19PM +0100, Dong-hyun Oh wrote: > Dear expeRt, > > I would like to know whether a function similar to str_replace() in > php exists in R. > > Looking forward to hearing from you. > > Best, > > > >

[R] function similar to str_replace() in php.

2008-02-15 Thread Dong-hyun Oh
Dear expeRt, I would like to know whether a function similar to str_replace() in php exists in R. Looking forward to hearing from you. Best, = Center of Excellence for Science and Innovation Studies, Royal Institute of Technology Drott

Re: [R] Softmax in nnet

2008-02-15 Thread Prof Brian Ripley
Looks like you meant to use 'TRUE' not 'T'. The latter is probably a variable you defined of length > 1. Double-posting at least halves your chances of getting help, so please stop doing it. On Fri, 15 Feb 2008, G Ilhamto wrote: > Hi R help, > > I run my data in nnet with skip layer, factor r

[R] Softmax in nnet

2008-02-15 Thread G Ilhamto
Hi R help, I run my data in nnet with skip layer, factor response (with 0 & 1 values) and explicitly put softmax=T to compare the result of the default nnet with no softmax specification. I assume this should give me the same result. I got the result the default one, but not the softmax version an

[R] lineplot.CI problem

2008-02-15 Thread Dieter Vanderelst
Hi List, I have a problem plotting data using the lineplot.CI command in the sciplot package. I want to plot the data of 2 experimental cases using different lines (traces). Time is on the X-axis. The tricky thing is that the data collection in the second case started later than for the first

[R] Softmax in nnet

2008-02-15 Thread G Ilhamto
Hi R help, I run my data in nnet with skip layer, factor response (with 0 & 1 values) and explicitly put softmax=T to compare the result of the default nnet with no softmax specification. I assume this should give me the same result. I got the result the default one, but not the softmax version an

[R] lmer in package of lme4

2008-02-15 Thread WANG
Dear Sir/madam, I use lmer to extract model in your package of lme4. It seems works well. But the problem is when I use anova/summary the extracted model, no p-value is shown at all. In previous version(nlme), I mainly use p-value to judge which term is significant or not, and then make a decision

Re: [R] Analysis with spatstat and Kcross() requires to much memory

2008-02-15 Thread Roger Bivand
Rainer M Krug gmail.com> writes: > > Hi > > I am running analysis with Kcross from the package spatstat and I am getting > a message that R can not allocate enough memory for a vector of 900MB. > R seems to be running towards the 2GB limit per process. > > The dataset is not to big (ca 3000 p

Re: [R] write output in a custom format

2008-02-15 Thread Charilaos Skiadas
Perhaps I am missing the obvious, but can't you simply write a small function that, given each particle "object", returns a string with the required output format (probably a couple of "paste" calls with sep and collapse set), and then use sapply and this function on the list of particles t

[R] No response for help

2008-02-15 Thread G Ilhamto
Dear R admin, I sent so many emails but none was posted. What happened? Thanks Ilham __ 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 prov

Re: [R] For Subset or Reshaping the Table

2008-02-15 Thread hadley wickham
On Thu, Feb 14, 2008 at 7:53 PM, dinesh kumar <[EMAIL PROTECTED]> wrote: > Hi R users > I am a new user in the field of R. > I want to subset or reshape a data.frame. > For example I have a matrix like > >A B C D E F G > a 1 2 3 4 5 6 7 > b 4 6 8 9 5 5 6 > c 3 4

Re: [R] Controling width of boxes in boxplots

2008-02-15 Thread Henrique Dallazuanna
Try this: x <- sample(5, 100, rep=T) y <- rnorm(100) plot(x,y, xlim=c(min(x)-.5, max(x)), ylim=c(min(y), max(y)+1)) boxplot(y, pars=list(boxwex=0.3), at=min(x)-.5, add=T) boxplot(x, pars=list(boxwex=0.3), at=max(y)+1, add=T, horizontal=T) On 15/02/2008, Marcin Kozak <[EMAIL PROTECTED]> wrote: >

[R] Error with stop()

2008-02-15 Thread jgarcia
Hello; I've used stop() previously without any problem. Now, I'm using a condition and getting an error when stop() is called. Mi condition is: if(dim(r.temp)[1] != (length(jul.names)+6)) stop("buffered data not available") An the R' response is: > source("my_program.R") Error in eval.with.vis

Re: [R] write output in a custom format

2008-02-15 Thread baptiste Auguié
Fair point! I guess I'll see how long it takes with a pure R solution, and maybe then try some optimization if needed. Thanks again, baptiste On 14 Feb 2008, at 21:27, jim holtman wrote: > There is nothing wrong with a loop for handling this case. Most of > your time is probably going to b

[R] help on loop function

2008-02-15 Thread mohamed nur anisah
Dear lists, Anysuggestion on how to write a loop function which has nx2 matrix as an input, where each of the row represents an interval. the function should return a mx2 matrix containing the no matched interval of x?? i've tried my own function but it's only applies for 2x2 matrix.

[R] R help

2008-02-15 Thread Susann Fält
Hello, I am trying to set up the oneChannelGUI in R to analyse exon arrays but I can not start up the package. I receive the error message “ Tcl/Tk Extensions not found” I have followed the suggestion: “If you don't know how to set environment variables in Windows, one way to make sure that

[R] Controling width of boxes in boxplots

2008-02-15 Thread Marcin Kozak
Hi, I want to add boxplots to a scatterplot: plot(x,y, xlim=c(80,120),ylim=c(80,120)) boxplot(y,add=TRUE,at=118) boxplot(x,add=TRUE,at=118,horizontal=TRUE) How can I control the width of the boxes (say, I'd like them to be of width 3 in the variables' scales). I've tried the "width" parameter bu

Re: [R] LMER

2008-02-15 Thread Douglas Bates
Could you send us the output of sessionInfo() please so we can see which version of the lme4 package you are using? In recent versions, especially the development version available as install.packages("lme4", repos = "http://r-forge.r-project.org";) the PQL algorithm is no longer used. The Lapl

[R] GAUSS (Aptech) & R

2008-02-15 Thread Naji Nassar
Hi Is there a correspondance between R commands and other software commands (GAUSS mainly).. I'd like to translate some Gauss into R.. Thanks for your help Naji __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEAS

Re: [R] setting color ranges

2008-02-15 Thread Jim Lemon
samsr wrote: > Hi, > > I need to plot a matrix using image() such that negative values are easily > distinguishable from posittive values, while also maintaining a gradation in > color with magnitude. How can I set ranges for colors in order to achieve > this. Thanks. > Hi Sam, This will give y

Re: [R] Latent class analysis

2008-02-15 Thread Tom Backer Johnsen
Thanks! Ingmar Visser wrote: > and also check packages: flexmix, polca, depmix and a few others ... > > On 15 Feb 2008, at 11:01, Dimitris Rizopoulos wrote: > >> check function lca() in package 'e1071'. >> >> Best, >> Dimitris >> >> >> Dimitris Rizopoulos >> Ph.D. Student >> Biostatistical

[R] Poisson-lognormal probability calculations

2008-02-15 Thread k . jewell
Hi, just for the record, although I don't think it's relevant (!) - > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUM

Re: [R] Latent class analysis

2008-02-15 Thread Ingmar Visser
and also check packages: flexmix, polca, depmix and a few others ... On 15 Feb 2008, at 11:01, Dimitris Rizopoulos wrote: > check function lca() in package 'e1071'. > > Best, > Dimitris > > > Dimitris Rizopoulos > Ph.D. Student > Biostatistical Centre > School of Public Health > Catholic Uni

Re: [R] question about calling winbugs in R

2008-02-15 Thread Uwe Ligges
Xin wrote: > Dear All: > > Do you have any experience on calling winbugs in R enviorment? I uploaded So you installed them, I assume? > R2winbgus, pktools, BRugs, ect. in order to call winbugs. In the end, I try > to use bugs(). The error message still displays that bugs() can not find.

[R] Help, Statistics Question. Testing for equality of frequncies of an event

2008-02-15 Thread si.fu
Hi All, I have a basic statistics question you might be able to help. I have some data collected within a single population (say of chronic illness) over a period of time (number under observation is constant, say 100 subjects). The question is how could I test whether the frequency of an even

Re: [R] LMER

2008-02-15 Thread Abderrahim Oulhaj
your r2 model corresponds to method = "Laplace". r4=lmer(Y~X+(1|Subject),family=binomial(link="logit"),method="Laplace") is equivalent to r2. Bests, Abderrahim - Original Message - From: "Daniel Malter" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Friday, February 15, 2008 12:5

Re: [R] For Subset or Reshaping the Table

2008-02-15 Thread Henrique Dallazuanna
Try this: cbind(Row=rownames(x), stack(x)[,2:1])[cbind(Row=rownames(x), stack(x)[,2:1])[,3]>3,] On 14/02/2008, dinesh kumar <[EMAIL PROTECTED]> wrote: > Hi R users > I am a new user in the field of R. > I want to subset or reshape a data.frame. > For example I have a matrix like > >A B

[R] question about calling winbugs in R

2008-02-15 Thread Xin
Dear All: Do you have any experience on calling winbugs in R enviorment? I uploaded R2winbgus, pktools, BRugs, ect. in order to call winbugs. In the end, I try to use bugs(). The error message still displays that bugs() can not find. Do you have any similar issue? If so, could you give your

Re: [R] Latent class analysis

2008-02-15 Thread Dimitris Rizopoulos
check function lca() in package 'e1071'. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/

Re: [R] storing ggplot objects as components of a vector

2008-02-15 Thread ONKELINX, Thierry
You'll need to store it in a list rather than a vector. library(ggplot2) DF<-data.frame(A=rnorm(12),B=c(1:12),C=rep(c(1:4),each=3)) Q <- list() PAC<-geom_point(mapping=aes(x=A,y=B),data=DF[DF$C==1,]) P<-ggplot()+PAC Q[[length(Q) + 1]] <- P Q[[1]] You could shorten this into library(ggplot2) DF<-

[R] Latent class analysis

2008-02-15 Thread Tom Backer Johnsen
Which package(s) contain something on latent class analysis? Tom -- ++ | Tom Backer Johnsen, Psychometrics Unit, Faculty of Psychology | | University of Bergen, Christies gt. 12, N-5015 Bergen, NORWAY | | Tel : +47-5558-9185

Re: [R] storing ggplot objects as components of a vector

2008-02-15 Thread Uwe Ligges
Gallego Liberman, Matias wrote: > Hi. > > I have a lot of plots that i need to store as components of a vector. > Here you have an example > >> DF<-data.frame(A=rnorm(12),B=c(1:12),C=rep(c(1:4),each=3)) >> Q<-c() >> length(Q)<-3 You need a list, hence replace the last two lines by: Q <- vec

Re: [R] lm, coefficient 'not defined because of singularities'? What does this mean?

2008-02-15 Thread Martin Waller
Ah yes - you're right, and its also a tiny number (10^-18) Thanks... Martin Patrick Burns wrote: > I think it is saying that there is only one (unique) > number in 'x1'. If that is right, then you could do: > > lm(y1 ~ x1 - 1) > > Patrick Burns > [EMAIL PROTECTED] > +44 (0)20 8525 0696 > http:/

Re: [R] data manipulation for plotting

2008-02-15 Thread Jim Lemon
[EMAIL PROTECTED] wrote: >Hi, > >i'd like to plot some data that I have with the value on the x axis and > freq >on the y axis. > >So, I need to calculate the freq a value is seen within my data vector > >for example, say i have a vector of data > >data=c(1,1,1,4,5,5,6)

Re: [R] problem with heatmap.2

2008-02-15 Thread Uwe Ligges
Ng Stanley wrote: > Hi, > >> temp1[1:6,] > _XXX BB_XXX C_XXX D_XXX E_XXX SkHep1_XXX > 500.75285 0.30630 0.56330 0.45755 0.496650.74685 > 630.35930-0.22725 0.04725 0.53955 0.563900.51170 > 69 -1.57515-1.67610 -1.61695 -1.11685 -0.00085

[R] storing ggplot objects as components of a vector

2008-02-15 Thread Gallego Liberman, Matias
Hi. I have a lot of plots that i need to store as components of a vector. Here you have an example > DF<-data.frame(A=rnorm(12),B=c(1:12),C=rep(c(1:4),each=3)) > Q<-c() > length(Q)<-3 > PAC<-geom_point(mapping=aes(x=A,y=B),data=DF[DF$C==1,]) > P<-ggplot()+PAC > P #generates the plot > Q[1]<-P W

Re: [R] finding source for a function

2008-02-15 Thread Uwe Ligges
Or just read the article Ligges, U. (2006): R Help Desk: Accessing the Sources. R News 6 (4), 43-45. http://cran.r-project.org/doc/Rnews/ which was written particularly for answering this kind of questions. Best, Uwe Ligges Gabor Csardi wrote: > RSiteSearch is your friend. E.g.: > > http:/

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