Re: [R] Line numbers in error messages

2004-04-12 Thread Thomas Lumley
On Tue, 13 Apr 2004, Jason Turner wrote: Webb Sprague wrote: I already use ESS. If it would give line numbers, my life would be perfect! It does, if you don't use source(). Have your R code in one buffer, and the R session running, and (from the code buffer), type C-c C-l. Yes, yes,

Re: [R] Line numbers in error messages

2004-04-12 Thread Thomas Lumley
/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ [EMAIL PROTECTED] mailing list https

Re: [R] getting data frame rows out of a by object

2004-04-08 Thread Thomas Lumley
On Thu, 8 Apr 2004, Ed L Cashin wrote: One thing I notice is that I get funny row names using this method. I can change them back easily enough, though. I think you can use interaction() rather than the factor(paste()) approach interaction(d$a, d$b, drop=TRUE) gives a factor with one level

Re: [R] R on MacOS X

2004-04-08 Thread Thomas Lumley
On Thu, 8 Apr 2004, Peter Dalgaard wrote: Martin Maechler [EMAIL PROTECTED] writes: Richard a designated sysadmin, which I'm not. Is there any Richard alternative to downloading a source distribution Richard and doing the classic ./configure;make;make install Richard

Re: [R] R on MacOS X

2004-04-08 Thread Thomas Lumley
On Thu, 8 Apr 2004, Thomas Lumley wrote: I believe, though I haven't yet tried, that the 1.9.0 setup will be better. I think you can put the R Framework in ~/Library/Frameworks and then put R.app anywhere. Almost true. You need to edit R.app/Contents/MacOS/R and change the first line

Re: [R] predict( ..., type=terms)

2004-04-07 Thread Thomas Lumley
On Wed, 7 Apr 2004, Giovanni Petris wrote: Hello, After reading the help for predict.lm and predict.glm, it is not clear to me what are the values returned by predict( ..., type=terms). Anybody willing to enlighten me? For each term in the formula, extract its coefficients and the

RE: [R] Deep copy in R

2004-04-06 Thread Thomas Lumley
On Mon, 5 Apr 2004, Shin, Daehyok wrote: Hm. Smarter than I expected. But, any special reason why the 6th line clones another vector? To me, just reference copy seems to be enough for the purpose. 6 xf = date.frame(x=x) You would have to look at the code for data.frame to see this, but I

Re: [R] Index of a Loop Variable?

2004-04-06 Thread Thomas Lumley
On Tue, 6 Apr 2004, Jim Java wrote: Hi Everyone:-- Is it possible, within a for loop not explicitly using whole-number indexing, to find out the index value of the loop variable within the vector or list that's being looped through? For example, in -- x - seq(5, 50, by=5) index.in.x - 1

Re: [R] assert( condition )

2004-04-06 Thread Thomas Lumley
On Tue, 6 Apr 2004, ivo welch wrote: hi R wizards: I think it would be a good idea for me to use basic argument checking (type, length) in function calls via an assert() like function. How do people usually do this? Should I define my own assert() function (or are there some predefined

Re: [R] assert( condition )

2004-04-06 Thread Thomas Lumley
On Tue, 6 Apr 2004, A.J. Rossini wrote: Thomas Lumley [EMAIL PROTECTED] writes: A more elegant solution would use the new R condition mechanism and allow assertion failures to be caught independently of errors. A pointer to this would be appreciated. help(tryCatch) -thomas

Re: [R] Very slow start of R under MacOS X

2004-04-05 Thread Thomas Lumley
On Mon, 5 Apr 2004, Laurence Loewe wrote: Hi, Since R 1.4.1 I am using R for various purposes on my Mac (OS9 and OSX10.3) and I am quite happy with it. However, recently I tried to update the binaries to 1.7.1 or 1.8, only to find that I have to wait for a painfully long time after

Re: [R] Selecting Best Regression Equation

2004-04-05 Thread Thomas Lumley
On Mon, 5 Apr 2004, WilDscOp wrote: Dear all, Does R or S-plus or any of their packages provide any command to form any of the following procedures to find Best Regression Equation - 1. 'All Possible Regressions Procedures' (is there any automated command to perform 2^p

Re: [R] Deep copy in R

2004-04-05 Thread Thomas Lumley
On Mon, 5 Apr 2004, Shin, Daehyok wrote: I am handling spatial data of huge volumes, so sensitive to the silent duplication of data in script programs. In the following R program, exactly when is the vector data deeply copied? Thanks in advance. 1 v - 1:1 2 z - f(v) -

Re: [R] Seeking help for outomating regression (over columns) and storing selected output

2004-04-03 Thread Thomas Lumley
On Sat, 3 Apr 2004, Gabor Grothendieck wrote: 2. Another possibility is to create a giant regression that does all the usergroup specific regressions at once and then repeat it without the usergroup variable to get the rest. df2 is a new data frame that strings out all the x variables into

Re: [R] R fft on 2D matrix

2004-04-01 Thread Thomas Lumley
On Thu, 1 Apr 2004, Anne Gosset wrote: Hi, I am a brand new user of R and I have a really stupid problem: I am having troubles applying fft on 2D matrices. I import a data file of 256*256 elements with read.table (it is actually a grey scale image, the corresponding data file being

Re: [R] Generating file names

2004-04-01 Thread Thomas Lumley
On Thu, 1 Apr 2004, Mark O. Kimball wrote: I read a data set into a data.frame. I then operate on the set, add columns to the frame etc. and now want to output the frame into a file. Trouble is, I want the file to have a name based upon the original data set name. I cannot figure out how to

Re: [R] RAqua and gcc

2004-03-30 Thread Thomas Lumley
__ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle

Re: [R] Where: package licenses

2004-03-30 Thread Thomas Lumley
On Tue, 30 Mar 2004 [EMAIL PROTECTED] wrote: R: This stems from my curiosity about the previous thread about a request for glm.nb code. The issue of package licenses was brought up and I was hoping for some clarification on that. Using the function license() or licence() gives info on

Re: [R] Runing S-plus add-on in R (Binary and Smoothed Binary Regression Quantiles)

2004-03-30 Thread Thomas Lumley
On Tue, 30 Mar 2004, Joao Pedro W. de Azevedo wrote: Hello, I would like to know if it is possible to run a s-plus package in R. I'm particularly interested on The add-on written by Walter Belluzzo and Gregory Kordas to estimate Binary and Smoothed Binary Regression Quantiles using the

Re: [R] data usage

2004-03-29 Thread Thomas Lumley
On Mon, 29 Mar 2004, Edwin Leuven wrote: Stata tends to store data as float, integer, or even byte where appropriate for the precision. This is one source of space saving. A factor of 2 is not atypical. i was suspecting something like this. what does R do? default to double always (or

RE: [R] how to modify variables of another frame (but not global)

2004-03-23 Thread Thomas Lumley
__ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University

RE: [R] how to modify variables of another frame (but not global)

2004-03-23 Thread Thomas Lumley
On Tue, 23 Mar 2004, Thomas Lumley wrote: I also note that in general - and eval.parent() are not related. It is a bad idea to confuse the enclosing and parent environments, even though they are often the same. I should probably also point out that one source of confusion is that we have

Re: [R] nlme question

2004-03-23 Thread Thomas Lumley
On Tue, 23 Mar 2004 [EMAIL PROTECTED] wrote: I have a need to call and pass arguments to nlme() from within another function. I use R version 1.8. I have found an apparent way to make this work, but I would appreciate some comments on whether this fix is really appropriate, or there is

Re: [R] building data object on iteration

2004-03-23 Thread Thomas Lumley
/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ [EMAIL PROTECTED] mailing

Re: [R] dots in function names

2004-03-23 Thread Thomas Lumley
On Tue, 23 Mar 2004, Robert W. Baer, Ph.D. wrote: There has been mention of S3 objects on the list. Is this relevant here? Is 'plot.default' a method (or perhaps a type-dependent object instantiation?) of the plot function object, or is 'plot.default' just a second function object that

Re: [R] multivariate analysis

2004-03-22 Thread Thomas Lumley
On Mon, 22 Mar 2004, Francesca Demichelis wrote: Dear, I'm using R to make multivariate analysis on bio/pathological data. In particular I use: coxph(Surv(time,status)~x+y+z). How to evaluate the hazard ratios and CI for each covariate? Could you suggest me a function or a set of function

Re: [R] detach()

2004-03-22 Thread Thomas Lumley
On Mon, 22 Mar 2004, Rolf Turner wrote: If, more realistically, you did melvin - grep(women,search()) detach(melvin) I would expect the data set ``women'' to be detached. My expectations would of course be dashed. The current structure of detach() seems to me to be a counterintuitive

RE: [R] substitute question

2004-03-18 Thread Thomas Lumley
On Wed, 17 Mar 2004, Gabor Grothendieck wrote: I left out the brackets in my last email but the problem (a reappears after have been substituted out) still remains: z - substitute( function(){a+1}, list(a=quote(b)) ) z function() { b + 1 } eval(z) function(){a+1} Interesting.

RE: [R] substitute question

2004-03-18 Thread Thomas Lumley
On Thu, 18 Mar 2004, Gabor Grothendieck wrote: Tony, Thomas. Thanks for your help. Your comments were very useful. Unfortunately, my next step gives me a new round of problems. The following is the same as the last example except that instead of hard coding the function into the

Re: [R] substitute question

2004-03-18 Thread Thomas Lumley
On Thu, 18 Mar 2004, Gabor Grothendieck wrote: From: Peter Dalgaard [EMAIL PROTECTED] (The real pain in these examples is that substitute autoquotes its expr argument. Therefore, when you want to modify an expression that is already stored in a variable, you need an extra outer layer

Re: [R] substitute question

2004-03-18 Thread Thomas Lumley
On Thu, 18 Mar 2004, Gabor Grothendieck wrote: I don't think I expressed myself very well on that. Looking at what we get from the example: z - substitute(substitute(expression(f),list(a=quote(b))),list(f=f)) z substitute(expression(function () { a + 1 }), list(a = quote(b)))

Re: [R] substitute question

2004-03-18 Thread Thomas Lumley
On Thu, 18 Mar 2004, Gabor Grothendieck wrote: I am not sure where this came from about not operating on functions. Are you sure? I know just about everyone is saying this but the help page does not refer to that and the example I gave where we do use list(f=f) for f a function does seem to

Re: [R] build on Irix failed reg-tests

2004-03-17 Thread Thomas Lumley
On Wed, 17 Mar 2004, Liaw, Andy wrote: Dear R-devel, Has anyone seen this problem? We tried building R-1.8.1 (and R-1.9.0 alpha 2004-03-17) on an Irix 6.5 box using ./configure CC=cc -64 F77=f77 -64 --with-tcltk=no --enable-R-shlib make check failed because NA + 0 gave NaN instead of NA.

RE: [R] build on Irix failed reg-tests

2004-03-17 Thread Thomas Lumley
On Wed, 17 Mar 2004, Liaw, Andy wrote: Sorry for being dense: So What is the likely source of the problem, then? Is it the compiler, the OS, R itself, or some combination of these? Any suggestion on how to resolve this? In a sense it is R itself, making assumptions that hold on many, but

Re: [R] glm questions

2004-03-16 Thread Thomas Lumley
On Tue, 16 Mar 2004, David Firth wrote: I am unclear what you are asking here. I assume by scaled deviance you mean deviance divided by phi, a (known) scale parameter? (I'm sorry, I don't know SAS's definition.)In many applications (eg binomial, Poisson) deviance and scaled deviance are

Re: [R] imputation of sub-threshold values

2004-03-15 Thread Thomas Lumley
need imputations. Otherwise you may be stuck with some ad hoc imputation with a sensitivity analysis to see how the results depend on the imputed value. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle

Re: [R] spss

2004-03-12 Thread Thomas Lumley
On Tue, 4 Mar 1997, Margarida [iso-8859-1] Júlia Rodrigues Igreja wrote: hi, i can´t download a file in access. when i type: library(foreign) read.spss(H:\Desktop\bd1\experiencia1) comes the error: Error in read.spss(H:Desktop\bd1experiencia1) : unable to open file do you know

Re: [R] No traceback available when using try(...)

2004-03-12 Thread Thomas Lumley
On Fri, 12 Mar 2004, Roger D. Peng wrote: Funny, it works for me on R-patched f - function(a) { return(log(a)) } f(A) Error in log(x) : Non-numeric argument to mathematical function traceback() 2: log(a) 1: f(A) try(f(A)) Error in log(x) : Non-numeric argument to mathematical

Re: [R] Xeon CPU and ATLAS

2004-03-12 Thread Thomas Lumley
On Fri, 12 Mar 2004 [EMAIL PROTECTED] wrote: I am about to get a new machine at work - an IBM Intellistation with the Xeon 2.8 GB processor. It will run Windows 2000. I would like to install the proper ATLAS dll for this machine, but I am not sure if Xeon is P4? Does anybody have any

Re: [R] Problems startin RAqua for Mac

2004-03-12 Thread Thomas Lumley
On Fri, 12 Mar 2004, Michael Mifek wrote: I am a user of a i book G4 with OS X 10.3 and I installed RAqua 1.8.1 without any problems. When I want to start RStart the R Symbol appers for one second and then disappers again and nothing else happens. I've tried to reinstall the program and I

RE: [R] Summary: do.call and environments

2004-03-11 Thread Thomas Lumley
On Thu, 11 Mar 2004, Liaw, Andy wrote: Gabor, From: Gabor Grothendieck Note that R and S are fundamentally different when it comes to scoping. R uses lexical scoping, i.e. the parent environment of a function is the environment at the point where it is *defined* whereas S uses

Re: [R] No traceback available when using try(...)

2004-03-11 Thread Thomas Lumley
On Thu, 11 Mar 2004, Edouard DUCHESNAY wrote: Hello, 1. The Situation : The stack traceback is not available when error ouccured in a try() It's a bug in 1.8.1. It has been fixed. -thomas __ [EMAIL PROTECTED]

Re: [R] Problem with Integrate

2004-03-02 Thread Thomas Lumley
On Tue, 2 Mar 2004, Anon. wrote: The background: I'm trying to fit a Poisson-lognormal distrbutuion to some data. This is a way of modelling species abundances: N ~ Pois(lam) log(lam) ~ N(mu, sigma2) The number of individuals are Poisson distributed with an abundance drawn from a

Re: [R] boxplot notches

2004-03-02 Thread Thomas Lumley
On Tue, 2 Mar 2004, P. B. Pynsent wrote: A Google search showed that all this was discussed in April 1988 with an extensive reply to the question from M Maechler. I, as a non-statistician, blindly believed what was written in the boxplot() help file, I am sure many would be grateful to this

Re: [R] Problem with Integrate

2004-03-02 Thread Thomas Lumley
On Tue, 2 Mar 2004, Anon. wrote: Thomas Lumley wrote: The help page for integrate() says When integrating over infinite intervals do so explicitly, rather than just using a large number as the endpoint. This increases the chance of a correct answer - any function whose

Re: [R] boxplot notches

2004-03-01 Thread Thomas Lumley
On Mon, 1 Mar 2004, Christoph Scherber wrote: Dear list members, Can anyone tell me how the notches in boxplot(Y~X,notch=T) are calculated? What do these notches represent exactly? I´d suppose they are Conficence Intervals for the median, but I´ve also been told they might show Least

Re: [R] load data for mypkg-Ex.R

2004-02-27 Thread Thomas Lumley
On Fri, 27 Feb 2004, Jason Sinnwell wrote: Using R 1.7.1 in Solaris I'm developing a package for both Splus and R, and I'm trying to use all the same files for R and Splus, both function files and help files. I have two questions. 1) The file made by R CMD check to run .Rd-examples posts

Re: [R] Help with multicolored points in one plot

2004-02-26 Thread Thomas Lumley
On Thu, 26 Feb 2004, David Thibault wrote: Hello all, I have a situation where I'd like to plot points from multiple groups of data in one plot. I'd like each group's points to be colored a different color. I've seen people comment on how you can alternate colors by providing a range of

Re: [R] variance estimator for the cumulative incidence function

2004-02-26 Thread Thomas Lumley
On Thu, 26 Feb 2004, Pintilie, Melania wrote: Hi everyone, I am using the package cmprsk in R to estimate the cumulative incidence function and its variance. In the manual it is mentioned that the variance is calculated based on Dr. Aalen's paper (1978, Nonparametric estimation of partial

Re: [R] read.spss defaults

2004-02-25 Thread Thomas Lumley
On Wed, 25 Feb 2004, Robert W. Baer, Ph.D. wrote: The read.spss parameter defaults are: use.value.labels=TRUE, to.data.frame=FALSE, Is there some reasoning other than historical for this choice? In most instances, it seems that the opposite default choice (use.value.labels=FALSE,

Re: [R] PWM Help

2004-02-25 Thread Thomas Lumley
On Wed, 25 Feb 2004, Jonathan Wang wrote: I saw a Help e-mail related to MLE. Does R have a probability weighted method (PWM) estimator function? I can't seem to find anything on PWM, unless my eyes are playing trick on me. The survey package has a function for maximising

Re: [R] would be nice ...

2004-02-24 Thread Thomas Lumley
On Tue, 24 Feb 2004, Martin Maechler wrote: or (slightly nicer) % echo sum(c(1,2,3)); 3*2 | R --quiet --vanilla sum(c(1,2,3)); 3*2 [1] 6 [1] 6 but it still echoes the input by default You can use --slave to suppress the input [al:~] thomas% echo print(sum(1:3))

Re: [R] Nonlinear Optimization

2004-02-24 Thread Thomas Lumley
On Tue, 24 Feb 2004, Kissell, Robert [EQRE] wrote: Hi, I have been brought back to the R-Side from MatLab. I have used R in graduate econometrics but only for statistics and regression (linear and nonlinear). But now I need to run general nonlinear optimization. I know about the add-in

Re: [R] passing object names in a vector to save?

2004-02-20 Thread Thomas Lumley
On Fri, 20 Feb 2004, wolski wrote: for(x in nam) { #reads the objects and assigns the names. assign(x,simFromEmboss(Simmatrix(),x)) nnam-paste(x,.rda,sep=) print(nnam) save(x,file=nnam) } I knew that it fails. (It saves object x containing a char.) There

RE: [R] Area between CDFs

2004-02-19 Thread Thomas Lumley
On Wed, 18 Feb 2004, Samuelson, Frank* wrote: You may not want to integrate cdfs. They're already probabilities. :) Nice analytic statistics exist for just the maximum distance between the cdfs, for example. And for the area between cdfs, which is perhaps better known as the difference in

Re: [R] filling the area between two curves in a plot

2004-02-19 Thread Thomas Lumley
On Thu, 19 Feb 2004, Rajarshi Guha wrote: Hi, does anybody know how I can color the area enclosed between two curves on a plot? There is an example of this in demo(graphics). -thomas __ [EMAIL PROTECTED] mailing list

Re: [R] Obtaining SE from the hessian matrix

2004-02-19 Thread Thomas Lumley
On Thu, 19 Feb 2004, Timur Elzhov wrote: So, what is the _right_ way for obtatining SE? Why two those formulas above differ? If you are maximising a likelihood then the covariance matrix of the estimates is (asymptotically) the inverse of the negative of the Hessian. The standard errors are

RE:[R] reshape direction=wide

2004-02-19 Thread Thomas Lumley
__ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED

Re: [R] How to repeat a procedure

2004-02-18 Thread Thomas Lumley
On Wed, 18 Feb 2004, Haiyan Chen wrote: Hello, 1. After I generate a 100x50 matrix by x3-matrix(0,100,50);for (i in 1:100) {x1-rpois(50, mu[i]);x2-x1; x2[runif(50).01]-0; x3[i,]-x2}, YOu can do this without the loop, eg x3-rpois(50*100, rep(mu,each=100)) x3-ifelse(runif(50*100)0.01, 0, x3)

Re: [R] interfacing C++ using .Call

2004-02-17 Thread Thomas Lumley
On Tue, 17 Feb 2004, Sundar Dorai-Raj wrote: Hi folks, I apologise if this is in the documentation somewhere, but I can't seem to find it. I also did a search of CRAN without any success. I'm using R-1.8.1 (pre-compiled) on Windows 2000 with Rtools and mingw 2.0.0 (which includes gcc/g++

RE: [R] How to write efficient R code

2004-02-17 Thread Thomas Lumley
On Wed, 18 Feb 2004, Ko-Kang Kevin Wang wrote: One way to make your codes more efficient is to use vectorisation -- vectorise your codes. I'm not sure where you can find more information about it, but an example would be to use the apply() function on a data frame instead using a loop.

Re: [R] Error Installing dse Package

2004-02-14 Thread Thomas Lumley
local relocation entries in non-writable section (__TEXT,__const) This seems to be a common symptom when packages fail to build under RAqua, but I don't know what causes it. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University

Re: [R] R: lags

2004-02-10 Thread Thomas Lumley
On Tue, 10 Feb 2004, allan clark wrote: hi all how does one simulate a random walk process? i.e y(0)=0 y(t)=y(t-1)+ e(t) where e(t) is normal(0,1) say. e-rnorm(100) y-cumsum(e) -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED

Re: [R] coxph error

2004-02-10 Thread Thomas Lumley
On Tue, 10 Feb 2004, Fredrick Schumacher wrote: R list: I am using a 'for' loop to run a number of different models (stratified by different variables) with coxph. The data becomes sparse when some strata are used causing the model to become unstable. The following error occurs and the

Re: [R] citing a package?

2004-02-09 Thread Thomas Lumley
On Mon, 9 Feb 2004, Ramon Diaz-Uriarte wrote: Dear Martin, I'd suggest you check the DESCRIPTION file and ask the author(s) of the package (e.g., a package might be related to a tech report which might, now, be in press, or whatever). The posted suggestions seem to be that you don't cite

Re: [R] simple question on picking out some rows of a matrix/data frame

2004-02-09 Thread Thomas Lumley
On Mon, 9 Feb 2004, Roger Levy wrote: Hi, I have a simple question about matrix/data frame manipulation. I have a data frame that looks a something like this XYZ 10apples -1 -1 oranges ... 0-1 bananas and I'd like to pull out all the rows for which

Re: [R] how to use try()

2004-02-09 Thread Thomas Lumley
On Mon, 9 Feb 2004, r.ghezzo wrote: Hello, I have a program with this section: .. for(i in 1:20){ lo - nls(y~y0+a/(1+(x/x0)^b),start=list(y0=0.1,a=a0,x0=x00,b=-8.1)) beta[i] - lo$m$getPars()[4] } .. If the fit works this is OK but if the fit fails, the whole program fails so: ..

Re: [R] iterating over files in a directory with R

2004-02-08 Thread Thomas Lumley
On Sun, 8 Feb 2004, femke wrote: Hello, I'm an R newbie and was wondering whether there are R commands for iterating over files in a directory. Basically what I want to do is to iterate over many files and apply some R functions to each file seperately. e.g. for (each file in a

RE: [R] Incomplete Factorial design

2004-02-06 Thread Thomas Lumley
On Fri, 6 Feb 2004, Simon Fear wrote: One could also fit fit - lm(y~A*B - 1, data.frame(y=..., A=..., B=..,) which will give a direct a:b term (as the negative of the intercept in Spenser's formulation). Arguably this is more natural in a setting where there is no placebo so that an

RE: [R] rgamma question

2004-02-06 Thread Thomas Lumley
know who they are. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE

Re: [R] Using huge datasets

2004-02-05 Thread Thomas Lumley
On Wed, 4 Feb 2004, Roger D. Peng wrote: As far as I know, R does not have a memory limitation -- the only limit is the memory installed on your computer. The only practical limitation is the pointer size of your machine, so 32-bit machine can't address more than 4Gb, and R probably won't

Re: [R] rgamma question

2004-02-05 Thread Thomas Lumley
On Thu, 5 Feb 2004, Icabalceta, Jorge L. wrote: I was trying to generate random numbers with a gamma distribution. In R the function is: rgamma(n, shape, rate = 1, scale = 1/rate). My question is that if X~gamma(alpha, beta) and I want to generate one random number where do I plug alpha and

Re: [R] lm coefficients

2004-02-03 Thread Thomas Lumley
On Tue, 3 Feb 2004, Timur Elzhov wrote: Dear R experts, Excuse me if my question will be stupid... I'd like to fit data with x^2 polynomial: snip out - lm(T ~ poly(X, 4), data = d) out Call: lm(formula = T ~ poly(X, 2), data = d) Coefficients: (Intercept) poly(X, 2)1 poly(X,

Re: [R] Stepwise regression and PLS

2004-02-02 Thread Thomas Lumley
effective approximation to model averaging. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman

Re: [R] Variable substitution in grep pattern

2004-01-29 Thread Thomas Lumley
On Thu, 29 Jan 2004, Alberto Fornasier wrote: I've tried to use a for loop as follows: for(i in Licenza.elenco) { + Licenza.elenco.prova[Licenza.elenco==i] - length(grep(.*i.*,as.character(Licenza)))} In which Licenza.elenco is a character vector containing all unique values I need to

Re: [R] Re: Help with Hmisc/Design installation in R-aqua (apple)

2004-01-28 Thread Thomas Lumley
On Wed, 28 Jan 2004, Bema Bonsu wrote: Thanks thomas and pj. As requested I am attaching the generated error message when I attempt to install the Hmisc and Design packages. What do I do next? * Installing *source* package 'Hmisc' ... ** libs g77 -fno-common -g -O2 -c cidxcn.f -o

Re: [R] lm function

2004-01-22 Thread Thomas Lumley
] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle

Re: [R] Graphical Windows

2004-01-22 Thread Thomas Lumley
On Thu, 22 Jan 2004, Sebastien Durand wrote: Hello, Here is my problem. I am trying to run and learn R trough the terminal application of my Mac (it runs on Panther). So here it goes I just recently installed R, in unix mode (terminal) by following the attached web page. The trouble is

Re: [R] Bug in termplot?

2004-01-22 Thread Thomas Lumley
, package:modreg, package:nls, package:ts, Autoloads, package:base --- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley

Re: [R] matrix exponential: M^0

2004-01-20 Thread Thomas Lumley
at ucl.ac.uk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics [EMAIL

Re: [R] ecdf function

2004-01-16 Thread Thomas Lumley
On Fri, 16 Jan 2004, Maya Sanders wrote: I am trying to use the ecdf function to find p-values (using a vector of numbers to represent my new distribution and a test specific t-statistic value). I am using : 1-ecdf(vector)(t-stat) vector-c(5.386, 3.701717, 3.8289, 3.602, 4.469, 5.2087,

Re: [R] Resend: help with Hmisc/ Design installation in R-aqua (apple).

2004-01-15 Thread Thomas Lumley
On Thu, 15 Jan 2004, Bema Bonsu wrote: Hello again. This is a resend (first sent on the 12th of January); I would truly appreciate a response. I have tried, unsuccessfully, to install the Hmisc and Design libraries (Harrell FE Jr) in R-aqua (Apple). These libraries are in source code only

Re: [R] empty string

2004-01-15 Thread Thomas Lumley
version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics

Re: [R] Doubly interval-censored data

2004-01-14 Thread Thomas Lumley
list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle

Re: [R] edit windows in RAqua

2004-01-10 Thread Thomas Lumley
On Fri, 9 Jan 2004, Roger Koenker wrote: I'm just beginning to explore Raqua on a new G5 machine. Generally, it feels very natural, but I'm puzzled by the behavior of editing windows. When you use fix() or vi() or edit() you get a new window; this is fine, but is there a way to: o

Re: [R] Poisson distribution help requested

2004-01-09 Thread Thomas Lumley
On Fri, 9 Jan 2004, Mark St.John wrote: Could somebody help me to understand the syntax of R's ppois function? I'm looking to calculate the cumulative probability density of an observed value (y) given the expected mean (mu) and the level of significance (alpha). I'm coming from using SAS to

Re: [R] Call and memory

2004-01-09 Thread Thomas Lumley
On Fri, 9 Jan 2004, Bob Wheeler wrote: I use a large real matrix, X, in C code that is passed from R and transposed in place in the C code. I would like to conserve memory and, if possible, allocate space for only one copy of X -- hence I would like to pass a pointer to the data in the X

Re: [R] Installing R on 64-bit Solaris 2.8 --- follow-up

2004-01-08 Thread Thomas Lumley
On Thu, 8 Jan 2004 [EMAIL PROTECTED] wrote: Hello R-users, thanks to Brian Ripley and Roger Peng for there prompt replies on installing R on a Solaris 64-bit machine. R is now running and seems to be doing fine. I realy would like to have access to the manuals so I can climb most of the

Re: [R] Strange parametrization in polr

2004-01-08 Thread Thomas Lumley
__ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University

Re: [R] Sweave xtable

2004-01-08 Thread Thomas Lumley
On Thu, 8 Jan 2004, michaell taylor wrote: I have successfully incorporated simple graphics and outputs, but am having trouble getting a latex (xtable) table to function properly. Latex is seemingly treating the xtable code as input or verbatim text. That is, if I run Sweave('myfile.Snw',

Re: [R] Survival, Kaplan-Meier, left truncation

2004-01-07 Thread Thomas Lumley
or counting data. The `interval' type is for interval-censored data. Left-truncated, right-censored data are so easy to handle with hazard-based models that they are the default. You want roland - survfit(Surv(age.enter, age.exit, status)) -thomas Thomas Lumley Assoc

Re: [R] Sweave and X11 on OSX 10.3

2004-01-07 Thread Thomas Lumley
before the X server was started. I don't know any automatic way to have DISPLAY set correctly when the server is running and unset when it isn't. The result is that you either need to have DISPLAY set in .tcshrc or equivalent, or remember to set it when needed. -thomas Thomas Lumley

Re: [R] Sweave and X11 on OSX 10.3

2004-01-07 Thread Thomas Lumley
On Wed, 7 Jan 2004 [EMAIL PROTECTED] wrote: I see, could in this case R for the Mac be smarter about what the default graphics device should be? This is not an Sweave issue, it simply means that under the setup described above any call to plot() ---without actively opening a device

Re: [R] optim function : BFGS vs L-BFGS-B

2004-01-05 Thread Thomas Lumley
converge and the other might not. There aren't a lot of guarantees in numerical optimisation. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ [EMAIL

Re: rsync (was: [R] MASS package and lda)

2003-12-31 Thread Thomas Lumley
On Wed, 31 Dec 2003, [iso-8859-1] Göran Broström wrote: On Wed, Dec 31, 2003 at 11:02:36AM +0100, Göran Broström wrote: I read your conversation and tried this advice, but got rsync not found. I searched CRAN, and found links to 'rsync.r-project.org' and 'www.rsync.org', none of which

Re: [R] Assignments in loops

2003-12-30 Thread Thomas Lumley
, New Zealand Email: [EMAIL PROTECTED]Fax 7 838 4155 Phone +64 7 838 4773 wk+64 7 849 6486 homeMobile 021 1395 862 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help Thomas

Re: [R] odd results from polr vs wilcoxon test

2003-12-30 Thread Thomas Lumley
On Tue, 30 Dec 2003, Jonathan Williams wrote: summary(fit1) Call: polr(formula = ordered(dat) ~ grp, control = c(maxiter = 1, trace = 0)) Coefficients: Value Std. Errort value grp -15.82468 169.3329 -0.0934531 Intercepts: ValueStd. Error t value 2|3

Re: [R] installing packages on MAC os X

2003-12-29 Thread Thomas Lumley
On Mon, 29 Dec 2003, Sara Good-Avila wrote: Hello, I've just downloaded and installed the RAqua onto my Mac and I have R up and running fine. Now I'm trying to get 'ape' downloaded and installed and having quite the difficulty. I am following the directions specified under 'Installing

RE: [R] draft of posting guide

2003-12-26 Thread Thomas Lumley
Rather than a separate beginners' mailing list or a posting guide, perhaps what we need is a separate mailing list for discussing posting style? -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help

Re: [R] What's latex for?

2003-12-23 Thread Thomas Lumley
On Tue, 23 Dec 2003, [EMAIL PROTECTED] wrote: As an R absolute beginner when I update my R 1.8.1, after installing the packages I see the various updated commands orderly running in a table on the screen where, among other things, latex and example are indicated. 1) Being an old user of

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