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Just thought I would mention that there is a new O'Reilly book out, "Developing Bioinformatics Computer Skills", which is ok, pretty superficial about some things but at least it lets you know what is happening and where. R gets a few pages in there, 394-396, mostly nice press and accurate except that Bill Venables (hi Bill) may be surprised to find out that he is a member of the

> From: Robert Gentleman [mailto:rgentlem@jimmy.harvard.edu] > > Greg, > you might be better off writing a wrapper, > > R->foo where foo has less than 65 args and does nothing more than > unpack them and calls bar (the original) with as many args as you > want, not much code change and not much cost... Hi Rob, [BTW, sorry about the crosspost

Prof. Gentleman (and R-help), Here's an example of what didn't work. I still don't understand why. Function: trycon <- function(file, n) { f.con <- file(file, open="rt") on.exit(close(f.con)) i <- 0 while( length(readln <- readLines(f.con, 1)) > 0 ) { x <- unlist(strsplit(readln, " ")) if(length(x) <= 6 && x[3] ==

Robert Gentleman wrote: > On Tue, Oct 16, 2001 at 04:40:34PM +0100, Rita Ribeiro wrote: > > Hi, > > > > In order to avoid deep copies by passing large arguments to functions or > > > > returning values, I'm trying to do the assignment of variables in a > > given environment. The problem is when I try to assign a structure: a > > list for example.

Dear R-help, I think I have kinda isolated the problem I had to the following: i <- 0 while( {i <- i + 1} < 5) { if(i < 3) next print(i) } This seems to go into an infinite loop. After I break the execution, i has the value 1. At the R prompt, if I start from i <- 0 and keep typing {i <- i + 1} < 5, it eventually evaluate to TRUE. So why does the while loop not work?

Byron Ellis has been making some progress on a hdf5 library for microarray data (and any other thing you want to put in there). In doing so some issues have arisen that are of more general interest. 1) hdf5 supports annotation (through comments) so it would be nice if the comment function in R became generic. I think this is backward compatible and basically not really an issue of any

Prof. Tierney, Thanks very much for the info. Why does the loop work if I move the assignment out of the condition? E.g., the following works: i <- 0 while(i < 5) { i <- i + 1 if(i < 3) next print(i) } Regards, Andy > -----Original Message----- > From: Luke Tierney [mailto:luke at nokomis.stat.umn.edu] > Sent: Tuesday, October 02, 2001 3:36 PM > To: Liaw, Andy

Is there an implementation of a reasonable k-nearest neighbor finder already in one of the packages? -- +---------------------------------------------------------------------------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: not yet

My mistake :( Seems that there's another R installed by root. So when I use .libPaths() there're two of them: > .libPaths() [1] "/disk/hopper/projects/class/cse514/R/library" [2] "/usr/lib/R/library" How could the second path be enabled then? The R_LIBS have already been set to as the [1] only. Thanks, yan On Mon, 3 Mar 2003, Robert Gentleman wrote: > You

Yeah!! I finally get SJava examples run on linux. The problems is that there's an old version installed on the machine, with static library. Unfortunately, the path of the old version is set before the new version, thus every time when R command is conducted, the old version is invoked (but I didn't know), and since the libR.so is not exist in that version, I always got linkage errors :(

Here is part 1 of my long saga towards a more flexible modeling paradigm. Comments and hints are especially welcome. The simple version: Starting with a formula and data R goes through 3 main steps to get the data into a form suitable for fitting. 1) application of terms 2) application of model.frame (subset and na.action occur in 2). 3) application of model.matrix To be concrete

I have a, no doubt, simple question. I wish to write a function such that a <- 9 b <- 10 changer _ function(x,y) { if (y>x){ x <<- Y+1}} Of course there are easier ways to accomplish the task above, but I am more interested in how to have the "x <<- Y+1" part of the function to change x in place for purposes of a much larger function. I have been wrestling with

Dear all, Does anyone knows how I could extract the p-value in: > survdiff(Surv(tempo,status) ~ grupo,data=dados1,rho=1) Call: survdiff(formula = Surv(tempo, status) ~ grupo, data = dados1, rho = 1) N Observed Expected (O-E)^2/E (O-E)^2/V grupo=1 21 5.12 12.00 3.94 14.5 grupo=2 21 14.55 7.68 6.16 14.5 Chisq= 14.5 on 1 degrees of freedom,

Dear all, The Norwegian Institute for Nature Research (NINA) seeks a post doc or Ph.D. candidate in mapping and valuation of ecosystem services from green infrastructure in Oslo. The candidate has preferably skills in Open Source GIS (OSGeo) and a M.Sc./Ph.D. in geomatics with an interest in urban ecosystem services, or a M.Sc./Ph.D. in nature management, landscape architecture, geography,

"An Introduction to R" says that arithmetic operators coerce logical vectors to numeric vectors. This doesn't seem to be true for unary "-" however: > x <- 1:10 > p1 <- (x > 5) > p2 <- (-p1) > is.logical(p2) [1] TRUE > is.numeric(p2) [1] FALSE Since "==" always does binary comparison, this can lead to some bizarre behavior: > p1

The standard R boxplot appears to use quartiles to determine the height of the rectangles and a range parameter - RNG - (default=1.5 I think) that determines the length of the whiskers as <= RNG x Interquartile Range. Is it possible to instead define the range as extending to the 95th percentile? If so, how would this be done? nb, I'm plotting multiple boxplots on a single chart so a

----- Forwarded message from Stelios Zimeras <szimeras at irisa.fr> ----- Date: Wed, 20 Oct 1999 11:35:52 +0200 From: Stelios Zimeras <szimeras at irisa.fr> Organization: IRISA, Campus de Beaulieu, 35042 Rennes Cedex, FRANCE X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.5 sun4m) X-Accept-Language: en To: rgentlem at stat.auckland.ac.nz Subject: R installation problem Dear Sir, I try

The following appears to be a bug in 0.90 > x<-sample(10,1:4,rep=T) > x [1] 8 > ?sample > x<-sample(10,1:4,rep=T) > x [1] 5 Of course, I forgot the syntax but I still don't like the result. -- +-------------------------------------------------------------------------+ | Robert Gentleman voice: (617) 632-5045 | | Senior Lecturer

Hello all, Since I got no answer to my first mail, I suspect I did not formulate my question adequately, so I try again. In R, one can debug or trace a function 'foo' with debug(foo) or trace(foo), respectively. This leads to a special treatment of the function 'foo' until one enter undebug(foo) or untrace(foo). I would like to know if there is a convenient way to know at any

Environment variables set with Sys.putenv() disappear (i.e. become "") after a while, especially after heavy-duty I/O. Example: R> x <- matrix(1., 3000, 3000) R> save(x, file="myx.RData") R> Sys.putenv(HOME="/tmp") R> while (Sys.getenv("HOME") != "") {cat("ok\n"); load("myx.RData")} The loop prints