Re: [R] demo(scoping)

2005-07-11 Thread Prof Brian Ripley
Why have you sent a message about this, which no indication except the non-English word `entercount'? Note that the message came from within try(), so it was intentional. If you look at the source it says try(ross$withdraw(500)) # no way.. It is helpful to learn how the code being

Re: [R] timezone problems

2005-07-11 Thread Prof Brian Ripley
For the record, this was covered by an answer to your bug report. The problem is your OS which mishandles a timezone of `GMT', so Sys.getenv(TZ) as `GMT' is not actually setting your OS to GMT. Hence NA is the correct answer. I know no way to set Windows to GMT as distinct from the timezone of

Re: [R] Dependence of bundle dse on setRNG (was Misbehaviour of DSE)

2005-07-11 Thread Prof Brian Ripley
As the posting guide says, there is no R 2.1. The first message suggests this is R 2.1.0, and the posting guide does ask you to use the latest version (and to quote versions accurately). The dse bundle depends on package setRNG, which you have not installed, so you need to do that. Look at

Re: [R] bug in chdir option of source

2005-07-12 Thread Prof Brian Ripley
Please read the posting guide (as we do ask) and use the current version as it asks to see if the `bug' has already been fixed. This was fixed a while ago, definitely in 2.1.1. On Tue, 12 Jul 2005 [EMAIL PROTECTED] wrote: I'm on R 2.1.0. In the source function there is a bug preventing the

Re: [R] what is the .Machine$double.xmin for a 64 bit machine?

2005-07-12 Thread Prof Brian Ripley
It's a floating-point quantity: `64 bit' refers to the pointer size (only). Almost all current R platforms use IEC60559 arithmetic for real numbers and 32-bit integers for integers, so differ only in the way the compiler orders operations and stores to memory (thereby losing precision on some

Re: [R] bug in chdir option of source

2005-07-12 Thread Prof Brian Ripley
are reluctant to upgrade, I would suggest never installing a .0 release (of any software, not just R). Thanks again, Stefan On Tue, 2005-07-12 at 13:02, Prof Brian Ripley wrote: Please read the posting guide (as we do ask) and use the current version as it asks to see if the `bug' has already

Re: [R] Puzzled at ifelse()

2005-07-12 Thread Prof Brian Ripley
This is working exactly as documented. Nothing `breaks'! What does the help page say? 'ifelse' returns a value with the same shape as 'test' which is filled with elements selected from either 'yes' or 'no' depending on whether the element of 'test' is 'TRUE' or 'FALSE'.

[R] : Re: Dispersion in glm (was (no subject))

2005-07-12 Thread Prof Brian Ripley
Actually, glm() does not estimate the dispersion at all, so you will need to be more specific. For example, summary.glm() and predict.glm() use the Pearson statistic if dispersion=NULL (the default) for most families. You can supply any other value you choose, and the MASS package makes use of

Re: [R] write.foreign, SPSS on Mac OS X

2005-07-13 Thread Prof Brian Ripley
On Tue, 12 Jul 2005, EJ Nikelski wrote: I have jut installed the foreign package (v 0.8-8) on my OS X machine, and have a bit of a problem writing out a data frame in SPSS format. Specifically, the code file (the .sps format file) seems to write 3 unprintable hex values instead of double

Re: [R] How to increase memory for R on Soliars 10 with 16GB and 64bit R

2005-07-13 Thread Prof Brian Ripley
On Tue, 12 Jul 2005, Dongseok Choi wrote: My machine is SUN Java Workstation 2100 with 2 AMD Opteron CPUs and 16GB RAM. R is compiled as 64bit by using SUN compilers. I trying to fit quantile smoothing on my data and I got an message as below.

Re: [R] Boxcox transformation / homogeneity of variances

2005-07-13 Thread Prof Brian Ripley
Please consult the reference on the help page of that function: it _is_ support software for a book. It implements the Box-Cox procedure (as it says). The original Box-Cox paper has three aims, two of which you have mentioned (but perhaps the most inportant one is the one you have not

Re: [R] How to use the function plot as Matlab

2005-07-13 Thread Prof Brian Ripley
For most purposes it is easiest to use matplot() to plot superimposed plots like this. E.g. x - 0.1*(0:20) matplot(x, cbind(sin(x), cos(x)), pl, pch=1) On Wed, 13 Jul 2005, Robin Hankin wrote: Hi Ted makes a good point... matlab can dynamically rescale a plot in response to

Re: [R] nlme, MASS and geoRglm for spatial autocorrelation?

2005-07-13 Thread Prof Brian Ripley
You seem to want to model spatially correlated bernoulli variables. That's a difficult task, especially as these are bernoulli and not binomial(n1). With a much fuller description of the problem we may be able to help, but I at least have no idea of the aims of the analysis. glmmPQL is

Re: [R] write.foreign, SPSS on Mac OS X

2005-07-13 Thread Prof Brian Ripley
, and it will not be if the labels are not ASCII. BTW, `8-bit ASCII' are mutually exclusive terms in file encodings. look into filing a bug report on this to the foreign package maintainer. Which is R-core, and we are already working on a fix. Thanks, Jim Prof Brian Ripley wrote: On Tue, 12 Jul 2005, EJ

Re: [R] Efficient testing for +ve definiteness

2005-07-14 Thread Prof Brian Ripley
On Wed, 13 Jul 2005, Makram Talih wrote: Dear R-users, Is there a preferred method for testing whether a real symmetric matrix is positive definite? [modulo machine rounding errors.] The obvious way of computing eigenvalues via E - eigen(A, symmetric=T, only.values=T)$values and returning

Re: [R] Name for factor's levels with contr.sum

2005-07-14 Thread Prof Brian Ripley
One way to do this generally is to make a copy of contr.sum, rename it, and set the dimnames appropriately. I think contr.treatment is misleading (it labels contrasts of two levels by just one of them), and Christoph's labels are informative but impractically long. But if you want to label

Re: [R] Memory question

2005-07-14 Thread Prof Brian Ripley
On Thu, 14 Jul 2005, Kenneth Cabrera wrote: Thank you Dr. Spencer Graves for your answer. What kind of matrices? They come form an image of about 3000x5000, and I need to generate arround 1024 matrices of the same size, they are not sparse matrices. What function can I use to, once

Re: [R] Fwd: Re: Problem installing R packages

2005-07-14 Thread Prof Brian Ripley
What Fortran compiler (g77) are you using, obtained from where? See http://www.astro.gla.ac.uk/users/norman/note/2004/restFP/ Your lines are wrapped in ways that make parsing impossible, but my guess at the link line does not include -lcc_dynamic. See also the list archives, e.g.

Re: [R] read.xport

2005-07-14 Thread Prof Brian Ripley
On Thu, 14 Jul 2005, Nelson, Gary (FWE) wrote: I have the latest version of foreign, but it still doesn't work. I Are you sure: a new version was released a few hours ago? It may not answer your question, but please do give actual version numbers (as the posting guide asks). -- Brian D.

Re: [R] Using system to run a stand alone program that requires input in Windows

2005-07-14 Thread Prof Brian Ripley
You want shell() not system(), I suspect, as you specified a shell command and I gather you are using Windows (not `DOS'). On Thu, 14 Jul 2005, Dr Carbon wrote: system(foo.exe params.txt) Alas that hangs just opens a window with foo.exe; params.txt is not passed to it. That's why I

Re: [R] Variance components from lm?

2005-07-15 Thread Prof Brian Ripley
In any case, the question was about lm, not lme. The short answer is that this is easiest from aov, a wrapper for lm, and for balanced data will be equivalent to as using lme. Steve can find worked examples for interlaboratory data in MASS (the book, see the FAQ). On Thu, 14 Jul 2005, Spencer

Re: [R] Fwd: Re: East Asian language

2005-07-15 Thread Prof Brian Ripley
On Fri, 15 Jul 2005, Peter Dalgaard wrote: Gabor Grothendieck [EMAIL PROTECTED] writes: I am not sure how generally this works but I was able to get it to switch back and forth between two languages within a single R session like this: The posting guide does ask people to read the

Re: [R] Fwd: Re: East Asian language

2005-07-15 Thread Prof Brian Ripley
On Fri, 15 Jul 2005, Uwe Ligges wrote: Pingping Zheng wrote: I think what Nan Lin wanted is How to change the language used in R console by re-setting something within R? For a non-english user, sometime we prefer to set the system default language to a native one and use english in

Re: [R] glm(family=binomial(link=logit))

2005-07-15 Thread Prof Brian Ripley
On Fri, 15 Jul 2005, Robin Hankin wrote: I am trying to make glm() work to analyze a toy logit system. I have a dataframe with x and y independent variables. I have L=1+x-y (ie coefficients 1,1,-1) then if I have a logit relation with L=log(p/(1-p)), p=1/(1+exp(L)). Not quite,

Re: [R] Passing character strings from C code to R

2005-07-15 Thread Prof Brian Ripley
Why invent your own function to do the same thing as the builtin one mkString? Please discuss C programming questions on the R-devel list *as the posting guide asks* On Fri, 15 Jul 2005, mkondrin wrote: Tuszynski, Jaroslaw W. wrote: Hi, I have a C code which produces array of integers

Re: [R] Cannot update some packages after upgrade to 2.1.1

2005-07-16 Thread Prof Brian Ripley
-lf77blas is part of ATLAS, so I do suspect the RPM builder had ATLAS installed. lme4 needs a compatible Matrix installed. I do think installing from the sources would solve this, but probably you need to discuss this with the RPM maintainer as a dependency appears to be missing. On Fri, 15

Re: [R] xfig device - depth

2005-07-17 Thread Prof Brian Ripley
There are no plans, and the means to do so was not documented in the file format docs used, nor does the R graphics model have a concept of `depth'. On Sat, 16 Jul 2005, Thomas Zanon wrote: Hi, I hope this is the right list for my posting, since I've never posted to any R list before. I'm

Re: [R] column-wise deletion in data-frames

2005-07-18 Thread Prof Brian Ripley
On Mon, 18 Jul 2005, Peter Dalgaard wrote: Chuck Cleland [EMAIL PROTECTED] writes: data - as.data.frame(cbind(X1,X2,X3,X4,X5)) So only X1, X3 and X5 are vars without any NAs and there are some vars (X2 and X4 stacked in between that have NAs). Now, how can I extract those former vars

Re: [R] Survival dummy variables and some questions

2005-07-18 Thread Prof Brian Ripley
This is almost unreadable. On Mon, 18 Jul 2005, Stephen wrote: Hi 1. To clarify: There is a posting saying that dummy regression using the coxph function is not possible... That posting may be outdated Clarification needs 1) an explanation of what you mean by `dummy regression' and 2) a

Re: [R] how to change bar colours in plot.stl

2005-07-18 Thread Prof Brian Ripley
On Mon, 18 Jul 2005, Michael Townsley wrote: Dear helpeRs, Is it possible to change the shading colour of the range bars in the plot generated by plot.stl? By default they are grey, but I would prefer them white (I am preparing some graphics for a powerpoint presentation so I'm inverting

Re: [R] column-wise deletion in data-frames

2005-07-18 Thread Prof Brian Ripley
On Mon, 18 Jul 2005, Peter Dalgaard wrote: Prof Brian Ripley [EMAIL PROTECTED] writes: On Mon, 18 Jul 2005, Peter Dalgaard wrote: Chuck Cleland [EMAIL PROTECTED] writes: data - as.data.frame(cbind(X1,X2,X3,X4,X5)) So only X1, X3 and X5 are vars without any NAs and there are some vars

Re: [R] read large amount of data

2005-07-18 Thread Prof Brian Ripley
On Mon, 18 Jul 2005, Thomas Lumley wrote: On Mon, 18 Jul 2005, Weiwei Shi wrote: Hi, I have a dataset with 2194651x135, in which all the numbers are 0,1,2, and is bar-delimited. I used the following approach which can handle 100,000 lines: t-scan('fv', sep='|', nlines=10)

Re: [R] listing datasets from all my packages

2005-07-19 Thread Prof Brian Ripley
I did manage eventually to reproduce this via data(package=makecdfenv) which is a BioC package with a non-standard use of the data directory. (There are no objects in the single R file in the data directory, which from its name I suggest is a dummy and the data directory should be removed

Re: [R] definition of index.array and boot.return in the code for boot

2005-07-19 Thread Prof Brian Ripley
Or read the *sources* for package boot, and find the original code with all the comments. On Mon, 18 Jul 2005, Spencer Graves wrote: Excellent question. Try 'getAnywhere(index.array)'. It's hidden in namespace:boot. Ditto for boot.return. spencer graves Obrien, Josh

Re: [R] help: how to change the column name of data.frame

2005-07-19 Thread Prof Brian Ripley
Just change the names! E.g. names(DF)[c(4,6)] - names(DF)[c(6,4)] Strictly a data frame has names, not column names, hence the use the names() and names-() functions here. On Tue, 19 Jul 2005, wu sz wrote: I have a data frame with 15 variables, and want to exchange the data of 4th column

Re: [R] help: how to change the column name of data.frame

2005-07-19 Thread Prof Brian Ripley
On Tue, 19 Jul 2005, Prof Brian Ripley wrote: Just change the names! E.g. names(DF)[c(4,6)] - names(DF)[c(6,4)] Strictly a data frame has names, not column names, hence the use the names() and names-() functions here. That answered the subject line. If you want to exchange the columns

Re: [R] help: how to change the column name of data.frame

2005-07-19 Thread Prof Brian Ripley
On Tue, 19 Jul 2005, wu sz wrote: Thanks a lot! But DF[c(4,6)] - DF[c(6,4)] seems to just exchange the data, not the names. If exchanging the columns(both data and names) needs two steps? DF[c(4,6)] - DF[c(6,4)] names(DF)[c(4,6)] - names(DF)[c(6,4)] Yes, it does. You did however say in

Re: [R] colnames

2005-07-19 Thread Prof Brian Ripley
On Tue, 19 Jul 2005, Adaikalavan Ramasamy wrote: First, your problem could be boiled down to the following example. See how the colnames of the two outputs vary. df - cbind.data.frame( 100=1:2, 200=3:4 ) df/df X100 X200 111 211 That one is probably unintentional. m -

Re: [R] writing matrices (no subject)

2005-07-20 Thread Prof Brian Ripley
Please use a current version of R: they are much better at this! write.table was rewritten in R 2.1.0 to use *much* less memory. There _is_ a `R Data Import/Export Manual' that dicsusses this. write.table was designed to write `tables' (data frames) not matrices. write.matrix (package MASS) does

Re: [R] CPU Usage with R 2.1.0 in Windows

2005-07-20 Thread Prof Brian Ripley
It probably is not a problem to leave hyperthreading on: we found little performance difference on a P4 either way. The Windows task manager is misleading, as `50%' is about as much as a P4-class processor with hyperthreading can actually deliver. On Tue, 19 Jul 2005, Lukasz Komsta wrote:

Re: [R] Problems with date-format (R 2.1.1 + chron)

2005-07-20 Thread Prof Brian Ripley
x - as.Date(21-07-2005,%d-%m-%y) is base R, and gives you a object of class Date. days() is not part of R, and I guess from your subject is part of chron. Its help page does not say what it actually does, but my guess is that it finds days of the month, *for a dates object not a Date object*.

Re: [R] .gct file

2005-07-20 Thread Prof Brian Ripley
On Tue, 19 Jul 2005, Marc Schwartz (via MN) wrote: For the TAB delimited columns, adjust the 'sep' argument to: read.table(data.gct, skip = 2, header = TRUE, sep = \t) The 'quote' argument is by default: quote = \' which should take care of the quoted strings and bring them in as a

Re: [R] problem in Krig function of Fields package

2005-07-20 Thread Prof Brian Ripley
My guess is that you have two data points which are very close together. The normal way out is to included a nugget effect in your model, but it can also be appropriate to leave out one of a pair of points. On Tue, 19 Jul 2005, orkun wrote: hello I try to build DEM using Krig function of

Re: [R] Need R Help

2005-07-20 Thread Prof Brian Ripley
You are probably not running a X server on your Windows machine, or if you are, you are not forwarding X connections. Even then, this is likely to be unsatisfactory unless you have a very good X server and a fast connection. Please read the help page for png, and note the See Also section

Re: [R] Cannot update some packages after upgrade to 2.1.1

2005-07-20 Thread Prof Brian Ripley
not to? It is a good idea unless you share R systems between different architectures (even down to the vintage of P4 or Xeon chips). We do and so tend to avoid ATLAS (which gets statically compiled in by default). Prof Brian Ripley wrote: -lf77blas is part of ATLAS, so I do suspect the RPM builder had ATLAS

Re: [R] Prefix for colnames

2005-07-20 Thread Prof Brian Ripley
On Wed, 20 Jul 2005 [EMAIL PROTECTED] wrote: Hi, I would like to add a prefix to colnames in a matrix but I can't get the prefix option in colnames to work. What am I doing wrong? X-matrix(NA,3,4) colnames(X)-c(test,test,test,test) colnames(X)-colnames(X,prefix=PREFIX.) X test

Re: [R] Cannot update some packages after upgrade to 2.1.1

2005-07-20 Thread Prof Brian Ripley
On Wed, 20 Jul 2005, Uwe Ligges wrote: Prof Brian Ripley wrote: On Wed, 20 Jul 2005, Kevin E. Thorpe wrote: Thank you for the information. I have contacted the RPM maintainer and am awaiting a response. It occurs to me that my problem could also be fixed by putting ATLAS on my

Re: [R] is.Date ?!!!

2005-07-20 Thread Prof Brian Ripley
If you mean of class Date, use inherits(x, Date). On Wed, 20 Jul 2005, Omar Lakkis wrote: Is there a way to test if a variable is a date? -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford,

Re: [R] predict.lm - standard error of predicted means?

2005-07-20 Thread Prof Brian Ripley
On Wed, 20 Jul 2005, Peter Dalgaard wrote: mark salsburg [EMAIL PROTECTED] writes: Can someone please refer me to a function or method that resolves this structuring issue: I have two matrices with identical colnames (89), but varying number of observations: matrix A

Re: [R] family

2005-07-21 Thread Prof Brian Ripley
You want to aim to write a family for R, not find the equivalents of S constructs -- they are different and so exact equivalents do not exist. In particular, an R family has several components which an S family does not. There are lots of example families for you to follow (e.g. see ?family

Re: [R] Problem with read.table()

2005-07-21 Thread Prof Brian Ripley
On Thu, 21 Jul 2005, Kristian Skrede Gleditsch wrote: Dear all, I have encountered a strange problem with read.table(). Most `strange problems' are user error, so please try not to blame your tools. When I try to read a tab delimited file I get an error message for line 260 not being

Re: [R] sapply(NULL, ...) returns a list?!?

2005-07-22 Thread Prof Brian Ripley
On Fri, 22 Jul 2005, Henrik Bengtsson wrote: Hi, I bet this one has be asked before, but doing sapply(x, FUN=as.character) where 'x' is a vector, then the result should [] be simplified to a vector according to ?sapply, correct? However, x - 1:10 sapply(x, FUN=as.character) [1]

Re: [R] About object of class mle returned by user defined functions

2005-07-22 Thread Prof Brian Ripley
confint has to be able to re-fit the function to form the profile likelihood. The fit you return refers to values inside the function you used, and those are not available in the environment you call confint from. You need to ensure that those values are substituted and not referred to.

Re: [R] memory cleaning

2005-07-22 Thread Prof Brian Ripley
See help(gc) and read up about garbage collection. Memory measurements without a preceding gc() are meaningless. You have not told us your version of R, but 2.1.0 and later do use much less memory in write.table. Nevertheless, they do have to convert each column to character and that does

Re: [R] problems with submitting an eps-file created in R

2005-07-22 Thread Prof Brian Ripley
On Fri, 22 Jul 2005, Christian Bieli wrote: Dear all I've got some problems submitting a manuscript, because I can't manage creating the favourable eps-file of a graph created in R. The journal's graphic requirements are as followed: format: eps width: max. 6 inches resolution: min. 1000

Re: [R] setting weights for such a two-class problem in nnet and svm

2005-07-22 Thread Prof Brian Ripley
On Fri, 22 Jul 2005, Baoqiang Cao wrote: Dear All, I have such a two-class problem, one class is very large(~98% of total), and the other is just 2%. According to manual of nnet, I need setup weights, so I intend to set 1 for class one, 49 for class 2. How do I do that? Just weights=49?

Re: [R] poisson fit for histogram

2005-07-23 Thread Prof Brian Ripley
What does fit.dist do that fitdistr (MASS) does not in this context? (It plots, but that is very easy to do in base R. However, to see if a Poisson fits you need a test of goodness-of-fit.) BTW, `decompress and store the files in your library folder' is on no OS (you did not mention one but

Re: [R] Lattice: reversing order of panel placement in conditional histograms

2005-07-23 Thread Prof Brian Ripley
From what I understand, you want to set up a factor with the levels reversed. It is not that `5 is larger than 1', but that you created a factor with the levels in alphabetic order. Lattice plots in the order of the levels. Something like f - factor(f, levels=rev(levels(f))) will do this.

Re: [R] %03d in the pdf command

2005-07-23 Thread Prof Brian Ripley
On Sat, 23 Jul 2005, Dennis Fisher wrote: The pdf man page contains the following text: pdf(file = ifelse(onefile, Rplots.pdf, Rplot%03d.pdf), width = 6, height = 6, onefile = TRUE, family = Helvetica, title = R Graphics Output, fonts = NULL, version = 1.1,

Re: [R] problem building R packages in windows xp

2005-07-24 Thread Prof Brian Ripley
On Sun, 24 Jul 2005, Uwe Ligges wrote: Dirk Eddelbuettel wrote: On 24 July 2005 at 13:44, Gabor Grothendieck wrote: | hhc.exe is the Microsoft help compiler. You have to download that | and then put hhc.exe somewhere in your path. The Windows | console command | | path | | will give

Re: [R] problem building R packages in windows xp

2005-07-24 Thread Prof Brian Ripley
On Sun, 24 Jul 2005, Jordi wrote: I am having problems building R packages in Windows xp. I have followed the instructions from Peter E. Rossi in Documentation - Other, except for the Better to follow the accurate official documentation. TeX version (fpTeX), since when I go to the

Re: [R] how to get the group mean deviation data ?

2005-07-25 Thread Prof Brian Ripley
if n id quite large,say n=1000 and t=3, it require too much time.so i want to know any more efficient way to do it? Why is about 0.4 second (which is what it takes on my system) too long? Given that you want to operate on 3000 cells, a second does not look unreasonable. This is a toy

Re: [R] apply and arrays

2005-07-25 Thread Prof Brian Ripley
On Mon, 25 Jul 2005, Uwe Ligges wrote: Laura Holt wrote: Hi R! I have a 3 dimensional array, which is 21 x 3 x 3 I want to use apply to sum on each 21x3 matrix, which is fine. Is there a way that I can do this in 1 step instead of a loop (3), please? Don't know which direction you

Re: [R] computation time gls()

2005-07-25 Thread Prof Brian Ripley
I find arima() fits such models very much faster. On Mon, 25 Jul 2005, Sebastian Leuzinger wrote: dear R users i try to fit a gls model to a rather large dataset with an AR(1) error structure: attach(sf.a1filt) m1.a.gls - gls(fluxt~co2+light+vpd+wind, correlation = corAR1(0.8))

Re: [R] how to write a periodic function in R?

2005-07-25 Thread Prof Brian Ripley
On Mon, 25 Jul 2005 [EMAIL PROTECTED] wrote: My question is how to write a periodic function in R. for example if there is a function f(x) that f(x)=f(x+4), for -2x2, f(x)=x how to write it in R? f((x+2)%%4 - 2) is one way. -- Brian D. Ripley, [EMAIL PROTECTED] Professor

Re: [R] ANOVA/aov question

2005-07-25 Thread Prof Brian Ripley
On Mon, 25 Jul 2005 [EMAIL PROTECTED] wrote: I'm a bit confused about the anova/aov functions. Both seem to rely on data models, where the relationship between the dependent variables and the independent variables can be expressed as a formula. In what I am trying to do, all of my

Re: [R] passing formula arguments cv.glm

2005-07-26 Thread Prof Brian Ripley
Adai, using traceback() helps, as does giving a reproducible example when reporting a problem. However, the problem is I think the line d.glm - update(glmfit, data = data[j.in, , drop = FALSE]) in cv.glm. I think that should be d.glm - eval.parent(update(glmfit,

Re: [R] passing formula arguments cv.glm

2005-07-26 Thread Prof Brian Ripley
On Tue, 26 Jul 2005, Adaikalavan Ramasamy wrote: Dear Prof. Ripley, Thank you for your response. See below for my comments. On Tue, 2005-07-26 at 10:57 +0100, Prof Brian Ripley wrote: Adai, using traceback() helps, as does giving a reproducible example when reporting a problem. You

Re: [R] text on some lines

2005-07-26 Thread Prof Brian Ripley
On Tue, 26 Jul 2005, Uwe Ligges wrote: Navarre Sabine wrote: I would like to write text on 2 lines for example. For example, if you have a long sentence and you want to cut it at the 45 caracter and put the continuation underneath! Is it possible? Do you mean for output to console / in

Re: [R] passing formula arguments cv.glm

2005-07-26 Thread Prof Brian Ripley
On Tue, 26 Jul 2005, Adaikalavan Ramasamy wrote: It works ! Thank you very much. Can I request this fix in the next version of boot package please if it is likely not to break compatibility with other functions. The modified cv.glm function can be found at

Re: [R] Assign new observations to Clara clusters

2005-07-26 Thread Prof Brian Ripley
On Tue, 26 Jul 2005, Nestor Fernandez wrote: Dear all, I need to assign new observations to cluster groups previously identified for a different dataset. The original clustering was performed using Clara. I gess one way is to assign each new observation to the nearest medioid of the

Re: [R] A question about par.plot in gamlss

2005-07-27 Thread Prof Brian Ripley
As the posting guide says, please ask the package maintainer -- I believe he does not read R-help regularly. Your layout is hard to read (please do use spaces and indentation in posted code), but probably there is a scoping problem with par.plot used inside a function. On Wed, 27 Jul 2005,

Re: [R] rpart.permutation, snow, rsprng binary files

2005-07-27 Thread Prof Brian Ripley
They rely on multiprocessing infrastructure not normally available on Windows. If you have this (and I don't know if it can be compiled on Windows but dome at least of the options cannot) you should be able to compile the source packages against the versions you have. On Wed, 27 Jul 2005, Jan

Re: [R] default family object in glm

2005-07-27 Thread Prof Brian Ripley
On Wed, 27 Jul 2005, luk wrote: what is the default family object in glm? I cannot find it from the doc. It would be great if you could tell me where I should look into. Try the help page: glm(formula, family = gaussian, data, weights, subset, It

Re: [R] make.names() does not return what is expected

2005-07-27 Thread Prof Brian Ripley
about how to discover already fixed bugs (not including this one). Prof Brian Ripley vas escriure el dia dc, 27 jul 2005: It's a bug, soon to be fixed in R-patched. -- Xavier Fernández i [EMAIL PROTECTED] [EMAIL PROTECTED] mailing listhttps://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read

Re: [R] how to generate 00Index.html from Rd or html

2005-07-27 Thread Prof Brian Ripley
On Wed, 27 Jul 2005, Jonathan Baron wrote: I'd like to generate 00Index.html for a bunch of libraries for my R search page. I think you mean for a package, not a library, that is the file /path/to/library/some_pky/html/00index.html ? I have now almost all the html help files for

Re: [R] unable to source a .R file using RJava

2005-07-27 Thread Prof Brian Ripley
Please, this is R-help, not the list for SJava questions. SJava is part of the Omegahat project (not the R project) and that used to have its own mailing lists. I believe they are currently non-operational, but please check. The R posting guide suggests that you first ask the maintainer and

Re: [R] How to delete rows

2005-07-27 Thread Prof Brian Ripley
To delete duplicate rows, use unique(TAB1): see its help page. It looks to me as if the names are missing values NA and *not* start with NA. If so, you want to use TAB1[!is.na(TAB1$Name), ] Otherwise, perhaps TAB1[substr(TAB1$Name, 1, 2) == NA, ]. On Wed, 27 Jul 2005, Michael Graber wrote:

Re: [R] how to get actual value from predict in nnet?

2005-07-27 Thread Prof Brian Ripley
Ask predict.nnet for a type other than class, as described on its help page. Please do read the help pages for yourself (as the posting guide asks). On Wed, 27 Jul 2005, Baoqiang Cao wrote: Dear All, After followed the help of nnet, I could get the networks trained and, excitedly, get the

Re: [R] Running Internet Explorer from Withing R

2005-07-29 Thread Prof Brian Ripley
On Thu, 28 Jul 2005, Peter Dalgaard wrote: Walter R. Paczkowski [EMAIL PROTECTED] writes: Good morning, Is it possible to open an html file using IE but from within R? I wrote a small function to generate tables in html but I'd like to write another function to call IE and open the html

Re: [R] Console not found

2005-07-29 Thread Prof Brian Ripley
Sounds like you have corrupted your Rconsole file. Fire up rterm and try ?Rconsole and/or read the rw-FAQ to find the file that it is use. It is not removed by uninstalling, and you do need to remove it. (The console settings have nothing whatsoever to do with memory settings.) Your matrices

Re: [R] R: graphics devices

2005-07-29 Thread Prof Brian Ripley
This is for Windows only, and documented in ?windows README.rw2011 (or whatever) It's more usual to switch recording on when you need it, either in the windows() call or from a menu. ?options only tells you about the standard options, not those used on specific platforms or by packages (and

Re: [R] Error Downloading Matrix Package

2005-07-29 Thread Prof Brian Ripley
Possible answers: 1) You do not have permission to remove the package from its previous location. 2) Windows mistakenly thinks that some file in the package is still open. Try deleting the directory from Windows Explorer. If 2) you may have to log out or reboot Windows before you can do so.

Re: [R] Error Downloading Matrix Package

2005-07-29 Thread Prof Brian Ripley
. (like do-it-yourself lobotomy.) Then I had to install.packages, because much of it got deleted and it wouldn't work any more. spencer graves Prof Brian Ripley wrote: Possible answers: 1) You do not have permission to remove the package from its previous location

Re: [R] Way to make R idle for some time and try something again later

2005-07-29 Thread Prof Brian Ripley
This depends on what else is going on. My guess is that you are running the Aqua GUI, and it is servicing the GUI which is taking the time, not R itself. On all of Linux, Solaris and Windows (RGui or Rterm) Sys.sleep() does use very close to zero resources at the beginning of a session, but

Re: [R] How to hiding code for a package

2005-07-30 Thread Prof Brian Ripley
What you ask is impossible. For a function to be callable it has to be locatable and hence can be printed. One possibility is to have a namespace, and something like foo - function(...) foo_internal(...) where foo is exported but foo_internal is not. Then foo_internal is hidden from casual

Re: [R] Updating to nlme 3.1-62 failing from source (OS X)

2005-08-01 Thread Prof Brian Ripley
This is an internal compiler/assembler error - please check that your tools are consistent and if so report this as a MacOS X error. (It is the sort of thing which happens if gcc targetted for one assembler is used with another, for example on Solaris with GNU vs Sun assemblers.) Given that

Re: [R] linux compile options (64-bit)

2005-08-02 Thread Prof Brian Ripley
We find it equally strange that you posted this! The advice _is_ in the R-admin manual which the INSTALL file asks you to read if you have any questions. It covers using enhanced BLAS libraries. R builds out of the box on FC3, FC4 and Suse on AMD64. I use Goto's BLAS, but ATLAS can be used

Re: [R] Rgdal windows binary warning message

2005-08-02 Thread Prof Brian Ripley
This is a consequence of how VC++ compiled gdal. R is protecting itself against that. Since R did not crash, there is nothing to worry about. On Tue, 2 Aug 2005, Tony Gill wrote: Hi all, I just downloaded windows binaries of RGDAL (from

Re: [R] can we manage memory usage to increase speed?

2005-08-02 Thread Prof Brian Ripley
On Mon, 1 Aug 2005, Haibo Huang wrote: Please refer to the following post. Which is about Windows only, not Linux. (And on Windows, the answer given is on the help page for memory.size. together with a better one.) Ed --- Mike Lawrence [EMAIL PROTECTED] wrote: Date: Mon, 1 Aug 2005

Re: [R] linux compile options (64-bit)

2005-08-02 Thread Prof Brian Ripley
On Tue, 2 Aug 2005, Göran Broström wrote: On Tue, Aug 02, 2005 at 07:34:39AM +0100, Prof Brian Ripley wrote: We find it equally strange that you posted this! The advice _is_ in the R-admin manual which the INSTALL file asks you to read if you have any questions. It covers using enhanced BLAS

Re: [R] Putting all elementes of the list in an enviorment of a function

2005-08-02 Thread Prof Brian Ripley
?with will help you. I would avoid using 'list' as a function name, as it will confuse people and might confuse R too. On Tue, 2 Aug 2005, [iso-8859-2] Alea }iberna wrote: Hello! I have two functions. The first one prepares the arguments for the second one. What is the best way to put

Re: [R] Putting all elementes of the list in an enviorment of a function

2005-08-02 Thread Prof Brian Ripley
only to create a list, it is not one of my functions. You used it as a variable within second()! Thanks again, Ales Ziberna - Original Message - From: Prof Brian Ripley [EMAIL PROTECTED] To: Ales Ziberna [EMAIL PROTECTED] Cc: R-help r-help@stat.math.ethz.ch Sent: Tuesday, August 02

Re: [R] linux compile options (64-bit)

2005-08-02 Thread Prof Brian Ripley
On Tue, 2 Aug 2005, Göran Broström wrote: On Tue, Aug 02, 2005 at 09:33:45AM +0100, Prof Brian Ripley wrote: On Tue, 2 Aug 2005, Göran Broström wrote: [...] Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with debian-amd64 (unstable) and ATLAS. Both 'make' and 'make

Re: [R] Read from data frame, and not from global environment

2005-08-02 Thread Prof Brian Ripley
I don't think that is the best way to do what I guess you intended. Try something like test - function(formula, data , weights) { Call - match.call() Call[[1]] - as.name(glm) Call$family - quote(poisson) glm1 - eval.parent(Call) } which is probably giving the

Re: [R] prcomp eigenvalues

2005-08-03 Thread Prof Brian Ripley
The eigenvalues are the squares of the singular values (although you need to watch the scalings used, in particular n vs n-1). (This is standard theory.) Since both are non-negative, given one you can get the other. On Tue, 2 Aug 2005, Sundar Dorai-Raj wrote: Rebecca Young wrote: Hello,

Re: [R] how to test this

2005-08-03 Thread Prof Brian Ripley
On Wed, 3 Aug 2005, Simon Blomberg wrote: This is two tests: Whether the slope != 1 and whether the intercept != 0. Neither model given has an intercept To do this, include an offset in your model: fit - lm(y ~ x + offset(x), data=dat) but no intercept, so use summary(lm(y ~ 0 + x +

Re: [R] Multilevel logistic regression using lmer vs glmmPQL vs. gllamm in Stata

2005-08-03 Thread Prof Brian Ripley
On Wed, 3 Aug 2005, Bernd Weiss wrote: I am trying to replicate some multilevel models with binary outcomes using R's lmer and glmmPQL and Stata's gllmm, respectively. That's not going to happen as they are not using the same criteria. The data can be found at

Re: [R] regexpr and portability issue

2005-08-03 Thread Prof Brian Ripley
On Tue, 2 Aug 2005, Marco Blanchette wrote: I am still forging my first arms with R and I am fighting with regexpr() as well as portability between unix and windoz. I need to extract barcodes from filenames (which are located between a double and single underscore) as well as the directory

Re: [R] make error: X11/Intrinsic.h: No such,,,

2005-08-03 Thread Prof Brian Ripley
On Wed, 3 Aug 2005, Jake Michaelson wrote: Hi all, I'm trying to build R 2.1.1 on Ubuntu 5.04 i686-SMP. Configure goes well with: ./configure --with-BLAS --with-readline=no but once I run 'make', I get the following error: In file included from devX11.c:64: devX11.h:57:74:

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