Dear All:
I updated my R program as well as associated packages yesterday. Currently
my R version is 2.2.1 running under WINXP SP-2.
When I tried to list (summary) an nlme object that I developed before, I got
the following error message:
[ Error in .C(ARMA_constCoef, as.integer(attr(object,
Dear Michael
Please remark that merge calculates all possible combinations if
you have repeated elements as you can see in the example below.
?merge
... If there is more than one match, all possible matches
contribute one row each. ...
Maybe you can apply aggregate in a reasonable way on your
And here is one with a working setHook call.
options(show.signif.stars=FALSE)
setHook(packageEvent(grDevices, onLoad),
function(...) grDevices::ps.options(horizontal=FALSE))
set.seed(1234)
options(repos=c(CRAN=http://cran.uk.r-project.org;))
On Thu, 5 Jan 2006, Petr Pikal wrote:
Hi
It's a bug. So nothing in the test suites uses this (nor any example in
any package on CRAN, which were tested prior to release).
Note that 3.1-68 is not the version of nlme which ships with R 2.2.1
(deliberately not introducing a new feature until after release).
Look for 3.1-68.1 in due
madhurima bhattacharjee wrote:
Hello Everybody,
I am running a R script through a perl code from command line.
The perl script is like:
my $cmd= 'R CMD BATCH D:/try5.R';
system($cmd);
I run the perl code from command line.
Now I want to pass some command line arguments to the R
gynmeerut wrote:
Dear All,
I am using R and I am putting my problem in form of an example:
X-c(128,34,153,987,345,45,3454,23,123)
I want to remove the entries which are lesser than 100(? How to compare every
element with 100 and how to create subsets )
and I need two vectors y and
At 11:56 05.01.2006 +1100, John Maindonald wrote:
I've changed the heading because this really is another thread. I
think it inevitable that there will, in the course of time, be other
lists that are devoted, in some shape or form, to the concerns of
practitioners (at all levels) who are
On 01/04/06 11:04, Franois Pinard wrote:
I'm in the process of learning R. While tutorials are undoubtedly very
useful, and understanding that working and studying methods vary between
individuals, what I (for one) would like to have is a fairly complete
reference manual to the library.
Of
David Forrest wrote:
[...]
Any volunteers?
Yes, me (well, partly...)! Here is what I propose: this is a very
lengthy thread in R-Help, with many interesting ideas and suggestions. I
fear that, as it happens too often, those nice ideas will be lost
because of the support used: email! By
[Jonathan Baron]
[the current reference manual] is organised by library and, within
each library, by function name: this organisation means that the
manual is mainly used as a reference, or else, that it ought to be
studied from cover to cover, dauntingly.
I think that many search
François Pinard wrote:
[David Forrest]
[...] A few end-to-end tutorials on some interesting analyses would be
helpful.
I'm in the process of learning R. While tutorials are undoubtedly very
useful, and understanding that working and studying methods vary between
individuals, what I
Roger Bivand wrote:
Gabor Grothendieck wrote:
For example, consider this introductory session in Stata:
http://www.stata.com/capabilities/session.html
Could I ask for comments on:
source(url(http://spatial.nhh.no/R/etc/capabilities.R;), echo=TRUE)
as a reproduction of the Stata
I don't think splitting the list is a good idea, neither according to the
level of questions (which will kill the beginners list), nor according
to geographic boundaries.
I totally agree with Heinz Tuechler's position : a (short) code on the
sublect of the e-mail seems a good ideau if people feel
Hello,
I'm using R version 2.2.0 installed on windows XP machine, with SP2 (maybe
it's also interesting to note it's laptop, so it outputs to a laptop screen)
a l and I wanted to draw a line in a graph, but it does not seem to work.
To test it I use the following code:
x = c(-1,0,1)
y =
Dear Sir,
I use the followoing command to install the library(kidpack). BTW I
install Biobase already.
install.packages(kidpack,type=source)
However, there is an error message occurred as follows.
library(kidpack)
Error in library(kidpack) : 'kidpack' is not a valid package
I think you need abline(v = 0).
I hope it helps.
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:
On 1/5/06, John Maindonald [EMAIL PROTECTED] wrote:
I've changed the heading because this really is another thread. I
think it inevitable that there will, in the course of time, be other
lists that are devoted, in some shape or form, to the concerns of
practitioners (at all levels) who are
Yufen wrote:
Dear Sir,
I use the followoing command to install the library(kidpack). BTW I
install Biobase already.
install.packages(kidpack,type=source)
However, there is an error message occurred as follows.
library(kidpack)
Error in library(kidpack) : 'kidpack'
R's week when handling large data file.
I has a data file : 807 vars, 118519 obs.and its CVS format.
Stata can read it in in 2 minus,but In my PC,R almost can not handle.
my pc's cpu 1.7G ;RAM 512M.
--
Deparment of Sociology
Fudan University
__
Another possibi8lity, of course, is language-based lists. Any interest for
r-spanish@ ...?
Kjetil
I am ready to contribute traducing original English texts into Spanish, but
not to produce original ones (I'm too new with these matters).
Ahimsa
Ahimsa Campos Arceiz
The University
Dear R-helpers,
First of all, a happy new year to everyone!
I succesfully used the daisy function (from package cluster) to find which two
rows from a dataframe differ by only one value, and I now want to come up with
a simpler way to find _which_ value makes the difference between any such
PhGr == Philippe Grosjean [EMAIL PROTECTED]
on Wed, 04 Jan 2006 20:35:17 +0100 writes:
PhGr David Forrest wrote:
[...]
Any volunteers?
PhGr Yes, me (well, partly...)! Here is what I propose: this is a very
PhGr lengthy thread in R-Help, with many interesting ideas
John Maindonald wrote:
...
(4) When should students start learning R?
[Students should get their first exposure to a high-level programming
language, in the style of R then Python or Octave, at age 11-14.
There are now good alternatives to the former use of Fortran or
Pascal, languages
Dear all,
I recently started using the deal package for learning Bayesian
networks. When using the jointprior function on a particular dataset, I
get the following message:
tor.prior-jointprior(tor.nw)
Error in array(1, Dim) : 'dim' specifies too large an array
What is the problem? How can I
Hi all,
Roger thanks for the reproduction.
As a user of Stata R, for common analysis I do use Stata and often, I have
to adapt some computations or to do some complex hierarchical modeling and
then I switch to R.
For me switching from Stata (or other statistical software, SO) to R (or
other
Dear all,
I recently started using the deal package for learning Bayesian
networks. When using the jointprior function on a particular dataset, I
get the following message:
tor.prior-jointprior(tor.nw)
Error in array(1, Dim) : 'dim' specifies too large an array
What is the problem? How can I
As someone who has been using Stata for a while now (and I started without a
programming background), I recently had to
move to R because of the rich spatial packages. Here is my 0.001 cent to this
thread.
-WHAT I LOVE ABOUT STATA--
a) Total control
In
Hi
On 5 Jan 2006 at 11:27, Edwin Commandeur wrote:
From: Edwin Commandeur [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Date sent: Thu, 5 Jan 2006 11:27:01 +0100
Subject:[R] problem with using lines command on windows XP
I am newbie in R, trying to understand and compare syntax in nlme and
lme4. lme() model from the nlme package I am interested in is:
lme.m1.1 = lme(Y~A+B+C,random=~1|D/E,data=data,method=ML)
(for simplicity reason, I am giving generic names of factors)
If I understand well, there are three
R Version 2.2.0
Platform: Windows
When I use barplot but select a ylim value greater than zero, the graph
is distorted. The bars extend below the bottom of the graph.
For instance the command produces a problematic graph.
barplot(c(200,300,250,350),ylim=c(150,400))
Any help
Peter Dalgaard writes:
Patrick Burns [EMAIL PROTECTED] writes:
whereas you could quite conceivably do it in R. (What *is* the
equivalent of rnorm(25) in those languages, actually?)
In SAS, it would go along the lines of:
data randvec(drop=seed);
seed = 459437845;
do obs = 1 to
Peter:
Almost correct. You need to add the variance component for the highest
level of nesting, so your model would be
lmer.m1.1 = lmer(Y~A+B+C+(1|D:E) + (1|E), data=data,method=ML)
But, yes, the : is used to note implicit nesting in lmer similar to the
syntax used for / in lme. The syntax
Martin Maechler writes:
If you go to the bottom of that wikipedia page,
you see that there is an R Wiki -- and has been for several
years now (!) at a Hamburg (De) university.
http://fawn.unibw-hamburg.de/cgi-bin/Rwiki.pl?RwikiHome
(...)
So, are you sure that another R Wiki is
From: Patrick Burns
John Maindonald wrote:
...
(4) When should students start learning R?
[Students should get their first exposure to a high-level
programming
language, in the style of R then Python or Octave, at age 11-14.
There are now good alternatives to the former use
Kjetil Halvorsen writes:
Another possibi8lity, of course, is language-based lists. Any interest for
r-spanish@ ...?
Kjetil
Since you´ve mentioned the topic, anyone reading this thread
knows of currently active R language-based lists? I am a member of R_STAT,
an R list for
On Thu, 2006-01-05 at 14:01 +0100, Bliese, Paul D LTC USAMH wrote:
R Version 2.2.0
Platform: Windows
When I use barplot but select a ylim value greater than zero, the graph
is distorted. The bars extend below the bottom of the graph.
For instance the command produces a problematic
Bliese, Paul D LTC USAMH paul.bliese at us.army.mil writes:
R Version 2.2.0
Platform: Windows
When I use barplot but select a ylim value greater than zero, the graph
is distorted. The bars extend below the bottom of the graph.
The problem is that barplot() is really designed to
Hi Petr and Eric,
Thanks for your comments.
To plot a vertical line, using lines(0) does not work, but
lines(c(-1,0),c(0,1))
does the work in my simple test example. I just interpreted the ?lines
documentation wrong.
So the lines command does work on my pc. Off course abline(v=0) will
also do
Ben Bolker bolker at ufl.edu writes:
Bliese, Paul D LTC USAMH paul.bliese at us.army.mil writes:
R Version 2.2.0
Platform: Windows
When I use barplot but select a ylim value greater than zero, the graph
is distorted. The bars extend below the bottom of the graph.
PaulB == Bliese, Paul D LTC USAMH [EMAIL PROTECTED]
on Thu, 5 Jan 2006 14:01:17 +0100 writes:
PaulB R Version 2.2.0
PaulB Platform: Windows
PaulB When I use barplot but select a ylim value greater
PaulB than zero, the graph is distorted. The bars extend
PaulB below
Thanks a lot. setHook is
Currently not in my knowledge set
But it's great to save these
Thing so I can look them up
When I feel more comfortable.
Just to add to that Stata versus R discussion :
I believe, anyone who uses
any other package than R, is probably missing
out in the long run. It's
lines() connects the `dots' given. If you want straight lines spanning the
entire graph, you are better off with abline().
Andy
From: Edwin Commandeur
Hi Petr and Eric,
Thanks for your comments.
To plot a vertical line, using lines(0) does not work, but
lines(c(-1,0),c(0,1))
does
predict.svm() can give you the decision values which are the distances
you are looking for (up to a scaling constant).
Regards,
David
Hi,
I know this question has been posed before, but I didnt find the answer in
the R-help archive, so please accept my sincere apologies for being
repetitive:
On 1/5/06, Liaw, Andy [EMAIL PROTECTED] wrote:
From: Patrick Burns
John Maindonald wrote:
...
(4) When should students start learning R?
[Students should get their first exposure to a high-level
programming
language, in the style of R then Python or Octave, at age 11-14.
On Wed, 4 Jan 2006, Peter Muhlberger wrote:
One comment in advance: please use a more meaningful subject. I would have
missed this mail if a colleague hadn't pointed me to it.
I'm someone who from time to time comes to R to do applied stats for social
science research.
[snip]
I would also
Dear all,
I'm now working on some programming on interactive displays from R.
So I'm creating an R display and want some interactive selection to be
available. I know ggobi and things like that, but it doesn't cope with
dendrogram.
So, if I go back to R graphics, as far as I know, --
For the
[ronggui]
R's week when handling large data file. I has a data file : 807 vars,
118519 obs.and its CVS format. Stata can read it in in 2 minus,but In
my PC,R almost can not handle. my pc's cpu 1.7G ;RAM 512M.
Just (another) thought. I used to use SPSS, many, many years ago, on
CDC machines,
Only or the record:
There is a wiki for R in general, used by only but a few people, annouced here
some year(s) ago:
http://fawn.unibw-hamburg.de/cgi-bin/Rwiki.pl
The question is: one or more wikis?
Detlef
On Wed, 04 Jan 2006 20:35:17 +0100
Philippe Grosjean [EMAIL PROTECTED] wrote:
David
-Original Message-
[ronggui]
R's week when handling large data file. I has a data file : 807 vars,
118519 obs.and its CVS format. Stata can read it in in 2 minus,but In
my PC,R almost can not handle. my pc's cpu 1.7G ;RAM 512M.
Just (another) thought. I used to use SPSS,
Dear Peter,
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Peter
Muhlberger
Sent: Wednesday, January 04, 2006 2:43 PM
To: rhelp
Subject: [R] A comment about R:
. . .
Ex. 1) Wald tests of linear hypotheses after max. likelihood
or even
As John and myself seem to have written our replies in parallel, hence
I added some more clarifying remarks in this mail:
Note that the Anova() function, also in car, can more conveniently compute
Wald tests for certain kinds of hypotheses. More generally, however, I'd be
interested in your
Hello there,
I did a few graphics but only one looks like the attached. Why the line
is not straight and how I can fix it?
thank you very much
Lisa Wang
Princess Margaret Hospital
Toronto, Canada__
R-help@stat.math.ethz.ch mailing list
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
Sent: Thursday, January 05, 2006 6:26 AM
To: 'Patrick Burns'; John Maindonald
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] A comment about R
[snip]
Any suggestion on how to go about
Another possibility is to make use of the several DBMS interfaces already
available for R. It is very easy to pull in a sample from one of those,
and surely keeping such large data files as ASCII not good practice.
One problem with Francois Pinard's suggestion (the credit has got lost) is
If what you are reading in is numeric data, then it would require (807 *
118519 * 8) 760MB just to store a single copy of the object -- more memory
than you have on your computer. If you were reading it in, then the problem
is the paging that was occurring.
You have to look at storing this in a
John Fox wrote:
Dear Peter,
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Peter
Muhlberger
Sent: Wednesday, January 04, 2006 2:43 PM
To: rhelp
Subject: [R] A comment about R:
. . .
Ex. 1) Wald tests of linear hypotheses after max.
2006/1/6, jim holtman [EMAIL PROTECTED]:
If what you are reading in is numeric data, then it would require (807 *
118519 * 8) 760MB just to store a single copy of the object -- more memory
than you have on your computer. If you were reading it in, then the problem
is the paging that was
It is often convenient to quickly set the working directory to a path
copied onto the windows clipboard. A simple trick I have been using for
a while is along the lines given in the previous posts.
setwd.clip-function()
{
options(warn=-1)
setwd(gsub(,/,readLines(clipboard)))
PaulB When I use barplot but select a ylim value greater
PaulB than zero, the graph is distorted. The bars extend
PaulB below the bottom of the graph.
PaulB For instance the command produces a problematic graph.
PaulB barplot(c(200,300,250,350),ylim=c(150,400))
Well, my
On 1/5/06 11:27 AM, Achim Zeileis [EMAIL PROTECTED] wrote:
As John and myself seem to have written our replies in parallel, hence
I added some more clarifying remarks in this mail:
Note that the Anova() function, also in car, can more conveniently compute
Wald tests for certain kinds of
Robert Baer rbaer at atsu.edu writes:
Well, consider this example:
barplot(c(-200,300,-250,350),ylim=c(-99,400))
It seems that barplot uses ylim and pretty to decide things about the axis
but does some slightly unexpected things with the bars themselves that are
not just at the 'zero' end
On 1/5/2006 2:11 PM, Berton Gunter wrote:
In a similar vein, a GUI version is:
setwd(dirname(choose.files()))
This gives you a standard Windows file browser -- you just click on any file
in the directory you want to set. Obviously, dirname(choose.files()) is an
easy interactive way to get
Dear Aaron,
I am really a tool user and not a tool maker (actually an ecologist
doing some biostatistics)... so, I take the liberty of sending a copy of
this e-mail to the r-help list where capable computer persons and true
statisticians may provide more relevant information and also to Paulo
ronggui wrote:
If i am familiar with
database software, using database (and R) is the best choice,but
convert the file into database format is not an easy job for me.
Good working knowledge of a DBMS is almost invaluable when it comes to
working with very large data sets. In addition, learning
Hi,
I've been using the package graph in the BioConductor assortment and
writing some functions based on its classes. My question is not specific to
this package or BioConductor (I think), but it serves as a useful example.
I recently wanted to look at the code for the function edgeMatrix for
Thanks Z, it's coming more into focus. I don't know what would work, though
maybe it's not impossible to have a richer set of cross-references by
interest area--e.g. People interested in econometrics may wish to
examine The views help in this regard, tho something in help itself
would be
At 19:07 04/01/06, fabio crepaldi wrote:
Hi,
I need to create the correlation table of a set of categorical data
(sex, marital_status, car_type, etc.) for a given population.
Basically what I'm looking for is a function like cor( ) working on
factors (and, if possible, considering NAs as
Something about the way R processes backslashes is defeating me.
Perhaps this is because I have only just started using R for text processing.
I would like to change occurrences of the ampersand into ampersand
preceded by a backslash.
temp - R D
sub(, \, temp)
[1] R D
sub(, \\, temp)
Michael Dewey [EMAIL PROTECTED] writes:
Something about the way R processes backslashes is defeating me.
Perhaps this is because I have only just started using R for text processing.
I would like to change occurrences of the ampersand into ampersand
preceded by a backslash.
temp - R
Briefly, S4 classes and methods are entirely different -- and often do not
comfortably coexist with -- the older S3 class/method system (which really
isn't, since the classes of the objects aren't really guaranteed as one
would expect).
Probably the best place to learn about S4 is The Green Book
Peter Muhlberger wrote:
But, there is a second point here, which is how difficult it
was for me [...] to find what seem to me like standard key
features I've taken for granted in other packages.
There is another side to this. Don't consider only how difficult it
was to find what you were
Thanks a lot Jim. Forwarded to Aaron (who rised the question) and the
R-help list...
Patrick
jim holtman a écrit :
The size matrix you are allocating (18227 x 18227) would require 2.6GB
of memory and that is what the error message is saying that you only
have 0.5GB (512MB) available.
Hi all,
Suppose I have a 4 x 2 matrix A and I want to select the values in
second column such that the value in first column equals to k.
I gave the colnames as alpha beta, so I was trying to access the info
using
A$beta[A[,1]==k], however, I was told it's not a data frame, I can get
Rongui,
I'm not familiar with SQLite, but using MySQL would solve your problem.
MySQL has a LOAD DATA INFILE statement that loads text/csv files rapidly.
In R, assuming a test table exists in MySQL (blank table is fine), something
like this would load the data directly in MySQL.
library(DBI)
I feel that as long as people continue to provide help on r-help wikis
will not be successful. I think we need to move to a central wiki or
discussion board and to move away from e-mail. People are extremely
helpful but e-mail seems to be to always be memory-less and messages get
too long
Thanks for the reference, it looks very interesting.
Best,
R.
-Original Message-
From: Weiwei Shi [mailto:[EMAIL PROTECTED]
Sent: Thu 1/5/2006 9:01 PM
To: Diaz.Ramon
Cc: Frank Duan; r-help
Subject:Re: [R] Looking for packages to do Feature Selection and
Frank makes an intersting point. For those interested, A site I spend
quite a bit of time on for Linux related stuff is IMHO really well done.
There are fora for many different linux distrubtions. There is a wiki,
a collection of tutorials, etc. If you want to take a look, the url is
Hi all,
what a great help list! I hope someone can help me with this puzzle...
I'm trying to find a simple way to do:
boxplot(obs~factor)
so that the factors are ordered left-to-right along the x-axis by
median, not alphabetically by factor name.
Complicated ways abound, but I'm hoping for a
On Thu, 2006-01-05 at 20:27 -0600, Joseph LeBouton wrote:
Hi all,
what a great help list! I hope someone can help me with this puzzle...
I'm trying to find a simple way to do:
boxplot(obs~factor)
so that the factors are ordered left-to-right along the x-axis by
median, not
A few thoughts about R vs SAS:
I started learning SAS 8 years ago at IBM, I believe it was version 6.10.
I started with R 7 months ago.
Learning curve:
I think I can do everything in R after 7 months that I could do in SAS after
about 4 years.
Bugs:
I suffered through several SAS version
[Brian Ripley]
I rather thought that using a DBMS was standard practice in the
R community for those using large datasets: it gets discussed rather
often.
Indeed. (I tried RMySQL even before speaking of R to my co-workers.)
Another possibility is to make use of the several DBMS interfaces
Leif Kirschenbaum wrote:
A few thoughts about R vs SAS:
I started learning SAS 8 years ago at IBM, I believe it was version 6.10.
I started with R 7 months ago.
Learning curve:
I think I can do everything in R after 7 months that I could do in SAS
after about 4 years.
Bugs:
I
Leif Kirschenbaum wrote:
A few thoughts about R vs SAS:
I started learning SAS 8 years ago at IBM, I believe it was version 6.10.
I started with R 7 months ago.
Learning curve:
I think I can do everything in R after 7 months that I could do in SAS
after about 4 years.
Bugs:
I
Hi
On 5 Jan 2006 at 15:11, Chia, Yen Lin wrote:
Date sent: Thu, 5 Jan 2006 15:11:18 -0800
From: Chia, Yen Lin [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Subject:[R] convert matrix to data frame
Hi all,
Suppose I have
Selecting a sample is easy. Yet, I'm not aware of any SQL device for
easily selecting a _random_ sample of the records of a given table. On
the other hand, I'm no SQL specialist, others might know better.
There are a number of such devices, which tend to be rather SQL
variant specific. Try
On Thursday 05 January 2006 12:13, Achim Zeileis wrote:
. . . snip
Whether you find this simple or not depends on what you might want to
have. Personally, I always find it very limiting if I've only got a switch
to choose one or another vcov matrix when there is a multitude of vcov
matrices
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