-- sorry but the code I posted yesterday wasn't self-contained; here
it is again --
well, these are *approximate* confidence intervals (i.e., big enough
sample sizes are required for the asympotics to work), check Section
2.4.3 in Pinheiro and Bates (2000), and also the code below
Hello again
I think now I can refine my problem: I want to run R scripts
non-interactively in batch-mode or invoked in Perl scripts, with
interactive rgl windows (responding to my mouse actions). Ideally the R
script finishes when I close the rgl window and executes some last
commands in the
On 03/01/2008 5:58 PM, Peter Waltman wrote:
Hi Gabor -
Thanks for the 2 suggestions (and to Charilaos Skiadas as well, who also
suggested looking at proto).
I think I'm leaning towards using the new environment idea you
suggested, however, I don't quite get what a promise is (beyond
Hi all,
I'm trying to plot an svm model and I'm the following error:
plot(model, data= dados[,-1], formula=formula(dados[,2]~dados[,3]),svSymbol =
1, dataSymbol = 2, symbolPalette = rainbow(4),color.palette = terrain.colors)
Error in terms.default(x) : no terms component
Anyone knows how to
On Jan 3, 2008 5:11 PM, Nayeem Quayum [EMAIL PROTECTED] wrote:
Hello List,
I do have R version 2.3 installed in my SUSE linux environment and I am
trying to upgrade it to 2.6. Can any body tell me how to upgrade R 2.3 to R
2.6. I tried to uninstall R from the installed directory using the
Hello,
If I run the script : a-2 ; a-a+5 ; a whith the submit buton in
Rcmdr the result is 12 !!!
But if I run the script a-2 ; b-a+5 ; b there is no problem and the
result is 7.
I think there is a bug in the function onSubmit.
Thanks,
[[alternative HTML version deleted]]
On 03/01/2008 6:29 PM, kyselad wrote:
I'm trying to put Greek letters in factor labels on a boxplot. Using the
expression() format works great in axis labels, but seems not to cooperate
when applied to factor labels. More precisely, I'm assigning the labels from
a factor variable using:
I suggest you consult the source code, specifically src/unix/system.c and
src/unix/sys-std.c.
interactive() reports the value of the C-level variable R_Interactive, and
standard Unix-alike R runs an event loop only if that is true. I suspect
RGL is relying on that event loop, but reading its
Thank you all very much for your swift and useful replies! I know of
few software packages where the user support is so good..
I now resolved my problems, there turned out to be two distinct ones.
For anybody who might have a similar problem in the future, here are
the solutions that worked for
I'm trying to plot an svm model and I'm the following error:
plot(model, data= dados[,-1], formula=formula(dados[,2]~dados[,
3]),svSymbol = 1, dataSymbol = 2, symbolPalette = rainbow(4),color.
palette = terrain.colors)
Error in terms.default(x) : no terms component
Anyone knows how to
I am trying to establish an interface between FAME and R.
I have downloaded the zip file containing the documentation regarding
this interface from the CRAN website, but I am still having problems.
Thus far, what I have done is as follows:
1. I ran the ClientServer.R file.
2. Then I ran
Dear All - Any help/advice appreciated
OSX 10.5.1, R 2.6.1, survival 2.34
I am trying to fit an interval censored model with cluster or frailty
term (first 20 lines of the data set are below).
---MODEL
m1-survreg(Surv(start,stop,event,type=interval)~tree+hag+entcir
Good morning and I appreciate the availability of a help-list. I am a
professional hydrologist, but not a professional statistician. Yet I
find myself using statistical tools at least part of the time. My
discovery of the R-project through a friend has been most helpful.
Here is my problem:
Dear Jeremy,
As it says in ?Commander, the script window in the R Commander doesn't
provide a true console to R. One of the things it doesn't do is handle lines
with multiple commands separated by semicolons. In fact, I wonder what
version of the Rcmdr package you're using, since (for me) in the
James,
the first non-regular message you got in the output was:
made use of undefined node nSeaW,
so what about defining nSeaW (or did you mean to write mSeaW)?
If this is not the problem, please provide the data so that we can try
to reproduce your error, as the psoting guide (of R-help) ask
On 1/4/2008 10:44 AM, mika03 wrote:
Hello,
I think this might be a beginner question, but I couldn't find the answer in
the manual...
http://www.nabble.com/file/p14618947/at-modality.png
I created this image with R by using the following code:
modality -
Hello,
I think this might be a beginner question, but I couldn't find the answer in
the manual...
http://www.nabble.com/file/p14618947/at-modality.png
I created this image with R by using the following code:
modality - read.table(results.table, header=TRUE, sep=,)
color -
Hi all,
I have a dataframe called 'table' in which both factors and numerical
values are stored.
dim(table)
[1] 990 6
The fist 10 lines of table, to get an idea:
table[1:10,]
QueryNoQuery type Ret Prec Rec
11 Sports exact 11 0.01
25 Office exact 0
Dear Richard and Jeremy,
I suspect this is coming from how assignments are handled, and may be hard
to fix. I'll take a look.
Oddly, I can't duplicate this error when the commands are entered on a
single line separated by semicolons; then I get the error message
unexpected ';' in
I need arguments pro-S-PLUS and against SAS for a meeting I will
have next week. S-Plus is (90 - 99)% compatible with R, so using
S-Plus will make things much easier for everyone. But I can't use
this argument. What other arguments could I use?
Alberto Monteiro
John,
It's worse than a semi-colon problem. It is an error in a self-referential
statement 'a - a+5'. Type those lines as three separate lines in the Rcmdr
Script Window
and you still get the wrong answer. This is from 1.3-9.
a-2
a-a+5
a
[1] 12
Rich
-Original Message-
From:
Try this:
plot(subset(df[,c(3,5)], type %in% c(exact, broader1, narrower4)))
On 04/01/2008, Laura Hollink [EMAIL PROTECTED] wrote:
Hi all,
I have a dataframe called 'table' in which both factors and numerical
values are stored.
dim(table)
[1] 990 6
The fist 10 lines of table, to get
Tukey's HSD is only appropriate when you are interested in ALL pairwise
comparisons between the means.
If there are specific contrasts that are of interest a priori, then other
methods for controlling
the type I error over the family of contrasts are available (e.g. Bonferroni,
Holm).
Regards,
?subset
The select argument allows to select the columns and the subset argument
the rows.
domenico
Laura Hollink wrote:
Hi all,
I have a dataframe called 'table' in which both factors and numerical
values are stored.
dim(table)
[1] 990 6
The fist 10 lines of table, to get an
On 1/4/2008 12:25 PM, John Fox wrote:
Dear Richard and Jeremy,
I suspect this is coming from how assignments are handled, and may be hard
to fix. I'll take a look.
Oddly, I can't duplicate this error when the commands are entered on a
single line separated by semicolons; then I get the
See FAQ 7.12 and the R Language Definition manual on scoping.
R uses lexical scoping which means here that s does not exist in the
enclosing environment of inner(), which is the global environment.
Bert Gunter
Genentech Nonclinical Statistics
7-7374
-Original Message-
From: [EMAIL
I'm fitting generalized linear mixed models to using several fixed effects
(main effects and a couple of interactions) and a grouping factor (site) to
explain the variation in a dichotomous response variable (family=binomial). I
wanted to compare the output I obtained using PROC GLIMMIX in SAS
Dear Duncan,
Thanks for this. I haven't yet had a chance to look at the code but will
probably later today. I think that I understand what's going on and how to
fix it.
Regards,
John
John Fox, Professor
Department of Sociology
McMaster University
Hamilton,
Hi,
I would like start R in BATCH mode and submit my own parameters. Or in other
words, I would like to specify variables from the command line and execute a
script using those.
I have been looking at commandArgs and calling R from the command line under
bash:
R CMD BATCH --no-save --args
Maybe you can time this and see if this is any better:
%$% = function(data,field) data[, pmatch(field,dimnames(data)[[2L]])]
# test
mat - matrix(1:24, 6, dimnames = list(NULL, letters[1:4]))
mat%$%c
On Jan 4, 2008 2:29 PM, Dan Dube [EMAIL PROTECTED] wrote:
hello,
i have been trying to
Hi all,
I am working with the package popbio (demographic work) at the moment and
there is an included dataset, whale, that includes to matrices of equal
dimensions. One represents transition values and one represents recruitment
of new individuals (whale$T and whale$F respectively). I have
Here are three ways:
1. Define inner inside outer:
outer - function() { s - 1; inner - function() s; inner() }
outer() # 1
2. Use parent.frame:
inner - function() parent.frame()$s
outer - function() { s - 1; inner() }
outer() # 1
3. Pass s explicitly:
inner - function(s) s
outer -
I'm using R Version 2.6.1 under Windows XP.
search()
[1] .GlobalEnvs s
package:cairoDevice
[5] package:datasets package:foreign package:graphics
package:grDevices
[9] package:gWidgetsrJava package:gWidgets
Hi there! Happy new year to everyone!
There's a piece of code that I must write that's driving me crazy.
Maybe any of you has previous experiences in something similar. Any help
will be greatly appreciated!
The problem is as follows. I have a matrix Z with dimensions c(m,
p). I
hello,
i have been trying to convert my data frames to matrices in the hopes of
speeding up some of my more complicated scripts.
to assist with this, i am trying to create a matrix column operator
like $:
%$% = function(data,field) {
Hello, Peter,
I talked with SPSS: there is a known bug with character encoding. They
will fix it in the next release.
Regards,
Matthias
-Ursprüngliche Nachricht-
Von: Peter Dalgaard [mailto:[EMAIL PROTECTED]
Gesendet: Mittwoch, 2. Januar 2008 16:55
An: Matthias Wendel
That's a good point. Using the mat we used earlier we have:
%$% - function(data, field) data[, as.character(subsitute(field))]
mat %$% c
Note that there is one difference between $ and [ . Namely,
$ does not evaluate its right hand argument whereas [ does.
On Jan 4, 2008 3:05 PM, Bert Gunter
Dear all,
As you can see from the attachment I'm using R to automatically annotate
peptide fragmentation mass spectra, which are represented by impulse plots.
I'd like to poll you on approaches of how to deal as generally as possible
with the two biggest annotation issues I run into:
1) very
Why do you want to do this? X[,cname] gives the column named cname of
matrix X (as a vector, unless drop=FALSE). The $ operator on data frames is
essentially equivalent to this, anyway (see ? Extract).
-- Bert Gunter
Genentech
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL
Suppose I have a two-way table of nominal category (party
affiliation) X ordinal category (political ideology):
party affiliation X (3 levels) - democratic, independent, and republic
political ideology Y (3 levels) - liberal, moderate, and conservative
The dependent variable is the frequency
On 1/4/08, Alberto Monteiro [EMAIL PROTECTED] wrote:
I need arguments pro-S-PLUS and against SAS for a meeting I will
have next week. S-Plus is (90 - 99)% compatible with R, so using
S-Plus will make things much easier for everyone. But I can't use
this argument. What other arguments could I
Dear Duncan, Rich, and Jeremy,
Duncan has fixed the problems with semicolons and with the evaluation of
expressions with a variable on both sides of the assignment. I've
incorporated his code inTO the development version (1.3-11) of the Rcmdr
package, which is available at
On Fri, 4 Jan 2008, Dan Dube wrote:
hello,
i have been trying to convert my data frames to matrices in the hopes of
speeding up some of my more complicated scripts.
to assist with this, i am trying to create a matrix column operator
like $:
%$% = function(data,field) {
predict.lm keeps row names when working from several rows in
newdata, but always removes rowname from a single row.
The rownames are removed by the line in predict.lm
predictor - drop(X[, piv, drop = FALSE] %*% beta[piv])
What is the reason for that decision? I usually want to
retain the row
José Luis Aznarte M. ha scritto:
Hi there! Happy new year to everyone!
There's a piece of code that I must write that's driving me crazy.
Maybe any of you has previous experiences in something similar. Any help
will be greatly appreciated!
The problem is as follows. I have a
Hi R users !
I'm trying to use odfWeave package
I have a problem with unzipping files : when I try to run the example given in
odfWeave help I get this error message :
Copying C:/Documents and Settings/stgduclos/Mes
documents/R/win-library/2.6/odfWeave/examples/simple.odt Setting wd
Hi,
I am trying to do a PCA on my data but I keep getting the error message
svd(x, nu=0) infinite or missing values
From the messages posted on the subject, I understand that the NAs in my
data might be the problem, but I thought na.omit would take care of that.
Less than 5% of my cells are
Dear List,
I am trying to assess the prediction accuracy of an ordinal model fit with
LRM in the Design package. I used predict.lrm to predict on an independent
dataset and am now attempting to assess the accuracy of these predictions.
From what I have read, the AUC is good for this because it
On 04/01/2008 2:06 PM, sylvie ahoussou wrote:
Hi R users !
I'm trying to use odfWeave package
I have a problem with unzipping files : when I try to run the example given
in odfWeave help I get this error message :
Copying C:/Documents and Settings/stgduclos/Mes
On 04/01/2008 2:06 PM, sylvie ahoussou wrote:
I already downloaded Wiz from Info-zip in my Program Files directory. I've
also copied the directory in my Path in the Environment Variables as I
was suggested to do but I keep on getting the same message. I've seen a
message in this list
One simple reason: graphic.
On Jan 5, 2008 5:23 AM, Liviu Andronic [EMAIL PROTECTED] wrote:
On 1/4/08, Alberto Monteiro [EMAIL PROTECTED] wrote:
I need arguments pro-S-PLUS and against SAS for a meeting I will
have next week. S-Plus is (90 - 99)% compatible with R, so using
S-Plus will
Please read the help page:
## S3 method for class 'formula':
prcomp(formula, data = NULL, subset, na.action, ...)
## Default S3 method:
prcomp(x, retx = TRUE, center = TRUE, scale. = FALSE, tol = NULL, ...)
So there is no na.action argument for the form you used, and
This is an inconsistency in drop:
x - matrix(1:4, 4,1, dimnames=list(letters[1:4], NULL))
x
[,1]
a1
b2
c3
d4
drop(x)
a b c d
1 2 3 4
drop(x[1,,drop=FALSE])
[1] 1
S does not do that, and I don't think R should, given its documentation.
(Note that x[1,] also drops names in R
On Fri, 4 Jan 2008, Bernd Jagla wrote:
Hi,
I would like start R in BATCH mode and submit my own parameters. Or in other
words, I would like to specify variables from the command line and execute a
script using those.
I have been looking at commandArgs and calling R from the command line
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