On Tue, 7 Sep 2004, Liaw, Andy wrote:
A small drawback to Gabor's proposal:
aa %:% dd
[1] b c d
00 %:% 99
character(0)
Defining it as a seq() method for characters is probably not a terribly good
idea, as one should expect it to work for any character vectors as input.
(One can
On Tue, 7 Sep 2004, Sigal Blay wrote:
On Tue, Sep 07, 2004 at 04:57:57PM -0400, Duncan Murdoch wrote:
On Tue, 7 Sep 2004 12:46:55 -0700, S Blay [EMAIL PROTECTED] wrote :
I wrote an R wrapper function (phylpro) around a C function
(Rphylpro).
The first time I'm running my function, it
On Tue, 7 Sep 2004, Roger D. Peng wrote:
Are you using an optimized BLAS for both builds? That's one
possibility. Also, 64-bit builds use up more memory initially since the
pointers are bigger. I've tried both 64-bit and 32-bit builds on
Sparc/Solaris and haven't seen any slowdown.
It
Kevin Wang [EMAIL PROTECTED] writes:
Hi,
On Tue, 7 Sep 2004, Kathy DeRiemer wrote:
Hi there,
I downloaded version 1.9.1 WinZip file, 9.367 bytes ( so I can update my R
Uit doesn't sound right, 9 bytes
Or 9K ? Still not making sense. The windows install file is
On 8 Sep 2004, Peter Dalgaard wrote:
Kevin Wang [EMAIL PROTECTED] writes:
On Tue, 7 Sep 2004, Kathy DeRiemer wrote:
I downloaded version 1.9.1 WinZip file, 9.367 bytes (so I can update my R
Uit doesn't sound right, 9 bytes
Or 9K ? Still not making sense.
R-1.9.1.tgz
Hello,
I was just doing heatmaps myself ;-) and I had the same problem. It would be
nice to have such an example in the help file because it is not clear (thank
you).
you use (for example... this is my case, which I am doing the distance
matrix using vegdist function with Bray curtis
Thanks Rolf and Thomas,
It looks to me like what you are doing is trying to judge
significance of differences by non-overlap of single-sample
confidence intervals. While this is appealing, it's not quite
right.
Yes, this is what I am trying to do. Apparently, when the replicates are
the
Dear R-users,
I would like to change the labels size and format in the node ends of a dendrogram,
how can I do it?
How can I use different symbols/colors in each node ends ?
I manage to do it with plot.cluster, but heat map uses plot.dendrogram.
Can anyone help me please?
thank you
Marta
Thank you very much, Profs. Ripley and Peng! It corrected a big
misconception in my mind.
By the way, does the Sun Forte 7 compiler produce faster R than the GCC
3.4.1 compiler (which we use)?
Jason
--- Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Tue, 7 Sep 2004, Roger D. Peng wrote:
On Wed, 8 Sep 2004, Jason Liao wrote:
Thank you very much, Profs. Ripley and Peng! It corrected a big
misconception in my mind.
By the way, does the Sun Forte 7 compiler produce faster R than the GCC
3.4.1 compiler (which we use)?
Not in my experience, although libsunperf helps a lot on
Hi all,
We have a genuine requirement for
Statistical Programmer with experience and knowledge of:
. R programming, and
. Oracle data base
This is to work on an a short term project for a research centre in italy.
If anyone would like further information, please feel free to
Dear List:
I have a question regarding an MDS procedure that I am accustomed to
using. I have searched around the archives a bit and the help doc and
still need a little assistance. The package isoMDS is what I need to
perform the non-metric scaling, but I am working with similarity
matrices, not
Hi All,
I am in the middle of doing an analysis of a Case-Cohort design. I had three questions
about the analysis:
a) Does any one know of some public code for developing the patient risk sets (indexed
by failure time) or is there a better way to organize the data?
b) I was planning to use
Try setting something like cex=0.5 in the plot. It works for at least
hclust. Here is a quick example using hclust to show how you can get
away with set the colours.
data(USArrests)
hc - hclust(dist(USArrests), ave)
plot(hc, hang=-1, cex=0.5)
labels - rownames(USArrests)[ hc$order]; n -
On Wed, 8 Sep 2004, Doran, Harold wrote:
1)Can isoMDS work only with dissimilarities? Or, is there a way
that it can perform the analysis on the similarity matrix as I have
described it?
Yes. The method, as well as the function in package MASS. All other
MDS packages are doing a
Ich werde ab 09/08/2004 nicht im Büro sein. Ich kehre zurück am
09/27/2004.
Ich werde Ihre Nachricht nach meiner Rückkehr beantworten.
Ursprüngliches Thema: R-help Digest, Vol 19, Issue 8
[[alternative HTML version deleted]]
__
[EMAIL
Hi again everyone
I have an arbitrarily dimensional array a and a list jj of length
length(dim(a)).The elements of jj are vectors of indexes.
How do I use do.call() to extract a[ jj[[1]], jj[[2]], jj[[3]], ...] ?
Toy example follows:
a - matrix(1:30,5,6)
jj - list(5:1,6:1)
I want the following
Hi Robin,
you could try the following:
lis - lapply(seq(1, length(dim(a))+1), function(x,a.,jj.) if(x==1) a.
else jj.[[x-1]] ,a.=a, jj.=jj)
do.call([,lis)
I hope this helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University
Distances cannot always be constructed from similarities. This can be done
only if the matrix of similarities is nonnegative definite. With the
nonnegative definite condition, and with the maximum similarity scaled so
that s_ii=1, d_ik=(2*(1-s_ik))^-.5
Check out the vegan package.
Alex
Robin Hankin [EMAIL PROTECTED] writes:
Hi again everyone
I have an arbitrarily dimensional array a and a list jj of length
length(dim(a)).The elements of jj are vectors of indexes.
How do I use do.call() to extract a[ jj[[1]], jj[[2]], jj[[3]], ...] ?
Toy example follows:
a -
On Wed, 8 Sep 2004, Hanke, Alex wrote:
Distances cannot always be constructed from similarities. This can be done
only if the matrix of similarities is nonnegative definite. With the
nonnegative definite condition, and with the maximum similarity scaled so
that s_ii=1, d_ik=(2*(1-s_ik))^-.5
Hi!
I observed it also. There are cases where it is not desirable. It will be quite
helpfull, if possible, to have a parameter that allows one to switch of removing the
#comments.
/E
*** REPLY SEPARATOR ***
On 9/6/2004 at 1:30 PM Thomas Petzoldt wrote:
Hello,
I try to
I don't understand.
If isoMDS does not work with distances, why does the help for isoMDS
indicate that the Data are assumed to be dissimilarities or relative
distances ?
Equally confusing is the loose use of the terms dissimilarities and
distances in the literature. As you point out in your book
Is anyone working on interfacing local linear embedding (Saul and Roweis) to
R?
The only mention I found was in the article Dimension Reduction for Data
Mapping (Edwards and Oman) in RNews 3/3.
Adele
__
[EMAIL PROTECTED] mailing list
This worked very well for me:
do.call([, c(list(a), jj))
What about you?
Kevin
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Robin Hankin
Sent: Wednesday, September 08, 2004 7:08 AM
To: [EMAIL PROTECTED]
Subject: [R] do.call([, ...) question
Hi
Hi Adele,
The Matlab code at http://www.cs.toronto.edu/~roweis/lle/code/lle.m seems
fairly straightforward to translate to R, so that would be the first thing
I'd try. However, one can obviously use better algorithms for sub-tasks
within that code, e.g., for finding k-NNs.
Best,
Andy
From:
Hi,
I'm looking for pointers/references on calculating den DF's for fixed
effects when using crossed random effects. Also, is there an implementation
of simulate.lme that I could use in lme4?
Thanks,
Elizabeth Lynch
Douglas Bates wrote:
Alexandre Galvão Patriota wrote:
Hi, I'm having some
Prof Brian Ripley wrote:
Well, we don't know what you are doing! RODBC does work with system DSNs,
but did you try odbcDriverConnect? Let me read the help page for you
odbcDriverConnect(DSN=foo) works, but odbcConnect(foo) fails as
described earlier. Is this as intended?
This seems weird,
Thanks Marta (and Andy). Between the two of you I think I got the result I
was looking for. I ended up doing the following:
heatmap(x, distfun=function(x) as.dist(x))
Thanks again.
-Original Message-
From: Marta Rufino [mailto:[EMAIL PROTECTED]
Sent: Wednesday, September 08, 2004
On my computer, it seems that (binary?) packages installed through the
GUI in RAqua are not used available to the command line version of R,
while (source) packages installed with R CMD INSTALL are available to
both. This is a problem when I run R CMD CHECK on a package that I am
creating that
Thank you. Quick clarification. isoMDS only works with dissimilarities.
Converting my similarity matrix into the dissimilarity matrix is done as
(from an email I found on the archives)
d- max(tt)-tt
Where tt is the similarity matrix. With this, I tried isoMDS as follows:
tt.mds-isoMDS(d)
and
I have just installed R 1.9.1 on an old Sun Sparc
with the following specs:
version
Machine hardware: sun4u
OS version: 5.6
Processor type: sparc
Hardware: SUNW,Ultra-4
The following components are installed on your system:
Sun Visual WorkShop C++ 3.0
Sun WorkShop
You should be able to get the behavior you want using the fit.glh() (short
for fit general linear hypothesis) function from the gregmisc/gmodels
package.
-G
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of
Fernando Henrique
Ferraz P. da Rosa
Sent:
Haven't you sent this before?
d_sign is part of the Fortran runtime support. Since you are running
sunperf, you should not have been building libRlapack at all.
Please don't try to outsmart R, but let it decide what configuration to
try. Once that works, feel free to try to improve it. My
typeof applied to a factor always seems to return integer,
independently of the type of the levels.
This has a strange side effect.
When a variable is imported into a data frame,
its type changes.
character variables automatically are converted
to factors when imported into data frames.
Here is an
?data.frame says:
Details:
A data frame is a list of variables of the same length with unique
row names, given class 'data.frame'.
'data.frame' converts each of its arguments to a data frame by
calling 'as.data.frame(optional=TRUE)'. As that is a generic
function,
In some cases it makes sense to store character variables as factors
(integers with labels) since this can take up much less memory. If
you really want to store `v2' as character, just do
data.frame(v1, I(v2))
-roger
Erich Neuwirth wrote:
typeof applied to a factor always seems to return
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XLSolutions Corporation (www.xlsolutions-corp.com) is proud to
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On Wed, 8 Sep 2004, Erich Neuwirth wrote:
typeof applied to a factor always seems to return integer,
independently of the type of the levels.
typeof is telling you the internal structure. From ?factor
'factor' returns an object of class 'factor' which has a set of
integer codes the
Hi all,
I have two questions stated below:
1. How to draw an observation uniformly from a given data?
For example, I have a dataset (or dataframe) with 10 observations (with a
set of variables) and I want to uniformly select an observation from this
given dataset, that is, the probability of
On Wed, 8 Sep 2004 [EMAIL PROTECTED] wrote:
Hi all,
I have two questions stated below:
1. How to draw an observation uniformly from a given data?
For example, I have a dataset (or dataframe) with 10 observations (with a
set of variables) and I want to uniformly select an observation from
[EMAIL PROTECTED] wrote:
Hi all,
I have two questions stated below:
1. How to draw an observation uniformly from a given data?
For example, I have a dataset (or dataframe) with 10 observations (with a
set of variables) and I want to uniformly select an observation from this
given dataset, that
Dear all,
I have a problem with adding columns to a data structure, using 'cbind':
I create an array, to which I want to cbind one new colum for every
iteration of a loop. Without the loop, the code works and looks like this:
Min- array(0,c(129,0))
Min
[1,]
[2,]
[3,]
[4,]
etc..
file -
The function I need is
valtype-function(x)
typeof(ifelse(is.factor(x),levels(x),x))
It is easy enough to write.
Are there any other special cases where the values
and the storage mode differ?
The background for all this is that I am transferring data
from R to Excel with VBA and I have to
Jan Wantia wrote:
Dear all,
I have a problem with adding columns to a data structure, using 'cbind':
I create an array, to which I want to cbind one new colum for every
iteration of a loop. Without the loop, the code works and looks like this:
Min- array(0,c(129,0))
Min
[1,]
[2,]
[3,]
Thanks David first.
Probably, David misunderstood my points.
source vector = (1,2)
the length of the target vector = 3
My expected complete outputs should be:
111, 112, 121, 122, 211, 212, 221, 222.
sample(c(1,2),3,replace=TRUE) just gives me one randomly sampled
combination at a time.
You should be able to make small modifications to the ci.lme function
provided in the gregmisc/gmodels package.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Spencer Graves
Sent: Friday, September 03, 2004 11:58 AM
To: [EMAIL PROTECTED]
Cc:
Try:
m - as.matrix(expand.grid(1:2, 1:2, 1:2))
x - m[,1] * 100 + m[,2] * 10 + m[,3]
x
1 2 3 4 5 6 7 8
111 211 121 221 112 212 122 222
Note that if the `source vector' is not 1:k for some integer k, you need to
coerce the output of expand.grid, as that returns a data frame of
Therefore, I would like to know if there are other types of variables
(besides factors) which give a misunderstandable answer about
the type
of their values when asked typeof.
Your question is a bit combative, don't you think? R performs as documented,
so I think your characterization is
Hi,
Loren Grimes wrote:
I realize that this is pretty basic, and I should be able to figure this out: but, how do I write a function [with a text editor] and then load it into an interactive R session?
Thanks
Try ?source
HTH,
Kevin
--
Ko-Kang Kevin Wang
PhD Student
Centre for Mathematics and
Doran, Harold wrote:
Thank you. Quick clarification. isoMDS only works with dissimilarities.
Converting my similarity matrix into the dissimilarity matrix is done as
(from an email I found on the archives)
d- max(tt)-tt
Mardia, kent Bibby defines the standard transformation from a
Dear all,
I wish to generate a lattice boxplot which skips an empty cell in a design.
I have trawled r-help, scruitinized xyplot(lattice) help page, and merrily
reproduced examples of using skip from a couple of previous r-help queries
and the example given in Pinheiro Bates. But I must be
On Wednesday 08 September 2004 23:18, Leon Barmuta wrote:
Dear all,
I wish to generate a lattice boxplot which skips an empty cell in a
design. I have trawled r-help, scruitinized xyplot(lattice) help
page, and merrily reproduced examples of using skip from a couple of
previous r-help
Note that I(v2) stores v2 as type character but not as class character.
For example,
R DF - data.frame(x = c(a, b), y = I(c(a, b)), z = I(c(a, b)))
R class(DF$z) - character
R sapply(DF, typeof) # y and z do have the same type
x y z
integer character character
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