The C stdin is used *always* to read commands from on Unix R, and even on
console versions stdin() is where the commands are read from.
R CMD BATCH is approximately giving you
R --vanilla --slave my.R
and piping to such a command is going to do nothing for you.
Your command
Dear R-helpers,
I'm dealing with large datasets, say tables of 60 000 times 12 or so, and
some of the functions are (too ) slow and I'm therefore trying to find ways
to speed them up.
I've found that for instance for-loops are slow in R (both by testing and by
searching through mail archives etc
On Fri, 6 Aug 2004 [EMAIL PROTECTED] wrote:
Dear R-helpers,
I'm dealing with large datasets, say tables of 60 000 times 12 or so, and
some of the functions are (too ) slow and I'm therefore trying to find ways
to speed them up.
I've found that for instance for-loops are slow in R (both by
I would like to see an example of a data matrix for cclust and how to
import it to cclust.
In fact, i don't know how to give my imput for cclust program!
i test this file
1 0.23 1.52
2 0.52 1.25
3 0.13 1.89
4 0.78 1.11
i do
library(cclust)
x-scan(test.matrice.phyl)
Is there any fonction in R package which can transform a multiple
protein alignement
in a matrix for cclust?
--
ARMOUGOM Fabrice
CNRS UPR 2589 -Laboratoire Information genonique et structurale-
31 chemin Joseph Aiguier
13402 Marseille cedex 20, FRANCE
tel. +33 (0)4 91 16 44 51
Please read the help on the function (in package cclust, not mentioned by
you). It contains two examples, and
x: Data matrix where columns correspond to variables and rows to
observations
Your first attempt is a vector and your second is a data frame. cclust
requires a
Hi,
I have a lattice xyplot that contains panels according to FactorA, and
curves for the 2 levels of Factor B within a panel.
I try to add text in the panels of a lattice graph. I suppose I have to
write a custom function (panel.txt).
What I really would like is to adapt the text in the panel
you might want to turn your data into a matrix. You get much much faster
for loops doing that.
Jean,
On Fri, 6 Aug 2004 [EMAIL PROTECTED] wrote:
Dear R-helpers,
I'm dealing with large datasets, say tables of 60 000 times 12 or so, and
some of the functions are (too ) slow and I'm therefore
Folks,
S_t = (x_t, y_t) is the state of a system at time t. There is an
iterative function which converts S_t into S_{t+1}. I can easily write
this in R like this:
iterate - function(S) {
list(S$x+1, S$y+1)
}
So this function eats S_t and makes S_{t+1} and I can say
S2 -
Hi, can you help? I am really struggling to find the answer to the
following question.
I have conducted a standard multiple regression using SPSS. The dependent
variable is CE, and the independent variables are Ibelieve and Tbelieve.
Because the independent variables are highly correlated I have
Hello
I have a longitudinal dataframe organized in the long format and would like to make
comparison between successive rows if certain conditions apply. Specifically, I have
four variables of interest: grade, score, year, and schid, associated with each school
with 3 measurements per school
Tinn-R
The Tinn is an editor in development with the Delphi 5 of the Borland,
addressed to programmers, of free code under GPL (GNU Public License),
developed under the operational system Windows.
The Tinn-R version contains enhancements to allow syntax highlighting
of S language (in *.R, *.r,
I would sort the data frame by the grouping variables and order of the
scores, then use tapply and diff to compute the successive differences by
groups. You may want to pad the output by a zero to make it the same length
as the original scores.
Andy
From: Doran, Harold
Hello
I have a
N == N Callow [EMAIL PROTECTED]
on Fri, 06 Aug 2004 11:48:00 +0100 writes:
N Hi, can you help? I am really struggling to find the
N answer to the following question.
N I have conducted a standard multiple regression using SPSS.
so why do you ask here?
R-help is for
Please, this is a mailing list about R, not SPSS. And what exact is
`semi-partial correlation'?
Andy
From: N.Callow
Hi, can you help? I am really struggling to find the answer to the
following question.
I have conducted a standard multiple regression using SPSS.
The dependent
Dear List,
At 32 degrees Celsius in the office, I was too lazy to figure out
the correct xapplytion for a simple lookup problem
and regressed to well-known c-style. Only to see my
computer hang forever doing 1 indexed offset calculation.
Boiled down, the problem is shown below; needs a few
I found the following strange behavior using qnorm() and pnorm():
x-8.21;x-qnorm(pnorm(x))
[1] 0.0004638484
x-8.22;x-qnorm(pnorm(x))
[1] 0.01046385
x-8.23;x-qnorm(pnorm(x))
[1] 0.02046385
x-8.24;x-qnorm(pnorm(x))
[1] 0.03046385
x-8.25;x-qnorm(pnorm(x))
[1] 0.04046385
On Friday 06 August 2004 04:16, Joris DeWolf wrote:
Hi,
I have a lattice xyplot that contains panels according to FactorA,
and curves for the 2 levels of Factor B within a panel.
I try to add text in the panels of a lattice graph. I suppose I have
to write a custom function (panel.txt).
-Original Message-
From: Trenkler, Dietrich
Sent: Friday, August 06, 2004 3:13 PM
To: 'r-help'
Subject: [R] Bug in qnorm or pnorm?
I found the following strange behavior using qnorm() and pnorm():
x-8.21;x-qnorm(pnorm(x))
[1] 0.0004638484
x-8.22;x-qnorm(pnorm(x))
On Friday 06 August 2004 08:13, Trenkler, Dietrich wrote:
Given that pnorm(8.30) delivers 1 shouldn't we get Inf
for x-8.30;x-qnorm(pnorm(x)) ?
Why?
pnorm(8.30)
[1] 1
qnorm(pnorm(8.30)) ## same as qnorm(1)
[1] Inf
8.30 - qnorm(pnorm(8.30)) ## same as 8.30 - Inf
[1] -Inf
This seems
You will have to sort out the list before assigning. I am not sure if
there is an auto-sort ability in any of the function. Try this :
list1 - list(x=2, y=3)
list2 - list(y=7, x=8)
out - data.frame( matrix(NA, nc=2, nr=5) )
colnames(out) - c(x, y)
out[1, ] - unlist( list1[ colnames(out) ] )
R-help,
I have a list of several data frames.
I want to compute the rowSums of the columns of these data frames but first one.
Something like this
lapply(my.list,rowSums)
Thank you
Luis Ridao Cruz
Fiskirannsóknarstovan
Nóatún 1
P.O. Box 3051
FR-110 Tórshavn
Faroe
-Original Message-
From: Deepayan Sarkar
Sent: Friday, August 06, 2004 3:31 PM
To: [EMAIL PROTECTED]
Subject: Re: [R] Bug in qnorm or pnorm?
On Friday 06 August 2004 08:13, Trenkler, Dietrich wrote:
Given that pnorm(8.30) delivers 1 shouldn't we get Inf
for
From: Luis Rideau Cruz
R-help,
I have a list of several data frames.
I want to compute the rowSums of the columns of these data
frames but first one.
Something like this
lapply(my.list,rowSums)
You're almost there:
lapply(my.list, function(x)
Luis Rideau Cruz wrote:
R-help,
I have a list of several data frames.
I want to compute the rowSums of the columns of these data frames but first one.
... but first data.frame or but first column?
but first data.frame:
lapply(my.list[-1], rowSums)
but first column:
lapply(my.list, function(x)
I've been watching with interest on this one. I've had problems with
looping a randomForest procedure within R, and despite heroic efforts
by the R developers this problem hasn't been solved.
I was thinking that if I could loop through the data extraction (from a
MySQL) in the system, then
Ok, found it out. Things are really speedy when you first store result in a
vector, and cbind the vector to the data frame later.
Assuming that copying is involved, this would explain to me that my first
approach was so much slower, but I don't understand why time goes up more
than linearily
On Fri, 6 Aug 2004, Dieter Menne wrote:
Ok, found it out. Things are really speedy when you first store result in a
vector, and cbind the vector to the data frame later.
Assuming that copying is involved, this would explain to me that my first
approach was so much slower, but I don't
Hi!
Could you tell me what is p.value.raw in a hmtest object?
And what are the others properties of hmtest object
Thanks
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
The first 2 solutions are vastly slower than the last 3 simply because
they use the for() loop. The vectorised versions are definitely faster.
# Solution 1 : list extraction operator
aa - rep(NA, n); bb - rep(NA, n)
system.time( for (i in 1:n) {
aa[i] - PatDay$Day[i] -
Adaikalavan,
thanks for your phantastic summary. Solution 5 is the version I was looking
for, but I left out the cbind in good old c-fashion.
# Solution 5 : Vectorised operation with list extractor
system.time( ee - PatDay$Day - StartDay[ cbind(PatDay$Treat,PatDay$Pat)
Dieter
On other notes, try to leverage R's vector capabilities when
possible. Your DayOff variable can also be computed via
DayOff = PatDay$Day - StartDay[cbind(PatDay$Treat,PatDay$Pat)]
Gardar
At 04:06 PM 8/6/2004 +0200, Dieter Menne wrote:
Ok, found it out. Things are really speedy when you first
Hi all:
I solved the previous stated problem in something of a brute force way
(but it works). I seem to now be running into one little hiccup using
reshape. Here is a quick snip of the data in long format:
grade stability year schid
6 Grade 4 3 2001 15
7 Grade 4
Hi,
Is there a way to plot more than one trend surface using the functions
contourplot() and wireframe(). I have found an add=T in contour(), but
no equivalent argument in contourplot() and wireframe()?
I have taken the example 11-2 (pages 441-451) from Design and analysis
of experiments
On Thu, 5 Aug 2004, Wolfram Fischer wrote:
Hello
Is there a possibility to import and add a bitmap image (png or
similar) to a R graphics display. It would be helpful e.g. to
locate positions of points of a scanned map or to add a background
to a R graphic.
Wolfram
I found
My dataset consists of maps of deforestation in Chile (in GIS), and I want to analyse
whether distance from roads, soil type, altitude etc are important determinants of
deforestation rate. I had hoped to do this using GLS models, to handle spatial
autocorrelation, but I have only been able to
On Fri, 6 Aug 2004, Doran, Harold wrote:
Hi all:
I solved the previous stated problem in something of a brute force way
(but it works). I seem to now be running into one little hiccup using
reshape. Here is a quick snip of the data in long format:
snip
Now, I want to reshape this into
Hi R-users:
I've got a problem with lme.
In Rail data,I try to model the next one
lme(travel ~ Rail, data = Rail, random = ~ Rail | Rail)
I want travel = Rail(i) + Rail(j) + epsilon(i,j)
say, an effect fixed for every Rail and other for Rail(j) random, R says
fewer observations or false
On Friday 06 August 2004 10:47, Peter Ho wrote:
Hi,
Is there a way to plot more than one trend surface using the
functions contourplot() and wireframe(). I have found an add=T in
contour(), but no equivalent argument in contourplot() and
wireframe()?
I have taken the example 11-2 (pages
I have contributed a gam library to CRAN,
which implements Generalized Additive Models.
This implementation follows closely the description in
the GAM chapter 7 of the white book Statistical Models in S
(Chambers Hastie (eds), 1992, Wadsworth), as well as the philosophy
in Generalized Additive
On Fri, 6 Aug 2004, Cere Davis wrote:
I want to perform a regex substitution on line #1 in a file based on the
contents of line #2. same is true for line 11 and line 12 etc...
With the look at each line of a file rolling forward method it seems to
me that I will not be able to use
I am looking to attend an R course this summer
in Atlanta area. Any help?
Thanks alot
Eugene
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
see attached link
http://tolstoy.newcastle.edu.au/R/help/04/07/1491.html
Mihai Nica
Jackson State University
155 B Parkhurst Dr.
Jackson, MS 39202
601 969 5423
- Original Message -
From: eugene dalt [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Friday, August 06, 2004 2:27 PM
Subject:
Hi
I suspect that what you want to do is to have a randon intercept for Rails.
i.e.:
m-lme(travel ~ Rail, data = Rail, random = ~ 1 | Rail)
You might want to try the documentation under C:\Program
Files\R\rw1091\library\lme4\doc and also the book Mixed-effect models in S
and S-Plus by Pinheiro
In case the suggested model is NOT what you want, the book by
Pinheiro and Bates describes other models that may be closer to what you
want. Also, you might wish to consider lme in both packages nlme and
lme4. They are different, and overall lme4 is better, though it may not
be in any
Dear all.
I need to draw a scatter plot of 23 chromosome copy numbers (y axes) against
chromosome and physical location within each chromosome in one plot. The
data matrix looks as below:
chr location copy_num
1 118345 1.320118
1 3776202 1.133879
1 4798845 0.989997
1 5350951
Hello:
I am using R 1.9.1 under windows.
I am interested in the permax package for analyzing DNA microarray data.
I see, from install.packages(), that the windows binary version is 1.2.1, but that
source code exists for version 2.2.
Version 2.2 has much more functionality, especially for
Richards, Thomas [EMAIL PROTECTED] writes:
Hello:
I am using R 1.9.1 under windows. I am interested in the permax
package for analyzing DNA microarray data. I see, from
install.packages(), that the windows binary version is 1.2.1, but
that source code exists for version 2.2.
Er, did
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