DMackay == Duncan Mackay [EMAIL PROTECTED]
on Fri, 27 Jan 2006 11:46:11 +1030 writes:
DMackay Hi all,
DMackay Can someone tell me how to justify (right or left) the labels on
the
DMackay branches of a dendrogram tree? I have produced a dendrogram via
agnes and
DMackay
yes, the error message was extremely clear; but what was also very clear was
that the file definitely exists under c:\ directory...
On 1/26/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
The error message seems pretty clear in this case. It can't
find the file. Try this instead:
x -
Markus == Markus Preisetanz [EMAIL PROTECTED]
on Thu, 26 Jan 2006 20:48:29 +0100 writes:
Markus Dear R Specialists,
Markus when trying to cluster a data.frame with about 80.000 rows and 25
columns I get the above error message. I tried hclust (using dist), agnes
(entering the
Hi Dale,
Unfortunately, you didn't say in what for format your
data is saved into, so I presume it's saved as a list
of strings. Perhaps there is a faster/better way, but
this should suffice if your datasize isn't enormous.
data = list()
data[1] = icsrvepf
data[2] = fpevrsci
data[3] = ics
Here is one example using the page option in xyplot:
library(lattice)
library(grid)
add.footnote - function(string=Hello World, col=grey,
lineheight=0.5, cex=0.7){
grid.text(string,
x=unit(1, npc) - unit(1, mm),
y=unit(1, mm), just=c(right, bottom),
Michael wrote:
thanks everyone, another problem is I cannot load Rcmdr at all in SCIView...
what might be the problem?
Not a problem, but a version incompatibility: SciViews is compiled for a
given version of R and Rcmdr (the one on the Web site is for R 2.2.0 and
Rcmdr 1.0-3... that is, not
Try:
data[lower.tri(data)]
(the same as data[col(data) row(data)], but using the dedicated function).
Best,
Philippe Grosjean
Christos Hatzis wrote:
Try
s - matrix(rnorm(36,0,1),nrow=6)
s[col(s)row(s)]
Courtesy of VR.
-Christos
-Original Message-
From: [EMAIL
Hi,
I am trying to use sub, regexpr on expressions like
log(D) ~ log(N)+I(log(N)^2)+log(t)
being a model specification.
The aim is to produce:
ln D ~ ln N + ln^2 N + ln t
The variable names N, t may change, the number of terms too.
I succeded only partially, help on regular
Briggs, Meredith M wrote:
exportData(MU.Cost,paste(C:/RAUDSL/S,as.character(MU.Cost$Run.Id[1]),
.,as.character(MU.Cost$MU.Id[1]),.MU.PRICE.OUTPUT.txt,sep=),append
= FALSE,type=ASCII,quote=FALSE)
Looks like perfectly good R to me.
Except there's no exportData function. I assume this is an
Dear all,
Are there any functions to convert decimals to fractions in R?
I have the result:
summary(as.factor(complete.ID))
0 0.0133 0.04
2256488230
0.0667 0.0933
Folks,
I'm doing fine with using orthogonal polynomials in a regression context:
# We will deal with noisy data from the d.g.p. y = sin(x) + e
x - seq(0, 3.141592654, length.out=20)
y - sin(x) + 0.1*rnorm(10)
d - lm(y ~ poly(x, 4))
plot(x, y, type=l); lines(x, d$fitted.values,
Note that [:alpha:] is a pre-defined character class and should only be
used inside []. And metacharacters need to be quoted. See ?regexp.
f - log(D) ~ log(N)+I(log(N)^2)+log(t)
f1 - deparse(f)
f1
[1] log(D) ~ log(N) + I(log(N)^2) + log(t)
Now we have a string.
(f2 - gsub(I\\((.*)\\) ,
G'day Muhammad,
MS == Muhammad Subianto [EMAIL PROTECTED] writes:
MS Are there any functions to convert decimals to fractions in R?
MS I have the result:
Something like:
library(MASS)
as.fractions(c(0, 0.0133, 0.04,
0.0667, 0.0933,
library(MASS)
?fractions
help.search(fractions) gets you there.
On Fri, 27 Jan 2006, Muhammad Subianto wrote:
Dear all,
Are there any functions to convert decimals to fractions in R?
I have the result:
summary(as.factor(complete.ID))
0 0.0133
I have updated some mail list traffic plots I created a while back
however I wouldn't consider the data verified. The reply stats are from
In-Reply-To headers.
http://brewiki.org/tmp/r-help_traffic.png
The data set is http://brewiki.org/tmp/r-help.zip
if it happens to know the denominator, then a simple approach could
be:
frac.fun - function(x, den){
dec - seq(0, den) / den
nams - paste(seq(0, den), den, sep = /)
sapply(x, function(y) nams[which.min(abs(y - dec))])
}
###
frac.fun(c(0, 1, 0.827, .06,
Hello,
Here is what I got after playing a little bit with your problem:
# First of all, if you prefer 'ln' instead of 'log', why not to define:
ln - function(x) log(x)
ln2 - function(x) log(x)^2
ln3 - function(x) log(x)^3
ln4 - function(x) log(x)^4
# ... as many function as powers you need
#
There are some interactive regex tools around. I use a python one
sometimes. You just then have to be careful re escaping and the style
of regular expressions used in the tool you worked with and the target
environment.
Christian Hoffmann wrote:
Hi,
I am trying to use sub, regexpr on
helpeRs,
I have a nice looking mosaic plot in an article to be published
soon. Sadly, the published version will be in black and white and so ruin
the advantage of the default shading scheme of tiles.
What would readers suggest as an alternative shading scheme? If I have a
black-and-white
On Thu, 26 Jan 2006 22:10:23 +0530 Ajay Narottam Shah wrote:
Folks,
I'm doing fine with using orthogonal polynomials in a regression
context:
# We will deal with noisy data from the d.g.p. y = sin(x) + e
x - seq(0, 3.141592654, length.out=20)
y - sin(x) + 0.1*rnorm(10)
d - lm(y
For the dissimilarity metric I would suggest manhattan, as provided by dist
(base package), daisy, agnes (both cluster package), for in your case a common
0 is meaningful - means that both pysicians didn't see the patient.
When using complete linkage you can see exactly how many patients
On this day 27/01/2006 11:51, Berwin A Turlach wrote:
library(MASS)
as.fractions(c(0, 0.0133, 0.04,
0.0667, 0.0933, 0.107,
0.133, 0.147, 0.16,
0.187,0.2,
Thanks you for your help.
Best wishes, Muhammad Subianto
On this day 27/01/2006 12:08, Dimitris Rizopoulos wrote:
if it happens to know the denominator, then a simple approach could
be:
frac.fun - function(x, den){
dec - seq(0, den) / den
nams - paste(seq(0, den), den, sep = /)
This particular call to exportData is probably equivalent in effect to
the R call:
write.table(MU.Cost,
file = paste(C:/RAUDSL/S,
as.character(MU.Cost$Run.Id[1]),
.,as.character(MU.Cost$MU.Id[1]),
Hi,
I installed R from one of the mirror sites (actually UK mirror site).
Once installed the interface is in German. Can you please suggest how to
change the R interface from German to English?
Thanking you and looking forward to your reply.
Best Regards,
Chanchal
Is there any function in R like
is.not.found(x, y)
meaning if you can't find object x, then use object
y??
Mikkel Grum
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
rm(list=ls())
a - 1
ifelse(exists(b), b, a)
[1] 1
b - 2
ifelse(exists(b), b, a)
[1] 2
Gabor
On Fri, Jan 27, 2006 at 04:38:39AM -0800, Mikkel Grum wrote:
Is there any function in R like
is.not.found(x, y)
meaning if you can't find object x, then use object
y??
Mikkel Grum
This is an FAQ from Windows users, who seem not to consult the rw-FAQ.
It is right there on the 'Help' menu and contains lots of useful
information.
If perchance you are not using Windows, it is also in the R-admin manual
which INSTALL asked you to read before installation.
I installed R
On 1/27/2006 7:48 AM, Gabor Csardi wrote:
rm(list=ls())
a - 1
ifelse(exists(b), b, a)
[1] 1
b - 2
ifelse(exists(b), b, a)
[1] 2
That's not quite right. ifelse() is meant for vectors of conditions;
you really want just plain old if here:
if (exists(b)) b else a
For example, with no b
You may recall that there was a discussion of a technical
report from the statistical consulting group at UCLA.
I have a draft of a comment on that report, which you
can get from
http://www.burns-stat.com/pages/Flotsam/uclaRcomment_draft1.pdf
I'm interested in comments: corrections, additions,
Michael comtech.usa at gmail.com writes:
yes, the error message was extremely clear; but what was also very clear was
that the file definitely exists under c:\ directory...
what happens with
file.exists('c:\\.txt')
?
(presumably the same error)
also try
f=file.choose()
select
Hi,
Am Donnerstag, 26. Januar 2006 19:39 schrieb Kort, Eric:
I have a variety of standard image processing functions written in R,
but have yet to distribute them because most people choose not to
perform image analysis in R for the previously stated reasons.
I encourage you to distribute
This does not answer your question directly but this
can relate to calling functions and also to inheritance
in object oriented systems. The common thread in
1b and 2 is that if a variable is not found in the current
environment R will look into the parent environment so if we
give our variables
On 1/26/06, Ajay Narottam Shah [EMAIL PROTECTED] wrote:
Folks,
I'm doing fine with using orthogonal polynomials in a regression context:
# We will deal with noisy data from the d.g.p. y = sin(x) + e
x - seq(0, 3.141592654, length.out=20)
This has already been answered but note that pi is
Hi everyone
Can anyone tell me how I normalise a power spectral density (PSD) plot of a
periodical time-series. At present I get the graphical output of spectrum VS
frequency.
What I want to acheive is period VS spectrum? Are these the same things but the
x-axis scale needs transformed ?
Any
Hi,
I was a happy user of Peter Parks' package (see http://www.chip.org/
~ppark/Supplements/PNAS05/) and could compile it without error under
Mac OS X 10.4. I then had a disk crash and had to re-install the
developer tools and now I get hideous messages such as the one
below. I
On 27 Jan 2006, [EMAIL PROTECTED] wrote:
Is there any function in R like
is.not.found(x, y)
meaning if you can't find object x, then use object
y??
Along with exists(), you might find mget() useful since it allows you
to specify an ifnotfound value.
--
+ seth
Hi, I' m having a hard time understanding the computation of degrees of freedom
when runing nlme() on the following model:
formula(my data.gd)
dLt ~ Lt | ID
TasavB- function(Lt, Linf, K) (K*(Linf-Lt))
my model.nlme - nlme (dLt ~ TasavB(Lt, Linf, K),
data = my data.gd,
fixed =
The entire message Re: [R] regular expressions, sub, originally sent to you
by [EMAIL PROTECTED] ([EMAIL PROTECTED]), has been forwarded to you from the
Antigen Quarantine area.
This message may have been re-scanned by Antigen and handled according to the
appropriate scan job's settings.
On Fri, 27 Jan 2006, Isaac Kohane wrote:
Hi,
I was a happy user of Peter Parks' package (see http://www.chip.org/
~ppark/Supplements/PNAS05/) and could compile it without error under
Mac OS X 10.4. I then had a disk crash and had to re-install the
developer tools and now I get
Hi, I would like to identify a few points on a clusplot generated from a
fanny clustering.
The manpage for clusplot indicates that setting labels=5 allows me to
identify the points. However I only need to identify a subset.
I tried setting the 'Labels' attribute of my data matrix (23 rows) as:
Eric:
I use R to quantify the efficacy of ultrasonic inspections of metal
components (e.g. looking for nonmetallic inclusions in forgings) and use R
for image processing, but my methods have been rather a kluge. I am
interested in your R functions, if you will make them available.
Unfortunately,
Charles Annis, P.E. writes...
Eric:
I use R to quantify the efficacy of ultrasonic inspections of metal
components (e.g. looking for nonmetallic inclusions in forgings) and
use R
for image processing, but my methods have been rather a kluge. I am
interested in your R functions, if you will
On 1/27/06, gabriela escati peñaloza [EMAIL PROTECTED] wrote:
Hi, I' m having a hard time understanding the computation of degrees of
freedom
So do I and I'm one of the authors of the package :-)
when runing nlme() on the following model:
formula(my data.gd)
dLt ~ Lt | ID
TasavB-
Hi,
Is it possible that I could see some of your functions and/or results of
those functions(Eric, Charles, Stephan). It's more about that I'd like
to see what already has been accomplished and the way that was chosen
thus circumventing reinvention and getting an overview.
Cheers
Thomas
Being a Stata user in transition to R I have to say that it would be
fair to mention that data handling for large amounts of data might
take an extra step in R.
I understand that there are good reasons for R consuming more memory
(than Stata) when handling large datasets, but it is necessary to
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Hi,
Is it possible that I could see some of your functions and/or results
of
those functions(Eric, Charles, Stephan). It's more about that I'd like
to see what already has been accomplished and the way that was chosen
thus circumventing
This worked great but I'm a bit confused about how to access the names
(keys?) of a list in a loop, and why this is failing for me:
I want to cross the entries in mylist (like entry0001) with the
columns of a dataframe ginput:
$entry0001
[1] AB0032 CF32134 DF34334
$entry0002
[1] AB0033
I'm using an SVM as I've seen a paper that reported extremely good
results. I'm not having such luck. I'm also interested in ideas for
other approaches to the problem that can also be applied to general
problems (no assuming that we're looking for spirals).
Here is my code:
library(mlbench)
Degrees of freedom for mixed models is a delicate issue - except in certain
orthogonal designs.
However, I'll just point out that for lmer models, there is a simulate()
function which can simulate data from a fitted model. simulate() is very fast -
just like lmer(). So one way to get around
On 27 Jan 2006, [EMAIL PROTECTED] wrote:
But mylist$entrylabel is not working inside the loop.
'$' doesn't evaluate its argument. You want mylist[[entrylabel]].
I haven't been able to found my way with R lists, maybe because I'm
comparing them with perl's hashes.
R lists do have names, but
In this post:
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/30590.html
Thomas Lumley provided a function to traverse a formula recursively.
We can modify it as shown to transform ln(m)^n to ln^n(m) producing
proc2. We then bundle everything up into proc3 which uses substitute
to
First of all,
I apologize for posting this question in this mailing list.
BTW, I walked around the problem.
1. English can be used if you add 'LANGUAGE=en' to the end of target field
of property window of the shortcut to R. I found this solution in the
Windows FAQ.
2. If I setup SciView R, then
I am very new to factor analysis as well as R. I am trying to run a factor
analysis on the residual returns on common stock (residual to some model) and
trying to determine if there are any strong factors remaining. After running
factanal, I can obtain the factor loadings but how do I get
Deepayan, thank you for your help!!
After much trial and error (and re-reading the help
files), I was able to
come up with what I wanted by making sure the first
line of my panel
function looked like this:
panel = function(y,x,...)
The complete set of code I ended up using:
I used the following command to train a randomForest model
train.rf - randomForest(grp ~ ., data=tr, ntree=100, mtry=50)
My question is how to save the trained model so that it can be loaded later
for testing new samples?
Thanks,
Luk
Use save().
Andy
From: luk
I used the following command to train a randomForest model
train.rf - randomForest(grp ~ ., data=tr, ntree=100, mtry=50)
My question is how to save the trained model so that it can
be loaded later for testing new samples?
Thanks,
Luk
You don't really expect SVM to give you good performance with no parameter
tuning at all, do you?
Try:
m2 - best.svm(class~., data=spiral, gamma=2^(-3:3), cost=2^(0:5))
plot(m2, spiral)
Andy
From: Joshua Gilbert
I'm using an SVM as I've seen a paper that reported extremely good
results.
On Fri, 27 Jan 2006, Krish Krishnan wrote:
I am very new to factor analysis as well as R. I am trying to run a
factor analysis on the residual returns on common stock (residual to
some model) and trying to determine if there are any strong factors
remaining. After running factanal, I can
I have two datasets, big and small.
s_date-c(2005-12-02, 2005-12-01,
2004-11-02,2002-10-05,2000-12-15)
s_id-c(a,a,b,c,d)
b_date- c(2005-12-31, 2005-12-31,
2004-12-31,2002-10-05,2001-10-31,1999-12-31)
b_id-c(a,b,c,d,e,c)
Thanks to all for the helpful suggestions, I was able to get good start from
there.
Cheers,
Dylan
On Thursday 26 January 2006 12:03 pm, Gabor Grothendieck wrote:
Would this do?
boxplot(Sepal.Length ~ Species, iris, horizontal = TRUE)
library(Hmisc)
summary(Sepal.Length ~ Species, iris,
---
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I'll address two issues. The first is today's error message and the other is
change management for contributed packages on CRAN.
TODAY'S ERROR MESSAGE
I switched from the 0.995-1 versions of lme4 and Matrix to those referenced in
the subject line this afternoon. Prior to using these packages
White, Charles E WRAIR-Wash DC wrote:
I'll address two issues. The first is today's error message and the other is
change management for contributed packages on CRAN.
TODAY'S ERROR MESSAGE
I switched from the 0.995-1 versions of lme4 and Matrix to those referenced
in the subject line
When armed with barely enough information to be dangerous you would be
amazed at what I am willing to believe.
Thank you for pointing out how foolish I was.
Josh.
On 1/27/06, Liaw, Andy [EMAIL PROTECTED] wrote:
You don't really expect SVM to give you good performance with no parameter
Dear all,
does anyone know a command to shut 'lme' (nlme) up? :)
I have a loop
for(i in 1:M){
lme(..)
}
and for each i i get the warning message
Fewer observations than random effects in all level 1
groups in: ...
I know I'm using fewer observations..., I just don't
want to see the message
Søren Højsgaard [EMAIL PROTECTED] writes:
Along similar lines, I've noticed that the anova() function for lmer
models now only reports the mean squares to go into the numerator
but nothing for the denominator of an F-statistic; probably in
recognition of the degree of freedom problem. It
Isaac,
On Mac OS 10. 4.4 with Xcode 2.2 installed, after setting:
sudo gcc_select 3.3, I get:
Robs-Laptop:~ rob$ gcc_select
Current default compiler:
gcc version 3.3 20030304 (Apple Computer, Inc. build 1819)
Robs-Laptop:~ rob$ cd Downloads/
Robs-Laptop:~/Downloads rob$ R CMD INSTALL
See the argument `warn' in ?options.
Andy
From: Marco Geraci
Dear all,
does anyone know a command to shut 'lme' (nlme) up? :)
I have a loop
for(i in 1:M){
lme(..)
}
and for each i i get the warning message
Fewer observations than random effects in all level 1
groups in: ...
I
Hello,
I am interested in doing a partial canonical correlation (identical to
the SAS function, Proc Cancorr with the Partial statement).
By this I mean, I have 3 sets of data, a vegetation matrix (columns of
abundances of species in rows of plots), an environment matrix
(columns of
On 1/27/06, Søren Højsgaard [EMAIL PROTECTED] wrote:
Degrees of freedom for mixed models is a delicate issue - except in certain
orthogonal designs.
However, I'll just point out that for lmer models, there is a simulate()
function which can simulate data from a fitted model. simulate() is
On 27 Jan 2006 23:08:28 +0100, Peter Dalgaard [EMAIL PROTECTED] wrote:
Søren Højsgaard [EMAIL PROTECTED] writes:
Along similar lines, I've noticed that the anova() function for lmer
models now only reports the mean squares to go into the numerator
but nothing for the denominator of an
Douglas Bates [EMAIL PROTECTED] writes:
Of course, Monte Carlo p-values have their problems, but the world
is not perfect
Another approach is to use mcmcsamp to derive a sample from the
posterior distribution of the parameters using Markov Chain Monte
Carlo sampling. If you are
Hello,
I was curious if there was a complex valued matrix exponential function
available for R? I have some Laplace transforms of occupation times
for a hidden Markov model. The matrix exponential function in the msm
package does not seem to handle complex values. For example
R-users,
I am new user of Linux (have been using Win XP Pro) and wanted to install R.
Since I am just beginning to learn Linux I was wondering, where in the
directory structure do users of Linux usually install R? Most of the
instructions I have read simply say to untar the tarball where you
On Thu, 2006-01-26 at 21:55 -0500, Duncan Murdoch wrote:
On 1/26/2006 9:45 PM, Manuel Morales wrote:
Dear list members,
I'm looking for a way to write nested functions similar to the
function Nest or NestList in Mathematica.
E.g.,
f-function(x) x+2*x
f(f(f(2)))
might
Dear Patrick:
Thanks for doing this.
Just picking nits: To end the second paragraph in Sec. 2, you say,
If your goal is to find what is in your data, then almost surely R will
be the best tool for you sooner or later. I think this is an
overstatement. R is for people
On 1/27/2006 9:07 PM, Manuel Morales wrote:
On Thu, 2006-01-26 at 21:55 -0500, Duncan Murdoch wrote:
On 1/26/2006 9:45 PM, Manuel Morales wrote:
Dear list members,
I'm looking for a way to write nested functions similar to the
function Nest or NestList in Mathematica.
E.g.,
f-function(x)
Try this:
merg - merge(big, small, by = id)
f - function(x) {
x$date_.y - max(x$date_.y)
x[x$date_.y = x$date_.x, date_.y] - NA
x
}
do.call(rbind, by(merg, merg$date_.x, f))
On 1/27/06, r user [EMAIL PROTECTED] wrote:
I have two datasets, big and small.
Thank you for providing such a marvelous example. I wish I could
reward your dilligence with a simple, complete answer. Unfortunately,
the best I can offer at the moment is a guess and a reference. First, I
believe you are correct in that the weights argument describes the
On 1/27/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Hi all,
I am using xyplot (lattice) to generate a figure like Figure 4.18 in
MASS4, but I have the following two questions (1) how to change the font
of x(y)lab?
Something like
xyplot(...
xlab = list(foo, font = 3),
On Fri, 27 Jan 2006, Daniel Nordlund wrote:
R-users,
I am new user of Linux (have been using Win XP Pro) and wanted to
install R. Since I am just beginning to learn Linux I was wondering,
where in the directory structure do users of Linux usually install R?
Most of the instructions I
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