On Thu, 5 Oct 2006, Christos Hatzis wrote:
Jue,
On a second look, it appears that wilcox.test does report the
offset-adjusted statistic U, as also mentioned in the help page.
wilcox.test returns W=6 (instead of 12 as your example showed, unless
wilcox_test is a different function).
This is taken from the help for the hist function:
Typical plots with vertical bars are not histograms. Consider barplot
or plot(*, type = h) for such bar plots.
For example:
x - rchisq(100, df = 4)
op-hist(x, freq = FALSE, ylim = c(0, 0.2))
plot(op$mids,op$counts,type=h)
On 06/10/06,
Ferdinand Alimadhi [EMAIL PROTECTED] writes:
lm(dep ~ as.factor(WKDY)
but if you want WKDYs as character you can make the appropriate changes
in your dataset
days-c(mon,tue,wed,thu,fri,sat,sun)
for(i in 1:7)
+ D$WKDY[D$WKDY==i]-days[[i]]
suppossing that D is your dataframe
I am trying to optimize a likelihood function using constrOptim. I
know from prior research that, e.g. x1x2. Is there a way to include
that constraint into the optimization routine, i.e. the ci
constraint? The examples I found only use absolute numeric values for
the constraint and not
Dear all,
someone knows if there is an already implemented function
for drawing a back to back barplot (something similar to
histbackback of the Hmisc package but for categorical data)?
Thanks in advance,
domenico vistocco
Chiacchiera con i tuoi amici in tempo reale!
See the Bioconductor project, http://www.bioconductor.org
Uwe Ligges
Baoqiang Cao wrote:
Dear All,
I'm thinking of visualizing the original binary data from
affymetrix. Would you recommend any package? Not necessarily limited
to R packages. Thanks!
Best,
-Cao
Hi all
I have to generate some test data for import in an sql database. The
database is meant for web-based data entry in a study taking place in a
german speaking region, so factor levels of the variables include umlauts.
The variables in the dataframe t.muster are generated e.g. like this:
Hello Alexander,
try package CRAN package 'vars'.
Best,
Bernhard
Hi,
does anybody know how to predict a multivariate AR within R?
If I just estimate a multi AR-object and plug it into predict I get an
error from the aperm - just works for univariates.
thx
alex
Dear R-help,
Has anyone implemented sparklines in the strips of a lattice plot? What I have
in mind is, say, highlighting that part of a time series that one is examining
in more detail in a set of lattice plots.
Regads,.
Mark Difford.
PS: (Andreas Loffler has implemented a simple but
Hi,
(I addressed the JRI issues I had in my previous email below
http://article.gmane.org/gmane.comp.lang.r.general/70322
by working with the precompiled version of JRI
that is part of the rJava package.)
So I can now run the JRI examples as expected but am having difficulty
getting the Rengine
And of course for NEdit, all one needs to do is select:
Preferences | Default Settings | Customize menus | Macro Menu
Then select the New option at the top of the menu list,
Give it a name (I call this r_comment),
Enter the following code:
replace_in_selection(^,#,regex)
click on Apply and
Richard A. O'Keefe wrote:
Commenting code out and providing documentation comments are easily
done with a good editor, although R documentation comments really belong
in files where help() can find them.
R documentation comments belong in .Rd files at the moment, but how
joyous would it
Note that if you only have block comments in a language, its much harder
to do this:
http://www.xkcd.com/c156.html
Barry
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
Domenico Vistocco wrote:
Dear all,
someone knows if there is an already implemented function
for drawing a back to back barplot (something similar to
histbackback of the Hmisc package but for categorical data)?
Hi Domenico,
Have a look at pyramid.plot in the plotrix package if you want
Baoqiang Cao wrote:
Hi there,
I really couldn't find out how to plot histogram with point/line instead of
rectangle for each bin? Any help please? Thanks!
This is a guess, but...
y-hist(rnorm(100,3),plot=FALSE)$counts
x-barplot(y,width=0.01,space=20)
points(x,y)
Jim
Dear R cracks,
I need to process data in R which consist of strings like
AAABAVVABNN
ABVVNNAA
What I would like to know is whether there are commands that deliver
-the length of a string
-one specified character of a string (e.g. the 3rd letter)
-that allow to concatenate
Dear R-Experts,
I was wondering how to fit a cumulative gaussian to a set of empirical
data using R. On the R website as well as in the mail archives, I found
a lot of help on how to fit a normal density function to empirical data,
but unfortunately no advice on how to obtain reasonable
Florian Menzel wrote:
Dear R cracks,
We prefer to be called 'R souls'.
I need to process data in R which consist of strings like
AAABAVVABNN
ABVVNNAA
What I would like to know is whether there are commands that deliver
-the length of a string
-one specified
And of course in emacs you can select the region to comment then hit
Ctrl-x r t and type #: all the lines in that region will have a # at the
beginnig
To uncomment Ctrl-x r d
Stefano
On Fri, Oct 06, 2006 at 07:05:52PM -0400, Jim Lemon wrote:
JimAnd of course for NEdit, all one needs to do is
I was off for few days and as nobody seems to answer I will try
again.
It is probably not trivial with matrix (possibly with combination of
outer and some subsequent selection) but if you can transfer it to
data frame (or list) you could use mapply
tj - 1:5
vj - matrix(1:25, 5,5)
mapply(*,
Commenting code out and providing documentation comments are easily
done with a good editor, although R documentation comments really belong
in files where help() can find them.
R documentation comments belong in .Rd files at the moment, but how
joyous would it be if they could be
Stefano == Stefano Calza [EMAIL PROTECTED]
on Fri, 6 Oct 2006 12:55:38 +0200 writes:
Stefano And of course in emacs you can select the region to comment then
hit
Stefano Ctrl-x r t and type #: all the lines in that region will have a #
at the
Stefano beginnig
Stefano To
Reparameterize replacing x1 with x2+delta constraining delta
to be positive or else replace x1 with x2 + delta^2 and
no constraint.
On 10/6/06, Felix Eggers [EMAIL PROTECTED] wrote:
I am trying to optimize a likelihood function using constrOptim. I
know from prior research that, e.g. x1x2. Is
Cool, didn't know that!
Thanks,
Stefano
On Fri, Oct 06, 2006 at 01:46:03PM +0200, Martin Maechler wrote:
MartinStefano To uncomment Ctrl-x r d
Martin
Martinwell, if we really talk emacs --- we shouldn't here --
Martinyou definitely should learn to use M-;
Martin
MartinIt does use ## in ESS
Dear R-helpers,
I don't see a difference between the following two plots of effect
objects, which I understand should be different. What am I missing?
require(doBy)
require(effects)
data(budworm)
m1 - glm(ndead/20 ~ sex + log(dose), data=budworm, weight=ntotal,
family=binomial)
m1.eff -
The two models that you compare differ in their fixed effects. As far as lme
had been concerned, the anova gave a warning because one should not compare two
models differing in their fixed effects if they had been estimated with REML
(Pinheiro Bates, 2000).
I guess the issue is still the same
Dear Michael,
Look more closely at the two plots: With rescale.axis=TRUE (the default),
the vertical axis is on the scale of the linear predictor (i.e., the logit
scale), but the tick marks are labelled in the scale of the response (i.e.,
the probability scale); this preserves the linear
Hi,
What about computational aspect for the job you intend to realise ? What will
be the use of R ? R can do a lot in statistic but you can't ask help for a
topic so far far of R. Be more precise.
Justin BEM
Elève Ingénieur Statisticien Economiste
BP 294 Yaoundé.
Tél (00237)9597295.
-
Thank you, Gabor, for all your suggestions.
Best,
John
On 10/5/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
On 10/4/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Also see package caTools.
On 10/4/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
See:
Laurent Rhelp laurentRhelp at free.fr writes:
Dear R-List,
I would like to convert my rnw files written with Sweave from LaTeX
to html. I discovered on the list the following link :
http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/SweaveConvert
Is this document only for linux
And of course vim, emacs, nedit, tinn-r...
Should R be editor specific? Or should it be editor neutral?
In my view blocks comments are a desirable, editor-neutral approach.
Note that most of the more recent languages have some form of block
comment capability.
I'd like to announce three new packages on CRAN: pmg, gWidgets, and
gWidgetsRGtk2.
--John Verzani
1 PMG
*=*=*=
The pmg package for R provides a relatively simple graphical user
interface for R in a manner similar to the more mature RCmdr package.
Basically this means a menu-driven interface
Gamer, Matthias gamer at uni-mainz.de writes:
Specifically, I have data from a psychometric function relating the
frequency a subject's binary response (stimulus present / absent) to the
strength of a physical stimulus. Such data is often modeled using a
cumulative gaussian function.
AgusSusanto gusanto at gmail.com writes:
I obtained error messages when I run these commands in UNIX, but I
obtained correct result when I run these command in WINDOWS. Can
somebody point out the problem and give the solution. Thanks.
dt-read.table(file=Fall.dat)
dim(dt)
[1] 1941
Does any one know why wilcox.exact sometimes doesn't agree with wilcox_test on
the estimate of the difference of medians in two levels ?
Thank you
Jue Wang, Biostatistician
Contracted Position for Preclinical Research Biostatistics
PrO Unlimited
(908) 231-3022
Example 1: (wilcox_test gives
If the data asymptote at 0 and 1, then you can use glm with the
binomial family
with either the logistic or probit links. If the data are from an
n-alternative
forced choice procedure or if the data do not asymptote at 0 and 1 for
some
reason or other, then you need to try other procedures.
Hi, I need installation instructions. library(pmg) seems not to be enough.
Thanks.
library(pmg)
Loading pmg()
Loading required package: gWidgets
Loading required package: gWidgetsRGtk2
Loading required package: RGtk2
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to
-Original Message-
From: Chuck Cleland [mailto:[EMAIL PROTECTED]
Sent: Friday, October 06, 2006 5:32 AM
To: Afshartous, David
Subject: Re: [R] treatment effect at specific time point within
mixedeffects model
Afshartous, David wrote:
The data structure is a repeated measures
When I do lmer models I only get Estimate, Standard Error and t value in
the output for the fixed effects.
Is there a way I get degrees of freedom and p values as well?
I'm a very new to R, so sorry if this a stupid question.
Thank you
- Mike
Mike Ford
Centre for Speech and Language
On Fri, 2006-10-06 at 17:05 +0100, Mike Ford wrote:
When I do lmer models I only get Estimate, Standard Error and t value in
the output for the fixed effects.
Is there a way I get degrees of freedom and p values as well?
I'm a very new to R, so sorry if this a stupid question.
Thank
On 10/6/06, Mark Difford [EMAIL PROTECTED] wrote:
Dear R-help,
Has anyone implemented sparklines in the strips of a lattice plot? What I
have in
mind is, say, highlighting that part of a time series that one is examining
in more
detail in a set of lattice plots.
It's not particularly
Hi,
In the Linux (FC3) version of R, ctrl-\ quits R. This wouldn't be so
bad, but on my keyboard, it's right next to ctrl-p and I tend to hit it
by accident.
Is there any way to turn that off?
Best,
Martin
__
R-help@stat.math.ethz.ch mailing list
A new version of mclust is now available as a contributed package on CRAN.
The associated manual is located at
http://www.stat.washington.edu/www/research/reports/2006/tr504.pdf
The main feature in terms of new functionality is the option to include
a Bayesian prior in the mixture model for
Martin C. Martin wrote:
In the Linux (FC3) version of R, ctrl-\ quits R. This wouldn't be
so bad, but on my keyboard, it's right next to ctrl-p and I tend to
hit it by accident.
And what is the use of ctrl-p?
Alberto Monteiro
__
previous command. Very helpful when you want to repeat something you
recently did, perhaps after modifying it a bit.
- Martin
Alberto Monteiro wrote:
Martin C. Martin wrote:
In the Linux (FC3) version of R, ctrl-\ quits R. This wouldn't be
so bad, but on my keyboard, it's right next to
Alberto Monteiro [EMAIL PROTECTED] writes:
Martin C. Martin wrote:
In the Linux (FC3) version of R, ctrl-\ quits R. This wouldn't be
so bad, but on my keyboard, it's right next to ctrl-p and I tend to
hit it by accident.
And what is the use of ctrl-p?
Same as up-arrow, but some
On Fri, 2006-10-06 at 14:46 -0400, Martin C. Martin wrote:
Hi,
In the Linux (FC3) version of R, ctrl-\ quits R. This wouldn't be so
bad, but on my keyboard, it's right next to ctrl-p and I tend to hit it
by accident.
Is there any way to turn that off?
Open your favorite terminal
Hi Folks,
Given a series of n independent Bernoulli trials with
outcomes Yi (i=1...n) and Prob[Yi = 1] = Pi, I want
P = Prob[sum(Yi) = r] (r = 0,1,...,n)
I can certainly find a way to do it:
Let p be the vector c(P1,P2,...,Pn).
The cases r=0 and r=n are trivial (and also are exceptions
for
Thanks! I put it in my .bashrc, now it will never bother me again.
Marc Schwartz (via MN) wrote:
BTW, you might want to consider updating your FC distro, as FC3 is now
EOL
Unfortunately, this is my work machine and they're still using FC3.
Although I've heard various grumblings about it,
Henrik Parn henrik.parn at bio.ntnu.no writes:
Dear all,
Given the discussions and issues of d.f., p-values and mcmcsamp-CIs in
mixed models, I wonder if anyone could recommend one or two papers (or
other citable sources for that sake) that summarizes the arguments
for/against
Hi all,
Is there a way to fill a rectangle or polygon with a color and/or
transparency gradient? This would be extremely useful for me in terms
of adding some additional information to some plots I'm making,
especially if I could define the gradient on my own by putting
functions into rgb
In nonlinear mixed effects models, SAS doesn't allow for free manipulation of
the covariance matrix (you can only specify a type, and our type doesn't
exist). Can R accomplish this? For example:
Parameters:
B1= Beta 1i
B2= Beta 2i
G1= Gamma i
y = B1 -(B1 - B2) exp { - G1 time} + e
the
On Fri, 2006-10-06 at 16:15 -0400, Eric Harley wrote:
Hi all,
Is there a way to fill a rectangle or polygon with a color and/or
transparency gradient? This would be extremely useful for me in terms
of adding some additional information to some plots I'm making,
especially if I could define
hi,
I tried to keep my workspace as small as possible when i tried to
save.image(). Sometimes, I am not sure whether obj in workspace will
be needed in future or not. However, I want to delete some big ones
when I use save.image(). BTW, I know I could use save, but I would
like to know : how to
First of all, I apologize for asking a question that has appeared
recurrently in this mailing list. However, I have googled for it, have
looked at the mailing list archives, and also looked at Pinheiro Bates book
(although not very thoroughly, I must confess), to no avail.
Here is the question:
Hi,
Can somebody tell me, which is the fastest way to make comparisons between all
rows in a matrix (here A) and put the results to the new symmetric matrix? I
have here used cosine distance as an example, but the comparison function can
be any other, euclidean dist etc.
On 10/6/06, Ted Harding [EMAIL PROTECTED] wrote:
Hi Folks,
Given a series of n independent Bernoulli trials with
outcomes Yi (i=1...n) and Prob[Yi = 1] = Pi, I want
P = Prob[sum(Yi) = r] (r = 0,1,...,n)
I can certainly find a way to do it:
Let p be the vector c(P1,P2,...,Pn).
The
?dist
Bert Gunter
Nonclinical Statistics
7-7374
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Atte Tenkanen
Sent: Friday, October 06, 2006 1:54 PM
To: r-help@stat.math.ethz.ch
Subject: [R] Row comparisons to a new matrix?
Hi,
Can somebody tell me,
Many thanks for your comments, Deepayan; and I liked your
recursive solution! Fun indeed.
Just a comment (below) on one of your comments (the rest
snipped).
On 06-Oct-06 Deepayan Sarkar wrote:
On 10/6/06, Ted Harding [EMAIL PROTECTED] wrote:
Hi Folks,
Given a series of n independent
I have to focus my question a little. I'd like to get rid of those for-loops
and use, if possible, some faster method for creating the symmetric result
matrix.
Atte
?dist
Bert Gunter
Nonclinical Statistics
7-7374
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL
There is a generalized inner product here:
http://tolstoy.newcastle.edu.au/R/help/05/04/3709.html
On 10/6/06, Atte Tenkanen [EMAIL PROTECTED] wrote:
Hi,
Can somebody tell me, which is the fastest way to make comparisons between
all rows in a matrix (here A) and put the results to the new
On 10/6/06, Ted Harding [EMAIL PROTECTED] wrote:
Many thanks for your comments, Deepayan; and I liked your
recursive solution! Fun indeed.
Just a comment (below) on one of your comments (the rest
snipped).
On 06-Oct-06 Deepayan Sarkar wrote:
On 10/6/06, Ted Harding [EMAIL PROTECTED]
I haven't been using R very long, so it's possible that I'm just
missing something, but I haven't found anything like this in the help
files. I've tried to poke around in graphics, grid, and ggplot,
without any luck so far. I really like some of the functionality in
ggplot, and it does some
Weiwei Shi helprhelp at gmail.com writes:
hi,
I tried to keep my workspace as small as possible when i tried to
save.image(). Sometimes, I am not sure whether obj in workspace will
be needed in future or not. However, I want to delete some big ones
when I use save.image(). BTW, I know I
Hi all,
Indeed, block comment is more clean and elegant than line by line.
If the R interpreter will recognizes it (I'm not sure if already recognizes),
we
will spend no more than few hours to make the syntax of the main editors
compatible, isn't it?
Regards,
--
Jose Claudio Faria
Hello all,
Just uploaded to CRAN updates for RSQLite, RMySQL, and DBI.
The primary svn repository for these packages is now hosted by the
Gentleman Lab in Seattle and our group is working with David James to
help with maintenance. Details on the updates are below.
RMySQL_0.5-9.tar.gz
*
Hi all
I have a question regarding differences in the way gregpexr works in R 2.3.0
and R 2.4.0.
In R 2.3.0, this is what happens:
gregexpr( [a-z] [a-z] , a b c d e f , perl=T)
[[1]]
[1] 1 3 5 7 9
attr(,match.length)
[1] 5 5 5 5 5
... while in R 2.4.0, this is what happens:
gregexpr(
You can get that by using zero width lookahead assertions. They must
match but are not consuming so the next match will not be forced
to start past them. See ?regex and
http://www.regular-expressions.info/lookaround.html
for more.
gregexpr( [a-z](?= [a-z] ), a b c d e f , perl = TRUE)
On
On 10/6/2006 10:00 PM, Stefan Th. Gries wrote:
Hi all
I have a question regarding differences in the way gregpexr works in R 2.3.0
and R 2.4.0.
In R 2.3.0, this is what happens:
gregexpr( [a-z] [a-z] , a b c d e f , perl=T)
[[1]]
[1] 1 3 5 7 9
attr(,match.length)
[1] 5 5 5 5 5
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