Hi
I am a little bit confused. You create two sample (from a gamma
distribution) and you do a wilcoxon test with this two samples.
Then you use the same monotone transformation (log) for both
samples and redo the wilcoxon test.
But since the transformations keeps the order of your samples
the
[EMAIL PROTECTED] wrote:
Hi R Users
This is a code I wrote and just want to confirm if the first 1000 values are
raw
gamma (z) and the next 1000 values are transformed gamma (k) or not. As I get
2000 rows once I import into excel, the p - values beyond 1000 dont look that
good, they
Hi everybody,
I have a large fasta file(15M) which contains a lot of DNA sequence in fasta
format.And i want to get probabilities matrix for 2nd order markov china
from this background.Here is a web tool,
http://tandem.bu.edu/markov.html.But i can not upload a large file. I wonder
if there is
As the posting guide says, please ask the package maintainer -- I believe
he does not read R-help regularly.
Your layout is hard to read (please do use spaces and indentation in
posted code), but probably there is a scoping problem with par.plot used
inside a function.
On Wed, 27 Jul 2005,
McClatchie, Sam (PIRSA-SARDI) wrote:
Background:
OS: Linux Mandrake 10.1
release: R 2.0.0
editor: GNU Emacs 21.3.2
front-end: ESS 5.2.3
-
Colleagues
I want to increase the size of the axis markings and labels on some trellis
graphs, and I am having some
Dear R-users,
Does anyone of you have binary files for the packages rpart.permutation,
snow and rsprng. I would like to use them in my classification tree. I
know they are still at the 0.x development stage, though.
Where can I get information on how to compile tar.gz files? I'm using
windows XP
Dear expeRts,
Currently, my colors are as follows:
mycol -
c(blue1,blue2,blue3,blue4,black,yellow4,yellow3,yellow2,y
ellow1)
heatmap(snp, Rowv=NA, Colv=NA, col=mycol)
However, I would like to have the following colors:
bright blue - dark blue: for intensity range from 0 to 2 in steps
On the omegahat site, you can read:
There is currently no binary available for Windows. I hope to release
one wihtin a few weeks (i.e. near the end of September, 2004).
You can ask to developers an unofficial binary version for you. Maybe
they have, or maybe they're esperiencing problems in
They rely on multiprocessing infrastructure not normally available on
Windows. If you have this (and I don't know if it can be compiled on
Windows but dome at least of the options cannot) you should be able to
compile the source packages against the versions you have.
On Wed, 27 Jul 2005, Jan
Dear R users:
I have two set of data, as follow:
x-c(0,0,0.28,0.55,1.2,2,1.95,1.85,
1.6,0.86,0.78,0.6,0.21,0.18)
y-c(0,0,0,0.53,1.34,1.79,2.07,1.88,
1.52,0.92,0.71,0.55,0.32,0.19)
i-1:length(x)
I want to sum each (x[i]-y[i])^2/x[i] together,
like:
Sum -sum((x[i]-y[i])^2/x[i])
Sum
[1]
Adaikalavan Ramasamy [EMAIL PROTECTED] writes:
I think it is doing what is supposed to do but I never used read.spss,
so take this with a pinch of salt.
In R when you use as.integer on a factor, the one with the lowest level
gets a value of 1 and so on. The lowest level of the factor can
look at ?sum() and use the `na.rm' argument, i.e.,
sum((x - y)^2 / x, na.rm = TRUE)
I hope it helps.
Best,
Dimitris
p.s., R is vectorized, you don't have to use `x[i]' in your example.
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of
What about
x-c(0,0,0.28,0.55,1.2,2,1.95,1.85,
1.6,0.86,0.78,0.6,0.21,0.18)
y-c(0,0,0,0.53,1.34,1.79,2.07,1.88,
1.52,0.92,0.71,0.55,0.32,0.19)
sum(((x-y)^2/x)[x!=0])
Regards,
Christoph Buser
--
Christoph Buser [EMAIL
The simplest way would be to ignore them in the sum
sum( ( x - y )/x, na.rm=T )
and notice that I have utilised the vectorised operation. But if you
want to, you can explicitly remove them with
good - which( x != 0 )
sum( ( x[good] - y[good] )/ x[good] )
Regards,
Simon Blomberg [EMAIL PROTECTED] writes:
Actually, atoms are originally a Lisp concept. Objects are either atoms or
not. Atoms are data types that cannot be taken apart, such as numbers or
symbols. Lists and vectors (of length 1) are examples of non-atomic data
types. Did you pass a
Narcyz Ghinea [EMAIL PROTECTED] writes:
MY THEORY:
I think it has something to do with the fact that the function
argument is a vector in CASE 2. Hope this doesn't mean I have to
re-write the function in a way that it doesn't require vector
inputs.
You do. The innards of mle has
Dear all,
we are trying to model some data from rare plants so we always have less than 50
1x1 km presences, and the total area is about 550.000 square km. So we have a
real problem, when we perform a GAM, if we consider only the same amount of
absences than presences.
We have thought to use a
Dear R-helpers,
Is it possible to create a type of 'movie' in R based on the output of
several figures (e.g., jpegs) via the plot() function. I obtained dynamic
results with the plotting function and would like to save these as a movie
(e.g., avi or other formats)?
Regards,
Jan
hi
what is the default family object in glm? I cannot find it from the doc. It
would be great if you could tell me where I should look into.
thanks,
lu
-
Stay connected, organized, and protected. Take the tour
[[alternative HTML
From ?glm() you get:
...
Usage
glm(formula, family = gaussian, data, weights, subset,
na.action, start = NULL, etastart, mustart,
offset, control = glm.control(...), model = TRUE,
method = glm.fit, x = FALSE, y = TRUE, contrasts = NULL, ...)
...
So the default family is the
Dear Sean
Thank you, however the heatmap() function from the stats package does not
have this option.
Browsing around I see that you mean heatmap.2() from package gplots, which
we have not
installed yet.
Is there also another possibility besides heatmap.2() since I would also
need this option
Hello,
I don't know if it's only me, but I can't get make.names() transform '_' in
the way it is expected when I add the allow_ option. A simple example trying
to replicate the example provided in the help page gives:
-8---
make.names(c(a and b, a_and_b), unique=TRUE,
Deart R-help,
I could not transfer ordered data into a matrix, does anybody knows if there is
something wrong in the code below please?
Thanks in advance, Tom
Y - ordered( unlist( Q[,1:2] ) )
z - matrix(0, nrow(Q), 2)
z - Y
is.ordered(z)
[1] T
is.matrix(z)
[1] F
i.e. Is it possibile
On Wed, 27 Jul 2005, luk wrote:
what is the default family object in glm? I cannot find it from the doc.
It would be great if you could tell me where I should look into.
Try the help page:
glm(formula, family = gaussian, data, weights, subset,
It
On Mon, 25 Jul 2005 14:12:41 +0200,
Gorjanc Gregor (GG) wrote:
Hello R-users!
I have tried to use Sweave within LyX* and found two ways to accomplish
this. I have attached LyX source file for both ways as well as generated
PDFs.
I have copied Gregor's files at
On Wed, 27 Jul 2005 15:28:54 +0200,
Gorjanc Gregor (GG) wrote:
[...]
Nope. That's what I also thought, but I was really amaized when discovered
that
there is no need for this. You only need to set up noweb stuff as mentioned
at
I wonder if anyone can help me find a text or reference to the
probabilistic under pinnings of simulation techniques. I come from an
econometrics background where the approach to Monte Carlo is a bit cook
booky, most of the focus is on the implementation rather than the
theoretical justification.
[...]
Nope. That's what I also thought, but I was really amaized when discovered
that
there is no need for this. You only need to set up noweb stuff as
mentioned at
http://thread.gmane.org/gmane.editors.lyx.general/18847
and use article(noweb) for document style. Then everything
On Wed, 27 Jul 2005, Xavier [utf-8] Fernández i Marín wrote:
Ok, thanks.
BTW, before writing the email I've been trying to search in the bugsweb
interface athttp://r-bugs.biostat.ku.dk/cgi-bin/R
searching for make.names, but with no success. Is this the way to procede?
See the posting guide
Sorry, my mistake, I did not realize that image() has breaks and that
heatmap() inherits from image().
However, I have the following problem, maybe I am doing something wrong.
I have defined:
mycol -
c(blue1,blue2,blue3,blue4,black,yellow4,yellow3,yellow2,yel
low1)
_Monte Carlo Statistical Methods_
by Christian P. Robert, George Casella
Springer, 2nd ed 2005
This book (I have edition 1) is a dandy. It will be rough sledding unless
you have a reasonable background in math stats but I think it is just what
you are looking for.
Charles Annis, P.E.
[EMAIL
hi all
I wish to thanks every body on the R mailing list for answering very fast,
directly in my mail box ;).
I've finish my work with R and i can say that it is very difficult at the
beginning, and when you succeed you are stopped by a stack overflow when you
call your nice recursive
[Jan Verbesselt]
Is it possible to create a type of 'movie' in R based on the output
of several figures (e.g., jpegs) via the plot() function. I obtained
dynamic results with the plotting function and would like to save
these as a movie (e.g., avi or other formats)?
You may also peek at an
Good afternoon,
I REALLY try to answer to my question as an autonomous student searching in
the huge pile of papers on my desk and on the Internet but I can't find out
the solution.
Would you mind giving me some help? Please.
#
I'm trying to use glm
Hello all,
I'm trying to setup a simple construct that will email me all errors,
warnings, and output of a sample R script. My initial thought was to use
sink() and tryCatch around the script such that at the end of the script
any output would be mailed to me, i.e.:
sinkFile - tempfile()
On Wed, 27 Jul 2005, Peter Dalgaard wrote:
Adaikalavan Ramasamy [EMAIL PROTECTED] writes:
I think it is doing what is supposed to do but I never used read.spss,
so take this with a pinch of salt.
In R when you use as.integer on a factor, the one with the lowest level
gets a value of 1 and
On Wed, 27 Jul 2005, McGehee, Robert wrote:
However, the sink() does not seem to be capturing the error messages as
I would have hoped. That is, if the R-script is {print(abc);
stop(def)}, the print output is captured to the file, the stop error
message is not, and instead sent to the
Jan Verbesselt [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Dear R-helpers,
Is it possible to create a type of 'movie' in R based on the output of
several figures (e.g., jpegs) via the plot() function. I obtained dynamic
results with the plotting function and would like to save
Most of time, I prefer to use randomForest of R though it really
depends on your problem. And don't forget Leo's Random Forest if you
don't use it for commercial purpose.
weiwei
On 7/26/05, Marc R. Feldesman [EMAIL PROTECTED] wrote:
--- Adaikalavan Ramasamy [EMAIL PROTECTED] wrote:
add me.
I really appreciate r-help mail list VERY MUCH! I learn a lot. You
guys are doing a great and very important job.
thanks.
On 7/27/05, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
hi all
I wish to thanks every body on the R mailing list for answering very fast,
directly in my mail
Ahh, I misunderstood the help page. I took that since the default values
for type were c(output, message), that both the output _and_ the
messages were simultaneously being redirected (else why not just make
the default output). I see that this is not the case (as noted in the
details).
After
*Dear R-user,
*
I try to run Winbugs from R using bugs function in R2WinBUGS.My model works
well in Winbugs except that I can't get DIC. Since I don't need DIC, when I
try to run Winbugs from R , I set DIC=FALSE. My model is as following:
model {
for (i in 1:N) {
for(j in 1 : T ) {
x[i, j] ~
On 27-Jul-05 Jan Verbesselt wrote:
Dear R-helpers,
Is it possible to create a type of 'movie' in R based on the
output of several figures (e.g., jpegs) via the plot() function.
I obtained dynamic results with the plotting function and would
like to save these as a movie (e.g., avi or other
Dear R-list,
I'm surprised that no one on this list has mentioned anything about the
ffmpeg tools! Hands down these are the tools to use for generating
animations and movies.
Processing the images is much quicker than imagemagick and with a little
tweaking, you can add additional filter effects
I have two questions:
1. If I want to do a binomial logit, how to handle the
categorical response variable? Data for the response
variables are not numerical, but text.
2. What if I want to do a multinomial logit, still
with categorical response variable? The variable has 5
non-numerical
using ./RJava --example --gui-none to invoke t.test core dumps. The line of R
works if I go directly thru R and not RJava.
Version info and code are below. Any help would be appreciated.
--Laura O'Brien
Applications Architect
Version info
Java: jdk1.5.0_03
R:
I am unable to source a .R file using RJava. I tried a couple of different
tests:
1) using java and the evaluation method core dumps
2) using ./RJava --example --gui-none to invoke source core dumps.
3) The line of R works if I go directly thru R and not RJava.
Version info
Dear R-users,
I am very new to R, so maybe my question is very easy to answer.
I have the following table:
TAB1-data.frame(Name,Number), Name and Number are all character
strings,
it looks like this:
Name Number
ab 2
ab 2
NA 15
NA 15
NA 15
cd 3
ef 1
NA
d-data.frame(y=sample(letters[1:2],100,T),x=rnorm(100))
head(d,10)
y x
1 b 0.55915620
2 b 0.87575380
3 b -0.13093156
4 b 0.75925729
5 b 0.40233427
6 b 1.34685918
7 a 1.10487752
8 a -2.27456596
9 a 1.65919787
10 b 0.05095611
glm(y~x,data=d,family=binomial)
Call:
Hello Hank,
thank you for your interest in simulating ODEs with R. Unfortunately, I am
out of office until end of August and I have no acces to a Mac with R.
Maybe, Woodrow Setzer has an idea, and as an alternative I would suggest
to post a minimal reproducible example to the R-help mailing
On Wed, 27 Jul 2005, Jonathan Baron wrote:
I'd like to generate 00Index.html for a bunch of libraries for my
R search page.
I think you mean for a package, not a library, that is the file
/path/to/library/some_pky/html/00index.html
?
I have now almost all the html help files for
Please, this is R-help, not the list for SJava questions.
SJava is part of the Omegahat project (not the R project) and that used to
have its own mailing lists. I believe they are currently non-operational,
but please check.
The R posting guide suggests that you first ask the maintainer and
To delete duplicate rows, use unique(TAB1): see its help page.
It looks to me as if the names are missing values NA and *not* start with
NA. If so, you want to use
TAB1[!is.na(TAB1$Name), ]
Otherwise, perhaps TAB1[substr(TAB1$Name, 1, 2) == NA, ].
On Wed, 27 Jul 2005, Michael Graber wrote:
Please excuse what is obviously a trivial matter...
I have a large 3-d array. I wish to set the third dimension (z) to NA
if there are any NA values in the first two dimnesions (xy). So, given
array foo:
foo - array(data = NA, dim = c(5,5,3))
foo[,,1] - matrix(rnorm(25), 5, 5)
foo[,,2] -
Newbies (and others!) may find useful the R Reference Card made available by
Tom Short and Rpad at http://www.rpad.org/Rpad/Rpad-refcard.pdf or through
the Contributed link on CRAN (where some other reference cards are also
linked). It categorizes and organizes a bunch of R's basic, most used
Dear Ed,
See ?glm for fitting binomial logit models, and ?multinom (in the nnet
package) for multinomial logit models. Neither function will handle a
character (text) variable as the response, but you could easily convert
the variable to a factor.
John
John Fox
Dear Dr Carbon,
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Dr Carbon
Sent: Wednesday, July 27, 2005 12:19 PM
To: [EMAIL PROTECTED]
Subject: [R] setting elements to NA across an array
Please excuse what is obviously a trivial matter...
I
Sorry for being obtuse.
How can I build a logical statement that will set foo[2,2,] - NA and
foo[3,5,] - NA? Something like, if any row and column are NA, then
set NA to that row and column to NA for the entire array
On 7/27/05, John Fox [EMAIL PROTECTED] wrote:
Dear Dr Carbon,
What platform are you working on? On windows you can also create an
animated gif file using ImageMagik (http://www.imagemagick.org/) from the
cmd or you can use the more user friendly UnFREEz downloadable at
http://www.whitsoftdev.com/unfreez/ ot Microsoft GIF animator(search for it
on
Dear Dr Carbon,
Actually, it appears that I'm the one who was being obtuse. To make sure
that I'm now interpreting what you want correctly, you'd like to set all
entries in a layer to NA if any entry in a layer is NA. If that's correct,
then how about the following?
foo[array(apply(foo, c(1,2),
hi,
rgev function gives me random deviates and I have a data
set which I am fitting to an EVD,IS there a way I can plot
both observed and ideal evd on the same plot
thankyou
Rangesh
__
R-help@stat.math.ethz.ch mailing list
Hi,
I am wirting a R script to process some data routinely and have a problem
when try to get the content of object in ls()?
Here is the script:
ls()
[1] a b
[3] files.num fll92_1a_gpr
[5] fll92_1a_gpr_norm fll92_1a.gpr.norm.scale
[7] fname fullnames
[9] gal galfile
[11] i readGalfile2
[13]
Hi,
Here was a short tutorial about howto do that:
http://r.vsthost.com/wordpress/2005/07/01/creating-video-files-on-gnulinux-using-r/
PS: You can submit such short articles or tutorials, if you have time. I
was thinking to add more stuff, but these days I don't have much time.
--Vehbi Sinan
It's easiest to reshape foo first:
d - dim(foo)
dim(foo) - c(d[1]*d[2],d[3])
m - rowSums(is.na(foo))
and then assign
foo[m,] - NA
and reshape
dim(foo) - d
(Reshaping just makes the indexing easier).
Reid Huntsinger
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL
See ?get.
Andy
From: Meng Cheng
Hi,
I am wirting a R script to process some data routinely and
have a problem
when try to get the content of object in ls()?
Here is the script:
ls()
[1] a b
[3] files.num fll92_1a_gpr
[5] fll92_1a_gpr_norm fll92_1a.gpr.norm.scale
[7] fname
Hi
You are right but here I am taking into account the p values I get from the
tests on the raw and the transformed samples. And then I calculate the power of
the tests based on the # of rejections of the p values.
DO you think its a good way to determine the power of a test?
thanks
-dev
Dear All,
After followed the help of nnet, I could get the networks trained and,
excitedly, get the prediction for other samples. It is a two classes data set,
I used N and P to label the two. My question is, how do I get the predicted
numerical value for each sample? Not just give me the
Hi. Day three and Im still struggling with this. Any advice to overcome the
final hurdle will be enormously appreciated. I now have all the right Java
applications etc. in their right places and have managed to get rid of most
errors but still get this:
Making package SJava
Building
Martin Henry H. Stevens [EMAIL PROTECTED] writes:
Hi -
I am getting different results when I run the numerical integrator
function lsoda (odesolve package) on a Mac and a PC. I am trying to
simulating a system of 10 ODE's with two exogenous pulsed inputs to the
system, and have had
Hi Duncan
Thank you for responding... I apologise for being so ignorant. I presume
that is a UNIX command - so have just downloaded cygwin (read about that
today) and ran your suggested line. I get:
Chmod: cannot acess 'configure.win'. No such file or directory
I am assuming that isn't good. Is
Hi,
I'd like to return the rows of sampled values of a vector. Can't figure
out how to do it.
For example: I start with [3, 1, 7, 4, 10] that have position
[1,2,3,4,5]. I sample [10,1,4] and I want to return [5,2,4].
I'm sure there's a simple way to do that but haven't been able to figure
On 7/27/05 5:44 PM, Mike Jones [EMAIL PROTECTED] wrote:
Hi,
I'd like to return the rows of sampled values of a vector. Can't figure
out how to do it.
For example: I start with [3, 1, 7, 4, 10] that have position
[1,2,3,4,5]. I sample [10,1,4] and I want to return [5,2,4].
I'm sure
Mike Jones wrote:
Hi,
I'd like to return the rows of sampled values of a vector. Can't figure
out how to do it.
For example: I start with [3, 1, 7, 4, 10] that have position
[1,2,3,4,5]. I sample [10,1,4] and I want to return [5,2,4].
I'm sure there's a simple way to do that but
Hi
I ran your code. I think it should give me the number of p values below 0.05
significance level (thats what i could understand from your code), but after
running your code there is neither any error that shows up nor any value that
the console displays.
thanks in advance
-dev.
Quoting Uwe
Aah, OK. Thanks for the correction. I learn something new every day. That's
why I like this list! Serves me right for relying on my Lisp knowledge.
Cheers,
Simon.
At 07:26 PM 27/07/2005, Peter Dalgaard wrote:
Simon Blomberg [EMAIL PROTECTED] writes:
Actually, atoms are originally a Lisp
I am using read.csv to read a CSV file (produced by saving an Excel file
as a CSV file). The columns containing dates are being read as factors.
Because of this, I can not compute follow-up time, i.e.
Followup-postDate-preDate. I would appreciate any suggestion that would
help me read the dates as
If this is a question about plotting 2 series on a plot then in general terms
you can plot 2 series as per this example in the list
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/5463.html
If it is about the use of rgev you should tell us the name of the package.
If you read the posting
I am using read.csv to read a CSV file (produced by saving an Excel file
as a CSV file). The columns containing dates are being read as factors.
Because of this, I can not compute follow-up time, i.e.
Followup-postDate-preDate. I would appreciate any suggestion that would
help me read the dates as
On Wed, 2005-07-27 at 23:07 -0400, John Sorkin wrote:
I am using read.csv to read a CSV file (produced by saving an Excel file
as a CSV file). The columns containing dates are being read as factors.
Because of this, I can not compute follow-up time, i.e.
Followup-postDate-preDate. I would
Which rgev are you using? There are at least two in at least three
different packages: evd, evir, and fExtremes. I found this by using
'help.search(rgev)', which will however only identify related material
I already have installed locally. 'RSiteSearch(rgev)' produced 22
hits,
Thanks to the R creators for such a great statistical system. Thanks to
the R help list, I have (finally) gotten far enough in R to have a
question I hope to be worth posting.
I'm using the recode function from John Fox's car package and have
encountered some unexpected behavior.
Consider the
'RSiteSearch(wishart)' just produced 45 hits for me, the first of
which was for function 'Simnu.mix' in package 'SharedHT2'. If this does
not help you, PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html. It can improve the chances
that you will get a
I just got zero hits from 'RSiteSearch(SETAR)'. When I Googled for
SETAR, I got 219,000 hits, but nothing on the first page looked like
it might be your SETAR. Then I Googled for SETAR Model and got
something that suggested threshold autoregressive ... Then and
If you still are interested in help with your problem, PLEASE do read
the posting guide! http://www.R-project.org/posting-guide.html. It can
increase the likelihood of you getting a useful reply.
See other comments in line.
spencer graves
Werner Bier wrote:
Have you considered aggregate in library(zoo)? If you are not
familiar with zoo, I suggest you install it, then run
'vignette(zoo)' and 'edit(vignette(zoo))' [NOTE: If you use Emacs,
'edit(vignette(...))' won't work. There is something that will, but I
don't remember what it is.
I can't help you much, because you did not include a simple example
that is sufficiently complete for me to run it myself and play with the
results.
I ran the example glm.D93 - glm(counts ~ outcome + treatment,
family=poisson()) in the glm help file. Then I looked at
Ask predict.nnet for a type other than class, as described on its help
page.
Please do read the help pages for yourself (as the posting guide asks).
On Wed, 27 Jul 2005, Baoqiang Cao wrote:
Dear All,
After followed the help of nnet, I could get the networks trained and,
excitedly, get the
87 matches
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