Yang Jie [EMAIL PROTECTED] writes:
Dear Sir:
I am a chinese researcher who interested in miRNA, and I want
to use
R to analysis my data.I have download R-2.4.0-win32.exe and install it
smoothly on my
computer,but when I want to use this software, error occurs,it
shows R
for
library(nlme)
fm1 - gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
+correlation = corARMA(form = ~ 1 | Mare, p = 2))
summary(fm1)
Generalized least squares fit by REML
Model: follicles ~ sin(2 * pi * Time) + cos(2 * pi * Time)
Data: Ovary
AIC BIClogLik
Do any of you know any simple programming editors for R scripts which offer
basic colour-coding and bracket-matching facilities?
Dregging through scripts to find a missing comma or parentheses is something
I'd rather do less of...
Jon Minton
[[alternative HTML version
Hello all.
I have encountered at problem when using the Hmisc package to generate
latex-tabels.
I can't seem to control the number of digits in the latex-file. I have
used the Design and Hmisc packages for a while without this problem, but
after upgrading to R-2.4.0 the problem has
Tinn-R
From: [EMAIL PROTECTED] on behalf of Jon Minton
Sent: Mon 06/11/2006 9:11 AM
To: R-help@stat.math.ethz.ch
Subject: [R] Colour-coded Editor for R Code
Do any of you know any simple programming editors for R scripts which offer
basic colour-coding and
Hello John,
you can derive these estimators by considering a step-wise approach:
1) Derive the estimators by evaluating a model with demeaned variables,
i.e.
consider (\tilde{X}'\tilde{x})^-1 \tilde{x}'\tilde{y}, where \tilde{...}
refers to the demeaned variables.
2) Obtain the estimate of the
Hi,
I make a weibull survival regression using suvreg function. Bu when I try to
get the P values from anova, it give me NAs:
I'm using R 2.4.0 and survival 2.29
Look:
m - survreg(Surv(tempo,censor)~grupo*peso)
anova(m)
Df Deviance Resid. Df-2*LL P(|Chi|)
NULL NA
Jon,
are you using Windows? If so, try WinEdt with library(RWinEdt).
It has all the features you want and need.
For Linux/Unix use EMACS.
There is a section on CRAN about editors.
Cheers,
Dan Bebber
Department of Plant Sciences
University of Oxford
Prof Brian Ripley wrote:
On Fri, 3 Nov 2006, Zheng Yuan wrote:
Dear all experts,
Does anyone know if there is a R function which can perform Ridge
regression for logistic models?
multinom and nnet in the package of that name.
You can also use the lrm function in the Design package,
Dear All,
I'm analysing a negative binomial dataset from a population-based
study. Many covariates were determined on household level, so all
members of a household have the same value for those covariates.
In STATA, there seems to be an option for 'clustered analysis' for
neg-bin regression.
Hello,
You have a rather large list of editor that support R syntax
highlighting listed in: http://www.sciviews.org/_rgui/projects/Editors.html.
Best,
Philippe Grosjean
Dan Bebber wrote:
Jon,
are you using Windows? If so, try WinEdt with library(RWinEdt).
It has all the features you want
Hello all.
Sorry for reposting this message, but I accedently sent it in
HTML-format the first time.
I have encountered at problem when using the Hmisc package to generate
latex-tabels.
I can't seem to control the number of digits in the latex-file. I have
used the Design and Hmisc packages
Emacs and ESS for both Unix and Windows.
emacs for Windows from
ftp://ftp.gnu.org/pub/gnu/emacs/windows/emacs-21.3-fullbin-i386.tar.gz
emacs for Unix from
ftp://ftp.gnu.org/pub/gnu/emacs/emacs-21.4a.tar.gz
ESS from
http://ess.r-project.org/
Click on Source for the package itself.
Other items
I'm not certain, but I think you should be able to use the robcov
function in the Design package in conjunction with glm.nb, perhaps
with a bit of tweaking. Another alternative might be to use the quasi
family in lmer.
On 06/11/06, Lutz Ph. Breitling [EMAIL PROTECTED] wrote:
Dear All,
I'm
Also check out the package glmpath which can incorporate both ridge (L2)
and lasso (L1) type penalties.
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric
On 11/5/06, Shravan Vasishth [EMAIL PROTECTED] wrote:
I'm trying to install lme4 (after having installed R 2.4.0 from source, and
having installed the latest Matrix package). lme4 fails with the following
message:
pedigree.o definition of _lme4_xSym in section (__DATA,__common)
pedigree.o
Gregor Gorjanc gregor.gorjanc at bfro.uni-lj.si writes:
Hello!
I am working on breed composition of animals in my project. Say I have
an animal 1 with parents 2 (father) and 3 (mother). If father is of
breed A and mother of breed B, then their descendant is of breed AB or
50 % of A and 50 %
Henrik Frederik Thomsen HFTH at DCE.AU.DK writes:
I have encountered at problem when using the Hmisc package to generate
latex-tabels.
I can't seem to control the number of digits in the latex-file. I have
used the Design and Hmisc packages for a while without this problem, but
after
Hi all!
i have done a fitting of experimental data using optim function and
setting up my mixed distribution logliklehood (it is a linear
combination of a normal and a weibull distribution). How can i test
the goodness of fit? I want to be able to say that my distribution fit
the data at 90%,
Jerome == Jerome Goudet [EMAIL PROTECTED]
on Sun, 05 Nov 2006 16:08:33 +0100 writes:
Jerome Dear all,
Jerome I am trying to use the Matrix package to do some calculations on
rather
Jerome large and sparse matrices. An example of such a matrix is given
below.
Jerome
But in Win you could try Tinn-R which is quite good!!
Mihai Nica
170 East Griffith St. G5
Jackson, MS 39201
601-914-0361
- Original Message
From: Richard M. Heiberger [EMAIL PROTECTED]
To: Jon Minton [EMAIL PROTECTED]; R-help@stat.math.ethz.ch
Sent: Monday, November 6, 2006 7:45:54
Dear friends,
I have three variables ,x,y and z, and i want to get two plots:
1.three-dimensionel plot: z is the vertical axis, x and y is on the same
horizontal plane;
2.contour plot:x is the horizontal axis, and y is vertical axis, and z is
used to plot the contour line.
I can't finish it
Hy,
In my case I just invoked as root (on a linux box) the command R CMD
javareconf and checked if my system and root vm did match the version of
the user vm. After this the
command .jinit(parameters=c(-Xmx512m,-Xmx128m)) could be executed
without errors. I got this information from
I noticed that RMySQL is now at version 0.5-10, but the libMySQL.dll and
RMySQL.dll files that are required for Windows are missing from the
distribution. These files were present in previous versions of RMySQL,
and the installation instructions still state they are needed.
I have an older
The R-package glmmADMB (not on CRAN) can do negative binomial response with
one level of Gaussian random effects. It also allows zero inflation.
Download site:
http://otter-rsch.com/admbre/examples/glmmadmb/glmmADMB.html
Regards,
hans
Dear All,
I'm analysing a negative binomial dataset from
Hello All.
I would like to repeat a multi-screen, multivariate time series plot across
multiple units.
Consider the following data:
r-help@stat.math.ethz.ch UNIT TRIAL Y1Y2 Y3 Y4
Y5 Y6
1109 1 NANA NA 13718 3655 15240
2109 2 15000
And Mac:
emacs for the Mac native environment
http://aquamacs.org/
At 8:45 AM -0500 11/6/06, Richard M. Heiberger wrote:
Emacs and ESS for both Unix and Windows.
emacs for Windows from
ftp://ftp.gnu.org/pub/gnu/emacs/windows/emacs-21.3-fullbin-i386.tar.gz
emacs for Unix from
Hi R users
Having both a faster CPU and more memory will boost computing power. I was
wondering if only adding more memory (1GB - 2GB) will significantly reduce
R computation time?
Taka,
_
Get FREE company branded e-mail
Nelson,
I do not know of any formal hypothesis testing mechanism, but I recommend a
QQ plot regardless. Venables and Ripley (2002, 4th edition MASS) have a
detailed example for the mixed normal case (see page 440 in particular) that
could be adapted for your normal + weibull case. Or you could
Thanks,
i wonder if I can use a kolmogorov smirnov test or a similar test
(but what test?). I use QQ-plot but the people i'm working to asked me
numbers... :) and not sum of square error.
The told about chi-square test and Kolmogorov Smirnov Test...
I produce QQ- plots, but they doesn't like
Hi,
I've written some MCMC algorithms that repeatedly evaluate exp(Xb)
where X is a design matrix and b a parameter vector. For certain
combinations of X and b I get numerical overflow, and would like a
way of rescaling the columns of X so that the range of exp(Xb) is
maximised without
Taka Matzmoto wrote:
Hi R users
Having both a faster CPU and more memory will boost computing power. I was
wondering if only adding more memory (1GB - 2GB) will significantly reduce
R computation time?
If your computations consume just a few Mb, it won't make it faster, if
it
Hi, I've got a very simple problem but cannot find the solution. I'm using two
data frames (say X and Y) and I want to get a subset of one according to the
different levels of a variable code of the other data frame. I tried
something like
Z-subset(X, code==levels(Y$code))(1)
Since the databases that I handle with are very large, I need answers to some
questions:
1) Can I work with R data frames like databases in SAS, that is, storing data
frames in files instead of in memory?
2) Can I use SQL codes to work with R data frames? Note that I ask for the
direct use,
Dear Readers,
The Annals of Applied Statistics, newest journal from the Institute of
Mathematical Statistics, began accepting papers on November 1, 2006.
Computational statistics is an area of particular interest. Please visit
the journal website at
http://www.imstat.org/aoas
to
Hi Florent,
A simple example with the expected output would help. If I understood
correctly what you want, perhaps the following would work:
X[ X$code %in% levels(Y$code), ]
assuming Y$code is a factor. If not, you can used instead unique(Y$code) in
the above.
-Christos
-Original
Dear All,
I am hoping to implement a barchart using trellis graphics where all
elements have a line width of 2.
Using trellis.par.set(), I am able to make most elements lwd=2, but not
all. In particular, the top of the box (above the upper most strip) and
the left y-axis remain one point.
Matthias Voigt [EMAIL PROTECTED] writes:
Dear list,
I am new to this all and therefore have following Newbie question:
How can I receive and read R-help mailings in a newsreader like thunderbird?
Use gmane.comp.lang.r.general on gmane.org
HTH,
Jens
On 11/6/06, Daniel E. Bunker [EMAIL PROTECTED] wrote:
Dear All,
I am hoping to implement a barchart using trellis graphics where all
elements have a line width of 2.
Using trellis.par.set(), I am able to make most elements lwd=2, but not
all. In particular, the top of the box (above the
Hi,
I''ve a question about comparing 2 dataframes: RRC_db1 and RRC_db2 of
different length.
For example:
RRC_db1:
CUSTOMER_ID CUSTOMER_RR
1 1000786BR 5+
2 1002047BR4
3 10127BR 5+
4 1004166834BR2
5
Hi
Deepayan Sarkar wrote:
On 11/6/06, Daniel E. Bunker [EMAIL PROTECTED] wrote:
Dear All,
I am hoping to implement a barchart using trellis graphics where all
elements have a line width of 2.
Using trellis.par.set(), I am able to make most elements lwd=2, but not
all. In particular, the
Hi,
Is there any package or code to compare and display correlated ROC curves in
R?
Thanks,
Reza
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the
On 11/6/06, Paul Murrell [EMAIL PROTECTED] wrote:
Hi
Deepayan Sarkar wrote:
On 11/6/06, Daniel E. Bunker [EMAIL PROTECTED] wrote:
Dear All,
I am hoping to implement a barchart using trellis graphics where all
elements have a line width of 2.
Using trellis.par.set(), I am able to
Lutz--
In addition to the previous suggestions, you might also have a look at the
following paper:
Kelvin K. W. Yau, Kui Wang and Andy H. Lee. Zero-Inflated Negative Binomial
Mixed Regression Modeling of Over-Dispersed Count Data with Extra Zeros.
Biometrical Journal 45 (2003) 4, 437–452
In trying to get NULL members into a list, I found out about alist().
x-alist()
x$one-1
x$two-NULL
but x$two doesn't exist.
It seems, though, that an alist is just a list.
How can one put NULL members into a list?
__
R-help@stat.math.ethz.ch
one of the newsletters ( about a year ago ) has something about an ROC
package but I don't remember which one it is.
If you do a search for ROC on the search thing in www.project.org, I'm
sure you will find something
about it.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL
On 11/6/2006 3:36 PM, Glen Herrmannsfeldt wrote:
In trying to get NULL members into a list, I found out about alist().
x-alist()
x$one-1
x$two-NULL
but x$two doesn't exist.
It seems, though, that an alist is just a list.
How can one put NULL members into a list?
x - c(x,
Nelson,
I did a quick Google search on the phrase goodness of fit mixture models
and found this thread. There seems to be some good info in there:
http://www.biostat.wustl.edu/archives/html/s-news/2000-07/msg00166.html
Hope that helps,
Bill
---
Bill Pikounis, PhD
Glen Herrmannsfeldt [EMAIL PROTECTED] writes:
In trying to get NULL members into a list, I found out about alist().
x-alist()
(that is the same as x - list(). I don't think alist() is relevant.)
x$one-1
x$two-NULL
but x$two doesn't exist.
It seems, though, that an alist is just a
Seyed Reza Jafarzadeh wrote:
Hi,
Is there any package or code to compare and display correlated ROC curves in
R?
Thanks,
Reza
There are ways to compare ROC areas. This will not have very good
power. The Hmisc package's rcorrp.cens function provides a test that
deals with pairs of
You need to start by first allocating the list. The problem is that you
cannot reference a list member that does not exist yet (as in x$two):
x - vector(list, 10)
x
List x has 10 NULL elements by default. You can then assign values to these
as needed.
-Christos
-Original Message-
Hello all,
I have 300 clusters of fixed size 2 and I need to do resampling with
replacement to run some regression models. I've searched through the
archive and the only thing I found was that I could use 'boot()'
function. but it's not clear to
me how I can do this. Has anyone done it? I would
Dear R Users,
Do you have a sample code for developing a nomogram with competing-risks?
Any help is appreciated.
Kind regards,
ND Nguyen
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting
Peter Dalgaard [EMAIL PROTECTED] wrote:
(regarding adding NULL elements to a list)
x[two] - list(NULL)
This seems to work.
In the actual case, it is assigning from a variable that may
or may not be null,
for example:
two-NULL
x[two]-list(two)
It seems to work, and not do what it looks
[EMAIL PROTECTED] writes:
Peter Dalgaard [EMAIL PROTECTED] wrote:
(regarding adding NULL elements to a list)
x[two] - list(NULL)
This seems to work.
In the actual case, it is assigning from a variable that may
or may not be null,
for example:
two-NULL
x[two]-list(two)
Great! Thanks to both Paul and Deepayan for these efficient approaches!
-Dan
Deepayan Sarkar wrote:
On 11/6/06, Paul Murrell [EMAIL PROTECTED] wrote:
Hi
Deepayan Sarkar wrote:
On 11/6/06, Daniel E. Bunker [EMAIL PROTECTED] wrote:
Dear All,
I am hoping to implement a barchart
hi,
I have a conversion table for colnames like this:
Probe_ID HUMAN_LLID
1 AF106325_PROBE1 7052
2 NM_019386_PROBE1 7052
3 NM_012907_PROBE1339
4 AW917796_PROBE1 84196
5L27651_PROBE1 10864
The Probe_ID contains a list of colnames for another
Hi, Weiwei.
You probably want to look at a combination of merge() to combine your data with
your conversion table followed by aggregate(). Read up on the help for those
two functions and that should do it, if I understand what you want to do.
However, keep in mind that averaging the
Hello,
I need to identify all elements which have a sequence of 3 consecutive upper
case letters, anywhere in the string.
I tested my grep expression on this site: http://regexlib.com/RETester.aspx
But when I try it in R, it does not filter anything.
str -c(AGH, this WOUld be good, Not Good at
Try
str[grep('[[:upper:]]{3}',str)]
On 06/11/06, Lapointe, Pierre [EMAIL PROTECTED] wrote:
Hello,
I need to identify all elements which have a sequence of 3 consecutive upper
case letters, anywhere in the string.
I tested my grep expression on this site: http://regexlib.com/RETester.aspx
hi,
I played around with these two functions but did not get what i want.
So I wrote a function by using a loop to do it and it is done in a
reasonable time:
system.time(t3 - iconix.convert(processed, 9, 7486,
probes2llid.genego[,c(2,5)]))
[1] 12.356 4.494 16.836 0.000 0.000
dim(t3)
[1]
Quoting David Barron [EMAIL PROTECTED]:
Try
str[grep('[[:upper:]]{3}',str)]
or more efficiently :
grep('[[:upper:]]{3}', str, value = TRUE)
On 06/11/06, Lapointe, Pierre [EMAIL PROTECTED] wrote:
Hello,
I need to identify all elements which have a sequence of 3 consecutive upper
case
Hi,
I am working with one array of data point. The value of the data points
fluctuate and I tried to locate the peak point in this array. It is like
you are going through the valleys and mountains, and I want to identify all
the mountain peak location.
I assume this is a very common problem to
Lapointe, Pierre [EMAIL PROTECTED] writes:
Hello,
I need to identify all elements which have a sequence of 3 consecutive upper
case letters, anywhere in the string.
I tested my grep expression on this site: http://regexlib.com/RETester.aspx
But when I try it in R, it does not filter
Try some of the threads at RSiteSearch(nomogram).
Cheers,
Francisco
Nguyen Dinh Nguyen wrote:
Dear R Users,
Do you have a sample code for developing a nomogram with competing-risks?
Any help is appreciated.
Kind regards,
ND Nguyen
__
Peter Dalgaard [EMAIL PROTECTED] wrote:
x[two] - list(NULL)
This seems to work.
In the actual case, it is assigning from a variable that may
or may not be null,
for example:
two-NULL
x[two]-list(two)
It seems to work, and not do what it looks like, add a list of
length
Dan Rie wrote:
I had a very similar problem installing RMySQL with R 2.4.0 on
Windows XP.
I beleive that the cause may have been that the RMySQL build used a
slightly older version of the MySQL compiled library functions than
was installed on my machine (I updated both MySQL, DBI, and
Hi,
Can anyone suggest a good way to draw level curves of a function with
R? I am thinking of something analogous to curve. If there is a
package I should be looking at for this kind of mathematical stuff,
I'd like to know too...
cheers
d
__
Thanks.
I do have readline.so. I just did not paste that part. Look.
[EMAIL PROTECTED] myuserid]$ slocate readline.so
/home/scratch/myuserid/usr/local/lib/python2.4/lib-dynload/readline.so
/home/scratch/myuserid/usr/local/lib/python2.4/libreadline.so.4
hi all : i have the data below and then below that, i call the hist
function three times using the Scott method for the widths of the bins.
the bin width is different for the three histograms but I would like it
to always be 0.05 regfardless of the data
set being histogrammed.
I'm sure there
There are several ways to do this, probably the easiest is to use
truehist from MASS. i.e
require(MASS)
par(mfrow=c(3,1)) #3 rows of histograms, one column
truehist(x,h=.05)
truehist(y,h=.05)
truehist(z,h=.05)
I hope this helps,
Francisco
--
Dr. Francisco J. Zagmutt
College of Veterinary
I don’t know if this question properly belongs on this list, but I’ll ask it
here because I’ve been using R to run linear regression models, and it is only
in using R (after switching from using SPSS) that I have discovered the process
of fitting a linear model. However, after reading Crowley
Hi,
I am trying to run a multilevel model with time nested in people and
people nested in dyads (3 levels of nesting) by initially running a
series of models to test whether the slope/intercept should be fixed or
random. The problem that I am experiencing appears to arise between the
random
How to make it correct?
[1]
Error in parse(file, n = -1, NULL, ?) : syntax error at
1: {\
#source('c:/Documents and Settings/xxx/My Documents/Archives/R/test.r')
#source(c:\\Documents and Settings\\xxx\\My
Documents\\Archives\\R\\test.r)
[2]
Error in file(file, r, encoding
Hi,
I am looking for an R package that would calculate multivarite (mostly
2d and 3d, tensor) cubic interpolating splines, so that I could
evaluate these splines (and their derivatives) at many points (unkown
at the time of calculating the spline polynomials) repeatedly.
To make things concrete,
I have drawn a map in which the X and Y axes are latitude and
longitude. Now I need to draw one circle on the map - the center is a
point with specific latitude and longitude, but the challenge is that
the radius is in miles. Is there a way to do this? I'd very much
appreciate your response.
*I am a very new user of R. I've spent several hours trying to import
data, I am successful in importing data from Excel. After having the data on
R console, I am not understanding how to make a file for imported data,so I
feel okay asking the list for help. *
*I have used save workspace option
specify is the first row containts variables names by h=T (header=T), and the
column separator symbol. In Excel save your file as Text File with tab
separator and then sep=\t
Justin BEM
Elève Ingénieur Statisticien Economiste
BP 294 Yaoundé.
Tél (00237)9597295.
- Message d'origine
Try this :
it-seq(0,2*pi, l=100)
xt-r*cos(it)
yt-r*sin(it)
points(xt,yt,type=l,col=blue)
a circle of radium r is define by
xt=r*cos(t)
yt=r*sin(t)
Justin BEM
Elève Ingénieur Statisticien Economiste
BP 294 Yaoundé.
Tél (00237)9597295.
- Message d'origine
De :
this have been discuss
try RSiteSearch(peak)
Justin BEM
Elève Ingénieur Statisticien Economiste
BP 294 Yaoundé.
Tél (00237)9597295.
- Message d'origine
De : Waverley [EMAIL PROTECTED]
À : r-help R-help@stat.math.ethz.ch
Envoyé le : Lundi, 6 Novembre 2006, 23h57mn 33s
Objet : [R]
Dear all R user,
Please forgive me if my problem is too simple.
Actually my problem is basically Statistical rather
directly R related. Suppose I have return series ret
with mean zero. And I want to fit a Garch(1,1)
on this.
my is r[t] = h[i]*z[t]
h[t] = w +
On Tue, 7 Nov 2006, justin bem wrote:
Try this :
it-seq(0,2*pi, l=100)
xt-r*cos(it)
yt-r*sin(it)
points(xt,yt,type=l,col=blue)
a circle of radium r is define by
xt=r*cos(t)
yt=r*sin(t)
Isn't this suggestion on the plane, when the question was about finding
the
Dear Rusers,
I want to know which function in R can perform the following tasks:
1.surface-data grid(x,y,z) #which could be done in splus, the name was from
splus's options of graph
2. contourplot(x,y,z) #which could be done in splus
By the way, where can i find some useful materials to
Hi
Maybe this example can help you to find your solution:
dat1 - data.frame(CUSTOMER_ID = c(1000786BR, 1002047BR, 10127BR,
1004166834BR, 1004310897BR, 1006180BR,
10064798BR, 1007311BR, 1007621BR,
1008195BR, 10126BR, 95323994BR),
84 matches
Mail list logo