Duncan == Duncan Murdoch [EMAIL PROTECTED]
on Thu, 07 Jul 2005 15:44:38 -0400 writes:
Duncan On 7/7/2005 3:38 PM, Weiwei Shi wrote:
Hi there:
I have a question on random foresst:
recently i helped a friend with her random forest and i came with this
problem:
Hi,
It's about 2 weeks that I think about a graph to translate my datas. But I
don't have an really idea.
I 'm going to expose you my problem:
I have a questionnaire with 15 questions and you have more possibilties to
answer to these.
For example:
The trainer is competent: Yes No
Hi R experts,
I am trying to do a prognostic model validation study, using cancer
survival data. There are 2 data sets - 1500 cases used to develop a
nomogram, and another of 800 cases used as an independent validation
cohort. I have validated the nomogram in the original data (easy with
On Fri, 8 Jul 2005, yyan liu wrote:
Hi:
I have two time series y(t) and x(t). I want to
regress Y on X. Because Y is a time series and may
have autocorrelation such as AR(p), so it is not
efficient to use OLS directly. The model I am trying
to fit is like
Hi,
It's about 2 weeks that I think about a graph to translate my
datas. But I don't have an really idea. I 'm going to expose
you my problem:
I have a questionnaire with 15 questions and you have more
possibilties to answer to these. For example:
The trainer is competent:
Hello,
The estimate of glm dispersion can be based on the deviance or on the
Pearson statistic.
I have compared output from R glm() to another statastical package and
it appears that R uses the Pearson statistic.
I was wondering if it is possible to make use R the deviance instead by
modifying
I used R on OS X 10.3x quite some time with no serious problems.
Sometimes R stopped when I tried to execute a bigger program. After
updating to OS X to version 10.4 R worked but I still had the problem
with bigger programs. Therefore I re-installed R on top of the
existing R version. The
Hello all,
I am planning to redeploy my workstation under KUBUNTU.
Does any body has any r experience installing/using r on this platform?
Best regards.
--
Constant Depièreux
Managing Director
Applied QUality Technologies Europe sprl
Rue des Déportés 123, B-4800 Verviers
(Tel) +32 87 292175
Constant Depièreux [EMAIL PROTECTED] writes:
Hello all,
I am planning to redeploy my workstation under KUBUNTU.
Does any body has any r experience installing/using r on this platform?
I don't think it's any different than any other Debian-derived
platform.
--
O__ Peter
Constant Depièreux wrote:
Hello all,
I am planning to redeploy my workstation under KUBUNTU.
Does any body has any r experience installing/using r on this platform?
Best regards.
Hi,
I've just moved from SuSE 9.1 to Ubuntu 5.04. The instalation is clean
and easy, although you have to
Hello,
plot(cox.zph(my.ph),var=1,xlab=Year)
gives the error:
Error in plot.default(range(xx), yr, type = n, xlab
= Time, ylab = ylab[i], : formal argument xlab
matched by multiple actual arguments
How can I customize the xlab and ylab for plots of
cox.zph?
Thanks,
Dan Bebber
Department of
Hi,
Does anyone know how to check the significance (p-values/t-values) of the
estimated parameters via the estVARXar function (in the dse package)?
Thanks in advance,
Sam.
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch
Please try to use a meaningful subject line. See below for comments.
On Mon, 2005-07-11 at 11:30 +0200, Smit, R. (Robin) wrote:
Hello,
The estimate of glm dispersion can be based on the deviance or on the
Pearson statistic.
I have compared output from R glm() to another statastical
I am not sure if there is an easy way around this. An ugly hack is to
make a copy the function survival:::plot.cox.zph and make your
modified function. But there are others in the list who might know
neater solutions.
Regards, Adai
On Mon, 2005-07-11 at 11:10 +0100, Dan Bebber wrote:
Hello,
No problem at all.
If you allow universe packages, many binary R packages are available (from
the GNU/Linux Debian sid).
On Monday 11 July 2005 11:54, Constant Depièreux wrote:
Hello all,
I am planning to redeploy my workstation under KUBUNTU.
Does any body has any r experience
Hi
When using Sweave, most of my functions get called with complex
arguments.
They get typeset in with additions that I don't want; 1+1i appears
as 1 + (0 + 1i)
and I would rather have plain old 1+1i.
Example follows:
\documentclass[a4paper]{article}
\title{A Test File}
\author{Robin
When we analyse ordered categorical data, with categories II,
should we expect an equivalent analysis if the ordering is changed to
II ? Not with a cloglog link (see example below). However, I
suspect the cloglog analysis on the reordered categories is equivalent
to a loglog analysis on
Adaikalavan Ramasamy wrote:
I am not sure if there is an easy way around this. An ugly hack is to
make a copy the function survival:::plot.cox.zph and make your
modified function. But there are others in the list who might know
neater solutions.
This hack is uglier (and might not work
Robin Hankin wrote:
Hi
When using Sweave, most of my functions get called with complex
arguments.
They get typeset in with additions that I don't want; 1+1i appears
as 1 + (0 + 1i)
and I would rather have plain old 1+1i.
Example follows:
\documentclass[a4paper]{article}
Folks,
I am finding problems with using dse:
library(dse1)
Loading required package: tframe
Error: c(package '%s' required by '%s' could not be found, setRNG, dse1)
library(dse2)
Loading required package: setRNG
Error: package 'setRNG' could not be loaded
In addition: Warning message:
there
AdaiR == Adaikalavan Ramasamy [EMAIL PROTECTED]
on Mon, 11 Jul 2005 03:04:44 +0100 writes:
AdaiR Just an addendum on the philosophical aspect of doing
AdaiR this. By selecting the 5% and 95% quantiles, you are
AdaiR always going to get 10% of the data as extreme and
AdaiR
Dear all,
I would appreciate a lot, if someone could explain to me in a simple
way, why the assignment class- is not always working and one has to
take as() like in the example below.
(v - matrix(1:9, 3))
[,1] [,2] [,3]
[1,]147
[2,]258
[3,]369
Williams Scott wrote:
Hi R experts,
I am trying to do a prognostic model validation study, using cancer
survival data. There are 2 data sets - 1500 cases used to develop a
nomogram, and another of 800 cases used as an independent validation
cohort. I have validated the nomogram
Dear R :
Sorry for the off topic question, but does anyone know the reference for
the -2 Ln Lambda following a Chi Square distribution, please?
Possibly one of Bartlett's?
Thanks in advance!
Sincerely,
Laura Holt
mailto: [EMAIL PROTECTED]
__
Duncan Murdoch [EMAIL PROTECTED] writes:
Question: why does \verb=c(1,1+1i)= get printed as
\verb=c(1,1 + (0+1i))= ?
The R parser only understands pure imaginary constants as complex
numbers. It parses 1+1i as the sum of the real constant 1 and the
complex constant 0+1i.
This
Duncan, your solution could be simplified using ann=FALSE in the plot
fit - coxph( Surv(futime, fustat) ~ age + rx, ovarian)
plot( cox.zph(fit), ann=F )
title( xlab=My own label, ylab=A new label, main=A clever title)
Now, why did I not think of this before ?
Regards, Adai
On Mon,
On 7/11/2005 9:10 AM, Adaikalavan Ramasamy wrote:
Duncan, your solution could be simplified using ann=FALSE in the plot
fit - coxph( Surv(futime, fustat) ~ age + rx, ovarian)
plot( cox.zph(fit), ann=F )
title( xlab=My own label, ylab=A new label, main=A clever title)
Now, why did I not
Hi,
I am trying to install the misc3d package on a Windows (XP) installation of R
2.0.1 using install.packages(misc3d) but with no success. I have used this
approach with other packages OK, but for misc3d I get the following output...
trying URL
Dear All,
I just came across the same error message (running a gnls{nlme}
model). [R-2.1.1 on Mac OS 10.4]
For a reproducible example, please download the file:
http://mit.edu/costas/www/GR.txt
and run the following:
GR - read.table(GR.txt,header=T)
attach(GR)
myyear - year-1969
On Mon, 11 Jul 2005, Mark Edmondson-Jones wrote:
Hi,
I am trying to install the misc3d package on a Windows (XP) installation
of R 2.0.1 using install.packages(misc3d) but with no success. I have
used this approach with other packages OK, but for misc3d I get the
following output...
Try
On 7/11/2005 9:57 AM, Mark Edmondson-Jones wrote:
Hi,
I am trying to install the misc3d package on a Windows (XP) installation of R
2.0.1 using install.packages(misc3d) but with no success. I have used this
approach with other packages OK, but for misc3d I get the following output...
misc3d is a very new package.
CRAN's windows binary repository for R-2.0.x is no longer updated, hence
does not contain the package. The corresponding ReadMe tells us: Last
update: 19.04.2005.
Either upgrade to R-2.1.1 and try again, or compile the package from
sources yourself.
Uwe Ligges
On Mon, 11 Jul 2005, Adaikalavan Ramasamy wrote:
I am not sure if there is an easy way around this. An ugly hack is to
make a copy the function survival:::plot.cox.zph and make your
modified function. But there are others in the list who might know
neater solutions.
If you then send a patch
What do you want? Consider the following:
v - matrix(1:9, 3)
class(v[1,1])
[1] integer
class(as.vector(v))
[1] integer
v2 - v
dim(v2) - NULL
class(v2)
[1] integer
spencer graves
[EMAIL PROTECTED] wrote:
Dear all,
I would appreciate a lot, if someone
Thanks.
Many people pointed that out. (It was due to that I only knew lappy by
that time :).
On 7/11/05, Martin Maechler [EMAIL PROTECTED] wrote:
Duncan == Duncan Murdoch [EMAIL PROTECTED]
on Thu, 07 Jul 2005 15:44:38 -0400 writes:
Duncan On 7/7/2005 3:38 PM, Weiwei Shi wrote:
However according to:
http://packages.ubuntu.com/hoary/math/r-base
you will have to live with R version 2.0.1 until the next version of
Ubuntu is released. (If I understood the Ubuntu policy...)
Or is there some other repository providing more updated binaries for
Ubuntu 5.04?
Cheers, Henrik
Dear all,
I've modified the plot.cox.zph function to allow
customized xlab and ylab (see below). Someone might
like to confirm that it works.
Thanks for all the assistance.
Dan
___
plot.cox.zph - function (x, resid = TRUE, se = TRUE,
df = 4, nsmo = 40, var,
Hi Heinz,
Can you send me your version of: '~/Library/Preferences/org.R-
project.R.plist'?
Most Mac OS questions are posted/answered on R-SIG-Mac.
Thanks,
Rob
On Jul 11, 2005, at 2:42 AM, Heinz Schild wrote:
I used R on OS X 10.3x quite some time with no serious problems.
Sometimes R
If you meant the lambda as the likelihood ratio test statistic, the
asymptotic chi-squared distribution comes from the asymptotic normality of
the MLEs. The proof is in a paper by Abraham Wald in 1943. See Stuart
Ord (Kendall's Advanced Statistics) for discussion (e.g., vol. 2, 5th
edition).
On 7/11/05, Henrik Andersson [EMAIL PROTECTED] wrote:
However according to:
http://packages.ubuntu.com/hoary/math/r-base
you will have to live with R version 2.0.1 until the next version of
Ubuntu is released. (If I understood the Ubuntu policy...)
Or is there some other repository
On Monday 11 July 2005 16:44, Henrik Andersson wrote:
Or is there some other repository providing more updated binaries for
Ubuntu 5.04?
I don't think, but I'm fine with R 2.0.1 ...
The next ubuntu release, Ubuntu 5.10 (The Breezy Badger), is for October 2005
and will include R 2.1.1
On Mon, 11 Jul 2005 11:18:55 -0400, Liaw, Andy wrote:
LA If you meant the lambda as the likelihood ratio test statistic, the
LA asymptotic chi-squared distribution comes from the asymptotic
LA normality of the MLEs. The proof is in a paper by Abraham Wald in
LA 1943. See Stuart Ord (Kendall's
Hi all,
What I'd like to do is to is to be able to extract a string corresponding to
only the file name from a string containing the complete path, i.e. from the
following path string:
/Users/ken/Desktop/test/runs/file1
I would like to end up with:
file1
This would be most ideally done in a
Dan, I think this works fine now.
I think the 'ylab' argument in other plot function take only a single
value whereas in the case of plot.cox.zph, it needs a vector. It is
especially confusing when this function does plots everything on a
single page by default and all you see is the last plot.
Ken Termiso [EMAIL PROTECTED] wrote:
Hi all,
What I'd like to do is to is to be able to extract a string
corresponding to only the file name from a string containing the
complete path, i.e. from the following path string:
/Users/ken/Desktop/test/runs/file1
I would like to end up with:
x - /Users/ken/Desktop/test/runs/file1.txt
basename(x)
[1] file1.txt
On Mon, 2005-07-11 at 16:13 +, Ken Termiso wrote:
Hi all,
What I'd like to do is to is to be able to extract a string corresponding to
only the file name from a string containing the complete path, i.e. from the
Hi,
I'm trying to produce 6 graphs on a single page using code I've borrowed
from an example by Paul Murrell:
(http://www.stat.auckland.ac.nz/~paul/RGraphics/custombase-xmastree.R).
It involves placing 6 horizontal barplots on one page and adding common
labels.
The problem is the first
Hi there,
If I do an lm, I get p-vlues as
p-value: 2.2e-16
Suppose am interested in exact value such as
p-value = 1.6e-16 (note = and not )
How do I go about it?
stephen
__
R-help@stat.math.ethz.ch mailing list
Hello,
Just a quick question about ppr in library modreg.
I have looked at Ripley and Venables 2002 and it says that projection
pursuit works by projecting X in M carefully chosen directions
I want to know how it choses the directions? I presume it moves around the
high-dimensional space of
Hi there,
If I do an lm, I get p-vlues as
p-value: 2.2e-16
This is obtained from F =39540 with df1 = 1, df2 = 7025.
Suppose am interested in exact value such as
p-value = 1.6e-16 (note = and not )
How do I go about it?
stephen
__
You can compile the newest version...
EJ
Henrik Andersson wrote:
However according to:
http://packages.ubuntu.com/hoary/math/r-base
you will have to live with R version 2.0.1 until the next version of
Ubuntu is released. (If I understood the Ubuntu policy...)
Or is there some other
On Mon, 11 Jul 2005, S.O. Nyangoma wrote:
Hi there,
If I do an lm, I get p-vlues as
p-value: 2.2e-16
This is obtained from F =39540 with df1 = 1, df2 = 7025.
Suppose am interested in exact value such as
p-value = 1.6e-16 (note = and not )
How do I go about it?
You can always
Why have you sent a message about this, which no indication except the
non-English word `entercount'?
Note that the message came from within try(), so it was intentional.
If you look at the source it says
try(ross$withdraw(500)) # no way..
It is helpful to learn how the code being
For the record, this was covered by an answer to your bug report.
The problem is your OS which mishandles a timezone of `GMT', so
Sys.getenv(TZ) as `GMT' is not actually setting your OS to GMT.
Hence NA is the correct answer.
I know no way to set Windows to GMT as distinct from the timezone of
Please do your homework, as the posting guide asks you to.
1. From the Example section of ?nls:
## weighted nonlinear regression
Treated - Puromycin[Puromycin$state == treated, ]
weighted.MM - function(resp, conc, Vm, K)
{
## Purpose: exactly as white book p.451 -- RHS for nls()
##
I just checked:
pf(39540, 1, 7025, lower.tail=FALSE, log.p=TRUE)
[1] -Inf
This is not correct. With 7025 denominator degrees of freedom, we
might use the chi-square approximation to the F distribution:
pchisq(39540, 1, lower.tail=FALSE, log.p=TRUE)
[1]
Google can be helpful. The 10th hit I got from projection pursuit
regression is http://www.scs.gmu.edu/~jgentle/csi991/03f/ppreg1024.rtf,
which gives some rough outline of the algorithm. If you want more detail,
Ripley (1996) PRNN would suffice, I believe.
Andy
From: Oliver Lyttelton
Rundle, Daniel [EMAIL PROTECTED] writes:
Dear R Community,
I am attempting to perform a weighted non-linear least squares fit.
It has already been noted that the weights option is not yet
implemented for the nls function, but no one seems to offer any
suggestions for getting around this
Scot,
Here is your toy example in more condensed form:
x11()
par(mar=c(0.5, 1, 5, 5))
par(mfrow=c(3,2))
plot(1:10)
par(mex) # mex=1.0 here
par(cex.axis=1.0, mex=0.5) # Now you change it
for (i in 1:5) plot(1:10)
When you build your first plot (effectively at the plot.new()
Compare the following
t.test( 1:100, 101:200 )$p.value
t.test( 1:100, 101:200 )
In the latter, the print method truncates to 2.2e-16.
You can go as far as (depending on your machine)
.Machine$double.xmin
[1] 2.225074e-308
before it becomes indistinguishable from zero.
But there
I would like to be able to exert certain types of control over the
plotting of dendrograms (representing hierarchical clusterings) that I
think is best achieved by modifying the dendrogram object
prior to plotting. I am using the dendrogram class and associated
methods.
Define the cluster number
Hi, all,
I just recently upgraded my computer though I'm using the same OS (XP).
But now I'm having difficulty building packages and I cannot seem to
solve the problem. I'm using R-2.1.1pat on Windows XP.
Here is what I tried:
D:\Users\sundard\slib\sundar\RR CMD CHECK sundar
* checking for
On 7/11/2005 3:21 PM, Sundar Dorai-Raj wrote:
Hi, all,
I just recently upgraded my computer though I'm using the same OS (XP).
But now I'm having difficulty building packages and I cannot seem to
solve the problem. I'm using R-2.1.1pat on Windows XP.
Here is what I tried:
Duncan Murdoch wrote:
On 7/11/2005 3:21 PM, Sundar Dorai-Raj wrote:
Hi, all,
I just recently upgraded my computer though I'm using the same OS (XP).
But now I'm having difficulty building packages and I cannot seem to
solve the problem. I'm using R-2.1.1pat on Windows XP.
Here is what
On 7/11/05, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 7/11/2005 3:21 PM, Sundar Dorai-Raj wrote:
Hi, all,
I just recently upgraded my computer though I'm using the same OS (XP).
But now I'm having difficulty building packages and I cannot seem to
solve the problem. I'm using R-2.1.1pat
Probably not answering your questions here, but have you considered the
functions prune.tree and snip.tree from package tree or prune.rpart and
snip.rpart from the package rpart ?
On Mon, 2005-07-11 at 11:48 -0700, Jenny Bryan wrote:
I would like to be able to exert certain types of control
Hi there,
Actually my aim was to compare anumber of extreme values (e.g. 39540)
with df1=1, df2=7025 via p-values.
Spencer mentions that
However, I have also used numbers like
exp(-19775.52) to guestimate relative degrees of plausibility for
different alternatives.
Can someone point to me
As the posting guide says, there is no R 2.1. The first message suggests
this is R 2.1.0, and the posting guide does ask you to use the latest
version (and to quote versions accurately).
The dse bundle depends on package setRNG, which you have not installed,
so you need to do that. Look at
On 11-Jul-05 Martin Maechler wrote:
AdaiR == Adaikalavan Ramasamy [EMAIL PROTECTED]
on Mon, 11 Jul 2005 03:04:44 +0100 writes:
AdaiR Just an addendum on the philosophical aspect of doing
AdaiR this. By selecting the 5% and 95% quantiles, you are
AdaiR always going to get
Dear R users,
It's possible to install newer versions of R from the Ubuntu depositories,
but the new version of R can only be found in 'breezy', the 'unstable'
version of Ubuntu. You can however create a mixed system with most of your
packages
from the old 'hoary' and only some (like R) from the
FWIW:
I have been an enthusiastic user of boxplots for decades. Of course, the
issue of how to handle the whiskers (outliers] is a valid one, and indeed
sample size related. Dogma is always dangerous. I got to know John Tukey
somewhat (I used to chauffer him to and from meetings with a group of
Dear All,
I am trying to put some Confidence intervals on some regressions from a linear
model with no luck. I can extract the fitted values using 'predict', but am
having difficulty in getting at the confidence intervals, or the standard
errors.
Any suggestions would be welcome
Cheers
Guy Forrester [EMAIL PROTECTED] writes:
Dear All,
I am trying to put some Confidence intervals on some regressions from a
linear model with no luck. I can extract the fitted values using 'predict',
but am having difficulty in getting at the confidence intervals, or the
standard
At 08:40 AM 12/07/2005, Guy Forrester wrote:
Dear All,
I am trying to put some Confidence intervals on some regressions from a
linear model with no luck. I can extract the fitted values using
'predict', but am having difficulty in getting at the confidence
intervals, or the standard errors.
On 11/07/2005, at 8:00 PM, Heinz Schild wrote:
I used R on OS X 10.3x quite some time with no serious problems.
Sometimes R stopped when I tried to execute a bigger program. After
updating to OS X to version 10.4 R worked but I still had the problem
with bigger programs. Therefore I
Hello,
I am running this script from Pinheiro Bates book in R Version 2.1.1 (WinXP).
But, I can't plot Figure 2.3.
What's wrong?
TIA.
Rod.
-
library(nlme)
names( Orthodont )
[1] distance age Subject Sex
levels( Orthodont$Sex
Hello,
I am running this script from Pinheiro Bates book in R (Version 2.1.1,WinXP).
But, I can't plot Figure 2.3.
What's wrong?
Thanks, Rod.
-
library(nlme)
names( Orthodont )
[1] distance age Subject Sex
levels( Orthodont$Sex )
Hi there,
I have data on earnings of 12000 individuals at two points in time. I intend to
construct a transition matrix, where the typical element, p_ij, gives the
probability that an individual ends at the j-th decile of the earnings
distribution given that he was was initially at the i-th
On 7/11/05, R V [EMAIL PROTECTED] wrote:
Hello,
I am running this script from Pinheiro Bates book in R Version 2.1.1
(WinXP).
But, I can't plot Figure 2.3.
What's wrong?
There was a change in the way that R handles assignments of names of
components and that affected the construction of
I don't have a reference, but you could look under data mining and p
values / Bonferroni.
spencer graves
S.O. Nyangoma wrote:
Hi there,
Actually my aim was to compare anumber of extreme values (e.g. 39540)
with df1=1, df2=7025 via p-values.
Spencer mentions that
I'll bite: How does one detect bimodalidty from a boxplot?
spencer graves
Berton Gunter wrote:
FWIW:
I have been an enthusiastic user of boxplots for decades. Of course, the
issue of how to handle the whiskers (outliers] is a valid one, and indeed
sample size related.
Dear R Users,
When I installed e1071 use R CMD INSTALL, I got
configure: WARNING: g++ 2.96 cannot reliably be used with this package.
configure: error: Please use a different C++ compiler.
But how to let R CMD INSTALL use a different C++ compiler? and which
C++ compiler is good?
-Luke
MailMarshal has quarantined the following message you sent:
Message: B42d3485f0001.0001.0002.mml
From:[EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: Good day
With the proliferation of mass mailer type viruses, Massey University has
had to implement a policy that
Couple of questions:
1. How can I obtain the frequency tables for a histogram chart?
2. Is there a short cut to obtain the frequency polygons directly without
having to generate the frequency table and doing a line plot?
Thanks ina dvance for any reply.
j.
Example data:
On 7/12/05, Tan Hui Hui Jenny [EMAIL PROTECTED] wrote:
Couple of questions:
1. How can I obtain the frequency tables for a histogram chart?
2. Is there a short cut to obtain the frequency polygons directly without
having to generate the frequency table and doing a line plot?
res - hist(x)
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