On Wed, 8 Mar 2006, Paulo Brando wrote:
summary(model.fit) # just one species from one treatment shown below
Call: survfit(formula = Surv(time, censo) ~ treatment + species, data =
wsuv)
treatment=0, species=1
time n.risk n.event survival std.err lower 95% CI upper 95% CI
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with that
setup.? As above, when I close my R session, I always say no to the
save question.
?
HTH,
?
Roger
?
On 3/10/06, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Thu, 9
Mar 2006, Thomas Lumley wrote:
On Thu, 9 Mar 2006, mark garey wrote:
hello all, i'm forwarding this question for a colleague
On Fri, 10 Mar 2006, Adaikalavan Ramasamy wrote:
The attach function appears to have two functions now :
Since R 1.1.0, in fact.
a) attach(lala.rda) loads objects from lala.rda into the search path
b) attach(obj) makes the named columns of a dataframe or list available
in the search path.
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with sprintf() you
probably want cat(), but if you have a vector of formatted text and you
want to look at it (as data), print() would be better.
-thomas
On 3/10/06, Thomas Lumley [EMAIL PROTECTED] wrote:
On Fri, 10 Mar 2006, Michael wrote:
something like sprintf in C?
so I can do
On Mon, 13 Mar 2006, John McHenry wrote:
Hi All,
I'm looking for some hints on idiomatic R usage using 'lapply' or similar.
What follows is a simple example from which to generalize my question...
# Suppose, in this simple example, I want to plot a number of different
lines in
, predict(lm(Y~X)), col=color)),
with(d, split(d,D)),
color=colors
)
Thomas Lumley [EMAIL PROTECTED] wrote:
You can't get lapply to increment i, but you can use mapply and write your
function with two arguments.
mapply( function(z,colour) with(z, lines(X, predict(lm(Y~X
On Tue, 14 Mar 2006, Gabor Grothendieck wrote:
On 3/14/06, Thomas Lumley [EMAIL PROTECTED] wrote:
It is probably worth pointing out here that the R documentation does not
specify the order in which lapply() does the computation.
I suspect that a huge amount of application code takes
On Tue, 14 Mar 2006, Gabor Grothendieck wrote:
On 3/14/06, Thomas Lumley [EMAIL PROTECTED] wrote:
On Tue, 14 Mar 2006, Gabor Grothendieck wrote:
On 3/14/06, Thomas Lumley [EMAIL PROTECTED] wrote:
It is probably worth pointing out here that the R documentation does not
specify the order
it, but I may not have been looking
for the right name, etc.
wilcox.test() computes this.
(I think it's false advertising to call something that assumes a location
shift model nonparametric)
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED
On Wed, 15 Mar 2006, Heinz Tuechler wrote:
Dear All,
a Surv object I put in a data frame behaves somehow unexpected (see example).
If I do a Cox regression on the original Surv object it works. If I put it
in a data.frame and do the regression on the data frame it does not work.
Seemingly
On Wed, 15 Mar 2006, Philippe Grosjean wrote:
the for() loop is very slow in S-PLUS. This is probably one of the
motivation of developing the apply() family of functions (as well as the
ugly For() loop) under this system.
Now, for() loops are much faster in R. Also, if you look at the R code
On Thu, 16 Mar 2006, Heinz Tuechler wrote:
Thank you, Thomas. You are right, it works, but why then I find on the help
page for Surv{survival} the following sentence:
To include a survival object inside a data frame, use the I() function.
Surv objects are implemented as a matrix of 2 or 3
On Thu, 16 Mar 2006, Heinz Tuechler wrote:
Dear All,
there seems to be some strange influence of the Design package on
data.frame. If I build a data.frame containing a Surv object without
loading the package Design, the data frame is usable to coxph. If instead I
just load Design and build
On Mon, 20 Mar 2006, Darren Weber wrote:
Dear Erich and John, thankyou for providing RColorBrewer!
Are you working on options for CMYK or RGB return values?
col2rgb() will give RGB values. convertColor() (or the colorspace
package) will give other conversions (but not CMYK)
-thomas
On Mon, 20 Mar 2006, johan Faux wrote:
Hello,
Is it possible to pass R matrix as a parameter to an internal C procedure?
From the documentation I got the impression that only 1-dim vectors can be
passed.
Why the following wont work for me?
a-matrix(1:15,3,5)
.C(pr,as.integer(a))
On Tue, 21 Mar 2006, Gregor Gorjanc wrote:
Hello!
Looking on how people use optim to get MLE I also noticed that one can
use returned Hessian to get corresponding standard errors i.e. something
like
result - optim( snip , hessian=T)
result$par # point estimates
vc -
On Tue, 21 Mar 2006, Ingmar Visser wrote:
The optim help page says:
hessian Logical. Should a numerically differentiated Hessian matrix be
returned?
I interpret this as providing a finite differences approximation of the
Hessian (possibly based on exact gradients?). Is that the case or
On Wed, 22 Mar 2006, Domenico Vistocco wrote:
Dear All,
It is difficult to summarize the question in few words. So, please,
look at the following example.
Thanks in advance,
domenico
,
IARC Scientific Publications.
which I think is the best reference. There's probably stuff on the web,
too.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
On Thu, 23 Mar 2006, Ingmar Visser wrote:
Dear expeRts,
I came across the following error in using model.frame:
# make a data.frame
jet=data.frame(y=rnorm(10),x1=rnorm(10),x2=rnorm(10),rvar=rnorm(10))
# spec of formula
mf1=y~x1+x2
# make the model.frame
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PLEASE
. The ideal
solution is Danyu Lin's semiparametric maximum partial likelihood
estimator, but I don't know of any implementations (the URL describe in
the paper lists the software as 'under development').
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL
situations this is all you need, because the correlation does not
prevent a sensible interpretation of your regression coefficients. In
other cases you want a different model that will give different regression
coefficients.
-thomas
Thomas Lumley Assoc. Professor
On Fri, 24 Mar 2006, Ingmar Visser wrote:
On Thu, 23 Mar 2006, Ingmar Visser wrote:
Dear expeRts,
I came across the following error in using model.frame:
# make a data.frame
jet=data.frame(y=rnorm(10),x1=rnorm(10),x2=rnorm(10),rvar=rnorm(10))
# spec of formula
mf1=y~x1+x2
# make the
.
-thomas
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tests are (approximately) score tests against particular
one-dimensional alternatives and so are more powerful against those
alternatives than a test based on the supremum of the score process.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED
On Sun, 2 Apr 2006, Gabor Grothendieck wrote:
Some functional languages have a feature called tail recursion that
can provide performance improvements if you write your recursions
to take advantage of it:
http://en.wikipedia.org/wiki/Tail_recursion
but I don't think R supports it. Is
On Mon, 3 Apr 2006, Monty B. wrote:
Hello all,
As this is my first time posting to this mailing list, I think I
should thank all the people who have contributed to the project. Many
man-hours have been saved on my part!
My question is simple - when i run a longer simulation, I would like
?
You can use cox.zph(), or you can just put in interactions between X and
start.
-thomas
Thank you in advance
Jean-Fran?ois Boudreau
Sherbrooke University
[[alternative HTML version deleted]]
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a vignette? Documenting a process involving multiple
functions is exactly what vignettes are designed for.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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processor you can usually run either 64-bit or 32-bit builds
of R, and the 64-bit one will be able to access more memory but will be
slower.
This doesn't mean that a 32-bit build of R on a 64-bit processor will be
slower than a 32-bit build of R on a 32-bit processor.
-thomas
Thomas Lumley
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. This is good behaviour for a
default, especially if you assume that anyone with an actual hypothesis as
to g(t) will specify transform= explicitly.
An obvious disadvantage is the lack of ready interpretation of beta*g(t).
-thomas
Thomas Lumley Assoc. Professor
On Mon, 10 Apr 2006, Omar Lakkis wrote:
Can someone, please, help explain to me why the following two calls
return the same set:
seq(from=as.POSIXlt('2005-12-4'), to=as.POSIXlt('2006-4-2'), by='weeks')
[1] 2005-12-04 EST 2005-12-11 EST 2005-12-18 EST 2005-12-25 EST
[5] 2006-01-01 EST
model with the same number of observations for each person
and no covariates that vary within a person. The independence and
exchangeable working correlations will give identical answers.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED
mean by the Sitter algorithm. Prof Sitter has
written several papers on bootstrapping survey data -- can you give a more
precise reference?
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington
On Tue, 11 Apr 2006, justin bem wrote:
Hi
you should use the package boot to compute bootsrap and jacknife
Not if he wants to get the right answers. This was for a stratified
multistage cluster-sampled survey.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
On Tue, 11 Apr 2006, Prof Brian Ripley wrote:
On Tue, 11 Apr 2006, Thomas Lumley wrote:
He has a linear model with the same number of observations for each person
Not so: some have 3 and some have 2, and the two levels of T are not quite
balanced (29/28).
and no covariates that vary
automatically is with the
package.skeleton function.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
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}
and then execute
foo - make.foo()
How would I go about accompishing the same (toy) task making use of the
local() function?
foo - local({
n - 4
function(x) {x^n}
})
-thomas
Thomas Lumley Assoc
expands to non-language object
Any help?
Thanks,
Chad R. Bhatti
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On Fri, 14 Apr 2006, Murray Jorgensen wrote:
I found myself wanting to average a vector [vec] within each level of a
factor [Fac], returning a vector of the same length as vec. After a
while I realised that
lm1 - lm(vec ~ Fac)
fitted(lm1)
did what I want.
But there must be another way
3
21890 8989 108
is.integer( dat$haspdat0 )
[1] TRUE
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On Wed, 12 May 2004, [iso-8859-1] Göran Broström wrote:
Is it the data? Let's try 'coxreg' (eha):
---
Call:
coxreg(formula = Surv(yrs2, ratify) ~ haz.wst + pol.free, data = dat)
Covariate Mean CoefRR
On Tue, 11 May 2004, Heike Heidemeier wrote:
Dear list-members,
I am trying to use R to conduct a meta-analysis, i.e. I'd like to use a
multi-level model to integrate the findings of a number of primary research
studies.
I set up a simple two level-model (only summary statistics are
of Kansas
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On Thu, 13 May 2004, Paul Johnson wrote:
I still don't quite understand your point about the reason that coxph
crashes. Why does the difference of scale between the variables cause
trouble?
Because exp(beta*x) is very, very, large for many values of beta when x
is that large. If exp(beta*x)
On Sun, 9 May 2004, Liaw, Andy wrote:
Dear R-help,
I've encounter what seems to me a strange problem with names-. Suppose I
define the function:
fun - function(x, f) {
m - tapply(x, f, mean)
ans - x - m[match(f, unique(f))]
names(ans) - names(x)
ans
}
which subtract
On Mon, 10 May 2004, Christophe Pallier wrote:
The use of tapply(x,f,mean)[match(f,unique(f))] assumes a particular
order in the result of tapply, no? It seems a bit dangerous to me.
My original code for the group means problem used rowsum(,reorder=FALSE)
rather than tapply(), and we do know
ideas how to do that ?
:
: Yours sincerly
: Felix Eschenburg
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or other garbage.
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On Mon, 3 May 2004, Francis Dimzon wrote:
Hi all,
Please help on this. We will be teaching epidemiology using opensource
software. What are R built-in functions or functions in available packages
that are capable of doing these:
a) Logistic regression (glm?)
glm
b) Conditional
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Thomas LumleyAssoc. Professor, Biostatistics
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Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
On Mon, 3 May 2004 [EMAIL PROTECTED] wrote:
Hi R-Helpers
Is there a way to access the parameters passed to a function all at
once? I want something like:
misc.params = list(...)
except such that it works with formal named parameters.
match.call() or sys.call()
-thomas
On Fri, 30 Apr 2004, Gordon Fredericks wrote:
Hello,
Has anyone written up code to estimate for example a simple logit using
quasi-likelihood? I know that glm() already does this, but I'd like to do
some tinkering with the variance function beyond what glm() allows.
This should just be a
On Fri, 30 Apr 2004, Phillip Good wrote:
Before I duplicate effort are there existing programs for computing the coefficients
for
a) LAD regression
LAD regression is a special case of quantile regression, which is handled
by the quantreg package.
-thomas
On Wed, 28 Apr 2004, Peter Dalgaard wrote:
Looks like a classic signed/unsigned confusion. Negative numbers
stored in ones-complement format in single bytes, but getting
interpreted as unsigned. A bug report could be a good idea if the
resident Stata expert (Thomas, I believe) is unavailable
On Wed, 28 Apr 2004, Paul Johnson wrote:
The read.dta has translated the negative values as (256-deml).
Is this the kind of thing that is a bug, or have I missed something in
the documentation about the handling of negative numbers? Should a
formal bug report be filed?
A fixed version of
On Thu, 29 Apr 2004, John Maindonald wrote:
This is, of course, not strictly about R. But if there should be
a decision to pursue such matters on this list, then we'd need
another list to which such discussion might be diverted.
Ted Harding started such a list (stats-discuss) quite some
On Thu, 29 Apr 2004, [iso-8859-1] Susana Bird wrote:
Dear all,
my problem is following. I know Stata, but currently I have to use R.
Could You please help in finding the analogy to R.
(1) creating of City-Dummy.
(2) Create a Time-Dummy-Variable
Andy Liaw has described how to do this, but
On Thu, 29 Apr 2004, Thomas Petzoldt wrote:
If you want to make a subsample, you can select cases (rows) using
sub(), see ?sub for details, e.g. somethink like:
I think you mean subset(). sub() is a regular expression substitution
function.
-thomas
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On Tue, 18 May 2004, Shin, Daehyok wrote:
Is there any way to define a destructor method of an object,
which is called automatically when garbage collector reclaims it?
yes, there is support for finalizers at both the C and R levels. For the R
level see ?reg.finalizer. I thought there was
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On Fri, 21 May 2004, array chip wrote:
Hi,
I am wondering how to specify interval-censored data
in coxph? The example in the help page
summary(coxph(Surv(start, stop, event) ~ x, data =
test2))
is for counting process data, is the counting process
data the same as interval-censored
On Mon, 24 May 2004, Peter Dalgaard wrote:
Whereas we cannot reasonably require people to test code on platforms
that they haven't got, we can and should require them to adhere to
reasonable standards and test procedures (which, mind you, other
people have invested a serious amount of time in
On Mon, 24 May 2004, Andrew Robinson wrote:
Greetings R-community,
I'm running simulations within R that I wrote in C. The simulations
require fitting that occasionally fails to finish. I was wondering if
there is any kind of tool for process control in R, such that after e.g.
15 minutes
://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
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On Thu, 27 May 2004, Mark Fowle wrote:
I'm a bit over my head hear, but my understanding is that R is a derivative
of S and is fully endorsed by the S group(I can not find any references at
the moment, but I believe that there is information on this somewhere with
in the R web site).
No,
W is looking for the vector cross product (a specifically
three-dimensional object important in physics and engineering). The
crossproduct() function provides a matrix product so that crossprod(x,y)
is t(x)%*%y, something completely different.
For the three-dimensional case you could define the
of model?
Thanks in advance
Aurélie Cohas
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Schweitzer
B.P. 118 Lambaréné (GABON)
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?
Use print().
-thomas
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On Thu, 3 Jun 2004, Rajarshi Guha wrote:
Hi,
I have a matrix, m, over whose rows I want to apply a function. I also
have a vector, r, whose length is equal to the rows of m.
The obvious way is:
result - apply( m, c(1), fun )
However the function call requires the row from m and the
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On Sat, 12 Jun 2004, Ajay Shah wrote:
R is very fancy. You won't get mundane things like ordered probit off
the shelf. (I will be very happy if someone will show how to use glm()
to do a vanilla probit!)
glm(y~x+z, family=binomial(probit))
Be happy,
-thomas
On Sun, 13 Jun 2004, Rong-En Fan wrote:
On Tue, May 25, 2004 at 04:38:44PM +1200, Richard A. O'Keefe wrote:
In R 1.9.0 running under Solaris 2.9 on a SunBlade 100,
with Sun WorkShop 6 update 2 C++ 5.3 2001/05/15 as the
C++ compiler, I just did
How worried should I be?
I guess the
On Mon, 14 Jun 2004, Patrick Connolly wrote:
It seems as though the first simulation makes it easier for
subsequent simulations of the same type AND also for simulations of a
somewhat different type also. The degree to which it helps varies
according to just what is being run (no surprise
On Mon, 14 Jun 2004, John Maindonald wrote:
I have found it helpful, in trying to explain (to myself and others)
what happens, to say that there is both a lexical stack and a call
stack. Is that a legitimate use of terminology?
I think this is helpful, despite being inaccurate. If you
On Mon, 14 Jun 2004, Laura Quinn wrote:
Is there a way to increase the sensitivity of the color palette in order
to more clearly represent certain sections of data? For example I am
wanting to clearly differentiate between height data for a rolling
landscape but because of the extremes of the
On Mon, 14 Jun 2004, Gabor Grothendieck wrote:
Thomas Lumley tlumley at u.washington.edu writes:
The distinction between environment and frame is important. The frame
is what you find things in with get(, inherits=FALSE) and the environment
uses get(, environment=TRUE).
The thing I find
On Mon, 14 Jun 2004, Small, Dylan wrote:
I'm trying to use the glmmML package on a Windows machine. When I try to install
the package, I get the message:
{pkg - select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)}
Error in dyn.load(x,
On Tue, 15 Jun 2004, Yev Kirpichevsky wrote:
I'm trying to install a package in windows. I have a package directory,
which contains all the essentials: .Rd in the Man directory, DESCRIPTION
file, etc. I copied it to my R\bin directory, where the Rcmd file is located.
Then, when I try to run
various tasks it may be more
useful to have vignettes than examples.
-thomas
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[EMAIL PROTECTED] University of Washington, Seattle
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On Wed, 16 Jun 2004, Prof Brian Ripley wrote:
You will have to tell us more. Exporting how: to what format using what
device and what exact command on what operating system?
The only device I know of that even knows about dpi is bitmap() and that
has no such limit unless imposed by your
On Thu, 17 Jun 2004, Rishi Ganti wrote:
I've got a few issues with the x-axes in the histogram and density plots. First,
often the default x-axis doesn't even extend to the length of my data. R often draws
histogram bars (or density lines) farther than the drawn x-axis extends. For
On Fri, 18 Jun 2004, Jari Oksanen wrote:
On 18 Jun 2004, at 8:26, Deepayan Sarkar wrote:
On Thursday 17 June 2004 22:57, Patrick Bennett wrote:
yes, i can reproduce that same graph when i print to the pdf-device.
but the panel titles do not appear when I print to the Quartz-device.
On Sun, 20 Jun 2004, Zhen Chen wrote:
I have problem evaluating the expression h = exp(x)/(exp(exp(x))-1) for
large negative x. This expression is actually the probability
that y = 1 when y is a Poisson random variable truncated at 0, hence
must satisfy 0 = h = 1. However, when
You would be
On Fri, 25 Jun 2004, Henrik Andersson wrote:
The last newsletter found on www.r-project.org is from December 2003.
I was looking forward to the next issue, will there be one soon, or what
happened ?
Yes, there will be one very soon.
-thomas
BTW: the last issue, while titled
On Thu, 8 Jul 2004, Gijs Plomp wrote:
Dear expeRts,
I fail to succesfully pass strings to functions. It comes down to the
observation that
plot(someVariable,anotherVariable)
works fine, but
x - someVariable
y - anotherVariable
plot(x,y)
does not.
Does this have something
The new issue of the R Newsletter (1/2004) is out on http://www.r-project.org/
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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