Hi everyone,
I'm witnessing an odd modelling phenomenon that I can't explain. If
anyone has seen this before, or can explain what's going on would let
me know, I'd be very grateful! Especially if I'm just being dim.
I'm fitting a pair of continuous variates and their interaction to
some
By at least some definitions, a `large file' is one over 2Gb, so yours is
hardly `huge'.
I don't know what .dat format is (or, rather, I know many different
definitions of it). But your problem seems a small one
for the current limits of 32-bit R for Windows, and on more capable
platforms
Hi,
Is there a function taking a function as an argument, which returns all the
functions it calls, and all the the functions those functions call, and so
on?I could use Rprof, but that would involve executing the function,
which may miss some branches of code. I'd really like a function
G'day Andrew,
AR == Andrew Robinson [EMAIL PROTECTED] writes:
AR I would have expected any term to explain less Sum Sq if
AR listed second than if listed first. Is my intuition awry?
Yes. :-)
I would not expect that *any* term explains less Sum Sq if listed
second, then life and
Hello all,
I'd like to create a function which would do some analysis on a particular
object, which should be specified in advance. Something like:
ls()
[1] aa bb cc
Object - bb
var.name - q2
testfunction - function(obj.name, var.name) {
temp - give.me.the.object.called(Object)
hello,
I am using the ROC package to evaluate predictive models
I have successfully plot the ROC curve, however
¿is there anyway to obtain the value of operating point=optimal threshold
value (i.e. the nearest point of the curve to the top-left corner of the
axes)?
thank you very much,
jose
Try
test.fn - function(obj.name, var.name=q2){
stopifnot( is.character(obj.name) is.character(var.name) )
x - subset( get(obj), select=var.name )
table(x)
}
On Fri, 2006-03-31 at 12:44 +0300, Adrian DUSA wrote:
Hello all,
I'd like to create a function which would do some analysis
Berwin A Turlach [EMAIL PROTECTED] writes:
Don't know if the following example, which shows the same behaviour,
leads to any insight.
n - 100
x1 - runif(n, -1,1)
x2 - runif(n, -1,1)
y - x1*x1*x2 + rnorm(n, sd=0.05)
y - y - mean(y)
anova(lm(y~x1+x2))
Here's another (paraphrased
Hello,
I have a problem with adding texts to my plots: The code is
/plot(dates(as.character(tam[,tkolon])),d[,i],ylab=names(d[i]),ylim=c(galt,gust),type=l)
abline(orta,0,lty=3,col=3)
text(//length(d[,i]//),0.025+(orta),expression(mu),col=3)
abline(orta+l2,0,lty=4,col=2)
Thanks, it's exactly what I want.
Adrian
On Friday 31 March 2006 12:59, Adaikalavan Ramasamy wrote:
Try
test.fn - function(obj.name, var.name=q2){
stopifnot( is.character(obj.name) is.character(var.name) )
x - subset( get(obj), select=var.name )
table(x)
}
--
Adrian DUSA
Nice trick, thx...
Stéphane.
On Wed, 2006-03-29 at 11:17 -0500, jim holtman wrote:
try 'by':
x
S_id AF_Class count... R_gc_percent S_length
5 82644971 30 0.4835678
6 826449737 0.4835678
8 82645541 31
Hello useRs,
I have a Liquid Chromatography data of mixtures. I have a 13 variables which
are integrals of peaks, and 40 observations as chromatography samples, and
concentrations of subtances as response variablse Y.
I am trying to bild the best regression model with MLM and PLS for these
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様々なイベント企画等のお知らせもございますのでお楽しみに♪
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〜 新番組いよいよＯＰＥＮ 〜
無料で簡単に遊べるオトナのセフレ探し♪
「ラブフレ’ＮＯ.１を使って良かった！」きっとそう思ってもらえるはずです。
☆★ラブフレ’ＮＯ.１★☆★☆★☆
Dear all,
I use the Andersen plot to check for proportional hazards assumption for a
factor (say x) in the Cox regression model and obtained a straight line that
pass through the origin. However, the formal test done by the R-function
cox.zph, which is based on the plot of Schonefeld residuals
Hello all!
From my current code, I need to call either a batch file or shell script,
depending on what operating system R is running. But before that I need to
find out, whether the machine is running Windows or Linux. I found the
getBuiltinOs() command in the utils package, but I cant get it to
Hi,
I'm trying to plot a bubbles plot wich I do with the cex argument. The
problem is that it looks like it fails the conditioning and reuses the
first 100 elements of the cex vector. See the code
x - rep(rep(1:10,10),2)
y - rep(rep(c(1:10),rep(10,10)),2)
z - rep(1:2,c(100,100))
w -
On Fri, 31 Mar 2006, Frank Rossdeutscher wrote:
From my current code, I need to call either a batch file or shell script,
depending on what operating system R is running. But before that I need to
find out, whether the machine is running Windows or Linux. I found the
getBuiltinOs() command in
I use model comparison with glms without mixed effects with
anova(modelA,modelB),
with mixed effects glm (glmmPQL), this doesn't work. Is there a way to
compare model fits with glmmPQL's?
Paula M. den Hartog
Behavioural Biology
Institute of Biology Leiden
Leiden University
Jose -
I've struggled a bit with the same question, said another way: how do you find
the value in a ROC curve that minimizes false positives while maximizing true
positives?
Here's something I've come up with. I'd be curious to hear from the list
whether anyone thinks this code might get
Guiseppe,
there are several things unclear with this question.
On Thu, 30 Mar 2006, Giuseppe Pagnoni wrote:
Dear all,
I have a BIG dissimilarity matrix (around one thousand by one thousand),
that I would like to cluster. Most of the elements of the matrix are
zero or close to zero. Is
Hi Tim and José,
Date: Fri, 31 Mar 2006 11:58:14 +0200
From: Anadon Herrera, Jose Daniel [EMAIL PROTECTED]
Subject: [R] ROC optimal threshold
I am using the ROC package to evaluate predictive models
I have successfully plot the ROC curve, however
?is there anyway to obtain the value of
This might help:
http://tolstoy.newcastle.edu.au/R/help/05/04/2263.html
On 3/31/06, Matthew Dowle [EMAIL PROTECTED] wrote:
Hi,
Is there a function taking a function as an argument, which returns all the
functions it calls, and all the the functions those functions call, and so
on?I
On 3/31/06, ernesto [EMAIL PROTECTED] wrote:
Hi,
I'm trying to plot a bubbles plot wich I do with the cex argument. The
problem is that it looks like it fails the conditioning and reuses the
first 100 elements of the cex vector. See the code
x - rep(rep(1:10,10),2)
y -
Is there is a way to make square bars in xyplot with type=h?
dat - data.frame(foo = rep(1:10,2), bar = rep(1:10,2))
xyplot(foo~bar, data = dat, type=h,lwd=20)
Thanks! Andy
__
R-help@stat.math.ethz.ch mailing list
If you define a cost function for a given threshold k as
cost(k) = FP(k) + lambda * FN(k)
then choose k that minimises cost. FP and FN are false positives and
false negatives at threshold k.
You change lambda to a value greater than 1 if you want to penalise FN
more than FP. There are many
On Fri, 31 Mar 2006, singyee ling wrote:
Dear all,
I use the Andersen plot to check for proportional hazards assumption for a
factor (say x) in the Cox regression model and obtained a straight line that
pass through the origin. However, the formal test done by the R-function
cox.zph, which
Michael Kubovy wrote:
Hi Tim and José,
Date: Fri, 31 Mar 2006 11:58:14 +0200
From: Anadon Herrera, Jose Daniel [EMAIL PROTECTED]
Subject: [R] ROC optimal threshold
I am using the ROC package to evaluate predictive models
I have successfully plot the ROC curve, however
?is there anyway to
I had a similar need and found package mvbutils, function foodweb().
From the help file:
'foodweb' is applied to a group of functions (e.g. all those in a
workspace); it produces a graphical display showing the hierarchy
of which functions call which other ones. This is handy, for
Andy Bunn wrote:
Is there is a way to make square bars in xyplot with type=h?
dat - data.frame(foo = rep(1:10,2), bar = rep(1:10,2))
xyplot(foo~bar, data = dat, type=h,lwd=20)
Thanks! Andy
Hi, Andy,
I don't think lattice supports this since it uses
trellis.par.get(plot.line) to
On 3/31/06, Sundar Dorai-Raj [EMAIL PROTECTED] wrote:
Andy Bunn wrote:
Is there is a way to make square bars in xyplot with type=h?
dat - data.frame(foo = rep(1:10,2), bar = rep(1:10,2))
xyplot(foo~bar, data = dat, type=h,lwd=20)
Thanks! Andy
Hi, Andy,
I don't think lattice
Dear all, I want to compute the NPMLE for interval censored data using
the EMICM function in Icens package, but I didn't find much detailed
instructions on how to use this. I couldn't even figure out how to
specify the status of right censored, interval censored, observed.
(probably due to my
Hi, Doug:
I just confirmed a discrepancy (reported by Paul Cossens) between the
output of lme and lmer using the Oxide example in Pinheiro and Bates,
pp. 167-170. It appears that coef(lmer(...)) adds only the ranef for
Wafer and omits the one for Lot.
Consider the
Hi:
I have been writing some functions in R that are about 500-1000 lines long,
and when I copy and paste the code into the R console, it takes about 20-30
seconds for R to print and run the code at the console command line (and
this is just for function definition - R isn't actually executing
On 3/31/06 12:20 PM, Toby Daniel Ahrens [EMAIL PROTECTED] wrote:
Hi:
I have been writing some functions in R that are about 500-1000 lines long,
and when I copy and paste the code into the R console, it takes about 20-30
seconds for R to ³print² and run the code at the console command
On Fri, 31 Mar 2006, Sean Davis wrote:
On 3/31/06 12:20 PM, Toby Daniel Ahrens [EMAIL PROTECTED] wrote:
Hi:
I have been writing some functions in R that are about 500-1000 lines long,
and when I copy and paste the code into the R console, it takes about 20-30
seconds for R to ³print² and run
Dr. Harrell,
Thank you for your response. I had noted, and appreciate, your perspective on
ROC in past listserv entries and am glad to have an opportunity to delve a
little deeper.
I (and, I think, Jose Daniel Anadon, the original poster of this question) have
a predictive model for the
I am using the R 2.2.1 in a Windows XP environment.
I have a dataframe with 12 columns and 1,000 rows.
(Some of the rows have 1 or fewer values.)
I am trying to use rowVars to calculate the variance
of each row.
I am getting the following message:
Error in na.remove.default(x) : length of
Hi,
I have a problem with my the R help system. I have
been searching through the help archives but I can't
find anything about it and I don't know how to specify
my search better.
When I type for instance ?hist, just the next
command line prompt shows but nothing actually
happens. There is no
Dear all, I want to compute the NPMLE for interval censored data using the
EMICM function in Icens package, but I didn't find much detailed
instructions on how to use this. I couldn't even figure out how to specify
the status of right censored, interval censored, observed. (probably due to
my
Dear R users,
I am estimating Poisson mixed models using glmmPQL
(MASS) and lmer (lme4). We know that glmmPQL do not
provide the correct loglikelihood for such models (it
gives the loglike of a 'pseudo' or working linear
mixed model). I would like to know how the loglike is
calculated by lmer.
A
In addition, I think people should always explore ways
to repackage exclusive S-Plus facilities and libraries
into R. By rewritting them or using GPL loopholes.
It seems to me that Insightful is very good at
protecting whatever they create and the same time
feels very comfortable taking R stuff
eugene dalt [EMAIL PROTECTED] writes:
It seems to me that Insightful is very good at
protecting whatever they create and the same time
feels very comfortable taking R stuff to keep they
clients happy. In essence they are selling free stuff.
I must defend Insightful on this point. As an
I have been trying for a year to get approval to install R on a work
computer and am not optimistic of a positive reply in the near future. I
was considering whether an option might be to run R from a CD/USB stick. I
looked through the installation manual but could see no mention of this
I have to come to the defence of Insightful here. In my
experience, they have been one of the better software companies
I've dealt with. (Try getting Microsoft to fix something.)
I think that their new packages initiative is an excellent idea.
Peter Ehlers
eugene dalt wrote:
In addition, I
If it is possible to run R from a CD or a USB stick without installation to
a computer
YES
On 3/31/06, Bob Green [EMAIL PROTECTED] wrote:
I have been trying for a year to get approval to install R on a work
computer and am not optimistic of a positive reply in the near future. I
was
Bob Green wrote:
I have been trying for a year to get approval to install R on a work
computer and am not optimistic of a positive reply in the near future. I
was considering whether an option might be to run R from a CD/USB stick. I
looked through the installation manual but could see no
On Sat, 2006-04-01 at 06:45 +1000, Bob Green wrote:
I have been trying for a year to get approval to install R on a work
computer and am not optimistic of a positive reply in the near future. I
was considering whether an option might be to run R from a CD/USB stick. I
looked through the
Tim Howard wrote:
Dr. Harrell,
Thank you for your response. I had noted, and appreciate, your perspective on
ROC in past listserv entries and am glad to have an opportunity to delve a
little deeper.
I (and, I think, Jose Daniel Anadon, the original poster of this question)
have a
I don't typically post to r-help but I could not pass up responding.
While I don't use S+ any longer many folks in my lab do use it and there
is a viable and useful market for it. Personally I welcome the
direction Insightful is taking. I don't know David Smith but I take my
hat off to him
Hello,
I have a question about the add1() function and quasilikelihoods for GLMs.
I am fitting quasi-Poisson models using glm(, family = quasipoisson).
Technically, with the quasilikelihood approach the deviance does not have
the interpretation as a likelihood-based measure of sample
Hello there,
Please shed some light on how to change the background color of trellis
graphic background.
Thanks a lot
lisa Wang
Toronto, Ca
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the
On Fri, 31 Mar 2006, Frank Rossdeutscher wrote:
From my current code, I need to call either a batch
file or shell script, depending on what operating system
R is running. But before that I need to find out, whether
the machine is running Windows or Linux. I found the
getBuiltinOs() command
On Fri, 31 Mar 2006, Marc Schwartz (via MN) wrote:
On Sat, 2006-04-01 at 06:45 +1000, Bob Green wrote:
I have been trying for a year to get approval to install R on a work
computer and am not optimistic of a positive reply in the near future. I
was considering whether an option might be to
On Fri, 2006-03-31 at 22:26 +0100, Prof Brian Ripley wrote:
On Fri, 31 Mar 2006, Marc Schwartz (via MN) wrote:
On Sat, 2006-04-01 at 06:45 +1000, Bob Green wrote:
I have been trying for a year to get approval to install R on a work
computer and am not optimistic of a positive reply in the
Point well taken. You should, however, expect R users
to bring up concerns. This isn't a win-win situation
as
you sound...and you want to keep s-news in the dark
too.
Frankly, you didn't address the real issue. How would
Insightful reacts for example if they find R users
repackaging your
Sorry to be late coming to this discussion. I was just talking with
Harold on the telephone and we decided why the inconsistency exists.
The lme function is designed to fit models with strictly nested random
effects. (It can be used to fit models with crossed random effects
but the process is
Take a look at trellis.par.set().
For example, trellis.par.set(theme = col.whitebg()) changes things to look
more or less like the default from the standard R graphics functions. But
you can change one option at a time too.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL
Sandra,
hard to tell where the error message originates from without having the data
at hand (perhaps you could provide that to me off-list?), but I am almost
sure things will work when you train the model the standard way:
cd1.svm-svm(Acode~EXT+TOF, data = boot.dist.dat, cost=100, gamma=20)
Please read the man pages.
?trellis.par.set
which leads you also to ?trellis.device
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
-Original Message-
I have run into this several times now. I leave a copy of
R running for days at a time. At some point in time, the
temporary directory R uses no longer exists. Once that
happens, installs (and other basic operations) stop
functioning. Currently I recreate the directory manually
by failing some
Is there a global option somewhere that can completely
disable the LazyLoad option? I want all my packages
in source format for searching purposes, crippled by
the conversion to database format.
--
SIGSIG -- signature too long (core dumped)
Point well taken. You should, however, expect R users
to bring up concerns.
Indeed, and I encourage them to do so.
This isn't a win-win situation as you sound...and you want
to keep s-news in the dark too.
As far as I can tell, your messages never appeared on s-news. Perhaps you're
not a
On 3/31/2006 5:15 PM, Paul Roebuck wrote:
Is there a global option somewhere that can completely
disable the LazyLoad option? I want all my packages
in source format for searching purposes, crippled by
the conversion to database format.
Why not just keep the source? Maybe I misunderstood
Dear R users
given a numeric array (a sequence of reals), I am interested in
finding the subsets of sequences (each with start and end index) which match a
given sd range.
I read the docs on match and which and the see also but could not come up
with a way. I could loop with a stepping
On Fri, 31 Mar 2006, Duncan Murdoch wrote:
On 3/31/2006 5:15 PM, Paul Roebuck wrote:
Is there a global option somewhere that can completely
disable the LazyLoad option? I want all my packages
in source format for searching purposes, crippled by
the conversion to database format.
Why
Dear R-list.
I would need to know if the centroid of a cluster, whose coordinates are the
average of the coordinates of the points in the cluster,
is also the point that minimizes the sum of its distances from all the
points in the cluster.
If so, where could I find a proof?
Since I
Hi All,
I'm looking for some reference paper about SOM (self organizing map)
algorithm. I tried the paper which is mentioned in
the help page of function som (package:som):
http://www.cis.hut.fi/research/papers/som_tr96.ps.Z
But I can't open it for some reason. Could you please help
On 31 March 2006 at 16:15, Paul Roebuck wrote:
| Is there a global option somewhere that can completely
| disable the LazyLoad option? I want all my packages
| in source format for searching purposes, crippled by
| the conversion to database format.
AFAICT setting LazyLoad=No in DESCRIPTION
Hi, All:
I only have 4 samples. I wish to get a confidence interval around the mean.
Is it reasonable? If not, is there a way to compute a confidence interval
for such small sample size's mean?
Many thanks,
U
[[alternative HTML version deleted]]
I am trying to fit a nonlinear regression model to data. There are
several predictor variables and 8 parameters. I will write the model as
Y ~ Yhat(theta1,...,theta8)
OK, I can do this using nls() - but only just as there are not as many
observations as might be desired.
Now the problem is
Dear r-helpers,
I am developing a smoothing function that performs a casewise deletion of all
the non-informative observations in a bivariate dataset following the Poisson -
D'Avril algorythm.
But I am now facing two problems:
1)Being based on loops, the function takes a lot of time before
On Fri, 31 Mar 2006, Dirk Eddelbuettel wrote:
On 31 March 2006 at 16:15, Paul Roebuck wrote:
| Is there a global option somewhere that can completely
| disable the LazyLoad option? I want all my packages
| in source format for searching purposes, crippled by
| the conversion to database
See McCullagh and Nelder (1989) (and the source code).
On Fri, 31 Mar 2006, Chad Reyhan Bhatti wrote:
Hello,
I have a question about the add1() function and quasilikelihoods for GLMs.
I am fitting quasi-Poisson models using glm(, family = quasipoisson).
Technically, with the
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