On Wed, 2006-06-07 at 01:14 -0400, Dan Rabosky wrote:
Hello.
I am creating an R package that I'd like to submit to CRAN (OS Windows
XP). How do I distinguish among 'public' functions, e.g., those that are
intended to be called by users of the package and for which I am providing
10-fold cross-validation is easily done at R level: there is generic code
in MASS, the book knn was written to support.
knn and lda have options for leave-one-out cross-validation just because
there are compuiationally efficient algorithms for those cases.
On Tue, 6 Jun 2006, Liaw, Andy wrote:
On Tue, 6 Jun 2006, Jennifer Lai wrote:
Hi,
Has anyone had success in building R source with Visual Studio? I
followed the instructions in README.packages, but failed on the very
first step, where it's looking for R.dll. I looked through R source and
couldn't find the file. Can someone
This is an S4-using package but missing a dependence on 'methods'.
To run R CMD check the package has to load under minimal conditions, e.g.
R_DEFAULT_PACKAGES=NULL R
...
library(foo)
should work. 'methods' is quite expensive to load, and so is only used in
checking if explicitly requested.
It's confusing to have time values that are different but `match', so
first you want to reduce your times to hh:mm (e.g. with substr).
Then you can cbind() the data frames, and use tapply() to do the
averaging. E.g.
d1 - read.table(foo1)
d2 - read.table(foo2)
d - cbind(d1, d2)
d$time -
Dan Rabosky wrote:
Hello.
I am creating an R package that I'd like to submit to CRAN (OS Windows
XP). How do I distinguish among 'public' functions, e.g., those that are
intended to be called by users of the package and for which I am providing
documentation examples, and 'private'
1. If you have time to change internal functions naming, you can rename
internal functions by putting a leading '.'.
Even without namespace, I have noticed there is no check for corresponding
docs for such functions.
2. If you don't want to rename all internal functions, the best way is
writing
Thanks everybody - it's working
Rainer
Dimitris Rizopoulos wrote:
try something like:
lapply(f, summary)
sapply(f, function(x) AIC(logLik(x)))
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Spencer Graves a écrit :
I agree it would be great to sort the variables in a correlation
matrix to make it easier to read and see patterns. I don't know any
functions for doing that. If it were my problem, I might order the
variables by their first principal component. There may
Hi All,
I am using plot(x, type = 'l') for some plotting, but I would like rounded
edges
rather than jagged edges in the plot (purely for aestetic reasons).
How could I achieve that?
Cheers,
Federico
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College,
probably you want to use the `lend' argument of ?par(); I hope it
helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Dimitris Rizopoulos wrote:
probably you want to use the `lend' argument of ?par(); I hope it helps.
Does not seem to work in my case.
F
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 7594
Le 07.06.2006 11:20, [EMAIL PROTECTED] a écrit :
Spencer Graves a écrit :
I agree it would be great to sort the variables in a correlation
matrix to make it easier to read and see patterns. I don't know any
functions for doing that. If it were my problem, I might order the
On Wed, 7 Jun 2006, Federico Calboli wrote:
Hi All,
I am using plot(x, type = 'l') for some plotting, but I would like
rounded edges rather than jagged edges in the plot (purely for aestetic
reasons).
How could I achieve that?
It I understand you aright, that is done by par(lend) but
On 6/7/06, Romain Francois [EMAIL PROTECTED] wrote:
Le 07.06.2006 11:20, [EMAIL PROTECTED] a écrit :
Spencer Graves a écrit :
I agree it would be great to sort the variables in a correlation
matrix to make it easier to read and see patterns. I don't know any
functions for doing
Prof Brian Ripley wrote:
It I understand you aright, that is done by par(lend) but the default is
round. So maybe your graphics device (unstated) on your OS (unstated)
does not support this.
graphics device = X11 (xserver-xorg)
OS = Debian GNU/Linux, Kernel 2.4.27-2-686-smp
We need
Federico Calboli wrote:
Hi All,
I am using plot(x, type = 'l') for some plotting, but I would like rounded
edges
rather than jagged edges in the plot (purely for aestetic reasons).
How could I achieve that?
Perhaps you want something like:
x-rnorm(50)
plot(spline(1:50,x),type=l)
Jim
If I understood correctly in irregular time series (its) objects, values are
indexed by time stamps in POSIX format.
But if I try to select the value of my time series corresponding to specific
time stamp in the following way:
x - its object
i - as.POSIXct(2006-05-19 15:30:00)
x[i,] or x[i] or
Dear all R users,
I have a query on Edit function. Suppose I have a data frame named data.
I can use EDIT function to see the materials contained in data, by using the
command:
edit(data)
But when I close the window then again the materials contained in data is
displayed in
[Presuming you mean monotone; many matrices are already monotonous.]
General solutions to this problem are discussed in
@ARTICLE{Friendly:02:corrgram,
author = {M. Friendly},
title = {Corrgrams: Exploratory displays for correlation matrices},
journal = {The American Statistician},
See: ?itsSubset
On 6/7/06, Ivan Kalafatic [EMAIL PROTECTED] wrote:
If I understood correctly in irregular time series (its) objects, values are
indexed by time stamps in POSIX format.
But if I try to select the value of my time series corresponding to specific
time stamp in the following way:
On Wed, 7 Jun 2006, stat stat wrote:
Dear all R users,
I have a query on Edit function. Suppose I have a data frame named
data. I can use EDIT function to see the materials contained in data,
by using the command:
edit(data)
But when I close the window then again the materials
I am trying to learn how to use the graphics from the lattice package (
and am very new to R).
I am trying to replicate the example plot referenced below, by using the
lattice xyplot lpolygon to create panels. I get what appears to be the
correct shape of the filled region, but cannot get
Hi!
I am trying to install in my R environment the rhdf5 package and
library but it seems to have vanished from either the CRAN or
BioConductors sites.
Can you tell me where it would be possible to find it or any R
library (or function) able to read hdf files?
Sincerely,
Nicolas
I have three completely different(!) but workable solutions. Thanks much
for your help.
=Randy=
R. Zelick email: [EMAIL PROTECTED]
Department of Biology voice: 503-725-3086
Portland State University fax: 503-725-3888
mailing:
On Wed, 7 Jun 2006, Nicolas Degallier wrote:
I am trying to install in my R environment the rhdf5 package and
library but it seems to have vanished from either the CRAN or
BioConductors sites.
Can you tell me where it would be possible to find it or any R
library (or function) able to read
I am trying to learn how to use the graphics from the lattice package (
and am very new to R).
I am trying to replicate the example plot referenced below, by using the
lattice xyplot lpolygon to create panels. I get what appears to be the
correct shape of the filled region, but cannot get
fix(data)
will invoke edit(data) and store changes you make in data without
displaying anything.
stat stat schrieb:
Dear all R users,
I have a query on Edit function. Suppose I have a data frame named
data. I can use EDIT function to see the materials contained in data, by
using
Antonio, Fabio Di Narzo [EMAIL PROTECTED] writes:
1. If you have time to change internal functions naming, you can rename
internal functions by putting a leading '.'.
Even without namespace, I have noticed there is no check for corresponding
docs for such functions.
2. If you don't want to
If you want to change the data,_fix_ will be a good option.But if you
just want to browse the data ,then invisible(edit(data)) is better
one.
I remember this question showed up some time ago.
2006/6/7, Ulrich Keller [EMAIL PROTECTED]:
fix(data)
will invoke edit(data) and store changes you
I have generated some some survival times and censoring indicators.
Thus I have an ordered pair for each observation. How do I sample these
ordered paris? I only know how to sample from a vector? I would
appreciate any help I could get.
Thanks
Matt
try something like:
surv.data - data.frame(times = rexp(100, 1/10), events = rbinom(100,
1, 0.7))
surv.data[sample(nrow(surv.data), replace = TRUE), ]
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of
I couldn't help but respond to this one, it's not often I see my own name.
Using data from the survival library:
library(survival)
lung[1:10, c('time', 'status')]
Surv(lung$time, lung$status)[1:10]
--Matt
Matt Austin
Statistician
Amgen, Inc
800 9AMGEN9 x77431
805-447-7431
-Original
Hi Mike,
If you're not committed to using a panel function, another option is to
use the function lineplot.CI, available in the package sciplot at
http://mutualism.williams.edu/sciplot
E.g.
# Define and generate variables in long format
range - vector()
voice - vector()
string -
Hello,
I am learning how to use R, and I cannot figure out how to plot more
than one data set on a single plot. Can you help me out?
Cheers,
Mark
--
Mark Sessing
CIMMS Research Fellow Meteorologist
NWS Warning Decision Training Branch
3200 Marshall Ave Ste. 202
Norman, OK 73072
Phone:
The best rebuttal I've heard recently to arguments like that is Linux
(www.linux.org): It's distributed under the same general public license
(GNU) license as R.
A perspective that I don't recall having seen on this list is that
the cost of producing and distributing
Without more inormation about what you are specifically trying
to do, see
?line
?points
Sarah
On 6/7/06, Mark L Sessing [EMAIL PROTECTED] wrote:
Hello,
I am learning how to use R, and I cannot figure out how to plot more
than one data set on a single plot. Can you help me out?
Cheers,
I use a simple-minded, dirty wrapper on edit:
view - function(x) {
warnopt - options()$warn
options(warn=-1)
on.exit({sink(); options(warn=warnopt)})
edit(x)
invisible()
}
I say dirty, because sometimes the output is re-directed from stdout
somewhere else as an unintended side effect,
On Wed, 2006-06-07 at 10:30 -0500, Mark L Sessing wrote:
Hello,
I am learning how to use R, and I cannot figure out how to plot more
than one data set on a single plot. Can you help me out?
Cheers,
Mark
It depends upon the type of plot (scatter, lines, bar, etc.) and whether
or not you
Dear Rusers,
As we all know , there are many methods to do multiple comparison in the
parametric statistical analysis, But i can't find some in nonparametric
statistical analysis.
Could anybody give some suggestions?
[[alternative HTML version deleted]]
On 6/7/06, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
I am trying to learn how to use the graphics from the lattice package (
and am very new to R).
I am trying to replicate the example plot referenced below, by using the
lattice xyplot lpolygon to create panels. I get what appears to be
Perfect. Thank-you!
Deepayan Sarkar [EMAIL PROTECTED]
06/07/2006 11:19 AM
To
[EMAIL PROTECTED] [EMAIL PROTECTED]
cc
r-help@stat.math.ethz.ch
Subject
Re: [R] Fw: Help needed using lattice for area plots lpolygon, xyplot.
On 6/7/06, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
I am
On Thu, 2006-06-08 at 00:10 +0800, zhijie zhang wrote:
Dear Rusers,
As we all know , there are many methods to do multiple comparison in the
parametric statistical analysis, But i can't find some in nonparametric
statistical analysis.
Could anybody give some suggestions?
Have you looked at
Also Consider Bonferroni Hochberg Holm type procedures or .
Dunn OJ. Multiple contrasts using rank sum tests. Technometrics
1964;6:241#/52.
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
Dear R-list,
I have made a simple kernel density estimation by
x - c(2,1,3,2,3,0,4,5,10,11,12,11,10)
kde - density(x,n=100)
Now I would like to know the estimated probability that a
new observation falls into the interval 0x3.
How can I integrate over the corresponding interval?
In several
Not a direct answer to your question, but if you use a logspline density
estimate rather than a kernal density estimate then the logspline
package will help you and it has built in functions for dlogspline,
qlogspline, and plogspline that do the integrals for you.
If you want to stick with the
Spencer,
I agree that there exist biases within large organizations toward
commercial software packages, but I humbly disagree that this can be
reduced to geopolitical differences. I work for a US Government Agency
and while there is some truth to the feeling [they] refuse to believe
that
Pedro wrote:
I have made a simple kernel density estimation by
x - c(2,1,3,2,3,0,4,5,10,11,12,11,10)
kde - density(x,n=100)
Now I would like to know the estimated probability that a
new observation falls into the interval 0x3.
How can I integrate over the corresponding interval?
In
Not a direct answer to your question, but if you use a logspline density
estimate rather than a kernal density estimate then the logspline
package will help you and it has built in functions for dlogspline,
qlogspline, and plogspline that do the integrals for you.
If you want to stick with the
hello:
I have 3 data.frame objects.
First df object:
Of dim (149,31). Columns 2:31 are marked as T1..T14
and N1..N16.
Name T1T2N1 T3 N2 N3 N4 T4
mu1 1010910 9 9 8 10
mu2 1111911 9 9 9 11
...
muN 1212911 9
Nicolas Degallier wrote:
Hi!
I am trying to install in my R environment the rhdf5 package and
library but it seems to have vanished from either the CRAN or
BioConductors sites.
Can you tell me where it would be possible to find it or any R
library (or function) able to read hdf
[Pikounis, Bill [CNTUS]]
view - function(x) {
warnopt - options()$warn
options(warn=-1)
on.exit({sink(); options(warn=warnopt)})
edit(x)
invisible()
}
I'm surprised by the necessity of sink(). Presuming it is necessary
indeed, the above could be simplified a bit like this
Hello all,
Here is the code that I am using for finding differentially expressed genes.
#Normalization
library(affy)
library(Biobase)
library(limma)
library(gcrma)
pd-read.phenoData(file.txt,header=TRUE,row.names=1,as.is=TRUE,sep=\t)
Data -
I am not sure I understand what you want to do, but maybe some of this
will be helpful. I first generate some data that should resemble yours:
dat-expand.grid(Region=1:3, Species=1:4, Sex=c(M,F))
dat-do.call(rbind,lapply(1:10,function(x) dat))
dat$Bodysize-rnorm(nrow(dat),10,2)
Now what the
Hello much more experienced R-users,
I have got a txt - file which contains data formated like this:
MM DD HH data1 data2 ... data31
2002 12 01 01 0.002 0.003 ... 312.0
The single columns are divided by at least one space.
Is their an easy and fast way to make R understand that the
I was trying quantreg package,
lm1 - lm(y~x)
rq1 - rq(y~x)
plot(summary(rq1)) #then got a warning says singular value, etc. but this
line can be omited
plot(lm1) #crash here
It happened every time on my PC, Windows XP Pro Serv. Pack 1, Pentium(4)
3.00G.
[[alternative HTML version
I forgot to mention my R version is 2.3.1 and quantreg is the most updated
too.
On 6/7/06, Mu Tian [EMAIL PROTECTED] wrote:
I was trying quantreg package,
lm1 - lm(y~x)
rq1 - rq(y~x)
plot(summary(rq1)) #then got a warning says singular value, etc. but this
line can be omited
plot(lm1)
Since the crash occurs plotting the lm object it is unclear what
this has to do with quantreg, but maybe you could explain
1. what you mean by crash,
2. something about x,y,
This is best addressed to the maintainer of the package rather than to
R-help, provided, of
Without y and x we cannot reproduce this.
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
On Wed, 7 Jun 2006, Mu Tian wrote:
I forgot to mention my R version is 2.3.1 and quantreg is the most updated
too.
It has a version number, which the posting guide tells
I attached the data file here. I restarted the PC but it still happens. It
says a memory address could not be written. I am not sure it is a problem of
R or quantreg but I plot without problems before I load quantreg.
Thank you.
Tian
On 6/7/06, Prof Brian Ripley [EMAIL PROTECTED] wrote:
Dear list members,
In some of my functions, I attach the data internally to allow subset
commands or to specify a data frame. This works well except for cases
where there is a masking conflict (which returns a warning). I see
some alternative listed in ?attach, but I'm not sure which of them do
On Wed, 7 Jun 2006, roger koenker wrote:
Since the crash occurs plotting the lm object it is unclear what
this has to do with quantreg, but maybe you could explain
1. what you mean by crash,
2. something about x,y,
This is best addressed to the maintainer of the package
I suggest you investigate with().
On Wed, 7 Jun 2006, Manuel Morales wrote:
Dear list members,
In some of my functions, I attach the data internally to allow subset
commands or to specify a data frame. This works well except for cases
where there is a masking conflict (which returns a
hi.
i'm a statistics student and studying bootstrap in R.
i'm trying to draw bootstrap samples from a sample, using the following R
code:
*boot = numeric(200)*
* {for (i in 1:200)*
* boot [i] = (sample(data,replace=T))}*
i obtain 200 samples but all of them are the same.
i want to obtain
R-help doesn't foward attached data files like this, but Brian
kindly forwarded it to me.
You need to restrict X so that it is full rank, it now has
rank 19 and column dimension 29 (with intercept). See
for example svd(cbind(1,x)).
I'll add some better checking for this, but it will basically
2006/6/7, Recep Aykaya [EMAIL PROTECTED]:
hi.
i'm a statistics student and studying bootstrap in R.
i'm trying to draw bootstrap samples from a sample, using the following R
code:
*boot = numeric(200)*
* {for (i in 1:200)*
* boot [i] = (sample(data,replace=T))}*
i obtain 200
Try this which reads in the data as a data frame and appends a
chron variable datetime:
Lines - MM DD HH data1 data2
2002 12 01 01 0.002 0.003
DF - read.table(textConnection(Lines), header = TRUE)
library(chron)
DF$datetime - with(DF, chron(paste(MM, DD, , sep = /)) + HH/24)
DF
On
Hello,
I have a simple function in the form as follows:
f-function(x){sum(v^x)}
where v is a vector. I was trying to integrate f using the command
I-integrate(f,0,1)
However, this will not work and seems that the reason is to use
integrate, the f must be a function that with input and
Have you tried RSiteSearch(spatial ecology)? I just got 47 hits
from that. Some of them might be relevant to your question.
If that fails, you might consider providing this group with the math
behind the automata models you are considering. I might expect them to
be
Dear friends,
I have a dataset: response var--y, class var-group, and the third variable-x.
I want to test whether there is statistical significance bewteen
group for y with the controlled x. First, i want to use analysis of
covariance in SAS, but i found that y isn't noramal and can't become
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