before getting scolded for submitting a (non-)bug report:
when using the 'symbols' function for plotting boxplot data (i.e. using
'boxplots' symbols), I noted that the x/y-position of the symbols is
associated with the center of the box.
while this is obviously natural for a usual plotting symb
I think you want print or summary rather than anova. anova() is not very
useful for aov() models even without error strata. The point of the aov
classes is that they present the results of lm() fits in ways which are
more conventional for designed experiments, including giving conventional
AN
Andris Jankevics wrote:
> Hello useRs,
>
> I can't figure out how can I store a data frame of values of X and D from
> this loop:
>
> Z <- c(1:10)
>
> for (i in 1:(length(Z)-2))
> {D <- x[1:(2+i)];
> X <- paste("x",sep="",i)
> print (X)
> print (D)
> }
Assign
You could try nested ifelse statements,
something like (untested)
x <- seq(-1, 3, 0.1)
y <- ifelse( x <= 3,
ifelse( x <= 2,
ifelse( x <= 1,
ifelse( x <= 0, 0, x^2/2), 2 * x - (x^2/2) -1), 1) )
plot(x, y)
**
Thi
Fred J. wrote:
> Dear R users
>
> I have read somewhere which I don't remember that some variable names
> are not to be used for conflict avoidance. and those were (c, q, T, F,
> T)
> I ran this
> > conflicts(detail=TRUE)
> $.GlobalEnv
> [1] "ts"
>
> $"package:methods"
> [1] "body<-
Jacob van Wyk wrote:
> This might be a trivial question, but I would appreciate if anybody
> could suggest an elegant way of plotting a function such as the
> following (a simple distribution function):
> F(x) = 0 if x<=0
>=(x^2)/2 if 0=2x-((x^2)/2)-1 if 1=1 if x>2
> This i
This might be a trivial question, but I would appreciate if anybody
could suggest an elegant way of plotting a function such as the
following (a simple distribution function):
F(x) = 0 if x<=0
=(x^2)/2 if 02
This is just an example. In this case it is a continuous function. But
how to do it
Hello useRs,
I can't figure out how can I store a data frame of values of X and D from
this loop:
Z <- c(1:10)
for (i in 1:(length(Z)-2))
{D <- x[1:(2+i)];
X <- paste("x",sep="",i)
print (X)
print (D)
}
Thank You,
Andris Jankevics
_
Hi Uwe,
thanks for the reply! I used postscript() instead of dev.copy2eps(), but the
problem remained; furthermore, its the same on the screen and in a physical
print.
After some more testing, I figured out that I can produce the desired output
if I do not use the pre-defined line type "dotte
Probabilities can't be greater than 1 but densities can.
On 3/29/06, Taka Matzmoto <[EMAIL PROTECTED]> wrote:
> Hi R users
> I have a question for yaxis for plot(density(...)).
>
> plot(density(rnorm(100,.25,0.0701361)),xlim=c(-.5,1),col="red",xlab="",main="")
>
> I expected that yaxis is a pr
Dear list,
Can someone please help me here? Is it not possible to use the R library for
optimization and other routines calling from C?
Thank you!!
AarEm Trotter
--- Globe Trotter <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I have read R's Writing Extensions manual and am still confused about how to
I have found a similar problem when constructing formulae and passing
them to glmmPQL. My solution was to use do.call(glmmPQL,...). See ?do.call.
HTH,
Simon.
pencer Graves wrote:
> Please try again after upgrading to the versions of R and MASS.
>
> If you still have a problem, P
Hi R users
I have a question for yaxis for plot(density(...)).
plot(density(rnorm(100,.25,0.0701361)),xlim=c(-.5,1),col="red",xlab="",main="")
I expected that yaxis is a probabilty (from 0 to 1) but it wasn't
I got 1 to 5 or 6 on yaxis.
How do I interpret yaxis values ?
Thanks
TM
___
Have you read Pinheiro and Bates (2000) Mixed-Effects Models in S and
S-Plus (Springer)? The figures and tables in this book should give you
some ideas that you can adapt to summarizing the results of fits to
nonnormal data.
If you've tried this and still have questions for
Please try again after upgrading to the versions of R and MASS.
If you still have a problem, PLEASE do read the posting guide!
"www.R-project.org/posting-guide.html" before you submit another post.
Most of the people who donate their time to answer questions on this
listserv
Try this:
lapply(names(mylist), function(nm) c(nm, mylist[[nm]]))
On 3/29/06, Thomas Girke <[EMAIL PROTECTED]> wrote:
> I have a question regarding accessing the names of list
> components when applying a function with lapply.
>
> Here is an example that demonstrates what I'd like to do.
>
> I ha
I have a question regarding accessing the names of list
components when applying a function with lapply.
Here is an example that demonstrates what I'd like to do.
I have a list like this one:
mylist <- list(a=letters[1:10], b=letters[10:1], c=letters[1:3])
Now I would like to ap
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
The current randomForest package stores the entire proximity matrix (3 x
3 in your case), which is needed for imputation. Breiman and Cutler's
Fortran code stores the largest nrnn element of each row. If you really
want to do it that way, use the Fortran version.
Andy
From: Zhu Ailing
>
While we wait for others to provide the best way, here's
one way (if I understand your question correctly):
numrows <- 10
x <- rnorm(25 * numrows)
dat <- as.data.frame(matrix(x, nc = 25))
newdat <- as.data.frame(matrix(0, nr = numrows, nc = 14))
for(j in 1:14) newdat[, j] <- rowMeans(dat[, j:(j +
I realized that the script I included in my original post (see below)
was written for an older version of rmetasim and will not work with the
current version. The only change that need be made to get my script to
run with the latest release of rmetasim is to change the command
'simulate.landsc
In addition to Brian's comment, Gordon's book, already in 2nd edition, is
all about clustering, but the title is simply `Classification'.
Andy
From: Sean Davis
>
> We have to be careful here. Classification (which is the
> terminology that the original poster used) is NOT the same as
> cluste
Hi all --
So I have a very simple dataset, which consists of 60 subjects,
who watched one of three videos, drank one of two drinks, and
completed a task. The response variable is the time to complete the
task. The ANOVA command is simple enough: anova(aov(time ~ drink *
video, data = df));
Hello,
I'm trying to find out if something has been written in R regarding data
assimilation and inverse modeling.
These searches do not return anything that look like Kalman filter
variations (EK, SEEK, ROEK, etc.)
help.search("assimilation")
help.search("inverse model")
Regards,
*
Correct: I'm not an attorney, but I've read the GPL. It clearly
says that if you have software that has functionality independent of GPL
code, the GPL applies to the code you use to connect to GPL code not to
your original code. Thus, Insightful would have to make publicly
availabl
I have a dataframe of 25 columns and 100,000 rows
called testdf.
I wish to build a new dataframe, with 14 columns and
100,000 rows.
I wish the new dataframe to have the trailing 12
column mean. That is, I want column 1 of the new
dataframe to have soemthing like:
( mean(testdf[,1:12],na.rm
XLSolutions Corporation (www.xlsolutions-corp.com) is proud to
announce 2-day "R/S-plus Fundamentals and Programming
Techniques" at 2 locations this April
www.xlsolutions-corp.com/Rfund.htm
San Francisco - April 27th-28th, 2006
New York City ---
David Smith wrote:
> The GPL code is available as separately-downloaded packages for S-PLUS, as
> has been done for many years. My own Oswald library for S-PLUS was published
> under the GPL in 1997, for example, and many other authors produce
> open-source libraries for S-PLUS under a variety of l
The GPL code is available as separately-downloaded packages for S-PLUS, as
has been done for many years. My own Oswald library for S-PLUS was published
under the GPL in 1997, for example, and many other authors produce
open-source libraries for S-PLUS under a variety of licenses. The only
differen
Dear R users
I have read somewhere which I don't remember that some variable names
are not to be used for conflict avoidance. and those were (c, q, T, F,
T)
I ran this
> conflicts(detail=TRUE)
$.GlobalEnv
[1] "ts"
$"package:methods"
[1] "body<-"
$"package:stats"
[1] "ts"
$"pac
That is interesting to find out since on RMySQL module site
(http://stat.bell-labs.com/RS-DBI/download/) it says the following for
the latest version: "RMySQL 0.5-7 built with R 2.2.1 and MySQL 5.0.18"
which is now obviously not entirely true, seeing as how that is what I
am using. :)
It there any
This is an excellent initiative! But how can you integrate GPL code in a
software that is not GPL? As far as I understand it, GPL is a
contaminant license, imposing to the whole software to be GPL too (or
providing at least similar freedom). I have no doubt that you solved
this problem. I am ju
> From: [EMAIL PROTECTED]
>
> I have plotted a map of the Barents Sea and surrounding coastline using:
>
> map('worldHires',ylim=c(50,85),xlim=c(5,65),fill=T,resolution=0)
> map.axes()
> map.scale(x=30,metric=T)
>
> Next, I imported a shapefile with depth contours for the sea:
>
> contours<-rea
[Sorry about the duplicate posting; this one comes from the correct address.
Please respond to me with any questions about this -- David.]
Dear R-help readers,
As Insightful announced at the DSC2005 meeting in Seattle, the next
release of S-PLUS will introduce a new package system. Our g
Here are two ways:
# method 1. nest an extra alwaysEven
alwaysEven <- function(x) {
alwaysEven <- function(x) {
handleOdd <- function(x) {
alwaysEven(x-1)# use Recall-like here
}
return(if (x %% 2) handleOdd(x) else x)
}
alwaysEven(x)
}
any2even <- alwaysEven
rm(alwaysEven
From: [EMAIL PROTECTED]
Reply-to: [EMAIL PROTECTED]
Subject: S-PLUS 8 Beta Program
Time to go out: As soon as possible
Dear R-help readers,
As Insightful announced at the DSC2005 meeting in Seattle, the next
release of S-PLUS will introduce a new package system. Our goal is to pr
What's the best way to simulate Recall for parent function?
Consider this one-time recursive code:
alwaysEven <- function(x) {
handleOdd <- function(x) {
alwaysEven(x-1)# use Recall-like here
}
return(if (x %% 2) handleOdd(x) else x)
}
any2even <- alwaysEven
rm(alwaysEven)
For general maxiimum likelihood estimation, have you considered the
function "mle" in library(stats4)? I've learned some things (a) reading
the documentation for "mle" and for other topics listed under "See Also"
and (b) working the "Examples" in the documentation.
Regardin
I'm trying to use a contributed package (rmetasim) to generate simulated
genetic datasets. My scripts work fine when I run them on a Sun
workstation running Solaris 7 and when I run them on a ~4 year old
laptop PC that I have. However, when I run them on my new laptop (Dell
Latitude D410 purc
1. Have you read Pinheiro and Bates (2000) Mixed-Effects Models in S
and S-Plus (Springer)? If no, I believe your study of that book will be
well rewarded; mine has.
2. If you've looked at Pinheiro and Bates and still have questions
about this, PLEASE do read the posting
Paul:
I may have found the issue (which is similar to your conclusion). I
checked using egsingle in the mlmRev package as these individuals are
strictly nested in this case:
library(mlmRev)
library(nlme)
fm1 <- lme(math ~ year, random=~1|schoolid/childid, egsingle)
fm2 <- lmer(math ~ year +(1|s
On Thu, 30 Mar 2006, Wuming Gong wrote:
> Dear list,
>
> Given a vector of logical values, say
>
> >a <- c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE)
>
> Are there any R functions that can tell whether there are two or more
> "TRUE" in a row in this vector?
?rle (a very useful func
Try this:
with(rle(a), any(lengths[values]>1))
On 3/29/06, Wuming Gong <[EMAIL PROTECTED]> wrote:
> Dear list,
>
> Given a vector of logical values, say
>
> >a <- c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE)
>
> Are there any R functions that can tell whether there are two or more
>
Wuming,
which(a) will identify the TRUE values and sum(a) will tell you how many
TRUE values there are.
David
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Wuming Gong
Sent: 29 March 2006 18:21
To: r-help@stat.math.ethz.ch
Subject: [R] Sub-vector
*
Dear list,
Given a vector of logical values, say
>a <- c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE)
Are there any R functions that can tell whether there are two or more
"TRUE" in a row in this vector?
Thanks,
Wuming
__
R-help@stat.math.
Prof Brian Ripley wrote:
>
[...]
> And only the designers can say
>
> 'but atan2 wasn't originally designed for complex arguments.'
>
> but the code suggests otherwise.
I was not referring to the _coding_ of the function... I was
referring to the _design_. The design of the "atan2" function
Taking that matrix, stripping out the quoted row and column i.d.s and
entering it into MATLAB R14 (7.01) as M, I get from the eig(M) operation:
E = eig(M)
E =
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0
in regards to the dynamic resizing, one would think that
commands like
plot.default {package:graphics} does it, as I am exploring other
commands from graphics it seams like tkrplot may not be needed,
I am
not sure as I just started with graphics in R, maybe a bett
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 0.5138894
9 82645542 11 0.5138894
10 826455431
> "Simon" == Simon Wood <[EMAIL PROTECTED]>
> on Wed, 29 Mar 2006 16:14:14 +0100 (BST) writes:
>> It looks like there might be a bug in the symmetry detection routine of
>> eigen. When I do
>>
>> eigen(M, symmetric=FALSE)
>>
>> it works fine.
Simon> - b
Hi
Does anyone who uses R know if there are any new R packages available -
I imagine under Bioconductor - that process SNP microarray data and
determine copy number and Loss of heterozygosity?
Thanks
Natalie Twine
--
__
R-help@stat.math.ethz.ch mail
Dear all,
trying to get some insights in a data set resulting from a microarray
experiment, I used the Limma package and its graphical function plotMA
and plotMA3by2. I am wondering if there might be a problem with the
zero.weights option.
Here are the command lines I have tried, and their resu
Dear R users,
I have some trouble with the aggregate function. Here are my data
> daf
S_id AF_Class count... R_gc_percent S_length
5 82644971 30 0.4835678
6 826449737 0.4835678
8 82645541 31 0.5138894
9 8264
> It looks like there might be a bug in the symmetry detection routine of
> eigen. When I do
>
> eigen(M, symmetric=FALSE)
>
> it works fine.
- but the matrix is symmetric, which seems to be correctly detected
(since eigen() hangs whether symmetric=TRUE is supplied or not).
> Eigenvalues (after
>On Wed, 29 Mar 2006, Sean Davis wrote:
>
>> We have to be careful here. Classification (which is the terminology that
>> the original poster used) is NOT the same as clustering, although the two
>> are often confused.
>
>Well, in one of its two English senses it is the same. From a recent talk
Hello,
Is it possible to derive Pan's QIC (2001 Biometrics 57:120) from
either a fitted gee() object in the gee package or from a geese() fit
in the geepack package? If so, would anyone be kind enough to provide
me with code to do so? I realize that QIC is part of the output from
yags() but I woul
Prof Brian Ripley <[EMAIL PROTECTED]> writes:
> [As an aside, I wonder whether compress=TRUE should not be the default for
> binary save/save.image. It adds little time and may save a lot of disc
> space.]
Here's one user who thinks that is a great idea. I often have to
remind developers who c
Jose: You might want to check out the multiresponse permutation procedure
(MRPP) family of statistics as they can perform permutation tests of
common distributions among groups of multivariate response data or perform
tests of equality of multivariate means among groups (i.e., a permutation
ve
running
pictex()
plot(1:11,(-5:5)^2, type='b', main="Simple_Example_Plot")
dev.off()
(as in the pictex example, but with underscores instead of spaces).
the TeX file contains
\put {Simple_Example_Plot} [lB] <0.00pt,0.00pt> at 124.00 275.33
the underscores have a special meaning in
> "Hugh" == Hugh Chipman <[EMAIL PROTECTED]>
> on Tue, 28 Mar 2006 12:17:44 -0400 writes:
Hugh> I'd like to announce the availability of a new library for hybrid
Hugh> hierarchical clustering, "hybridHclust". The library has been
uploaded
Hugh> to CRAN and is now availabl
Hello,
I'm working on 30 natural populations of Aster amellus L. a threatened
plant species. My aim is to see if the population size influence on several
fitness trait. I build a multi-factorial ANOVA. The independents variables
are altitude, humidity, soil component, maintenance and populat
On Wed, 29 Mar 2006, Thibaut Jombart wrote:
> Hello list,
>
> does anyone know if Monmonier algorithm is available in R? I've checked
> several spatial libraries, but I didn't find anything related to it.
> However, there is a huge documentation and I may have missed it.
>
> Before coding it,
Sven Schaltenbrand wrote:
> dear list,
>
> i have a problem using the adaboost function from the package boost.
> running the example of leukemia works out very well, but so it does not on
> my own data.
>
> i always get the following 22 warnings:
>
> 1: cannot compute exact p-value with tie
Try this:
options(warn = 2)
Now rerun it and it will fail with an error at the point of the warning
and you can issue a:
traceback()
to find the exact point at which it failed so you can investigate further.
On 3/29/06, Sven Schaltenbrand <[EMAIL PROTECTED]> wrote:
> dear list,
>
> i have a pr
dear list,
i have a problem using the adaboost function from the package boost.
running the example of leukemia works out very well, but so it does not on
my own data.
i always get the following 22 warnings:
1: cannot compute exact p-value with ties in: wilcox.test.default(x[which(y
== 0)], x
On 3/29/2006 2:49 AM, Prof Brian Ripley wrote:
> On Tue, 28 Mar 2006, Duncan Murdoch wrote:
>
>> On 3/28/2006 11:00 AM, Prof Brian Ripley wrote:
>>> Rgui now supports \r in the same way as rterm.
>> I notice that there's a slight change to the colour scheme: now the prompt
>> ">" is in foregroun
Hello list,
does anyone know if Monmonier algorithm is available in R? I've checked
several spatial libraries, but I didn't find anything related to it.
However, there is a huge documentation and I may have missed it.
Before coding it, I'd like to be sure it doesn't already exist.
Cheers,
Thi
On Wed, 29 Mar 2006, Sean Davis wrote:
We have to be careful here. Classification (which is the terminology that
the original poster used) is NOT the same as clustering, although the two
are often confused.
Well, in one of its two English senses it is the same. From a recent talk
of mine (G
Dear All,
This is probably a very basic question but:
I have plotted a map of the Barents Sea and surrounding coastline using:
map('worldHires',ylim=c(50,85),xlim=c(5,65),fill=T,resolution=0)
map.axes()
map.scale(x=30,metric=T)
Next, I imported a shapefile with depth contours for the sea:
cont
stat stat wrote:
> hi all,
>
> Somewhere I got a phrase - the function returns a S3 object of class
> "hclust" - can anyone tell me what is "S3 objects"?
Simply an object with a "class" attribute.
See chapter "Object-oriented programming" in the R Language Definition
manual.
Uwe Ligges
We have to be careful here. Classification (which is the terminology that
the original poster used) is NOT the same as clustering, although the two
are often confused. If the original poster wants to do clustering and
examine the results for the presence of three clusters, that is fine and
there
Hi,
My code is:
andeti1 <- read.csv(file='andarai1.csv',head=T,sep=";")
andeti1lm <- lm(formula = valor ~ area+salao+quarto3+play+vaga+frente, data =
andeti1)
step(andeti1lm,direction=c("both"),steps=1000,k=2)
How can I specify "scope" parameter in "step" command?
Thanks.
--
Sávio Martins
On Wed, 29 Mar 2006, Henrik Bengtsson wrote:
> Hi. R can do all of this for you. See ?save.image and especially the
> 'compress' argument.
It is nice to know that we anticipated your needs. It is actually even
easier. If you do (using the Rtools or other sources, or on a Unix-alike)
gzip file
I apologize for my lack of knowledge.
Thank you very much for the suggestions.
These are exactly what I was looking for.
> ?zip.file.extract
Help for 'zip.file.extract' is shown in the browser
Maybe I must re-run and re-save again to compress my R workspace.
> ?save.image
Help for 'save.image'
On Wed, 29 Mar 2006, Muhammad Subianto wrote:
> Dear R users,
> My situation:
> (1) I have limited workspace for my work harddisk (about 10 GiB).
> (2) I have a lot of data files in R workspace (*.RData) which most of
> them > 200 MiB. For some reason I zip some of them, for instance
> "filename.R
On Wed, Mar 29, 2006 at 11:44:03AM +0200, Muhammad Subianto wrote:
> How can I open/load "filename.zip"? Is there any function to open R
> workspace which it store in zip file?
I think you have two options:
1) use zip.file.extract() to unzip the file before loading
2) save your data with save.im
Hi. R can do all of this for you. See ?save.image and especially the
'compress' argument.
/Henrik
On 3/29/06, Muhammad Subianto <[EMAIL PROTECTED]> wrote:
> Dear R users,
> My situation:
> (1) I have limited workspace for my work harddisk (about 10 GiB).
> (2) I have a lot of data files in R work
Prof Brian Ripley <[EMAIL PROTECTED]> writes:
> On Fri, 24 Mar 2006, Dieter Menne wrote:
>
> > Leonardo D Bacigalupe sheffield.ac.uk> writes:
> >
> >> I'm trying to plot e.g. fitted vs residuals for each level of the
> >> random effects, and i'm getting the same error.
> >> I guess this might be
HI,
I have data set of 3 record with 162 features. when I try to fill out the
missing values using rfImpute(), I got kicked out becz:
tra.imputed <- rfImpute(tra.na[,-163],tra.na[,163],iter=5,ntree=10)
Error in matrix(0, n, n) : cannot allocate vector of length 9
I wonder how to
Dear R users,
My situation:
(1) I have limited workspace for my work harddisk (about 10 GiB).
(2) I have a lot of data files in R workspace (*.RData) which most of
them > 200 MiB. For some reason I zip some of them, for instance
"filename.RData (250 MiB)" to "filename.zip (3MiB)". In this work I
ha
Prof Brian Ripley wrote:
> On Tue, 28 Mar 2006, Duncan Murdoch wrote:
>
>
>>On 3/28/2006 11:00 AM, Prof Brian Ripley wrote:
>>
>>>Rgui now supports \r in the same way as rterm.
>>
>>I notice that there's a slight change to the colour scheme: now the prompt
>>">" is in foreground colour, rather
On Fri, 24 Mar 2006, Dieter Menne wrote:
> Leonardo D Bacigalupe sheffield.ac.uk> writes:
>
>> I'm trying to plot e.g. fitted vs residuals for each level of the
>> random effects, and i'm getting the same error.
>> I guess this might be a problem of the graphic capabilities of R.
>>
>> Is there a
On 3/28/06, Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
>
> You need to learn to supply adequate information. The current
> version of sn *does* have such an argument, and I was careful to check.
> So it seems that you are using an unstated obselete version of sn.
> Do ugrade as the posting guide
The hitcounters show a lot of interest. I have now updated
http://www.cuddyvalley.org/psychoR/
by putting index files in every (well, almost every) subdirectory.
This makes
browsing the subdirectories much easier, and it also protects
some stuff that nobody needs to see anyway.
In addition, th
You cannot observe a time series in continuous time. So either you have
regularly spaced observations (and see ?spectrum), or irregular ones
(and there may be something in one of the packages for irregular time
series, but there is no support in R itself).
On Tue, 28 Mar 2006, Martin Albers wr
On Wed, 29 Mar 2006, Robin Hankin wrote:
> Hi guys
>
> perhaps my original message wasn't so clear.
>
> My point was that the documentation is inconsistent with the
> function.
I think it is _your reading_ of the documentation that is inconsistent.
An equally plausible reading is that both x and
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