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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Tamas
first of all, Thank You for a really well-posed, interesting problem.
Answer follows.
do.index - function(a,f){
jj - function(i){seq_len(dim(a)[i])}
index - as.matrix(expand.grid(sapply(1:length(dim
(a)),jj,simplify=FALSE)))
a[index] - apply(index,1,f)
return(a)
}
f -
This appears to be about Windows, unstated!
On Thu, 16 Nov 2006, Charles Annis, P.E. wrote:
Greetings:
I've installed Rtools, MikTeX, perl, minGW, and HTML Help Workshop, and have
succeeded in making, checking (using R CMD check mypkg) then building the
simple example
The details and address for package 'dna' *are* in the R FAQ section 5.1.
For some reason he calls 'MS executables' the non-executable binary
packages for Windows users of R.
On Thu, 16 Nov 2006, Marwan Khawaja wrote:
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL
On Thu, 16 Nov 2006, Hong Ooi wrote:
Not sure if this counts as a bug or not, but I just noticed in R 2.4.0
that : and interaction are not quite equivalent. For example:
Well, that depends on what you mean by 'equivalent', a word that is not
used in the help you quote but is used in help(:).
Dear friends,
I am beginning to use R software in my academic research and I'm having some
problems regarding the use of PCA.
I have a table with 24445 rows and 9 columns, and I used the function
prcomp() to do the analysis.
Working with an example…:
x-read.table(test.txt, header=T)
Dear all,
Many thanks for your help and advice. Now I understand the situation
much better.
Concerning the multiplication workaround, I would - as already indicated
in my first email - prefer to use core() rather than the deviation to a
zoo object.
(im - its(mat))
core(im) - core(im) * scale
Dear all,
I have three concerns:
1)
I am running models with the lme4 package. I cannot find a way to pull
out a vector of the fitted values and the residuals. Does anybody know
how to do it?
2)
How can I nest a random effect variable into a two-level fixed effect
variable?
3)
Suppose I have the
Jeff,
Does anyone know what happened to the dna library or the dotmatrix
function? For the life of me, I can't find it anywhere with the
exception of this reference:
http://rss.acs.unt.edu/Rdoc/library/dna/html/dotmatrix.html
Thanks!
Jeff.
you may also have a look at the
Gabor
Tamas
yet again I find myself trumped by Gabor because I forget that
TRUE is a perfectly acceptable argument to [.
Heh.
I'll stick do.index2() in the magic package.
best wishes
rksh
On 16 Nov 2006, at 11:27, Gabor Grothendieck wrote:
Here is minor simplification:
do.index2 -
Yes, I am using WindowsXP on a 3 year old DELL machine with 2 gig. I
apologize to Professor Ripley and our other helpers for my omission.
I also tried R CMD build --binary mypkg, as was suggested by Benilton
Carvalho, and with a similar error message. I don't think I want binaries
in any event.
Thank you, Benilton.
I started over from scratch, and this time, using R CMD build --binary mypkg
I was successful. I am not sure where I made my original mistake, but I
think it was in overlooking one of the instruction/comment lines in
mypkg-package.Rd
Thank you again for your help.
Dear All
For my calculations, I am needing to use more floating-point precision
than the default one of R. Is that possible? And, if yes, how?
Thanks in advance,
Paul
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Hi R-Experts,
I'm currently using R 2.4.0 in Windows XP. I'm trying to download data
from Bloomberg using the package RBloomberg, but it fails to install
the three needed packages zoo, chron and 'Rbloomberg. Moreover I
am not able to find RBloomberg package as windows binary in CRAN
site as
The Brown-Forsyth homogeneity of variance test, including
a graph, is included in the HH package that you can download
from CRAN
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PLEASE do read the posting guide
On Thu, 16 Nov 2006, Paul Smith wrote:
For my calculations, I am needing to use more floating-point precision
than the default one of R. Is that possible? And, if yes, how?
See package gmp (but that will be slow and cumbersome for all but simple
calculations).
The real issue is that R
Dear colleagues,
Im a new R-help user. Ive read the advertisements about
the good manners and I hope to propose a good question.
Im using R to build an epidemiological SEIR model based
on ODEs. The odesolve package is very useful to solve
deterministic ODE systems but Id like to perform a
Never used it but if you look down the check list on Windows:
http://cran.r-project.org/bin/windows/contrib/checkSummaryWin.html
for RBloomberg we see it has an error in attempting to access one of its
dependent packages. See if building it yourself or going back to R 2.3.1
helps.
On
Hi,
I have a list with the names of tables, e.g.
l - c(t1,t2,t3)
and I want to change the colnames of each of the
tables in a for loop like this:
for (x in l) {
colnames(eval(x)) - lower.case(colnames(eval(x)))
}
This does not work but could someone give me some help
to get on the right
Hello Carlos,
# let me save you a couple steps here
x-read.table(test.txt, header=T, row.names=1)
pca-prcomp(x, scale=T)
names(pca)
## here begin my problems… know what…??##
Try this for a graphical view of your data:
biplot(pca)
You might also want to work through the examples given
in
On Thu, Nov 16, 2006 at 02:55:07PM +0100, Massimo Fenati wrote:
Dear colleagues,
Im a new R-help user. Ive read the advertisements about
the good manners and I hope to propose a good question.
Im using R to build an epidemiological SEIR model based
on ODEs. The odesolve package is very
The RDCOMClient is available from a different repository
http://www.omegahat.org/R
You can include it in the list of repositories being
searched on Windows using the Packages menu in the R GUI
and then select the entry Select repositories
and include Omegahat in the selection.
Or just install
how about:
for (x in l) colnames(get(x)) - lower.case(colnames(get(x)))
b
On Nov 16, 2006, at 9:01 AM, Werner Wernersen wrote:
Hi,
I have a list with the names of tables, e.g.
l - c(t1,t2,t3)
and I want to change the colnames of each of the
tables in a for loop like this:
for (x in l) {
Yes...And the dependent package is RDCOMClient. I was using R
2.2.0...The downloading process was smooth...But not in R 2.4.0...why is
this so? Could you reply me ASAP?
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Gabor
Grothendieck
Sent:
Dear Max,
Check out the BUGS software available (free) at
http://www.mrc-bsu.cam.ac.uk/bugs/. It is easy to use and there are
several packages in R which comport with the varying BUGS programs
(R2WinBUGS, bRugs, rbugs, etc.).
Best wishes,
Amy Paternostro
Hello Experts,
This is error I get in downloading RDCOMClient...
/**/
install.packages(RDCOMClient,
+ repos = http://www.omegahat.org/R;)
Warning: unable to access index for repository
http://www.omegahat.org/R/bin/windows/contrib/2.4
Warning in
Shubha Vishwanath Karanth wrote:
Hello Experts,
This is error I get in downloading RDCOMClient...
/**/
install.packages(RDCOMClient,
+ repos = http://www.omegahat.org/R;)
Warning: unable to access index for repository
Thanks for your reply...
Then...Is it not good to download bloomberg data from R? I also saw that
the RBloomberg package has some error in the site
http://cran.r-project.org/bin/windows/contrib/checkSummaryWin.html;
specified by you. Also, while downloading intraday data, even after
specifying
Hi all,
I ran a discriminant analysis with some data and want to get a general idea
of prediction error rate. Some have suggested using X-fold cross validation
procedure. Anyone know if there is a function for this in R?
Thanks,
Wade
[[alternative HTML version deleted]]
That's almost perfect! Only the operation
colnames(get(x)) -
seems not to be defined.
Now I can't figure out how to assign the colnames of
the object in the original environment.
Thanks, Benilton!
--- Benilton Carvalho [EMAIL PROTECTED] schrieb:
how about:
for (x in l) colnames(get(x))
Patrick Drechsler patrick at pdrechsler.de writes:
Knut M. Wittkowski wrote:
Apologies if this is the wrong list, but could somebody put the
information on how to create the graphs on
http://www.r-project.org/screenshots/screenshots.html (or a link to
these instructions) next to the
Yes...just now I tried it in my Bloomberg machine and yupp it is
working...
Thank you so much on this... But this works on any R version?
Also, some times while downloading the data, with the code, I get
warning message, NA's introduced due to Coersion...then I will not see
the data
Dear Michael,
If I follow what you want to do, which is not altogether certain, what
you're describing as the design matrix is intended to constitute the
left-hand side of the model. That is, your d1,1, ..., d1,12 are the 12
response variables. If so, I'm not sure why you think that my original
Thanks for your fast advises.
A simple examples of SEIR model is shown below:
#expample of very simple SEIR model#
library(odesolve)
times-seq(0,1200,1)
parms-c(
b=0.35, #BETA OR COEFFICIENT OF TRANSMISSION
pl=1/7, #LATENCY
g=1/21, #RECOVERY
try the following (untested):
tb1 - tb2 - tb3 - matrix(1:100, 10, 10, dim = list(NULL,
LETTERS[1:10]))
lis - list(tb1, tb2, tb3)
for(i in seq(lis)){
tb - get(lis[[i]])
colnames(tb) - tolower(colnames(tb))
assign(lis[[i]], tb)
}
I hope it helps.
Best,
Dimitris
Dimitris
Jue:
In R, wilcox.test does not actually do the Wilcoxon, but the Mann Whitney test.
While the tests are equivalent, the former is based on the rank sum, while the
latter is based on the sum of u-scores. Thus the need to convert the rank sum
into the sum of u-scores.
In S, in contrast,
I was trying to create a multi-color silhouette plot (each cluster a different
color) from clusters created by trimkmeans. This works straighforwardly on an
object created from pam however my colors are interwoven when I try the same
approach on clusters from trimkmeans. I also tried sorting
Hello!
I have some data stored into 2 separate csv file. 1 file (called A.csv) (12
results named Group1, Group2, Group3, etc...) odds ratios, 2 file (called
B.csv) 12 corresponded errors.
How to import that data into R and make forest plot like I saw inside help file
Rmeta and meta with
I am having a problem with a gantt chart since
moving to R2.4.0. from 2.3.1
I made some adaptations to the code from
http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=74
and successful produced a simple gantt chart. However
when I upgraded to 2.4.0 it no longer works as
desired.
Dear Joe,
I'd try to think it over if you sent me a reproducible example, i.e.,
example data, and code showing what you did with the pam output (how you'd like
to
have it) and with the trimkmeans output (which should be improved).
Best,
Christian
On Thu, 16 Nov 2006, Joseph Retzer wrote:
I
Robin == Robin Hankin [EMAIL PROTECTED]
on Thu, 16 Nov 2006 11:54:38 + writes:
Robin Gabor
Robin Tamas
Robin yet again I find myself trumped by Gabor because I forget that
Robin TRUE is a perfectly acceptable argument to [.
Robin Heh.
Robin I'll stick
Hello,
I am interested in using the capscale function of vegan package of R. I
already have a dissimilarity matrix and I am intended to use it as
'distance' argument. But then, I don't know what kind of data must be in
'comm' argument. I don't understand what type of data must be referred
as
Thanks Phil and Dimitris!
This works perfectly!
At this stage I am not concerned about efficiency
although I am curious if there is a way to do without
copying, for instance with pointers like in C.
Thanks again,
Werner
--- Dimitris Rizopoulos
[EMAIL PROTECTED] schrieb:
try the following
how hard is it to write one though?
On 11/16/06, Wade Wall [EMAIL PROTECTED] wrote:
Hi all,
I ran a discriminant analysis with some data and want to get a general idea
of prediction error rate. Some have suggested using X-fold cross validation
procedure. Anyone know if there is a function
Hi, Wade:
Some functions in R have n-fold cv themselves. For example, if you are
looking for a linear discriminant analysis (lda {MASS}), it comes with
a leave-one-out cv in which n equals the size of training sample,
and it gives you pretty good estimation of error rate. But be advised,
this
One option is the Bioconductor package MLInterfaces that provides a unified
interface for several machine learning alrogirithms and methods for
cross-validation etc. See the algorithms web site for details.
-Christos
Christos Hatzis, Ph.D.
Nuvera Biosciences, Inc.
400 West Cummings Park
Suite
Apologies for the typos there.
I meant to say see the Bioconductor web site for details.
-Christos
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Christos Hatzis
Sent: Thursday, November 16, 2006 11:53 AM
To: 'Wensui Liu'; 'Wade Wall'
Cc:
Dear Massimo
This site have some code that may help you to get started.
http://www.statistik.lmu.de/~hoehle/software/
Also if you want to take an agent-based approach, you may want to take a
look at the simecol package
Regards,
Francisco
Massimo Fenati wrote:
Thanks for your fast
I had some code that used to work in an old version of multcomp:
herbcover -
read.delim(http://anthony.darrouzet-nardi.net/downloads/herbcover.txt;)
herbcover$date - as.POSIXct(strptime(herbcover$date, %Y-%m-%d))
herbcover$block - factor(herbcover$block)
herbcover$treatment -
Hi Alicia,
On 11/16/06, Alicia Amadoz [EMAIL PROTECTED] wrote:
'comm' argument. I don't understand what type of data must be referred
as 'species scores' and 'community data frame' since my data refer to
nucleic distances between different sequences.
comm would be the original data from
Sorry, one additional note:
You don't need to specify comm to use capscale. Ignore what I said about
modifying the function.
Sarah
--
Sarah Goslee
http://www.functionaldiversity.org
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Dear helpeRs,
anyone knows how to obtain a stacked area chart in R?
I mean one of the graph that is used for representing compositional
data along time.
Thanks in advance,
domenico
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R-help@stat.math.ethz.ch mailing list
Hi,
Overwriting existing functions with new versions is done pretty easily by
sourcing the altered versions.
I tried the same for a S4 package method, but this resulted in an error message
(complaining about arguments). The new method version is the old one but with
an additional argument.
On Thu, 2006-11-16 at 17:25 +0100, Alicia Amadoz wrote:
Hello,
I am interested in using the capscale function of vegan package of R. I
already have a dissimilarity matrix and I am intended to use it as
'distance' argument. But then, I don't know what kind of data must be in
'comm' argument.
Dear list,
I am trying to plot 4 overlapping ellipse showing the overlap among 4 data
sets. Could any one suggest how to make this plot with R?
Thanks!
/Mike
_
Stay up-to-date with your friends through the Windows Live Spaces
Nice catch, Gavin - I missed that part of the original post. The
nucleic distances need to be included as the left-hand-side of
the formula, not as the distance argument.
comm is still optional, though, but it's not a good idea to omit
it if there's any way you can provide the original data. From
--- Domenico Vistocco [EMAIL PROTECTED] wrote:
Dear helpeRs,
anyone knows how to obtain a stacked area chart in
R?
I mean one of the graph that is used for
representing compositional
data along time.
Thanks in advance,
domenico
Hello:
When I use SPSS I execute the AGGREGATE DATA comand for the next data:
2112141123212213212213334
3143244113442312121213344
2114141123112214212113344
2112211122212413421213221
311123442414343413344
231223122321323223322
2143241123212313131213234
21132411132123131
Try this:
tb1 - tb2 - tb3 - matrix(1:100, 10, 10, dim = list(NULL,
LETTERS[1:10]))
head(tb1)
lis - c(tb1, tb2, tb3)
for(d in lis) colnames(.GlobalEnv[[d]]) - tolower(colnames(.GlobalEnv[[d]]))
head(tb1)
lis - list(tb1 = data.frame(1:100, 10, dim = list(NULL, LETTERS[1:10]), 3)
lis -
Having no SPSS I have to resort to deductive inference. It seems that you want
to make a frequency table of the occurence of these 25 digit strings, hence
?xtab
?table
spring to mind. I have the faint suspicion that seeing this as 25 variables
might be less efficient than seeing it as one 25
Reposting this because I had the wrong subject on the the last message...
I had some code that used to work in an old version of multcomp:
herbcover -
read.delim(http://anthony.darrouzet-nardi.net/downloads/herbcover.txt;)
herbcover$date - as.POSIXct(strptime(herbcover$date, %Y-%m-%d))
Hi, all,
In order to save simulation time, I need to call C in R. For the C codes, I
need integrate certain functions ( both continous and discrete ), I wonder
how to realize the integration in C?
I try to use qsimp and trapzd subroutines from Numerical Recipes. But the
error continues to
On 11/16/06, Frank Johannes [EMAIL PROTECTED] wrote:
Dear all,
I have three concerns:
1)
I am running models with the lme4 package. I cannot find a way to pull
out a vector of the fitted values and the residuals. Does anybody know
how to do it?
The fitted() and resid() extractor functions
Dears,
I d like to know, whether the nonpar package still exists in R? That
including function chisq.gof? Since I want to know whether my data were
fitted well with the chosen distribution function? I use ks.test that works
fine but function chisq.test does not work good it require more work...
Piet van Remortel [EMAIL PROTECTED] writes:
Hi all,
[...]
Intuitively, I would like to be able to slice the data in a 'data-
cube' kind of way to query, analyze, cluster, fit etc., which
resembles the database data-cube way of thinking common in de db
world these days. (
R has integration routines in its C API: see `Writing R Extensions'.
On Thu, 16 Nov 2006, Lynette Sun wrote:
Hi, all,
In order to save simulation time, I need to call C in R. For the C codes, I
need integrate certain functions ( both continous and discrete ), I wonder
how to realize the
Perhaps I do not understand, but the array (?array) and manipulation of
array objects and their components are a fundamental paradigm of R. How is
this not **exactly** what you want to do? Perhaps a specific reproducible
example might be informative...
Bert Gunter
Nonclinical Statistics
7-7374
Airon,
I'm not sure I have understood your question. Anyway, it
seems to me that you'll have to code a little. Take a look
at ?modwt. I think you'll have to put zeros each scale a time
except the one you want to reconstruct. Then do imodwt.
After some small loop, I think you'll get the desired
In my code below tempa and tempb are numeric vectors that I combined
into a dataframe along with the deciles of tempa.
I have an lapply statement that goes through the dataframe and does ten
plots according to the appropriate decile.
The code is below and it works fine. There are no bugs so I
RSiteSearch(lme and aov) returned 350 hits for me just now. I'm
sure that many are not relevant to your question, but I believe some
are. Beyond this, there is now and R Wiki, accessible via
www.r-project.org - Documentation: Wiki (or directly as
Nothing personal against Spencer. However, I feel that the response was
similar to just saying, Let's not use the listserv anymore. Personally, I
find most, if not all, of the questions to be very helpful. I use them to
learn the language. When something looks over-my-head, I put it in a folder
Vicki,
take a look at P. 47 of the book by Pinheiro and Bates, if you have a copy
(if not, get one!) They show the analysis of a split-plot design using
lme there.
Here, both aov and lme are estimating two levels of variation. The key
difference is that with aov the Ring-level variation is not
Hi,
Thank you for your suggestions. But I also realized I didn't make myself
clear. I actually don't just need the integration results in R. The
integration in C is part of my C codes. I need the integration results in C.
How to realize that? Any suggestions? Thanks a lot!
Best,
Lynette
Help! I accidentally saved my work as an .rdata format instead of .txt
I need to somehow get it saved as a .txt file otherwise i'm really in trouble!
Does anyone know how to convert .rdata to .txt files??
I also tried re-loading the file into R to see if i can re-save it but it
doesnt work!
i've
Mark
In my code below tempa and tempb are numeric vectors that I
combined into a dataframe along with the deciles of tempa.
I have an lapply statement that goes through the dataframe
and does ten plots according to the appropriate decile.
The code is below and it works fine. There are no
I seem to get that error/warning NA's introduced due to Coercion when
I ask for too much intraday data at once. There are limits to what can
come back in one call, and probably the error checking/correcting needs
help.
Why not take a look at the R code and see if you have any ideas.
It might be a
see also:
http://www.zoo.ufl.edu/bolker/eid/
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal,
Hi there!
I need a piece of advice obtaining the average of 4 samples from
different sample sizes.
lets's see that my numbers are:
6,3,6 and 15
and each one comes from:
100,130,125 and 33 sample sizes.
I need a command in R to solve this!
I guess it should not be complicated but... it happens
How about
?weighted.mean
Dan
Daniel J. Nordlund
Research and Data Analysis
Washington State Department of Social and Health Services
Olympia, WA 98504-5204
-Original Message-
From: [EMAIL PROTECTED] [mailto:r-help-
[EMAIL PROTECTED] On Behalf Of Pablo Andres
Sent: Thursday,
i've attached a solution. it works perfectly here (R2.4, win XP) and is
really fast. there's no way you can go wrong using it.
(read the posting guide, ?load, and ?write.table)
On 11/17/06, tt [EMAIL PROTECTED] wrote:
Help! I accidentally saved my work as an .rdata format instead of .txt
I
2006/11/16, Douglas Bates [EMAIL PROTECTED]:
On 11/16/06, Frank Johannes [EMAIL PROTECTED] wrote:
Dear all,
I have three concerns:
1)
I am running models with the lme4 package. I cannot find a way to pull
out a vector of the fitted values and the residuals. Does anybody know
how to do
Hi,
I have problem of reordering in the heatmap.
Followering is an example code:
require(graphics)
x - as.matrix(mtcars)
rc - rainbow(nrow(x), start=0, end=.3)
cc - rainbow(ncol(x), start=0, end=.3)
hv - heatmap(x, col = cm.colors(256), scale=column,
Is it possible to add standard error bars to the means on interaction plots?
Thanks
Murray
--
Murray Pung
Statistician, Datapharm Australia Pty Ltd
0404 273 283
[[alternative HTML version deleted]]
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Hi.
I am trying to get data from mysql database using a couple of queries.
I do one query to find out the indexes. Then i need to use these
indexes in another query, but i keep getting errors.
Here is something:
numb - dbSendQuery(con2, select distinct(comparison) from table1)
count -
On Thu, 16 Nov 2006 20:21:29 -0800
Rahul Thathoo [EMAIL PROTECTED] wrote:
Hi.
I am trying to get data from mysql database using a
couple of queries.
I do one query to find out the indexes. Then i need to
use these
indexes in another query, but i keep getting errors.
Here is something:
Hi R-Experts,
I'm having a problem with reading a large data file which is
in .csv format and size is 120 MB (app.). I was trying to use RODBC
package but I found RODBCconnectExcel function only. And can I convert
this file to .dbf format? How can I read this file? And also let me
Sumanta
consider using read.csv which is a special case of read.table
?read.csv
as for the RODBC functions, you probably found odbcConnectExcel, but the
help file there mentions a .dbf connections
?odbcConnectDbase
from there using sqlQuery it should be possible to write a .dbf file.
?load should be entered into R. you should probably consider reading the
intro to R documents to get a better grasp of the basics. Were I a fortune
teller, I would predict a poor grade in you class if you are required to use
R and don't take the time to read the intro docs.
Now, say you have an
Well, I would not call R packages 'MS executables'!
But Jim is critical of some R conventions -- see his notes on the webpage
http://popgen.unimaas.nl/~jlindsey/rcode.html
Bestest Marwan
--
Marwan Khawaja http://staff.aub.edu.lb/~mk36
On Thu, 16 Nov 2006, Lynette Sun wrote:
Hi,
Thank you for your suggestions. But I also realized I didn't make myself
clear. I actually don't just need the integration results in R. The
integration in C is part of my C codes. I need the integration results in C.
How to realize that? Any
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