Hi
I can never remember what melt, cast and all that means, hence I simpy
use reshape() which does not even require any additional package:
reshape(dat, direction=long, idvar = ID,
varying=list(2:4), v.names=Value, times=names(dat)[2:4])
Uwe Ligges
www
ID T0 T1 T2
1 A 1 2 3
Dear R users,
It would be really helpful if I got to know the names of the packages which
use the following for testing:
pkg-Ex. Rout.save files
(examples of testing)
If possible some testing links: to see how testing is done.
Thanks in advance.
Regards
Vikram
[[alternative HTML
On 09/23/2011 01:49 AM, Benedikt Drosse wrote:
Hello R-Users,
it might be a rather simple problem I have, but I couldn't find any
solution online. Thus, here is my problem:
I would like to adjust the y-axis range in a barplot, since all my
values are 70. Therefore I would like to only visualize
Problem solved.
It had something to do with calling expm(-array(c(K_1, 0, 0, K_2),
c(2,2))*h).
2011/9/22 Kristian Lind kristian.langgaard.l...@gmail.com
Dear R users,
When running the program below I receive the following error message:
fit - optim(parm, objective, yt = tyield, hessian =
Thanks Martin, it worked.
I will post on BioC next time.
Cheers.
--
View this message in context:
http://r.789695.n4.nabble.com/chippeakanno-package-getAllPeakSequence-problem-tp3830284p3836422.html
Sent from the R help mailing list archive at Nabble.com.
To separate the parts of a formula, use as.character
(check the examples in ?character)
Helios
22 Sep 2011 16:14:05 -0400
From: Jean-Christophe BOU?TT? jcboue...@gmail.com
Hello,
You can check ?model.frame.
I do not know however to extract only the right-hand of left-hand
part
of a formula.
hello,
thank you for your help!
I was not successfull using the XLConnect-package. Anyway, I have to
postpone this problem for now as I have to sort out some other other
problems at the moment.
marion
2011/9/16 Greg Snow greg.s...@imail.org
Look at the XLConnect package.
--
Gregory (Greg) L.
I have a bunch of benchmark measurements that look something like this:
sample.10.000.0625000.0583300.058330
0.058330
sample.20.0583300.0583300.0583300.058330
0.058330
sample.30.062500
I am a relative novice with R and am having some difficulty using 'clusplot'
(package Cluster).
I have performed PCA analysis (using vegan) on a large set of morphometric
measurements and revealed up to 4 principal components. To examine the
grouping of the data I have used PAM followed by
A nice alternative,
Many thanks Achim
Wesley
Achim Zeileis achim.zeil...@uibk.ac.at 22/09/2011 14:46
On Thu, 22 Sep 2011, Gabor Grothendieck wrote:
On Thu, Sep 22, 2011 at 6:48 AM, Wesley Roberts wrobe...@csir.co.za wrote:
Dear R users,
I am currently working in subsetting a zooreg()
You've got to state the problem little bit more clear.
What do you mean by set? Is it a list of certain possible values,
available as outcomes of each single measurement (variate)? Or is it
something else?
How many variates do you have inside each sample?
What is it exactly that you want to find?
Szeptember 12-től 26-ig irodán kívül vagyok, és az emailjeimet nem érem el.
Sürgős esetben kérem forduljon Kárpáti Edithez (karpati.e...@gyemszi.hu).
Üdvözlettel,
Mihalicza Péter
I will be out of the office from 12 till 26 September with no access to my
emails.
In urgent cases please contact
Hi,
I'm new to R, and I have searched helpfiles and this forum on my 2
questions. Hope you guys can help me out! :-)
Many thanks in advance!
Cheers,
Lars
Q1: I imported a csv file with columnames subject and class. There are about
1000 different classes...
It looks like this:
subject1,
[R] Newbie question: Converting Table
Hi,
I'm new to R, and I have searched helpfiles and this forum on my 2
questions. Hope you guys can help me out! :-)
You did not search enough. You probably want table or xtabs
Q1
untested
res - xtabs(~subject+class, data=your.file)
ifelse(res==1,
On 23.09.2011 10:16, Vikram Bahure wrote:
Dear R users,
It would be really helpful if I got to know the names of the packages which
use the following for testing:
pkg-Ex. Rout.save files
(examples of testing)
Simply take a look, there are really many. The source packages are all
As Jim suggested, the duplicated() function should help.
If I understand what you're after, you could try something like this. I
assumed that the name of your data frame was df.
selrows - df$WorkerID %in% df$WorkerID[duplicated(df$WorkerID)]
# SubjectNumbers with duplicate WorkerIDs
Allan Carson acarson at unbc.ca writes:
[snip]
When I try to conduct a
multiple comparison, I get an error (See below):
fm3- lme(abovegroundbiomass.m.2~medium*amelioration*fertilizer*treatment,
random=~1|block/medium/amelioration/fertilizer)
tukeytest-glht(fm3,
Also, if your formula is really of the form y ~x1+...+xn
you can have a look at the last example for ?formula for a simple way
to generate the formula.
HTH,
JC
2011/9/23 Helios de Rosario helios.derosa...@ibv.upv.es:
To separate the parts of a formula, use as.character
(check the examples in
Look at the help page for Surv to see how to code left censored data.
Be aware of the difference between left censored (we know the event
happened before fecha) and left truncated (the subject entered
observation at fecha) -- they are different concepts. The survival code
can deal with both.
1) The p values in the printout are a Wald test. The Wald, score, and
likelihood ratio tests are asymptotically equivalent, but may differ
somewhat in finite samples. (The Wald and score are both Taylor series
approximations to the LR). If you want to do an LR test, fit the two
models and use
On Thu, Sep 22, 2011 at 2:54 PM, trekvana trekv...@aol.com wrote:
Hello all,
So I am using the (formula entry) method for randomForests:
randomForest(y~x1+x2+...+x39+x40,data=xxx,...) but the issue is that some of
the items in that package dont take a formula entry - you have to explicitly
Hello,
I created an array to hold the results of a series of simulations I'm
running:
d.eta - array(0,dim=c(3,3,200))
simulation goes here and populates the array but it's not important
Then I tried to save the results using this:
save(d.eta,file=D:/Simulation Results/sim 9-23-11 deta)
When
A more compact example might be helpful:
g - array(0,dim=c(4,4))
g
save(g,file=D:/g)
h - load(file=D:/g)
h
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Downey, Patrick
Sent: Friday, September 23, 2011 9:32 AM
To:
Hi,
did you try
load(file=D:/Simulation Results/sim 9-23-11 deta)
without the assignment ?
look at ?load
2011/9/23 Downey, Patrick pdow...@urban.org:
Hello,
I created an array to hold the results of a series of simulations I'm
running:
d.eta - array(0,dim=c(3,3,200))
simulation goes here
--- begin inclusion --
Hi everybody. I'm trying to fit a weibull survival model with a spline
basis for the predictor, using the survival library. I've noticed that
it
doesn't seem to be possible to use the aic method to choose the degrees
of
freedom for the spline basis in a parametric
This is one of the rare cases in R where you don't want to save
the return value. You loaded d.eta, and then promptly overwrote it
with the return value, which is just the name of the object.
ls()
character(0)
d.eta - array(0,dim=c(3,3,200))
dim(d.eta)
[1] 3 3 200
save(d.eta, file=deta)
Thank you Jean Christophe and Sarah. You are both, of course, absolutely
correct.
-Original Message-
From: Jean-Christophe BOUËTTÉ [mailto:jcboue...@gmail.com]
Sent: Friday, September 23, 2011 9:44 AM
To: Downey, Patrick
Cc: r-help@r-project.org
Subject: Re: [R] 'save' saved object
On 23/09/2011 9:31 AM, Downey, Patrick wrote:
Hello,
I created an array to hold the results of a series of simulations I'm
running:
d.eta- array(0,dim=c(3,3,200))
simulation goes here and populates the array but it's not important
Then I tried to save the results using this:
Hi,
i think the right to fit a GARCH-model is to use garchFit of the fGARCH
package. My problem is that the time-series is definitly not normal
distributed. So i can not use the QMLE method. How can i do it right?
thanks
Roland
--
View this message in context:
Dear Mr. Tuszynski,
I would like to request what I believe would be a beneficial update / patch
to the runmean() function in the caTools package.
Consider the following
R x = 1:100
R is.integer(x)
[1] TRUE
R library(caTools)
R head(runmean(x, 5, alg=exact))
[1] 8.487983e-314 1.060998e-313
Dear Helios,
I've now had a chance to look at your code for the factorltest.mlm() function.
I agree that the function makes it easier to test hypotheses in
repeated-measures ANOVAs. When I have some more time, I'll make a few
suggestions (off list) for improving the user interface to the
See FAQ for windows 2.7! - 2.7 How do I UNinstall R?.
John
On Thursday, 22 September 2011, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
On 22.09.2011 14:47, Andrey A wrote:
Dear R users
How does one completely uninstall R from their machine? Going to control
panelprograms does not
Dear all
I have a bit off topic question. I need to compare some measured values
with people's subjective estimation (was not done yet). Before I start the
experiment I would like to consult some appropriate literature.
Basically I will have several samples and several people can evaluate all
I guess that I have just to consider the means of each subject,
as indicated here.
http://www-users.york.ac.uk/~mb55/intro/corrsim.htm
Thanks
On Thu, Sep 22, 2011 at 9:16 PM, Heverkuhn Heverkuhn heverk...@gmail.comwrote:
Hello
I have a dataframe that looks like this:
Date Min
Hi R-experts,
I am using the envfit function over an ordination of floristic data.
The problem is that every time that I run it changes the results. Sometimes
dramatically, selecting variables that the first time were not significant.
I do not get what could be the problem or if is normal given
Thanks, I will read the posting guide.
Q1: thanks for helping me out!
Q2: What I mean is that given the dataset:
subject1,class1_yes, class2_no, class3_yes, class4_no
subject2, class1_no, class2_no, class3_no, class4_yes
subject3, class1_yes, class2_no, class3_yes, class4_no
I want to count
Hello All,
I am trying to estimate the parameters of a stochastic differential equation
(SDE) using quasi-maximum likelihood methods but I am having trouble with
the 'optim' function that I am using to optimise the log-likelihood
function.
After simulating the SDE I generated samples of the
Yuta,
Thanks for the response.
Yuta wrote:
You've got to state the problem little bit more clear.
What do you mean by set? Is it a list of certain possible values,
available as outcomes of each single measurement (variate)? Or is it
something else?
How many variates do you have inside
Dear Dr. Snow,
I would like to ask for help on my three questions regarding Kolmogorov
Smirnov test.
1.
'With a sample size over 10,000 you will have power to detect differences
that are not practically meaningful. '
-Is sample size of 3000 for each sample okay for using Kolmogorov
Smirnov
Hi group,
code:
m-read.table(test.txt,sep='\t',header=TRUE,colClasses=c('character','integer','integer','numeric','numeric'))
s-data.frame(c(rle(m$Sample1)[[2]],rle(m$Sample2)[[2]]),c(rle(m$Sample1)[[1]],rle(m$Sample2)[[1]]))
names(s)=c(Values,Probes)
G=1
for(i in 1:length(s$Probes)){
+
Dear Community
I am at my wits end and seek advice.
My wish is to plot coordinates (x,y in WGS84_UMTS for the ones interested)
of sampling points.
This I can do by the standard spatstat prodcedure via owin. I then try to
add an image, which is
a map/satellite photo in the background.
Firstly
Take a look at http://biostat.mc.vanderbilt.edu/SweaveConvert
The most general approach is to convert from PDF to word using one of the
web sites. An example is given (input + output) in the above site.
Frank
Joshua Wiley-2 wrote:
Hi Tal,
Just another note, I recently joined the R2HTML
Hello,
I would like to know if it exists a package including something equivalent
to this page:
http://www.developpez.net/forums/d740403/autres-langages/algorithmes/contribuez/image-geometrie-projective-homography/
Hi everybody!
I'm trying to install the tikzDevice package, and I keep on getting the
ERROR: dependency filehash is not available for package tikzDevice
I tried install.packages('filehash') and I get
package filehash is not available
Does anybody have the same problem or any hint?
thank
Thanks very much to both of you. Duplicated does exactly what I'm looking
for.
Sorry -- I didn't realize that I was supposed to provide a subset of my data
frame. A little late now, but here it is -- the data frame is called
SubInfo, and it gives background informations on subjects from a
Dear R users,
we would like to announce that on the CRAN a new package (SeleMix
version 0.8.1) for selective editing is available.
This package includes functions for identification of outliers and
influential errors in numerical data. For each unit, it provides also
anticipated values
On 23.09.2011 16:39, Helena Peña wrote:
Hi everybody!
I'm trying to install the tikzDevice package, and I keep on getting the
ERROR: dependency ‘filehash’ is not available for package ‘tikzDevice’
I tried install.packages('filehash') and I get
package ‘filehash’ is not available
Which
Hi,
I have a question about how to sort a matrix for multiple columns.
dat-sample(0:1,1000,replace=T)
matrix(dat,ncol=5,nrow=200)-x
I want to order like the following:
x[order(x[,1],x[,2],x[,3],x[,4],x[,5]),]-x
My problem: the number of columns of the matrix to be sorted is variable, in
Use do.call(func, listOfArgs) when you don't
know how many arguments will be passed to func.
E.g.,
x - cbind(round(sin(1:10)), round(cos(1:10)), round(tan(1:10)))
x[do.call(order, split(x, col(x))), , drop=FALSE]
[,1] [,2] [,3]
[1,] -1 -11
[2,] -1 -11
[3,]
Hello, I have run a linear discriminant analysis for the simple 2 group case
using the MASS package lda() function. With priors fixed at 0.5 and unequal n
for each group, the output basically provides the group means and the LD1
value. There is no automatic output of the cutoff (decision
This is not an R question. Post it on a statistics site like stackexchange,
instead.
http://stats.stackexchange.com/
-- Bert
On Fri, Sep 23, 2011 at 9:49 AM, B Jessop deel...@hotmail.com wrote:
Hello, I have run a linear discriminant analysis for the simple 2 group
case using the MASS
Hi,
I have a question concerning the image function and how to generate custom
axis labels:
dat-sample(0:1,1000,replace=T)
matrix(dat,ncol=5,nrow=200)-x
x[order(x[,1],x[,2],x[,3],x[,4],x[,5]),]-x
I would like to have a heatmap kind of thing like this:
image(t(x),col=c(0,1),axes=F)
This has got to be incredibly simple but I nevertheless can't figure it out
as I am apparently brain dead.
I just want to convert the elements of a character vector to variable names,
so as to then assign formulas to them, e.g:
z = c(model1,model2); I want to assign formulas, such as lm(y~x[,1])
On Fri, 23 Sep 2011, B Jessop wrote:
Hello, I have run a linear discriminant analysis for the simple 2
group case using the MASS package lda() function. With priors fixed
at 0.5 and unequal n for each group, the output basically provides
the group means and the LD1 value. There is no
Sorry that forgot to put R-forum in the loop...
-Original Message-
From: Bogaso Christofer [mailto:bogaso.christo...@gmail.com]
Sent: 23 September 2011 22:53
To: 'Prof Brian Ripley'
Cc: 'leighton155'
Subject: RE: [R] ARIMA - Skipping intermediate lags
Dear Prof. Ripley,
The usual response to this sort of question is usually something like the
following:
assign() will do what you want; get() runs the other direction. But the more
R way to do it is to put all the models in a list.
Michael
On Fri, Sep 23, 2011 at 1:03 PM, Jim Bouldin bouldi...@gmail.com wrote:
On 23.09.2011 19:03, Maxim wrote:
Hi,
I have a question concerning the image function and how to generate custom
axis labels:
dat-sample(0:1,1000,replace=T)
matrix(dat,ncol=5,nrow=200)-x
x[order(x[,1],x[,2],x[,3],x[,4],x[,5]),]-x
I would like to have a heatmap kind of thing like this:
Hi,
image() resizes the range of the data to roughly 0-1 , as you can see with
par()$usr
so what you need is:
axis(1, 1:5/5, colnames(x))
or something similar.
the c() c(colnames(x)) is unnecessary, since colnames(x) already returns a
character vector, but in the example you provided (thanks!),
Hi, I'm wondering why the spectrum() phase of quadrature
couple isn't purely +/-pi.
But mostly, I'm looking for a recommended way to take a 2-D
spectrum and convert it into a single complex array.
Kindly consider:
# 10 Hz sine wave 10 seconds long sampled at 50 Hz
deltaT = 1/50
t =
Dear R users,
I know, the topic is more related to the r-sig-ecology. I decided to
post it to the r-help as some specific topics of my question deals
with NA-values and RDA (R vegan) and an adaptated RDA code due to a
specific study design (including a second matrix).
I am calculating a
OS linux 2.6.38
R version 2.12.1
I tried the CRAN german mirrors
http://mirrors.softliste.de/cran/
http://ftp5.gwdg.de/pub/misc/cran
and others from the UK...
--
View this message in context:
http://r.789695.n4.nabble.com/tikzDevice-install-problem-tp3837315p3837457.html
Sent from the R
Hello R-user community,
I am applying the function metaMDS. However, I would like to know if there
is any option to export the data I got from the axis as a data frame.
I have tried as.data.frame.list but is not working. Any suggestion?
Thank you in advance for your help,
Lineth
On Sep 23, 2011, at 11:00 AM, PtitBleu wrote:
Hello,
I would like to know if it exists a package including something
equivalent
to this page:
http://www.developpez.net/forums/d740403/autres-langages/algorithmes/contribuez/image-geometrie-projective-homography/
Jim Bouldin wrote on 09/23/2011 12:03:47 PM:
This has got to be incredibly simple but I nevertheless can't figure it
out
as I am apparently brain dead.
I just want to convert the elements of a character vector to variable
names,
so as to then assign formulas to them, e.g:
z =
Yes, I tried to do it using assign. I couldn't get that to work. E.g:
z=1:2; zz=rep(model,2);zzz = paste(zz,z,sep='');zzz
[1] model1 model2
y = 1:10; v = rnorm(10,0,2); x2 = y + v; x3 = y + v^0.5
x = data.frame(x2,x3)
for (i in 1:2){assign(zzz[i],lm(y~x[,i]))};zzz
[1] model1 model2
stumped
Lineth Contreras wrote on 09/23/2011 11:35:10 AM:
Hello R-user community,
I am applying the function metaMDS. However, I would like to know if
there
is any option to export the data I got from the axis as a data frame.
I have tried as.data.frame.list but is not working. Any suggestion?
What exactly is the problem? Like I said, I'd personally put this in a list,
but this seems like exactly what you wanted...
model1
Call:
lm(formula = y ~ x[, i])
Coefficients:
(Intercept) x[, i]
1.0489 0.7175
model2
Call:
lm(formula = y ~ x[, i])
Coefficients:
(Intercept)
OK, I see. I thought R was just returning the character strings of the
model names without doing any assigning, since that's what it displayed. I
had it right all along. Thanks for your help.
On Fri, Sep 23, 2011 at 1:45 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
What exactly
assign() doesn't return anything in this case. It's your addtional
(unnecessary?) call to zzz at the end which triggers a print statement.
Michael
On Fri, Sep 23, 2011 at 1:56 PM, Jim Bouldin bouldi...@gmail.com wrote:
OK, I see. I thought R was just returning the character strings of the
Am 21.09.2011 17:05, schrieb Uwe Ligges:
On 21.09.2011 11:53, Duarte Viana wrote:
Hello all,
Can someone tell me why the following mixture of two log-normal
distributions does not get truncated? What puzzles me is that the
function works almost always, but for certain combinations (like
OK. I was assuming that the call to zzz would print the model formulae, not
the object names. That's what threw me.
Jim
On Fri, Sep 23, 2011 at 1:59 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
assign() doesn't return anything in this case. It's your addtional
(unnecessary?) call
Two things:
I think you are not aware of the R difference between a formula and a lm
object. A formula is part of the input to the lm function while the output
is a complicated object of lm class. If you want the formulas back from the
model object, you can access them by way of
model1$call with
On Sep 23, 2011, at 8:43 AM, Metronome123 wrote:
Thanks, I will read the posting guide.
Please do it NOW. Before any further postings.
Q1: thanks for helping me out!
Q2: What I mean is that given the dataset:
subject1,class1_yes, class2_no, class3_yes, class4_no
subject2, class1_no,
You are not giving anyone much to go on. Please read the posting guide and see
how to ask your question in a way that's easier for others to answer. At the
_very_ least, show what commands you used, what your data looks like, etc.
Andy
-Original Message-
From:
I am looking for study materisl on how to conduct 'small area estimation' using
structural equations models in R for both longtudinal and repeated
cross-section data. Tried google did not work. There are other regression
technique my interest is on structural equation models.
Are you doing the 2 sample KS test? Comparing if 2 samples come from the same
distribution?
With 3,000 points you will still likely have power to find meaningless
differences, what exactly are you trying to accomplish by doing the comparison?
I am really only familiar with the KS test done in
I'm not at all sure that I understand your question, but since (as far
as I am aware) no-one else has answered, I'll give it a go.
The puzzle, to me, is what you mean by ``I would like to add weights
to optim.'' What do you mean ``add weights''?
If you want to minimize a weighted sum of
Thanks for your help, what I meant was that each observation x had a
corresponding count to them, and I wanted to use these counts as weights in
the optim (so that the optim process would give more weight to the
measurements that had more counts).
I had forgotten if the weights should accounted
Dear all,
I'm having issues with the installation of the ncdf package. It returns a
non-zero exit status. Can anyone suggest what I should do next? FYI, I do
not have problems installing other packages.
Thanks.
Muhammad
* installing *source* package ‘ncdf’ ...
checking for nc-config...
Perhaps start by reading the posting guidelines.
---
Jeff Newmiller The . . Go Live...
DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries
On 24/09/11 02:32, tkdweber wrote:
Dear Community
I am at my wits end and seek advice.
My wish is to plot coordinates (x,y in WGS84_UMTS for the ones interested)
of sampling points.
This I can do by the standard spatstat prodcedure via owin.
You appear to be rather confused from the very
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