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Department
.
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My code substracts the median absolute value. If you want to divide by it,
the code must be :
apply(some_dataset,2,function(
x){
x/median(abs(x))
})
Thanks to Peter Langfelder for pointing out my mistake.
On Tue, May 25, 2010 at 6:24 PM, Joris Meys jorism...@gmail.com wrote:
What kind
can't think of a formal method to check in a
nMDS framework how much dimensions are enough. Anybody an idea?
I use metaMDS from the vegan package, although it's not really meant to be
used on these data.
Cheers
Joris
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Gunter gunter.ber...@gene.com wrote:
?scale
is specifically written for this. See also ?sweep
Bert Gunter
Genentech Nonclinical Biostatistics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On
Behalf Of Joris Meys
Sent: Tuesday, May
commented, minimal, self-contained, reproducible code.
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On Tue, 25 May 2010, Joris Meys wrote:
Scale is written to do that IF you want to normalize according to the mean
and the sd. For any other form of normalization, apply or sweep constructs
will have to be used.
I couldn't really see a way of using the absolute median value in a
sweep
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sure all
branch lengths are interpreteable on the same scale. Therefor I want to
normalize the branch lengths, but I can't find a function to do that, nor
one to clock the tree. Anybody an idea?
Cheers
Joris
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for s(x1) and s(x2).
Cheers
Joris
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Statistical Consultant
Ghent University
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Department of Applied mathematics, biometrics and process control
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-contained, reproducible code.
--
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Statistical Consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
Coupure Links 653
B-9000 Gent
tel : +32 9 264 59 87
joris.m...@ugent.be
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
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=Basis function,xlab=X,type=l,lwd=2)
plot(x1,Z[,2],ylab=Basis function,xlab=X,type=l,lwd=2)
plot(x1,Z[,1],ylab=Basis function,xlab=X,type=l,lwd=2)
par(op)
On Wed, May 19, 2010 at 8:38 PM, Simon Wood s.w...@bath.ac.uk wrote:
On Wednesday 19 May 2010 15:08, Joris Meys wrote:
Dear all
.
The models are essentially the same, the shift is mainly in the intercept.
But the centering got a bit a reflex.
Cheers
Joris
On Wed, May 19, 2010 at 8:20 PM, Simon Wood s.w...@bath.ac.uk wrote:
On Wednesday 19 May 2010 15:29, Joris Meys wrote:
Could you specify the package you use
.
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PM, Joris Meys wrote:
On Sat, May 8, 2010 at 7:02 PM, Bak Kuss bakk...@gmail.com wrote:
Just wondering.
The smallest the p-value, the closer to 'reality' (the more accurate)
the model is supposed to (not) be (?).
How realistic is it to be that (un-) real?
That's a common
doesn't work
combn(test,2,all.equal)
Cheers
Joris
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8, 2010 at 4:04 PM, David Winsemius dwinsem...@comcast.netwrote:
On May 8, 2010, at 9:43 AM, Joris Meys wrote:
Dear all,
I want to apply a function to list elements, two by two. I hoped that
combn
would help me out, but I can't get it to work. A nested for-loop works,
but
seems highly
.
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]]
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PLEASE do read the posting guide
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PLEASE do read the posting guide
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Statistical Consultant
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Faculty
-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Statistical Consultant
Ghent University
Faculty of Bioscience Engineering
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
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://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
Joris Meys
Statistical Consultant
Ghent University
Faculty of Bioscience Engineering
Department
and provide commented, minimal, self-contained, reproducible code.
--
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Statistical Consultant
Ghent University
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Department of Applied mathematics, biometrics and process control
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the posting guide
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and provide commented, minimal, self-contained, reproducible code.
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Statistical Consultant
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the posting guide
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Ghent University
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Department of Applied mathematics, biometrics and process control
code.
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that is more extreme than the observed
pvalue
I use the central limit theorem in a way, assuming the distribution of the
statistic for the bootstrap sample is symmetric.
Best wishes,
Cheba
2010/5/7 Joris Meys jorism...@gmail.com
depends on how you interprete absolute median difference
guide
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) |
www.r-statistics.com (English)
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On Thu, May 6, 2010 at 2:25 PM, Joris Meys jorism...@gmail.com wrote:
Hi Tal,
The problem is not the analysis, but the data. You have 2 weeks that only
have
.
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Department of Applied mathematics, biometrics and process control
Coupure Links 653
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PS : level, you might want to consider stopping to spam the help-list.
You're not making yourself popular by asking -in one day- 3 questions that
can be solved by using Google and reading the introductions given on the R
homepage.
On Thu, May 6, 2010 at 5:57 PM, Joris Meys jorism...@gmail.com
-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Statistical Consultant
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/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Statistical Consultant
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-project.org mailing list
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PLEASE do read the posting guide
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Faculty of Bioscience
For completeness.
On Thu, May 6, 2010 at 8:03 PM, Joris Meys jorism...@gmail.com wrote:
Table - matrix(ncol=3,nrow=4,c(0,0,0,0,7,2,1,3,4,0,3,4))
# one way
t(t(Table)/colSums(Table))
# another way
apply(Table,2,function(x){x/sum(x)})
Take in mind that your solution is wrong. If you
the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
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[mailto:r-help-boun...@r-
project.org] On Behalf Of Joris Meys
Sent: Thursday, May 06, 2010 9:57 AM
To: Dimitri Liakhovitski
Cc: r-help@r-project.org; level
Subject: Re: [R] T-test for loop
Hehe,
those homeworks. If you can explain this code to the professor, you
surely
passed.
n
-help
PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
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Statistical Consultant
Ghent University
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-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joris Meys
Statistical Consultant
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Department of Applied mathematics, biometrics and process control
Coupure Links 653
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tel : +32 9
and provide commented, minimal, self-contained, reproducible code.
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Joris Meys
Statistical Consultant
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Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
Coupure Links 653
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tel : +32 9 264 59 87
joris.m...@ugent.be
way of splitting my
vector in a list of the subvectors or so.
Anybody an idea?
Cheers
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PM, jim holtman jholt...@gmail.com wrote:
Try this:
x - 1:10
pos - c(1,4,7)
pat - rep(seq_along(pos), times=diff(c(pos, length(x) + 1)))
split(x, pat)
$`1`
[1] 1 2 3
$`2`
[1] 4 5 6
$`3`
[1] 7 8 9 10
On Tue, May 4, 2010 at 11:29 AM, Joris Meys jorism...@gmail.com wrote:
Dear
-guide.html
and provide commented, minimal, self-contained, reproducible code.
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joris.m
, reproducible code.
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Department of Applied mathematics, biometrics and process control
Coupure Links 653
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tel : +32 9 264 59 87
joris.m...@ugent.be
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and provide commented, minimal, self-contained, reproducible code.
--
Joris Meys
Statistical Consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
Coupure Links 653
B-9000 Gent
tel : +32 9 264 59 87
joris.m
://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joris Meys
Statistical Consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
Coupure Links 653
B-9000 Gent
tel
and provide commented, minimal, self-contained, reproducible code.
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Joris Meys
Statistical Consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
Coupure Links 653
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tel : +32 9 264 59 87
joris.m...@ugent.be
on this subject.
What confuses me most, is the use of the intercept in the random factor.
Does this mean the intercept is seen as random, has a random component or is
it just notation? In different mails from this list I found different
explanations.
Thank you in advance.
Cheers
Joris
--
Joris Meys
in advance.
Cheers
Joris
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Statistical Consultant
Ghent University
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Department of Applied mathematics, biometrics and process control
Coupure Links 653
B-9000 Gent
tel : +32 9 264 59 87
joris.m...@ugent.be
---
Disclaimer
, mohamed.laj...@inserm.fr wrote:
Hi Joris
Try Is.element function: is.element (x,y)
Regards
mohamed
Joris Meys jorism...@gmail.com a écrit :
Dear all,
I have a vector, and for each element I want to check whether it is equal
to
any element from another vector. I want a vector of logical
in
the package limma too, but I didn't use that before.
Anybody who knows what happened to R.basic?
Cheers
Joris
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-project.org mailing list
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
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Statistical Consultant
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Faculty of Bioscience
-contained, reproducible code.
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Statistical Consultant
Ghent University
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Department of Applied mathematics, biometrics and process control
Coupure Links 653
B-9000 Gent
tel : +32 9 264 59 87
joris.m...@ugent.be
Thank you both for your answers.
On Fri, Feb 26, 2010 at 7:58 PM, Duncan Murdoch murd...@stats.uwo.cawrote:
You aren't seeing the print method, you are seeing a newly created print
generic function. As Uwe mentioned, print() is not an S4 generic, so when
you create your print method, a new
, but the print method is gone. Am
I forgetting something somewhere? It's rather inconvenient to have to run
the definition files every time I want to clear the memory.
Cheers
Joris
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Statistical Consultant
Ghent University
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Department of Applied
Dear all,
I'm currently applying a mixed model approach to meta analysis using the
package metafor. I use the model.matrix() function to create dummy
variables. The option btt gives me the combined test for the dummies.
Problem is, I don't know which indices I have to use, and can't really
figure
Hi Tyler,
sorry, I missed your response. Don't know if it's solved already, but
some remarks.
the predict uses a princomp object, so your second command should work.
I guess the problem is either the data format of B (should contain
exactly the same amount of columns, with the same names), or
Hi all,
I'm currently programming my first complete package in S4. (thanks to
Christophe Genolini for the nice introduction he wrote). I have an
object Data with a number of slots. One of those slots is meteo.
Now Meteo is on itself a class with again a number of slots (like
rainfall,
The problem is easily solved by plotting salaries$salary/100
Cheers
Joris
On Thu, Dec 3, 2009 at 5:16 PM, Wells Oliver we...@submute.net wrote:
Hello all. I have the following:
plot(salaries$yearID, salaries$salary, type='n', xaxt='n', xlab='',
yaxt='n', ylab='')
axis(1,
Please provide minimal and self-contained code. Without being able to
read in the dataset, it's impossible to check the code.
Cheers
Joris
On Thu, Nov 26, 2009 at 9:13 AM, Markus Häge markus_ha...@gmx.de wrote:
Hello,
sorry for incomplete code...
with this I read the file and calculate my
On Thu, Nov 26, 2009 at 1:04 AM, Tyler82 procaccianti.clau...@gmail.com wrote:
Hi all!
I am working with R package cluster and I have a little problem:
let's say I have two datasets...first one (A) is divided into 4 clusters
by means of Pam algorythm.
Let's say I want to project the second
I run your script from the windows console (evidently), and as said, I
can't reproduce your error. Can you give me the exact command you use
to run it from the windows console?
Cheers
Joris
On Tue, Nov 24, 2009 at 7:33 PM, yonosoyelmejor
yonosoyelme...@hotmail.com wrote:
Sure,but my problem is
Hi,
The log of the mean is not the same as the mean of the logs, that's a
no-brainer. Guess you use the beanplot from the package with the same
name.
beanplot(As1988,log=)
gives the correct plot.
Next time, could you provide a minimal code example we can run
ourselves? If we don't know what
I can't reproduce the error you have. With me, it runs all fine. In
fact, readline apparently flushes automatically, as I didn't have to
use the flush.console() at all.
test.r
---
cat(1- 24horas\n)
cat(2- 12horas\n)
cat(3- 8horas\n)
selection-readline(prompt=\nSelecciona numero de horas:)
wrote:
On Mon, Nov 16, 2009 at 07:28, joris meys jorism...@gmail.com wrote:
Hi all,
I tried plotting a horizontal dendrogram, but it seems as if the
labels are not taken into account in the function plot.dendrogram().
A minimal example :
Test - data.frame(
x1x = c(1:10),
x2x
Dear all,
I'm looking for a function comparable to switch, to categorize a
continuous variable in a few levels. Off course that can be done with
a series of ifelse statements, but that looks rather clumsy. I looked
at switch, but couldn't figure out how to use it for this. I guess
that's not
Never mind, found the function :
cut(test,breaks=c(0,10,50,90,100),labels=c(lowest,low,high,highest),include.lowest=T,right=F)
Cheers
Joris
On Mon, Nov 23, 2009 at 2:14 PM, joris meys jorism...@gmail.com wrote:
Dear all,
I'm looking for a function comparable to switch, to categorize
Hi all,
I tried plotting a horizontal dendrogram, but it seems as if the
labels are not taken into account in the function plot.dendrogram().
A minimal example :
Test - data.frame(
x1x = c(1:10),
x2x = c(2:11),
x3x = c(11:2)
)
TestDist - daisy(data.frame(t(Test)))
I was missing something. Thx Dennis.
-- Forwarded message --
From: Dennis Murphy djmu...@gmail.com
Date: Tue, Nov 17, 2009 at 12:34 AM
Subject: Re: dendrogram
To: jorism...@gmail.com
Hi,
There are a couple of things you could do to pull the text back into
the dendrogram plot,
Hi Rene,
the problem is probably due to the fact that R will send all plots to
the same graphical output window. Each next plot just replaces the
previous one.
if it's only a few plots, you can divide the graphical window with the
commands par(mfrow=...) (see ?par) or layout(matrix(...)) (see
()
}
}
par(mfrow=(3,2))
kk(1:3)
Thanks a lot!
Rene
-Original Message-
From: joris meys [mailto:jorism...@gmail.com]
Sent: Tuesday, 20 October 2009 12:11 a.m.
To: Rene
Subject: Re: [R] loop and plot
Hi Rene,
the problem is probably due to the fact that R will send
2 problems :
test seems to be a data frame or list with one variable. So you have
to specify :
as.numeric(test$classcol)
But this will make the internal factor levels the real values, not the
numbers you specified. What you need, is
as.numeric(as.character(test$classcol))
Cheers
Joris
On Mon,
Hi Ian,
first of all, take a look at the functions sapply, mapply, lapply,
tapply, ... : they are the more efficient way of implementing loops.
Second, could you elaborate a bit further on the data set : the amount
of the month ago, is that one value from another row, or the sum of
all values in
Don't know if it will work, but did you try ?layout ?
Cheers
Joris
On Thu, Oct 15, 2009 at 2:39 PM, Jesse Poland jap...@cornell.edu wrote:
I would like to combine multiple pairs plots (each one being a matrix of
correlation plots) into a single graphic. I have tried the par() function,
which
Don't know if it will work, but did you try ?layout ? Otherwise you
can take a look at ?split.screen too.
Cheers
Joris
On Thu, Oct 15, 2009 at 2:39 PM, Jesse Poland jap...@cornell.edu wrote:
I would like to combine multiple pairs plots (each one being a matrix of
correlation plots) into a
I tried :
test - 0:1
test2 - f(0:1)
plot(test,test2)
plot(test,log(test2))
and
test - seq(0,1,by=0.1)
test2 - sapply(test,f)
plot(test,log(test2))
plot(test,test2)
with the values you gave.
And according to this result, you did nothing wrong. Zero is the only
root of
On Tue, Oct 13, 2009 at 6:48 PM, PDXRugger j_r...@hotmail.com wrote:
II just want to create a new object with the first two numerals of the data.
Not sure why this isnt working, consider the following:
EmpEst$naics=c(238321, 624410, 484121 ,238911, 81, 531110, 621399,
541613,
524210
Josh,
One way would be to convert the numeric vector to a character and use
the function substr(). Following code returns a numeric vector with
the 2 first digits of every element.
naics=c(238321, 624410, 484121 ,238911, 81, 531110,
621399,541613,524210 ,236115 ,811121 ,236115 ,236115
On Wed, Oct 14, 2009 at 2:45 PM, Robert Baer rb...@atsu.edu wrote:
The problem is the limit of 8 characters long on variable
names.
And again, my answer is that one approach would be to map SHORT names to
long variable LABELS. This was a common use of labels before variable names
supported
Well,
it might be wise to elaborate a bit more about the variables and what
exactly you want e.g. death-time to be. I'd interprete it as time of
death, but the fact that it is 0/1, means it is a logical (?) binary
variable of some sort.
Please ask your question in such a way that somebody who
resources.
The great thing would be to support long variables names on read.spss.
Thanks guys for everything
Caveman
On Wed, Oct 14, 2009 at 4:52 PM, joris meys jorism...@gmail.com wrote:
Hi Orvalho,
question : where do the .dat files come from and what do you have to
do with the SPSS syntax
On Wed, Oct 14, 2009 at 9:19 PM, quaildoc just.strut...@gmail.com wrote:
Some suggested that go into more detail on what I wanted to accomplish and
the rest of my code. I want to accomplish exactly what Fox did in this
article( http://www.nabble.com/file/p25897307/appendix-cox-regression.pdf
Sorry to be so blunt, but I cannot believe PSPP can't save a dataset
as a .csv file for example. That should be the prefered format to
transport a dataset to any other statistical package, including R. csv
files are universal.
Cheers
Joris
On Tue, Oct 13, 2009 at 3:30 PM, Orvalho Augusto
The easy way out is to send the file containing only the function to
the people willing to use it. They can load the function from the file
foo.R using :
source (path/foo.R)
The hard way out is to write a package. For that, see :
http://cran.r-project.org/doc/manuals/R-exts.html
Cheers
Joris
On Tue, Oct 13, 2009 at 5:30 PM, Barry Rowlingson
b.rowling...@lancaster.ac.uk wrote:
On Tue, Oct 13, 2009 at 2:41 PM, Thomas Lumley tlum...@u.washington.edu
wrote:
On Tue, 13 Oct 2009, AJ83 wrote:
I need to create a function to find all the prime numbers in an array. Can
anyone point me
see ?hist
On Tue, Oct 13, 2009 at 1:06 PM, Dmitry Gospodaryov
gospodar...@rambler.ru wrote:
Dear R developers,How I can build a histogram from matrix:
0 0.5 1
0.25 34 43 65
1 23 35 54
4 22 29 42
10 21 22 29
20 15 17 20
(first string is represented names of columns,
first column is
On second thought,
You'll have to reorganize your data first, and then check the function
histogram() in the package lattice.
cheers
On Wed, Oct 14, 2009 at 12:43 AM, joris meys jorism...@gmail.com wrote:
see ?hist
On Tue, Oct 13, 2009 at 1:06 PM, Dmitry Gospodaryov
gospodar...@rambler.ru
Dear Roman,
could you give us the trace given by traceback() ? I suspect the error
is resulting from the permutations and/or jackknife procedure in the
underlying functions specaccum and specpool.
You can take a look at the package R.huge, but that one is deprecated
already. There are other
(integer, length)
6: integer(nbins)
5: tabulate(bin, pd)
4: as.vector(data)
3: array(tabulate(bin, pd), dims, dimnames = dn)
2: table(y[, factor])
1: accumcomp(PoCom, y = PoEnv, factor1 = HM_sprem, method = exact)
Cheers,
Roman
On Mon, Oct 12, 2009 at 12:52 PM, joris meys jorism
I'm basically put off by the question itself. Plotting a 4-dimensional
graph is rather complicated if the world has only 3 dimensions. A
4-dimensional representation is typically a movie (with time as the
4th dimension). You could try to project a heatmap on a 3D surface
graph, but I doubt this
allocate vector of size 1.2 Gb
To: joris meys jorism...@gmail.com
I hope this workspace file attached is what you were looking for.
Cheers,
Roman
On Mon, Oct 12, 2009 at 2:07 PM, joris meys jorism...@gmail.com wrote:
It's easier if you just load the data in R, save the workspace and
send that one
Hi Emkay,
If you want to look at different plots together, you can also plot
them side by side in the same plot window.
You can specify this using for example:
par(mfcol=c(2,2))
( see ?par and check mfrow and mfcol)
or
layout(matrix(1:4,2,2))
(see ?layout and ?matrix)
eg :
x -
graph where. It's pretty straight forward.
Kind regards
Joris
On Sun, Oct 11, 2009 at 12:50 AM, joris meys jorism...@gmail.com wrote:
Hi Emkay,
If you want to look at different plots together, you can also plot
them side by side in the same plot window.
You can specify this using
First, you should define your function as :
test - function(cand2,phi,lambda,
whatever-arguments-you-want-to-use-further){... insert code here ...}
All variables you use inside a function only exist within that
function. Your parameters/arguments is the interface between the
function and the
Quite a strange error. The function installed.packages should be in
the utils package.
Try ?installed.packages and see if you get a help file. If it doesn't
find that function, there is a problem with your R installation.
It might be something went wrong with downloading the package itself.
DAAG
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