[R] Hierarchical clustering : analysis of the cluster
Hi R lovers!
I am using the agnes function of the package cluster to compute a
hierarchical clustering.
I'd like to know if somebody has ever developped a function which could
give the names/label of the individuals merged together with respect to the
number of cluster the user eventually wants to keep.
Namely, If I have the dendogram and I choose to cut it to get , say 5
cluster, how can I get the names of the individuals in each of the 5
clusters?
I am looking for an algorithm that could do that.
I have tried to find one using the $merge component of the agnes.object or
the $order.lab component but with no result.
If by chance it exists already...
Thank you very much.
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[R] error message in fitdistr
Hi R lovers
Here is a numerical vector test
> test
[1] 206 53 124 112 92 77 118 75 48 176 90 74 107 126 99 84 114
147 99 114 99 84 99 99 99 99 99 104 1 159 100 53
[33] 132 82 85 106 136 99 110 82 99 99 89 107 99 68 130 99 99
110 99 95 153 93 136 51 103 95 99 72 99 50 110 37
[65] 102 104 92 90 94 99 76 81 109 91 98 96 104 104 93 99 125
89 99 99 108 90 105 92 106 103 99 99 99 94 102 103
[97] 97 99 118 91 110 99 99 99 98 105 99 97 99 101 95 98 99
102 99 99 99 99 95 93 86 96 113 87 112 120 71 99
[129] 99 81 96 113 85 116 112 84 120 88 97 104 99 105 153 103 92
99 99 99 90 108 104 99 105 97 94 93 99 85 91 99
[161] 118 99 91 99 103 101 102 96 99 123 85 101 88 99 93 73 97
89 94 69 74 99 97 91 92
Assuming it follows a lognormal distribution I'd like to determine the mean
and the sd thanks to maximum likelihood estimation
> fitdistr(test,"lognormal",start=list(200,10))
Error in print.fitdistr(structure(list(estimate = c(4.54666263736726, :
more elements supplied than there are to replace
I chose the parameter start randomly
I don't understand the error message. Has anybody ever encountered such
one?
thanks for the help
have a wonderful day
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[R] defining and plotting functions thanks to equation
Hi R lovers!
Are there any means to define and plot a function given the equation that
specifies the function?
For example I'd like to plot and work with the Gumbel Distribution density
defined by
Lambda(x)=exp(-exp(-x))
My question may appear very simple but I haven't got an idea yet about how
to do that. I could plot something with x a vector/set of value but I don't
know how to proceed with x belonging to a continuous interval
Thanks for any help.
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Re: [R] named list 'start' in fitdistr
Oups! I should have read further the help file...
Thank you very much
|-+>
| | [EMAIL PROTECTED]|
| | F.COM|
| ||
| | 07/25/03 05:02 PM|
| ||
|-+>
>--|
|
|
| To: Vincent STOLIAROFF/fr/[EMAIL PROTECTED]
|
| cc: [EMAIL PROTECTED]
|
| Subject: Re: [R] named list 'start' in fitdistr
|
>--|
An example in help(fitdistr) (R 1.7.1 for Windows) is "fitdistr(x,
dgamma, list(shape = 1, rate = 0.1), lower = 0.01)". Based on this,
have you tried the following:
>>fitdistr(test,"lognormal", start=list(meanlog=0, sdlog=1))
hope this helps. spencer graves
[EMAIL PROTECTED] wrote:
> Hi R lovers!
>
> I'd like to know how to use the parameter 'start' in the function
> fitdistr()
> obviously I have to provide the initial value of the parameter to
optimize
> except in the case of a certain set of given distribution
>
>
> Indeed according to the help file for fitdistr
> " For the following named distributions, reasonable starting values
> will be computed if `start' is omitted or only partially
> specified: `cauchy', `gamma', `logistic', `negative binomial' (R
> only, parametrized by `mu' and `size'), `t', `uniform', `weibull'.
"
>
>
> However I cannot fit an univariate distribution named 'test'
>
> I get this:
>
>
>>fitdistr(test,"lognormal")
>
> Error in fitdistr(test, "lognormal") : `start' must be a named list
>
>
>>fitdistr(test,"lognormal",start$meanlog=0,start$sdlog=1)
>
> Error: syntax error
>
> How I am supposed to type a value for start depending on the distribution
> on which I am fitting my set
>
> thanks
>
>
>
>
> **
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[R] named list 'start' in fitdistr
Hi R lovers!
I'd like to know how to use the parameter 'start' in the function
fitdistr()
obviously I have to provide the initial value of the parameter to optimize
except in the case of a certain set of given distribution
Indeed according to the help file for fitdistr
" For the following named distributions, reasonable starting values
will be computed if `start' is omitted or only partially
specified: `cauchy', `gamma', `logistic', `negative binomial' (R
only, parametrized by `mu' and `size'), `t', `uniform', `weibull'. "
However I cannot fit an univariate distribution named 'test'
I get this:
>fitdistr(test,"lognormal")
Error in fitdistr(test, "lognormal") : `start' must be a named list
> fitdistr(test,"lognormal",start$meanlog=0,start$sdlog=1)
Error: syntax error
How I am supposed to type a value for start depending on the distribution
on which I am fitting my set
thanks
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RE: [R] clearing some part of a graph
Many thanks
I don't see any other solution than what you've proposed.
I have tried the par(mfg=c(i,j,k,l))
But it overwrites rather than replaces the previous graph
take care
vincnet
|-+>
| | [EMAIL PROTECTED]|
| | .uk |
| ||
| | 07/15/03 03:53 PM|
| ||
|-+>
>--|
|
|
| To: Vincent STOLIAROFF/fr/[EMAIL PROTECTED], [EMAIL PROTECTED]
|
| cc:
|
| Subject: RE: [R] clearing some part of a graph
|
>--|
Dear Vincent,
You can't clear a title only. The idea is to plot without one, like
plot(...,main="",sub="",xlab="",ylab="")
and add the title by hand (as you mentioned).
Moreover, AFAIK you can't clear one plot in a multiple figure environment,
since you can only clear the graphics device (not the plot),
but you can put a new plot onto a specific part of your m.f.e. using
par(mfg=c(i,j))
see ?par and "An Introduction to R" for more details.
(I have to admit that I am unsure whether that will remove a plot there,
or create the new one on top of it - hiding the old one. That matters
with respect to dev.copy() I assume.)
HTH
Thomas
---
Thomas Hotz
Research Associate in Medical Statistics
University of Leicester
United Kingdom
Department of Epidemiology and Public Health
22-28 Princess Road West
Leicester
LE1 6TP
Tel +44 116 252-5410
Fax +44 116 252-5423
Division of Medicine for the Elderly
Department of Medicine
The Glenfield Hospital
Leicester
LE3 9QP
Tel +44 116 256-3643
Fax +44 116 232-2976
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED]
> Sent: 15 July 2003 14:31
> To: [EMAIL PROTECTED]
> Subject: [R] clearing some part of a graph
>
>
> Hi R lovers
>
> 2 questions:
>
> 1) I'd like to know how to clean the title, the sub title or
> the labels of
> a graph. I know how to redefine it with the function title() but it
> overwrites the previous title and do not replace it
>
> 2) How could I clear a whole plot (for example in a multiple figure
> environment)
>
> thanks for your help
> vincent
>
>
>
>
>
>
> **
> The sender's email address has changed to
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> personal address book. Please see http://www.sgcib.com for more
> information.
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[R] function acf in package ts
Hi R lovers!
I'd like to know if the 2 blue lines in the graph produced by the function
acf in the package ts represents the level for the test of significance of
the autocorrelation
thanks for help
vincent
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[R] clearing some part of a graph
Hi R lovers
2 questions:
1) I'd like to know how to clean the title, the sub title or the labels of
a graph. I know how to redefine it with the function title() but it
overwrites the previous title and do not replace it
2) How could I clear a whole plot (for example in a multiple figure
environment)
thanks for your help
vincent
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[R] R and Latex's tables
Hi R lovers!
I have discovered recently that graph can be exported from R in a Latex
compatible file
thanks to the pictex command
I would like to know if there is the equivalent while exporting datas.
Let's say I have a matrix, a data.frame or a list that I would like to
export as a flat text file that is immediatly transcripted into a table
into latex
Is there a macro or package that could transcript it with the tabular or
array environment command, ...
\begin{tabular/array}
..&.&. \\
etc
It would be easier than to use the write.table() function and then
transform my txt file into a latex table manually
thanks a lot
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RE: [R] writing comments within a function
Thanks you everybody for all your answers
|-+>
| | [EMAIL PROTECTED]|
| | .uk |
| ||
| | 06/06/03 01:32 PM|
| ||
|-+>
>--|
|
|
| To: Vincent STOLIAROFF/fr/[EMAIL PROTECTED], [EMAIL PROTECTED]
|
| cc: [EMAIL PROTECTED]
|
| Subject: RE: [R] writing comments within a function
|
>--|
> -Original Message-
> From: Ott Toomet [mailto:[EMAIL PROTECTED]
> Sent: 06 June 2003 12:05
> To: [EMAIL PROTECTED]
> Cc: [EMAIL PROTECTED]
> Subject: Re: [R] writing comments within a function
>
>
> | From: [EMAIL PROTECTED]
> | Date: Fri, 6 Jun 2003 11:57:32 +0200
>
> Hallo,
>
> | Hi R lovers!
> |
> | I would like to know how you can write comments inside the
> code of a
> | function
> |
> | is it latex style
> | % ?
> | or any other language style?
>
> It's #, otherwise like tex. The same character is used by gnuplot and
> many configuration scripts and probably by many programming languages
> too.
>
> You may also consider
>
> if(FALSE) {
> ...
> }
>
> But this "comment" must be syntactically correct. You may also
> consider emacs+ESS which includes possibilities to commenting and
> uncommenting large program blocks.
>
> I don't know where it is mentioned explicitly (I did not see it in "S
> Programming" (a book)), but most examples include comments, I guess.
It is stated in the "R Language Definition" manual, section 10.2, which
usually comes with the distribution.
Best wishes
Thomas
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[R] writing comments within a function
Hi R lovers!
I would like to know how you can write comments inside the code of a
function
is it latex style
% ?
or any other language style?
thanks a lot
*
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[R] counting missing values
Hello R lovers
I have written a little cute function to count the number of missing value
per row in a matrix and return the percentage of missing value
it takes a lot of time to run with a 1000 rows matrix
I'd like to know if there is a function already implemented to count the
number of occurence of a given values in a vector
For information,
here is the function
count<-0
for (i in 1:nrow(Matrix))
{
for (j in 1:ncol(Matrix)) {if (is.na(Matrix[i,j])) count<-count+1}
Result[i,1]<-((count/(ncol(Matrix)))*100);
count<-0
}
Result
thanks for any help
Vincent
*
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[R] authorized characters and symbols
Hi R lovers
Obviously I cannot use the underscore "_ " character to name an object in R
Is there a special reason for that ?
I want to use it to rename a function
maybe the problem is due to the nature of the object I work on
thanks for any comments on that very little and not very bothering trouble
*
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RE: [R] writing several command line in R console
Thanks to all
1) OK for the "+" sign and the problem of syntactelly unbreaking when you
open a { or a (
2) Thanks for the advise to use another editor for the functions. And then
the source() function. I tried it succesfully
Long life to R!
From: "Henrik Bengtsson" <[EMAIL PROTECTED]>
To: "'Vincent Stoliaroff'" <[EMAIL PROTECTED]>,
<[EMAIL PROTECTED]>
Subject: RE: [R] writing several command line in R console
Date: Tue, 4 Mar 2003 14:04:13 +1100
The R prompt should be though of as a one line editor or rather one
expression editor. You can not "step" between lines etc while editing an
expression. The "+" in front of each row placed there by R indicating
that even if you have typed ENTER the expression is not finished and
that R expect you to close it (normally by closing brackets, parentesis
etc). The "+" is just an indicator and will not be included in your
expression.
What you really want to do when you create functions etc is to write the
up in an external text editor, save them with the extension *.R, e.g.
"twosam.R", and the use source to read the function in to R, i.e.
> source("twosam.R")
Make sure to save your twosam.R file as *text*. If you're using Windows
you can use Notepad to do this. Also, you have to save the file in the
working directory of R. You can find the current working directory of R
by
> getwd()
Alternatively, you'll have to specify the full path to the file when
using source
> source("C:/My Documents/hb/twosam.R")
Hope this helps!
Henrik Bengtsson
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Vincent
> Stoliaroff
> Sent: den 4 mars 2003 13:36
> To: [EMAIL PROTECTED]
> Subject: [R] writing several command line in R console
>
>
>
> Hi R lovers
>
> I would like to know how to step to the next line in the R
> console editor
> without breaking the continuity of my code
> more clearly : if for example I write a function, so far i
> have to write the
> all code inside on the same line wich may become obscure as
> the function is
> more and more complex.
> I would like to do like in the example of the manuels:
>
> >twosam <- function(y1, y2) {
> n1 <- length(y1); n2 <- length(y2)
> yb1 <- mean(y1); yb2 <- mean(y2)s1 <- var(y1);
> s2 <- var(y2)
> s <- ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2)
> tst <- (yb1 - yb2)/sqrt(s2*(1/n1 + 1/n2))tst }
>
>
> all I can do is something like that:
>
> >twosam <- function(y1, y2) {n1 <- length(y1); n2 <- length(y2)
>
> +yb1 <- mean(y1); yb2 <- mean(y2)s1 <- var(y1);
> s2 <- var(y2)
> +s <- ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2)
> + tst <- (yb1 - yb2)/sqrt(s2*(1/n1 + 1/n2))tst }
>
> with the sign "+" in front of each line
> What does this sign mean? and how could I solve my problems Thanks
>
> __
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[R] writing several command line in R console
Hi R lovers
I would like to know how to step to the next line in the R console editor
without breaking the continuity of my code
more clearly : if for example I write a function, so far i have to write the
all code inside on the same line wich may become obscure as the function is
more and more complex.
I would like to do like in the example of the manuels:
twosam <- function(y1, y2) {
n1 <- length(y1); n2 <- length(y2)
yb1 <- mean(y1); yb2 <- mean(y2)s1 <- var(y1);s2 <- var(y2)
s <- ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2)
tst <- (yb1 - yb2)/sqrt(s2*(1/n1 + 1/n2))tst }
all I can do is something like that:
twosam <- function(y1, y2) {n1 <- length(y1); n2 <- length(y2)
+yb1 <- mean(y1); yb2 <- mean(y2)s1 <- var(y1);s2 <- var(y2)
+s <- ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2)
+ tst <- (yb1 - yb2)/sqrt(s2*(1/n1 + 1/n2))tst }
with the sign "+" in front of each line
What does this sign mean? and how could I solve my problems
Thanks
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RE: [R] Clustering partition and memory
Thanks. Clara() is performing well. I had a dataset of 7500 rows and the clustering was produced very quickly From: "Adaikalavan Ramasamy" <[EMAIL PROTECTED]> To: "Vincent Stoliaroff" <[EMAIL PROTECTED]>,<[EMAIL PROTECTED]> Subject: RE: [R] Clustering partition and memory Date: Sun, 9 Feb 2003 19:50:24 +0800 What distance metric are you using? See if clara() in cluster library etc is more appropriate. -----Original Message- From: Vincent Stoliaroff [mailto:[EMAIL PROTECTED]] Sent: Sunday, February 09, 2003 7:33 PM To: [EMAIL PROTECTED] Subject: [R] Clustering partition and memory Dear R-help list members i would like to use R to produce clustering or partitioning of a dataset. I am trying to use the functions: - hierclust() of the package multiv -pam(), agnes() and fanny() of the package cluster But I cannot get any result because of lack of memory. Would you know any clustering function not to greedy in memory? I have tried to expand my memory limit with memory.limit() but no significant results. Thank you for any answer that could help. Vincent __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Clustering partition and memory
Dear R-help list members i would like to use R to produce clustering or partitioning of a dataset. I am trying to use the functions: - hierclust() of the package multiv -pam(), agnes() and fanny() of the package cluster But I cannot get any result because of lack of memory. Would you know any clustering function not to greedy in memory? I have tried to expand my memory limit with memory.limit() but no significant results. Thank you for any answer that could help. Vincent __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] correspondance analysis & clustering
Hi 1) I am using the function ca() of the package multiv to make a correspondance analysis of a matrix of categorical datas which are numericaly coded. I would like to be sure that it is considered as a matrix of categorical datas and not numerical. I cannot find any explicit mention of that in the help file for this function 2) I would like to take the resulting matrix rproj to do a clustering. I use hierclust() and partition() of the package multiv regarding hierclust() when I use the method number 1 i get this error: Error in hclust(a, method) : invalid clustering method when I change the number of the method I get Error in pmatch(x, table, duplicates.ok) : argument is not of mode character As for the partition() function, I also have some troubles. It seems I should mention a vector of clustered centers for initiating the iterative optimization process. But I do not know where to enter it. I get the following message Error in matrix(0, ng, m) : non-numeric matrix extent Has anybody ever encountered those problems? Thanks a lot _ MSN Search, le moteur de recherche qui pense comme vous ! __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Downloading Package
Thank you very much to you 3 I didn't know it was possible to download, update and load the package directly within R. It is pretty convenient... Eventhough my system was not correctly set up because I cannot open any url from R I finally succeed in installing the package after downloading it directly from http://www.stat.math.ethz.ch/CRAN/bin/windows/contrib/multiv.zip and then installing it "from a local zip file" Thanks again. From: "Warnes, Gregory R" <[EMAIL PROTECTED]> To: "'Peter von Rohr'" <[EMAIL PROTECTED]>, Vincent Stoliaroff <[EMAIL PROTECTED]> CC: [EMAIL PROTECTED] Subject: RE: [R] Downloading Package Date: Thu, 30 Jan 2003 10:03:35 -0500 If your system is set up appropriately, you should be able to use the menu "Packages -> Install Packages from Cran" to get a list of packages, then select the desired package and press OK. -Greg > -Original Message- > From: Peter von Rohr [mailto:[EMAIL PROTECTED]] > Sent: Thursday, January 30, 2003 6:57 AM > To: Vincent Stoliaroff > Cc: [EMAIL PROTECTED] > Subject: Re: [R] Downloading Package > > > Hello Vincent, > > > > I am a beginner in using R so my question could seem very > simple. I would > > like to download the package multiv to do multivariate data > analysis. The > > package I download seems to be a file meant for UNIX and I > am using a Window > > OS. How could I download and install correctly this file? > > although i am not using R for windows, but there are binaries for > windows available for multiv at: > http://www.stat.math.ethz.ch/CRAN/bin/windows/contrib/multiv.zip > > you may want to read the documentation about how to install > pakages from > http://stat.ethz.ch/CRAN/doc/manuals/R-admin.pdf (chapter 5). > > depending on where you are physically, you may want to select another > cran mirror for a list of mirrors see: > http://cran.r-project.org/mirrors.html > > hth, peter > > -- > Peter von Rohr http://www.inf.ethz.ch/~vonrohr > Institute of Scientific Computing[EMAIL PROTECTED] > ETH-Zentrum, HRS H23 phone: +41 1 632 7473 > CH - 8092 Zurich fax: +41 1 632 1374 > > __ > [EMAIL PROTECTED] mailing list > http://www.stat.math.ethz.ch/mailman/listinfo/r-help > LEGAL NOTICE\ Unless expressly stated otherwise, this message is ... [[dropped]] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help _ MSN Search, le moteur de recherche qui pense comme vous ! __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Downloading Package
Hello, I am a beginner in using R so my question could seem very simple. I would like to download the package multiv to do multivariate data analysis. The package I download seems to be a file meant for UNIX and I am using a Window OS. How could I download and install correctly this file? Thanks a lot _ MSN Messenger : discutez en direct avec vos amis ! http://www.msn.fr/msger/default.asp __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
