Re: [R] Re:How to create a R -application
On 7 Oct 2004 at 17:49, Adaikalavan Ramasamy wrote: This is not answering your question directly. I usually use the BATCH command for running R non-interactively. You can also use commandArgs() to get any arguments from the command line. For more information, see help(BATCH) or help(commandArgs). Or you can make a function from your commands and use it to process your data. See ?function and Writing your own functions in intro docs. Or you can copy/paste to some suitable text editor, save it as plain text and copy/paste it back to R later (with any modifications). Cheers Petr On Thu, 2004-10-07 at 16:14, Kunal Shetty wrote: Dear R- users and Helpers I am a beginner for R. I am using R to implement EM algorithm for treating Missing values. I would like to know how can save or compile my logical R commands to an application; so that the next time I could just execute the R- file. Example for calculating the mean of a data set x - c(8,11,16,18,6,4,20,25,9,13) u - mean(x) u Now I would like to save these commands as batch or an application Anybody could please help or direct me in this problem Thank you Regards Kunal __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Petr Pikal [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] reading partial file content
hi,
I'd like to extract data from very large files (ca 1-2 Mio lines),
and I already know which lines of these files I need.
Is there a way to do it without filling the memory with the whole file content?
The lines I need are randomly distributed within the files.
Thanks,
Marc
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Kunal Shetty
Sent: Friday, October 08, 2004 5:16 AM
To: Austin, Matt
Cc: R-help
Subject: RE: [R] Read.Table Reading a Text file
thanks austin, it worked..it was exactly what I was looking for
regards
Kunal
Austin, Matt [EMAIL PROTECTED] wrote:
x.1$V1
or
x.1[,1]
or
x.1['V1']
and you shouldn't need to call print.default() directly, just call
print().
--Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Kunal Shetty
Sent: Thursday, October 07, 2004 18:44 PM
To: [EMAIL PROTECTED]
Cc: R-help
Subject: Re: [R] Read.Table Reading a Text file
James
Thank you for response. I am working on treatment for missing
data for both bivariate and multivariate normal data. Coming back to
example. My problem was that once we do execute this command
x.1 - read.table('/tempxx.txt', fill=T)
How can access the particular column say X8 and all it's values so that I
could assign some other operations on them.
Because if I say
print.default(x.1)
the result..
V1 V2
1 Xy
2 810
3 11 1 4
4 16 16
5 18 15
6 620
7 4 4
8 20 18
9 2522
and I want to access V1 values.
thank you
regards
Kunal
[EMAIL PROTECTED] wrote:
If you have an unequal number of columns, then use 'fill=T' onread.table
It putsNAs.
Is this what youwant?
Here is what happens on the input file which is your data and someextra
columns:
8 10
11 14
16 16
18 15 12
6 20
44 12
20 18
x.1 - read.table('/tempxx.txt',fill=T)
x.1
X8X10
11 14 NA
16 16 NA
18 15 12
6 20 NA
4 4 12
20 18 NA
__
James HoltmanWhat is the problem you are trying tosolve?
Executive Technical Consultant -- Office of Technology,Convergys
[EMAIL PROTECTED]
+1 (513)723-2929
KunalShetty
[EMAIL PROTECTED] To:[EMAIL PROTECTED]
.educc:
Sent by: Subject: [R] Read.Table Reading a Textfile
[EMAIL PROTECTED]
ath.ethz.ch
10/07/200416:18
Dear R users andHelpers
I am beginner with using R and interested in carrying out certaintask
for
my statisticalresearch.
I am reading data for a text file, which could contain data infollowing
pattern
x y
8 10
11 14
16 16
18 15
6 20
4 4
20 18
As per the example I have two columns and 7 rows of data ineach.
However is real life data situation I may not know how many columnsare
present and how rows are present and also with the certain datais
missing. Yes I am assuming the data is delimited myTab.
My question or rather problem is I want read data from each colum saycol
x
(8,11,16,18âEUR¦.20) and store it into a variable so that I couldperform
some
operations onthem.
I have also looked into certain R-help for Read.table and data.framebut
still struggling on my requirement. Theyare
http://tolstoy.newcastle.edu.au/R/help/04/07/2040.html
http://tolstoy.newcastle.edu.au/R/help/04/07/3152.html
Regards
Kunal
__
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Re: [R] reading partial file content
Please do not tack your question on to a different one (as the posting guide does ask you not to). On Fri, 8 Oct 2004, Marc Mamin wrote: hi, I'd like to extract data from very large files (ca 1-2 Mio lines), and I already know which lines of these files I need. Is there a way to do it without filling the memory with the whole file content? Yes, several, and it has been discussed on this list on Wednesday, in a thread entitled `Performing Analysis on Subset of External data' Please look in the archives. The lines I need are randomly distributed within the files. [irrelevant other message discarded here.] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Read.Table Reading a Text file
On 7 Oct 2004 at 20:18, Kunal Shetty wrote: Dear R users and Helpers I am beginner with using R and interested in carrying out certain task for my statistical research. I am reading data for a text file, which could contain data in following pattern x y 8 10 1114 1616 1815 6 20 4 4 2018 As per the example I have two columns and 7 rows of data in each. However is real life data situation I may not know how many columns are present and how rows are present and also with the certain data is missing. Yes I am assuming the data is delimited my Tab. My question or rather problem is I want read data from each colum say col x (8,11,16,18?.20) and store it into a variable so that I could perform some operations on them. Hi Better to read by appropriate read.whatever() function to data frame, see eg. ?read.table I hope you have already read some intro documents in which there is stated how you could read your data and organize them. I also recommend to go through Paul Johnsons Rtips. You can find it by e.g. Google. Cheers Petr I have also looked into certain R-help for Read.table and data.frame but still struggling on my requirement. They are http://tolstoy.newcastle.edu.au/R/help/04/07/2040.html http://tolstoy.newcastle.edu.au/R/help/04/07/3152.html Regards Kunal __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Petr Pikal [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Read.Table Reading a Text file
Hi
you really should spend some time to go through introductory
documentation and do some examples provided.
snip
On 8 Oct 2004 at 3:15, Kunal Shetty wrote:
you probably read it by read.table without saying/specifying
header=TRUE so your X and y is included to your data not as
names but as values. Therefore V1 and V2 are factors.
Please consult especially R-intro manual in doc directory. It helps
you to save a lot of frustration and misunderstanding, especially at
the begging of your work with R.
And consider help list as a last source of help as what you have
learned yourself you remember better and you understand better.
Cheers
Petr
V1 V2
1 Xy
2 810
3 11 1 4
4 16 16
5 18 15
6 620
7 4 4
8 20 18
9 2522
and I want to access V1 values.
thank you
regards
Kunal
[EMAIL PROTECTED] wrote:
If you have an unequal number of columns, then use 'fill=T'
onread.table
It putsNAs.
Is this what youwant?
Here is what happens on the input file which is your data and
someextra
columns:
8 10
11 14
16 16
18 15 12
6 20
44 12
20 18
x.1 - read.table('/tempxx.txt',fill=T)
x.1
X8X10
11 14 NA
16 16 NA
18 15 12
6 20 NA
4 4 12
20 18 NA
__
James HoltmanWhat is the problem you are trying tosolve?
Executive Technical Consultant -- Office of Technology,Convergys
[EMAIL PROTECTED]
+1 (513)723-2929
KunalShetty
[EMAIL PROTECTED] To:[EMAIL PROTECTED]
.educc:
Sent by: Subject: [R] Read.Table Reading a Textfile
[EMAIL PROTECTED]
ath.ethz.ch
10/07/200416:18
Dear R users andHelpers
I am beginner with using R and interested in carrying out
certaintask
for
my statisticalresearch.
I am reading data for a text file, which could contain data
infollowing
pattern
x y
8 10
11 14
16 16
18 15
6 20
4 4
20 18
As per the example I have two columns and 7 rows of data ineach.
However is real life data situation I may not know how many
columnsare present and how rows are present and also with the
certain datais missing. Yes I am assuming the data is delimited
myTab.
My question or rather problem is I want read data from each colum
saycol
x
(8,11,16,18EUR.20) and store it into a variable so that I
couldperform
some
operations onthem.
I have also looked into certain R-help for Read.table and
data.framebut still struggling on my requirement. Theyare
http://tolstoy.newcastle.edu.au/R/help/04/07/2040.html
http://tolstoy.newcastle.edu.au/R/help/04/07/3152.html
Regards
Kunal
__
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https://stat.ethz.ch/mailman/listinfo/r-help
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Petr Pikal
[EMAIL PROTECTED]
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RE: [R] library in R2.0.0 - summary
Thanks to Andy Liaw and prof.Ripley for their comments. I finally managed my function set work without need for proper installation. However I must try it sometimes. I got tools from http://www.murdoch-sutherland.com/Rtools/tools.zip but I did not install Pearl yet. I tried make pkg-fun which resulted in sequence of errors which I corrected according what I was told by screen and documentation (best thanks to all who provided it) and finally I end with 1. modified DESCRIPTION file 2. functional set of my functions 3. error message perl: not found So next step will be trying to install perl (if I am allowed by suspicious network administrator) and completing the whole installation. Thanks again. Petr From: Petr Pikal Hi all I upgraded to 2.0.0 version and did everything as I used to do before. I installed windows binary, copy/paste other than bundled packages. I got e.g. library(chron) Error in library(chron) : 'chron' is not a valid package -- installed 2.0.0? so I loaded it from CRAN and everything worked OK except my own personal functions (they are not on CRAN). So I went through NEWS file which says: o Packages must have been re-installed for this version, and library() will enforce this. I have never done it, my simple set of functions was never actually installed. I used copy/paste the directory from old R version to new one and I used library(fun) in personal .Rprofile to load my function set. Doing that again I got: Error in library(fun) : There is no package called 'fun' I know I can use source source(D:/programy/R/rw2000/library/fun/R/fun) but I feel library way is better way and I think I could try it. Before I start to try transferring my function set to a real package I would like to ask simple ***question***. Is the error message result of not installing package fun correctly (at all) or I shall do something more than follow instructions in README.packages and other documentation? -- --- Thank you. Petr Pikal [EMAIL PROTECTED] Petr Pikal [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Bug in nlme under version 2.0.0
Dear all, Under version 2.0.0, I get the error below when calling summary() on a lme-object, whereas it works under version 1.9.1 (well, it did last week, before I upgraded). Any help on this? Thx in advance Søren library(nlme) mf - formula(Weight~Cu*(Time+I(Time^2)+I(Time^3))) lme1 - lme(mf, data = dietox, random=~1|Pig) summary(lme1) Linear mixed-effects model fit by REML Data: dietox AIC BIClogLik 4748.664 4815.081 -2360.332 Random effects: Formula: ~1 | Pig (Intercept) Residual StdDev:6.360083 3.116751 Fixed effects: Error in as.vector(x, list) : cannot coerce to vector __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Evaluating Assignment-Operator R 2.0.0
Dear Helpers, in which way I have to use the assignment-operator evaluating left to right with R 2.0.0? With R 2.0.0 (w2k-installation) the superassignment operator '-' seems to have a different behaviour compared with R 1.9.1 : x-4 x [1] 4 attr(x,'y')-5 Error: Object x not found Using earlier versions of R I never got this error. In the NEWS file and the docs coming along with R 2.0.0 I did not found anything concerning this problem. AFAIK '=' instead of '-' works - but is allowed only for toplevel- assignments. Thanks in advance, Friedemann __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] confidence interval for nls
Henrik Andersson [EMAIL PROTECTED] writes: I tried the example and it works fine, but why o why, do I not get any gradient from another prediction? Apparently this depends on whether you supply an RHS which returns the gradient. The built-in SS all do that. ##plot(yran~x) mich - function(x,K,rmax) rmax*x/(x+K) mm.nls - nls(yran~mich(x,K,rmax),start=list(K=5,rmax=3)) So: Here you need to add a gradient computation to mich(). One simple way (and pretty much what nls does internally) is mich - function(x,K,rmax) numericDeriv(quote(rmax*x/(x+K)),c(K,rmax), parent.frame()) (well, figuring out the parent.frame() bit wasn't all *that* trivial!) Or, nice when dealing with simple functions: mmDeriv - deriv(quote(rmax*x/(x+K)),c(K,rmax)) mich - function(x,K,rmax) eval.parent(mmDeriv) -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Evaluating Assignment-Operator R 2.0.0
On Fri, 8 Oct 2004, friedemann wrote: Dear Helpers, in which way I have to use the assignment-operator evaluating left to right with R 2.0.0? - is the operator you should normally use. With R 2.0.0 (w2k-installation) the superassignment operator '-' seems to have a different behaviour compared with R 1.9.1 : x-4 x [1] 4 attr(x,'y')-5 Error: Object x not found Using earlier versions of R I never got this error. In the NEWS file and the docs coming along with R 2.0.0 I did not found anything concerning this problem. Did you not notice NEWS contains o Complex superassignments were wrong when a variable with the same name existed locally, and were not documented in R-lang. AFAIK '=' instead of '-' works - but is allowed only for toplevel- assignments. = is allowed almost everywhere - is, and not just at top-level. I don't know what you are really trying to do, but x - 4 testit - function() attr(x,'y') - 5 testit() x works as documented, and that is the normal type of usage of superassignments. As the NEWS entry says, R-lang (`The R Language Definition') gives fuller details (and I guess the help page for - should point there). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Evaluating Assignment-Operator R 2.0.0
friedemann [EMAIL PROTECTED] writes: With R 2.0.0 (w2k-installation) the superassignment operator '-' seems to have a different behaviour compared with R 1.9.1 : x-4 x [1] 4 attr(x,'y')-5 Error: Object x not found Using earlier versions of R I never got this error. In the NEWS file and the docs coming along with R 2.0.0 I did not found anything concerning this problem. It's there. Look for complex superassignment. AFAIK '=' instead of '-' works - but is allowed only for toplevel- assignments. Eh? You mean assignments in the current environment? Why do you want to use - at top level (the command-line) anyway? -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-(wiki)-pedia?
Here's a function for searching the Rwiki from R:
rwiki.search - function(string){
RwikiURL=http://fawn.unibw-hamburg.de/cgi-bin/Rwiki.pl;
RwikiSearchURL=paste(RwikiURL(),?search=,string,sep='')
browseURL(RwikiSearchURL)
return(invisible(0))
}
Then you can do rwiki.search(gabor) and the results pop up in your
browser.
Perhaps we need some more documentation-getting functions in R, such as
this, something to search the mailing list archives, and maybe a
readPostingGuide() function...
Or is this spoonfeeding too much, and people should be able to go to a
web page and stick something in the search box?
Baz
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[R] submitting to R
Dear Colleagues, would you like to explain in which way we can get possibility to use some version of R for Window. Sincerely yours Ziedonis Greislis *** Dr. Ziedonis Grislis Head of Laboratory of Quantitative Genetics Department of Animal Science LatviaUniversity of Agriculture 2, Liela Str, Jelgava, LV-3001 LATVIA Tel.: +371-30-05661, +371-30- 05663 Fax: +371- 30-27238 E-mail: [EMAIL PROTECTED] ** __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Correlation Matrix
Hi, I'm dealing with a datamining analysis: I've a lot of categories of product sold per week (n. week =26, n. categories about 50. my dataframe is like this: Settimana ALIMENTI..ALTRI. ALIMENTI.APROTEICI 1 13 19 2 22 0 3 31 22 4 42 6 I computed correlation coefficents among categories having a correlation matrix (53X53). Now I will extract from this matrix only significative correlations, or, in alternative correlations 0.5 and -0.5, excluding the other, and put this coefficients in a dataframe. I'm looking for significative correlations among categories. Is someone could help me? Many thanks in advance. Is also someone using R for dataminig analysis like me? Vito = Diventare costruttori di soluzioni The business of the statistician is to catalyze the scientific learning process. George E. P. Box Visitate il portale http://www.modugno.it/ e in particolare la sezione su Palese http://www.modugno.it/archivio/cat_palese.shtml __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] submitting to R
Read the (Windows-)FAQ. Next time, please read the FAQ and the posting guide before posting to r-help... Christian On Fri, 8 Oct 2004, Ziedonis Grislis wrote: Dear Colleagues, would you like to explain in which way we can get possibility to use some version of R for Window. Sincerely yours Ziedonis Greislis *** Dr. Ziedonis Grislis Head of Laboratory of Quantitative Genetics Department of Animal Science LatviaUniversity of Agriculture 2, Liela Str, Jelgava, LV-3001 LATVIA Tel.: +371-30-05661, +371-30- 05663 Fax: +371- 30-27238 E-mail: [EMAIL PROTECTED] ** __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] submitting to R
try these urls: http://www.cran.mirrors.pair.com/bin/windows/ http://www.cran.mirrors.pair.com/bin/windows/base/ Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/16/396887 Fax: +32/16/337015 Web: http://www.med.kuleuven.ac.be/biostat/ http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm - Original Message - From: Ziedonis Grislis [EMAIL PROTECTED] To: '[EMAIL PROTECTED]' [EMAIL PROTECTED] Sent: Friday, October 08, 2004 1:21 PM Subject: [R] submitting to R Dear Colleagues, would you like to explain in which way we can get possibility to use some version of R for Window. Sincerely yours Ziedonis Greislis *** Dr. Ziedonis Grislis Head of Laboratory of Quantitative Genetics Department of Animal Science LatviaUniversity of Agriculture 2, Liela Str, Jelgava, LV-3001 LATVIA Tel.: +371-30-05661, +371-30- 05663 Fax: +371- 30-27238 E-mail: [EMAIL PROTECTED] ** __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Correlation Matrix
Vito Ricci wrote: Hi, I'm dealing with a datamining analysis: I've a lot of categories of product sold per week (n. week =26, n. categories about 50. my dataframe is like this: Settimana ALIMENTI..ALTRI. ALIMENTI.APROTEICI 1 13 19 2 22 0 3 31 22 4 42 6 I computed correlation coefficents among categories having a correlation matrix (53X53). Now I will extract from this matrix only significative correlations, or, in alternative correlations 0.5 and -0.5, excluding the other, and put this coefficients in a dataframe. I'm looking for significative correlations among categories. Is someone could help me? Many thanks in advance. Is also someone using R for dataminig analysis like me? Vito Assuming `x' is your data above, how about the following: r - cor(x) y - which(lower.tri(r), TRUE) z - data.frame(row = rownames(r)[y[, 1]], col = colnames(r)[y[, 2]], cor = r[y]) subset(z, abs(cor) 0.5) #row colcor # 1 ALIMENTI..ALTRI. Settimana -0.6324555 --sundar __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Correlation Matrix
Hi Sundar, many thanks for your suggestion: it's just I wished! Best Vito --- Sundar Dorai-Raj [EMAIL PROTECTED] ha scritto: Vito Ricci wrote: Hi, I'm dealing with a datamining analysis: I've a lot of categories of product sold per week (n. week =26, n. categories about 50. my dataframe is like this: Settimana ALIMENTI..ALTRI. ALIMENTI.APROTEICI 1 13 19 2 22 0 3 31 22 4 42 6 I computed correlation coefficents among categories having a correlation matrix (53X53). Now I will extract from this matrix only significative correlations, or, in alternative correlations 0.5 and -0.5, excluding the other, and put this coefficients in a dataframe. I'm looking for significative correlations among categories. Is someone could help me? Many thanks in advance. Is also someone using R for dataminig analysis like me? Vito Assuming `x' is your data above, how about the following: r - cor(x) y - which(lower.tri(r), TRUE) z - data.frame(row = rownames(r)[y[, 1]], col = colnames(r)[y[, 2]], cor = r[y]) subset(z, abs(cor) 0.5) #row colcor # 1 ALIMENTI..ALTRI. Settimana -0.6324555 --sundar = Diventare costruttori di soluzioni The business of the statistician is to catalyze the scientific learning process. George E. P. Box Visitate il portale http://www.modugno.it/ e in particolare la sezione su Palese http://www.modugno.it/archivio/cat_palese.shtml __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RWinEdt
Hi, I have troubles getting RWinEdt with the R2.0.0 Version startet. Do I have to install a different version of RWinEdt or WinEdt? I have RWinEdt 1.6.1 and WinEdt 5.3. Thanks Anna Hennig __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] RWinEdt
Anna: That is the most current version of RWinEdt. Uwe Ligges is working on a version for 2.0.0 so check back soon for a new release. http://cran.r-project.org/contrib/extra/winedt/ Also, when inquiring about a specific package it is often helpful to contact the maintainer directly and not R-help. HTH, Andy -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Friday, October 08, 2004 8:14 AM To: [EMAIL PROTECTED] Subject: [R] RWinEdt Hi, I have troubles getting RWinEdt with the R2.0.0 Version startet. Do I have to install a different version of RWinEdt or WinEdt? I have RWinEdt 1.6.1 and WinEdt 5.3. Thanks Anna Hennig __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RWinEdt
[EMAIL PROTECTED] wrote: Hi, I have troubles getting RWinEdt with the R2.0.0 Version startet. Do I have to install a different version of RWinEdt or WinEdt? I have RWinEdt 1.6.1 and WinEdt 5.3. You have either to wait for RWinEdt_1.6-2 (which already has been uploaded to CRAN's incoming area and waits for the CRAN maintainers to move it) or to follow the alternative way for installation described in the ReadMe, or to get it right now (but only temporarily available) from the following link: http://www.statistik.uni-dortmund.de/~ligges/RWinEdt_1.6-2.zip Maybe of interest to all the other R-WinEdt users (some of them already wrote private messages, which is the appropriate way in this case!): The new version of R-WinEdt is updated for use with R-2.0.0. Installation has been simplified, because Omegahat's SWinRegistry package is no longer required. The complete code from SWinRegistry has been included in the RWinEdt package, therefore many thanks to Duncan Temple Lang. Uwe Ligges Thanks Anna Hennig __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] submitting to R
On Fri, 8 Oct 2004 13:34:42 +0200, Dimitris Rizopoulos [EMAIL PROTECTED] wrote : try these urls: http://www.cran.mirrors.pair.com/bin/windows/ http://www.cran.mirrors.pair.com/bin/windows/base/ The pair.com mirror can certainly handle the traffic, but you might find one of the European mirrors (see the list at http://cran.r-project.org/mirrors.html) is faster from Leuven or Jelgava. Duncan Murdoch Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/16/396887 Fax: +32/16/337015 Web: http://www.med.kuleuven.ac.be/biostat/ http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm - Original Message - From: Ziedonis Grislis [EMAIL PROTECTED] To: '[EMAIL PROTECTED]' [EMAIL PROTECTED] Sent: Friday, October 08, 2004 1:21 PM Subject: [R] submitting to R Dear Colleagues, would you like to explain in which way we can get possibility to use some version of R for Window. Sincerely yours Ziedonis Greislis *** Dr. Ziedonis Grislis Head of Laboratory of Quantitative Genetics Department of Animal Science LatviaUniversity of Agriculture 2, Liela Str, Jelgava, LV-3001 LATVIA Tel.: +371-30-05661, +371-30- 05663 Fax: +371- 30-27238 E-mail: [EMAIL PROTECTED] ** __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] testing for differences in parameter estimates from parametric bootstrapping
Based on a rather complicated model I do parametric bootstrapping to obtain bootstrap distributions of the parameters of interest. What is the proper way to test whether the parameter estimates are significantly different (the differences in parameter estimates are expected from including different covariates in the model)? __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Bug in nlme under version 2.0.0
Søren Højsgaard wrote: Dear all, Under version 2.0.0, I get the error below when calling summary() on a lme-object, whereas it works under version 1.9.1 (well, it did last week, before I upgraded). Any help on this? Thx in advance Søren library(nlme) mf - formula(Weight~Cu*(Time+I(Time^2)+I(Time^3))) lme1 - lme(mf, data = dietox, random=~1|Pig) summary(lme1) Linear mixed-effects model fit by REML Data: dietox AIC BIClogLik 4748.664 4815.081 -2360.332 Random effects: Formula: ~1 | Pig (Intercept) Residual StdDev:6.360083 3.116751 Fixed effects: Error in as.vector(x, list) : cannot coerce to vector I can't reproduce this problem on a simple example like library(nlme) example(lme) summary(fm1) Can you give us more information on your platform, the version of nlme, and perhaps make the data set available on the Internet so we can try to reproduce the problem? Just as a guess, do you happen to have the lme4 package loaded before loading nlme? The two packages cannot be loaded simultaneously. This is detected if you load them in the order nlme, lme4 but not if you load them in the other order. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] provide extra variables to environment in call
Hi all,
Situation:
there is a function `f' already defined by someone and
provided in package. `f' looks like that:
f - function() {
x+1
}
i.e. `f' is not closed i.r.t. term `x'
now I have my own function `g', where I'd like
to override variable `x' while calling `f':
x - dummy gloabal value
g - function() {
x - 42
eval(f(), environment()) # how to make loacl `x' visible in `f'?
}
g() # = Error in x + 1 : non-numeric argument to binary operator
Here comes the question:
What is the right way to call `f' in order to override
global value of `x' with the local value defined within
of function `g' ?
I see that i've missed something in docs for eval/environments and related.
Thank you in advance.
--
Valery.
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RE: [R] provide extra variables to environment in call
Not an direct answer to your question, but why not do something like:
f - function() x + 1
x - 10
f()
[1] 11
g - function(x, ...) {
+ my.f - f
+ formals(my.f) - c(list(x=NULL), formals(f))
+ my.f(x, ...)
+ }
g(5)
[1] 6
Andy
From: Khamenia, Valery
Hi all,
Situation:
there is a function `f' already defined by someone and
provided in package. `f' looks like that:
f - function() {
x+1
}
i.e. `f' is not closed i.r.t. term `x'
now I have my own function `g', where I'd like
to override variable `x' while calling `f':
x - dummy gloabal value
g - function() {
x - 42
eval(f(), environment()) # how to make loacl `x' visible in `f'?
}
g() # = Error in x + 1 : non-numeric argument to binary operator
Here comes the question:
What is the right way to call `f' in order to override
global value of `x' with the local value defined within
of function `g' ?
I see that i've missed something in docs for
eval/environments and related.
Thank you in advance.
--
Valery.
__
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http://www.R-project.org/posting-guide.html
__
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Re: [R] provide extra variables to environment in call
Khamenia, Valery V.Khamenia at biovision-discovery.de writes:
:
: Hi all,
:
: Situation:
:
: there is a function `f' already defined by someone and
: provided in package. `f' looks like that:
:
: f - function() {
: x+1
: }
:
: i.e. `f' is not closed i.r.t. term `x'
:
: now I have my own function `g', where I'd like
: to override variable `x' while calling `f':
:
: x - dummy gloabal value
:
: g - function() {
: x - 42
: eval(f(), environment()) # how to make loacl `x' visible in `f'?
: }
:
: g() # = Error in x + 1 : non-numeric argument to binary operator
:
: Here comes the question:
:
: What is the right way to call `f' in order to override
: global value of `x' with the local value defined within
: of function `g' ?
:
: I see that i've missed something in docs for eval/environments and related.
f - function() x+1
g - function() {
x - 42
environment(f) - environment()
f()
}
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[R] polr and optim question
Hello again I am trying to fit an ordinal logistic model using the polr function from MASS. When I run model.loan.ordinal - polr(loancat~age + sex + racgp + yrseduc + needlchg + gallery + sniffball + smokeball + sniffher + smokeher + nicocaine + inject + poly(year.of.int,3) + druginj + inj.years) I get an error Error in optim(start, fmin, gmin, method = BFGS, hessian = Hess, ...) : non-finite value supplied by optim I checked in the MASS book, and in John Fox's book An R and S-Plus Companion to Applied Regression, I also checked in R-help, where a similar problem was solved by using as.ordered, but that did not help here. Any help appreciated Thanks Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] provide extra variables to environment in call
On Fri, 8 Oct 2004, Khamenia, Valery wrote:
Hi all,
Situation:
there is a function `f' already defined by someone and
provided in package. `f' looks like that:
f - function() {
x+1
}
i.e. `f' is not closed i.r.t. term `x'
now I have my own function `g', where I'd like
to override variable `x' while calling `f':
x - dummy gloabal value
g - function() {
x - 42
eval(f(), environment()) # how to make loacl `x' visible in `f'?
}
g() # = Error in x + 1 : non-numeric argument to binary operator
Here comes the question:
What is the right way to call `f' in order to override
global value of `x' with the local value defined within
of function `g' ?
This is messy because f() should not have been defined that way.
You can't do it without modifying (a copy of) f().
If the package has a namespace, so that you can't override the definition
of f() it may be impossible.
If you can override the definition of f() you can do something like
environment(f)-environment()
inside g(). On the other hand, you could then just replace the definition
of f() with one that takes x as an argument.
-thomas
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[R] constrained opt with lagrange multiplier example?
I'm curious to find out if there is an example of R code for optimization of two variable function, with contraints, using lagrange multiplier (using optim/nlm?). I have a problem that contains one discrete variable, but need a simple problem/example to start with. I haven't been able to find any examples and thought I should ask here before I plunged into writing a few miles of R code. Thanks, Jeff. -- Jeff D. Hamann Forest Informatics, Inc. PO Box 1421 Corvallis, Oregon 97339-1421 office 541-753-4218 fax 541-752-0288 home 541-754-1428 [EMAIL PROTECTED] http://www.forestinformatics.com __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] polr and optim question
Dear Peter, It's hard to know from your message what the source of the problem might be, but a good guess is that data are ill-conditioned in some way. Some things to check: What's the distribution of the response variable? (Are there many categories, some with very few observations?) How ill-conditioned is the model matrix? I hope this helps, John -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peter Flom Sent: Friday, October 08, 2004 9:18 AM To: [EMAIL PROTECTED] Subject: [R] polr and optim question Hello again I am trying to fit an ordinal logistic model using the polr function from MASS. When I run model.loan.ordinal - polr(loancat~age + sex + racgp + yrseduc + needlchg + gallery + sniffball + smokeball + sniffher + smokeher + nicocaine + inject + poly(year.of.int,3) + druginj + inj.years) I get an error Error in optim(start, fmin, gmin, method = BFGS, hessian = Hess, ...) : non-finite value supplied by optim I checked in the MASS book, and in John Fox's book An R and S-Plus Companion to Applied Regression, I also checked in R-help, where a similar problem was solved by using as.ordered, but that did not help here. Any help appreciated Thanks Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] problem Installing R 2.0.0 on SuSe 9.1
Hello: I first tried it by using ./configure with the source files, but found that there is a huge problem with the gcc-g77 package, then I tried using the RPM obtained from CRAN, getting the following, the first of which appears to be another manifestation of the g77 problem: linux:/tmp # rpm -i R-base-2.0.0-1.i586.rpm warning: R-base-2.0.0-1.i586.rpm: V3 DSA signature: NOKEY, key ID a3278da3 error: Failed dependencies: libg2c.so.0 is needed by R-base-2.0.0-1 libglade-gnome.so.0 is needed by R-base-2.0.0-1 libglade.so.0 is needed by R-base-2.0.0-1 Do you have a suggestion about what I (a suse beginner) should do in order to get R up and running under suse 9.1? I have done some looking around and I do not see any package on suse for version 3.3.3 of the gcc-g77 package that corresponds to the gcc-g++ version 3.3.3, and I don't know if I am up to changing the versions of everything, so I hope I don't have to do that. Thanks in advance. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Java and help.start() search engine
The latest Sun Java release is jre-1_5_0, and unlike the recent versions of j2re-1_4_2-0[2345], this one does work with Firefox 1.0PR, Mozilla 1.7.3 and Netscape 7.1 (and hopefully other Mozilla-based browsers). From http://plugindoc.mozdev.org/faqs/java.html: Java Runtime Environment 5.0 has been released, and fixes many problems users are having with Java. Go get it!. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Chernoff faces
Kenneth == Kenneth Cabrera [EMAIL PROTECTED] writes: Kenneth Hello everybody: Does any one has a function to build Chernoff Kenneth faces? Many of us don't think it's worth them. But we know that opinions differ and gladly incorporate (good quality) submissions of source code. R *is* an open source project and to some extent a community effort. Please don't hesitate to contribute and enter the hall of fame of R contributors :-) Martin An example code from H.P. Wolf (2003) can be found at: http://www.wiwi.uni-bielefeld.de/~wolf/ : S/R - functions : faces Wolfram __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Number of characters per line
Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit Received-SPF: none (hypatia: domain of [EMAIL PROTECTED] does not designate permitted sender hosts) X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch X-Spam-Checker-Version: SpamAssassin 2.63 (2004-01-11) on hypatia.math.ethz.ch X-Spam-Level: * X-Spam-Status: No, hits=1.9 required=5.0 tests=AWL,NO_REAL_NAME,RCVD_IN_BL_SPAMCOP_NET autolearn=no version=2.63 Hi all, how can I tell R after how many characters it should do a line break in its output? For example, instead of this output [1] 0.692927557 0.016564402 0.053789695 0.457274207 0.320261162 0.343467947 [7] 0.289319881 0.820783841 0.737314682 0.305060765 0.009107208 0.271747209 I'd like to have that output: [1] 0.692927557 0.016564402 0.053789695 0.457274207 [5] 0.320261162 0.343467947 0.289319881 0.820783841 [9] 0.737314682 0.305060765 0.009107208 0.271747209 Running R 1.9.1 (2004-06-21), ESS 5.1.21 from within XEmacs 21.4.15 (April 2004), Suse 9.1 I've tried to find out in FAQ and R-help archive, without success, so thanks a lot in advance for any help. Tobi __ Mit WEB.DE FreePhone mit hoechster Qualitaet ab 0 Ct./Min. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] creating named elements of lists on the fly
HI Folks, I'm trying to create a list with named elements. Only, I don't know the names of the elements a priori (they come from the data being calculated). Currently, my approach is to create an environment, then assign things to the environement, then as.list the environment to get a list. Running the code gives, for example: e2 - new.env(FALSE, NULL) assign(dude, 123, env=e2) assign(chick, 456, env=e2) as.list(e2) Error in as.vector(x, list) : cannot coerce to vector Is this the best way to make a list like this? Thanks, Ben __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Number of characters per line
Dear Tobi, You can use options(width=n.of.characters). I hope this helps, John -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, October 08, 2004 11:36 AM To: [EMAIL PROTECTED] Subject: [R] Number of characters per line Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit Received-SPF: none (hypatia: domain of [EMAIL PROTECTED] does not designate permitted sender hosts) X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch X-Spam-Checker-Version: SpamAssassin 2.63 (2004-01-11) on hypatia.math.ethz.ch X-Spam-Level: * X-Spam-Status: No, hits=1.9 required=5.0 tests=AWL,NO_REAL_NAME,RCVD_IN_BL_SPAMCOP_NET autolearn=no version=2.63 Hi all, how can I tell R after how many characters it should do a line break in its output? For example, instead of this output [1] 0.692927557 0.016564402 0.053789695 0.457274207 0.320261162 0.343467947 [7] 0.289319881 0.820783841 0.737314682 0.305060765 0.009107208 0.271747209 I'd like to have that output: [1] 0.692927557 0.016564402 0.053789695 0.457274207 [5] 0.320261162 0.343467947 0.289319881 0.820783841 [9] 0.737314682 0.305060765 0.009107208 0.271747209 Running R 1.9.1 (2004-06-21), ESS 5.1.21 from within XEmacs 21.4.15 (April 2004), Suse 9.1 I've tried to find out in FAQ and R-help archive, without success, so thanks a lot in advance for any help. Tobi __ Mit WEB.DE FreePhone mit hoechster Qualitaet ab 0 Ct./Min. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] creating named elements of lists on the fly
Dear Ben, Is this the kind of thing you had in mind? lst - list() element - a lst[[element]] - 1:5 element - b lst[[element]] - letters[1:5] lst $a [1] 1 2 3 4 5 $b [1] a b c d e I hope this helps, John -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ben Shapiro Sent: Friday, October 08, 2004 11:46 AM To: [EMAIL PROTECTED] Subject: [R] creating named elements of lists on the fly HI Folks, I'm trying to create a list with named elements. Only, I don't know the names of the elements a priori (they come from the data being calculated). Currently, my approach is to create an environment, then assign things to the environement, then as.list the environment to get a list. Running the code gives, for example: e2 - new.env(FALSE, NULL) assign(dude, 123, env=e2) assign(chick, 456, env=e2) as.list(e2) Error in as.vector(x, list) : cannot coerce to vector Is this the best way to make a list like this? Thanks, Ben __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Number of characters per line
[EMAIL PROTECTED] wrote: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit Received-SPF: none (hypatia: domain of [EMAIL PROTECTED] does not designate permitted sender hosts) X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch X-Spam-Checker-Version: SpamAssassin 2.63 (2004-01-11) on hypatia.math.ethz.ch X-Spam-Level: * X-Spam-Status: No, hits=1.9 required=5.0 tests=AWL,NO_REAL_NAME,RCVD_IN_BL_SPAMCOP_NET autolearn=no version=2.63 Hi all, how can I tell R after how many characters it should do a line break in its output? For example, instead of this output [1] 0.692927557 0.016564402 0.053789695 0.457274207 0.320261162 0.343467947 [7] 0.289319881 0.820783841 0.737314682 0.305060765 0.009107208 0.271747209 I'd like to have that output: [1] 0.692927557 0.016564402 0.053789695 0.457274207 [5] 0.320261162 0.343467947 0.289319881 0.820783841 [9] 0.737314682 0.305060765 0.009107208 0.271747209 ?options which states... 'width': controls the number of characters on a line. You may want to change this if you re-size the window that R is running in. Valid values are 10...1 with default normally 80. (The valid values are in file 'Print.h' and can be changed by re-compiling R.) Gav -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] [EMAIL PROTECTED] UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] creating named elements of lists on the fly
Ben Shapiro wrote: HI Folks, I'm trying to create a list with named elements. Only, I don't know the names of the elements a priori (they come from the data being calculated). Currently, my approach is to create an environment, then assign things to the environement, then as.list the environment to get a list. Running the code gives, for example: e2 - new.env(FALSE, NULL) assign(dude, 123, env=e2) assign(chick, 456, env=e2) as.list(e2) Error in as.vector(x, list) : cannot coerce to vector Is this the best way to make a list like this? Thanks, Ben You can use the [[ operator for list objects: nm - c(dude, chick) e2[[nm[1]]] - 123 e2[[nm[2]]] - 456 HTH, --sundar __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] creating named elements of lists on the fly
Ben Shapiro bshapiro-lists-R at getdown.org writes:
:
: HI Folks,
:
: I'm trying to create a list with named elements. Only, I don't know the
names of the elements a priori (they
: come from the data being calculated). Currently, my approach is to create an
environment, then assign
: things to the environement, then as.list the environment to get a list.
:
: Running the code gives, for example:
: e2 - new.env(FALSE, NULL)
: assign(dude, 123, env=e2)
: assign(chick, 456, env=e2)
: as.list(e2)
: Error in as.vector(x, list) : cannot coerce to vector
:
: Is this the best way to make a list like this?
:
: Thanks,
: Ben
If you need to add them one at a time then John Fox has
already provided an answer. If you want to create it
all at once and you have the contents in a list and
the names in a vector like this:
nams - letters[1:3]
contents - list(1:3, 4:5, 6:9)
# then here are two ways:
# 1
mapply({, nams, contents, SIMPLIFY = FALSE)
# 2
names(contents) - nams
contents
# Actually in your example the elements are all homogeneous so
# you could alternately use a vector to hold the results:
# 1a
contents - c(1, 2, 3)
mapply({, nams, contents)
# 2a
names(contents) - nams
contents
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[R] nlme vs gls
Dear List:
My question is more statistical than R oriented (although it originates
from my work with nlme). I know statistical questions are occasionally
posted, so I hope my question is relevant to the list as I cannot turn
up a solution anywhere else. I will frame it in the context of an R
related issue.
To illustrate the problem, consider student achievement test score data
with multiple observations available for each student. One way of
modeling these data might be
Y_{ti} = (\mu + \mu_{i} ) + (\beta_0 + \beta_{i} )*(time) +
\epsilon_{ti} ; t indexes time and i indexes student
The nlme code is
tt-lme(reponse~time, data, random=~time|ID)
With this, I can extract the growth rate for each individual in the data
set. Conceptually this is the sum of the main effect for time plus the
empirical bayes estimate for each individual:
\beta_0 + \beta_{i}
I can use the coef(tt, ...) to extract these coefficients.
Now, assume that I do not want to include random effects associated with
the slope and intercept, but instead use a gls to account for the
variances and covariances through an unstructured covariance matrix.
For example, assume the following model fit to the same data
Y_{ti} = \mu + \beta_0 * (time) + \epsilon_{ti}; where e~N(0, \Sigma)
With Sigma forming a more complex covariance matrix. We can use the gls
option as follows for example,
tt1-gls(response~time, data, correlation=corSymm(form=~1|ID),
weights=varIdent(form=~1|time))
On p. 254 of PB, they note that the mixed model gives as a by-product,
estimates for the random effects, which may be of interest in
themselves. And in my situation they are. Specifically, I want to
estimate the growth rate for each individual student.
My questions boils down to:
1) Is there any way possible to extract or to compute (estimate) the
growth rate of individual i when the data have been modeled using gls?
2) Can anyone point me to an example or reference where this has been
done? I have searched but have really turned up empty handed.
It seems that there must be a methodology for doing so as we are
accomplishing a similar task. Would there be information in the new
covariance matrix, Sigma, that would help play this role?
These only illustrate the issue, the actual model I am dealing with is
more complex, but the issue generalizes. Fitting random effects in the
current model I am dealing with is not a particularly attractive
solution. I actually have the issue layed out in more detail in a paper
I am working on and would be happy to share if requested.
I would appreciate any thoughts you might have on this problem.
Harold
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[R] reading Systat into R
How do I read a Systat file into R? The following email by Marc Schwartz http://tolstoy.newcastle.edu.au/R/help/04/06/1005.html deals with reading Systat on a Linux machine. I'm running R on Windows (precise version info below). A colleague sent me data in systat, a *.SYD file. Do I have to ask the colleague to re-save the data as Excel or text? (I tried opening it in SPSS, and SPSS also does not seem to recognize an SYD file.) Thanks for any info. Jake Wegelin version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor9.1 year 2004 month06 day 21 language R __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] reading Systat into R
On 10/08/04 12:02, Jacob Wegelin wrote: How do I read a Systat file into R? The following email by Marc Schwartz http://tolstoy.newcastle.edu.au/R/help/04/06/1005.html deals with reading Systat on a Linux machine. I'm running R on Windows (precise version info below). A colleague sent me data in systat, a *.SYD file. Do I have to ask the colleague to re-save the data as Excel or text? Unfortunately, yes, to my knowledge. Text, of course, could be SYC, or one of the various outputs that Systat produces. Because I used to use Systat, and many of my colleagues still do, I spent some time investigating this problem. Here are some excerpts from correspondence. Because one was just to me and not the list, I'm removing the From. I have the code, but I could not get it to work. I put it aside. I think it needs someone who is more familiar with c than I am (which doesn't take much). Jon --- Contact [EMAIL PROTECTED] because his dataload program will import from SYSTAT and output to an .rda file. But I fear that dataload is no longer available to new users, only those grandfathered in before a license issue came up. -Frank Thanks. DataLoad does have a free version, but the whole thing is Windows only. (Just search for dataload on Google.) If I had Windows, I'd have Systat. No, David gave me the ready-to-run linux executable. Never used it on windows. -- I've put three header files and two pre-ANSI C files in a tarball. I note that sys_errlist causes an error under compilation now, but for code last looked at 12 years ago, that's not bad. The reading code was written by me alone based on reverse engineering, but when I had a question - as you'll see from the code - someone I think called P. Fleury from Systat sent me some C that they'd been trying out, which I saw after writing my own. I think mine was more thorough. The endian-ness was because I needed to read and write on non-Intel machines (you may need the functions I used then - please ask if so, or substitute more modern ones if required). Please treat this as GPL - I think there was not difficulty with Systat at the time, and they knew that I had this on my ftp server then (a 1992 paper in Computers and Geosciences). I still have *.sys files that I could try it on if it works - please let me know if there are unresolved calls (walert() wrote an error message, for example). Best wishes, Roger [Bivand] From [EMAIL PROTECTED] Wed Jun 16 11:33:01 2004 The commercial package dbmscopy has a Linux version. I have used dbmscopy for several years and have been happy with it as it converts data files among many spreadsheets and statistics programs. http://www.conceptual.com/dbmscopt.htm However, somewhat recently they were purchased by SAS, so I'm not sure of current state of the program. There are probably other commercial packages as well. Anne Hi Jon and Anne! One other commercial product to check out is Stat/Transfer. More information on supported formats is at: http://www.stattransfer.com/html/formats.html They do support Windows, MacOS and Unix/Linux. Demo downloads are available from: http://www.stattransfer.com/html/download.html Unix/Linux pricing is available at: http://www.stattransfer.com/html/prices_-_unix.html. HTH, Marc Schwartz -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-(wiki)-pedia?
On Fri, 8 Oct 2004, Barry Rowlingson wrote:
Here's a function for searching the Rwiki from R:
rwiki.search - function(string){
RwikiURL=http://fawn.unibw-hamburg.de/cgi-bin/Rwiki.pl;
RwikiSearchURL=paste(RwikiURL(),?search=,string,sep='')
browseURL(RwikiSearchURL)
return(invisible(0))
}
Hmm, that's nice.
Then you can do rwiki.search(gabor) and the results pop up in your
browser.
Perhaps we need some more documentation-getting functions in R, such as
this, something to search the mailing list archives, and maybe a
readPostingGuide() function...
Or is this spoonfeeding too much, and people should be able to go to a
web page and stick something in the search box?
Some people need spoonfeeding, and sometimes its nice to be able to do
things more than one way.
rwiki.search('SearchFunctions')
help.search.archive-function(string){
RURL=http://www.google.com/u/newcastlemaths;
RSearchURL=paste(RURL,?q=,string,sep='')
browseURL(RSearchURL)
return(invisible(0))
}
help.search.archive('wiki')
Dave
--
Dave Forrest
[EMAIL PROTECTED](804)684-7900w
[EMAIL PROTECTED] (804)642-0662h
http://maplepark.com/~drf5n/
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Re: [R] reading Systat into R
Thanks to Jonathan and Marc for your swift replies. Here is how I solved the problem: I downloaded a 30 day trial version of systat from http://www.clecom.co.uk/science/systat/systat_download.html, installed it on my PC, opened the file in Systat, then used File, Save As and saved it in every imaginable format: Excel, ascii, SPSS, and SAS. The SPSS *.SAV file, when I opened it, proved not to have any data in it. It only contained the variable view not the data view. But the Excel file appears to contain the data. Jake Wegelin On Fri, 8 Oct 2004, Marc Schwartz wrote: On Fri, 2004-10-08 at 14:02, Jacob Wegelin wrote: How do I read a Systat file into R? The following email by Marc Schwartz http://tolstoy.newcastle.edu.au/R/help/04/06/1005.html deals with reading Systat on a Linux machine. I'm running R on Windows (precise version info below). A colleague sent me data in systat, a *.SYD file. Do I have to ask the colleague to re-save the data as Excel or text? (I tried opening it in SPSS, and SPSS also does not seem to recognize an SYD file.) Thanks for any info. Jake Wegelin Jacob, Stat/Transfer does support reading SYSTAT files on Windows. The W logos on the formats page (http://www.stattransfer.com/html/formats.html) indicate that those other particular formats are available on Windows only. SYSTAT file support is available on each supported OS. There are inexpensive academic/student prices available for Stat/Transfer if this is something that makes sense to invest in. If this is going to be a one-time issue, I would have your colleague re-save the data file to an ASCII CSV file, if possible. HTH, Marc __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] reading Systat into R
The SPSS *.SAV file, when I opened it, proved not to have any data in it. It only contained the variable view not the data view. But the Excel file appears to contain the data. My experience with getting spss files suggests that you might actually be seeing the file as a list. Look at help for ?read.spss. The most usable format to get a data frame is: dframe=read.spss(MyData.sav,to.data.frame=T) See if this doesn't do what you expect. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] nlme vs gls
One thing to be aware of (as Pinheiro and Bates point out on
the same page) is that the general random effects and gls
models are not nested. This means that the general covariance
matrix you estimate with gls may not correspond to *any*
random effects model. In that case there are no subject-
specific coefficients (e.g. slopes), in the random effects sense.
Rich Raubertas
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold
Sent: Friday, October 08, 2004 1:27 PM
To: [EMAIL PROTECTED]
Subject: [R] nlme vs gls
Dear List:
My question is more statistical than R oriented (although it
originates
from my work with nlme). I know statistical questions are occasionally
posted, so I hope my question is relevant to the list as I cannot turn
up a solution anywhere else. I will frame it in the context of an R
related issue.
To illustrate the problem, consider student achievement test
score data
with multiple observations available for each student. One way of
modeling these data might be
Y_{ti} = (\mu + \mu_{i} ) + (\beta_0 + \beta_{i} )*(time) +
\epsilon_{ti} ; t indexes time and i indexes student
The nlme code is
tt-lme(reponse~time, data, random=~time|ID)
With this, I can extract the growth rate for each individual
in the data
set. Conceptually this is the sum of the main effect for time plus the
empirical bayes estimate for each individual:
\beta_0 + \beta_{i}
I can use the coef(tt, ...) to extract these coefficients.
Now, assume that I do not want to include random effects
associated with
the slope and intercept, but instead use a gls to account for the
variances and covariances through an unstructured covariance matrix.
For example, assume the following model fit to the same data
Y_{ti} = \mu + \beta_0 * (time) + \epsilon_{ti}; where
e~N(0, \Sigma)
With Sigma forming a more complex covariance matrix. We can
use the gls
option as follows for example,
tt1-gls(response~time, data, correlation=corSymm(form=~1|ID),
weights=varIdent(form=~1|time))
On p. 254 of PB, they note that the mixed model gives as a
by-product,
estimates for the random effects, which may be of interest in
themselves. And in my situation they are. Specifically, I want to
estimate the growth rate for each individual student.
My questions boils down to:
1) Is there any way possible to extract or to compute (estimate) the
growth rate of individual i when the data have been modeled
using gls?
2) Can anyone point me to an example or reference where this has been
done? I have searched but have really turned up empty handed.
It seems that there must be a methodology for doing so as we are
accomplishing a similar task. Would there be information in the new
covariance matrix, Sigma, that would help play this role?
These only illustrate the issue, the actual model I am dealing with is
more complex, but the issue generalizes. Fitting random effects in the
current model I am dealing with is not a particularly attractive
solution. I actually have the issue layed out in more detail
in a paper
I am working on and would be happy to share if requested.
I would appreciate any thoughts you might have on this problem.
Harold
[[alternative HTML version deleted]]
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[R] Survey of moving window statistical functions - still looking f or fast mad function
Hi,
Lately I run into a problem that my code R code is spending hours performing
simple moving window statistical operations. As a result I did searched
archives for alternative (faster) ways of performing: mean, max, median and
mad operation over moving window (size 81) on a vector with about 30K
points. And performed some timing for several ways that were suggested, and
few ways I come up with. The purpose of this email is to share some of my
findings and ask for more suggestions (especially about moving mad
function).
Sum over moving window can be done using many different ways. Here are some
sorted from the fastest to the slowest:
1. runmean = function(x, k) {
n= length(x)
y= x[ k:n ] - x[ c(1,1:(n-k)) ] # this is a difference
from the previous cell
y[1] = sum(x[1:k]); # find the first sum
y= cumsum(y)# apply precomputed
differences
return(y/k) # return mean not sum
}
2. filter(x, rep(1/k,k), sides=2, circular=T) - (stats package)
3. kernapply(x, kernel(daniell, m), circular=T)
4. apply(embed(x,k), 1, mean)
5. mywinfun - function(x, k, FUN=mean, ...)
{ # suggested in news group
n - length(x)
A - rep(x, length=k*(n+1))
dim(A) - c(n+1, k)
sapply(split(A, row(A)), FUN, ...)[1:(n-k+1)]
}
6. rollFun(x, k, FUN=mean) - (fSeries package)
7. rollMean(x, k) - (fSeries package)
8. SimpleMeanLoop = function(x, k) {
n = length(x) # simple-minded loop used as a
baseline
y = rep(0, n)
k = k%/%2;
for (i in (1+k):(n-k)) y[i] = mean(x[(i-k):(i+k)])
}
9. running(x, fun=mean, width=k) - (gtools package)
Some of above functions return results that are the same length as x and
some return arrays with length n-k+1. The relative speeds (on Windows
machine) were as follow: 0.01, 0.09, 1.2, 8.1, 11.2, 13.4, 27.3, 63, 345. As
one can see there are about 5 orders of magnitude between the fastest and
the slowest.
Maximum over moving window can be done as follow, in order of speed
1. runmax = function(x, k) {
n = length(x)
y = rep(0, n)
m = k%/%2;
a = 0;
for (i in (1+m):(n-m)) {
if (a==y[i-1]) y[i] = max(x[(i-m):(i+m)]) # calculate
max of the window
else y[i] = max(y[i-1], x[i+m]); # max of the
window is =y[i-1]
a = x[i-m] # point that will be removed from the window
}
return(y)
}
2. apply(embed(x,k), 1, max)
3. SimpleMaxLoop(x, k) - similar to SimpleMeanLoop above
4. mywinfun(x, k, FUN=max) - see above
5. rollFun(x, k, FUN=max) - fSeries package
6. rollMax(x, k) - fSeries package
7. running(x, fun=max, width=k) - gtools package
The relative speeds were: 0.01, 3, 3.4, 5.3, 7.5, 7.7, 15.3
Median over moving window can be done as follows:
1. runmed(x, k) - from stats package
2. SimpleMedLoop(x, k) - similar to SimpleMeanLoop above
3. apply(embed(x,k), 1, median)
4. mywinfun(x, k, FUN=median) - see above
5. rollFun (x, k, FUN=median) - fSeries package
6. running(x, fun=max, width=k) - gtools package
Speeds: 0.01, 3.4, 9, 15, 29, 165
Mad over moving window can be done as follows:
1. runmad = function(x, k)
{
n = length(x)
A = embed(x,k)
A = abs(A - rep(apply(A, 1, median), k))
dim(A) = c(n-k+1, k)
apply(A, 1, median)
}
2. apply(embed(x,k), 1, mad)
3. mywinfun(x, k, FUN=mad) - see above
4. SimpleMadLoop(x, k) - similar to SimpleMeanLoop above
5. rollFun(x, k, FUN=mad) - fSeries package
6. running(x, fun=mad, width=k) - gtools package
Speeds: 11, 18, 25, 50, 50, 400
Some thoughts about those results:
* All functions from Stats package (runmed, filter, kernapply)
are fast and hard to improve on.
* In case of Mean and Max a simple un-optimized R codes are
much faster than specialized functions build for the same purpose.
* apply(embed(x,k), 1, fun) - seem to be always faster than
any functions from fSeries package or mywinfun
* running function from gtools package is horribly slow
compared to anything else
* mywinfun proposed as a faster version of
apply(embed(x,k), 1, fun) seems
Re: [R] RWinEdt
Hi,
All do also have troubles. In my case, I get the following message:
install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
package 'RWinEdt' successfully unpacked and MD5 sums checked
updating HTML package descriptions
local({pkg - select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Error in firstlib(which.lib.loc, package) :
couldn't find function lazyLoad
In addition: Warning message:
package RWinEdt was built under R version 2.0.0
Error in library(pkg, character.only = TRUE) :
.First.lib failed
Any help would be appreciated!!!
Emili
At 05:14 AM 10/8/2004, [EMAIL PROTECTED] wrote:
Hi,
I have troubles getting RWinEdt with the R2.0.0 Version startet.
Do I have to install a different version of RWinEdt or WinEdt?
I have RWinEdt 1.6.1 and WinEdt 5.3.
Thanks
Anna Hennig
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[R] Adding factor variable to a CoxPH
I think this is a pretty basic statistic question: If I have a variable which has 4 factors how can I add it to a coxph model? I have other variables added which have digits 1-4 instead of four factors. If I recode the variable will that work? Thanks Neil __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] polr problem solved
I'd like to thank John Fox and Chuck Cleland for their help in resovling this issue. It turned out to be something simple, but perhaps others have had similar problems In my original data frame, I had 4 categories of race/ethnicity. One of the categories (other) was very small, and not similar to any of the other three categories, so I created a new data frame deleting those people. However, the level other was still there, with no one in it. This didn't cause a problem for glm or lm, but it did for polr. When I eliminated that level, the problem disappeared. Thanks again for the help Peter Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RWinEdt
OK, now it's fine.
Thanks,
Emili
At 05:50 PM 10/8/2004, Emili Tortosa-Ausina wrote:
Hi,
All do also have troubles. In my case, I get the following message:
install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
package 'RWinEdt' successfully unpacked and MD5 sums checked
updating HTML package descriptions
local({pkg - select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Error in firstlib(which.lib.loc, package) :
couldn't find function lazyLoad
In addition: Warning message:
package RWinEdt was built under R version 2.0.0
Error in library(pkg, character.only = TRUE) :
.First.lib failed
Any help would be appreciated!!!
Emili
At 05:14 AM 10/8/2004, [EMAIL PROTECTED] wrote:
Hi,
I have troubles getting RWinEdt with the R2.0.0 Version startet.
Do I have to install a different version of RWinEdt or WinEdt?
I have RWinEdt 1.6.1 and WinEdt 5.3.
Thanks
Anna Hennig
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