Re: [R] Proba( Ut+2=1 / ((Ut+1==1) (Ut==1))) ? Thanks
Thank you all for all your answers. I see than there are many ways to solve my question ! Thank you very much. __ R-help@stat.math.ethz.ch 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] How to override coerion error in 'scan'
Kittler, Richard wrote: Uwe, Thanks. I did find something in the archives about using a custom colClass of 'num' with read.csv and using setAs to define a character - num function. From the read.table code this appears to force 'scan' to read it as character and then convert it later using 'as'. I'm not sure if there is any advantage in this approach to just reading it using a colClass of 'character' and then converting it myself afterward (?) No, I think you are looking for something fuzzy that does not exist, AFAIK. Sorry, I was too short, here. I mean read it in as character. Then use some function (e.g. using regular expressions) to detect what is numeric and what not (e.g. 03/15/200523:56:03), replace the latter by NA and convert to numeric. Uwe --Rich Richard Kittler AMD TDG 408-749-4099 -Original Message- From: Uwe Ligges [mailto:[EMAIL PROTECTED] Sent: Saturday, April 23, 2005 6:50 AM To: Kittler, Richard Cc: r-help@stat.math.ethz.ch Subject: Re: [R] How to override coerion error in 'scan' Kittler, Richard wrote: I am using 'read.csv' in V2.0.1 to read in a CSV file with the colClasses option and am getting an error from 'scan' when it encounters a non-numeric value for a 'numeric' column, i.e. ds - read.csv(in_file, nrows=irow, row.names=NULL, colClasses=zclass, comment.char=) Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : scan expected a real, got 03/15/200523:56:03 Is there a way to override this and just have it convert those values to NA? The dataset is large so I would prefer not to have to import the columns as character and convert them to numeric afterward. I think you have to read it in as character - or write your own C-level facility... Uwe Ligges --Rich Richard Kittler AMD TDG 408-749-4099 __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Garbled plot label
Marc Schwartz (MSchwartz at MedAnalytics.com) wrote Here is another option. One issue is that given the way in which plot.lm () is coded, some of the axis labels are hard coded when passed to the four underlying plot functions and as far as I can tell, there is no way to use a 'par' and just blank out the x axis labels only. Thus, both x and y axis labels need to be blanked and then separately created using title(). Thus, here is a plot.lm2() function. It's a bit kludgy, but it seems to work, though other eyes should look at it for any errors. What it effectively does is to do each of the four plots in plot.lm() individually without labels (ann = FALSE) and then adds them, generally based upon the way it is done in plot.lm(). The x axis labels are paste ()'d to the wrapped model expression to create a multi-line sub.title for each plot. The wrap.len argument is the 'width' argument for strwrap indicating the target line wrapping length. Note that if you get to around 3 lines, you will likely need to modify the margins in the plot for side 1 to provide for more room. I cannot see how to set this up so that it works in every situation. The only clean and simple way that I can see to handle the problem is to set a default that tests whether the formula is broken into multiple text elements, and if it is then omit it. Users can then use their own imaginative skills, and such suggestions as have been made on r-help, to construct whatever form of labeling best suits their case, their imaginative skills and their coding skills. The web page http://wwwmaths.anu.edu.au/~johnm/r/plot-lm/ has image files plot.lm.RData and plot6.lm.RData that are proposals for a revised version of plot.lm(). The changes made so far do not deal with the long formula issue, but if nothing better turns up my proposal will be to proceed as I have just indicated. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Bioinformation Science, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. __ R-help@stat.math.ethz.ch 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] Problems installing and updating packages for 2.1.0 on Windows 2000
Greg Blevins wrote: Hello, I am running R 2.1.0 on Windows 2000. When I attempt to install or update packages, regardless of whether I use the menu or command line, I get the following error. utils:::chooseCRANmirror() utils:::menuInstallPkgs() Warning message: unable to connect to 'cran.cnr.Berkeley.edu' on port 80. Warning: unable to access index for repository http://cran.cnr.Berkeley.edu/bin/windows/contrib/2.1 Warning message: unable to connect to 'www.stats.ox.ac.uk' on port 80. Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.1 Error in install.packages(NULL, .libPaths()[1], dependencies = TRUE, type = type) : no packages were specified I have uninstalled and reinstalled R 2.1.0 to no avail. I read through the recent treads on similar problems, but if an answer to my problem we given, I missed it. It sounds as though you need to configure a proxy for Internet access. See the discussion in the R for Windows FAQ (which gives other possibilities too). Duncan Murdoch __ R-help@stat.math.ethz.ch 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] writing a data frame in excel format
I save my data(frames) in csv format, which can be opened by any spreadsheet application: R write.table( myData, myFile.csv, col.names = NA, sep = , ) Arne On Tuesday 26 April 2005 04:28, Mario Morales wrote: Hello I know how read a file in excel format into a R data frame using the RODBC library, but I don't know how write a R data frame in excel format. I don't understand the instructions from RODBC user manual. To read an excel file I use. library(RODBC); conex-odbcConnectExcel(fis_quim.xls); sqlTables(conex); data-sqlFetch(conex,hoja1); Suppose I modify data and I want to save it as an excel file, How do I do that? Thanks for your help Mario Alfonso Morales Rivera Profesor Auxiliar. Departamento de Matemáticas y Estadistica. Universidad de Córdoba. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ R-help@stat.math.ethz.ch 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] Index matrix to pick elements from 3-dimensional matrix
Hello Juhana
try this (but there must be a better way!)
stratified.select - function(A,J){
out - sapply(J,function(i){sample(A[,,i],1)})
attributes(out) - attributes(J)
return(out)
}
A - array(letters[1:12],c(2,2,3))
J - matrix(c(1,2,3,3),2,2)
R stratified.select(A,J)
[,1] [,2]
[1,] b i
[2,] g k
R stratified.select(A,J)
[,1] [,2]
[1,] d j
[2,] f l
R
best wishes
Robin
On Apr 26, 2005, at 05:16 am, juhana vartiainen wrote:
Hi all
Suppose I have a dim=c(2,2,3) matrix A, say:
A[,,1]=
a b
c d
A[,,2]=
e f
g h
A[,,3]=
i j
k l
Suppose that I want to create a 2x2 matrix X, which picks elements
from the above-mentioned submatrices according to an index matrix J
referring to the depth dimension:
J=
1 3
2 3
In other words, I want X to be
X=
a j
g l
since the matrix J says that the (1,1)-element should be picked from
A[,,1], the (1,2)-element should be picked from A[,,3], etc.
I have A and I have J. Is there an expression in A and J that creates
X?
Thanks
Juhana
[EMAIL PROTECTED]
--
Juhana Vartiainen
docent in economics
Director, FIEF (Trade Union Foundation for Economic Research,
Stockholm), http://www.fief.se
gsm +46 70 360 9915
office +46 8 696 9915
email [EMAIL PROTECTED]
homepage http://www.fief.se/staff/Juhana/index.html
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Uncertainty Analyst
Southampton Oceanography Centre
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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Re: [R] writing a data frame in excel format
Hi Arne On 26 Apr 2005 at 9:29, Arne Henningsen wrote: I save my data(frames) in csv format, which can be opened by any spreadsheet application: R write.table( myData, myFile.csv, col.names = NA, sep = , ) Or you can write it as write.table(r.data.frame, excel.file.xls, sep=\t, na=, row.names=F) which I can usually open in Excel just by clicking on it. Cheers Petr Arne On Tuesday 26 April 2005 04:28, Mario Morales wrote: Hello I know how read a file in excel format into a R data frame using the RODBC library, but I don't know how write a R data frame in excel format. I don't understand the instructions from RODBC user manual. To read an excel file I use. library(RODBC); conex-odbcConnectExcel(fis_quim.xls); sqlTables(conex); data-sqlFetch(conex,hoja1); Suppose I modify data and I want to save it as an excel file, How do I do that? Thanks for your help Mario Alfonso Morales Rivera Profesor Auxiliar. Departamento de Matemticas y Estadistica. Universidad de Crdoba. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ R-help@stat.math.ethz.ch 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] __ R-help@stat.math.ethz.ch 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] R - C programm. calling load() from within C code
Hi!
This is the first time I'm trying to write a C program to be linked with R by
my own and I've got one (main) problem
1) I've got a stack of big matrixes, so to manage them I' using save() in the
preparation process to save workspace (they are about 1000 matrixes and each
one occupies 4.2 MB in my hard disk):
for ( i in 1:1000) {
...
save(temp, file=paste(temp_matrix,i,R.sav,sep=))
}
Later on, I would need to be able to use something like
load(paste(temp_matrix,i,R.sav,sep=))
to reload the corresponding matrix in each of the loops running within the C
code, and to be able to load this matrix, (called temp) into the C code.
I've tried to load the vector into the R workspace using load(a[i]) where a
is a vector with names of the maps, and also passing a list a in the call to
the C code, where each element of the list a[[i]] is the name of each map,
and tried to extract this names in the list to be used along with the
expresion, but nothing works.
With the html R-extensions help I've been able to load existing R objects in
run time into C, but I'm not able to use load() to put saved R object into
the R workspace and load them in C afterwards. Please, have anyone tried to
use this succesfully? Or you have any clue?
Thanks a lot for your help
Best regards,
Javier
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Re: [R] panel ordering in nlme and augPred plots
Hi So FYI attached is source file limity.txt which, with the code limity.1 - dget(limity.txt) limity.gr - groupedData(konverze~tepl|spol.f, limity.1, order.groups=F) plot(limity.gr) # panel order is OK fit.nlsList1 - nlsList(SSfpl,limity.gr) fit.nlme1 - nlme(fit.nlsList1, random=xmid+scal~1) plot(augPred(fit.nlme1, level=0:1)) # panel order is mismatched gives me different ordering of these two plots. After ooo - order(limity.gr$zdrzeni, limity.gr$mvykon.c) limity.gr - update(limity.gr[ooo,]) both plots are in the same (correct) order. The key is probably in order of limity.gr file, which is different after updating. Cheers Petr On 25 Apr 2005 at 18:25, Deepayan Sarkar [EMAIL PROTECTED] wrote: Thank you. On 25 Apr 2005 at 10:29, Deepayan Sarkar wrote: On Monday 25 April 2005 09:40, Petr Pikal wrote: Dear all I am trying nlme together with Pinheiro/Bates book. I constructed grouped data object with suitable plotting layout (according to some common factor, panels from bottom to top are in increasing order). When I do nlme(... some stuff...) I get fitted object which I can plot with plot(augPred(fit.nlme6, level=0:1)) but it results in completely different ordering. Is there any way how I can plot panels in some defined order e.g. Could you give us a reproducible example? Following the example on the help page Not yet, I try. I made my grouped.data with ooo ordering limity.gr-groupedData(konverze~tepl|spol.f, limity[ooo,], order.groups=F) which led to correct ordering in plot(limity.gr) but it probably left limity.gr in the same order as limity head(limity[,1:2]) pokus vzorek 1 1 6 2 1 7 3 1 8 4 1 9 5 1 10 6 2 8 head(limity.gr[,1:2]) pokus vzorek 1 1 6 2 1 7 3 1 8 4 1 9 5 1 10 6 2 8 head(limity.gr[ooo,1:2]) pokus vzorek 3310 3 3410 4 3510 5 3610 7 3710 8 3810 9 head(limity[ooo,1:2]) pokus vzorek 26 7 5 27 7 6 28 7 7 7815 9 7915 10 8015 11 When I reordered the limity.gr file in desired order and I made the nlme analysis based on this newly ordered data, augPred plot was OK. snip Possibly. plot.augPred produces a Trellis plot, and usually arguments to the underlying plotting function can be passed on through the top-level call. e.g., with the Orthodont data plot(augPred(fm1, level = 0:1), skip = rep(c(F,T), c(16, 2))) That's it! Together with suitable layout I got what I wanted. Great. Thanks a lot Best regards Petr or p - plot(augPred(fm1, level = 0:1)) update(p, skip = rep(c(F,T), c(16, 2))) You would of course have to know what valid arguments are; for that see ?xyplot and ?update.trellis (in the lattice package). Deepayan Petr Pikal [EMAIL PROTECTED] structure(list(pokus = c(1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 9, 9, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21), vzorek = c(6, 7, 8, 9, 10, 8, 9, 10, 7, 8, 7, 8, 9, 10, 7, 8, 9, 10, 5, 6, 7, 10, 11, 3, 4, 5, 6, 7, 10, 11, 3, 4, 3, 4, 5, 7, 8, 9, 10, 2, 3, 4, 7, 8, 9, 3, 4, 5, 9, 10, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16), cas = c(150, 180, 210, 240, 270, 210, 240, 270, 180, 210, 180, 210, 240, 270, 180, 210, 240, 270, 120, 150, 180, 60, 90, 60, 90, 120, 150, 180, 60, 90, 60, 90, 60, 90, 120, 30, 60, 90, 120, 30, 60, 90, 30, 60, 90, 60, 90, 120, 90, 120, 60, 90, 120, 150, 0, 20, 40, 60, 80, 0, 20, 40, 60, 80, 0, 20, 40, 60, 80, 0, 10, 20, 30, 0, 20, 40, 60, 0, 10, 20, 30, 0, 10, 20, 30, 0, 10, 20, 0, 10, 20, 30, 0, 10, 20, 30, 0, 10, 20, 30, 0, 10, 20, 30, 0, 20, 40, 60, 0, 20, 40, 60, 80, 0, 20, 40, 60, 0, 10, 20, 30, 0, 10, 20, 30, 0, 10, 20, 30, 0, 10, 20, 30, 0, 10, 20, 30, 0, 20, 40, 0, 10, 20, 20, 0, 20, 40, 60, 0, 20, 40, 60, 0, 20, 40, 60, 0, 20, 40, 60, 0, 20, 40, 60, 0, 10, 20, 30, 0,
[R] Flip rows and columns of a table?
Any simple way to take a (2D) table and 'rotate' it so all the rows become columns and the columns rows? I'll wager there is a simple way ;) - but I can't find it :( __ R-help@stat.math.ethz.ch 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] Flip rows and columns of a table?
t( my.table ) -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc -- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dan Bolser Sent: Tuesday, April 26, 2005 11:18 AM To: R mailing list Subject: [R] Flip rows and columns of a table? Any simple way to take a (2D) table and 'rotate' it so all the rows become columns and the columns rows? I'll wager there is a simple way ;) - but I can't find it :( __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Flip rows and columns of a table?
Le 26.04.2005 11:18, Dan Bolser a écrit : Any simple way to take a (2D) table and 'rotate' it so all the rows become columns and the columns rows? I'll wager there is a simple way ;) - but I can't find it :( __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ?t -- ~ ~~ Romain FRANCOIS - http://addictedtor.free.fr ~~ Etudiant ISUP - CS3 - Industrie et Services ~~http://www.isup.cicrp.jussieu.fr/ ~~ Stagiaire INRIA Futurs - Equipe SELECT ~~ http://www.inria.fr/recherche/equipes/select.fr.html~~ ~ __ R-help@stat.math.ethz.ch 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] [R-pkgs] psy version 0.65 released
Dear R users, psy version 0.65 is on CRAN now. psy provides several methods used in psychometry (kappa, icc, cronbach, screeplot (with simulations), non linear mapping, etc.) A bug has been fixed in function wkappa (weighted kappa): in particular circumstances, the 2*2 table presented levels in an order different to what was suggested in the help file. The fpca function (PCA plot with pvalues and compatible with dependant/independant variables dichotomy) has been extended. As usual, any kind of feedback is the most welcome Bruno Bruno Falissard Département de santé publique Hôpital Paul Brousse 14 Avenue Paul Vaillant Couturier 94804 Villejuif cedex, France tel : (+33) 6 81 82 70 76 fax : (+33) 1 45 59 34 18 web site : http://perso.wanadoo.fr/bruno.falissard/ http://perso.wanadoo.fr/bruno.falissard/ [[alternative HTML version deleted]] ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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] simple question on graphics window
Dear All, This is a rather simple question. How do I open more than 1 graphics window? Dom __ R-help@stat.math.ethz.ch 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] simple question on graphics window
Dom Peters wrote: Dear All, This is a rather simple question. How do I open more than 1 graphics window? See ?x11 Uwe Ligges Dom __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] simple question on graphics window
Le 26.04.2005 11:36, Dom Peters a écrit : Dear All, This is a rather simple question. How do I open more than 1 graphics window? Dom __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html *REALLY DO IT ** ?x11 ?windows -- ~ ~~ Romain FRANCOIS - http://addictedtor.free.fr ~~ Etudiant ISUP - CS3 - Industrie et Services ~~http://www.isup.cicrp.jussieu.fr/ ~~ Stagiaire INRIA Futurs - Equipe SELECT ~~ http://www.inria.fr/recherche/equipes/select.fr.html~~ ~ __ R-help@stat.math.ethz.ch 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] missing values
Hello, Thanks for the instructive responses. But two questions arise. Firstable I can't manage to load the library mice. I'm using R 2.0.1 on my Debian I try just copying the package in my library /usr/lib/R/library . but when i do library() ... mice ** No title available (pre-2.0.0 install?) ** ... and when i do library(mice) Error in library(mice) : 'mice' is not a valid package --installed 2.0.0? The second question is more statistical: aregImpute() seems to give good results but i would like to compare the different methods not just graphically. It'is possible? I also have other meteorological stations that have correleted data with the data station I'm using? Can I use those data to improve my imputation method. Regards, Giordano __ R-help@stat.math.ethz.ch 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] missing values
Hello, On my experience, mice works fine with R 1.9 but not necessarily for newer versions... Bruno Bruno Falissard INSERM U669, PSIGIAM Paris Sud Innovation Group in Adolescent Mental Health Maison de Solenn 97 Boulevard de Port Royal 75679 Paris cedex 14, France tel : (+33) 6 81 82 70 76 fax : (+33) 1 45 59 34 18 web site : http://perso.wanadoo.fr/bruno.falissard/ -Message d'origine- De : [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] De la part de Giordano Sanchez Envoyé : mardi 26 avril 2005 11:58 À : r-help@stat.math.ethz.ch Objet : Re: [R] missing values Hello, Thanks for the instructive responses. But two questions arise. Firstable I can't manage to load the library mice. I'm using R 2.0.1 on my Debian I try just copying the package in my library /usr/lib/R/library . but when i do library() ... mice ** No title available (pre-2.0.0 install?) ** ... and when i do library(mice) Error in library(mice) : 'mice' is not a valid package --installed 2.0.0? The second question is more statistical: aregImpute() seems to give good results but i would like to compare the different methods not just graphically. It'is possible? I also have other meteorological stations that have correleted data with the data station I'm using? Can I use those data to improve my imputation method. Regards, Giordano __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] missing values
On 04/26/05 09:58, Giordano Sanchez wrote: Hello, Thanks for the instructive responses. But two questions arise. Firstable I can't manage to load the library mice. I'm using R 2.0.1 on my Debian The package called norm also has functions for missing data. When I tried it, the values it gave were not sensible for my problem, but I may have done something wrong. (This was a simple problem that did not involve multiple imputation.) The second question is more statistical: aregImpute() seems to give good results but i would like to compare the different methods not just graphically. It'is possible? What different methods? Compare how? Are you assuming that we remember your last post? I also have other meteorological stations that have correleted data with the data station I'm using? Can I use those data to improve my imputation method. This sounds like exactly what aregImput() is good for, or transcan(), depending on whether you need to make inferences (and hence do multiple imputation). Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ R-help@stat.math.ethz.ch 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] missing values
Jonathan Baron wrote: On 04/26/05 09:58, Giordano Sanchez wrote: Hello, Thanks for the instructive responses. But two questions arise. Firstable I can't manage to load the library mice. I'm using R 2.0.1 on my Debian The package called norm also has functions for missing data. When I tried it, the values it gave were not sensible for my problem, but I may have done something wrong. (This was a simple problem that did not involve multiple imputation.) The second question is more statistical: aregImpute() seems to give good results but i would like to compare the different methods not just graphically. It'is possible? What different methods? Compare how? Are you assuming that we remember your last post? I also have other meteorological stations that have correleted data with the data station I'm using? Can I use those data to improve my imputation method. This sounds like exactly what aregImput() is good for, or transcan(), depending on whether you need to make inferences (and hence do multiple imputation). Jon For those interested I have preprints of a paper comparing MICE, aregImpute, and transcan on the basis of simulations. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch 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] Problem with R-2.1.0: install.packages() doesn't work
On Fri, 22 Apr 2005, Uwe Ligges wrote: Roger D. Peng wrote: What happens if you don't set the 'CRAN' option via 'options()' first and just run 'install.packages()'? Should be the same as long as no CRAN mirror has been choosen and X11 is not accessible (see my other message). The code needs to be a bit more defensive here - or present a better error message. It was a bug, already (by last Friday) corrected in R-patched: o Typo in menu(graphics=TRUE) meant it failed on Unix if tcltk was not available. -- 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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Where to find out about fixed bugs (Re: [R] Problem with R-2.1.0: install.packages() doesn't work)
On Sat, 23 Apr 2005, Marc Schwartz wrote: On Sat, 2005-04-23 at 16:14 +0200, Uwe Ligges wrote: Thanks for your work on this topic, Marc, but the bug has already been fixed by Brian 4 days ago (see below). Uwe r33976 | ripley | 2005-04-19 05:38:51 -0400 (Tue, 19 Apr 2005) | 1 line Changed paths: M /trunk/NEWS M /trunk/src/library/utils/R/menu.R missing braces Thanks Uwe. It was a nice workout for these aging neurons... ;-) Did I miss a bug report on this? I don't recall seeing a report come through and a quick review of r-devel and the bug tracking system does not turn up anything. The vast majority of the bug fixes are not from formal bug reports but from things spotted by R-core members either when using R (as here) or from reading the code (normally to find something else). (90% of those documented for 2.1.0.) In either case, glad to see that it is fixed. I have also downloaded a copy of the 2.1.0 patched tarball and noted that it is fixed there (Version 2.1.0 Patched (2005-04-20)), so for anyone compiling from source get a copy of: ftp://ftp.stat.math.ethz.ch/Software/R/R-patched.tar.gz -- 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 __ R-help@stat.math.ethz.ch 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] missing values
On 26-Apr-05 Jonathan Baron wrote: On 04/26/05 09:58, Giordano Sanchez wrote: Hello, Thanks for the instructive responses. But two questions arise. Firstable I can't manage to load the library mice. I'm using R 2.0.1 on my Debian The package called norm also has functions for missing data. When I tried it, the values it gave were not sensible for my problem, but I may have done something wrong. (This was a simple problem that did not involve multiple imputation.) Hi Jonathan, Would you be kind enough to give sufficient detail to reproduce such a case? I've used 'norm' (and 'cat' and 'mix') quite extensively, without encountering non-sensible results (at any rate in situations where the packages were not being abused, which one can do in certain circumstances -- imputing missing values can depend quite strongly on supplying realistic constraints, and on not expecting too much when the proportion of missing data is substantial: this methodology does not have magical powers!). best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Apr-05 Time: 12:47:42 -- XFMail -- __ R-help@stat.math.ethz.ch 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] shared library configuration; Gnome GUI
This seems to have gone unanswered. The difference in building R as a shared library is in the R-admin manual. Quick summary: you slowed R down by ca 15%. Both my FC3 systems build gnomeGUI. In any case, the information about gnome version is also in the R-admin manual, and FC3 has gnome-libs-1.4.1.2.90-44 gnome-libs-devel-1.4.1.2.90-44 More likely you do not have these at all than you have `2.0X' On Fri, 22 Apr 2005, Paul Johnson wrote: Hello, everybody: On a Fedora Core 3 Linux system, I built R-2.1 using an updated version of the spec file that was used to make the RPMs for version 2.0.1 on the CRAN system. The build was fine, and packages updates perfectly. Thanks! Then I got curious about the package gnomeGUI. While trying to build that, I see errors = * Installing *Frontend* package 'gnomeGUI' ... Using R Installation in R_HOME=/usr/lib/R R was not built as a shared library Need a shared R library ERROR: configuration failed for package 'gnomeGUI' === So then I look back at re-building R, and see ./configure --help I see these two items that seem to contradict each other. Why is the first defaulted to no and the second one yes? What's the difference? --enable-R-shlibbuild R as a shared library [no] [...snip...] --enable-shared[=PKGS] build shared libraries [default=yes] I built with --enable-R-shlib and all seemed fine. Anyway, it turns out it was all for nothing, because the Gnome package wants the Gnome-1.4 libraries, whereas I have 2.0X. So, I'm going to forget about gnomeGUI, but I wonder: did I do any harm by building R with the non-default --enable-R-shared? Can it potentially break something? As far as I can see, new R runs great. -- 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 __ R-help@stat.math.ethz.ch 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] installing R-2.1.0 from source on Fedora Core 3 with tclt k
On Sun, 24 Apr 2005, Liaw, Andy wrote: On my FC3 for x86_64 (Athlon64 3000+) at home, R-patched from today compiled just fine, and tcltk works. The version of tcl, tcl-devel, tk and tk-devel are all 8.4.7-2. Indeed. Since FC3 is the platform used by two (at least) of R-core and both have 64-bit machines, it would be surprising if there were a problem there. From: Jonathan Baron I installed from source on Fedora Core 3 starting with the command ./configure --prefix=/usr --with-tcltk (The --with-tcltk may not be necessary, but there seems to be some correlation between using it and getting it to work.) It would not compile with tcltk, even though I had both tcl and tk rpms installed. Various fooling around let me to get http://www.murdoch-sutherland.com/Rtools/R_Tcl.zip (even though it is supposedly for Windows), unzip it in the R-2.0.0/ directory (where the tar file put itself), and also install rpms for tcl-devel and tk-devel, which I did not have. When I did both of these things, it worked. Either one of them alone (the ..devel rpms or the R_Tcl.zip) did not suffice. You need the non-devel rpms as well, and that is what I think you are picking up from the R_Tcl.zip (which is Tcl pre-compiled for Windows). (However, it isn't clear that a single trial experiment is sufficient to determine what works.) My own problem is solved for the moment. But others may benefit from this report, and it may be that the installation documentation needs minor tweaking. (Or it may be that I did something else wrong, but right now I doubt that.) -- 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 __ R-help@stat.math.ethz.ch 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] installing R-2.1.0 from source on Fedora Core 3 with tclt k
I was able to compile R-2.0.0 successfully on another fc3 computer, theoretically identical to the first three. I'm sorry for starting this thread. It does seem that I had a problem that resulted from having only tk and tcl, but not tk-devel and tcl-devel. Perhaps after I installed these I forgot to log out and log in again, so they weren't found. When I did it successfully, I installed the devel versions first, then logged in as root and did everything as root. (Initially I had done only the very last step - make install - as root.) Probably this doesn't matter either. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ R-help@stat.math.ethz.ch 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] Construction of a mean contengency table
Hi List,
Say I have a data.frame DF with 6 columns, 3 factors and 3 variables,
with different number of repetitions for each combination of factors.
I would like to build, for two given factors, a matrix per variable,
containing in each cell the mean or sd for a given couple of factors.
I have managed to get to the result I wanted step by step, but I would
like to have it in a function. I have not found what I was looking for
so I decided to try to write my own function, using aggregate( ) to
generate the mean values as a dataframe, and then display this as a
matrix.
I'd like it to be general enough so that I could use it in many cases.
From what I have tried and understood, table( ) cannot do what I want
(no mean or sd ...) neither does xtabs( ), i.e. asking for a formula not
a function to passed as an argument ...
My final aim would be to plot this with persp( ), and it seems that
persp( ) must be fed with 2 dimensional arrays ...
Below is what I have tried to write, but it is not working.
It might be awkward, but I think it can work ... I think it is a problem
about correctly receiving and passing arguments in the different
function calls.
Do you think there would be a smarter way of doing this ? Or can you see
what is going wrong with this ?
Any advice will be welcome
Pascal Boisson
matrixation-function(DF, var, factorlist, FUN, condition)
## DF is the original dataframe with raw results from my experiments
## var is the var that I want to print
## eg. DF$var1
## factorlist is a list of the two factor I want to mean against (but
I'm noot sure List is the best form for this argument),
## eg. list(DF$fact1, DF$fact2)
## FUN would be the function I want to use during aggregation,
## eg. Mean( )
## condition would be a condition for building a subset
## eg. DF$fact3==1
{
sDF - subset(DF, condition)
A - aggregate(sDF, factorlist, FUN)
M - matrix(data=NA, nrow = length(levels(factorlist[[1]])),
ncol = length(levels(factorlist[[2]])),
dimnames =
list(levels(factorlist[[1]]),levels(factorlist[[2]]) )
)
for (i in 1:length(A[,1]))
{
tPhii - A$Group.1[i]
tAppari - A$Group.2[i]
M[tPhii, tAppari] - A$pest_max_number[i]
}
return(M)
}
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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RE: [R] multiple autocorrelation coefficients in spdep?
Thanks for the reply. I will look into the suggestions you have given. Indeed, I have used an lme model with direct covariance representation via geostatistical models, where I was able to fit separate terms for different groups, but part of my point is to compare the outcome from both approaches. Ignacio -Original Message- From: Roger Bivand [mailto:[EMAIL PROTECTED] Sent: Tuesday, April 26, 2005 3:00 AM To: Ignacio Colonna Cc: R-help@stat.math.ethz.ch Subject: Re: [R] multiple autocorrelation coefficients in spdep? On Mon, 25 Apr 2005, Ignacio Colonna wrote: Hello, Has anyone modified the errorsarlm in the R package spdep to allow for more than a single spatial autocorrelation coefficient (i.e. 'lambda')? Or, if not, any initial suggestions on how to make that modification? I have looked at the source code for the function and realize that any attempt to do it on my own would require much dedication, so would like to check whether someone has done it already. My R programming skills are very elementary. Specifically I would need to specify 2 different lambdas in a dataset, one for each group. I am performing a regression of grain yield against a number of soil variables, for 2 different years, where the regression includes terms for year*soil variables interaction. The spatial structure of the error is clearly different between these years, and I would thus like to fit different lambdas to them, if possible. Of course one option is to just run 2 separate regressions, but if the possibility of fitting more than 1 lambda does not seem too remote, I think fitting a single model offers some advantages. As far as I am aware, as package maintainer, this has not been done, and is not easy to do, as you have noted. It might be possible to use the lm.gls() function in the MASS package once the compound weights matrix (including the coefficients) has been fixed, perhaps using optim(). Have you considered other options perhaps including some lme variant, and/or spatial panel variants? Thanks in advance, Ignacio -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] installing R-2.1.0 from source on Fedora Core 3 with tclt k
On Tue, 2005-04-26 at 09:05 -0400, Jonathan Baron wrote: I was able to compile R-2.0.0 successfully on another fc3 computer, theoretically identical to the first three. I'm sorry for starting this thread. It does seem that I had a problem that resulted from having only tk and tcl, but not tk-devel and tcl-devel. Perhaps after I installed these I forgot to log out and log in again, so they weren't found. When I did it successfully, I installed the devel versions first, then logged in as root and did everything as root. (Initially I had done only the very last step - make install - as root.) Probably this doesn't matter either. Logging in and out should not be needed. The header files (installed from the 'devel' RPMS) are installed in standard locations on Linux (ie. /usr/include) as are the libraries (ie. /usr/lib) and these are usually picked up by the configure script. There is really nothing in terms of environment variables for example, that would need to get updated via a logout/login cycle. Unlike Windows, which for example can require a full re-boot when certain components get installed, about the only time Linux needs a re-boot is to utilize a new kernel. Otherwise the majority of system updates are done hot. When building from source, I do it all as a regular user and as you reference above, then 'su' to root for the installation. Best regards, Marc Schwartz __ R-help@stat.math.ethz.ch 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] postscript (eps) / latex / par(mfg=...) / problem!
The same problem I am having has been reported here
http://tolstoy.newcastle.edu.au/R/devel/04a/0344.html
Namely that using par(mfg=...) with a postscript (eps) for inclusion with
latex makes the figure appear upside down and back to front (flipped)!
Converting the dvi to ps makes matters worse (the eps seems to be broken),
however, it appears fine with gv.
Here is (basically) the code I am using...
dat - read.table(x.dmp, header=1)
t(dat)
t(dat)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
CHAINS 1 2 3 4 5 6 7 8 9 10 11 12 13 14 16 20 23 24 26 28
FREQUENCY 886 792 136 201 16 58 6 21 3 9 3 9 1 4 3 1 1 1 1 1
postscript(
+ x.eps,
+ width = 6.0,
+ height = 6.0,
+ horizontal = FALSE,
+ onefile = FALSE,
+ paper = special,
+ )
par(mfg=c(1,1))
par(mar=c(3,4,1,2))
plot(dat,type='b')
par(mfg=c(2,1))
par(mar=c(4,4,0,2))
plot(dat,type='b', log='y')
dev.off()
Including the resulting file in a latex document like this...
begin{figure}
\centering
\includegraphics[width=\textwidth]{x.eps}
\caption[X]
{
Hello!
}
\label{xFig}
\end{figure}
The result is an upside down (flipped) version of my plot. I tried
rotating 180 degrees (based on similar problems people were having on the
list), but then it just gets worse (most of the plot is off the page). If
I convert the dvi to ps (dvips -Ppdf my.tex.dvi -o my.tex.ps) it gets
worse (a tiny speck where the image should be).
After removing the two mfg commands (which I use to add grid lines (not
shown for clarity)) everything is fine! Some how mfg is snarling things
up.
OK, I just had a brain wave (dont laugh). Here is a diff of the working
eps vs the broken eps...
diff broken working
78a79,80
%%Page: 1 1
bp
229c231
57.60 43.20 403.20 201.60 cl
---
57.60 57.60 403.20 216.00 cl
417c419
%%Pages: 0
---
%%Pages: 1
Does that help anyone debug my problem? Like I said, both look identical
via gv, and are 'conceptually' identical in R.
Here are my vitals
Linux 2.4.20-31.9 i686 athlon i386 GNU/Linux
R 2.0.0 (2004-10-04).
GNU Ghostscript 7.05 (2002-04-22)
Anything else you need?
Please help!
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[R] .libPaths()
Hello I use the function .libPaths() .libPaths() [1] /usr/local/lib/R/library .libPaths(c(/usr/local/lib/myRlib,/usr/local/lib/library)) .libPaths() [1] /usr/local/lib/R/library but it simply does not pick up the new path. Can anybody help? (The problem originates from the inability to install packages into /usr/local/lib/R/library, running R under linux suse 9.3) Sebastian Leuzinger __ R-help@stat.math.ethz.ch 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] .libPaths()
On Tue, 26 Apr 2005, Sebastian Leuzinger wrote: Hello I use the function .libPaths() .libPaths() [1] /usr/local/lib/R/library .libPaths(c(/usr/local/lib/myRlib,/usr/local/lib/library)) .libPaths() [1] /usr/local/lib/R/library but it simply does not pick up the new path. Can anybody help? (The problem originates from the inability to install packages into /usr/local/lib/R/library, running R under linux suse 9.3) It works for me as long as the paths actually exist -- it didn't work with your example because I don't have /usr/local/lib/myRlib or /usr/local/lib/library. -thomas __ R-help@stat.math.ethz.ch 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] .libPaths()
Did you check to make sure the new path exists? -roger Sebastian Leuzinger wrote: Hello I use the function .libPaths() .libPaths() [1] /usr/local/lib/R/library .libPaths(c(/usr/local/lib/myRlib,/usr/local/lib/library)) .libPaths() [1] /usr/local/lib/R/library but it simply does not pick up the new path. Can anybody help? (The problem originates from the inability to install packages into /usr/local/lib/R/library, running R under linux suse 9.3) Sebastian Leuzinger __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch 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] missing values
Dear Giordano, Library Hmisc, by Frank Harrell, contains several functions for imputation which I have found extremely useful. Best, R. On Tuesday 26 April 2005 11:58, Giordano Sanchez wrote: Hello, Thanks for the instructive responses. But two questions arise. Firstable I can't manage to load the library mice. I'm using R 2.0.1 on my Debian I try just copying the package in my library /usr/lib/R/library . but when i do library() ... mice ** No title available (pre-2.0.0 install?) ** ... and when i do library(mice) Error in library(mice) : 'mice' is not a valid package --installed 2.0.0? The second question is more statistical: aregImpute() seems to give good results but i would like to compare the different methods not just graphically. It'is possible? I also have other meteorological stations that have correleted data with the data station I'm using? Can I use those data to improve my imputation method. Regards, Giordano __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Ramón Díaz-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncológicas (CNIO) (Spanish National Cancer Center) Melchor Fernández Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. __ R-help@stat.math.ethz.ch 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] Error using e1071 svm: NA/NaN/Inf in foreign function call
Hello, As far I saw in archive mailing list, I am not the first person with this problem. Anyway I was not able to pass this error once the information I got from the archive it is not very conclusive for this case. I have used linear, radial and sigmoid kernels for the same data in the same conditions and everything is ok. This problem just happens with the polynomial kernel. I send the debuging result from a reproducible example. The error message is at the end. Thanks in advance Joao _ FEUP - Engineering Faculty, Porto University - Portugal DEMEGI/GEIN Tel.: +351 22 508 1639 Fax: +351 22 508 1538 Example: debugging in: svm(Fim ~ ., data = list(Inicio = c(25056, 28554, 32074, 33266, 39116, 40466, 41684, 42919, 46233, 47772, 48857, 50613, 52626, 56210, 58817, 62476, 25471, 27619, 28342, 29093, 29814, 31971, 32861, 34861, 35757, 36386, 38455, 42566, 43368, 46749, 47879, 48993, 49759, 50234, 51477, 51552, 51835, 52747, 53219, 54654, 55038, 56458, 58147, 58588, 59297, 60246, 61078, 61766, 62252, 64219, 64609, 66020, 67155, 67866, 71006, 71771, 72851, 73689, 24464, 25808, 29370, 34246, 37772, 38930, 42631, 46039, 47247, 49797, 50887, 54400, 58090, 59284, 62835, 69276, 75084, 27295, 31077, 32004, 33357, 34505, 35210, 39278, 40773, 48925, 51568, 52623, 54216, 59771, 60759, 64410, 67766, 71363, 23238, 23981, 24647, 26498, 29248, 29837, 30372, 31583, 33680, 35404, 35913, 37145, 39135, 39381, 41374, 42626, 44911, 48595, 49161, 50376, 50983, 51562, 51995, 53856, 57033, 57706, 57983, 58692, 59346, 60522, 64186, 69265, 70944, 72866, 73804, 25704, 27485, 29070, 29244, 30025, 34286, 35797, 36534, 37194, 38188, 39018, 39829, 42681, 43212, 46788, 47142, 49024, 51016, 52888, 53416, 54579, 55023, 56971, 58974, 65278, 66524, 73780, 23432, 24009, 24576, 25382, 26446, 28081, 28815, 29382, 30545, 31001, 32360, 32897, 33620, 34824, 35231, 36854, 39980, 40601, 43810, 47241, 50895, 52016, 52781, 53893, 55148, 57066, 57463, 60234, 60539, 62271, 63602, 63898, 67163, 25705, 26312, 27191, 29796, 31031, 32947, 34245, 35416, 42399, 43585, 45441, 47346, 49180, 51126, 52209, 52807, 53777, 55100, 56960, 57600, 58153, 59776, 60726, 61665, 62252, 63579, 65315, 67087, 69278, 71865, 74845, 23457, 27725, 28387, 29070, 29324, 30527, 32308, 33018, 33555, 34086, 36698, 37812, 38424, 43138, 44917, 47252, 47749, 48371, 49173, 49529, 50079, 50831, 52817, 54515, 56300, 56841, 59390, 60488, 61676, 63473, 66798, 68636, 69266, 69996, 72289, 73708, 25981, 28212, 31749, 32981, 34046, 36499, 37762, 40061, 41523, 45147, 46265, 48704, 49840, 52050, 53554, 54447, 55765, 58446, 60424, 61964, 62823, 65211, 66269, 67818, 69051, 70375, 30865, 35662, 36956, 40381, 41567, 42838, 44156, 45250, 47778, 48956, 51925, 52634, 58047, 59131, 60439, 60793, 63402, 68843, 73788, 29262, 30645, 31228, 32648, 35312, 36440, 37077, 38279, 40234, 41266, 44311, 46614, 47303, 47849, 48443, 49146, 49551, 50602, 52085, 57448, 59759, 61350, 70081, 23412, 24078, 25157, 25813, 26845, 27522, 28035, 29885, 33453, 34823, 36470, 38876, 43025, 45422, 46674, 48547, 49026, 51011, 52661, 55224, 56155, 56881, 58671, 59214, 60475, 61110, 61691, 68951, 70135, 73754, 23349, 24817, 25505, 26846, 29162, 31760, 32979, 33497, 34661, 35836, 40191, 44880, 45457, 46079, 47357, 48374, 49093, 50187, 51892, 54524, 55210, 55810, 56243, 57605, 58565, 59249, 60339, 62345, 65299, 66304, 67782, 71822, 23275, 24132, 24592, 25057, 28456, 32484, 32961, 33442, 34287, 34864, 35334, 37177, 48274, 49067, 50791, 52114, 52728, 54547, 56413, 56826, 59311, 60416, 61196, 61850, 63257, 67009, 69268, 70260, 73661, 23479, 23929, 24592, 25223, 25806, 26370, 27576, 29322, 30067, 31670, 32224, 33184, 33535, 34792, 35242, 36615, 37709, 39014, 40690, 43199, 45041, 46178, 46717, 47277, 47810, 50404, 50956, 52215, 52788, 53241, 54447, 55675, 56210, 57100, 58765, 63026, 63679, 68971, 71276, 72867, 73799, 24590, 29347, 30606, 34185, 37677, 39006, 40041, 43744, 46158, 48638, 49874, 52021, 55689, 58049, 60456, 62896, 63977, 65408, 67863, 69060, 73589, 30936, 33051, 34518, 38084, 39214, 40288, 41716, 45256, 46364, 47792, 48765, 49956, 54435, 55466, 58190, 62216, 63318, 70175, 71250, 74837, 25274, 26921, 27596, 28962, 29314, 29891, 33652, 37706, 39515, 40221, 40742, 44280, 44754, 46095, 47423, 49651, 51428, 57608, 58045, 60667, 61588, 62560, 68305, 71095, 72804, 23225, 26405, 26912, 28682, 29291, 32259, 34827, 35375, 38231, 40118, 44419, 45055, 45542, 46669, 47317, 47903, 48558, 49082, 49314, 50926, 51564, 52772, 53939, 56079, 57392, 58776, 59301, 61751, 63511, 66226, 70126, 73799, 24632, 26950, 27431, 31036, 31775, 32411, 33520, 34676, 36510, 37164, 40126, 40747, 41441, 42627, 44878, 46147, 47375, 49268, 49646, 50215, 56825, 59737, 62569, 69224, 70171, 24576, 27596, 29243, 29855, 30506, 31750, 32915, 34695, 35328, 36482, 37218, 38307, 39061, 44248, 44999, 46774, 47275, 48561, 49719, 50318, 50920, 51417, 53241,
[R] Advice for calling a C function
Hi,
I'm having some trouble with a bit of combined C R code. I'm trying to
write a C function to handle the for loops in a function I'm working on
to calculate a similarity matrix. Jari Oksanen has kindly added the
necessary changes to the vegan package so that I can use the vegdist
function, so this isn't absolutely necessary. However, I'm stubborn and
want to know why Jari's code works and mine doesn't! Other than, of
course, the obvious - one of us knows what their doing and the other
doesn't. I would appreciate any help. What I've done is:
pass a matrix x to my C function, as a double:
.C(gowsim, as.double(mat), as.integer(nrow(mat)), as.integer(ncol(mat)))
Then I try and reconstruct the matrix, in the form of a C array:
#include R.h
#include Rmath.h
#include math.h
void gowsim ( double *mat, int *OBJ, int *MATDESC)
{
double x [*MATDESC][*OBJ];
int i, j, nrow, ncol;
nrow = *OBJ;
ncol = *MATDESC;
/* Rebuild Matrix */
for (j=0; j ncol; j++) {
for (i=0; i nrow; i++) {
x[i][j] = *mat;
Rprintf(row %d col %d value %f\n, i, j, x[i][j]);
mat++;
}
}
for (i=0; i nrow; i++) {
Rprintf(%f %f %f %f\n, x[i][0], x[i][1], x[i][2], x[i][3]);
}
}
The Rprintf statements display what's going on at each step. It looks
for all the world as if the assignments are working properly, but when I
try and print the matrix I get very strange results. If mat is 3x3 or
4x4 everything seems ok. But if mat is not symetrical the resulting x
matrix is very strange. In the case of a 5x4 mat only the first column
works out, and for 3x4 mat the second and third positions in the first
column are replaced by the first and second positions of the last
column. I'm guessing that I've messed up something in my use of
pointers, or perhaps the for loop, but I can't for the life of me figure
out what!! Once I sort this out I'll be calculating the differences
between rows in the x array en route to producing a similarity matrix. I
looked at the vegdist code, which is fancier than this, and manages to
avoid rebuilding the matrix entirely, but it's a bit beyond me.
I'm using WindowsXP, R 2.1.0 (2005-04-18), and the MinGW compiler.
Thanks for your continued patience,
Tyler
--
Tyler Smith
PhD Candidate
Department of Plant Science
McGill University
21,111 Lakeshore Road
Ste. Anne de Bellevue, Quebec
H9X 3V9
CANADA
Tel: 514 398-7851 ext. 8726
Fax: 514 398-7897
[EMAIL PROTECTED]
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Re: [R] missing values
On 04/26/05 12:54, Ted Harding wrote: Would you be kind enough to give sufficient detail to reproduce such a case? I've used 'norm' (and 'cat' and 'mix') quite extensively, without encountering non-sensible results (at any rate in situations where the packages were not being abused, which one can do in certain circumstances -- imputing missing values can depend quite strongly on supplying realistic constraints, and on not expecting too much when the proportion of missing data is substantial: this methodology does not have magical powers!). OK. Here you go. First the data without any names: 41,43,41,43,44 43,40,40,42,41 43,44,NA,43,44 42,43,NA,44,44 41,44,42,42,42 43,43,41,42,42 47,48,46,47,46 39,35,35,39,38 40,39,36,40,38 40,40,40,40,40 48,46,46,48,46 45,45,42,44,45 41,40,40,41,41 40,39,37,40,38 41,42,40,41,41 41,42,41,43,43 46,46,45,46,46 40,40,41,40,41 39,41,40,41,41 40,43,38,40,39 37,36,37,36,39 45,46,45,46,46 43,44,42,43,44 42,42,48,42,43 45,46,45,46,45 37,36,36,36,38 37,34,39,37,39 NA,43,41,44,43 45,44,45,44,45 38,38,37,39,38 45,44,44,44,45 NA,42,43,43,43 45,45,44,44,45 40,35,37,40,38 43,43,43,43,43 39,34,37,36,39 38,38,38,39,39 43,41,40,42,43 46,43,42,45,45 46,45,41,44,44 40,40,38,39,40 39,37,39,38,39 Now the commands I used in norm, and the result: m1 - as.matrix(read.csv(test.data)) s1 - prelim.norm(m1) thetahat - em.norm(s1) rngseed(1234564) ximp - imp.norm(s1,thetahat,m1) ximp 1 41.0 43 41.0 43 44 2 43.0 40 40.0 42 41 3 43.0 44 43.72409 43 44 4 42.0 43 43.36864 44 44 5 41.0 44 42.0 42 42 6 43.0 43 41.0 42 42 7 47.0 48 46.0 47 46 8 39.0 35 35.0 39 38 9 40.0 39 36.0 40 38 10 40.0 40 40.0 40 40 11 48.0 46 46.0 48 46 12 45.0 45 42.0 44 45 13 41.0 40 40.0 41 41 14 40.0 39 37.0 40 38 15 41.0 42 40.0 41 41 16 41.0 42 41.0 43 43 17 46.0 46 45.0 46 46 18 40.0 40 41.0 40 41 19 39.0 41 40.0 41 41 20 40.0 43 38.0 40 39 21 37.0 36 37.0 36 39 22 45.0 46 45.0 46 46 23 43.0 44 42.0 43 44 24 42.0 42 48.0 42 43 25 45.0 46 45.0 46 45 26 37.0 36 36.0 36 38 27 37.0 34 39.0 37 39 28 44.13337 43 41.0 44 43 29 45.0 44 45.0 44 45 30 38.0 38 37.0 39 38 31 45.0 44 44.0 44 45 32 41.25152 42 43.0 43 43 33 45.0 45 44.0 44 45 34 40.0 35 37.0 40 38 35 43.0 43 43.0 43 43 36 39.0 34 37.0 36 39 37 38.0 38 38.0 39 39 38 43.0 41 40.0 42 43 39 46.0 43 42.0 45 45 40 46.0 45 41.0 44 44 41 40.0 40 38.0 39 40 42 39.0 37 39.0 38 39 What seemed odd to me, and maybe they aren't, were the imputed values in rows 3 and 4. They seemed high, knowing the rater in question and the students. Here is the output of transcan, for the same cases, which looks more in line with what I expected: 1 41.0 43 41.0 43 44 2 43.0 40 40.0 42 41 3 43.0 44 43.09469 43 44 4 42.0 43 43.39897 44 44 5 41.0 44 42.0 42 42 6 43.0 43 41.0 42 42 7 47.0 48 46.0 47 46 8 39.0 35 35.0 39 38 9 40.0 39 36.0 40 38 10 40.0 40 40.0 40 40 11 48.0 46 46.0 48 46 12 45.0 45 42.0 44 45 13 41.0 40 40.0 41 41 14 40.0 39 37.0 40 38 15 41.0 42 40.0 41 41 16 41.0 42 41.0 43 43 17 46.0 46 45.0 46 46 18 40.0 40 41.0 40 41 19 39.0 41 40.0 41 41 20 40.0 43 38.0 40 39 21 37.0 36 37.0 36 39 22 45.0 46 45.0 46 46 23 43.0 44 42.0 43 44 24 42.0 42 48.0 42 43 25 45.0 46 45.0 46 45 26 37.0 36 36.0 36 38 27 37.0 34 39.0 37 39 28 43.80165 43 41.0 44 43 29 45.0 44 45.0 44 45 30 38.0 38 37.0 39 38 31 45.0 44 44.0 44 45 32 42.91116 42 43.0 43 43 33 45.0 45 44.0 44 45 34 40.0 35 37.0 40 38 35 43.0 43 43.0 43 43 36 39.0 34 37.0 36 39 37 38.0 38 38.0 39 39 38 43.0 41 40.0 42 43 39 46.0 43 42.0 45 45 40 46.0 45 41.0 44 44 41 40.0 40 38.0 39 40 42 39.0 37 39.0 38 39 The commands here were s.imp - transcan(m1,asis=*,data=m1,imputed=T,long=T,pl=F) s.na - is.na(m1) # which ratings are imputed m1[which(s.na)] - unlist(s.imp$imputed) (I wish I could find a more elegant way to replace the NAs.) Jon - Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ R-help@stat.math.ethz.ch 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] Error using e1071 svm: NA/NaN/Inf in foreign function call
On Tue, 26 Apr 2005 15:46:20 +0100 João Mendes Moreira wrote: Hello, As far I saw in archive mailing list, I am not the first person with this problem. Anyway I was not able to pass this error once the information I got from the archive it is not very conclusive for this case. I have used linear, radial and sigmoid kernels for the same data in the same conditions and everything is ok. This problem just happens with the polynomial kernel. I send the debuging result from a reproducible example. The error message is at the end. I receive a different error message: Error in eval(expr, envir, enclos) : Object Fim not found So much for the reproducibility... Wouldn't it be possible to simply use a data set that is already available in R, *please*? Anyways, it seems that your specification of `nu' causes the problem: 0 might be a little bit too small. Z __ R-help@stat.math.ethz.ch 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] Finding 'ncp' for t
Hi Folks, I'm looking for a neat procedure for the following: Given t0 such that pt(t0,df,ncp=0) = alpha (given) find ncp0 such that for given beta pt(t0,df,ncp=ncp0) = (1 - beta) (In other words, what's the ncp such that you get power (1-beta) to detect it, using a 1-sided test with size alpha when ncp = 0?) In the past I've done the groping by hand, but this time it needs to be done many times over, so a good solver for ncp0 in this situation would be handy. With thanks, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Apr-05 Time: 15:02:24 -- XFMail -- __ R-help@stat.math.ethz.ch 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] Finding 'ncp' for t
(Ted Harding) [EMAIL PROTECTED] writes: Hi Folks, I'm looking for a neat procedure for the following: Given t0 such that pt(t0,df,ncp=0) = alpha (given) find ncp0 such that for given beta pt(t0,df,ncp=ncp0) = (1 - beta) (In other words, what's the ncp such that you get power (1-beta) to detect it, using a 1-sided test with size alpha when ncp = 0?) In the past I've done the groping by hand, but this time it needs to be done many times over, so a good solver for ncp0 in this situation would be handy. You might want to peek inside power.t.test(). Or just use it... -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch 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] Extending time series
I noticed that when one tries to extend a time series (ts) object by a single period using window() actually two observations (NAs) are added. See below for an example. Does anyone know the reason for this behavior and how to avoid it? Thanks. FS x-ts(c(1,2,3)) x1- window(x, start(x), end(x) + 1, extend = TRUE) x1 Time Series: Start = 1 End = 5 Frequency = 1 [1] 1 2 3 NA NA __ R-help@stat.math.ethz.ch 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] Error in nonlinear mixed-effects model
Dear all, I am trying to fit a mixed-effects non linear regression, but I have some trouble with it. My data are a balanced panel of 904 subjects with 8 observations (at regular periods) per subject. The functional form of my model is Y=Aexp(-BX1)X2 +e. I want to allow parameters A and B to vary among subjects and also include an autocorrelation term. I have already fitted a standard nonlinear regression to the data, but I keep having problems with NLME. I have defined my data as a groupedData object, and when I try to fit the model I get this error message: dat-groupedData(V~VAC|ID,data=dat) attach(dat) mod-nlme(V~A*exp(B*YEAR)*VAC, fixed=A+B~1, random=A+B~1, correlation=corCAR1(), start=c(A=1.2,B=0.2)) Error in getGroups.data.frame(dataMix, eval(parse(text = paste(~1, deparse(groups[[2]]), : Invalid formula for groups Do you have any clue of whats happening? Its the first time I fit a model like this in R, so the problem is probably pretty obvious, but I cannot see it. Thank you very much, Antonio __ R-help@stat.math.ethz.ch 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] mantelhaen.test for more than two groups?
Dear All, I'd like to perform the generalized Cochran-Mantel-Haenszel-Test (as described in Agresti (1990), Categorical Data Analysis) for my nominal data. My problem is that I have more than two groups. In fact I think I'd need an 5-dimensional array for the response variable, the control variable and three group variables. Could you please tell me if this is possible in R - and if yes how I am supposed to do this? By now I get an error message: MyData-array(c(21,6,0,18,8,1,46,9,2,12,8,1,35,3,7,9,2,8,58,5,11,3,2,4,14,0,0,21,0,0,26,0,0,12,0,0,32,0,0,25,0,0,62,0,0,16,0,0),dim=c(3,2,2,2,2)) mantelhaen.test(MyData) Error in mantelhaen.test(MyData) : x must be a 3-dimensional array I'm using R Version 1.9.1 on a Linux machine. I apologize in case I am completely wrong by choosing this test, which might be the fact as this is my very first struggle with statistics... :) In the hope of not losing it, thank you very much for any help, :) Kati __ R-help@stat.math.ethz.ch 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] mantelhaen.test for more than two groups?
On Tue, 26 Apr 2005, Katrin Schweitzer wrote: Dear All, I'd like to perform the generalized Cochran-Mantel-Haenszel-Test (as described in Agresti (1990), Categorical Data Analysis) for my nominal data. My problem is that I have more than two groups. In fact I think I'd need an 5-dimensional array for the response variable, the control variable and three group variables. Could you please tell me if this is possible in R - and if yes how I am supposed to do this? You're supposed to have a three-dimensional array: exposure x response x group. This means turning your three group variables into one variable. One way to do this is with the interaction() function. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@stat.math.ethz.ch 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] Extending time series
On Tue, 26 Apr 2005 11:52:00 -0400 Fernando Saldanha wrote: I noticed that when one tries to extend a time series (ts) object by a single period using window() actually two observations (NAs) are added. See below for an example. Does anyone know the reason for this behavior and how to avoid it? Yes: end(x) + 1 is not what you expect it to be. You can set equivalently end = 4 end = c(4, 1) to achieve what you want and you can compute one of those representations in various ways, e.g., tsp(x)[2] + 1. Z Thanks. FS x-ts(c(1,2,3)) x1- window(x, start(x), end(x) + 1, extend = TRUE) x1 Time Series: Start = 1 End = 5 Frequency = 1 [1] 1 2 3 NA NA __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] good editor for R sources ?
Dear all, (Sorry if the question has already been answered.) Could someone please suggest a good text editor for writing R sources ? (I know emacs exists ... but I find it a bit heavy). I use crimson (http://www.crimsoneditor.com) which is small and simple, but the R syntax seems not to be supported. Thanks for any advice __ R-help@stat.math.ethz.ch 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] mantelhaen.test for more than two groups?
Thomas Lumley [EMAIL PROTECTED] writes: On Tue, 26 Apr 2005, Katrin Schweitzer wrote: Dear All, I'd like to perform the generalized Cochran-Mantel-Haenszel-Test (as described in Agresti (1990), Categorical Data Analysis) for my nominal data. My problem is that I have more than two groups. In fact I think I'd need an 5-dimensional array for the response variable, the control variable and three group variables. Could you please tell me if this is possible in R - and if yes how I am supposed to do this? You're supposed to have a three-dimensional array: exposure x response x group. This means turning your three group variables into one variable. One way to do this is with the interaction() function. Or, if data are already counts, change the dimensions (as in dim(x) - c(2,3,8)), possibly after using aperm() to get the indices in the right order. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch 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] Extending time series
On 4/26/05, Fernando Saldanha [EMAIL PROTECTED] wrote: I noticed that when one tries to extend a time series (ts) object by a single period using window() actually two observations (NAs) are added. See below for an example. Does anyone know the reason for this behavior and how to avoid it? Thanks. FS x-ts(c(1,2,3)) x1- window(x, start(x), end(x) + 1, extend = TRUE) x1 Time Series: Start = 1 End = 5 Frequency = 1 [1] 1 2 3 NA NA Another way to do it is: ts(c(x, NA), start = start(x), freq = frequency(x)) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] good editor for R sources ?
Hi,
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of vincent
(Sorry if the question has already been answered.)
Could someone please suggest a good text editor for
writing R sources ?
(I know emacs exists ... but I find it a bit heavy).
I use crimson (http://www.crimsoneditor.com) which is
small and simple, but the R syntax seems not to be supported.
Thanks for any advice
although I prefer myself (X)Emacs, I suggest to people Tinn-R, it is
GPLed, has syntax highlighting, and something I haven't seen with any
other editor before:
You write for example:
mydata - read.table(.csv, header=TRUE, )
and while you are writing your code, a line pops up below the line you
are writing giving you the arguments and their default values for the
current function (I was impressed, I have to admit).
The homepage of this project is:
http://www.sciviews.org/Tinn-R/
Best,
Roland
+
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
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Re: [R] good editor for R sources ?
vincent wrote: Dear all, (Sorry if the question has already been answered.) Could someone please suggest a good text editor for writing R sources ? (I know emacs exists ... but I find it a bit heavy). I use crimson (http://www.crimsoneditor.com) which is small and simple, but the R syntax seems not to be supported. See http://www.sciviews.org/_rgui/projects/Editors.html The page tells us that there is support for Crimson editor. Uwe Ligges Thanks for any advice __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] good editor for R sources ?
At 18:22 26/04/2005 +0200, vincent wrote: Dear all, (Sorry if the question has already been answered.) Could someone please suggest a good text editor for writing R sources ? (I know emacs exists ... but I find it a bit heavy). I use crimson (http://www.crimsoneditor.com) which is small and simple, but the R syntax seems not to be supported. Thanks for any advice Tinn-R with Sciviews : http://www.sciviews.org/Tinn-R/index.html Cuvelier Etienne Assistant FUNDP - Institut d'Informatique rue Grandgagnage, 21 B-5000 Namur (Belgique) tel: 32.81.72.49.93fax: 32.81.72.49.67 __ R-help@stat.math.ethz.ch 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] random interactions in lme
The code below gives almost identical results for a split-block analysis in lme and SAS proc mixed, in terms of variance components and F statistics. It just extends the example in Pinheiro Bates (p.162) to a split block design. I am including below the SAS code and the data in case you want to try it. The only difference between both is in the df for the F denominator, which I wasn't able to compute correctly in lme, but this may be my ignorance on how to correctly specify the model. It is not a big issue though, as the F values are identical, so you can compute the p-values if you know how to obtain the correct DenDF. # a split block design spbl.an1-lme(yield~rowspace*ordered(tpop),random=list(rep=pdBlocked(list(pd Ident(~1), pdIdent(~rowspace-1),pdIdent(~ordered(tpop)-1,data=spblock) * SAS code proc mixed data=splitblock method=reml; class rep rowspace tpop; model yield=rowspace tpop rowspace*tpop; random rep rep*rowspace rep*tpop; run; # data rowspacetpoprep plotyield 9 60 1 133 19 9 120 1 101 19.5 9 180 1 117 22 9 240 1 132 19.4 9 300 1 116 23.9 18 60 1 134 15.8 18 120 1 102 26.2 18 180 1 118 21.9 18 240 1 131 20 18 300 1 115 23.3 9 60 2 216 20.6 9 120 2 233 22 9 180 2 201 23.4 9 240 2 217 28.2 9 300 2 232 25.9 18 60 2 215 19.7 18 120 2 234 30.3 18 180 2 202 22.4 18 240 2 218 27.9 18 300 2 231 28.5 9 60 3 309 20.8 9 120 3 308 21.6 9 180 3 324 24.6 9 240 3 340 25.3 9 300 3 325 35.3 18 60 3 310 17.2 18 120 3 307 23.6 18 180 3 323 24.9 18 240 3 339 30.7 18 300 3 326 33 9 60 4 435 15.6 9 120 4 403 20.4 9 180 4 430 24.4 9 240 4 414 21 9 300 4 419 23.2 18 60 4 436 17.7 18 120 4 404 23.6 18 180 4 429 21.7 18 240 4 413 24.4 18 300 4 420 26.2 Ignacio -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Douglas Bates Sent: Monday, April 25, 2005 6:40 PM To: Jacob Michaelson Cc: r-help@stat.math.ethz.ch Subject: Re: [R] random interactions in lme Jacob Michaelson wrote: On Apr 24, 2005, at 8:52 AM, Douglas Bates wrote: Jacob Michaelson wrote: Hi All, I'm taking an Experimental Design course this semester, and have spent many long hours trying to coax the professor's SAS examples into something that will work in R (I'd prefer that the things I learn not be tied to a license). It's been a long semester in that regard. One thing that has really frustrated me is that lme has an extremely counterintuitive way for specifying random terms. I can usually figure out how to express a single random term, but if there are multiple terms or random interactions, the documentation available just doesn't hold up. Here's an example: a split block (strip plot) design evaluated in SAS with PROC MIXED (an excerpt of the model and random statements): model DryMatter = Compacting|Variety / outp = residuals ddfm = satterthwaite; random Rep Rep*Compacting Rep*Variety; Now the fixed part of that model is easy enough in lme: DryMatter~Compacting*Variety But I can't find anything that adequately explains how to simply add the random terms to the model, ie rep + rep:compacting + rep:variety; anything to do with random terms in lme seems to go off about grouping factors, which just isn't intuitive for me. The grouping factor is rep because the random effects are associated with the levels of rep. I don't always understand the SAS notation so you may need to help me out here. Do you expect to get a single variance component estimate for Rep*Compacting and a single variance component for Rep*Variety? If so, you would specify the model in lmer by first creating factors for the interaction of Rep and Compacting and the interaction of Rep and Variety. dat$RepC - with(dat, Rep:Compacting)[drop=TRUE] dat$RepV - with(dat, Rep:Variety)[drop=TRUE] fm - lmer(DryMatter ~ Compacting*Variety+(1|Rep)+(1|RepC)+(1|RepV), dat) Thanks for the prompt reply. I tried what you suggested, here's what I got: turf.lme=lmer(dry_matter~compacting*variety+(1|rep)+(1|rc)+(1|rv), turf.data) Error in lmer(dry_matter ~ compacting * variety + (1 | rep) + (1 | rc) + : entry 3 in matrix[9,2] has row 3 and column 2 Just to see what the
Re: [R] postscript (eps) / latex / par(mfg=...) / problem!
Should I post this to 'bugs'?
On Tue, 26 Apr 2005, Dan Bolser wrote:
The same problem I am having has been reported here
http://tolstoy.newcastle.edu.au/R/devel/04a/0344.html
Namely that using par(mfg=...) with a postscript (eps) for inclusion with
latex makes the figure appear upside down and back to front (flipped)!
Converting the dvi to ps makes matters worse (the eps seems to be broken),
however, it appears fine with gv.
Here is (basically) the code I am using...
dat - read.table(x.dmp, header=1)
t(dat)
t(dat)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
CHAINS 1 2 3 4 5 6 7 8 9 10 11 12 13 14 16 20 23 24 26 28
FREQUENCY 886 792 136 201 16 58 6 21 3 9 3 9 1 4 3 1 1 1 1 1
postscript(
+ x.eps,
+ width = 6.0,
+ height = 6.0,
+ horizontal = FALSE,
+ onefile = FALSE,
+ paper = special,
+ )
par(mfg=c(1,1))
par(mar=c(3,4,1,2))
plot(dat,type='b')
par(mfg=c(2,1))
par(mar=c(4,4,0,2))
plot(dat,type='b', log='y')
dev.off()
Including the resulting file in a latex document like this...
begin{figure}
\centering
\includegraphics[width=\textwidth]{x.eps}
\caption[X]
{
Hello!
}
\label{xFig}
\end{figure}
The result is an upside down (flipped) version of my plot. I tried
rotating 180 degrees (based on similar problems people were having on the
list), but then it just gets worse (most of the plot is off the page). If
I convert the dvi to ps (dvips -Ppdf my.tex.dvi -o my.tex.ps) it gets
worse (a tiny speck where the image should be).
After removing the two mfg commands (which I use to add grid lines (not
shown for clarity)) everything is fine! Some how mfg is snarling things
up.
OK, I just had a brain wave (dont laugh). Here is a diff of the working
eps vs the broken eps...
diff broken working
78a79,80
%%Page: 1 1
bp
229c231
57.60 43.20 403.20 201.60 cl
---
57.60 57.60 403.20 216.00 cl
417c419
%%Pages: 0
---
%%Pages: 1
Does that help anyone debug my problem? Like I said, both look identical
via gv, and are 'conceptually' identical in R.
Here are my vitals
Linux 2.4.20-31.9 i686 athlon i386 GNU/Linux
R 2.0.0 (2004-10-04).
GNU Ghostscript 7.05 (2002-04-22)
Anything else you need?
Please help!
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[R] Multiple periodicities
Derar all, This is a problem that I am unable to solve. I am interested in analyzing some high-frequency data which show two periodicities (periods 5 and 260), It is clear how to estimate models with one periodicity with arima() but I have not been able to include both periodicities. Is there some good way to handle tis kind of problem? Thanks in advane, Miguel A. -- * Miguel A. Arranz Tol-Project [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
FW: [R] Advice for calling a C function
I think it is a problem with matrices in R and C being stored in different
row/column order
void gowsim ( double *mat, int *OBJ, int *MATDESC) {
double x [*MATDESC][*OBJ];
int i, j, nrow, ncol;
nrow = *OBJ;
ncol = *MATDESC;
/* Rebuild Matrix */
for (j=0; j ncol; j++) {
for (i=0; i nrow; i++) {
x[i][j] = *mat;
Swapping x[i][j] to x[j][i] should fix the problem. Sorry, I did not test
it.
Rprintf(row %d col %d value %f\n, i, j, x[i][j]);
mat++;
}
}
for (i=0; i nrow; i++) {
Rprintf(%f %f %f %f\n, x[i][0], x[i][1], x[i][2], x[i][3]);
}
}
Jarek
\===
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation \__,|
(703) 676-4192 \
[EMAIL PROTECTED] `\
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Re: [R] Index matrix to pick elements from 3-dimensional matrix
I'm assuming what you want to do is randomly sample from slices of A
selected on the 3-rd dimension, as specified by J. Here's a way that
uses indexing by a matrix. The cbind() builds a three column matrix of
indices, the first two of which are randomly selected. The use of
replace() is to make the result have the same attributes, e.g., dim and
dimnames, as J.
A - array(letters[1:12],c(2,2,3))
J - matrix(c(1,2,3,3),2,2)
replace(J, TRUE, A[cbind(sample(dim(A)[1], length(J), rep=T),
sample(dim(A)[2], length(J), rep=T), as.vector(J))])
[,1] [,2]
[1,] b l
[2,] f k
replace(J, TRUE, A[cbind(sample(dim(A)[1], length(J), rep=T),
sample(dim(A)[2], length(J), rep=T), as.vector(J))])
[,1] [,2]
[1,] b l
[2,] h i
replace(J, TRUE, A[cbind(sample(dim(A)[1], length(J), rep=T),
sample(dim(A)[2], length(J), rep=T), as.vector(J))])
[,1] [,2]
[1,] c l
[2,] h k
-- Tony Plate
Robin Hankin wrote:
Hello Juhana
try this (but there must be a better way!)
stratified.select - function(A,J){
out - sapply(J,function(i){sample(A[,,i],1)})
attributes(out) - attributes(J)
return(out)
}
A - array(letters[1:12],c(2,2,3))
J - matrix(c(1,2,3,3),2,2)
R stratified.select(A,J)
[,1] [,2]
[1,] b i
[2,] g k
R stratified.select(A,J)
[,1] [,2]
[1,] d j
[2,] f l
R
best wishes
Robin
On Apr 26, 2005, at 05:16 am, juhana vartiainen wrote:
Hi all
Suppose I have a dim=c(2,2,3) matrix A, say:
A[,,1]=
a b
c d
A[,,2]=
e f
g h
A[,,3]=
i j
k l
Suppose that I want to create a 2x2 matrix X, which picks elements
from the above-mentioned submatrices according to an index matrix J
referring to the depth dimension:
J=
1 3
2 3
In other words, I want X to be
X=
a j
g l
since the matrix J says that the (1,1)-element should be picked from
A[,,1], the (1,2)-element should be picked from A[,,3], etc.
I have A and I have J. Is there an expression in A and J that creates X?
Thanks
Juhana
[EMAIL PROTECTED]
--
Juhana Vartiainen
docent in economics
Director, FIEF (Trade Union Foundation for Economic Research,
Stockholm), http://www.fief.se
gsm +46 70 360 9915
office +46 8 696 9915
email [EMAIL PROTECTED]
homepage http://www.fief.se/staff/Juhana/index.html
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--
Robin Hankin
Uncertainty Analyst
Southampton Oceanography Centre
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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[R] Summarizing factor data in table?
I have a very simple query with regard to summarizing the number of factors present in a certain snippet of a data frame. Given the following data frame: foo - data.frame(yr = c(rep(1998,4), rep(1999,4), rep(2000,2)), div = factor(c(rep(NA,4),A,B,C,D,A,C)), org = factor(c(1:4,1:4,1,2))) I want to get two new variables. Object ndiv would give the number of divisions by year: 1998 0 1999 3 2000 2 Object norgs would give the number of organizations 1998 4 1999 4 2000 2 I figure xtabs should be able to do it, but I'm stuck without a for loop. Any suggestions? -Andy __ R-help@stat.math.ethz.ch 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] random interactions in lme
Thanks, Ignacio -- That was another thing I'd been wondering about (the DenDF in SAS vs. lme). Your example will give me something to chew on as I continue to try and reconcile proc mixed and lme. Thanks for the guidance. Jake On Apr 26, 2005, at 10:36 AM, Ignacio Colonna wrote: The code below gives almost identical results for a split-block analysis in lme and SAS proc mixed, in terms of variance components and F statistics. It just extends the example in Pinheiro Bates (p.162) to a split block design. I am including below the SAS code and the data in case you want to try it. The only difference between both is in the df for the F denominator, which I wasn't able to compute correctly in lme, but this may be my ignorance on how to correctly specify the model. It is not a big issue though, as the F values are identical, so you can compute the p-values if you know how to obtain the correct DenDF. # a split block design spbl.an1- lme(yield~rowspace*ordered(tpop),random=list(rep=pdBlocked(list(pd Ident(~1), pdIdent(~rowspace-1),pdIdent(~ordered(tpop)-1,data=spblock) * SAS code proc mixed data=splitblock method=reml; class rep rowspace tpop; model yield=rowspace tpop rowspace*tpop; random rep rep*rowspace rep*tpop; run; # data rowspacetpoprep plotyield 9 60 1 133 19 9 120 1 101 19.5 9 180 1 117 22 9 240 1 132 19.4 9 300 1 116 23.9 18 60 1 134 15.8 18 120 1 102 26.2 18 180 1 118 21.9 18 240 1 131 20 18 300 1 115 23.3 9 60 2 216 20.6 9 120 2 233 22 9 180 2 201 23.4 9 240 2 217 28.2 9 300 2 232 25.9 18 60 2 215 19.7 18 120 2 234 30.3 18 180 2 202 22.4 18 240 2 218 27.9 18 300 2 231 28.5 9 60 3 309 20.8 9 120 3 308 21.6 9 180 3 324 24.6 9 240 3 340 25.3 9 300 3 325 35.3 18 60 3 310 17.2 18 120 3 307 23.6 18 180 3 323 24.9 18 240 3 339 30.7 18 300 3 326 33 9 60 4 435 15.6 9 120 4 403 20.4 9 180 4 430 24.4 9 240 4 414 21 9 300 4 419 23.2 18 60 4 436 17.7 18 120 4 404 23.6 18 180 4 429 21.7 18 240 4 413 24.4 18 300 4 420 26.2 Ignacio -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Douglas Bates Sent: Monday, April 25, 2005 6:40 PM To: Jacob Michaelson Cc: r-help@stat.math.ethz.ch Subject: Re: [R] random interactions in lme Jacob Michaelson wrote: On Apr 24, 2005, at 8:52 AM, Douglas Bates wrote: Jacob Michaelson wrote: Hi All, I'm taking an Experimental Design course this semester, and have spent many long hours trying to coax the professor's SAS examples into something that will work in R (I'd prefer that the things I learn not be tied to a license). It's been a long semester in that regard. One thing that has really frustrated me is that lme has an extremely counterintuitive way for specifying random terms. I can usually figure out how to express a single random term, but if there are multiple terms or random interactions, the documentation available just doesn't hold up. Here's an example: a split block (strip plot) design evaluated in SAS with PROC MIXED (an excerpt of the model and random statements): model DryMatter = Compacting|Variety / outp = residuals ddfm = satterthwaite; random Rep Rep*Compacting Rep*Variety; Now the fixed part of that model is easy enough in lme: DryMatter~Compacting*Variety But I can't find anything that adequately explains how to simply add the random terms to the model, ie rep + rep:compacting + rep:variety; anything to do with random terms in lme seems to go off about grouping factors, which just isn't intuitive for me. The grouping factor is rep because the random effects are associated with the levels of rep. I don't always understand the SAS notation so you may need to help me out here. Do you expect to get a single variance component estimate for Rep*Compacting and a single variance component for Rep*Variety? If so, you would specify the model in lmer by first creating factors for the interaction of Rep and Compacting and the interaction of Rep and Variety. dat$RepC - with(dat, Rep:Compacting)[drop=TRUE] dat$RepV - with(dat, Rep:Variety)[drop=TRUE] fm - lmer(DryMatter ~ Compacting*Variety+(1|Rep)+(1|RepC)+(1|RepV), dat) Thanks for the prompt reply. I tried what you suggested, here's what I got:
Re: [R] Summarizing factor data in table?
Do you want to count the number of non-NA divisions and organizations in the data for each year (where duplicates are counted as many times as they appear)? tapply(!is.na(foo$div), foo$yr, sum) 1998 1999 2000 042 tapply(!is.na(foo$org), foo$yr, sum) 1998 1999 2000 442 Or perhaps the number of unique non-NA divisions and organizations in the data for each year? tapply(foo$div, foo$yr, function(x) length(na.omit(unique(x 1998 1999 2000 042 tapply(foo$org, foo$yr, function(x) length(na.omit(unique(x 1998 1999 2000 442 (I don't understand where the 3 in your desired output comes from though, which maybe indicates I completely misunderstand your request.) Andy Bunn wrote: I have a very simple query with regard to summarizing the number of factors present in a certain snippet of a data frame. Given the following data frame: foo - data.frame(yr = c(rep(1998,4), rep(1999,4), rep(2000,2)), div = factor(c(rep(NA,4),A,B,C,D,A,C)), org = factor(c(1:4,1:4,1,2))) I want to get two new variables. Object ndiv would give the number of divisions by year: 1998 0 1999 3 2000 2 Object norgs would give the number of organizations 1998 4 1999 4 2000 2 I figure xtabs should be able to do it, but I'm stuck without a for loop. Any suggestions? -Andy __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Summarizing factor data in table?
The three was a typo, which I regret very much. I don't know why I didn't think of apply. I was obsessed with doing it as a table. Thanks for your response, -Andy -Original Message- From: Tony Plate [mailto:[EMAIL PROTECTED] Sent: Tuesday, April 26, 2005 2:00 PM To: Andy Bunn Cc: R-Help Subject: Re: [R] Summarizing factor data in table? Do you want to count the number of non-NA divisions and organizations in the data for each year (where duplicates are counted as many times as they appear)? tapply(!is.na(foo$div), foo$yr, sum) 1998 1999 2000 042 tapply(!is.na(foo$org), foo$yr, sum) 1998 1999 2000 442 Or perhaps the number of unique non-NA divisions and organizations in the data for each year? tapply(foo$div, foo$yr, function(x) length(na.omit(unique(x 1998 1999 2000 042 tapply(foo$org, foo$yr, function(x) length(na.omit(unique(x 1998 1999 2000 442 (I don't understand where the 3 in your desired output comes from though, which maybe indicates I completely misunderstand your request.) Andy Bunn wrote: I have a very simple query with regard to summarizing the number of factors present in a certain snippet of a data frame. Given the following data frame: foo - data.frame(yr = c(rep(1998,4), rep(1999,4), rep(2000,2)), div = factor(c(rep(NA,4),A,B,C,D,A,C)), org = factor(c(1:4,1:4,1,2))) I want to get two new variables. Object ndiv would give the number of divisions by year: 1998 0 1999 3 2000 2 Object norgs would give the number of organizations 1998 4 1999 4 2000 2 I figure xtabs should be able to do it, but I'm stuck without a for loop. Any suggestions? -Andy __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Summarizing factor data in table?
Actually it can be done with xtabs if that's the approach you prefer. foo$yr - factor(foo$yr) margin.table(xtabs(~ div + yr, foo), 2) yr 1998 1999 2000 0 4 2 margin.table(xtabs(~ org + yr, foo), 2) yr 1998 1999 2000 4 4 2 On 4/26/05, Andy Bunn [EMAIL PROTECTED] wrote: The three was a typo, which I regret very much. I don't know why I didn't think of apply. I was obsessed with doing it as a table. Thanks for your response, -Andy -Original Message- From: Tony Plate [mailto:[EMAIL PROTECTED] Sent: Tuesday, April 26, 2005 2:00 PM To: Andy Bunn Cc: R-Help Subject: Re: [R] Summarizing factor data in table? Do you want to count the number of non-NA divisions and organizations in the data for each year (where duplicates are counted as many times as they appear)? tapply(!is.na(foo$div), foo$yr, sum) 1998 1999 2000 0 4 2 tapply(!is.na(foo$org), foo$yr, sum) 1998 1999 2000 4 4 2 Or perhaps the number of unique non-NA divisions and organizations in the data for each year? tapply(foo$div, foo$yr, function(x) length(na.omit(unique(x 1998 1999 2000 0 4 2 tapply(foo$org, foo$yr, function(x) length(na.omit(unique(x 1998 1999 2000 4 4 2 (I don't understand where the 3 in your desired output comes from though, which maybe indicates I completely misunderstand your request.) Andy Bunn wrote: I have a very simple query with regard to summarizing the number of factors present in a certain snippet of a data frame. Given the following data frame: foo - data.frame(yr = c(rep(1998,4), rep(1999,4), rep(2000,2)), div = factor(c(rep(NA,4),A,B,C,D,A,C)), org = factor(c(1:4,1:4,1,2))) I want to get two new variables. Object ndiv would give the number of divisions by year: 1998 0 1999 3 2000 2 Object norgs would give the number of organizations 1998 4 1999 4 2000 2 I figure xtabs should be able to do it, but I'm stuck without a for loop. Any suggestions? -Andy __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] good editor for R sources ?
From: Rau, Roland
Hi,
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of vincent
(Sorry if the question has already been answered.)
Could someone please suggest a good text editor for
writing R sources ?
(I know emacs exists ... but I find it a bit heavy).
I use crimson (http://www.crimsoneditor.com) which is
small and simple, but the R syntax seems not to be supported.
Thanks for any advice
although I prefer myself (X)Emacs, I suggest to people Tinn-R, it is
GPLed, has syntax highlighting, and something I haven't seen with any
other editor before:
You write for example:
mydata - read.table(.csv, header=TRUE, )
and while you are writing your code, a line pops up below the line you
are writing giving you the arguments and their default values for the
current function (I was impressed, I have to admit).
I believe the builtin editor in JGR can do that, too.
Andy
The homepage of this project is:
http://www.sciviews.org/Tinn-R/
Best,
Roland
+
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[R] PCA model
Hi, Another newbie question. Once I have generated a PCA model using the princomp command how can i use it to display a new dataset ? Thanks for your help Fred [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] PCA model
It has a predict method, and ?predict points you to it. predict() is the usual way to apply a model to new data: see `An Introduction to R' or any good book on S/R. On Tue, 26 Apr 2005, Frédéric Ooms wrote: Another newbie question. Once I have generated a PCA model using the princomp command how can i use it to display a new dataset ? Thanks for your help [[alternative HTML version deleted]] PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html As in the comment about HTML mail! -- 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__ R-help@stat.math.ethz.ch 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] how to add a column with string values to a data frame while still converting them to factors
I have 2 questions. In essence i am trying to create product categories based on product description and have it as an additional column of my dataframe. some products dont fit any category and i need a list of them. i am having some trouble in this simple (for most) task. Could you please provide suggestions. Thank you. avneet Question 1) I have a data frame agm.data=read.xls(agm.xls) i add a column to it by this and similar statements agm.data$ProdCategory[agm.data$Product.Description==PGX|agm.data$Product.Description==PGW|agm.data$Product.Description==PS|agm.data$Product.Description==PSX]=Molded Graphite if i do agm.data$ProdCategory i get: [1] Extruded Graphite Molded Graphite Molded Graphite [4] Extruded Graphite Extruded Graphite NA [7] Molded Graphite Extruded Graphite Extruded Graphite [10] Extruded Graphite Extruded Graphite Extruded Graphite [13] Extruded Graphite Porous Iso-Molded Graphite . . . . . [1222] Extruded Graphite Molded Graphite Extruded Graphite [1225] Extruded Graphite Extruded Graphite NA [1228] Iso-Molded Graphite Extruded Graphite NA if i check the class, i get is(agm.data$ProdC) [1] character vector i want this to have.. [1] factor oldClass ..like other columns have Question 2)some values of agm.data$ProdCategory are NA. i want to find corresponding values of agm.data$Product.Description so i give the following command agm.data$Product.Description[agm.data$ProdCategory==NA] i get: [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [17] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA . . . . . . [257] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [273] NA NA NA NA NA 165 Levels: 1.563x24 10x50x60 61x1.25 6x72 890S 8x6 9x7; 10x1.5 AGR ... YBDXX88 -- God created man because he was disappointed over the apes. After that he has given up any further experiments ~Mark Twain __ R-help@stat.math.ethz.ch 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] good editor for R sources ?
On 4/26/05, Uwe Ligges [EMAIL PROTECTED] wrote: (Sorry if the question has already been answered.) Could someone please suggest a good text editor for writing R sources ? (I know emacs exists ... but I find it a bit heavy). I use crimson (http://www.crimsoneditor.com) which is small and simple, but the R syntax seems not to be supported. See http://www.sciviews.org/_rgui/projects/Editors.html The page tells us that there is support for Crimson editor. And for Linux, what do you recommend? Paul __ R-help@stat.math.ethz.ch 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] good editor for R sources ?
From: Paul Smith On 4/26/05, Uwe Ligges [EMAIL PROTECTED] wrote: (Sorry if the question has already been answered.) Could someone please suggest a good text editor for writing R sources ? (I know emacs exists ... but I find it a bit heavy). I use crimson (http://www.crimsoneditor.com) which is small and simple, but the R syntax seems not to be supported. See http://www.sciviews.org/_rgui/projects/Editors.html The page tells us that there is support for Crimson editor. And for Linux, what do you recommend? There are suggestions on that page that Uwe mentioned above for Linux! First choice would be (X)Emacs/ESS. Then there are also vim, kate, bluefish, ... Andy Paul __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Re: how to add a column with string values to a data frame while still converting them to factors
i got the first part: agm.data$ProdCategory=as.factor(agm.data$ProdCategory) the second i am still struggling with On 4/26/05, avneet singh [EMAIL PROTECTED] wrote: I have 2 questions. In essence i am trying to create product categories based on product description and have it as an additional column of my dataframe. some products dont fit any category and i need a list of them. i am having some trouble in this simple (for most) task. Could you please provide suggestions. Thank you. avneet Question 1) I have a data frame agm.data=read.xls(agm.xls) i add a column to it by this and similar statements agm.data$ProdCategory[agm.data$Product.Description==PGX|agm.data$Product.Description==PGW|agm.data$Product.Description==PS|agm.data$Product.Description==PSX]=Molded Graphite if i do agm.data$ProdCategory i get: [1] Extruded Graphite Molded Graphite Molded Graphite [4] Extruded Graphite Extruded Graphite NA [7] Molded Graphite Extruded Graphite Extruded Graphite [10] Extruded Graphite Extruded Graphite Extruded Graphite [13] Extruded Graphite Porous Iso-Molded Graphite . . . . . [1222] Extruded Graphite Molded Graphite Extruded Graphite [1225] Extruded Graphite Extruded Graphite NA [1228] Iso-Molded Graphite Extruded Graphite NA if i check the class, i get is(agm.data$ProdC) [1] character vector i want this to have.. [1] factor oldClass ..like other columns have Question 2)some values of agm.data$ProdCategory are NA. i want to find corresponding values of agm.data$Product.Description so i give the following command agm.data$Product.Description[agm.data$ProdCategory==NA] i get: [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [17] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA . . . . . . [257] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [273] NA NA NA NA NA 165 Levels: 1.563x24 10x50x60 61x1.25 6x72 890S 8x6 9x7; 10x1.5 AGR ... YBDXX88 -- God created man because he was disappointed over the apes. After that he has given up any further experiments ~Mark Twain -- God created man because he was disappointed over the apes. After that he has given up any further experiments ~Mark Twain __ R-help@stat.math.ethz.ch 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] how to modify and compile R sourse codes
Dear All: I am working on writing some R functions to make statistical reports automatically. Dr. Harrell's Hmisc has all the wonderful stuff. But sometimes I need change some formats, so I want to read through it and make some modifications to fit my project. Ideally, I want proceed as following: 1. change some source of Hmisc 2. compile and install the modified Hmisc 3. debug my modified functions. And I am working on windows 2000. Could anyone give some suggestions on the tools and the best way to do this? Thanks __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 with clipping in Lattice, and closing a postscript device
I would appreciate any answer to the following two problems I am having with the Lattice package. First, in most instances of using Lattice, the produced graphs have some clipping, usually at the borders of the encompassing rectangles. An example of this is here: http://cs.uwm.edu/~vu/lattice.pdf where the clipping occurs in the first half of the X axis. Second, when printing to a postscript file, for example, using the command trellis.device(postscript, file = test.ps, color = TRUE) to initialize the output file and then the command dotplot(y ~ x | z, ...) to draw the graph, the postscript file test.ps still has zero size. If at this point I quit R, then test.ps will contain the output graphics. Is there a way to flush the trellis device without exiting R? Thank you very much in advance. Vu Ha, PhD. Information and Decision Technology Honeywell Aerospace 3660 Technology Dr. Minneapolis, MN 55418 612-951-7114 __ R-help@stat.math.ethz.ch 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] Problem with clipping in Lattice, and closing a postscript device
On Tuesday 26 April 2005 15:27, VU HA wrote: I would appreciate any answer to the following two problems I am having with the Lattice package. First, in most instances of using Lattice, the produced graphs have some clipping, usually at the borders of the encompassing rectangles. An example of this is here: http://cs.uwm.edu/~vu/lattice.pdf where the clipping occurs in the first half of the X axis. I've never seen this type of problem before. I suspect using dev.off() as described below would solve this too. Second, when printing to a postscript file, for example, using the command trellis.device(postscript, file = test.ps, color = TRUE) to initialize the output file and then the command dotplot(y ~ x | z, ...) to draw the graph, the postscript file test.ps still has zero size. If at this point I quit R, then test.ps will contain the output graphics. Is there a way to flush the trellis device without exiting R? You have to use dev.off() to properly finish creating a graphics file (this is true for R graphics in general, not just lattice). Deepayan __ R-help@stat.math.ethz.ch 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] good editor for R sources ?
On 4/26/05, Liaw, Andy [EMAIL PROTECTED] wrote: (Sorry if the question has already been answered.) Could someone please suggest a good text editor for writing R sources ? (I know emacs exists ... but I find it a bit heavy). I use crimson (http://www.crimsoneditor.com) which is small and simple, but the R syntax seems not to be supported. See http://www.sciviews.org/_rgui/projects/Editors.html The page tells us that there is support for Crimson editor. And for Linux, what do you recommend? Tere are suggestions on that page that Uwe mentioned above for Linux! First choice would be (X)Emacs/ESS. Then there are also vim, kate, bluefish, ... Thanks, Andy. Does somebody know how to install ess on xemacs? Paul __ R-help@stat.math.ethz.ch 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] survreg with numerical covariates
Does anyone know if the survreg function in the survival package can fit numerical covariates ? When I fit a survival model of the form survreg( Surv(time,censored) ~ x ) then x is always treated as a factor even if it is numeric (and even if I try to force it to be numeric using as.numeric(x). Thus, in the particular example I am analysing, a simple numerical covariate becomes a factor with 190 levels. Is this the expected behaviour ? Am I doing something wrong ? I am running R 2.0.1 on a 64bit Debian Linux system, and version 2.17 of the survival package Thanks Richard Mott -- Richard Mott | Wellcome Trust Centre tel 01865 287588 | for Human Genetics fax 01865 287697 | Roosevelt Drive, Oxford OX3 7BN __ R-help@stat.math.ethz.ch 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] Finding 'ncp' for t
On 26-Apr-05 Peter Dalgaard wrote: (Ted Harding) [EMAIL PROTECTED] writes: Hi Folks, I'm looking for a neat procedure for the following: Given t0 such that pt(t0,df,ncp=0) = alpha (given) find ncp0 such that for given beta pt(t0,df,ncp=ncp0) = (1 - beta) (In other words, what's the ncp such that you get power (1-beta) to detect it, using a 1-sided test with size alpha when ncp = 0?) In the past I've done the groping by hand, but this time it needs to be done many times over, so a good solver for ncp0 in this situation would be handy. You might want to peek inside power.t.test(). Or just use it... Thanks for reminding me of this, Peter. It can be persuaded to do what I want! Also to Rolf Turner for his suggestion. Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Apr-05 Time: 20:13:16 -- XFMail -- __ R-help@stat.math.ethz.ch 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] good editor for R sources ?
On 4/26/05, Paul Smith [EMAIL PROTECTED] wrote: On 4/26/05, Liaw, Andy [EMAIL PROTECTED] wrote: (Sorry if the question has already been answered.) Could someone please suggest a good text editor for writing R sources ? (I know emacs exists ... but I find it a bit heavy). I use crimson (http://www.crimsoneditor.com) which is small and simple, but the R syntax seems not to be supported. See http://www.sciviews.org/_rgui/projects/Editors.html The page tells us that there is support for Crimson editor. And for Linux, what do you recommend? Tere are suggestions on that page that Uwe mentioned above for Linux! First choice would be (X)Emacs/ESS. Then there are also vim, kate, bluefish, ... Thanks, Andy. Does somebody know how to install ess on xemacs? It comes with ESS built-in if you get the full distribution. But this would be better asked on the ess-help list. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] mantelhaen.test for more than two groups?
How about using logistic regression? When you have K dimensional tables and several potential confounders it might be better to go for a multivariable model. Take a look at function glm(stats) and lrm(Design). Cheers Francisco From: Peter Dalgaard [EMAIL PROTECTED] To: Thomas Lumley [EMAIL PROTECTED] CC: Katrin Schweitzer [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject: Re: [R] mantelhaen.test for more than two groups? Date: 26 Apr 2005 18:24:31 +0200 Thomas Lumley [EMAIL PROTECTED] writes: On Tue, 26 Apr 2005, Katrin Schweitzer wrote: Dear All, I'd like to perform the generalized Cochran-Mantel-Haenszel-Test (as described in Agresti (1990), Categorical Data Analysis) for my nominal data. My problem is that I have more than two groups. In fact I think I'd need an 5-dimensional array for the response variable, the control variable and three group variables. Could you please tell me if this is possible in R - and if yes how I am supposed to do this? You're supposed to have a three-dimensional array: exposure x response x group. This means turning your three group variables into one variable. One way to do this is with the interaction() function. Or, if data are already counts, change the dimensions (as in dim(x) - c(2,3,8)), possibly after using aperm() to get the indices in the right order. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Error in nonlinear mixed-effects model
Revilla,AJ (pgt) wrote: Dear all, I am trying to fit a mixed-effects non linear regression, but I have some trouble with it. My data are a balanced panel of 904 subjects with 8 observations (at regular periods) per subject. The functional form of my model is Y=Aexp(-BX1)X2 +e. I want to allow parameters A and B to vary among subjects and also include an autocorrelation term. I have already fitted a standard nonlinear regression to the data, but I keep having problems with NLME. I have defined my data as a groupedData object, and when I try to fit the model I get this error message: dat-groupedData(V~VAC|ID,data=dat) attach(dat) I don't think that attach'ing a groupedData object will propagate the grouping factors. I suggest that you avoid the construction of the groupedData object and also that you avoid attaching and detaching data frames. Just use mod - nlme(V~A*exp(B*YEAR)*VAC, dat, fixed=A+B~1, random=A+B~1|ID, correlation=corCAR1(), start=c(A=1.2,B=0.2)) You will also need to specify a formula for the corAR1 constructor. My guess is form = ~ YEAR | ID but you will need to decide if that is what you intend. Check the help page for corAR1 to see the list of possible arguments. Error in getGroups.data.frame(dataMix, eval(parse(text = paste(~1, deparse(groups[[2]]), : Invalid formula for groups Do you have any clue of whats happening? Its the first time I fit a model like this in R, so the problem is probably pretty obvious, but I cannot see it. Thank you very much, Antonio __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] making table() work
I am trying to do some verification across a large dataset, cuData, that has 23 columns. Column 23 (similarity) is the outcome 0 or 1 and the other columns are the features. I do this: verificationglm.model - glm(formula = similarity ~ ., family=binomial, data=cuData[1:1000,]) and produce the model: summary(verificationglm.model) Call: glm(formula = similarity ~ ., family = binomial, data = cuData[1:1000, ]) Deviance Residuals: Min 1Q Median 3Q Max -2.3885 -0.8943 -0.2918 0.8851 2.7025 Coefficients: Estimate Std. Error z value Pr(|z|) (Intercept) 26.3112869 21.2229690 1.240 0.215066 length-0.6249415 0.1906254 -3.278 0.001044 ** meanPitch -0.0110389 0.0053083 -2.080 0.037565 * minimumPitch 0.0002689 0.0024290 0.111 0.911845 maximumPitch -0.0013454 0.0038149 -0.353 0.724326 meanF1-0.0362153 0.0112499 -3.219 0.001286 ** meanF2 0.0016765 0.0115335 0.145 0.884430 meanF3 0.0073960 0.0076235 0.970 0.331964 meanF4 0.0063015 0.0016820 3.746 0.000179 *** meanF5-0.0022535 0.0024885 -0.906 0.365153 ratioF2ToF1 -1.2322825 7.0036532 -0.176 0.860334 ratioF3ToF1 -4.9643148 4.5973552 -1.080 0.280222 jitter-8.7535283 14.5273818 -0.603 0.546806 shimmer1.6706067 2.6327972 0.635 0.525731 percentUnvoicedFrames -0.4863219 1.1638115 -0.418 0.676042 numberOfVoiceBreaks -0.0335636 0.0634956 -0.529 0.597086 percentOfVoiceBreaks -2.9353239 0.8945600 -3.281 0.001033 ** meanIntensity -0.2931293 0.3355314 -0.874 0.382321 minimumIntensity 0.0689654 0.1531059 0.450 0.652392 maximumIntensity 0.2186570 0.2510906 0.871 0.383848 ratioIntensity-8.1777871 13.1676287 -0.621 0.534565 noSyllsIntensity 0.1714826 0.0695021 2.467 0.013614 * speakingRate -0.3564808 0.1507373 -2.365 0.018034 * startSpeech -1.3537348 6.7337461 -0.201 0.840669 --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 1384.0 on 999 degrees of freedom Residual deviance: 1084.7 on 976 degrees of freedom AIC: 1132.7 Number of Fisher Scoring iterations: 5 Now I want to use the model to predict on a different part of the dataset. I try this, and get my prediction: pred - predict(verificationglm.model, cuData[1001:2000,1:23]) pred 1001 1002 1003 1004 1005 1006 1007 -0.495901722 -2.406349629 -0.911082179 -0.965869553 -0.488695693 -1.849622304 -1.637722247 1008 1009 1010 1011 1012 1013 1014 -1.148952722 -0.191538278 -1.511895046 -2.989036645 -2.775775622 0.603852124 -0.838613048 1015 1016 1017 1018 1019 1020 1021 -0.434259674 -2.004230065 -0.234829011 1.666502334 2.039631718 -0.592192326 1.667700087 1022 1023 1024 1025 1026 1027 1028 0.104644531 1.748724399 0.391461247 1.356898357 1.468154760 1.090708994 1.071487227 1029 1030 1031 1032 1033 1034 1035 0.720596788 2.378350706 -0.128248232 0.969373318 0.315142756 1.372108172 -2.399517898 1036 1037 1038 1039 1040 1041 1042 -0.684530171 0.761198819 -1.298372615 1.185368711 -1.148974059 0.358234433 0.671495255 1043 1044 1045 1046 1047 1048 1049 0.683771224 0.663767266 2.009012643 0.196591464 2.063417812 0.823472345 0.696638161 [runs on to 2000] However, I then want to check for classAgreement (an e1701 package function). First I want a table. I do this: t = table(pred,cuData[1001:2000,24]) t pred 0 1 -8.900700989801060 1 -8.0484071844879 0 1 -7.792985487755231 0 -7.183383306090131 0 [runs on] when I expect this 0 1 0 ?? 1 ?? with the ?s being some count. When I look at my slice of cuData it looks like this: cuData[1001:2000,24] [1] 1 0 1 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 [38] 1 1 1 0 1 1 1 1 0 1 1 1 1 0 0 0 1 1 1 1 1 0 1 0 1 1 0 1 1 1 1 0 0 0 1 1 0 [75] 1 0 0 1 1 0 1 1 0 0 1 0 1 1 1 0 0 1 0 1 1 0 0 0 1 1 1 0 0 0 1 0 1 0 0 0 0 [112] 0 1 1 1 0 1 0 1 1 0 0 1 0 0 1 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [149] 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0 1 0 0 0 0 0 1 1 0 1 0 0 [186] 0 1 0 0 0 1 0 0 0 0 1 1 0 1 1 1 0 0 1 0 1 1 0 0 0 0 0 0 1 1 1 1 1 1 1 0 1 [223] 0 1 0 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 0 0 0 1 0 0 1 1 1 1 1 1 1 1 0 [260] 1 0 0
[R] lattice plot problem!
Hello everybody,
Could I consult you two questions?
Recently I write some code about lattice plot.
1) bwplot function
I know the lattice default background color is grey and the box color
is green, but I don't like the color. So I change the background color to white
use the
trellis.device(bg=white)
then I modify the
panel=function(...)
+{
+ panel.bwplot(col=black...)
+ }
But I find the the box color is still green, just change the color of
point which is in the box, I guss it is the mean or median value of the data.
So How to change the color of box, and how to change the shape of the point in
the box. I want it like other boxplot, like a horizontal line.
2) In every lattices, I want to add a mean line of the group. I try the
panel.abline(h)
But I find in very lattice add the same line. Then I try the
panel.linejoin etc. But I can not get my wish plot.
Could anyone help me to settle these problems?
Thanks very much!
Best Regards!
Ivy Li
YMS in Production Testing
Semiconductor Manufactory International(ShangHai) Corporation
#18 ZhangJiang Road, PuDong New Area, Shanghai, China
Tel: 021-5080-2000 *11754
Email: [EMAIL PROTECTED]
__
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[R] Time series indexes
I tried to assign values to specific elements of a time series and got in trouble. The code below should be almost self-explanatory. I wanted to assign 0 to the first element of x, but instead I assigned zero to the second element of x, which is not what I wanted. Is there a function that will allow me to do this without going into index arithmetic (which would be prone to errors)? FS x- ts(c(1,2,3,4), start = 2) x Time Series: Start = 2 End = 5 Frequency = 1 [1] 1 2 3 4 x[2] - 0 x Time Series: Start = 2 End = 5 Frequency = 1 [1] 1 0 3 4 __ R-help@stat.math.ethz.ch 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] lattice plot problem!
Lattice is not my forte but here goes.
?panel.bwplot specifically notes that pch, col, cex: graphical parameters
controlling the dot. If you look at the code for panel.bwplot you will see
where the colours come from in which case you can probably set up your own
colour scheme using trellis.par.set.
If you are trying to change the symbol so that it is a small line that can be
done using the pch parameter, however it sounds as if you are wanting to
substitute the symbol for a line in which case you might have to write your own
function. a good starting point would be the existing function. A quick look
suggests to me that all you would have to do is to replace the stats$stats[3]
code from grid.points to grid.lines.
Tom
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Ivy_Li
Sent: Wednesday, 27 April 2005 10:53 AM
To: r-help@stat.math.ethz.ch
Subject: [R] lattice plot problem!
Hello everybody,
Could I consult you two questions?
Recently I write some code about lattice plot.
1) bwplot function
I know the lattice default background color is grey and
the box color is green, but I don't like the color. So I
change the background color to white use the
trellis.device(bg=white)
then I modify the
panel=function(...)
+{
+ panel.bwplot(col=black...)
+ }
But I find the the box color is still green, just
change the color of point which is in the box, I guss it is
the mean or median value of the data. So How to change the
color of box, and how to change the shape of the point in the
box. I want it like other boxplot, like a horizontal line.
2) In every lattices, I want to add a mean line of the group.
I try the
panel.abline(h)
But I find in very lattice add the same line. Then I
try the panel.linejoin etc. But I can not get my wish plot.
Could anyone help me to settle these problems?
Thanks very much!
Best Regards!
Ivy Li
YMS in Production Testing
Semiconductor Manufactory International(ShangHai) Corporation
#18 ZhangJiang Road, PuDong New Area, Shanghai, China
Tel: 021-5080-2000 *11754
Email: [EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
