[R] Q: how to submit documentation patches?
I don't want to gripe here, but I would like to know the best method for
submitting suggestions and patches to the documentation.
It looks like for many help items, we need to track from the html file
which help.search(*)/help(*) presents, back to the authoritiative
documentation file from which they are generated. It seems the
installation process discards much of the .../{package}/man/*.Rd files, so
to build patches to the original documentation requires a download and
extraction from the source.
Is there a way to retain the authoritiative files, patch them, re-install
the patched documentation, and perhaps produce a useable patch for the
package maintainers?
Something like
R CMD INSTALL --docs-only pixmap_mine_0.4-1.tar.gz
# to rebuild the documentation
or
R CMD INSTALL --keep-docs --library=/usr/lib/R/library \
utils.xx.yy.tar.gz # to keep the authoritative documentation
with a:
diff -ru pixmap/man pixmap_mine/man pixmap_doc.patch
... as a convenient way to deliver the document criticism, correction, or
elaboration to the package maintainers.
As it is, one has to either download, patch and reinstall the packages, or
edit the .../help/, .../html/, derived files directly to make minor
improvements in the documentation.
I apologise for the complaining, but I did spend too much time today
rediscovering that 'pixmap' is a package for computing images, (I was
off-line, and knew there was something in R that read, plotted, or wrote
graphics files) and a small change like the patch to utils/help/methods
attached would also have saved me some time. R does many things, but the
documentation is hard to patch and improve.
And back to my subject:
Is producing patches against the authoritative documentation the
recommended way to improve the documentation?
Dave
--
Dave Forrest
[EMAIL PROTECTED](804)684-7900w
[EMAIL PROTECTED] (804)642-0662h
http://maplepark.com/~drf5n/diff -ur R-1.9.1-dist/src/library/utils/man/methods.Rd
R-1.9.1/src/library/utils/man/methods.Rd
--- R-1.9.1-dist/src/library/utils/man/methods.Rd 2003-12-09 02:24:25.0
-0500
+++ R-1.9.1/src/library/utils/man/methods.Rd2004-08-24 23:33:44.0 -0400
@@ -47,7 +47,8 @@
The original \code{methods} function was written by Martin Maechler.
}
\seealso{
- \code{\link{S3Methods}}, \code{\link[base]{class}}, \code{\link{getS3method}}
+ \code{\link{S3Methods}}, \code{\link[base]{class}}, \code{\link{getS3method}},
+ \code{\link[methods]{showMethods}}
}
\references{
Chambers, J. M. (1992)
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[R] R and Latex tables
Dear R users, I would like to know if there is any way that I can aumatically generate *.tex files with the output of my estimations from R. Many thanks in advance, Joao Pedro __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Problems with Heatmap
Hi I am having some problems getting my heatmap to be the right size! Let me explain. I am experienced at getting an hclust or a dendrogram object to be the right size. For example, I have a dataset which has 4000 rows, which I clustered using hclust and I wanted to plot it as a horizontal dendrogram. So I used jpeg(), set the image height to be 4000 and plotted the dendrogram and got the result I expected - ie the dendrogram filled up the whole image and I had roughly one pixel per row of data. However, if I run heatmap() instead of hclust(), the resulting image DOES NOT fill up the whole jpeg() - instead, it sits right in the middle of it, the same size as it would be if I had ran heatmap() normally into an x11() window. I've figured out how to use the margins= argument of heatmap() to set the margins, but how do I make my heatmap fill up all of the available space in a jpeg()? Mick __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R and Latex tables
Hi, On Wed, 25 Aug 2004, Joao Pedro W. de Azevedo wrote: Dear R users, I would like to know if there is any way that I can aumatically generate *.tex files with the output of my estimations from R. Take a look at the xtable package. HTH, Kevin Ko-Kang Kevin Wang PhD Student Centre for Mathematics and its Applications Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 0200 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7407 Ph (M): +61-40-451-8301 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R and Latex tables
Hi,
-Original Message-
From: [EMAIL PROTECTED]
[SMTP:[EMAIL PROTECTED] On Behalf Of Joao Pedro W. de
Azevedo
Sent: Wednesday, August 25, 2004 10:43 AM
To: [EMAIL PROTECTED]
Subject: [R] R and Latex tables
Dear R users,
I would like to know if there is any way that I can aumatically generate
*.tex files with the output of my estimations from R.
I am not sure what you exactly mean, but one of the two ways should
meet your needs.
a)
library(xtable)
?xtable
b)
library(utils)
?Sweave
Was this of some help for you?
Roland
P.S. I am using Sweave on a regular basis and I would like to thank
Friedrich Leisch for this great tool.
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[R] R-help
Dear R users, I have just start working with R and would need some help. If you have a matrix as: [,1][,2] [,3] [1,] 11 24 11 [2,] 16 29 16 [3,]215 2 and you want the position where you can find the maximum value, in this case row 2 and column 2. How could you get the position? The values in the matrix is likelihood function values, and each row and column represent values from two parameters. So the idea is to seek which parameter values maximise the likelihood and therefore I need boot row and column position. Regards Jim -- This e-mail and any attachment may be confidential and may also be privileged. If you are not the intended recipient, please notify us immediately and then delete this e-mail and any attachment without retaining copies or disclosing the contents thereof to any other person. Thank you. -- [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help
Hi Jim, you could try this: mat - matrix(sample(1:25), 5, 5) mat row(mat)[mat==max(mat)] col(mat)[mat==max(mat)] I hope it helps. Best, Dimitris Dimitris Rizopoulos Doctoral Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/16/396887 Fax: +32/16/337015 Web: http://www.med.kuleuven.ac.be/biostat/ http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm - Original Message - From: Jim Gustafsson [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Wednesday, August 25, 2004 11:07 AM Subject: [R] R-help Dear R users, I have just start working with R and would need some help. If you have a matrix as: [,1][,2] [,3] [1,] 11 24 11 [2,] 16 29 16 [3,]215 2 and you want the position where you can find the maximum value, in this case row 2 and column 2. How could you get the position? The values in the matrix is likelihood function values, and each row and column represent values from two parameters. So the idea is to seek which parameter values maximise the likelihood and therefore I need boot row and column position. Regards Jim -- This e-mail and any attachment may be confidential and may also be privileged. If you are not the intended recipient, please notify us immediately and then delete this e-mail and any attachment without retaining copies or disclosing the contents thereof to any other person. Thank you. -- [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Help using Hmisc / Latex
Hi, On Wed, 25 Aug 2004, Joao Pedro W. de Azevedo wrote: ## Annette Dobson (1990) An Introduction to Generalized Linear Models. ## Page 9: Plant Weight Data. summary(lm.D90 - lm(weight ~ group - 1))# omitting intercept out - latex(lm.D90) latex(out, model1, file=) When I run this code, I get an output which does not attend my needs. Just out of interest, have you read the documentation for latex()? Kevin Ko-Kang Kevin Wang PhD Student Centre for Mathematics and its Applications Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 0200 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7407 Ph (M): +61-40-451-8301 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Heckman estimation
Hi, I wrote a function to perform a two-step Heckman (also known as heckit) estimation. This function is mainly a wrapper function to glm (1st step probit estimation) and lm (2nd step OLS estimation). Though this function is not perfect yet, it is IMHO already very useful. Since there were some questions about Heckmann estimation in this list, I would like to release it to the public. I hope that useRs will become developeRs and help to improve and extend this function(s). I think it might be not very reasonable to start a new package just for this single small function. And my package micEcon for microeconomic analysis that I hope to release soon seems also not to be the right place, since heckman estimations are used in many other areas besides microeconomic analysis. Can anybody suggest me a package that is appropriate to include the Heckmann function and whose maintainer is willing to do that, too? (Of course, I will write the .Rd file and, if the maintainer wants, I will maintain this function.) Thanks, Arne -- 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/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Problems with Heatmap
By `filling up the page with heatmap', do you mean the image map on the lower right corner of a typical heatmap? If so, that's just image(), so you can use that directly. Andy From: michael watson (IAH-C) Hi I am having some problems getting my heatmap to be the right size! Let me explain. I am experienced at getting an hclust or a dendrogram object to be the right size. For example, I have a dataset which has 4000 rows, which I clustered using hclust and I wanted to plot it as a horizontal dendrogram. So I used jpeg(), set the image height to be 4000 and plotted the dendrogram and got the result I expected - ie the dendrogram filled up the whole image and I had roughly one pixel per row of data. However, if I run heatmap() instead of hclust(), the resulting image DOES NOT fill up the whole jpeg() - instead, it sits right in the middle of it, the same size as it would be if I had ran heatmap() normally into an x11() window. I've figured out how to use the margins= argument of heatmap() to set the margins, but how do I make my heatmap fill up all of the available space in a jpeg()? Mick __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Mapping PCA loadings on to map
Hello all,
I have performed PCA on stacked wind vector data for 20 different spatial
locations. In this case I therefore am in effect working out a PCA for 40
different stations (2 paired pieces of information [ie u and v vector
information] for each station), so have 40 PCs.
In my previous PCA (for none vector data) i have plotted the PC loadings
onto a map of the area of concern, and would like to represent
the results of this PCA in a similar way.
My previous code looks like this:
east-sort(unique(alt$east))
north-sort(unique(alt$north))
map.matrix-matrix(alt$Alt,nrow=length(north),byrow=TRUE)
site.data-read.table(siteinfo.dat,header=TRUE)
ts.data-read.table(met.dat,header=TRUE)
library(mva)
met.pca-prcomp(ts.data,retx=FALSE,scale=TRUE,center=TRUE)
scale-2
for(i in 1:4){
image(east,north,t(map.matrix),col=terrain.colors(50),axes=TRUE,
xlab=,ylab=)
text(site.data$east,site.data$north,labels=as.character(site.data$site))
pc-met.pca$rotation[,i]
pc.pos-(pc0)
if(any(pc.pos)){
symbols(site.data$east[pc.pos],site.data$north[pc.pos],
circles=scale*pc[pc.pos],lwd=2,fg=red,inches=FALSE,add=TRUE)}
if(any(!pc.pos)){
symbols(site.data$east[!pc.pos],site.data$north[!pc.pos],
circles=-scale*pc[!pc.pos],lwd=2,fg=blue,inches=FALSE,add=TRUE)}
box()
}
My problem is, how can i adjust this code so that I get a pair of loadings
at each site? I've been having real problems trying to sort the
subscripting out, as i need to be able to recognise the PC loadings as
pairs, (so have made a further u and v subscript to each station name
before the analysis) but then I they aren't in the same format as needed
to plot onto the map.
I guess there is probably a very obvious way around this and would be
extremely grateful if anyone could help me out!
Also, it occurs to me that another way of representing this information is
by using the arrows() function to add a vector to the map - but again this
relies on my subscripting problem
TIA,
Laura
Laura Quinn
Institute of Atmospheric Science
School of the Environment
University of Leeds
Leeds
LS2 9JT
tel: +44 113 343 1596
fax: +44 113 343 6716
mail: [EMAIL PROTECTED]
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[R] Testing Performance of R on AIX
Dear R Users, I compiled two R-1.9.1 environments on IBM P690 AIX platform, one with optimization level 3(-O3), another with optimization level 2(-O). I would like to do some performance comparison with these two environments. Can anybody give me some advices for how to do the performance test against R? Thanks in advance. Kexiao __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Testing Performance of R on AIX
Acovea is a nice tool for testing gcc optimization options, but you would probably have to do a lot of work to build tests for R. http://www.coyotegulch.com/products/acovea/index.html -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Liao, Kexiao Sent: Wednesday, August 25, 2004 9:28 AM To: [EMAIL PROTECTED] Subject: [R] Testing Performance of R on AIX Dear R Users, I compiled two R-1.9.1 environments on IBM P690 AIX platform, one with optimization level 3(-O3), another with optimization level 2(-O). I would like to do some performance comparison with these two environments. Can anybody give me some advices for how to do the performance test against R? Thanks in advance. Kexiao __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Missing Info on /bin/macosx/r-devel
A minor problem ... Since several weeks the Daily checking results for contributed packages with R-devel for MacOSX seems to be broken, respectively the check file is empty. Please follow the links http://cran.r-project.org/bin/macosx/ and http://cran.r-project.org/bin/macosx//r-devel. Does anybody know, where to find the checking results of R-packages for MacOSX? Many thanks in advance Diethelm Wuertz __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] ADE4
**Libre de Virus - Escaneado por la Universidad de Manizales** X-Virus-Scanned: by AMaViS perl-11 Solicito su ayuda para encontrar e instalar el ADE4, pues en la versión 1.9.1. que tengo instalada no la encuentro y estos son mis primeros ejercicios Le agradezco su colaboración __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Win-Edt and Sweave
Hello, Does anyone knows if there is any plugin for Sweave to run on WinEdt, or any other windows Latex editor? Many thanks, JP __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] sjava problem
hello, I am trying to install SJava on Windows XP as described on http://www.omegahat.org/RSJava/: at the level configure.win: $rhome/sjava/configure.win returned argument 'c:/...' ignored When i tried to install like the readme file, it returned in R library(SJava) using JAVA_HOME = C:\Program Files\Java\j2re1.4.2_04 .JavaInit() Error in .JavaInit() : Couldn't start Java Virtual Machine: Can't create Java Virtual Machine what can I do? version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor9.0 year 2004 month04 day 12 language R thank you thibaut pillas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Win-Edt and Sweave
What's wrong with (X)Emacs? If you want to use Sweave together with R and LaTeX, there's probably nothing else that's better. Andy From: Joao Pedro W. de Azevedo Hello, Does anyone knows if there is any plugin for Sweave to run on WinEdt, or any other windows Latex editor? Many thanks, JP __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Win-Edt and Sweave
Hi,
-Original Message-
From: [EMAIL PROTECTED]
[SMTP:[EMAIL PROTECTED] On Behalf Of Joao Pedro W. de
Azevedo
Sent: Wednesday, August 25, 2004 5:25 PM
To: [EMAIL PROTECTED]
Subject: [R] Win-Edt and Sweave
Does anyone knows if there is any plugin for Sweave to run on WinEdt, or
any
other windows Latex editor?
I use XEmacs 21.4.13 on Win32 here in my office and it works fine.
The second bullet point at the Sweave FAQ site at:
http://www.ci.tuwien.ac.at/~leisch/Sweave/FAQ.html
tells you what to have to insert into your .emacs file (or
.xemacs/init.el). And, of course, you need to have the ESS package installed
as well.
For me, it worked right away.
Best,
Roland
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[R] Re: R online manuals
[diverted from R-devel to R-help, since hopefully of much wider interest] PD == Peter Dalgaard [EMAIL PROTECTED] on 25 Aug 2004 17:17:55 +0200 writes: PD [EMAIL PROTECTED] writes: There is a mistake on the Weibull Distribution (base package) help page in the online docs (http://docs.stat.ufl.edu/R/doc/html/). The formula for Var(X) should have Gamma(1 + 1/a)^2 in place of Gamma(1 + 1/a). PD Looks like docs.stat.ufl.edu haven't been updated for a PD while. It still has the old organisation of the base PD packages. We can't fix bugs retrospectively, PD y'know... The 1.9.1 version does have the squared term PD (it has gamma instead of Gamma, though). Just as note to everyone listening: There are much more official ``R online manuals'' than the one you mention: 1) The most official ones, available by [Manuals] just off the R home page, which goes to CRAN http://cran.r-project.org/manuals.html but these are PDFs which---for the reference manual of all help pages---may be a bit frightening with its almost 2300 pages. Though, actually using acroread's [Find] , entering Weibull very quickly brings you to page 1141, and on p.1142 you see the formulae as nice mathematical equations. If you like these real formulae rather than their plain (or Html) text equivalents, I'd like to draw your attention to the much underused help(dweibull, offline = TRUE) which produces a nice postscript help file for the weibull distribution --- if LateX has been properly available when your R was built / installed. 2) The less official ones, particularly for R-developers are the help pages for current R-patched and R-devel, available by [Help Pages] off the R home page, which leads you to http://stat.ethz.ch/R-manual/ and there, you'll find (all the manuals, not just) the help pages in the usual ``help.start()'' like form, e.g., http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Weibull.html Martin Maechler __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Win-Edt and Sweave
Joao Pedro W. de Azevedo wrote: Hello, Does anyone knows if there is any plugin for Sweave to run on WinEdt, or any other windows Latex editor? Many thanks, JP __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html No plugin for WinEdt that supports LaTeX + R at the same time in the same editor windows is available yet (nor running Sweave from WinEdt). There are some plans to implement it in R-WinEdt, but other stuff is of higher priority on my list ... Uwe Ligges __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] ADE4
La manera mas facil seria haciendo clic en Packages -- Install Packages from CRAN -- ADE4. Despues que lo instales, usa la siguente orden para poder utilizar la libreria ADE4: library(ade4) Espero que esto te ayude, Danny -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Wednesday, August 25, 2004 11:59 AM To: [EMAIL PROTECTED] Subject: [R] ADE4 **Libre de Virus - Escaneado por la Universidad de Manizales** X-Virus-Scanned: by AMaViS perl-11 Solicito su ayuda para encontrar e instalar el ADE4, pues en la versión 1.9.1. que tengo instalada no la encuentro y estos son mis primeros ejercicios Le agradezco su colaboración __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] S - R
Hello! I would like to be able to read in list data objects in R/S created in R/S. (Ie R-S or S-R.) I have tried 'dput' and 'dump' in S, but neither of the created files could be read into R (with 'dget' nor 'source'). Is there any way that I can save a list object in S that can be read into R? Sincerely, Zachary Skrivanek, PhD Research Scientist Program Phase Statistics-Endocrine [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Measuring Variational Distance
R-Users, Does anyone know if there is a package or code somewhere in R that provides a measure of the maximum difference between 2 distributions defined on a common space? I think it is called variational distance? I have constructed several marginal distribution plots (proportion/sample where I defined bin-widths) showing the difference between 2 treatments and I have been trying to get a measure of the difference in area between the curves. I tried searches using variational distance on the R website and CRAN with no luck. TIA, Bret Collier Univ. Arkansas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] S - R
Have you tried following the advice in the R Data Import/Export manual? It suggests the following: Function data.restore reads S-PLUS data dumps (created by data.dump) with the same restrictions (except that dumps from the Alpha platform can also be read). It should be possible to read data dumps from S-PLUS 5.x and 6.x written with data.dump(oldStyle=T). -- Tony Plate At Wednesday 10:29 AM 8/25/2004, Zachary Skrivanek wrote: Hello! I would like to be able to read in list data objects in R/S created in R/S. (Ie R-S or S-R.) I have tried 'dput' and 'dump' in S, but neither of the created files could be read into R (with 'dget' nor 'source'). Is there any way that I can save a list object in S that can be read into R? Sincerely, Zachary Skrivanek, PhD Research Scientist Program Phase Statistics-Endocrine [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] S - R
Zachary Skrivanek wrote: Hello! I would like to be able to read in list data objects in R/S created in R/S. (Ie R-S or S-R.) I have tried 'dput' and 'dump' in S, but neither of the created files could be read into R (with 'dget' nor 'source'). Is there any way that I can save a list object in S that can be read into R? Have you read section 3.1 in R Data Import/Export? http://cran.r-project.org/doc/manuals/R-data.pdf --sundar __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Statistical Learning and Data Mining course
Short course: Statistical Learning and Data Mining Trevor Hastie and Robert Tibshirani, Stanford University Georgetown University Conference Center Washington DC September 20-21, 2004 This two-day course gives a detailed overview of statistical models for data mining, inference and prediction. With the rapid developments in internet technology, genomics and other high-tech industries, we rely increasingly more on data analysis and statistical models to exploit the vast amounts of data at our fingertips. This sequel to our popular Modern Regression and Classification course covers many new areas of unsupervised learning and data mining, and gives an in-depth treatment of some of the hottest tools in supervised learning. The first course is not a prerequisite for this new course. Most of the techniques discussed in the course are implemented by the authors and others in the S language (S-plus or R), and all of the examples were developed in S. Day one focuses on state-of-art methods for supervised learning, including PRIM, boosting, support vector machines, and very recent work on least angle regression and the lasso. Day two covers unsupervised learning, including clustering, principal components, principal curves and self-organizing maps. Many applications will be discussed, including the analysis of DNA expression arrays - one of the hottest new areas in biology! ### Much of the material is based on the book: Elements of Statistical Learning: data mining, inference and prediction Hastie, Tibshirani Friedman, Springer-Verlag, 2001 http://www-stat.stanford.edu/ElemStatLearn/ A copy of this book will be given to all attendees. ### For more information, and to register, visit the course homepage: http://www-stat.stanford.edu/~hastie/mrc.html Trevor Hastie [EMAIL PROTECTED] Professor, Department of Statistics, Stanford University Phone: (650) 725-2231 (Statistics) Fax: (650) 725-8977 (650) 498-5233 (Biostatistics) Fax: (650) 725-6951 URL: http://www-stat.stanford.edu/~hastie address: room 104, Department of Statistics, Sequoia Hall 390 Serra Mall, Stanford University, CA 94305-4065 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] S - R
Hi,
-Original Message-
From: [EMAIL PROTECTED]
[SMTP:[EMAIL PROTECTED] On Behalf Of Zachary Skrivanek
Sent: Wednesday, August 25, 2004 6:29 PM
To: [EMAIL PROTECTED]
Subject: [R] S - R
'source'). Is there any way that I can save a list object in S that can
be read into R?
With S you probably mean S-PLUS, right? Given that is the case, it
depends on the version of S-PLUS you are using. I had no problems to dump
a list and then load it into R as long as I was using S-PLUS 2000. When I
switched to S-PLUS 6, I suddenly could not do that anymore.
It was possible again to do it when I used the same specification of
dump by setting the argument oldStyle=T
This indicates that (excerpt from ?dump)
oldStyle
logical flag; should the file be written in a form that can be read
by earlier versions of S-PLUS? If F, then the file will not be readable by
versions of S-PLUS earlier than 5.0 (Unix) or 6.0 (Windows).
Hope this gets you going.
By the way, this has been discussed before on this list. Please
check (could be googled by using the keywords:
R-project S-PLUS dump; it is actually the first hit):
http://tolstoy.newcastle.edu.au/R/help/04/01/0650.html (for the
beginning of the thread)
http://tolstoy.newcastle.edu.au/R/help/04/01/0665.html (for the same
suggestion as given in my message here)
Roland
+
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
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RE: [R] Adding labels to variables
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin Maechler Sent: Wednesday, August 25, 2004 2:46 AM To: Austin, Matt Cc: [EMAIL PROTECTED] Subject: RE: [R] Adding labels to variables AustinM == Austin, Matt [EMAIL PROTECTED] on Tue, 24 Aug 2004 22:15:15 -0700 writes: AustinM Check out the Hmisc library. It's a *package*, not a library ! [ ... rest deleted ...] As long as the function to load a package is called *library*, I think your campaign to change common usage is doomed to failure. Rich Raubertas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ADE4
S'il vous plait: La lengua de esta listserve es inglés. Sé que es difícil expresarse en una lengua diferente de lo suyo, pero muchas personas apprendan leyendo las preguntans y contestaciones de esta lista. Muchos de los leyentes aquí no entienden francés o aleman o japones o ... . Por eso, yo les pido a ustedes utilicen la norma internacional de esta lista (o construyen una liste para R en Castellano puro). Vielen Dank. Spencer Graves Almirall, Daniel wrote: La manera mas facil seria haciendo clic en Packages -- Install Packages from CRAN -- ADE4. Despues que lo instales, usa la siguente orden para poder utilizar la libreria ADE4: library(ade4) Espero que esto te ayude, Danny -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Wednesday, August 25, 2004 11:59 AM To: [EMAIL PROTECTED] Subject: [R] ADE4 **Libre de Virus - Escaneado por la Universidad de Manizales** X-Virus-Scanned: by AMaViS perl-11 Solicito su ayuda para encontrar e instalar el ADE4, pues en la versión 1.9.1. que tengo instalada no la encuentro y estos son mis primeros ejercicios Le agradezco su colaboración __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] License for including datasets in packages
Dear All, I would like to publish a function for 'heckit' estimations together with two examples from Greene's and Wooldridge's econometric textbooks. These examples use the dataset of Mroz (1987) that is also available in John Fox' car package. However, not all variables that are used in my examples are available in the car package. Therefore, I want to put the full Mroz dataset in my package. This full dataset can be downloaded from some internet sites (e.g. pages.stern.nyu.edu/~wgreene/Text/econometricanalysis.htm, www.stata.com/texts/eacsap/), but I did not find any license information. Whom do I have to ask wether I am allowed to put these data in a GPLed R package? (Mr. Mroz, Mr. Greene, STATA, University of Michigan (PSID), . . . ) @John: Do you have any license information on these data? Thanks, Arne -- 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/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Help using Hmisc / Latex
I'm afraid you need to modify your approach. You're trying to pass latex an lm object, which latex doesn't know how to handle. Also, latex isn't supposed to produce a full .tex file; it generates just a core that's loaded into a shell when you run dvi. Here's an example of how you might use it appropriately: l - latex(summary(lm(b ~ a, data.frame(a = 1:5, b = 1:5)))$coefficients) d - dvi(l) d If you want the full .tex file, you can read the console output after running dvi(l) to find out where the .tex tempfile lives and copy it over to someplace usable. Obviously, you'll have to tweak the row and column names as well as the rounding to suit your preferences. If you're just looking for graphical output--not necessarily a .tex file--I have a function grid.table, now being rolled into a package I will soon release, which uses grid to place a data frame (neatly) on the graphics device. You could then wrap the command around a pdf(), postscript() or any other device to produce an appropriate display. Let me know if you'd like me to send over my working version of the binaries. Kevin -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Joao Pedro W. de Azevedo Sent: Wednesday, August 25, 2004 4:02 AM To: [EMAIL PROTECTED] Subject: [R] Help using Hmisc / Latex Dear R users, I'm trying to automatically generate a *.tex file with the output of an OLS estimation. Some people suggested to use the latex function on the Hmisc package. I'm having a bit of trouble to properly specify this function (I'm not a very experienced R user). Below you will find an example, of what I'm doing. ## Annette Dobson (1990) An Introduction to Generalized Linear Models. ## Page 9: Plant Weight Data. summary(lm.D90 - lm(weight ~ group - 1))# omitting intercept out - latex(lm.D90) latex(out, model1, file=) When I run this code, I get an output which does not attend my needs. First, I could not figure out how to print the variable names. Second I'm not sure how I can select only the coefficients and the std. errors to be inserted on the output. Third, I was wondering if there is any way I can automatically generate significance level indicators next to either the coefficients or the std erros. Forth, is there any way I can aumtomaticaly insert some of model fitting statistics? Fifth, is it possible to specify this function to save the std. error under the coefficient? I'm sure this are quite basic questions, but my attempts to fiddle with the parameters in the model took me nowhere. Many thanks once again, Joao Pedro __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] S - R
I'm puzzled by the discourse in this thread. Briefly, dput() and dget() seem to work just fine for me. I tried junk - list(x=rnorm(20),y=sample(1:100,12,TRUE)) dput(junk,junk.dat) in Splus (Version 6.1.2 Release 2 for Sun SPARC, SunOS 5.6 : 2002) and then in R junk - dget(junk.dat) R version: platform sparc-sun-solaris2.9 arch sparc os solaris2.9 system sparc, solaris2.9 status major1 minor9.1 year 2004 month06 day 21 language R There were no complaints, and typing ``junk'' in the R window and in the Splus window appeared to produce indentical results. So what's the problem? cheers, Rolf Turner [EMAIL PROTECTED] Tony Plate wrote: Have you tried following the advice in the R Data Import/Export manual? It suggests the following: Function data.restore reads S-PLUS data dumps (created by data.dump) with the same restrictions (except that dumps from the Alpha platform can also be read). It should be possible to read data dumps from S-PLUS 5.x and 6.x written with data.dump(oldStyle=T). -- Tony Plate At Wednesday 10:29 AM 8/25/2004, Zachary Skrivanek wrote: Hello! I would like to be able to read in list data objects in R/S created in R/S. (Ie R-S or S-R.) I have tried 'dput' and 'dump' in S, but neither of the created files could be read into R (with 'dget' nor 'source'). Is there any way that I can save a list object in S that can be read into R? Sincerely, Zachary Skrivanek, PhD Research Scientist Program Phase Statistics-Endocrine __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] S - R
I think the issue is that dput() and dget() don't work for some more complex structures (as you point out, they do appear to work for simple structures). The R Data Import/Export manual doesn't mention using dput and dget to transfer objects between R and S-PLUS, perhaps because these functions have limited coverage? E.g.: S-PLUS6.1 junk - list(f=as.name(g)) S-PLUS6.1 dput(junk,junk1.dat) S-PLUS6.1 data.dump(junk, file=junk2.dat, oldStyle=F) S-PLUS6.1 data.dump(junk, file=junk3.dat, oldStyle=T) R dget(junk1.dat) Error in eval(expr, envir, enclos) : Object g not found R # with package foreign loaded R data.restore(junk2.dat) Error in ReadSdump(TRUE, ) : S mode junk (near byte offset 45) not supported In addition: Warning message: NAs introduced by coercion R data.restore(junk3.dat) [1] junk3.dat R junk $f g -- Tony Plate At Wednesday 11:45 AM 8/25/2004, Rolf Turner wrote: I'm puzzled by the discourse in this thread. Briefly, dput() and dget() seem to work just fine for me. I tried junk - list(x=rnorm(20),y=sample(1:100,12,TRUE)) dput(junk,junk.dat) in Splus (Version 6.1.2 Release 2 for Sun SPARC, SunOS 5.6 : 2002) and then in R junk - dget(junk.dat) R version: platform sparc-sun-solaris2.9 arch sparc os solaris2.9 system sparc, solaris2.9 status major1 minor9.1 year 2004 month06 day 21 language R There were no complaints, and typing ``junk'' in the R window and in the Splus window appeared to produce indentical results. So what's the problem? cheers, Rolf Turner [EMAIL PROTECTED] Tony Plate wrote: Have you tried following the advice in the R Data Import/Export manual? It suggests the following: Function data.restore reads S-PLUS data dumps (created by data.dump) with the same restrictions (except that dumps from the Alpha platform can also be read). It should be possible to read data dumps from S-PLUS 5.x and 6.x written with data.dump(oldStyle=T). -- Tony Plate At Wednesday 10:29 AM 8/25/2004, Zachary Skrivanek wrote: Hello! I would like to be able to read in list data objects in R/S created in R/S. (Ie R-S or S-R.) I have tried 'dput' and 'dump' in S, but neither of the created files could be read into R (with 'dget' nor 'source'). Is there any way that I can save a list object in S that can be read into R? Sincerely, Zachary Skrivanek, PhD Research Scientist Program Phase Statistics-Endocrine __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] S - R
Thanks Tony. But the Mr. Skrivanek initially said he couldn't get dput() and dget() to work with ***lists***. It seems to turn out that lists, as such, are not the issue. The problem stems from having relatively weird components in the lists. Also, in your example, the issue is not an R -- S incompatibility problem. The example causes an error even if one stays entirely within Splus (or within R): ===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== junk - list(f=as.name(g)) dput(junk,junk.dat) crap - dget(junk.dat) Problem in dget(junk.dat): Object g not found Use traceback() to see the call stack ===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== And the same happens in R (except that the error message is phrased differently: ===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== Error in structure(list(f = g), .Names = f) : Object g not found ===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== cheers, Rolf Turner [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Newbie Question: Spatial Autocorrelation with R Tutorial?
Howdy All, I am looking for some good tutorials (books, websites, whatever) for calculating/testing for Spatial Autocorrelation using R. Specifically, I am wanting to test for autocorrelation of a number of variables measured at a set of discrete locations. Up to this point I have been exploring the spdep package and I can get moran.test to work, but I am concerned that somewhere along the line I may not be doing things correctly. Hence my request for a tutorial so that I may brush up on my autocorrelation basics, specifically autocorrelation with R, and reassure myself that the results I am getting aren't bogus. Thanks in advance for any suggestions! Jeff Hollister * Jeffrey William Hollister Ph.D. Candidate Environmental Data Center Department of Natural Resources Science University of Rhode Island office: (401) 874 5054 fax: (401) 874 4561 cell: (401)556 4087 http://www.edc.uri.edu/personal/jeff/home/jwh_cv_full.htm __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Censored (Tobit) Regression method
I need to give a quick description of Tobit Regression (TR), including how it differs from ordinary least squares (OLS). I am an ecologist who knows just enough about remote sensing and statistics to be dangerous in both. Now I have found myself doing a remote sensing project where I have used TR: survreg(Surv()). As far as I can tell, no form of Censored Regression has been used in analyzing satellite imagery, so the manuscript I am working on will effectively be introducing TR to the remote sensing community. The manuscript has gone through peer review, and the strongest comment was that I need to give a short description of TR compared to OLS. While I think I've got a reasonable understanding of how to use it, I must admit that I know nothing about the mathematics behind TR. Some references mention it being a combination of OLS and Probit Analysis. At least one econometrics book describes estimating an normal mean from data with a censored or truncated normal distribution. I also find lots of mentionings of y (dependant variable) being a 'latent' variable, though I cannot seem to find a definition for 'latent variable' anywhere, though my guess is that it simply is another way of referring to a censored or truncated variable. I've also seen mentionings of the use of the Tobit Model in Bayesian statistics... so maybe Tobit refers only to a linear model with a censored outcome and there may be multiple ways of getting to that? Here are some specific questions, in case that makes it easier to reply: (1) Does 'Tobit' refer only to y* = Bx + E where y* is censored, or does it also refer to the method for estimating the coefficients of significant variables? (Is it the model or the regression method?) (2) What is a 'latent' variable? (3) In the use of survreg(Surv()), are both OLS and Probit Analysis involved? (4) If OLS is involved, are there modifications made to estimating the means? Is this where Probit Analysis is involved? (5) I've also seen mentionings of maximum likelihood (ML), and ML values are given in the survreg output for the base and full models. Where does ML get involved in the calculations? Thanks! -Eric --- Eric B. Peterson, Ph.D. Vegetation Ecologist Lichenologist Nevada Natural Heritage Program and (adjunct) UNR Dept. NRES [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to Arrange character vector in alphabetic order
Hi, Is there any function that can arrange a character in alphabetic order? Thanks for answer -MY [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] License for including datasets in packages
Dear Arne, I'm not a lawyer, but I believe that data per se are not copyrightable. Regards, John -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Arne Henningsen Sent: Wednesday, August 25, 2004 12:06 PM To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Subject: [R] License for including datasets in packages Dear All, I would like to publish a function for 'heckit' estimations together with two examples from Greene's and Wooldridge's econometric textbooks. These examples use the dataset of Mroz (1987) that is also available in John Fox' car package. However, not all variables that are used in my examples are available in the car package. Therefore, I want to put the full Mroz dataset in my package. This full dataset can be downloaded from some internet sites (e.g. pages.stern.nyu.edu/~wgreene/Text/econometricanalysis.htm, www.stata.com/texts/eacsap/), but I did not find any license information. Whom do I have to ask wether I am allowed to put these data in a GPLed R package? (Mr. Mroz, Mr. Greene, STATA, University of Michigan (PSID), . . . ) @John: Do you have any license information on these data? Thanks, Arne -- 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/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] How to Arrange character vector in alphabetic order
You mean as in: x - c(aaa, abc, ab, d) sort(x) [1] aaa ab abc d ?? Andy From: Yao, Minghua Hi, Is there any function that can arrange a character in alphabetic order? Thanks for answer -MY __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to Arrange character vector in alphabetic order
Is there any function that can arrange a character in alphabetic order? Thanks for answer Check out sort(). vv - c(letters[5:10], letters[20:11], letters[21:26], letters[4:1]) vv [1] e f g h i j t s r q p o n m l k u v w[20] x y z d c b a sort(vv) [1] a b c d e f g h i j k l m n o p q r s[20] t u v w x y z __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to Arrange character vector in alphabetic order
Yao, Minghua wrote: Hi, Is there any function that can arrange a character in alphabetic order? Thanks for answer -MY [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ^ ?sort, ?order, etc --sundar __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RE: How to Arrange character vector in alphabetic order
Sorry for not asking the question clearly. The elements of the character vector may consist of numbers not just letter. How to do that. Thanks. -MY From: Yao, Minghua Sent: Wed 8/25/2004 2:20 PM To: R Help Subject: How to Arrange character vector in alphabetic order Hi, Is there any function that can arrange a character in alphabetic order? Thanks for answer -MY [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Pixmap problem
On Wed, 25 Aug 2004, Benjamin Lloyd-Hughes wrote:
Hi,
I'm having trouble writing .pnm images which I think is due to a problem
with my colour space. The pixmap object seems to be looking for 72 of 8
colours (one per cell?) which doesn't seem healthy...
library(pixmap)
x - pixmapIndexed(rep(1:8, 9), nrow=6, col=rainbow(8))
x
Pixmap image
Type : pixmapIndexed
Size : 6x12
Resolution: 1x1
Bounding box : 0 0 12 6
Nr. of colors : 72 of 8
write.pnm(x, file=D:/Temp/output.pnm)
Error in options(x) : evaluation nested too deeply: infinite recursion /
options(expression=)?
This one is in:
x - pixmapIndexed(rep(1:8, 9), nrow=6, col=rainbow(8))
as(x, pixmapRGB)
Error in options(x) : evaluation nested too deeply: infinite recursion /
options(expression=)?
and as(x, pixmapRGB) is called to make the indexed pixmap
an RGB pixmap, and hits:
setAs(pixmapIndexed, pixmapRGB,
function(from, to){
z = as(from, pixmapRGB)
in setAs(pixmapIndexed, pixmapRGB, ...
with traceback() saying, quite logically:
traceback()
140: options(x)
139: getOption(topLevelEnvironment)
138: identical(envir, matchThisEnv)
137: topenv(parent.frame())
136: exists(classMetaName(Class), where)
135: isClass(class1)
134: possibleExtends(cl, class2)
133: is(fdef, genericMethods)
132: getMethodsForDispatch(f, fdef)
131: getMethods(coerce)
130: .quickCoerceSelect(thisClass, Class)
129: as(from, pixmapRGB)
128: asMethod(object)
...
5: as(from, pixmapRGB)
4: asMethod(object)
3: as(from, pixmapRGB)
2: asMethod(object)
1: as(x, pixmap)
for me:
version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status Under development (unstable)
major2
minor0.0
year 2004
month08
day 06
language R
Until this is fixed, is it feasible for you to use pixmapRGB, not
pixmapIndexed, directly? pixmapRGB objects seem to pass through
write.pnm() without trouble.
Grey ones work but with a warning...
x - pixmapGrey(rep(1:8, 9), nrow=6)
x
Pixmap image
Type : pixmapGrey
Size : 6x12
Resolution: 1x1
Bounding box : 0 0 12 6
write.pnm(x, file=D:/Temp/output.pnm)
Warning message:
connection is already open
showConnections(TRUE)
description class mode text isopen can read can write
0 stdin terminal r text opened yesno
1 stdoutterminal w text opened no yes
2 stderrterminal w text opened no yes
suggests that this is caused by a coding infelicity:
con - file(file, open=w)
open(con, open=w)
in write.pnm() - the open() is unneeded, and will be removed in the next
release.
Any ideas?
Cheers, Ben
[R 1.9.1 and Pixmap 0.4-1 under windows]
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--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Breiviksveien 40, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93
e-mail: [EMAIL PROTECTED]
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RE: [R] Adding labels to variables
At 01:01 PM 08/25/2004, Raubertas, Richard wrote: As long as the function to load a package is called *library*, I think your campaign to change common usage is doomed to failure. Yes, and it's also annoyingly hard to remember -- at least for those of us who don't eat, sleep, and breathe R. MHP -- Michael Prager, Ph.D.[EMAIL PROTECTED] NOAA Center for Coastal Fisheries and Habitat Research Beaufort, North Carolina 28516 http://shrimp.ccfhrb.noaa.gov/~mprager/ NOTE: Opinions expressed are personal, not official. No government endorsement of any product is expressed or implied. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RE: How to Arrange character vector in alphabetic order
Yao, Minghua wrote: Sorry for not asking the question clearly. The elements of the character vector may consist of numbers not just letter. How to do that. Thanks. -MY Why won't ?sort do what you want? Please provide an example and the output you desire. --sundar __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] integrate function
Is possible to integrate this diferential equation: dN/dt = Nr(1-(N/K)) in R using the integrate() function? Or any other diferential equation? If yes, how? If no, anybody know any software on linux that make this? Inte Ronaldo -- O problema de ter os dois pés bem firmes no chão é que você não vai conseguir tirar as calças. --Anônimo -- | // | \\ [***] | ( õ õ ) [Ronaldo Reis Júnior] | V [UFV/DBA-Entomologia] |/ \ [36571-000 Viçosa - MG ] | /(.''`.)\ [Fone: 31-3899-2532 ] | /(: :' :)\ [EMAIL PROTECTED]] |/ (`. `'` ) \[ICQ#: 5692561 | LinuxUser#: 205366 ] |( `- ) [***] | _/ \_Powered by GNU/Debian Woody/Sarge __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] RE: How to Arrange character vector in alphabetic order
Please do read the posting guide, which suggests that you provide a simple example of what you want to achieve, instead of leaving people guessing what you have in mind. Andy From: Yao, Minghua Sorry for not asking the question clearly. The elements of the character vector may consist of numbers not just letter. How to do that. Thanks. -MY From: Yao, Minghua Sent: Wed 8/25/2004 2:20 PM To: R Help Subject: How to Arrange character vector in alphabetic order Hi, Is there any function that can arrange a character in alphabetic order? Thanks for answer -MY __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Adding labels to variables
Mike Prager [EMAIL PROTECTED] writes: At 01:01 PM 08/25/2004, Raubertas, Richard wrote: As long as the function to load a package is called *library*, I think your campaign to change common usage is doomed to failure. Who says it's common usage? It is of course a common fallacy to think that everyone else makes the same mistakes as you do... Yes, and it's also annoyingly hard to remember -- at least for those of us who don't eat, sleep, and breathe R. There's a good chance that R-2.x will introduce usePackage() and eventually remove library() as a tool for loading packages. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] integrate function
Ronaldo Reis Jr. [EMAIL PROTECTED] writes: Is possible to integrate this diferential equation: dN/dt = Nr(1-(N/K)) in R using the integrate() function? No. Or any other diferential equation? Only if the right hand side does not depend on the dependent variable (N in this case) -- just plain integrals. If yes, how? If no, anybody know any software on linux that make this? The odesolve package in R. Possibly, there's also stuff in Octave but I haven't looked lately. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] [Q] Apply Function Over Multiple Array Margins
Paul Roebuck [EMAIL PROTECTED] writes:
Is there a canonical means to apply a function
over multiple arrays simultaneously? For example,
if I wanted to plot each line with a different color?
Or is a for loop conversion my best option?
Try looking at matplot() and friends...
x - seq(0, 8, by = 2)
y - matrix(1:15, nrow = 5, byrow = TRUE)
my.colors - heat.colors(3)
drawLines - function(row) {
lines(x, row)# want corresponding 'my.colors' here
}
plotData - function(x, y) {
plot(x, type='n', axes = FALSE,
xlim = c(min(x), max(x)),
ylim = c(0, max(y)));
box();
axis(1, min(x):max(x))
axis(2, seq(0, max(y), by = 5))
axis(3, labels = FALSE)
axis(4, labels = FALSE)
apply(y, 1, drawLines)
}
plotData(x, t(y))
--
SIGSIG -- signature too long (core dumped)
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--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] [Q] Apply Function Over Multiple Array Margins
Is there a canonical means to apply a function over multiple arrays simultaneously? For example, Would mapply() get you what you're looking for? __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] gam plots
When smooths fitted by the gam package are plotted, what are the units of the vertical axis? Is there a simple way to change these units to units of the dependent variable? Thanks for any suggestions! Paul von Hippel Paul von Hippel Department of Sociology / Initiative in Population Research Ohio State University 300 Bricker Hall 190 N. Oval Mall Columbus OH 43210 614 688-3768 Office hours M-Th 3-5pm __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] brlr function
Hi,
I'm trying the brlr function in a penalized logistic regression function.
However, I am not sure why I am encountering errors. I hope to seek
your advice here. (output below)
Thank you! Your help is truly appreciated.
Min-Han
#No error here, the glm seems to work fine
genes.cox1.glm1-glm(as.formula(paste(paste('as.integer(sim.cv.cox.yhat1)~'),paste('sim.dat.tst[',genes.cox1.rows,',]',sep=,collapse='+'
#Something happened here ... I only substituted brlr for glm
genes.cox1.glm1-brlr(as.formula(paste(paste('as.integer(sim.cv.cox.yhat1)~'),paste('sim.dat.tst[',genes.cox1.rows,',]',sep=,collapse='+'
Error in eval(expr, envir, enclos) : y values must be 0 = y = 1
#using the test data in brlr gives the same error if the dependent is
reduced to one column, is it a problem with my dependent? It works
fine as per the original vignette with
brlr(cbind(grahami,opalinus)~height ...)
brlr(grahami~height+diameter,data=lizards)
Error in eval(expr, envir, enclos) : y values must be 0 = y = 1
#This is how the objects look
as.integer(sim.cv.cox.yhat1)
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 2 2 1 1 2 2 1 1 1 2 1 2 2 2
1 2 1 1 2 1 1 2 1 1 1 2 2 2 2
as.formula(paste(paste('as.integer(sim.cv.cox.yhat1)~'),paste('sim.dat.tst[',genes.cox1.rows,',]',sep=,collapse='+')))
as.integer(sim.cv.cox.yhat1) ~ sim.dat.tst[27, ] + sim.dat.tst[35,
] + sim.dat.tst[17, ] + sim.dat.tst[41, ] + sim.dat.tst[38,
] + sim.dat.tst[31, ] + sim.dat.tst[3, ] + sim.dat.tst[32,
] + sim.dat.tst[16, ] + sim.dat.tst[48, ] + sim.dat.tst[13,
] + sim.dat.tst[28, ]
sim.dat.tst[27,]
Sample 1 Sample 2 Sample 3 Sample 4 Sample 5 Sample 6 Sample 7
Sample 8 Sample 9 Sample 10 Sample 11 Sample 12 Sample 13 Sample 14
Sample 15
5.79 6.72 6.11 5.58 6.32 6.50 6.45
5.77 7.46 6.32 5.64 5.77 5.44 5.83
5.57
Sample 16 Sample 17 Sample 18 Sample 19 Sample 20 Sample 21 Sample 22
Sample 23 Sample 24 Sample 25 Sample 26 Sample 27 Sample 28 Sample 29
Sample 30
5.70 5.67 5.72 5.50 6.34 5.98 6.10
6.25 6.13 7.40 7.28 8.37 5.73 6.83
5.72
Sample 31 Sample 32 Sample 33 Sample 34 Sample 35 Sample 36 Sample 37
Sample 38 Sample 39 Sample 40 Sample 41 Sample 42 Sample 43 Sample 44
Sample 45
6.12 6.74 6.64 6.13 7.74 6.70 7.37
6.54 6.49 5.75 6.18 6.41 7.68 5.36
6.34
Sample 46 Sample 47 Sample 48
5.86 6.64 6.69
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RE: [R] Adding labels to variables
Sigh. I thought I was making a small innocuous observation, but it has apparently been taken as some kind of challenge. Martin's efforts to correct this usage seem (to me) frequent enough to justify calling the mistake 'common', but I guess others will disagree. And what grounds do you have for your implication that it is a mistake I make? Rich Raubertas -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peter Dalgaard Sent: Wednesday, August 25, 2004 4:37 PM To: Mike Prager Cc: [EMAIL PROTECTED] Subject: Re: [R] Adding labels to variables Mike Prager [EMAIL PROTECTED] writes: At 01:01 PM 08/25/2004, Raubertas, Richard wrote: As long as the function to load a package is called *library*, I think your campaign to change common usage is doomed to failure. Who says it's common usage? It is of course a common fallacy to think that everyone else makes the same mistakes as you do... Yes, and it's also annoyingly hard to remember -- at least for those of us who don't eat, sleep, and breathe R. There's a good chance that R-2.x will introduce usePackage() and eventually remove library() as a tool for loading packages. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Beginners Question: Make nlm work
Hello, I'm new to this and am trying to teach myself some R by plotting biological data. The growth curve in question is supposed to be fitted to the Verhulst equation, which may be transcribed as follows: f(x)=a/(1+((a-0.008)/0.008)*exp(-(b*x))) - for a known population density (0.008) at t(0). I am trying to rework the example from An Introduction to R (p. 72) for my case and am failing miserably. Could somebody glance over the code below and nudge me into the right direction - I must have some major conceptual problem which can't be solved by me staring at it ... Since I'm repeating something I have done with gnuplot I know that 3 and 4e-3 as starting values for the fit are appropriate ... Thanks for any hint, Joh setwd(~/Biology/R_versuch) mydata-read.table(YJG45-7_Growth.dat) x-mydata$V1 y-mydata$V2 VH - function(p) y ~ p[1]/(1+((p[1]-0.008)/0.008)*exp(-(p[2]*x))) plot(x, y, xlab=Time (h),ylab=expression(OD[600][~nm]),las=1) out - nlm(VH, p = c(3, 4e-3), hessian = TRUE) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Adding labels to variables
May I also point out the following section title in the R1091 FAQ for Windows: 3.1 Can I install packages (libraries) in this version? So I think that R's own documentation supports Rich's (gentle) comment. -- Bert Gunter Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Raubertas, Richard Sent: Wednesday, August 25, 2004 3:51 PM To: 'Peter Dalgaard' Cc: '[EMAIL PROTECTED]' Subject: RE: [R] Adding labels to variables Sigh. I thought I was making a small innocuous observation, but it has apparently been taken as some kind of challenge. Martin's efforts to correct this usage seem (to me) frequent enough to justify calling the mistake 'common', but I guess others will disagree. And what grounds do you have for your implication that it is a mistake I make? Rich Raubertas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Beginners Question: Make nlm work
- Original Message - From: Johannes Graumann [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Wednesday, August 25, 2004 7:07 PM Subject: [R] Beginners Question: Make nlm work Hello, I'm new to this and am trying to teach myself some R by plotting biological data. The growth curve in question is supposed to be fitted to the Verhulst equation, which may be transcribed as follows: f(x)=a/(1+((a-0.008)/0.008)*exp(-(b*x))) - for a known population density (0.008) at t(0). I am trying to rework the example from An Introduction to R (p. 72) for my case and am failing miserably. Could somebody glance over the code below and nudge me into the right direction - I must have some major conceptual problem which can't be solved by me staring at it ... Since I'm repeating something I have done with gnuplot I know that 3 and 4e-3 as starting values for the fit are appropriate ... Thanks for any hint, Joh setwd(~/Biology/R_versuch) mydata-read.table(YJG45-7_Growth.dat) x-mydata$V1 y-mydata$V2 VH - function(p) y ~ p[1]/(1+((p[1]-0.008)/0.008)*exp(-(p[2]*x))) Shouldn't this be VH - function(p) sum((y - p[1]/(1+((p[1]-0.008)/0.008)*exp(-(p[2]*x^2) Where you are minimizing the squared deviations from what your given equation is when you pass it to nlm? Maybe if you send some data that would make it more clear. Jim plot(x, y, xlab=Time (h),ylab=expression(OD[600][~nm]),las=1) out - nlm(VH, p = c(3, 4e-3), hessian = TRUE) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] labels on secondary y axis
On Thu, 26-Aug-2004 at 01:34AM +0100, Louize Hill wrote: | Hi, | I have plotted a graph and used a secondary axis as follows: | | plot (d$Year, d$HrFishing, type='l', col='1', xlab='Year', ylab='Effort | (hours/fishing)') | par(new=TRUE) | plot (d$Year, d$Landings, type='l', col='3', xlab='', ylab='') | axis(4) | | However, if I put a label in the 2nd ylab='' it is placed over the 1st ylab, | on the left hand side. | Clearly label in the axis command is not what I want as that erases my tick | marks, and ylab generates errors here! | Please can someone give me a pointer on what I should be using. mtext is your friend. -- Patrick Connolly HortResearch Mt Albert Auckland New Zealand Ph: +64-9 815 4200 x 7188 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ I have the world`s largest collection of seashells. I keep it on all the beaches of the world ... Perhaps you`ve seen it. ---Steven Wright ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: brlr function
Thank you all.
The reason was because the dependent should have been 0 and 1, rather
than 1 and 2!
Apologies for any trouble.
Min-Han
On Wed, 25 Aug 2004 18:40:38 -0400, Min-Han Tan
[EMAIL PROTECTED] wrote:
Hi,
I'm trying the brlr function in a penalized logistic regression function.
However, I am not sure why I am encountering errors. I hope to seek
your advice here. (output below)
Thank you! Your help is truly appreciated.
Min-Han
#No error here, the glm seems to work fine
genes.cox1.glm1-glm(as.formula(paste(paste('as.integer(sim.cv.cox.yhat1)~'),paste('sim.dat.tst[',genes.cox1.rows,',]',sep=,collapse='+'
#Something happened here ... I only substituted brlr for glm
genes.cox1.glm1-brlr(as.formula(paste(paste('as.integer(sim.cv.cox.yhat1)~'),paste('sim.dat.tst[',genes.cox1.rows,',]',sep=,collapse='+'
Error in eval(expr, envir, enclos) : y values must be 0 = y = 1
#using the test data in brlr gives the same error if the dependent is
reduced to one column, is it a problem with my dependent? It works
fine as per the original vignette with
brlr(cbind(grahami,opalinus)~height ...)
brlr(grahami~height+diameter,data=lizards)
Error in eval(expr, envir, enclos) : y values must be 0 = y = 1
#This is how the objects look
as.integer(sim.cv.cox.yhat1)
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 2 2 1 1 2 2 1 1 1 2 1 2 2 2
1 2 1 1 2 1 1 2 1 1 1 2 2 2 2
as.formula(paste(paste('as.integer(sim.cv.cox.yhat1)~'),paste('sim.dat.tst[',genes.cox1.rows,',]',sep=,collapse='+')))
as.integer(sim.cv.cox.yhat1) ~ sim.dat.tst[27, ] + sim.dat.tst[35,
] + sim.dat.tst[17, ] + sim.dat.tst[41, ] + sim.dat.tst[38,
] + sim.dat.tst[31, ] + sim.dat.tst[3, ] + sim.dat.tst[32,
] + sim.dat.tst[16, ] + sim.dat.tst[48, ] + sim.dat.tst[13,
] + sim.dat.tst[28, ]
sim.dat.tst[27,]
Sample 1 Sample 2 Sample 3 Sample 4 Sample 5 Sample 6 Sample 7
Sample 8 Sample 9 Sample 10 Sample 11 Sample 12 Sample 13 Sample 14
Sample 15
5.79 6.72 6.11 5.58 6.32 6.50 6.45
5.77 7.46 6.32 5.64 5.77 5.44 5.83
5.57
Sample 16 Sample 17 Sample 18 Sample 19 Sample 20 Sample 21 Sample 22
Sample 23 Sample 24 Sample 25 Sample 26 Sample 27 Sample 28 Sample 29
Sample 30
5.70 5.67 5.72 5.50 6.34 5.98 6.10
6.25 6.13 7.40 7.28 8.37 5.73 6.83
5.72
Sample 31 Sample 32 Sample 33 Sample 34 Sample 35 Sample 36 Sample 37
Sample 38 Sample 39 Sample 40 Sample 41 Sample 42 Sample 43 Sample 44
Sample 45
6.12 6.74 6.64 6.13 7.74 6.70 7.37
6.54 6.49 5.75 6.18 6.41 7.68 5.36
6.34
Sample 46 Sample 47 Sample 48
5.86 6.64 6.69
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Re: [R] Beginners Question: Make nlm work
Aaaa - there was my conceptual problem ... Thanks! ... but 'Oh, God!'! R sucks at fitting (when directed to do so by the simple minded)! Or am I really that off? I attach a plot that contains my data as well as two modeled curves: - the nice one fitted by gnuplot (nonlinear least-squares (NLLS) Marquardt-Levenberg) - the nasty one fitted by the code below. Both algorithms were started with the same values for p[1] and p[2]. Comments? Is there any way to access the 2 elements of 'out$estimate' from the program? Joh setwd(~/Biology/R_versuch) mydata-read.table(YJG45-7_Growth.dat) #plot(mydata$V1,mydata$V2,xlab=Time (h),ylab=expression(OD[600][~nm]),las=1) x-mydata$V1 y-mydata$V2 VH - function(p) sum( (y - p[1]/(1+((p[1]-0.008)/0.008)*exp(-(p[2]*x^2) plot(x, y, axes=FALSE, type=p, xlab=Time (min), ylab=expression(OD[600][~nm]), las=1, pch=20, tck=0.015, mgp=c(1.5,0.25,0), ) axis(1, at=NULL, tick=TRUE, tck=0.015, mgp=c(1.5,0.25,0) ) axis(2, at=NULL, tick=TRUE, tck=0.015, mgp=c(1.5,0.25,0) ) axis(3, at=c(300,600,900,1200,1500,1800,2100), labels=c(5,10,15,20,25,30,35), tick=TRUE, tck=0.015, mgp=c(1.5,0.25,0)) axis(4, labels=FALSE, at=NULL, tick=TRUE, tck=0.015, mgp=c(1.5,0.25,0) ) box() out - nlm(VH, p = c(3, 4e-3), hessian = TRUE) #Plot Results from Gnuplot fit yfit1 - 4.21632/(1+((4.21632-0.008)/0.008)*exp(-(0.00414403*x))) lines(spline(x, yfit1)) #Plot Results from 'out' yfit2 - 3.02050/(1+((3.02050-0.008)/0.008)*exp(-(0.004587924*x))) lines(spline(x,yfit2)) On Wed, 25 Aug 2004 21:06:24 -0400 Jim Brennan [EMAIL PROTECTED] wrote: - Original Message - From: Johannes Graumann [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Wednesday, August 25, 2004 7:07 PM Subject: [R] Beginners Question: Make nlm work Hello, I'm new to this and am trying to teach myself some R by plotting biological data. The growth curve in question is supposed to be fitted to the Verhulst equation, which may be transcribed as follows: f(x)=a/(1+((a-0.008)/0.008)*exp(-(b*x))) - for a known population density (0.008) at t(0). I am trying to rework the example from An Introduction to R (p. 72) for my case and am failing miserably. Could somebody glance over the code below and nudge me into the right direction - I must have some major conceptual problem which can't be solved by me staring at it ... Since I'm repeating something I have done with gnuplot I know that 3 and 4e-3 as starting values for the fit are appropriate ... Thanks for any hint, Joh setwd(~/Biology/R_versuch) mydata-read.table(YJG45-7_Growth.dat) x-mydata$V1 y-mydata$V2 VH - function(p) y ~ p[1]/(1+((p[1]-0.008)/0.008)*exp(-(p[2]*x))) Shouldn't this be VH - function(p) sum((y - p[1]/(1+((p[1]-0.008)/0.008)*exp(-(p[2]*x^2) Where you are minimizing the squared deviations from what your given equation is when you pass it to nlm? Maybe if you send some data that would make it more clear. Jim plot(x, y, xlab=Time (h),ylab=expression(OD[600][~nm]),las=1) out - nlm(VH, p = c(3, 4e-3), hessian = TRUE) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html plot1.eps Description: PostScript document __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Adding labels to variables
Dear Spencer et al., I agree with Spencer's point: It's one thing to introduce usePackage() and encourage its use, another to remove library(). Regards, John -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Spencer Graves Sent: Wednesday, August 25, 2004 9:03 PM To: Peter Dalgaard Cc: Mike Prager; [EMAIL PROTECTED] Subject: Re: [R] Adding labels to variables Mon Dieu! I realize that I'm not part of r-devel, but for what it's worth, I vastly prefer commands and programming styles that produce code that can run without change in both S-Plus and R. Any move to obsolete in R a command commonly used in S-Plus would just make life more difficult for those of us who have to live in both the S-Plus and R worlds. In my judgment, where S-Plus and R currently differ, there usually seems to be a good reason, and R is usually superior. One example is the log options in the probability functions. The suggestion to introduce usePackage and obsolete library reminds me of a 6 week delay in the introduction in France of a US automobile, because the French Royal Academy failed to produce without a substantial delay an official French word for a new technical term. The automobile could not be sold without the User's Manual in French, and it could not be printed without the approval of the French Royal Academy for new words. just my 2e-12 cents. spencer graves Peter Dalgaard wrote: Mike Prager [EMAIL PROTECTED] writes: At 01:01 PM 08/25/2004, Raubertas, Richard wrote: As long as the function to load a package is called *library*, I think your campaign to change common usage is doomed to failure. Who says it's common usage? It is of course a common fallacy to think that everyone else makes the same mistakes as you do... Yes, and it's also annoyingly hard to remember -- at least for those of us who don't eat, sleep, and breathe R. There's a good chance that R-2.x will introduce usePackage() and eventually remove library() as a tool for loading packages. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Adding labels to variables
Peter Dalgaard p.dalgaard at biostat.ku.dk writes: There's a good chance that R-2.x will introduce usePackage() and eventually remove library() as a tool for loading packages. We already have require(). __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Difficulties in starting up with its package
Folks, I'm trying to learn `its' and am stuck on many basics. Could you please help? I am on R 1.9.1 (2004-06-21) on Linux 2.4.17 #2. My its version says Packaged: Tue Apr 27 13:38:25 2004; HeywoodG Built: R 1.9.0; ; 2004-04-28 15:03:13; unix This part flows fine -- library(its) x1 - newIts(start=2000-01-01, end=2000-01-10, 1:30, ncol=3) print(x1) x2 - newIts(start=2000-01-01, end=2000-01-10, 1:30, ncol=3, extract=T, weekday=T) print(x2) Now I get into trouble -- str(x1)# works str(x2)# BREAKS For the str(x2) it says Error in object[1:ile] : subscript out of bounds Is this a bug? I try to go on. # Let's try writing and reading -- writecsvIts(x1, filename=/tmp/try.1) y - its(readcsvIts(filename=/tmp/try.1)) print(y) # looks fine print(x1) # looks fine y-x1 # BREAKS For the y-x1 command, he says Error in y - x1 : dates must match. But when I look at y and x1, the dates do seem to match. I read in two of my own data files like this -- nifty.its - readcsvIts(filename=nifty.d, header=F, sep= , col.names=c(date, r.nifty), informat=its.format(%Y%m%d), outformat=its.format(%Y-%m-%d)) inrusd.its - readcsvIts(filename=inrusd.d, header=F, sep= , col.names=c(date, r.inrusd), informat=its.format(%Y%m%d), outformat=its.format(%Y-%m-%d)) These seem to be fine. To help you diagnose my problem, I have put the results of dput() for both these at the end. Now when I say: union(nifty.its, inrusd.its) [1] 1.0149431 1.0093692 1.0126526 0.9845319 0.9804095 0.9846924 1.0105904 [8] 1.0311819 0.9986636 0.9950831 0.9922442 0.9510527 0.9833306 1.0131162 [15] 0.9966518 0.9970885 1.000 1.0065139 1.0093729 0.9991156 0.9975658 [22] 1.0042147 1.0039761 0.9988999 0.9955947 0.9953540 1.0046677 0.9993363 [29] 1.0015497 1.0022104 0.9984561 I find this odd: I thought union() was supposed to give me an its object. intersect(nifty.its, inrusd.its) numeric(0) I find this odd: the two series have plenty of dates in common. And, I thought intersect() would produce an its object. Here's the dput results for nifty.its and inrusd.its -- dput(nifty.its) structure(c(1.01494311428086, 1.00936924878702, 1.01265263274214, 0.984531863814928, 0.980409543074067, 0.98469241317728, 1.01059040709914, 1.03118189975644, 0.998663641731672, 0.995083089562457, 0.992244183137353, 0.951052697932426, 0.983330571665286), .Dim = as.integer(c(13, 1)), .Dimnames = list(c(2004-05-04, 2004-05-05, 2004-05-06, 2004-05-07, 2004-05-10, 2004-05-20, 2004-05-21, 2004-05-24, 2004-05-25, 2004-05-26, 2004-05-27, 2004-05-28, 2004-05-31), r.nifty)) dput(inrusd.its) structure(c(1.01311623699683, 0.996651785714286, 0.997088465845465, 1, 1.00651392632525, 1.00937290783307, 0.999115631218218, 0.997565833148927, 1.00421472937001, 1.00397614314115, 0.998899889989, 0.995594713656388, 0.995353982300885, 1.00466770393421, 0.99933628318584, 1, 1.00154970112907, 1.00221043324492, 0.998456109395677), .Dim = as.integer(c(19, 1)), .Dimnames = list(c(2004-05-03, 2004-05-05, 2004-05-06, 2004-05-07, 2004-05-10, 2004-05-11, 2004-05-12, 2004-05-13, 2004-05-14, 2004-05-17, 2004-05-18, 2004-05-19, 2004-05-20, 2004-05-21, 2004-05-24, 2004-05-25, 2004-05-26, 2004-05-27, 2004-05-28), r.inrusd)) -- Ajay Shah Consultant [EMAIL PROTECTED] Department of Economic Affairs http://www.mayin.org/ajayshah Ministry of Finance, New Delhi __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Plotting groupedData objects
I am trying to create a plot similar to Figure 3.2 in Bates and Pinheiro. I have repeated measurements on about 80 subjects from 2 treatment groups. I would like to have the panels for the two treatment groups in separate groups and within those groups have the panels ordered on maximum value (as is the default). I am ok with getting plots similar to Figs 3.1 and 3.2, but can't see how to change the ordering of the panels to what I want. Here is the definition of my groupedData object RAWlmeData - groupedData(RAW~Elapsed|ID, data=RAWData, labels=list(x=Elapsed time,y=Airways resistance), units=list(x=(hours),y=cm H20/L/sec)) I guess I could just plot the two treatment groups separately in turn but I feel there is something I am missing. I am using 1.9.1 on Windows XP. David Scott _ David Scott Department of Statistics, Tamaki Campus The University of Auckland, PB 92019 AucklandNEW ZEALAND Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000 Email: [EMAIL PROTECTED] Graduate Officer, Department of Statistics __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Difficulties in starting up with its package
Ajay Shah ajayshah at mayin.org writes: : : Folks, : : I'm trying to learn `its' and am stuck on many basics. Not sure about those issues but I am familiar with zoo and you could do the above in zoo like this. require(zoo) d - seq(as.Date(2000-01-01), as.Date(2000-01-10), by = day) x1 - zoo(matrix(1:30,ncol=3), d) dw - d[as.numeric(format(d,%w)) %in% 1:5] x2 - zoo(matrix(1:30,ncol=3), dw) print(x2) str(x1) str(x2) write.table(data.frame(time = time(x1), unclass(x1)), file = /mytest.txt) y - read.table(/mytest.txt, header = T, as.is = T) y - zoo(data.matrix(y[,-1]),as.Date(y[,1])) print(y) print(x1) # this works since y and x1 same times and are conformable but in general # you need to do a merge first to align them y-x1 nifty.its - structure(c(1.01494311428086, 1.00936924878702, 1.01265263274214, 0.984531863814928, 0.980409543074067, 0.98469241317728, 1.01059040709914, 1.03118189975644, 0.998663641731672, 0.995083089562457, 0.992244183137353, 0.951052697932426, 0.983330571665286), .Dim = as.integer(c(13, 1)), .Dimnames = list(c(2004-05-04, 2004-05-05, 2004-05-06, 2004-05-07, 2004-05-10, 2004-05-20, 2004-05-21, 2004-05-24, 2004-05-25, 2004-05-26, 2004-05-27, 2004-05-28, 2004-05-31), r.nifty)) inrusd.its - structure(c(1.01311623699683, 0.996651785714286, 0.997088465845465, 1, 1.00651392632525, 1.00937290783307, 0.999115631218218, 0.997565833148927, 1.00421472937001, 1.00397614314115, 0.998899889989, 0.995594713656388, 0.995353982300885, 1.00466770393421, 0.99933628318584, 1, 1.00154970112907, 1.00221043324492, 0.998456109395677), .Dim = as.integer(c(19, 1)), .Dimnames = list(c(2004-05-03, 2004-05-05, 2004-05-06, 2004-05-07, 2004-05-10, 2004-05-11, 2004-05-12, 2004-05-13, 2004-05-14, 2004-05-17, 2004-05-18, 2004-05-19, 2004-05-20, 2004-05-21, 2004-05-24, 2004-05-25, 2004-05-26, 2004-05-27, 2004-05-28), r.inrusd)) nifty.zoo - zoo(nifty.its, as.Date(rownames(nifty.its))) rownames(nifty.zoo) - NULL inrusd.zoo - zoo(inrusd.its, as.Date(rownames(inrusd.its))) rownames(inrusd.zoo) - NULL # merge.zoo is similar to union in its merge(nifty.zoo, inrusd.zoo) # merge.zoo with all = FALSE is similar to intersect in its merge(nifty.zoo, inrusd.zoo, all = FALSE) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Order with scientific notations
Hi, If a value like 8e-04 is in a data frame, is the following behaviour normal? final.df Chr P.values 11 0.0379 260.068 32 0.0025 4 138e-04 5 14 0.0244 63 0.0279 74 0.1561 85 0.9261 97 0.0011 10 9 0.5125 11 10 0.2196 12 11 0.6457 13 18 0.9272 final.sorted - data.frame(final.df[order(final.df$P.values), ], +row.names = 1:13) final.sorted Chr P.values 17 0.0011 22 0.0025 3 14 0.0244 43 0.0279 51 0.0379 660.068 74 0.1561 8 10 0.2196 99 0.5125 10 11 0.6457 11 5 0.9261 12 18 0.9272 13 138e-04 I'd think 8e-04 should be the smallest value...? It's R 1.9.1 on Windows XP if that helps. Cheers, Kevin -- Ko-Kang Kevin Wang PhD Student Centre for Mathematics and its Applications Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 0200 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7407 Ph (M): +61-40-451-8301 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] library() (was Adding labels to variables)
Can I remind people to use a relevant subject line -- this has gone way off the original topic. It is not proposed to just rename library() to usePackage() or similar. The need is for a new interface to the loading of packages, one that returns useful information in an object. We also need to sort out the mess of require() vs library(), especially as `require' does not actually require its argument (and almost no one tests the return value). I don't think it is going to make 2.0.0, though. Incidentally, the section heading Bert Gunter quoted does not indicate that `library' is a synonym for `package', but that packages are installed into libraries. In S, `library sections' are installed into libraries. Spencer should be very happy that data() will be almost completely optional come 2.0.0: that's the R/S difference that most hurts writing common documentation in my experience. On Wed, 25 Aug 2004, John Fox wrote: Dear Spencer et al., I agree with Spencer's point: It's one thing to introduce usePackage() and encourage its use, another to remove library(). Regards, John -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Spencer Graves Sent: Wednesday, August 25, 2004 9:03 PM To: Peter Dalgaard Cc: Mike Prager; [EMAIL PROTECTED] Subject: Re: [R] Adding labels to variables Mon Dieu! I realize that I'm not part of r-devel, but for what it's worth, I vastly prefer commands and programming styles that produce code that can run without change in both S-Plus and R. Any move to obsolete in R a command commonly used in S-Plus would just make life more difficult for those of us who have to live in both the S-Plus and R worlds. In my judgment, where S-Plus and R currently differ, there usually seems to be a good reason, and R is usually superior. One example is the log options in the probability functions. The suggestion to introduce usePackage and obsolete library reminds me of a 6 week delay in the introduction in France of a US automobile, because the French Royal Academy failed to produce without a substantial delay an official French word for a new technical term. The automobile could not be sold without the User's Manual in French, and it could not be printed without the approval of the French Royal Academy for new words. just my 2e-12 cents. spencer graves Peter Dalgaard wrote: Mike Prager [EMAIL PROTECTED] writes: At 01:01 PM 08/25/2004, Raubertas, Richard wrote: As long as the function to load a package is called *library*, I think your campaign to change common usage is doomed to failure. Who says it's common usage? It is of course a common fallacy to think that everyone else makes the same mistakes as you do... Yes, and it's also annoyingly hard to remember -- at least for those of us who don't eat, sleep, and breathe R. There's a good chance that R-2.x will introduce usePackage() and eventually remove library() as a tool for loading packages. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
