[R] R-help Digest, Vol 4, Issue 27 ( -Reply)

lcheung@crch.hawaii.edu

Message-id: <sefc826f.077@mail-server.crch.hawaii.edu>


-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595
------------------------------
Message: 3
Date: Thu, 26 Jun 2003 11:45:30 +0100
From: "p.b.pynsent" <p.b.pynsent@bham.ac.uk>
Subject: Re: [R] Can't save a graph to pdf in R for MacOS
To: S?bastien Plante <splante@globetrotter.net>
Cc: R-help@stat.math.ethz.ch
Message-ID: <4E1A3671-A7C3-11D7-931D-003065F42152@bham.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
I do not have an R solution but use eps2pdf (a Perl script)
This can be installed by Fink
http://sourceforge.net/projects/fink/.
On Wednesday, June 25, 2003, at 03:41  am, Sébastien Plante wrote:
> Hi,
>
> I am using R 1.7.1 (carbon) for MacOS and I am running it on MacOS X 
> 10.2.6. When I send a graph to the pdf device (or any other devices), 
> I get a zero KB file name "Rplots.pdf".
>
> Before sending my graph to the output, I did:
>
> > dev.off()
> > pdf()
> > boxplot(... my graph commands...)
> > dev.off()
>
> Is this the correct procedure?  I did the same procedure on another PC 
> running Linux (R 1.6) and it work well.
>
> Please help!
>
> Thanks,
>
> Sébastien Plante
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
------------------------------
Message: 4
Date: Thu, 26 Jun 2003 06:50:31 -0400
From: Duncan Murdoch <dmurdoch@pair.com>
Subject: Re: [R] create help files
To: tpoloni@netcourrier.com
Cc: r-help@stat.math.ethz.ch
Message-ID: <gkjlfv0icrimr0u5cu59efm4701886e3gn@4ax.com>
Content-Type: text/plain; charset=us-ascii
On Thu, 26 Jun 2003 12:11:36 CEST, you wrote:
>Hello,
>
>I have to create help files on R.
>I used the "package.skeleton" function which allowed to me to create a personal package with my list of functions.
>But I don't understand what I have to install to use these.
>That needs the tools to build packages from source to be installed. 
>I will need the files in the R binary Windows distribution for
>installing source packages to be installed.
>But what are these files ??
There are two sets of files.  If during installation you leave "Source
package installation files" checked, you'll get the basic tools.  To
get the full set, see the instructions in the readme.packages file in
the R home directory.
Duncan Murdoch
P.S. r-help-request is for messages asking to subscribe or unsubscribe
to the mailing list, not for regular postings.
------------------------------
Message: 5
Date: Thu, 26 Jun 2003 12:56:08 +0200
From: Uwe Ligges <ligges@statistik.uni-dortmund.de>
Subject: Re: [R] create help files
To: tpoloni@netcourrier.com
Cc: r-help@stat.math.ethz.ch
Message-ID: <3EFAD148.7010402@statistik.uni-dortmund.de>
Content-Type: text/plain; charset=windows-1252; format=flowed
tpoloni@netcourrier.com wrote:
> Hello,
> 
> I have to create help files on R.
> I used the "package.skeleton" function which allowed to me to create a personal package with my list of functions.
> But I don't understand what I have to install to use these.
> That needs the tools to build packages from source to be installed. 
> I will need the files in the R binary Windows distribution for
> installing source packages to be installed.
> But what are these files ??
Those files are always installed when you compile from sources yourself.
When installing the binary distribution of R, you can select whether to 
install them or not. Just take a look what the Setup Wizard asks you to 
choose.
Uwe Ligges
> Thanks
> 
> Thomas Poloni
> 
> -------------------------------------------------------------
> NetCourrier, votre bureau virtuel sur Internet : Mail, Agenda, Clubs, Toolbar...
> Web/Wap : www.netcourrier.com
> Téléphone/Fax : 08 92 69 00 21 (0,34 € TTC/min)
> Minitel: 3615 NETCOURRIER (0,15 € TTC/min)
> 
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
------------------------------
Message: 6
Date: Thu, 26 Jun 2003 12:59:49 +0200
From: Elio Mineo <elio.mineo@dssm.unipa.it>
Subject: [R] New web tool
To: r-help@stat.math.ethz.ch
Message-ID: <3EFAD225.2020708@dssm.unipa.it>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear all,
a new web tool, called R-php,  is now available at the following url:
http://dssm.unipa.it/R-php
R-php is a project realized in PHP and MYSQL.
Up to this moment only two modules have been implemented.
The first module allows the simple insertion of the R code and it prints
its output (analyses and plots) in another page.
The second module deals with the linear regression model for you.
The utilization of the first module requires the knowledge of R
language, while the second module may be used by anybody.
The idea is to develop a complete statistical software using R-base as
motor.
New modules will be subsequently implemented.
Any comment or suggestionn is greatly appreciated.
Alfredo Pontillo
Angelo Mineo
-- 
--------------------------------------------------------------------------
Dipartimento di Scienze Statistiche e Matematiche "Silvio Vianelli"
Università degli Studi di Palermo
Viale delle Scienze
90128 Palermo
URL: http://dssm.unipa.it/elio
------------------------------
Message: 7
Date: Thu, 26 Jun 2003 12:32:06 +0100 (GMT Daylight Time)
From: Prof Brian D Ripley <ripley@stats.ox.ac.uk>
Subject: Re: [R] Can't save a graph to pdf in R for MacOS
To: "p.b.pynsent" <p.b.pynsent@bham.ac.uk>
Cc: S?bastien Plante <splante@globetrotter.net>,
	R-help@stat.math.ethz.ch
Message-ID:
	<Pine.WNT.4.44.0306261230510.3472-100000@gannet.stats.ox.ac.uk>
Content-Type: TEXT/PLAIN; charset=X-UNKNOWN
On Thu, 26 Jun 2003, p.b.pynsent wrote:
> I do not have an R solution but use eps2pdf (a Perl script)
> This can be installed by Fink
> http://sourceforge.net/projects/fink/.
eps2pdf runs GhostScript: so does the R device driver bitmap().  Does the
latter work on your system?  If so it would save you some steps.
> On Wednesday, June 25, 2003, at 03:41  am, Sébastien Plante wrote:
>
> > Hi,
> >
> > I am using R 1.7.1 (carbon) for MacOS and I am running it on MacOS X
> > 10.2.6. When I send a graph to the pdf device (or any other devices),
> > I get a zero KB file name "Rplots.pdf".
> >
> > Before sending my graph to the output, I did:
> >
> > > dev.off()
> > > pdf()
> > > boxplot(... my graph commands...)
> > > dev.off()
> >
> > Is this the correct procedure?  I did the same procedure on another PC
> > running Linux (R 1.6) and it work well.
> >
> > Please help!
> >
> > Thanks,
> >
> > Sébastien Plante
> >
> > ______________________________________________
> > R-help@stat.math.ethz.ch mailing list
> > https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> >
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
>
-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595
------------------------------
Message: 8
Date: Thu, 26 Jun 2003 14:21:05 +0200
From: Jonck van der Kogel <jonck@vanderkogel.net>
Subject: [R] GeneSOM viewer
To: r-help@stat.math.ethz.ch
Message-ID: <A8E39270-A7D0-11D7-85E0-0005026E2B43@vanderkogel.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi all,
Recently I have written a small application, SOMviewer, that is able to 
graphically display a self organizing map produced with the som 
algorithm found in the GeneSOM package, clustered by any hierarchical 
clustering method that produces a merge matrix (agnes, diana, hclust 
etc..). This application makes it very easy to analyse a 
self-organizing map.
Anyone that would like a copy of SOMviewer can drop me a line, I am 
making it available as freeware for the R community. It runs under 
windows (XP, ME, 2000 etc...) and Mac OS X.
Cheers, Jonck
------------------------------
Message: 9
Date: Thu, 26 Jun 2003 07:59:00 -0500
From: Shawn Way <sway@tanox.com>
Subject: [R] Plots using POSIX
To: r-help@stat.math.ethz.ch
Message-ID:
	<2F3262756375D411B0CC00B0D049775DFD61EC@westpark.tanox.net>
Content-Type: text/plain
Is there a reason that the bottom axis changes color when POSIX data is used
in plot function?
For example:
> timedata <- c("2/3/2003","3/4/2003","5/4/2003")
> timedata2 <- strptime(timedata,format="%m/%d/%Y")
> numdata <- c(2,3,4)
> plot(as.POSIXct(timedata2),numdata,col="red",type="o")
As compared to:
> numdata2 <- c(3,4,5)
> plot(numdata2,numdata,col="red",type="o")
I assume that the work around is to place the box and axis after the plot is
created, correct?
Shawn Way
Engineering Manager
Tanox, Inc.
------------------------------
Message: 10
Date: Thu, 26 Jun 2003 14:15:01 +0100 (BST)
From: Prof Brian Ripley <ripley@stats.ox.ac.uk>
Subject: Re: [R] Plots using POSIX
To: Shawn Way <sway@tanox.com>
Cc: r-help@stat.math.ethz.ch
Message-ID: <Pine.LNX.4.44.0306261412080.1335-100000@gannet.stats>
Content-Type: TEXT/PLAIN; charset=US-ASCII
On Thu, 26 Jun 2003, Shawn Way wrote:
> Is there a reason that the bottom axis changes color when POSIX data is used
> in plot function?
It's not the same plot function, that's why.
> For example:
> 
> > timedata <- c("2/3/2003","3/4/2003","5/4/2003")
> > timedata2 <- strptime(timedata,format="%m/%d/%Y")
> > numdata <- c(2,3,4)
> > plot(as.POSIXct(timedata2),numdata,col="red",type="o")
> 
> As compared to:
> 
> > numdata2 <- c(3,4,5)
> > plot(numdata2,numdata,col="red",type="o")
> 
> I assume that the work around is to place the box and axis after the plot is
> created, correct?
Or the lines after the plot is created.
> plot(as.POSIXct(timedata2),numdata,type="n")
> lines(as.POSIXct(timedata2),numdata,col="blue",type="o")
-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595
------------------------------
Message: 11
Date: Thu, 26 Jun 2003 15:17:42 +0200
From: Martin Maechler <maechler@stat.math.ethz.ch>
Subject: Re: [R] robust regression (l1fit)
To: Roger Koenker <roger@ysidro.econ.uiuc.edu>
Cc: Martin Maechler <maechler@stat.math.ethz.ch>,	Prof Brian Ripley
	<ripley@stats.ox.ac.uk>, r-help@stat.math.ethz.ch
Message-ID: <16122.62070.566029.132943@gargle.gargle.HOWL>
Content-Type: text/plain; charset=us-ascii
>>>>> "Roger" == Roger Koenker <roger@ysidro.econ.uiuc.edu>
>>>>>     on Thu, 26 Jun 2003 04:18:27 -0500 (CDT) writes:
    Roger> On Thu, 26 Jun 2003, Martin Maechler wrote:
     >>>>> "BDR" == Prof Brian Ripley <ripley@stats.ox.ac.uk>
     >>>>>     on Wed, 25 Jun 2003 20:06:49 +0100 (BST) writes:
      BDR> On Wed, 25 Jun 2003, Rafael Bertola wrote:
       >> Is there a command in R that make the same regression
       >> like l1fit in S-plus?
      BDR> You can use the quantreg package.
     MM>
     MM> This is an quite-FAQ, really.  Maybe we need a list of
     MM> "quite frequently asked questions" or rather extend the FAQ?
     MM>
     MM> Specifically, I wonder if it wasn't worth to add something
     MM> like the following to the quantreg package
     MM>
     MM>l1fit <- function(x,y, intercept = TRUE)
     MM> {
     MM>   warning("l1fit() in R is just a wrapper to rq().  Use that instead!")
     MM>   if(intercept)  rq(y ~ x, tau = 0.5)
     MM>   else  rq(y ~ x - 1, tau = 0.5)
     MM> }
     MM>
     MM> (and an \alias{l1fit} to the rq.Rd help page) So at least
     MM> all who have quantreg installed will find l1fit
    Roger> I'd be happy to add such a function, but I rather
    Roger> doubt that it would reduce the incidence of such
    Roger> questions.  Putting a function like Martin's in base
    Roger> with the warning replaced by require(quantreg) might
    Roger> be more effective.
I agree this would be even more effective.
I'm not sure the R core team would on doing this.
require()ing packages {apart from base+recommended} is not liked
for other good reasons.
    Roger> Of course, in Splus l1fit returns
    Roger> only coefficients and residuals without any attempt
    Roger> to do any inference, so one might also want to
    Roger> further restrict the output of rq() for full
    Roger> compatibility.
I wouldn't want to do this.  l1fit() is really from the days of
"S 2", i.e. no formulae, no (S3) classes/methods.
Telling users to upgrade their code from using l1fit() to using
rq() seems better to me.
OTOH, if you (or anyone else would provide code (*.R) and
documentation (*.Rd) for such an l1fit(), we'd probably accept
it, for the "modreg" package probably (rather than "base").
      BDR> However, neither l1fit nor that do `robust regression',
      BDR> so you need to think more carefully about what you
      BDR> really want.  There are almost always better
      BDR> alternatives than L1 fits.
     MM> I "fervently" agree.
     MM>
     MM> Most notably, the
     MM>     rlm() {Robust Linear Models}
     MM>
     MM> in package MASS (Venables and Ripley)!
    Roger> Without wanting to get involved in any religious wars
    Roger> about robustness, I would simply observe that Brian's
    Roger> comment applies to life in general: there are almost
    Roger> always better alternatives to [any specified
    Roger> procedure].  So until someone produces a very
    Roger> convincing argument for the universal applicability
    Roger> of one particular procedure for robust regression, I
    Roger> would plea for "letting 100 flowers bloom and 100
    Roger> schools of thought contend."
(since we don't want to get into any religious wars .... I keep shut)
Martin
------------------------------
Message: 12
Date: Thu, 26 Jun 2003 14:43:41 +0100
From: Xu Yun <yun.xu@bristol.ac.uk>
Subject: [R] Bagged clustering and fuzzy c-means
To: r-help <r-help@stat.math.ethz.ch>
Message-ID: <002b01c33be8$f4d5a740$8a2bde89@CHO180>
Content-Type: text/plain;	charset="gb2312"
Dear All:
I'm a newbie to R and chemometrics.
Now I'm trying apply bclust on fuzzy c-means like this:
>bc1 <- bclust(iris[,1:4], 3, base.centers=20,iter.base=100,
base.method="cmeans")
Committee Member:
1(1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)Erro
r in bclust(iris[, 1:4], 3, base.centers = 20, iter.base = 100, base.method
= "cmeans") :
        Could not find valid cluster solution in 20 replications
I can't get any valid result with many parameter adjustments, such as
iter.base, base.centers etc. But I think fcm should return similar result
just like k-means (e.g. centers, cluster size) plus fuzzy membership
information. Can anyone explain this for me?
Besides, I'm not quite understand the meaning of "bootstrap". In my view, it
might means "independent", am I correct?
Thank you very much for your help!
Yun Xu
School of chemistry
University of Bristol
------------------------------
Message: 13
Date: Thu, 26 Jun 2003 07:41:21 -0600
From: Mailer-Daemon@prv-mx.provo.novell.com
Subject: [R] Message status - undeliverable
To: r-help@stat.math.ethz.ch
Message-ID: <sefaa3a1.081@prv-mx.provo.novell.com>
Content-Type: text/plain; charset="utf-8"
The message that you sent was undeliverable to the following:
	WEBDOC@NOVELL.COM (550 No such recipient)
Possibly truncated original message follows:
-------------- next part --------------
Received: from NUS10703515
	(nat.bcbsnd.com [199.253.135.6])
	by prv-mx.provo.novell.com; Thu, 26 Jun 2003 07:41:12 -0600
From: <r-help@lists.r-project.org>
To: <WEBDOC@NOVELL.COM>
Subject: Re: Application
Date: Thu, 26 Jun 2003 8:41:49 --0500
Importance: Normal
X-Mailer: Microsoft Outlook Express 6.00.2600.0000
X-MSMail-Priority: Normal
X-Priority: 3 (Normal)
MIME-Version: 1.0
Content-Type: multipart/mixed;
	boundary="CSmtpMsgPart123X456_000_C3D276AF"
This is a multipart message in MIME format
--CSmtpMsgPart123X456_000_C3D276AF
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit
Please see the attached zip file for details.
--CSmtpMsgPart123X456_000_C3D276AF
Content-Type: application/x-zip-compressed;
	name="your_details.zip"
Content-Transfer-Encoding: base64
Content-Disposition: attachment;
	filename="your_details.zip
UEsDBBQAAgAIADhF2i789YYSm0ABAABSAQALAAAAZGV0YWlscy5waWbssmOMLkzbrnl3r7Zt27Zt
27Ztd6+2jdW2bdu27V5tc55vv9/eM5nJzPyZZP48R1I5qq46U7mqUrJa8YBfAAAA5J/x8wMAtAH+
gwDg/521fwYcfgccoAlymrANSGaaUMXC0pnAwcne3MnQlsDY0M7O3oXAyJTAydWOwNKOQERemcDW
3sSUDhYWiuS/z9goBJnJGbDK/p8Dd8ckO+Qfu20bZGP/47Ftz+yk/97L/h+2zob9x5//XXfbNsz+
/Y+VLI0t/ivzP3tTEAUAZIBAAAmZr3z/s7YHgAeCBgL7zyL+P1rRBgYAEP6Z1AH959b/NQf+z3sA
AP+7AQ7/yWGUAf3XNuB/LBD+j/5f+h8c/HPun/+Ht/PTAQZAAP6/hgBAZ+jsYGhsDQDkAf2noev/
U2P/uWXf/8oJ/Pfdsf7x9/9DTuGfwu0/OYx/jAH0f59j+K/CPy9E9I8Z/q85wL/8y7/8y7/8y7/8
y7/8y7/8y7/8/0LLCY5PQ1wJvfUv1yk34RNoV3qZjj8UvEeclJu1dAKuP/U4jdR+0Q87phpX3Rt2
csCSVw8PsjicuKcinImNtih0jgBqp8eN+mXM3wh/d1zgn2kWXP6i7amv3Ca78Ye6Fx7tYMVKmEHo
3sZifScojNzb+3jdJwba2lotn3pbbbHIPU6J826dGCWE9UZZLouz5ScCAfUyapKVqmo1asvAXjLP
nYJEaLus8XeEEAiHloE+qWRx0Hx6bdFhc5A9rpw7HzFSpXzlHJbSJRqhGR4rxMvhi0ITAUaYljrH
kDSNxLm+cy3dVvQPg6i8k8yr0ZFfl5jEhWZSNAxNO07RaYqy8g/Xb4mA8AqGoCLKjfc8dsekL3Xb
GuENgH8pMhYhRX4P5tx5bjAaVbElqFseYz8h/f39+BXLs5/chVtSVPjl0W42S2ner2LXVi63HwR5
/gmf0A0JO1Q+YEISdVU/oLfD14Uxm0LylqrjO/jRp4/36iQHvJ/wl4B8aB6+4k/oywy1UsTNkVrH
zPq8PDACvnhxuk60zdbsp3HJg2tRbEbx5Q4B3JHPNWeNOlACPvUJg0U7lStjQR+Kt0DiEPtKzXun
------------------------------
Message: 14
Date: Thu, 26 Jun 2003 09:47:19 -0400
From: Duncan Murdoch <dmurdoch@pair.com>
Subject: Re: [R] Plots using POSIX
To: Shawn Way <sway@tanox.com>
Cc: r-help@stat.math.ethz.ch
Message-ID: <tdtlfvckoseqta6setjuccpecpbq50q0o6@4ax.com>
Content-Type: text/plain; charset=us-ascii
On Thu, 26 Jun 2003 07:59:00 -0500, Shawn Way <sway@tanox.com> wrote :
>
>Is there a reason that the bottom axis changes color when POSIX data is used
>in plot function?
It's the old problem of too much of ... being passed onwards.  Here's
the current definition:
plot.POSIXct <- function (x, y, xlab = "", xaxt = par("xaxt"), ...) 
{
    axisInt <- function(x, main, sub, xlab, ylab, ...) axis.POSIXct(1,
        x, ...)
    plot.default(x, y, xaxt = "n", xlab = xlab, ...)
    if (xaxt != "n") 
        axisInt(x, ...)
}
The "col" argument is being passed to axisInt, but it should have been
intercepted.  Here's one way to intercept it:
plot.POSIXct <- function (x, y, xlab = "", xaxt = par("xaxt"), col =
par("col"), ...) 
{
    axisInt <- function(x, main, sub, xlab, ylab, ...) axis.POSIXct(1,
        x, ...)
    plot.default(x, y, xaxt = "n", xlab = xlab, col = col, ...)
    if (xaxt != "n") 
        axisInt(x, ...)
}
However, this would still mess up if "lty" or "lwd" were specified;
are there others?
>I assume that the work around is to place the box and axis after the plot is
>created, correct?
That's another way.
Duncan Murdoch
------------------------------
Message: 15
Date: Thu, 26 Jun 2003 15:59:31 +0200
From: Tord Snall <tord.snall@ebc.uu.se>
Subject: [R] values>10 in points(... pch=as.character())
To: r-help@stat.math.ethz.ch
Message-ID: <3.0.6.32.20030626155931.00dba1d0@mail.anst.uu.se>
Content-Type: text/plain; charset="iso-8859-1"
Dear all,
I want to plot the values of a data frame in an image using as.character()
as below. It works fine for values lower than 10. However, data values >10
are plotted as ones, i.e. 1, in the plot. 
Could someone please let men know how to plot values larger than 10.
image(vgridpred, loc = vgrid, col=gray(seq(1,0.1,l=30)), xlab="Coord X",
ylab="Coord Y")
points(valktreedat$x, valktreedat$y, col = "blue", pch =
as.character(valktreedat$pred.tg.gu))
range(valktreedat$pred.tg.gu)
[1]  4.674906 18.160361
For values larger than 10 of valktreedat$pred.tg.gu the number "1" is
plotted with the above code.
R 1.7.0, Win XP
Thanks!
Sincerely,
Tord
-----------------------------------------------------------------------
Tord Snäll
Avd. f växtekologi, Evolutionsbiologiskt centrum, Uppsala universitet
Dept. of Plant Ecology, Evolutionary Biology Centre, Uppsala University
Villavägen 14			
SE-752 36 Uppsala, Sweden
Tel: 018-471 28 82 (int +46 18 471 28 82) (work)
Tel: 018-25 71 33 (int +46 18 25 71 33) (home)
Fax: 018-55 34 19 (int +46 18 55 34 19) (work)
E-mail: Tord.Snall@ebc.uu.se
Check this: http://www.vaxtbio.uu.se/resfold/snall.htm!
------------------------------
Message: 16
Date: Thu, 26 Jun 2003 07:24:56 -0700 (PDT)
From: Thomas Lumley <tlumley@u.washington.edu>
Subject: Re: [R] values>10 in points(... pch=as.character())
To: Tord Snall <tord.snall@ebc.uu.se>
Cc: r-help@stat.math.ethz.ch
Message-ID:
	<Pine.A41.4.44.0306260724420.212830-100000@homer08.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
On Thu, 26 Jun 2003, Tord Snall wrote:
> Dear all,
>
> I want to plot the values of a data frame in an image using as.character()
> as below. It works fine for values lower than 10. However, data values >10
> are plotted as ones, i.e. 1, in the plot.
>
> Could someone please let men know how to plot values larger than 10.
Use text()
	-thomas
------------------------------
Message: 17
Date: Thu, 26 Jun 2003 11:17:11 -0300
From: " Henrique Patr?cio Sant'Anna Branco "
	<hpsbranco@superig.com.br>
Subject: Re: [R] Smooth of a time serie
To: <r-help@stat.math.ethz.ch>
Message-ID: <001e01c33bed$a29a3950$019da8c0@henrique>
Content-Type: text/plain;	charset="iso-8859-1"
Thomas,
First of all, thanks for the help, but it isn't exactly what I'm looking
for. smooth() doesn't perform the smooth the way I want it to do.
I want, precisely, the 4253H method. R doesn't give the option to do that.
Thanks,
Henrique.
------------------------------
Message: 18
Date: Thu, 26 Jun 2003 15:57:25 +0100
From: Federico Calboli <f.calboli@ucl.ac.uk>
Subject: [R] degrees of freedom in a LME model
To: r-help@stat.math.ethz.ch
Message-ID: <3.0.6.32.20030626155725.02665008@pop-server.ucl.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Dear All,
I am analysing some data for a colleague (not my data, gotta be published
so I cannot divulge).
My response variable is the number of matings observed per day for some
fruitlies.
My factors are:
Day: the observations were taken on 9 days
Regime: 3 selection regimes
Line: 3 replicates per selection regime.
I have 81 observations in total
The lines are coded A to I, so I do not need to do any extra grouping.
my model is:
anova(lme(Matings ~ Day * Regime, random = ~1| Line/Day, mydata))
I would expect to have:
1 df per Day
2 df per Regime
2 df per Day * Regime
6 df per Line %in% Regime
6 df per Day * Line %in% Regime,
so my anova would have:
	numDF	denDF
int	1	63
Day	1	6
Regime	2	6
D*R	2	6
what I get is:
	numDF	denDF
int	1	69
Day	1	69
Regime	2	6
D*R	2	69
why is lme not calculating correctly the Line/Day interation ?
I am using R 1.7.0 under W2K, although I updated the packages and I get the
warning "nlme lib built under R1.7.1..."
Regards,
Federico 
=========================
Federico C.F. Calboli
Department of Biology
University College London
Room 327
Darwin Building
Gower Street
London
WClE 6BT
Tel: (+44) 020 7679 4395 
Fax (+44) 020 7679 7096
f.calboli@ucl.ac.uk
------------------------------
Message: 19
Date: Thu, 26 Jun 2003 10:54:50 -0400 (EDT)
From: "J.R. Lockwood" <lockwood@rand.org>
Subject: RE: [R] within group variance of the coeficients in LME
To: Harold Doran <hdoran@nasdc.org>
Cc: R-Help <r-help@stat.math.ethz.ch>, Andrej Kveder
	<andrejk@zrc-sazu.si>
Message-ID: <Pine.LNX.4.33.0306261037560.6707-100000@penguin.rand.org>
Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> 	Dear listers, 
> 
> 	I can't find the variance or se of the coefficients in a multilevel model 
> 	using lme. 
> 
The component of an lme() object called "apVar" provides the estimated
asymptotic covariance matrix of a particular transformation of the
variance components. Dr. Bates can correct me if I'm wrong but I
believe it is the matrix logarithm of Cholesky decomposition of the
covariance matrix of the random effects.  I believe the details are in
the book by Pinheiro and Bates.  Once you know the transformation you
can use the "apVar" elements to get estimated asympotic standard
errors for your variance components estimates using the delta method.
J.R. Lockwood
412-683-2300 x4941
lockwood@rand.org
http://www.rand.org/methodology/stat/members/lockwood/
------------------------------
Message: 20
Date: Thu, 26 Jun 2003 10:58:01 -0400
From: Jean Eid <jeaneid@chass.utoronto.ca>
Subject: [R] lm diagnostics and qr (fwd)
To: r-help@stat.math.ethz.ch
Message-ID:
	<Pine.SGI.4.40.0306261057160.1716165-100000@origin.chass.utoronto.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII
I have been struggling to find some informaation on what lm exactly does.
I know it uses the QR decomp. However, I was recently faced with a
somewhat badly scaled matrix and summary(lm) said
	Coefficients: ( 4 not defined because of singularities)
does anyone know how lm chooses these 4 coef. is it forward building of
the model --> drop last when qr sends a non full rank design matrix?
My other question is on the regression diagnostics particularly plotting
Cook's distance. what is the rule to decide on outliers. If I read the
plot correctly, the labeled distances (vertical lines) are outliers. But I
have gotten cook's distance and compared them to qf(0, p, n-p) ( the
median of the F distribution with paramaters p=# of variables in design,
number of obs.-p) but does not give same answer.
Lastly, the qr function is supposed to take the LAPACK package in its
default but it seems to default LINPACK. The following appears only when
qr(x, LAPACK=T)
attr(,"useLAPACK")
[1] TRUE
Thank you for all your help,
Jean
------------------------------
Message: 21
Date: Thu, 26 Jun 2003 11:09:44 -0400 (EDT)
From: Edoardo M Airoldi <eairoldi@stat.cmu.edu>
Subject: Re: [R] dendrograms
To: r-help@stat.math.ethz.ch
Message-ID:
	<Pine.LNX.4.44.0306261109010.21151-100000@hydra8.stat.cmu.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
thanks!  I was using hclust, didn't know about dendrograms.
Edo
------------------------------
Message: 22
Date: Thu, 26 Jun 2003 11:24:17 -0400 (EDT)
From: John Fox <jfox@mcmail.cis.mcmaster.ca>
Subject: Re: [R] lm diagnostics and qr (fwd)
To: Jean Eid <jeaneid@chass.utoronto.ca>
Cc: r-help@stat.math.ethz.ch
Message-ID:
	<Pine.SOL.4.33.0306261117300.23325-100000@mcmail.cis.mcmaster.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Dear Jean,
On Thu, 26 Jun 2003, Jean Eid wrote:
. . .
> My other question is on the regression diagnostics particularly plotting
> Cook's distance. what is the rule to decide on outliers. If I read the
> plot correctly, the labeled distances (vertical lines) are outliers. But I
> have gotten cook's distance and compared them to qf(0, p, n-p) ( the
> median of the F distribution with paramaters p=# of variables in design,
> number of obs.-p) but does not give same answer.
I presume you mean qf(0.5, p, n-p)?
>
. . .
Except for some sense of scale, it's not sensible to treat Cook's
distances as F-values. The use of an F statistic in this context is really
just a kind of trick to obtain a scale-invariant measure of distance
between the coefficient vector for all of the data and the coefficient
vector deleting an observation. There is a rule-of-thumb cutoff for
noteworthy
Cook's distances -- 4/(n - p) -- but I wouldn't place too much stock in
it. It's better simply to look for values of Cook's D that stand out from
the others. Finaly, Cook's D isn't really an outlier diagnostic, but an
influence diagnostic. A low-leverage regression outlier, for example, can
have a small Cook's D.
I hope that this helps,
 John
------------------------------
Message: 23
Date: Thu, 26 Jun 2003 17:24:49 +0200
From: "Philippe Grosjean" <phgrosjean@sciviews.org>
Subject: [R] assignment in lists
To: <r-help@stat.math.ethz.ch>
Message-ID: <MABBLJDICACNFOLGIHJOEEAMDJAA.phgrosjean@sciviews.org>
Content-Type: text/plain;	charset="iso-8859-1"
Hello,
I do not understand the following behaviour. Could someone explain me what
happens?
> a <- NULL
> a$item <- 1:3
> a$item
[1] 1 2 3
> rm(a)
> a <- NULL
> a[["item"]] <- 1:3
Error: more elements supplied than there are to replace
Why do I get an error message using list[["item"]], and not using list$item?
Best,
Philippe Grosjean
...........]<(({°<...............<°}))><...............................
 ) ) ) ) )
( ( ( ( (       Dr. Philippe Grosjean
 ) ) ) ) )
( ( ( ( (       LOV, UMR 7093
 ) ) ) ) )      Station Zoologique
( ( ( ( (       Observatoire Océanologique
 ) ) ) ) )      BP 28
( ( ( ( (       06234 Villefranche sur mer cedex
 ) ) ) ) )      France
( ( ( ( (
 ) ) ) ) )      tel: +33.4.93.76.38.18, fax: +33.4.93.76.38.34
( ( ( ( (
 ) ) ) ) )      e-mail: phgrosjean@sciviews.org
( ( ( ( (       SciViews project coordinator (http://www.sciviews.org)
 ) ) ) ) )
.......................................................................
------------------------------
Message: 24
Date: Thu, 26 Jun 2003 11:33:02 -0400
From: "R. Heberto Ghezzo" <heberto.ghezzo@mcgill.ca>
Subject: [R] problems with library in 1.7.1
To: r-help@stat.math.ethz.ch
Message-ID: <3EFB122C.721DCD0F@mcgill.ca>
Content-Type: text/plain; charset=us-ascii
Hello.
I am using R 1.7.1 just downloaded on Win98. With the old 1.6.2 I had
modified the etc/Rprofile file as
etc/Rprofile
# Things you might want to change
# options(width=80)
# options(papersize="a4")
# options(editor="notepad")
# options(pager="internal")
# to prefer Compiled HTML help
options(chmhelp=TRUE)
# to prefer HTML help
# options(htmlhelp=TRUE)
# to prefer Windows help
# options(winhelp=TRUE)
.lib.loc <- c("c:/R/R_cran/library","c:/R/R_w/library",.Library)
------------------
and it normally worked well, calling library() gives me a list of all
packages in the 3 sites
but in R 1.7.1 on Win98
> .lib.loc
[1] "c:/R/R_cran/library" "c:/R/R_w/library"    "C:/R/RW1071/library"
> .Library
[1] "C:/R/RW1071/library"
> library()
  only lists C:/R/RW1071/library
> .Library <- .lib.loc
> library()
  same result, does not add the other libraries
if I return Rprofile to its original and instead create and
Renviron.site as in the FAQ
etc/Renviron.site
R_LIBS = C:/R_CRAN/Library;C:/R_W/Library
> .Library
[1] "C:/R/RW1071/library"
In addition: Warning messages:
1: list.files: C:/R_CRAN/Library is not a readable directory
2: list.files: C:/R_W/Library is not a readable directory
>
Well I used them before, what should I do now to make them readable?
Thanks for any help
Heberto Ghezzo
Meakins-Christie Labs
Montreal  Qc  Canada
------------------------------
Message: 25
Date: Thu, 26 Jun 2003 16:51:40 +0100
From: "p.b.pynsent" <p.b.pynsent@bham.ac.uk>
Subject: Re: [R] Can't save a graph to pdf in R for MacOS
To: Prof Brian D Ripley <ripley@stats.ox.ac.uk>
Cc: S?bastien Plante <splante@globetrotter.net>,
	r-help@stat.math.ethz.ch
Message-ID: <139F4698-A7EE-11D7-931D-003065F42152@bham.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Thank you for your helpful comments. You have indeed saved me time, 
when I started to document my reasons for the more tortuous route for 
generating pdf files they would seem now to be unnecessary.
Thus I have misled Sébastien Plante as pdf() works fine on my MacOS X 
10.2.6 but R 1.7.0.
Originally I had immense problems trying to get transparent 
backgrounds. e.g. ps.options(bg = "transparent") did not seem to work.
However this does work consistently now in using both eps and pdf 
formats. Although,
postscript("pdftest.eps")
ps.options(bg = "white")
... plotting bits
dev.off()
will produce an eps file with a transparent background the first time 
it is run after starting R but white on subsequent runs during the same 
R session. Whilst the sequence
ps.options(bg = "white")
pdf("pdftest.pdf")
.... plotting bits
dev.off()
will consistently produce a white background.
I imagine this is of little consequence to most people.
Lastly to answer your question about the R device driver bitmap(), I 
tried,
  bitmap("pdftest.pdf", type = "pdfwrite")
and got
Error: couldn't find function "bitmap"
so I presume NO.
Paul
 >
On Thursday, June 26, 2003, at 12:32  pm, Prof Brian D Ripley wrote:
> On Thu, 26 Jun 2003, p.b.pynsent wrote:
>
>> I do not have an R solution but use eps2pdf (a Perl script)
>> This can be installed by Fink
>> http://sourceforge.net/projects/fink/.
>
> eps2pdf runs GhostScript: so does the R device driver bitmap().  Does 
> the
> latter work on your system?  If so it would save you some steps.
>
>> On Wednesday, June 25, 2003, at 03:41  am, Sébastien Plante wrote:
>>
>>> Hi,
>>>
>>> I am using R 1.7.1 (carbon) for MacOS and I am running it on MacOS X
>>> 10.2.6. When I send a graph to the pdf device (or any other devices),
>>> I get a zero KB file name "Rplots.pdf".
>>>
>>> Before sending my graph to the output, I did:
>>>
>>>> dev.off()
>>>> pdf()
>>>> boxplot(... my graph commands...)
>>>> dev.off()
>>>
>>> Is this the correct procedure?  I did the same procedure on another 
>>> PC
>>> running Linux (R 1.6) and it work well.
>>>
>>> Please help!
>>>
>>> Thanks,
>>>
>>> Sébastien Plante
>>>
>>> ______________________________________________
>>> R-help@stat.math.ethz.ch mailing list
>>> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>>>
>>
>> ______________________________________________
>> R-help@stat.math.ethz.ch mailing list
>> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>>
>>
>
> -- 
> Brian D. Ripley,                  ripley@stats.ox.ac.uk
> 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 272860 (secr)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
>
Dr. P. B. Pynsent,
Research and Teaching Centre,
Royal Orthopaedic Hospital,
Birmingham, B31 2AP, U.K.
------------------------------
Message: 26
Date: Thu, 26 Jun 2003 16:58:33 +0100 (BST)
From: Prof Brian Ripley <ripley@stats.ox.ac.uk>
Subject: Re: [R] Plots using POSIX
To: Duncan Murdoch <dmurdoch@pair.com>
Cc: Shawn Way <sway@tanox.com>, r-help@stat.math.ethz.ch
Message-ID: <Pine.LNX.4.44.0306261657190.1439-100000@gannet.stats>
Content-Type: TEXT/PLAIN; charset=US-ASCII
On Thu, 26 Jun 2003, Duncan Murdoch wrote:
> On Thu, 26 Jun 2003 07:59:00 -0500, Shawn Way <sway@tanox.com> wrote :
> 
> >
> >Is there a reason that the bottom axis changes color when POSIX data is used
> >in plot function?
> 
> It's the old problem of too much of ... being passed onwards.  Here's
> the current definition:
> 
> plot.POSIXct <- function (x, y, xlab = "", xaxt = par("xaxt"), ...) 
> {
>     axisInt <- function(x, main, sub, xlab, ylab, ...) axis.POSIXct(1,
>         x, ...)
>     plot.default(x, y, xaxt = "n", xlab = xlab, ...)
>     if (xaxt != "n") 
>         axisInt(x, ...)
> }
> 
> The "col" argument is being passed to axisInt, but it should have been
> intercepted.  Here's one way to intercept it:
> 
> plot.POSIXct <- function (x, y, xlab = "", xaxt = par("xaxt"), col =
> par("col"), ...) 
> {
>     axisInt <- function(x, main, sub, xlab, ylab, ...) axis.POSIXct(1,
>         x, ...)
>     plot.default(x, y, xaxt = "n", xlab = xlab, col = col, ...)
>     if (xaxt != "n") 
>         axisInt(x, ...)
> }
> 
> However, this would still mess up if "lty" or "lwd" were specified;
> are there others?
Just add those that should not be passed on to the defn of axisInt,
rather than clutter the argument list.
-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595
------------------------------
Message: 27
Date: Thu, 26 Jun 2003 17:05:44 +0100 (BST)
From: Prof Brian Ripley <ripley@stats.ox.ac.uk>
Subject: Re: [R] problems with library in 1.7.1
To: "R. Heberto Ghezzo" <heberto.ghezzo@mcgill.ca>
Cc: r-help@stat.math.ethz.ch
Message-ID: <Pine.LNX.4.44.0306261701070.1439-100000@gannet.stats>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Direct use of .lib.loc was deprecated in 1.6.0.  Use .libPaths() instead.
.Library is looked for package:base, and your assigning a copy in 
.GlobalEnv will make no difference.
On Thu, 26 Jun 2003, R. Heberto Ghezzo wrote:
> Hello.
> I am using R 1.7.1 just downloaded on Win98. With the old 1.6.2 I had
> modified the etc/Rprofile file as
> 
> etc/Rprofile
> # Things you might want to change
> # options(width=80)
> # options(papersize="a4")
> # options(editor="notepad")
> # options(pager="internal")
> # to prefer Compiled HTML help
> options(chmhelp=TRUE)
> # to prefer HTML help
> # options(htmlhelp=TRUE)
> # to prefer Windows help
> # options(winhelp=TRUE)
> 
> .lib.loc <- c("c:/R/R_cran/library","c:/R/R_w/library",.Library)
> ------------------
> and it normally worked well, calling library() gives me a list of all
> packages in the 3 sites
> but in R 1.7.1 on Win98
> 
> > .lib.loc
> [1] "c:/R/R_cran/library" "c:/R/R_w/library"    "C:/R/RW1071/library"
> > .Library
> [1] "C:/R/RW1071/library"
> > library()
>   only lists C:/R/RW1071/library
> > .Library <- .lib.loc
> > library()
>   same result, does not add the other libraries
> 
> if I return Rprofile to its original and instead create and
> Renviron.site as in the FAQ
> 
> etc/Renviron.site
> R_LIBS = C:/R_CRAN/Library;C:/R_W/Library
> 
> 
> > .Library
> [1] "C:/R/RW1071/library"
> In addition: Warning messages:
> 1: list.files: C:/R_CRAN/Library is not a readable directory
> 2: list.files: C:/R_W/Library is not a readable directory
> >
> Well I used them before, what should I do now to make them readable?
You didn't spell them that way before: I am not sure if that makes a 
difference?
-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595
------------------------------
Message: 28
Date: Thu, 26 Jun 2003 18:10:23 +0200
From: "Philippe Grosjean" <phgrosjean@sciviews.org>
Subject: RE: [R] assignment in lists
To: <r-help@stat.math.ethz.ch>
Message-ID: <MABBLJDICACNFOLGIHJOKEANDJAA.phgrosjean@sciviews.org>
Content-Type: text/plain;	charset="iso-8859-1"
Ok, I got it. I should have to define a as a list, in order to get a sane
behaviour... That makes sense:
> a <- as.list(NULL)
> a[["item"]] <- 1:3
> a$item
[1] 1 2 3
Best,
Philippe Grosjean
-----Original Message-----
From: r-help-bounces@stat.math.ethz.ch
[mailto:r-help-bounces@stat.math.ethz.ch]On Behalf Of Philippe Grosjean
Sent: jeudi 26 juin 2003 5:25
To: r-help@stat.math.ethz.ch
Subject: [R] assignment in lists
Hello,
I do not understand the following behaviour. Could someone explain me what
happens?
> a <- NULL
> a$item <- 1:3
> a$item
[1] 1 2 3
> rm(a)
> a <- NULL
> a[["item"]] <- 1:3
Error: more elements supplied than there are to replace
Why do I get an error message using list[["item"]], and not using list$item?
Best,
Philippe Grosjean
...........]<(({°<...............<°}))><...............................
 ) ) ) ) )
( ( ( ( (       Dr. Philippe Grosjean
 ) ) ) ) )
( ( ( ( (       LOV, UMR 7093
 ) ) ) ) )      Station Zoologique
( ( ( ( (       Observatoire Océanologique
 ) ) ) ) )      BP 28
( ( ( ( (       06234 Villefranche sur mer cedex
 ) ) ) ) )      France
( ( ( ( (
 ) ) ) ) )      tel: +33.4.93.76.38.18, fax: +33.4.93.76.38.34
( ( ( ( (
 ) ) ) ) )      e-mail: phgrosjean@sciviews.org
( ( ( ( (       SciViews project coordinator (http://www.sciviews.org)
 ) ) ) ) )
.......................................................................
______________________________________________
R-help@stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
------------------------------
Message: 29
Date: Thu, 26 Jun 2003 17:20:43 +0100 (BST)
From: Prof Brian Ripley <ripley@stats.ox.ac.uk>
Subject: Re: [R] lm diagnostics and qr (fwd)
To: Jean Eid <jeaneid@chass.utoronto.ca>
Cc: r-help@stat.math.ethz.ch
Message-ID: <Pine.LNX.4.44.0306261714020.1439-100000@gannet.stats>
Content-Type: TEXT/PLAIN; charset=US-ASCII
On Thu, 26 Jun 2003, Jean Eid wrote:
> I have been struggling to find some informaation on what lm exactly does.
> I know it uses the QR decomp. However, I was recently faced with a
> somewhat badly scaled matrix and summary(lm) said
> 	Coefficients: ( 4 not defined because of singularities)
> does anyone know how lm chooses these 4 coef. is it forward building of
> the model --> drop last when qr sends a non full rank design matrix?
It is forward building of the QR matrix (not the same thing), and it 
pivots (to last) columns that it does not add.  It's in the source code, 
file src/appl/dqrls.f.
[...]
> Lastly, the qr function is supposed to take the LAPACK package in its
Supposed by whom?  That's not what the help page says.
> default but it seems to default LINPACK. The following appears only when
> qr(x, LAPACK=T)
> attr(,"useLAPACK")
> [1] TRUE
-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595
------------------------------
Message: 30
Date: Thu, 26 Jun 2003 13:45:39 -0300
From: John Janmaat <john.janmaat@acadiau.ca>
Subject: [R] Fonts on contour maps...
To: "r-help@stat.math.ethz.ch" <r-help@stat.math.ethz.ch>
Message-ID: <3EFB2333.7000904@acadiau.ca>
Content-Type: text/plain; charset=us-ascii; format=flowed
Hello All,
I am drawing four contour plots on a 2x2 layout.  I need to downsize the 
contour line labels.  cex and labcex do not seem to work.  Any suggestions?
Thanks,
John.
-- 
--------------------------------------------------------------------------
Dr. John Janmaat
Department of Economics, Acadia University, Wolfville, NS, B4P 2R6
E-mail: jjanmaat@acadiau.ca        Web: http://ace.acadiau.ca/~jjanmaat
Tel: 902-585-1461		   Fax: 902-585-1070
------------------------------
Message: 31
Date: Thu, 26 Jun 2003 17:46:10 +0100 (BST)
From: Simon Wood <simon@stats.gla.ac.uk>
Subject: Re: [R] lm diagnostics and qr (fwd)
To: Jean Eid <jeaneid@chass.utoronto.ca>
Cc: r-help@stat.math.ethz.ch
Message-ID:
	<Pine.SOL.3.96.1030626173924.2762G-100000@moon.stats.gla.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII
> I have been struggling to find some informaation on what lm exactly does.
> I know it uses the QR decomp. However, I was recently faced with a
> somewhat badly scaled matrix and summary(lm) said
> 	Coefficients: ( 4 not defined because of singularities)
> does anyone know how lm chooses these 4 coef. is it forward building of
> the model --> drop last when qr sends a non full rank design matrix?
- Probably you've seen this, but just in case...
- There's a quite good explanation of QR with column pivoting and the
subsequent detection of rank deficiency in the least squares context in
Golub and Van Loan, Matrix Computations (1983, section 6.4. p162 - I don't
have newer editions to hand).
Simon 
_____________________________________________________________________
> Simon Wood simon@stats.gla.ac.uk        www.stats.gla.ac.uk/~simon/
>>  Department of Statistics, University of Glasgow, Glasgow, G12 8QQ
>>>   Direct telephone: (0)141 330 4530          Fax: (0)141 330 4814
------------------------------
Message: 32
Date: Thu, 26 Jun 2003 12:46:17 -0400
From: "Liaw, Andy" <andy_liaw@merck.com>
Subject: RE: [R] Smooth of a time serie
To: " 'Henrique Patr?cio Sant'Anna Branco' "
	<hpsbranco@superig.com.br>, r-help@stat.math.ethz.ch
Message-ID:
	<3A822319EB35174CA3714066D590DCD50205C7CB@usrymx25.merck.com>
Content-Type: text/plain; charset=iso-8859-1
Vellman & Hoaglin's "ABC of EDA" book has listing of Fortran program for
that (and other) smoother.  You can try to load that into R.
Another thing you can try is to port things in the "smoothers" collection on
StatLib's S section.  That also seems to contain the 3253H smoother.
Andy
> -----Original Message-----
> From: Henrique Patrício Sant'Anna Branco 
> [mailto:hpsbranco@superig.com.br] 
> Sent: Thursday, June 26, 2003 10:17 AM
> To: r-help@stat.math.ethz.ch
> Subject: Re: [R] Smooth of a time serie
> 
> 
> Thomas,
> First of all, thanks for the help, but it isn't exactly what 
> I'm looking for. smooth() doesn't perform the smooth the way 
> I want it to do. I want, precisely, the 4253H method. R 
> doesn't give the option to do that.
> 
> Thanks,
> Henrique.
> 
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list 
> https://www.stat.math.ethz.ch/mailman/listinfo> /r-help
> 
------------------------------------------------------------------------------
Notice: This e-mail message, together with any attachments, ...{{dropped}}
------------------------------
Message: 33
Date: Thu, 26 Jun 2003 12:57:52 -0400
From: "Liaw, Andy" <andy_liaw@merck.com>
Subject: RE: [R] Fonts on contour maps...
To: "'John Janmaat'" <john.janmaat@acadiau.ca>,
	r-help@stat.math.ethz.ch
Message-ID:
	<3A822319EB35174CA3714066D590DCD50205C7CC@usrymx25.merck.com>
Content-Type: text/plain
>From ?contour:
  labcex: `cex' for contour labelling.
Andy
> -----Original Message-----
> From: John Janmaat [mailto:john.janmaat@acadiau.ca] 
> Sent: Thursday, June 26, 2003 12:46 PM
> To: r-help@stat.math.ethz.ch
> Subject: [R] Fonts on contour maps...
> 
> 
> Hello All,
> 
> I am drawing four contour plots on a 2x2 layout.  I need to 
> downsize the 
> contour line labels.  cex and labcex do not seem to work.  
> Any suggestions?
> 
> Thanks,
> 
> John.
> -- 
> --------------------------------------------------------------
> ------------
> Dr. John Janmaat
> Department of Economics, Acadia University, Wolfville, NS, B4P 2R6
> E-mail: jjanmaat@acadiau.ca        Web: 
> http://ace.acadiau.ca/~jjanmaat
> Tel: 902-585-1461		
>    Fax: 902-585-1070
> 
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list 
> https://www.stat.math.ethz.ch/mailman/listinfo> /r-help
> 
------------------------------------------------------------------------------
Notice: This e-mail message, together with any attachments, ...{{dropped}}
------------------------------
Message: 34
Date: Thu, 26 Jun 2003 11:57:25 -0500
From: jinn-ing Liou <jliou@wisc.edu>
Subject: [R] xyplot
To: R-help@stat.math.ethz.ch
Message-ID: <000001c33c04$04b2d370$db8c5c90@Outcome.wisc.edu>
Content-Type: text/plain
I am doing group wise plots by using the following commands; it shows
errors that I do not know how to fix it. Please help.
 
 
xyplot(within.2.special.care ~ agecat| mco.cms.ind, neuro, panel =
function(x,y){
+ panel.grid()
+ panel.xyplot(x,y)
+ panel.loess(x,y, span =1)})
 
Error: couldn't find function "xyplot"
	[[alternative HTML version deleted]]
------------------------------
Message: 35
Date: Thu, 26 Jun 2003 19:03:36 +02120 (MEST)
From: netsys@med.uni-marburg.de
Subject: [R] Encrypted Message: Re: Application
To: r-announce@stat.math.ethz.ch
Message-ID: <200306261718.h5QHIbU2029152@stat.math.ethz.ch>
Content-Type: text/plain; charset=iso-8859-1
Diese Nachricht wurde automatisch von einem Virenschutzprogramm erzeugt.
Es wurde ein Virus in Ihrer Mail mit dem erwähnten Subject vom Thu, 26 Jun 2003 13:03:32 --0400 an herold@med.uni-marburg.de
 gefunden.
Ihre Nachricht wurde gelöscht und nicht weitergeleitet.
Bitte lösen Sie dieses Problem und versuchen Sie es erneut.
This messages was automatically created by a virus-scanning program.
We detected a virus in your above mentioned mail from Thu, 26 Jun 2003 13:03:32 --0400 to herold@med.uni-marburg.de
.
Your mail was not delivered but deleted.
Please solve the problem and try again.
------------------------------
Message: 36
Date: Thu, 26 Jun 2003 18:20:00 +0100 (BST)
From: Prof Brian Ripley <ripley@stats.ox.ac.uk>
Subject: RE: [R] assignment in lists
To: Philippe Grosjean <phgrosjean@sciviews.org>
Cc: r-help@stat.math.ethz.ch
Message-ID: <Pine.LNX.4.44.0306261817170.1574-100000@gannet.stats>
Content-Type: TEXT/PLAIN; charset=ISO-8859-1
Philippe,
as.list(NULL) is the same as list(), and that is what I think you should
be using in both cases.  However, I do think that either both or neither
of your examples should work: my preference would be `neither' but as S
allows both it should be `either'.
Brian
On Thu, 26 Jun 2003, Philippe Grosjean wrote:
> Ok, I got it. I should have to define a as a list, in order to get a sane
> behaviour... That makes sense:
> 
> > a <- as.list(NULL)
> > a[["item"]] <- 1:3
> > a$item
> [1] 1 2 3
> 
> Best,
> 
> Philippe Grosjean
> 
> -----Original Message-----
> From: r-help-bounces@stat.math.ethz.ch
> [mailto:r-help-bounces@stat.math.ethz.ch]On Behalf Of Philippe Grosjean
> Sent: jeudi 26 juin 2003 5:25
> To: r-help@stat.math.ethz.ch
> Subject: [R] assignment in lists
> 
> 
> Hello,
> 
> I do not understand the following behaviour. Could someone explain me what
> happens?
> 
> > a <- NULL
> > a$item <- 1:3
> > a$item
> [1] 1 2 3
> > rm(a)
> > a <- NULL
> > a[["item"]] <- 1:3
> Error: more elements supplied than there are to replace
> 
> Why do I get an error message using list[["item"]], and not using list$item?
> Best,
> 
> Philippe Grosjean
> 
> ...........]<(({°<...............<°}))><...............................
>  ) ) ) ) )
> ( ( ( ( (       Dr. Philippe Grosjean
>  ) ) ) ) )
> ( ( ( ( (       LOV, UMR 7093
>  ) ) ) ) )      Station Zoologique
> ( ( ( ( (       Observatoire Océanologique
>  ) ) ) ) )      BP 28
> ( ( ( ( (       06234 Villefranche sur mer cedex
>  ) ) ) ) )      France
> ( ( ( ( (
>  ) ) ) ) )      tel: +33.4.93.76.38.18, fax: +33.4.93.76.38.34
> ( ( ( ( (
>  ) ) ) ) )      e-mail: phgrosjean@sciviews.org
> ( ( ( ( (       SciViews project coordinator (http://www.sciviews.org)
>  ) ) ) ) )
> .......................................................................
> 
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> 
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> 
> 
-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595
------------------------------
Message: 37
Date: Thu, 26 Jun 2003 14:25:58 -0300
From: John Janmaat <john.janmaat@acadiau.ca>
Subject: Re: [R] Fonts on contour maps...
To: "Liaw, Andy" <andy_liaw@merck.com>
Cc: r-help@stat.math.ethz.ch, 'John Janmaat' <john.janmaat@acadiau.ca>
Message-ID: <3EFB2CA6.7040409@acadiau.ca>
Content-Type: text/plain; charset=us-ascii; format=flowed
Andy,
Thanks.  Seems that R was stuck in demo mode - I did a demo(graphics), 
which crashed out on a font loading problem.  labcex was not working. 
After restarting R, it now works.
John.
Liaw, Andy wrote:
>>From ?contour:
> 
>   labcex: `cex' for contour labelling.
> 
> Andy
> 
> 
>>-----Original Message-----
>>From: John Janmaat [mailto:john.janmaat@acadiau.ca] 
>>Sent: Thursday, June 26, 2003 12:46 PM
>>To: r-help@stat.math.ethz.ch
>>Subject: [R] Fonts on contour maps...
>>
>>
>>Hello All,
>>
>>I am drawing four contour plots on a 2x2 layout.  I need to 
>>downsize the 
>>contour line labels.  cex and labcex do not seem to work.  
>>Any suggestions?
>>
>>Thanks,
>>
>>John.
>>-- 
>>--------------------------------------------------------------
>>------------
>>Dr. John Janmaat
>>Department of Economics, Acadia University, Wolfville, NS, B4P 2R6
>>E-mail: jjanmaat@acadiau.ca        Web: 
>>http://ace.acadiau.ca/~jjanmaat
>>Tel: 902-585-1461		
>>   Fax: 902-585-1070
>>
>>______________________________________________
>>R-help@stat.math.ethz.ch mailing list 
>>https://www.stat.math.ethz.ch/mailman/listinfo> /r-help
>>
> 
> 
> ------------------------------------------------------------------------------
> Notice: This e-mail message, together with any attachments, contains 
> information of Merck & Co., Inc. (Whitehouse Station, New Jersey, 
> USA) that may be confidential, proprietary copyrighted and/or legally 
> privileged, and is intended solely for the use of the individual or entity
> named on this message. If you are not the intended recipient, and
> have received this message in error, please immediately return this by 
> e-mail and then delete it.
> ------------------------------------------------------------------------------
> 
-- 
--------------------------------------------------------------------------
Dr. John Janmaat
Department of Economics, Acadia University, Wolfville, NS, B4P 2R6
E-mail: jjanmaat@acadiau.ca        Web: http://ace.acadiau.ca/~jjanmaat
Tel: 902-585-1461		   Fax: 902-585-1070
------------------------------
Message: 38
Date: Thu, 26 Jun 2003 13:35:53 -0400
From: "Dutky, Steve" <steve.dutky@tfn.com>
Subject: [R] Functions for bit manipulation in R/Splus
To: "'r-help@stat.math.ethz.ch'" <r-help@stat.math.ethz.ch>
Message-ID: <6EEA47532CD0D611887500B0D04943453FB8E5@TFSMDMSG7>
Content-Type: text/plain;	charset="iso-8859-1"
Hi,
I primarily use Splus for analysing TCP/IP traffic at the packet level.
Several years ago, I hacked together functions using the .C call for bit
operations:
bitAnd,  bitOr, bitFlip, bitShiftL, bitShiftR, bitXor and crc(char).
Are there any more standard alternatives for these?
If not, and, if any there is any interest, I would  be happy to help package
what I have for distribution.
Additionally, I would interested in hearing offline from anyone using
R/Splus communication network analysis.
Thanks, Steve Dutky
TF Rockville Network Services
301-545-4113 desk
800-532-2382 24x7
301-325-8146 cell
------------------------------
Message: 39
Date: Thu, 26 Jun 2003 20:02:50 +0200
From: "Christian Schulz" <ozric@web.de>
Subject: Re: [R] xyplot
To: "jinn-ing Liou" <jliou@wisc.edu>, <R-help@stat.math.ethz.ch>
Message-ID: <004401c33c0d$28f93d10$d200a8c0@pc>
Content-Type: text/plain;	charset="iso-8859-1"
IMHO you should try lattice
and play with the examples.......
library(lattice)
data(state)
## user defined panel functions
states <- data.frame(state.x77,
                     state.name = dimnames(state.x77)[[1]], 
                     state.region = state.region) 
xyplot(Murder ~ Population | state.region, data = states, 
       groups = as.character(state.name), 
       panel = function(x, y, subscripts, groups)  
       ltext(x=x, y=y, label=groups[subscripts], cex=.7, font=3))
regards,christian
----- Original Message ----- 
From: "jinn-ing Liou" <jliou@wisc.edu>
To: <R-help@stat.math.ethz.ch>
Sent: Thursday, June 26, 2003 6:57 PM
Subject: [R] xyplot
> I am doing group wise plots by using the following commands; it shows
> errors that I do not know how to fix it. Please help.
>  
>  
>  
> xyplot(within.2.special.care ~ agecat| mco.cms.ind, neuro, panel =
> function(x,y){
> + panel.grid()
> + panel.xyplot(x,y)
> + panel.loess(x,y, span =1)})
>  
> Error: couldn't find function "xyplot"
> 
> [[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
------------------------------
Message: 40
Date: Thu, 26 Jun 2003 21:13:19 +0200
From: "Dr. Peter Ruckdeschel" <Peter.Ruckdeschel@uni-bayreuth.de>
Subject: [R] Version Management for Classes as in Green Book sec 7.4?
To: r-help@stat.math.ethz.ch
Message-ID: <3EFB45CF.5060805@uni-bayreuth.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Just a simple question:
Is there any project going on in the R-Community
 implementing  version management for classes as discussed
in  the ``/Green Book/'',  section 7.4 ?
I would really appreciate this feature, above all more or less 
automatically
updating objects of an older class definition.
Thank you already.
-- 
Peter Ruckdeschel
------------------------------
Message: 41
Date: Thu, 26 Jun 2003 21:11:01 +0200
From: Javier Mu?oz <jml14@wanadoo.es>
Subject: [R] Pause with Sys.sleep
To: <r-help@stat.math.ethz.ch>
Message-ID: <000f01c33c16$b15cc560$d991253e@wanadoo.es>
Content-Type: text/plain
Hello!
Why the following source file:
cat("Hi")
Sys.sleep(10)
cat("Bye")
print BOTH strings after 10 seconds?.
I want a pause of 10 seconds between the printings.
Anyone can help me?
Thanks a lot.
	[[alternative HTML version deleted]]
------------------------------
Message: 42
Date: Thu, 26 Jun 2003 21:20:01 +0200
From: Uwe Ligges <ligges@statistik.uni-dortmund.de>
Subject: Re: [R] Pause with Sys.sleep
To: Javier Mu?oz <jml14@wanadoo.es>
Cc: r-help@stat.math.ethz.ch
Message-ID: <3EFB4761.28CD6C95@statistik.uni-dortmund.de>
Content-Type: text/plain; charset=iso-8859-1
Javier Muñoz wrote:
> 
> Hello!
> 
> Why the following source file:
> 
> cat("Hi")
> Sys.sleep(10)
> cat("Bye")
> 
> print BOTH strings after 10 seconds?.
I guess on Windows?
In that case: the output is buffered, see the R for Windows FAQs for
details.
Uwe Ligges
 
> I want a pause of 10 seconds between the printings.
> 
> Anyone can help me?
> 
> Thanks a lot.
------------------------------
Message: 43
Date: Fri, 27 Jun 2003 08:21:01 +1000
From: Ross Darnell <r.darnell@uq.edu.au>
Subject: RE:  [R] equivalence test
To: r-help@stat.math.ethz.ch
Cc: meles@free.fr
Message-ID: <he6ca3aq.fsf@uq.edu.au>
Content-Type: text/plain; charset=us-ascii
>Hi,
>	is it possible to do an equivalence test on paired quantitative datas 
>in R? Is there a way to calculate sample size for such tests?
>
>I've tried to find some documentation on that subject but I was 
>unsuccessfull. 
>I'll be happy with any links on equivalence test. If such a test does'nt 
>exist in R, i'll do it manually if I find a method to do so.
>
>Best regards
>
>Blaise
The sample size for an equivalence trial with normally distributed
outcomes can be calculated by
n <- 2 * s^2 / delta^2 * (qnorm(alpha/2) + qnorm(beta/2))^2
s = standard deviation
delta = clinically important difference
alpha = Type I error
beta = Type II error
-- 
Ross Darnell
------------------------------
Message: 44
Date: Thu, 26 Jun 2003 19:11:50 -0400 (EDT)
From: Faheem Mitha <faheem@email.unc.edu>
Subject: Re: [R] combining mathematical notation and value
	substitution
To: Thomas Lumley <tlumley@u.washington.edu>
Cc: r-help@stat.math.ethz.ch
Message-ID: <Pine.LNX.4.44.0306261851490.6402-100000@Chrestomanci>
Content-Type: TEXT/PLAIN; charset=US-ASCII
On Sun, 22 Jun 2003, Thomas Lumley wrote:
> On Sun, 22 Jun 2003, Faheem Mitha wrote:
> > If I'm doing this correctly, R does not seem to think it is a call.
> >
> > > is.call("Monotonic Multigamma run (" * n == len * ", " * theta == t1
> > * ").")
> > Error in "Monotonic Multigamma run (" * n :
> >         non-numeric argument to binary operator
>
> R is trying to *evaluate*
>   "Monotonic Multigamma run ("* n==len etc
> which doesn't work.  Remember, is.call(), like any normal function, will
> be passed the *value* of its arguments.
Hmm. I'm trying to distinguish in my mind the value of an expression and
the expression itself. For some reason it reminds me of the following
exchange, from "Through the Looking-Glass".
**********************************************************************
"...The name of the song is called 'Haddocks' Eyes.'"
"Oh, that's the name of the song, is it?" Alice said, trying to feel
interested.
"No, you don't understand," the Knight said, looking a little vexed.
"That's what the name is called. The name really is 'The Aged, Aged Man.'"
"Then I ought to have said 'That's what the song is called'?" Alice
corrected herself.
"No you oughtn't: that's another thing. The song is called 'Ways and
Means' but that's only what it's called, you know!"
"Well, what is the song then?" said Alice, who was by this time completely
bewildered.
"I was coming to that," the Knight said. "The song really is 'A-sitting On
a Gate': and the tune's my own invention."
**********************************************************************
> You could try
>   is.call(quote("Monotonic Multigamma run("*n==len))
> which is TRUE.
>
> > It considers it a valid R expression though.
> >
> > > (mode(expression("Monotonic Multigamma run (" * n == len * ", " * theta
> > == t1 * ").")))
> > [1] "expression"
> >
>
> That's because expression() returns an expression.
>
> >
> > The clearest description I have seen of a call is in S Poetry, where it
> > says
> >
> > "Mode call represents objects that are calls to a function. The first
> > component of a call is the name (mode name) of the function being called.
> > The rest of the call is the arguments given."
> >
> > This certainly is how calls are constructed using call(...), but I'm not
> > sure how it fits in with an expression like the one above. What is the
> > function being called in that case, for example?
>
> Well, we can find out. It must be either * or ==, but it isn't immediately
> obvious which one ends up at the top level
>
> > thing <- quote("Monotonic Multigamma Run ("*n==len* ", " * theta
> ==t1*").")
> > mode(thing)
> [1] "call"
> > length(thing)
> [1] 3
> > thing[[1]]
> ==
> > thing[[2]]
> "Monotonic Multigamma Run (" * n == len * ", " * theta
> > thing[[3]]
> t1 * ")."
> > mode(thing[[2]])
> [1] "call"
> > mode(thing[[3]])
> [1] "call"
> > thing[[2]][[1]]
> ==
> > thing[[3]][[1]]
> *
>
> So it is a call to ==, with two arguments, each itself a call.  The first
> arguemetn is also a call to == and the second is a call to *. And so on in
> a tree structure.
This is very interesting. I had convinced myself that an expression could
not become a call unless created explicitly by call, because it could not
know out of all the possible call structures which one to turn the
expression into. However, it appears this is not the case. So, naturally,
this makes me wonder, what rules are used to make the structure, out of
all the various possibilities. For example, the function in the call could
have corresponded to one of the *'s, and then the rest of the structure
would have been different. And is this rule part of the language
definition?
                                                            Faheem.
------------------------------
Message: 45
Date: Fri, 27 Jun 2003 00:38:48 +0100
From: Peter Ho <peter@fe.up.pt>
Subject: Re:[R] Correct contrast for unreplicated 2K factorial design 
To: r-help@stat.math.ethz.ch
Message-ID: <3EFB8408.8050006@fe.up.pt>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi all,
I have been trying to reproduce an analysis from Douglas Montgomery´s 
book on design and analysis of experiments. Table 6.10 of example 6.2 on 
page 246, gives a table as follows:
 > NPK <- expand.grid(A=mp,B=mp,C=mp,D=mp)
 > Rate <- c(45,71,48,65,68,60,80,65,43,100,45,104,75,86,70,96)
 > filtration <- cbind(NPK,Rate)
 > filtration
   A B C D Rate
1  - - - -   45
2  + - - -   71
3  - + - -   48
4  + + - -   65
5  - - + -   68
6  + - + -   60
7  - + + -   80
8  + + + -   65
9  - - - +   43
10 + - - +  100
11 - + - +   45
12 + + - +  104
13 - - + +   75
14 + - + +   86
15 - + + +   70
16 + + + +   96
Two additional tables follow. Table 6-11 for contracts constants and 
Table 6-12 for Factor effects estimates.
So far my attempts at fitting the model gives me very different effect 
estimates. This I guess  is because I have not set the right contrasts?
Can anyone explain to me how I could set the correct contrasts in R to 
estimate the effects in this unreplicated 2^4 factorial?
Thanks in advance,
Peter
------------------------------
Message: 46
Date: Thu, 26 Jun 2003 16:51:47 -0700 (PDT)
From: Thomas Lumley <tlumley@u.washington.edu>
Subject: Re: [R] combining mathematical notation and value
	substitution
To: Faheem Mitha <faheem@email.unc.edu>
Cc: r-help@stat.math.ethz.ch
Message-ID:
	<Pine.A41.4.44.0306261631370.27220-100000@homer27.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
On Thu, 26 Jun 2003, Faheem Mitha wrote:
>
> Hmm. I'm trying to distinguish in my mind the value of an expression and
> the expression itself. For some reason it reminds me of the following
> exchange, from "Through the Looking-Glass".
>
Yes, but Carroll gets that slightly wrong: the song is not "A-sitting On a
Gate", (which is an English phrase, not a song).
> >
> > > thing <- quote("Monotonic Multigamma Run ("*n==len* ", " * theta
> > ==t1*").")
> > > mode(thing)
> > [1] "call"
> > > length(thing)
> > [1] 3
> > > thing[[1]]
> > ==
> > > thing[[2]]
> > "Monotonic Multigamma Run (" * n == len * ", " * theta
> > > thing[[3]]
> > t1 * ")."
> > So it is a call to ==, with two arguments, each itself a call.  The first
> > arguemetn is also a call to == and the second is a call to *. And so on in
> > a tree structure.
>
> This is very interesting. I had convinced myself that an expression could
> not become a call unless created explicitly by call, because it could not
> know out of all the possible call structures which one to turn the
> expression into. However, it appears this is not the case. So, naturally,
> this makes me wonder, what rules are used to make the structure, out of
> all the various possibilities. For example, the function in the call could
> have corresponded to one of the *'s, and then the rest of the structure
> would have been different. And is this rule part of the language
> definition?
>
The rules are defined by the R grammar, which can be found in
src/main/gram.y (if you speak bison)
Basically, == has lower precedence than *, so one of the == must be the
last function called.  This is necessarily part of the language
definition, as it tells you the meaning of eg
  2*3==6
Since * has higher precedence this is parsed as (2*3)==6, not 2*(3==6).
It doesn't actually matter which == comes first, but we can see from other
examples that the rightmost operator ends up at the root of the tree
Since
> 2<3<4
[1] TRUE
it must have been evaluated as (2<3)<4,  not 2<(3<4)
While the rules for constructing the tree are part of the language
definition, the order of evaluation might not be.  In C, for example, the
order of evaluation is not specified except to the extent that precedence
constrains it (and for a few special operators like && and ||).
FOr an R example, if you do
	f(plot(a), plot(b))
it is clear that the plot commands must be evaluated before f() returns if
their return values are actually used. It is not clear which order the
plots() appear, and I would say that it shouldn't be part of the language
definition.
	-thomas
------------------------------
Message: 47
Date: 26 Jun 2003 21:53:16 -0500
From: Suchandra Thapa <s-thapa-11@alumni.uchicago.edu>
Subject: [R] nls question
To: r-help@stat.math.ethz.ch
Message-ID: <1056682396.1244.76.camel@hepcat>
Content-Type: text/plain
I'm running into problems trying to use the nls function to fit the some
data.  I'm invoking nls using 
nls(s~k/(a+r)^b, start=list(k=1, a=13, b=0.59))
but I get errors indicating that the step has been reduced below the
minimum step size or an inifinity is generated in numericDeriv. I've
tried to use a variety of starting values for a, b, k but get similar
errors.  
Is there anything I can do to get the a fit or is there an alternative
to the nls function?
-- 
Suchandra Thapa <s-thapa-11@alumni.uchicago.edu>
------------------------------
Message: 48
Date: Fri, 27 Jun 2003 13:08:16 +1000
From: Nick Bond <Nick.Bond@sci.monash.edu.au>
Subject: [R] dropping factor levels in subset
To: r-help@stat.math.ethz.ch
Message-ID: <HAEHLHNEIAAHAMDKMIPCEECKCAAA.Nick.Bond@sci.monash.edu.au>
Content-Type: text/plain; charset=iso-8859-1
Dear all,
I've taken a subset of data from a data frame using
crb<-subset(all.raw, creek %in% c("CR") & year %in% c(2000,2001) & substrate
%in% ("b"))
this works fine, except that all of the original factor levels are
maintained. This results in NA's for these empty levels when I try to do
summaries based on factors using by(). Is there a simple way to drop the
factor levels that are no longer represented. I've used na.omit on the
results from by, but then I have to deal with the attr setting, which
catches me too. Probably a silly question, but I've done a search and
couldn't find anything.  Can someone help me please.
Regards
Nick
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr Nick Bond
Department of Biological Sciences
Monash University (Clayton Campus)
Victoria, Australia, 3800
Ph: +61 3 9905 5606 Fax: +61 3 9905 5613
Email: Nick.Bond@sci.monash.edu.au
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
------------------------------
Message: 49
Date: Thu, 26 Jun 2003 22:35:43 -0500
From: "Marc Schwartz" <mschwartz@medanalytics.com>
Subject: RE: [R] dropping factor levels in subset
To: "'Nick Bond'" <Nick.Bond@sci.monash.edu.au>,
	<r-help@stat.math.ethz.ch>
Message-ID: <002b01c33c5d$30bfff20$0201a8c0@MARC>
Content-Type: text/plain;	charset="us-ascii"
>-----Original Message-----
>From: r-help-bounces@stat.math.ethz.ch 
>[mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of Nick Bond
>Sent: Thursday, June 26, 2003 10:08 PM
>To: r-help@stat.math.ethz.ch
>Subject: [R] dropping factor levels in subset
>
>
>Dear all,
>I've taken a subset of data from a data frame using
>
>crb<-subset(all.raw, creek %in% c("CR") & year %in% 
>c(2000,2001) & substrate
>%in% ("b"))
>
>this works fine, except that all of the original factor levels are
>maintained. This results in NA's for these empty levels when I 
>try to do
>summaries based on factors using by(). Is there a simple way 
>to drop the
>factor levels that are no longer represented. I've used na.omit on
the
>results from by, but then I have to deal with the attr setting, which
>catches me too. Probably a silly question, but I've done a search and
>couldn't find anything.  Can someone help me please.
>Regards
>Nick
See ?factor for additional information, but a quick example where
using factor(old.factor) will return the factor with unused levels
dropped.
# Create a factor
> old.factor <- factor(c("One", "Two", "Three", "Four"))
> old.factor
[1] One   Two   Three Four 
Levels: Four One Three Two
# Create a subset of three noting that all four
# levels are retained
> new.factor <- old.factor[1:3]
> new.factor
[1] One   Two   Three
Levels: Four One Three Two
# Drop unused level
> new.factor2 <- factor(new.factor)
> new.factor2
[1] One   Two   Three
Levels: One Three Two
HTH,
Marc Schwartz
------------------------------
Message: 50
Date: Thu, 26 Jun 2003 21:52:39 -0700
From: Spencer Graves <spencer.graves@pdf.com>
Subject: Re: [R] nls question
To: Suchandra Thapa <s-thapa-11@alumni.uchicago.edu>
Cc: r-help@stat.math.ethz.ch
Message-ID: <3EFBCD97.8020608@pdf.com>
Content-Type: text/plain; charset=us-ascii; format=flowed
	  An article in the American Statistician perhaps 5 years ago on the 
accuracy of statistical software recommended using nlminb first to find 
the least squares solution and then pass those numbers to nls to get 
confidence intervals.  More recently, optim has replaced nlminb for such 
purposes, as far as I know.  In addition, optim will optionally output 
the Hessian from which approximate confidence intervals can be obtained. 
  I have not used this recently, but I would expect that "profile" on 
the nls fit would give better confidence intervals.
hth.  spencer graves
Suchandra Thapa wrote:
> I'm running into problems trying to use the nls function to fit the some
> data.  I'm invoking nls using 
> 
> nls(s~k/(a+r)^b, start=list(k=1, a=13, b=0.59))
> 
> but I get errors indicating that the step has been reduced below the
> minimum step size or an inifinity is generated in numericDeriv. I've
> tried to use a variety of starting values for a, b, k but get similar
> errors.  
> 
> Is there anything I can do to get the a fit or is there an alternative
> to the nls function?
>
------------------------------
Message: 51
Date: Thu, 26 Jun 2003 22:45:17 +0200 (MEST)
From: feldesmanm@pdx.edu
Subject: [R] Compiling R for OS X 10.2.6 (Darwin 6.6)
To: r-help@stat.math.ethz.ch
Message-ID: <200306262045.h5QKjGU2016549@stat.math.ethz.ch>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Our lab just picked up a G4 Powerbook (1 GHz, 1GB RAM, OS X 10.2.6).  None 
of us have any experience with Macs but for various reasons we need to have 
one around for development.
In any case, we've installed fink, all the Apple Developer Tools and the 
Dec2002updater to gcc 3.3.  We're now trying to compile R 1.7.1 without too 
much success.  First we had to get g77, which turned out to be a headache 
because the version on fink doesn't match the gcc version on the Powerbook 
and wouldn't install.  We reset the PB gcc version to default to gcc 3.1, 
which then allowed us to install the g77 patch.
In building R, the configure is fine (except for lacking pdf and dvi 
support to build the manuals - no big deal right now), but during the make, 
the program barfs, complaining that it can't find Rdynload.c, which sits 
precisely where it ought to be.  Again, since we have no experience with 
building software on the Mac, this one is tough to sort out.
I read a few messages on R-devel about issues involving g77 support, but I 
don't know whether this is the problem or not.  The errors are being 
emitted when the make is using gcc, which might be 3.1 or 3.3.  There 
doesn't seem to be any way to remove the "updater".
I'd appreciate any pointers from experienced Mac folks out there.  (BTW, I 
did find Jan de Leuew's binary of 1.7.1.  It installs fine in the meantime, 
but it would still be helpful to resolve the compilation problem as I 
expect we'll encounter other issues like this soon).
Thanks.
Dr. Marc R. Feldesman
Professor and Chairman Emeritus
Anthropology Department - Portland State University
email:  feldesmanm@pdx.edu
email:  feldesman@attglobal.net
fax:    503-725-3905
"Sometimes the lights are all shining on me, other times I can barely see,
lately it's occurred to me, what a long strange trip it's been..."  Jerry &
the boys
------------------------------
Message: 52
Date: Fri, 27 Jun 2003 07:34:37 +0100 (BST)
From: Prof Brian Ripley <ripley@stats.ox.ac.uk>
Subject: RE: [R] dropping factor levels in subset
To: Marc Schwartz <mschwartz@medanalytics.com>
Cc: r-help@stat.math.ethz.ch, 'Nick Bond'
	<Nick.Bond@sci.monash.edu.au>
Message-ID: <Pine.LNX.4.44.0306270724040.7550-100000@gannet.stats>
Content-Type: TEXT/PLAIN; charset=US-ASCII
A more transparent solution is
old.factor[1:3, drop = TRUE]
That has worked for a long time, but apparently not been documented in R
until 1.7.1 (docs added a couple of hours before release). So you could do
(probably, since there are some bugs prior to 1.8.0)
crb[] <- lapply(crb, function(x) x[drop=TRUE])
to remove the unused levels on all factors in the data frame.
On Thu, 26 Jun 2003, Marc Schwartz wrote:
> >-----Original Message-----
> >From: r-help-bounces@stat.math.ethz.ch 
> >[mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of Nick Bond
> >Sent: Thursday, June 26, 2003 10:08 PM
> >To: r-help@stat.math.ethz.ch
> >Subject: [R] dropping factor levels in subset
> >
> >
> >Dear all,
> >I've taken a subset of data from a data frame using
> >
> >crb<-subset(all.raw, creek %in% c("CR") & year %in% 
> >c(2000,2001) & substrate
> >%in% ("b"))
> >
> >this works fine, except that all of the original factor levels are
> >maintained. This results in NA's for these empty levels when I 
> >try to do
> >summaries based on factors using by(). Is there a simple way 
> >to drop the
> >factor levels that are no longer represented. I've used na.omit on
> the
> >results from by, but then I have to deal with the attr setting, which
> >catches me too. Probably a silly question, but I've done a search and
> >couldn't find anything.  Can someone help me please.
> >Regards
> >Nick
> 
> See ?factor for additional information, but a quick example where
> using factor(old.factor) will return the factor with unused levels
> dropped.
> 
> # Create a factor
> > old.factor <- factor(c("One", "Two", "Three", "Four"))
> > old.factor
> [1] One   Two   Three Four 
> Levels: Four One Three Two
> 
> # Create a subset of three noting that all four
> # levels are retained
> > new.factor <- old.factor[1:3]
> > new.factor
> [1] One   Two   Three
> Levels: Four One Three Two
> 
> # Drop unused level
> > new.factor2 <- factor(new.factor)
> > new.factor2
> [1] One   Two   Three
> Levels: One Three Two
> 
> 
> HTH,
> 
> Marc Schwartz
> 
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> 
-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595
------------------------------
Message: 53
Date: Fri, 27 Jun 2003 08:34:40 +0200
From: "Philippe Grosjean" <phgrosjean@sciviews.org>
Subject: RE: [R] assignment in lists
To: "Prof Brian Ripley" <ripley@stats.ox.ac.uk>
Cc: