Re: [R] 'non-standard' folder names in R package
Oops, somehow I missed that part. Thank you very much! Tao From: Uwe Ligges [EMAIL PROTECTED] To: Tao Shi [EMAIL PROTECTED] CC: r-help@stat.math.ethz.ch Subject: Re: [R] 'non-standard' folder names in R package Date: Tue, 31 Jul 2007 11:52:10 +0200 Tao Shi wrote: Hi list, I use a .xml file for a function's demo in the R package I'm creating. Since it doesn't belong to any of the 'standard' folders, i.e. those mentioned in the 'Writing R Extension', I put it in a folder call myXML, much like the 'iris.xl' file in 'xls' folder from 'gdata' package, for example. After running R CMD build, I could see the .xml file is in the ..tar.gz file. However, after running R CMD INSTALL -build, the file and the folder disappeared in both the .zip file and the installed package. (R CMD CHECK, of course, failed too before that, as myXML can't be installed.) Could anybody tell me what's the tricks to keep those folders in my installation? I'm using R-2.5.1 under WinXP. Thank you very much! If you want it to be in mypackage/myXML after installation, put it into mypackage/inst/myXML in the source package, as the manual you cited suggests. Uwe Ligges Tao _ Need a brain boost? Recharge with a stimulating game. Play now! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] 'non-standard' folder names in R package
Hi list, I use a .xml file for a function's demo in the R package I'm creating. Since it doesn't belong to any of the 'standard' folders, i.e. those mentioned in the 'Writing R Extension', I put it in a folder call myXML, much like the 'iris.xl' file in 'xls' folder from 'gdata' package, for example. After running R CMD build, I could see the .xml file is in the ..tar.gz file. However, after running R CMD INSTALL -build, the file and the folder disappeared in both the .zip file and the installed package. (R CMD CHECK, of course, failed too before that, as myXML can't be installed.) Could anybody tell me what's the tricks to keep those folders in my installation? I'm using R-2.5.1 under WinXP. Thank you very much! Tao _ Need a brain boost? Recharge with a stimulating game. Play now! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating windows binary R package (PowerArchiver vs. zip -r9X)
Thanks, Uwe! It workedTao Date: Fri, 27 Jul 2007 09:16:49 +0200 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@stat.math.ethz.ch Subject: Re: [R] Creating windows binary R package (PowerArchiver vs. zip -r9X)Tao Shi wrote: Hi list,I apologize if you see funny fonts, b/c I'm using the new Windows Live Hotmail and don't know how to turn off the rich text mode.I have successfully built and installed a R package in windowsXP for R-2.5.1. But when I tried to create a .zip file so I can use Packages/install package(s) from local .zip files... to install it, it seems R only recognizes the .zip file created by zip -r9X not by PowerArchiver. Do you know why? I vaguely remember I used WinZip before and it worked fine.The two threads I found on R-help and R-devel help me a lot, but don't really answer my question.http://tolstoy.newcastle.edu.au/R/help/06/06/29587.htmlhttp://tolstoy.newcastle.edu.au/R/devel/05/12/3336.htmlThanks,...Tao In order to provide a Windows binary package, type: R CMD INSTALL --build PackageName_vers.tar.gz and the zip file will be generated by R in the correct way. Uwe Ligges _ PC Magazine’s 2007 editors’ choice for best web mail—award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-usocid=TXT_TAGHM_migration_HMWL_mini_pcmag_0707 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Creating windows binary R package (PowerArchiver vs. zip -r9X)
Hi list,I apologize if you see funny fonts, b/c I'm using the new Windows Live Hotmail and don't know how to turn off the rich text mode.I have successfully built and installed a R package in windowsXP for R-2.5.1. But when I tried to create a .zip file so I can use Packages/install package(s) from local .zip files... to install it, it seems R only recognizes the .zip file created by zip -r9X not by PowerArchiver. Do you know why? I vaguely remember I used WinZip before and it worked fine.The two threads I found on R-help and R-devel help me a lot, but don't really answer my question.http://tolstoy.newcastle.edu.au/R/help/06/06/29587.htmlhttp://tolstoy.newcastle.edu.au/R/devel/05/12/3336.htmlThanks,...Tao _ Missed the show? Watch videos of the Live Earth Concert on MSN. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to extract R codes that embedded in a HTML file
Works perfectly!
Thank you very much, Fritz!
Tao
From: Friedrich Leisch [EMAIL PROTECTED]
To: Tao Shi [EMAIL PROTECTED], [EMAIL PROTECTED],
[EMAIL PROTECTED], r-help@stat.math.ethz.ch
Subject: Re: [R] How to extract R codes that embedded in a HTML file
Date: Fri, 18 May 2007 15:14:48 +0200
Original Message
Subject: Re: [R] How to extract R codes that embedded in a HTML file
usingStangle?
Date: Thu, 17 May 2007 17:01:30 +
From: Tao Shi [EMAIL PROTECTED]
To: [EMAIL PROTECTED], [EMAIL PROTECTED]
CC: r-help@stat.math.ethz.ch
: [EMAIL PROTECTED]
Hi Uwe,
Thanks for the answer, but I still need a bit more clearification. I
always
thought that a .rnw or .snw file is a file mixing word processing
markup
(e.g. tex or HTML) and R/S code using noweb syntax. Is the reason for
'Stangle' is not working with .rnw file with HTML due to there is no
proper
driver available (like RweaveHTML driver for Sweave)? If yes, does
R2HTML
package have plans to provide a such driver?
Tao
The following does the trick for me:
R mytangle - function ()
list(setup = RtangleSetup, runcode = utils:::RtangleRuncode,
writedoc = RtangleWritedoc,
finish = utils:::RtangleFinish, checkopts = RweaveHTMLOptions)
R Stangle(/PATH/TO/R/SITE-LIBRARY/R2HTML/samples/example1.snw,
driver=mytangle)
Writing to file example1.R
Best,
Fritz
_
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Re: [R] How to extract R codes that embedded in a HTML file using Stangle?
Hi Uwe, Thanks for the answer, but I still need a bit more clearification. I always thought that a .rnw or .snw file is a file mixing word processing markup (e.g. tex or HTML) and R/S code using noweb syntax. Is the reason for 'Stangle' is not working with .rnw file with HTML due to there is no proper driver available (like RweaveHTML driver for Sweave)? If yes, does R2HTML package have plans to provide a such driver? Tao From: Uwe Ligges [EMAIL PROTECTED] To: Tao Shi [EMAIL PROTECTED] CC: r-help@stat.math.ethz.ch Subject: Re: [R] How to extract R codes that embedded in a HTML file using Stangle? Date: Tue, 15 May 2007 22:23:09 +0200 Tao Shi wrote: I'm using R2HTML package to generate reports, but don't know how to extract R codes from .rnw files using Stangle. It seems Stangle only works on ..tex file that has R codes embedded. Stangle is meant for Rnw files, not for html ... Uwe Ligges Thanks, Tao _ Hotmail. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Hotmail. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to extract R codes that embedded in a HTML file using Stangle?
I'm using R2HTML package to generate reports, but don't know how to extract R codes from .rnw files using Stangle. It seems Stangle only works on ..tex file that has R codes embedded. Thanks, Tao _ Hotmail. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] can't use Sweave in a function?
Thank you very much for the pointer, Duncan!
BTW, one comment. While testing your suggestion, I found that only 'save'
works (exactly like you said!), not 'save.image' (see the following R
session). 'save.image' only sees .globalEnv. So I guess the
statement--'save.image()' is just a short-cut for save my current
workspace, i.e., 'save(list = ls(all=TRUE), file = .RData)'. in the
help file is not entirely true.
Tao
ls()
character(0)
f1 - function() {
+ y - 1:5
+ x - ABC
+ #save(x,y, file=tmp.RData)
+ #save(list=ls(all=TRUE), file=tmp.RData)
+ save.image(tmp.RData)
+ #Sweave(test.rnw, driver=RweaveHTML)
+ }
f1()
ls()
[1] f1
load(tmp.RData)
ls()
[1] f1
rm(list=ls())
ls()
character(0)
f1 - function() {
+ y - 1:5
+ x - ABC
+ #save(x,y, file=tmp.RData)
+ save(list=ls(all=TRUE), file=tmp.RData)
+ #save.image(tmp.RData)
+ #Sweave(test.rnw, driver=RweaveHTML)
+ }
f1()
ls()
[1] f1
load(tmp.RData)
ls()
[1] f1 x y
From: Duncan Murdoch [EMAIL PROTECTED]
To: Tao Shi [EMAIL PROTECTED]
CC: r-help@stat.math.ethz.ch
Subject: Re: [R] can't use Sweave in a function?
Date: Thu, 10 May 2007 21:46:27 -0400
On 10/05/2007 9:08 PM, Tao Shi wrote:
Hi List,
Please see the following simple example which illustrate the problem. I'm
using R-2.5.0 in WinXP and
R2HTML 1.58.
The code in an Sweave document needs to be self-contained. It won't see
variables in some other R session.
If you want to pass the values of x and y into your document, use save() to
save them to a file, then load() them in the document.
Duncan Murdoch
Thanks,
Tao
#=test.rnw =
html
body
div
h1 align=centerReport/h1
p
echo=FALSE,results=html=
print(y)
print(\n)
print(paste((, x, ), sep=))
@
/p
/div
/body
/html
#
#=== R session ==
ls()
character(0)
f1 - function() {
+ y - 1:5
+ x - ABC
+ Sweave(test.rnw, driver=RweaveHTML)
+ }
f1()
Writing to file test.html
Processing code chunks ...
1 : term html
Error: chunk 1
Error in print(y) : object y not found
debug(f1)
f1()
debugging in: f1()
debug: {
y - 1:5
x - ABC
Sweave(test.rnw, driver = RweaveHTML)
}
Browse[1]
debug: y - 1:5
Browse[1]
debug: x - ABC
Browse[1]
debug: Sweave(test.rnw, driver = RweaveHTML)
Browse[1] x
[1] ABC
Browse[1] y
[1] 1 2 3 4 5
Browse[1]
Writing to file test.html
Processing code chunks ...
1 : term html
Error: chunk 1
Error in print(y) : object y not found
undebug(f1)
y - 1:5
x - ABC
ls()
[1] f1 x y
Sweave(test.rnw, driver=RweaveHTML)
Writing to file test.html
Processing code chunks ...
1 : term html
file test.html is completed
R.Version()
$platform
[1] i386-pc-mingw32
$arch
[1] i386
$os
[1] mingw32
$system
[1] i386, mingw32
$status
[1]
$major
[1] 2
$minor
[1] 5.0
$year
[1] 2007
$month
[1] 04
$day
[1] 23
$`svn rev`
[1] 41293
$language
[1] R
$version.string
[1] R version 2.5.0 (2007-04-23)
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[R] can't use Sweave in a function?
Hi List,
Please see the following simple example which illustrate the problem. I'm
using R-2.5.0 in WinXP and
R2HTML 1.58.
Thanks,
Tao
#=test.rnw =
html
body
div
h1 align=centerReport/h1
p
echo=FALSE,results=html=
print(y)
print(\n)
print(paste((, x, ), sep=))
@
/p
/div
/body
/html
#
#=== R session ==
ls()
character(0)
f1 - function() {
+ y - 1:5
+ x - ABC
+ Sweave(test.rnw, driver=RweaveHTML)
+ }
f1()
Writing to file test.html
Processing code chunks ...
1 : term html
Error: chunk 1
Error in print(y) : object y not found
debug(f1)
f1()
debugging in: f1()
debug: {
y - 1:5
x - ABC
Sweave(test.rnw, driver = RweaveHTML)
}
Browse[1]
debug: y - 1:5
Browse[1]
debug: x - ABC
Browse[1]
debug: Sweave(test.rnw, driver = RweaveHTML)
Browse[1] x
[1] ABC
Browse[1] y
[1] 1 2 3 4 5
Browse[1]
Writing to file test.html
Processing code chunks ...
1 : term html
Error: chunk 1
Error in print(y) : object y not found
undebug(f1)
y - 1:5
x - ABC
ls()
[1] f1 x y
Sweave(test.rnw, driver=RweaveHTML)
Writing to file test.html
Processing code chunks ...
1 : term html
file test.html is completed
R.Version()
$platform
[1] i386-pc-mingw32
$arch
[1] i386
$os
[1] mingw32
$system
[1] i386, mingw32
$status
[1]
$major
[1] 2
$minor
[1] 5.0
$year
[1] 2007
$month
[1] 04
$day
[1] 23
$`svn rev`
[1] 41293
$language
[1] R
$version.string
[1] R version 2.5.0 (2007-04-23)
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] a question regarding 'lrm'
Hi List, I don't understand why 'lrm' doesn't recognize the '~.' formula. I'm pretty sure it was working before. Please see below: I'm using R2.3.0, WinXP, Design 2.0-12 thanks, ...Tao dat - data.frame(y=factor(rep(1:2,each=50)), x1=rnorm(100), x2=rnorm(100), x3=rnorm(100)) lrm(y~., data=dat, x=T, y=T) Error in terms.formula(formula, specials = strat) : '.' in formula and no 'data' argument lrm(y~x1+x2+x3, data=dat, x=T, y=T) Logistic Regression Model lrm(formula = y ~ x1 + x2 + x3, data = dat, x = T, y = T) Frequencies of Responses 1 2 50 50 Obs Max Deriv Model L.R. d.f. P CDxy Gamma 100 1e-08 3.61 3 0.3066 0.594 0.187 0.188 Tau-a R2 Brier 0.095 0.047 0.241 Coef S.E. Wald Z P Intercept -0.05224 0.2071 -0.25 0.8009 x1-0.30699 0.1952 -1.57 0.1159 x2 0.08093 0.2171 0.37 0.7093 x3 0.21450 0.2247 0.95 0.3398 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] an error message with 't.test' with R under Unix
Hi list,Could you please help me to explain the following error messages with 't.test' in R Unix 2.1.1? I don't see it in R under Windows (R 2.3.0) or Unix (R2.3.1). Is it really due to the different R versions?Thanks,...TaoUnix session: (R.2.1.1) R.version _ platform x86_64-unknown-linux-gnuarch x86_64 os linux-gnu system x86_64, linux-gnu status major2 minor1.1 year 2005month06 day 20 language Rt.test(extra ~ group, data = sleep)Welch Two Sample t-testdata: extra by group t = -1.8608, df = 17.776, p-value = 0.0794alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -3.3654832 0.2054832 sample estimates:mean in group 1 mean in group 2! 0.752.33 t.test((1:6)~rep(1:2,each=3))Error in terms.formula(formula[-3]) : invalid model formula in ExtractVars t.test(2^(1:6)~rep(1:2,each=3))Error in terms.formula(formula[-3]) : invalid power in formula t.test(2^extra ~ group, data = sleep)Error in terms.formula(formula[-3]) : invalid power in formulaUnix session: (R 2.3.1) R.version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 3.1 year 2006 month 06day 01svn rev38247 language R version.string Version 2.3.1 (2006-06-01) t.test(1:6~rep(1:2,each=! 3))Welch Two Sample t-testdata: 1:6 by rep(1:2, each = 3) t = -3.6742, df = 4, p-value = 0.02131alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -5.266958 -0.733042 sample estimates:mean in group 1 mean in group 2 2 5 Windows session:=== R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 3.0 year 2006 month 04day 24svn rev37909 language R version.string Version 2.3.0 (2006-04-24) help(t.test) t.test(extra ~ group, data = sleep)Welch Two Sample t-testdata: extra by group t = -1.8608, df = 17.7! 76, p-value = 0.0794alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -3.3654832 0.2054832 sample estimates:mean in group 1 mean in group 20.752.33 t.test(2^extra ~ group, data = sleep)Welch Two Sample t-testdata: 2^extra by group t = -1.6362, df = 10.718, p-value = 0.1308alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -18.641557 2.773344 sample estimates:mean in group 1 mean in group 23.448644 11.382751 t.test(1:6~rep(1:2,each=3))Welch Two Sample t-testdata: 1:6 by rep(1:2, each = 3) t = -3.6742, df = 4, p-value = 0.02131alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -5.266958 -0.733042 sample estimates:mean in group 1 mean in group 2 2 5 _ Use Messenger to talk to your IM friends, even those on Yahoo! 685ee3e858fe [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] an error message with 't.test' with R under Unix
Hi Peter, Thank you for the reply! Really sorry for the formating (forgot to change to plain text). Here is basically what I'm talking about: R.version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major2 minor1.1 year 2005 month06 day 20 language R t.test(1:6~rep(1:2,each=3)) Error in terms.formula(formula[-3]) : invalid model formula in ExtractVars Again, I don't see the error in R under Windows (R 2.3.0) or Unix (R2.3.1). Is this the bug you were talking about? ...Tao To: [EMAIL PROTECTED] CC: r-help@stat.math.ethz.ch Subject: Re: [R] an error message with 't.test' with R under Unix From: [EMAIL PROTECTED] Date: Wed, 13 Sep 2006 23:52:04 +0200 Tao Shi [EMAIL PROTECTED] writes: Hi list,Could you please help me to explain the following error messages with 't.test' in R Unix 2.1.1? This is completely unreadable! However, yes, there was at some point a bug where the LHS of model formulas was checked more rigorously than need be, using the same rules that apply to the RHS. This fact can be found in a recent NEWS file. I don't see it in R under Windows (R 2.3.0) or Unix (R2.3.1). Is it really due to the different R versions?Thanks,...TaoUnix session: (R.2.1.1) R.version _ platform x86_64-unknown-linux-gnuarch x86_64 os linux-gnu system x86_64, linux-gnu status major2 minor1.1 year 2005month06 day 20 language Rt.test(extra ~ group, data = sleep)Welch Two Sample t-testdata: extra by group t = -1.8608, df = 17.776, p-value = 0.0794alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -3.3654832 0.2054832 sample estimates:mean in group 1 mean in group 2 ! 0.752.33 t.test((1:6)~rep(1:2,each=3))Error in terms.formula(formula[-3]) : invalid model formula in ExtractVars t.test(2^(1:6)~rep(1:2,each=3))Error in terms.formula(formula[-3]) : invalid power in formula t.test(2^extra ~ group, data = sleep)Error in terms.formula(formula[-3]) : invalid power in formulaUnix session: (R 2.3.1) R.version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 3.1 year 2006 month 06 day01svn rev38247 language R version.string Version 2.3.1 (2006-06-01) t.test(1:6~rep(1:2,each =! 3))Welch Two Sample t-testdata: 1:6 by rep(1:2, each = 3) t = -3.6742, df = 4, p-value = 0.02131alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -5.266958 -0.733042 sample estimates:mean in group 1 mean in group 2 2 5 Windows session:=== R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 3.0 year 2006 month 04day24svn rev 37909 language R version.string Version 2.3.0 (2006-04-24) help(t.test) t.test(extra ~ group, data = sleep)Welch Two Sample t-testdata: extra by group t = -1.8608, df = 17. 7! 76, p-value = 0.0794alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -3.3654832 0.2054832 sample estimates:mean in group 1 mean in group 20.752.33 t.test(2^extra ~ group, data = sleep)Welch Two Sample t-testdata: 2^extra by group t = -1.6362, df = 10.718, p-value = 0.1308alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -18.641557 2.773344 sample
[R] a problem 'cor' function
Hi list, One of my co-workers found this problem with 'cor' in his code and I confirm it too (see below). He's using R 2.2.1 under Win 2K and I'm using R 2.3.0 under Win XP. === R.Version() $platform [1] i386-pc-mingw32 $arch [1] i386 $os [1] mingw32 $system [1] i386, mingw32 $status [1] $major [1] 2 $minor [1] 3.0 $year [1] 2006 $month [1] 04 $day [1] 24 $`svn rev` [1] 37909 $language [1] R $version.string [1] Version 2.3.0 (2006-04-24) data(iris) cor(iris[1:4]) Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length 1. -0.1176 0.8718 0.8179 Sepal.Width -0.1176 1. -0.4284 -0.3661 Petal.Length 0.8718 -0.4284 1. 0.9629 Petal.Width0.8179 -0.3661 0.9629 1. cor(iris[1:4])==1 Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length TRUE FALSEFALSE FALSE Sepal.Width FALSETRUEFALSE FALSE Petal.LengthFALSE FALSE TRUE FALSE Petal.Width FALSE FALSEFALSETRUE cor(iris[1:4], iris[1:4]) Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length 1. -0.1176 0.8718 0.8179 Sepal.Width -0.1176 1. -0.4284 -0.3661 Petal.Length 0.8718 -0.4284 1. 0.9629 Petal.Width0.8179 -0.3661 0.9629 1. cor(iris[1:4], iris[1:4])==1 Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length TRUE FALSEFALSE FALSE Sepal.Width FALSETRUEFALSE FALSE Petal.LengthFALSE FALSEFALSE FALSE Petal.Width FALSE FALSEFALSETRUE === The two ways of calculating correlation seem to generate the 'same' results, but the second one doesn't appear to be numerically stable (see the 3rd diagonal element of the last matrix). thanks, ...Tao _ Join the next generation of Hotmail and you could win the adventure of a lifetime __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] a problem 'cor' function
Hi Peter, Thank you very much for your quick reply! I'm aware of the accuracy issue of the numbers in R. I guess the thing I was puzzled is how come the same function when used in different way produce different results (it's supposed to use the same algorithm). The only explanation for this is when cor(x) is used, the function automatically assign all the diagonal elements to 1. But when cor(x, y) is used, since there is no way to check which two vectors are the same, the function gives the 'real' results. best, ...Tao Date: Wed, 31 May 2006 16:49:18 -0600 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@stat.math.ethz.ch Subject: Re: [R] a problem 'cor' function Looks like another case of the most F of all FAQs: FAQ 7.31. See if the following makes sense to you:pl - iris[101:150, 3] all.equal(cor(pl,pl), 1) [1] TRUE cor(pl,pl) == 1 [1] FALSE sprintf(%1.22g, cor(pl, pl)) [1] 0.99989 sprintf(%1.22g, pl) [1] 6 5.0996 5.9004 etc Peter Ehlers Tao Shi wrote: Hi list, One of my co-workers found this problem with 'cor' in his code and I confirm it too (see below). He's using R 2.2.1 under Win 2K and I'm using R 2.3.0 under Win XP.=== R.Version()$platform [1] i386-pc-mingw32$arch [1] i386$os [1] mingw32$system [1] i386, mingw32 $status [1] $major [1] 2$minor [1] 3.0 $year [1] 2006$month [1] 04$day [1] 24 $`svn rev` [1] 37909$language [1] R $version.string [1] Version 2.3.0 (2006-04-24) data(iris) cor(iris[1:4]) Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length 1. -0.1176 0.8718 0.8179 Sepal.Width -0.1176 1. -0.4284 -0.3661 Petal.Length 0.8718 -0.4284 1. 0.9629 Petal.Width 0.8179 -0.3661 0.9629 1. cor(iris[1:4])==1 Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length TRUE FALSEFALSE FALSE Sepal.Width FALSETRUEFALSE FALSE Petal.Length FALSE FALSE TRUE FALSE Petal.Width FALSE FALSEFALSETRUE cor(iris[1:4], iris[1:4]) Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length 1. -0.1176 0.8718 0.8179 Sepal.Width -0.1176 1. -0.4284 -0.3661 Petal.Length 0.8718 -0.4284 1. 0.9629 Petal.Width0.8179 -0.3661 0.9629 1. cor(iris[1:4], iris[1:4])==1 Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length TRUE FALSE FALSE FALSE Sepal.Width FALSETRUE FALSE FALSE Petal.LengthFALSE FALSEFALSE FALSE Petal.Width FALSE FALSEFALSETRUE ===The two ways of calculating correlation seem to generate the 'same' results, but the second one doesn't appear to be numerically stable (see the 3rd diagonal element of the last matrix).thanks,...Tao _ Join the next generation of Hotmail and you could win the adventure of a lifetime __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Peter Ehlers Chair, Division of Statistics and Actuarial Science Department of Mathematics and Statistics University of Calgary, 2500 University Dr. NW ph: 403-220-3936 Calgary, Alberta T2N 1N4, CANADA fax: 403-282-5150 email: [EMAIL PROTECTED] _ Its the future of Hotmail: Try Windows Live Mail beta [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] zlim for levelplot
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[R] hclust, centroid
Does anyone know how hclust (stats) calculates centroid linkage if only a distance matrix can be used as the input? ...Tao __ [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: [Rd] a simple suggestion for the next version of R windows
Hi, Andy:
Thanks! I think it also depends on people's working hobby.
What you suggested is a good way around it. But I'm still thinking since
the R window already has the big blue R logo to identify itself, the word R
console is really redundant and could be replaced by something more
informative. Not nesessarly everytime you change to a new diretory, you
need to change to a new identifier, but at least the every first .RData file
you loaded. I don't know... Something along that line. It will be
very helpful when you use Alt+Tab to move between windows, b/c all you see
are R consoles...
...Tao
Original Message Follows
From: Liaw, Andy [EMAIL PROTECTED]
To: 'Tao Shi' [EMAIL PROTECTED],[EMAIL PROTECTED]
CC: [EMAIL PROTECTED]
Subject: RE: [Rd] a simple suggestion for the next version of R windows
Date: Sat, 24 Apr 2004 23:18:06 -0400
I don't see how this can work. I frequently run only one R session (also in
SDI), but change working directories several times during the session, with
or without loading the workspace files in those directories, depending on
what I need to do. I don't think the Window title can change every time I
do setwd(somewhereElse); load(.RData).
One possibility that could probably help you is to change the R command
prompt from to the current working directory plus . I believe this
can be done with the taskCallbackManager().
Andy
From: Tao Shi
Is it possible to replace the word R Console on the title
bar (is it what
it's called? It's the blue area above menu bar) with the name
of the work
space file you're using or loaded, so people who are runing multple R
sessions at same time can identify them immediately. I'm
using 1.9.0 in SDI
mode.
Thanks,
...Tao
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[R] a question regarding 'cor' function
I'm a little bit confused with how exactly the 'cor' function handles missing values. Should the last two function calls give the same results? Thanks, ...Tao == x=rnorm(10) y=rnorm(10) x[1]=NA y[2]=NA cor(x,y,method=spearman) [1] -0.006060606 cor(x,y,use=pairwise.complete.obs,method=spearman) [1] -0.006060606 cor(x[3:10],y[3:10],method=spearman) [1] 0.167 == _ Create a Job Alert on MSN Careers and enter for a chance to win $1000! http://msn.careerbuilder.com/promo/kaday.htm?siteid=CBMSN_1Ksc_extcmp=JS_JASweep_MSNHotm2 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Why two chisq.test p values differ when the contingency tableis transposed?
I'm using R1.7.0 runing with Win XP. Thanks, ...Tao x [,1] [,2] [1,] 149 151 [2,]18 t(x) [,1] [,2] [1,] 1491 [2,] 1518 chisq.test(x, simulate.p.value=T, B=10) Pearson's Chi-squared test with simulated p-value (based on 1e+05 replicates) data: x X-squared = 5.2001, df = NA, p-value = 0.03774 chisq.test(t(x), simulate.p.value=T, B=10) Pearson's Chi-squared test with simulated p-value (based on 1e+05 replicates) data: t(x) X-squared = 5.2001, df = NA, p-value = 0.01642 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
