[R] .NAME in .Fortran
ROR Running examples in 'tweedie-Ex.R' failed The error most likely occurred in: ### Name: tweedie-package ### Title: Tweedie Distributions ### Aliases: tweedie-package Tweedie ### Keywords: models ### ** Examples # Generate random numbers set.seed(314) y <- rtweedie( 500, p=1.5, mu=1, phi=1) # With index p between 1 and 2, this produces continuous # data with exact zeros x <- rnorm( length(y), 0, 1) # Unrelated predictor # With exact zeros, index p must be between 1 and 2 # Fit the tweedie distribution; expect p about 1.5 out <- tweedie.profile( y~1, p.vec=seq(1.1, 1.9, length=9), do.plot=TRUE) 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 .Error in .Fortran(.NAME = "pdfun", as.double(power), as.double(phi[i]/(y[i]^(2 - : supplied argument name '.NAME' does not match 'name' Calls: tweedie.profile -> dtweedie.inversion -> .Fortran Execution halted ** running examples for arch 'x86_64' ... ERROR Running examples in 'tweedie-Ex.R' failed The error most likely occurred in: ### Name: tweedie-package ### Title: Tweedie Distributions ### Aliases: tweedie-package Tweedie ### Keywords: models ### ** Examples # Generate random numbers set.seed(314) y <- rtweedie( 500, p=1.5, mu=1, phi=1) # With index p between 1 and 2, this produces continuous # data with exact zeros x <- rnorm( length(y), 0, 1) # Unrelated predictor # With exact zeros, index p must be between 1 and 2 # Fit the tweedie distribution; expect p about 1.5 out <- tweedie.profile( y~1, p.vec=seq(1.1, 1.9, length=9), do.plot=TRUE) 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 .Error in .Fortran(.NAME = "pdfun", as.double(power), as.double(phi[i]/(y[i]^(2 - : supplied argument name '.NAME' does not match 'name' Calls: tweedie.profile -> dtweedie.inversion -> .Fortran Execution halted -- Dr Peter Dunn Biostatistician Faculty of Science, Health, Education and Engineering (T3.03; ML 33) Ph: +61 7 5456 5085 | Fax: +61 7 5430 2896 | Email: pdu...@usc.edu.au | Web: www.usc.edu.au <http://www.usc.edu.au/> University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland, 4558 Australia. CRICOS Provider No: 01595D Please consider the environment before printing this email. This email is confidential. If received in error, please delete it from your system. __ R-help@r-project.org 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] Sweave problem: lines repeated
Hi all
I'm having a problem when using Sweave. Here is a minimal example.
My input file (eg, test.Snw) looks like this:
<>=
data(cars)
m1 <- lm( dist~speed, data=cars ); coef( m1 )
@
<>=
<>
@
<>=
data(cars)
m1 <- lm( dist~speed, data=cars )
@
<>=
<>
@
After running Sweave over this file in R, the output file (eg. test.tex) looks
like this:
\begin{Schunk}
\begin{Sinput}
> data(cars)
> m1 <- lm( dist~speed, data=cars ); coef( m1 )
> m1 <- lm( dist~speed, data=cars ); coef( m1 )
\end{Sinput}
\begin{Soutput}
(Intercept) speed
-17.5790953.932409
\end{Soutput}
\end{Schunk}
\begin{Schunk}
\begin{Sinput}
> data(cars)
> m1 <- lm( dist~speed, data=cars )
\end{Sinput}
\end{Schunk}
For some reason I cannot fathom, the first two chunks end up giving me *part*
of the verbatim code twice (which is not what I was expecting), but the last
two chunks do things as I expect.
Can anyone point me to my error, or explain why this happens?
P.
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MASS_7.3-8
loaded via a namespace (and not attached):
[1] tools_2.12.0
> version
_
platform i386-apple-darwin9.8.0
arch i386
os darwin9.8.0
system i386, darwin9.8.0
status
major 2
minor 12.0
year 2010
month 10
day15
svn rev53317
language R
version.string R version 2.12.0 (2010-10-15)
Peter Dunn: Biostatistician (Room T4.15)
School of Health and Sport Science
Faculty of Science, Health and Education ML-34
University of the Sunshine Coast, Locked Bag 4
Maroochydore DC Qld 4558
Tel: +61 7 5456 5085
Fax: +61 7 5430 2896
Email: pdu...@usc.edu.au
www.usc.edu.au
CRICOS Provider Number: 01595D
This communication is intended for the recipient only and should not be
forwarded, distributed or otherwise read by others without express permission.
The views expressed in this email are not necessarily those of the University
of the Sunshine Coast.
--
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Re: [R] Using termplot() with transformations of x
Hi >the two models are identical because of having the same independent > variable and dependent variable.they produce different termplot()s because > of they base on different variables,one is x,the other is logx.see the > lateral axis. Sure; this is all obvious from the code and the plots. But my question is *why* two fundamentally identical models produce different termplot()s? As the original post asks: If this is intended, what is the logic? Or am I missing something? Let me place explain further. Suppose I try this m1 <- lm(y~x) termplot(m1) and I see that there is a problem. So I decide to use log(x) as a predictor instead of x; I could do this one of two ways: logx <- log(x) m2 <- lm(y~logx) termplot(m2) m3 <- lm(y~log(x)) termplot(x3) In the first case, the new termplot() tells me the model looks good. In the second case, I output is the same as for termplot(m1) produced, and I don't really learn anything new. So the original questions remain: If this is intended, what is the logic? Or am I missing something? Perhaps I could add: How do I explain and justify this behaviour to someone? Thanks. P. Peter Dunn: Biostatistician (Room T4.12) School of Health and Sport Science Faculty of Science, Health and Education ML-34 University of the Sunshine Coast, Locked Bag 4 Maroochydore DC Qld 4558 Tel: +61 7 5456 5085 Fax: +61 7 5430 2896 Email: pdu...@usc.edu.au www.usc.edu.au CRICOS Provider Number: 01595D This communication is intended for the recipient only and should not be forwarded, distributed or otherwise read by others without express permission. The views expressed in this email are not necessarily those of the University of the Sunshine Coast. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org 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] Using termplot() with transformations of x
Hi all I was playing with termplot(), and came across what appears to be an inconsistency. It would appreciate if someone could enlighten me: > # First, generate some data: > y <- rnorm(100) > x <- runif(length(y),1,2) > # Now find the log of x: > logx <- log(x) > > # Now fit two models that are exactly the same, but specified differently: > m1 <- lm(y~log(x)) # Using log in the call > m2 <- lm(y~logx) # Using the variable logx > > # The two termplots() are different: > par(mfrow=c(1,2)) > termplot(m1) > termplot(m2) I see two models that are identical, but produce different termplot()s. In both cases, the independent variable is log(x), but is just specified differently. If this is intended, what is the logic? Or am I missing something? Thanks. P. > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Peter Dunn: Biostatistician (Room T4.12) School of Health and Sport Science Faculty of Science, Health and Education ML-34 University of the Sunshine Coast, Locked Bag 4 Maroochydore DC Qld 4558 Tel: +61 7 5456 5085 Fax: +61 7 5430 2896 Email: pdu...@usc.edu.au www.usc.edu.au CRICOS Provider Number: 01595D This communication is intended for the recipient only and should not be forwarded, distributed or otherwise read by others without express permission. The views expressed in this email are not necessarily those of the University of the Sunshine Coast. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org 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] Sweave output from print.summary.glm is too wide
Hi all
I am preparing a document using Sweave; a really useful tool. But I am having
a problem.
Consider this toy example Sweave file:
\documentclass{article}
\begin{document}
<>=
options(width=40) # Set width to 40 characters
hide <- capture.output(example(glm)) # Create an example of the problem, but
hide the output
summary(glm.D93) # This is where the problem is evident
@
\end{document}
The intent of the options(width=40) command is to ensure the output does not
extend to far to the right of the page, as per the Sweave manual Section A.14.
And in most cases, this does the job.
Now, I run Sweave on the above file, run pdflatex. Feel free to run the above
code to see the actual result, but here is an edited text version of the output:
> options(width = 40)
> hide <- capture.output(example(glm))
> summary(glm.D93)
Call:
glm(formula = counts ~ outcome + treatment, family = poisson())
Deviance Residuals:
1 2 3 4
-0.67125 0.96272 -0.16965 -0.21999
5 6 7 8
-0.95552 1.04939 0.84715 -0.09167
9
-0.96656
Coefficients:
Estimate Std. Error
(Intercept) 3.045e+00 1.709e-01
outcome2 -4.543e-01 2.022e-01
outcome3 -2.930e-01 1.927e-01
treatment2 8.717e-16 2.000e-01
treatment3 4.557e-16 2.000e-01
z value Pr(>|z|)
(Intercept) 17.815 <2e-16 ***
outcome2 -2.247 0.0246 *
outcome3 -1.520 0.1285
treatment2 4.36e-15 1.
treatment3 2.28e-15 1.
The final pdf output file is mostly fine: but not all of the output of
print.summary.glm obeys the width=40 command.
The middle parts of the output are suitable wrapped (the coefficients, std
error, z and P-value bit), but the bits at the end (not shown) and the start
are not; for example, look at the Call: section of the output above.
I'd be expecting the initial part of the output to appear something like this,
suitably wrapped:
> summary(glm.D93)
Call:
glm(formula = counts ~ outcome +
treatment, family = poisson())
As far as I can recall, print.summary.glm and print.summary.lm are the only
times I have seen this behaviour. I found a similar thread posted June 2009
("overshoot of formula line in summary output of Sweave"); there appeared no
resolution in that thread, or after contacting the originator of the post.
So my question:
* What can I do to ensure my output is not extending too far to the right with
print.summary.glm?
Thanks as always.
P.
> sessionInfo()
R version 2.9.0 (2009-04-17)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GLMsData_0.7
loaded via a namespace (and not attached):
[1] tools_2.9.0
>
Peter Dunn: Biostatistician
School of Health and Sport Science
Faculty of Science, Health and Education ML-34
University of the Sunshine Coast, Locked Bag 4
Maroochydore DC Qld 4558
Tel: +61 7 5456 5085
Fax: +61 7 5430 2896
Email: pdu...@usc.edu.au
www.usc.edu.au ( http://www.usc.edu.au/ )
CRICOS Provider Number: 01595D
This communication is intended for the recipient only and should not be
forwarded, distributed or otherwise read by others without express permission.
The views expressed in this email are not necessarily those of the University
of the Sunshine Coast.
--
This message has been scanned for viruses and\ dangerous...{{dropped:8}}
__
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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.
Re: [R] Error building package: LaTeX error when creating PDF version
Duncan suggested R CMD check was not finding pdflatex, because there is no .log file in the same directory as the .tex file. However, the first line of output from R CMD check says: > * checking for working pdflatex ... OK Indeed: pdu...@pdunnubuntu:~/DSdata/GLMsData.Rchecks$ R CMD pdflatex This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. ** And it waits for input. So that doesn't seem to be the problem. Further suggestions? P. Peter Dunn: Biostatistician School of Health and Sport Science Faculty of Science, Health and Education ML-34 University of the Sunshine Coast, Locked Bag 4 Maroochydore DC Qld 4558 Tel: +61 7 5456 5085 Fax: +61 7 5430 2896 Email: pdu...@usc.edu.au www.usc.edu.au ( http://www.usc.edu.au/ ) >>> Duncan Murdoch 24/04/2009 10:40 am >>> On 23/04/2009 8:24 PM, Peter Dunn wrote: > Hi all > > I am trying to build an R package, which I have successfully done many times > before, but have an error I cannot trace. I hope someone can help me. > > Here's is some edited output (full output below if it is useful): > > pdu...@pdunnubuntu:~/DSdata$ R CMD build GLMsData > * checking for file 'GLMsData/DESCRIPTION' ... OK > * preparing 'GLMsData': > * checking DESCRIPTION meta-information ... OK > * removing junk files > * checking for LF line-endings in source and make files > * checking for empty or unneeded directories > * building 'GLMsData_0.7.tar.gz' > > pdu...@pdunnubuntu:~/DSdata$ R CMD check GLMsData > * checking for working pdflatex ... OK > * using log directory '/home/pdunn2/DSdata/GLMsData.Rcheck' > * using R version 2.9.0 (2009-04-17) > > > > * checking data for non-ASCII characters ... OK > * checking examples ... OK > * checking PDF version of manual ... WARNING > LaTeX errors when creating PDF version. > This typically indicates Rd problems. > * checking PDF version of manual without index ... ERROR > > > So there is an error making the PDf version of the package manual. That's > fine; I am happy to fix it. But first I need to find it. > > So I enter the directory GLMsData.Rcheck and find the corresponding tex file > for the manual, and run pdflatex on this tex file: > > pdu...@pdunnubuntu:~/DSdata$ cd GLMsData.Rcheck/ > pdu...@pdunnubuntu:~/DSdata/GLMsData.Rcheck$ pdflatex GLMsData-manual.tex > > > > Output written on GLMsData-manual.pdf (79 pages, 405091 bytes). > Transcript written on GLMsData-manual.log. > pdu...@pdunnubuntu:~/DSdata/GLMsData.Rcheck$ > > > So from what I gather: > * R CMD check finds an error when using pdflatex to make the PDF version > of the manual > * But when I manually run pdflatex on the tex file, it works OK. > > Obviously, I am missing something. Can someone tell me what it is? I can't > find enlightenment on the archives or the manuals. You should also have a .log file in the same directory as the .tex file. You probably have a new one now that pdflatex works; please move that one aside and run R CMD check again. If you get a .log file, it should list whatever the error was; you could compare it to the .log that worked if you can't spot it. If you don't get a new log, that means R CMD check couldn't run pdflatex. Duncan Murdoch > > Thanks everyone. > > P. > > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i486-pc-linux-gnu > > locale: > LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methodsbase > > > > > > FULL OUTPUT: > > pdu...@pdunnubuntu:~/DSdata$ R CMD build GLMsData > * checking for file 'GLMsData/DESCRIPTION' ... OK > * preparing 'GLMsData': > * checking DESCRIPTION meta-information ... OK > * removing junk files > * checking for LF line-endings in source and make files > * checking for empty or unneeded directories > * building 'GLMsData_0.7.tar.gz' > > pdu...@pdunnubuntu:~/DSdata$ R CMD check GLMsData > * checking for working pdflatex ... OK > * using log directory '/home/pdunn2/DSdata/GLMsData.Rcheck' > * using R version 2.9.0 (2009-04-17) > * using session charset: UTF-8 > * checking for file 'GLMsData/DESCRIPTION' ... OK > * checking extension type ... Package > * this is package 'GLMsData' version '0.7' > * checking package dependencies ... OK > * checking if this is a source packag
[R] Error building package: LaTeX error when creating PDF version
ival. Pub-lished on the in-ter-net [][]$\T1/p
cr/m/n/10 www . health . wa . gov . au / Publications /
[75]
Overfull \hbox (1.66795pt too wide) in paragraph at lines 3290--3290
[]\T1/ptm/m/n/10 the smok-ing sta-tus of the women in the \T1/ptm/m/it/10 orig-
i-nal \T1/ptm/m/n/10 sur-vey; a fac-tor with lev-els \T1/pcr/m/n/10 NonSmoker
[76] [77] [78]
No file GLMsData-manual.ind.
[79] (./GLMsData-manual.aux) )
(see the transcript file for additional information){/usr/share/texmf-texlive/f
onts/enc/dvips/base/8r.enc}
Output written on GLMsData-manual.pdf (79 pages, 405091 bytes).
Transcript written on GLMsData-manual.log.
pdu...@pdunnubuntu:~/DSdata/GLMsData.Rcheck$
--
Peter Dunn: Biostatistician
School of Health and Sport Science
Faculty of Science, Health and Education ML-34
University of the Sunshine Coast, Locked Bag 4
Maroochydore DC Qld 4558
Tel: +61 7 5456 5085
Fax: +61 7 5430 2896
Email: pdu...@usc.edu.au
www.usc.edu.au
CRICOS Provider Number: 01595D
This communication is intended for the recipient only and should not be
forwarded, distributed or otherwise read by others without express permission.
The views expressed in this email are not necessarily those of the University
of the Sunshine Coast.
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
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__
R-help@r-project.org mailing list
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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] OT: Adding verbatim R code text into LaTeX documents: texttt; verb or url?
Hi all
I use Sweave extensively to mix R and LaTeX, and often have R code appearing in
my LaTeX document.
Just a quick question then: What is the best way to add example of R commands
into LaTeX in-line? (That is, not using Sweave.) For example, suppose I wish
to place in my document this instruction:
...is done in R using the command \verb|lm( y ~ var.one + var.two )| as
follows:
I used \verb above, but I see three options: \verb, \url (package url), or
\texttt; there are probably others.
Here are my comments on these three:
- Using \texttt is OK, but it disappears my tildes and can hyphenate
- Using \verb is good, but it can hyphenate.
- Using \url is very good, but it:
* disappears my spaces; so for the above example, the spaces added for clarity
are gone.
* Minor: I like my verbatim text a little smaller (\small size), and change
the font size for verbatim using \def\verba...@font{\small\ttfamily} but \url
seems to ignore this and appears larger than if I used \text or \verb.
Also, using \url often adds line-breaks mid-variable at the dots (for example,
splitting var.one to have "var." on one line, and "one" on the next). I'm not
sure this is a problem or not; here it is just an observation.
Ideally, one would want a LaTeX function, say \rcode{}, that displayed in-text
using non-proportional font, kept tildes, kept spacing, uses my verb-font
changes, and broke at sensible places for R. (I don't want much, do I?)
So two questions:
* What do other people do? Maybe there is a solution I have over-looked.
* Is there an easy solution? I suppose writing such a command in LaTeX is
possible, but there is strong evidence to reject the hypothesis that I would be
able to write one. Maybe one of the above choices are easily adopted.
If no easy solutions exist or emerge, I'm happy to run with \url.
Thanks again.
P.
Peter Dunn
Biostatistician
School of Health and Sport Science
Faculty of Science, Health and Education
University of the Sunshine Coast
Tel: +61 7 5456 5085
Fax: +61 7 5430 2896
Email: pdu...@usc.edu.au
www.usc.edu.au
CRICOS Provider Number: 01595D
This communication is intended for the recipient only and should not be
forwarded, distributed or otherwise read by others without express permission.
The views expressed in this email are not necessarily those of the University
of the Sunshine Coast.
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
__
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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] Understanding glm family documentation: dev.resids
Hi all Consider the family function, as used by glm. The help page says the value of the family object is a list, one element of which is the following: dev.resids function giving the deviance residuals as a function of (y, mu, wt). But reading any of the family functions (eg poisson) shows that dev.resids is a function that computes the *square* of the deviance residuals (at least, by every definition I know of). Further, the deviance residuals returned by residuals.glm are essentially computed as the square root of dev.resids. Something seems amiss. The element dev.resids actually seems to compute the deviance residuals squared. I guess the help file could be changed to read: dev.resids function giving the square of the deviance residuals as a function of (y, mu, wt). ...but then, dev.resids still seems a misleading label, but that may so entrenched it will never changed. (By my definition, the square of the deviance residuals is not quite the unit deviance as the weights need to be incorporated differently, but others may disagree.) Of course, I could be way off track. I would appreciate enlightenment. P. Peter Dunn Biostatistician School of Health and Sport Science Faculty of Science, Health and Education University of the Sunshine Coast Tel: +61 7 5456 5085 Fax: +61 7 5430 2896 Email: [EMAIL PROTECTED] www.usc.edu.au CRICOS Provider Number: 01595D This communication is intended for the recipient only and should not be forwarded, distributed or otherwise read by others without express permission. The views expressed in this email are not necessarily those of the University of the Sunshine Coast. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org 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] Citing R in journal articles (or the failure to)
Hi all I was reading a paper recently in which I was surprised to see an R package of mine obviously used, without acknowledgement. Indeed, R itself was used without any acknowledgment. So I contact the author about these issues, who said (in part): Regarding the R packages, I used the "tweedie" and "statmod" for my analyses as you pointed out. The referee of this paper advised me that it is not needed to cite "R" because it is a kind of free software different from the commercial package such as SAS. What is the logic behind this? What can be done about it? That makes me quite angry... P. Peter Dunn Biostatistician School of Health and Sport Science Faculty of Science, Health and Education University of the Sunshine Coast Tel: +61 7 5456 5085 Fax: +61 7 5430 2896 Email: [EMAIL PROTECTED] www.usc.edu.au Peter Dunn Biostatistician School of Health and Sport Science Faculty of Science, Health and Education University of the Sunshine Coast Tel: +61 7 5456 5085 Fax: +61 7 5430 2896 Email: [EMAIL PROTECTED] www.usc.edu.au CRICOS Provider Number: 01595D This communication is intended for the recipient only and should not be forwarded, distributed or otherwise read by others without express permission. The views expressed in this email are not necessarily those of the University of the Sunshine Coast. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org 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] Bug/Error in formatC? (Was: Why doesn 't formatC( x, digits=2, format= " g")...)
Martin
I know you and Brian have been discussing this issue, and Brian
would officially declare it a 'buglet' if he used that word, but
for completeness (I should have done this anyway; my oversight):
> What are the exact platform details?
> sessionInfo()
R version 2.7.0 (2008-04-22)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.7.0
--
Dr Peter Dunn | dunn usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
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[R] Bug/Error in formatC? (Was: Why doesn 't formatC( x, digits=2, format= " g")...)
Hi all
After posting what follows, Duncan Murdoch suggested perhaps a bug
in formatC, or an error on documentation. Any comments?
In particular, bug, error or not, any ideas about how I can
consistently get two significant figures to print?
P.
-- Original Message --
Hi all
I am not a C programmer, but I am trying to understand formatC to
get consistent printing of reals to a given number of significant
digits.
Can someone please explain this to me? These first three give what
I expect on reading ?formatC:
> formatC(0.005, digits=2,format="fg",flag="#")
[1] "0.0060"
> formatC(0.5, digits=2,format="fg",flag="#")
[1] "0.60"
> formatC(5., digits=2,format="fg",flag="#")
[1] "6.0"
This seems consistent with what I read (but perhaps do not
understand) in ?formatC, where I read this:
digits the desired number of digits after the decimal
point (format = "f") or significant digits (format = "g",
= "e" or = "fg").
Since I am using format="fg" and digits=2, so I am expecting two
significant digits to always show, which I have above. So I fail to
understand this:
> formatC(0.5, digits=2,format="fg",flag="#")
[1] "0.6"
> formatC(0.59, digits=2, format="fg",flag="#")
[1] "0.59"
I was expecting both of these to produce "0.59". But in the
first case above, I get one significant digit only.
I'm obviously misunderstanding something; can someone enlighten me?
(No doubt, someone will point out a nuance of the help files I
didn't understand!)
Also, since the above obviously doesn't do what I hoped
(consistently printing two sig figs), could someone also explain
how I can consistently get two significant figures in situation
like above?
Thanks as always.
P.
--
Dr Peter Dunn | dunn usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
This email (including any attached files) is confidentia...{{dropped:15}}
__
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and provide commented, minimal, self-contained, reproducible code.
[R] Why doesn't formatC( x, digits=2, format="g") doesn't always give 2 sig figs?
Hi all
I am not a C programmer, but I am trying to understand formatC to
get consistent printing of reals to a given number of significant
digits.
Can someone please explain this to me? These first three give what
I expect on reading ?formatC:
> formatC(0.005, digits=2,format="fg",flag="#")
[1] "0.0060"
> formatC(0.5, digits=2,format="fg",flag="#")
[1] "0.60"
> formatC(5., digits=2,format="fg",flag="#")
[1] "6.0"
This seems consistent with what I read (but perhaps do not
understand) in ?formatC, where I read this:
digits the desired number of digits after the decimal point
(format = "f") or significant digits (format = "g", = "e" or
= "fg").
Since I am using format="fg" and digits=2, so I am expecting two
significant digits to always show, which I have above. So I fail to
understand this:
> formatC(0.5, digits=2,format="fg",flag="#")
[1] "0.6"
> formatC(0.59, digits=2, format="fg",flag="#")
[1] "0.59"
I was expecting both of these to produce "0.59". But in the
first case above, I get one significant digit only.
I'm obviously misunderstanding something; can someone enlighten me?
(No doubt, someone will point out a nuance of the help files I
didn't understand!)
Also, since the above obviously doesn't do what I hoped
(consistently printing two sig figs), could someone also explain
how I can consistently get two significant figures in situation
like above?
Thanks as always.
P.
--
Dr Peter Dunn | dunn usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
This email (including any attached files) is confidentia...{{dropped:15}}
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] tweedie model
I am.
What do you need to know now?
P.
On Thursday 06 March 2008 09:39, Roslina Zakaria wrote:
> Hi R users,
> Anybody using tweedie model to analyze rainfall data?
> Thanks in advance for your attention.
>
> __
> R-help@r-project.org mailing list
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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.
--
Dr Peter Dunn | dunn usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
This email (including any attached files) is confidentia...{{dropped:15}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] quantile-residual plot
> What is quantile residuals?
See
Dunn, Peter K. and Smyth, Gordon K. (1996). Randomized Quantile
Residuals. Journal of Computational and Graphical Statistics,
volume 5, issue 3, 236–244.
Or see ?qresid in R package statmod.
P.
--
Dr Peter Dunn | dunn usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
This email (including any attached files) is confidentia...{{dropped:15}}
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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] Adding LaTeX cross-references into Sweave plots
Hi all
I'm using Sweave and LaTeX, and love how they interact.
But here's a different interaction I'm not sure how to achieve; I
hope someone can help. I use a simple example, of course, to
demonstrate.
Suppose in my LaTeX document I have this:
Here is a linear equation:
\begin{equation}
y = -1 + 3 x
\label{EQ:example}
\end{equation}
This appears in the final product with an Equation number, say (1).
Now suppose I wish to produce a graphic in R:
<>=
plot( c(-1,1), c(-1,1), type="n",
main="Graph of Eq (1)")
abline(-1, 3)
@
All easy.
But... how to I ensure the correct LaTeX label appears in the plot?
You see, if I run LaTeX again, and my equation is no longer
labelled (1) and changes to (say) label (3), I have to manually fix
the Sweave code to read
<>=
plot( c(-1,1), c(-1,1), type="n",
main="Graph of Eq (3)")
abline(-1, 3)
@
Any ideas of how that can be automated? I guess something like this
(though this obviously will fail):
<>=
plot( c(-1,1), c(-1,1), type="n",
main="Graph of Eq (\label{EQ:equation})")
abline(-1, 3)
@
Thanks as always.
P.
--
Dr Peter Dunn | dunn usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
This email (including any attached files) is confidentia...{{dropped:15}}
__
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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.
Re: [R] Identity link in tweedie
Cristina
> I'm using the tweedie distribution package and I cant figure out
> how to run a model using an identity link. I know I can use a log
> link by having link.power=0 and I think identity would be
> link.power=1, but I'm not sure.
Yes, that is correct.
> Furthermore when I try running it
> with link.power=1 it requires starting values which I cant manage
> to give appropriately
Without any code to see, I will guess at what is happening. The
trouble with using an identity link is that the predicted means,
say mu, may be negative, where as the Tweedie distributions have mu
greater than zero. In using the identity link, you may be asking R
to fit the impossible.
Perhaps the question you need to ask is this: Why do you need an
identity link?
P.
--
Dr Peter Dunn | dunn usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
This email (including any attached files) is confidentia...{{dropped:15}}
__
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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.
Re: [R] Help! - boxcox transformations
> I am trying to detrend and transform variables to achieve
> normality and stationarity (for time series use, namely spectral
> analysis). I am using the boxcox transformations.
>
>
>
> As my dataset contains zeros, I found I need to add a constant to
> it in order to run "boxcox".
If your data are continuous with exact zeros, and contain a lot of
zeros, no transformation may help. You simply map a stack of zeros
to some other value. Box--Cox transforms are not really designed
for this.
If your data really is continuous with exact zeros, other options
exist such as hurdle models, Tweedie glms (package tweedie) and so
forth.
P.
--
Dr Peter Dunn | dunn usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
This email (including any attached files) is confidentia...{{dropped:15}}
__
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and provide commented, minimal, self-contained, reproducible code.
[R] Mixing lty specifications in legend
Hi all
I have a plot with lines, one specified as (say) lty=1,
using standard line types, and another as (say) my
own spec: lty="51".
I can't get legend to display both. Toy example:
> plot(1~1)
> legend("topright", lty=c("51",1), legend=c("My own","Standard"))
Error in segments(x1, y1, x2, y2, ...) : invalid line type: must be
length 2, 4, 6 or 8
>
Any ideas?
P.
> sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets"
"methods" "base"
other attached packages:
car xtable statmod
"1.2-2" "1.5-1" "1.3.1"
Dr Peter Dunn (USQ CRICOS No. 00244B)
Web:http://www.sci.usq.edu.au/staff/dunn
Email: dunn @ usq.edu.au
ACSC: http://www.usq.edu.au/acsc
This email (including any attached files) is confidentia...{{dropped:15}}
__
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and provide commented, minimal, self-contained, reproducible code.
[R] Problem using xtable on an array
Hi all
I know about producing a minimal example to show my problem. But I'm
having trouble producing a minimal example that displays this
behaviour, so please bear with me to begin with.
Observe: I create an array called model.mat. Some details on this:
> str(model.mat)
num [1:18, 1:4] -0.170 -0.304 -2.617 2.025 -1.610 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:18] "Amount: CP for VF" "Amount: CP for F" "Amount: CP for
M" "Amount: RD for VF" ...
..$ : chr [1:4] "beta_0" "P-value" "beta_1" "P-value"
It contains the following:
> model.mat[1:2,]
beta_0 P-valuebeta_1 P-value
Amount: CP for VF -0.1702877 0.7716153 0.5148616 2.020602e-03
Amount: CP for F -0.3042522 0.1966133 0.8795982 6.058299e-12
That's fine. Now to produce a LaTeX table using xtable,
I get:
> xtable(model.mat[1:2,])
Amount: CP for VF & $-$0.17 & 0.77 & 0.51 & 0.77 \\
Amount: CP for F & $-$0.30 & 0.20 & 0.88 & 0.20 \\
That is, the final column does *not* correspond to the final
column of model.mat itself. It is actually column 2 repeated.
What's going on? If I try repeating on a minimal type example,
xtable works as expected:
> fred <- array( seq(1,18*4), dim=c(18,4))
> fred[1:2, ]
[,1] [,2] [,3] [,4]
[1,]1 19 37 55
[2,]2 20 38 56
> xtable(fred[1:2, ])
% latex table generated in R 2.5.0 by xtable 1.4-6 package
% Thu Sep 13 14:09:46 2007
\begin{table}[ht]
\begin{center}
\begin{tabular}{r}
\hline
& 1 & 2 & 3 & 4 \\
\hline
1 & 1 & 19 & 37 & 55 \\
2 & 2 & 20 & 38 & 56 \\
\hline
\end{tabular}
\end{center}
\end{table}
So it is not a generic problem. But what could it be? I can't decide
where to look, so find a solution or produce a minimal example to display
this behaviour. I actually use this construct with xtable a lot, so
it disturbs me to find this error... which is probably is something
I am doing.
The problem exists for a smaller subsets of this array also; let's take
columns 2, 3 and 4 only:
> model.mat[1:2,2:4]
P-valuebeta_1 P-value
Amount: CP for VF 0.7716153 0.5148616 2.020602e-03
Amount: CP for F 0.1966133 0.8795982 6.058299e-12
> xtable(model.mat[1:2,2:4])
% latex table generated in R 2.5.0 by xtable 1.4-6 package
% Thu Sep 13 14:04:40 2007
\begin{table}[ht]
\begin{center}
\begin{tabular}{}
\hline
& P-value & beta\_1 & P-value \\
\hline
Amount: CP for VF & 0.77 & 0.51 & 0.77 \\
Amount: CP for F & 0.20 & 0.88 & 0.20 \\
\hline
\end{tabular}
\end{center}
\end{table}
Is it a problem with my particular array model.mat or something
I am doing wrong/silly? I don't know where to start.
Thanks all, as always.
P.
> sessionInfo()
R version 2.5.0 (2007-04-23)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=en_AU.UTF-8;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
[7] "base"
other attached packages:
car xtable statmod
"1.2-1" "1.4-6" "1.3.0"
--
Dr Peter Dunn | dunn usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
This email (including any attached files) is confidential an...{{dropped}}
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