Re: [R] OLS standard errors
Please check your statistical methods lecture notes. var(e) has divisor
n-1, and that is not an unbiased estimator of the residual variance when
'e' are residuals. From summary.lm (and you are allowed to read the code)
rdf - n - p
if (is.na(z$df.residual) || rdf != z$df.residual)
warning(residual degrees of freedom in object suggest this is not
an \lm\ fit)
p1 - 1:p
r - z$residuals
f - z$fitted.values
w - z$weights
if (is.null(w)) {
mss - if (attr(z$terms, intercept))
sum((f - mean(f))^2)
else sum(f^2)
rss - sum(r^2)
}
else {
mss - if (attr(z$terms, intercept)) {
m - sum(w * f/sum(w))
sum(w * (f - m)^2)
}
else sum(w * f^2)
rss - sum(w * r^2)
r - sqrt(w) * r
}
resvar - rss/rdf
the correct divisor is n-p. Since p=3 in your example, that explains a 2%
difference in variances and hence a 1% difference in SEs.
On Tue, 26 Feb 2008, Daniel Malter wrote:
Hi,
the standard errors of the coefficients in two regressions that I computed
by hand and using lm() differ by about 1%. Can somebody help me to identify
the source of this difference? The coefficient estimates are the same, but
the standard errors differ.
Simulate data
happiness=0
income=0
gender=(rep(c(0,1,1,0),25))
for(i in 1:100){
happiness[i]=1000+i+rnorm(1,0,40)
income[i]=2*i+rnorm(1,0,40)
}
Run lm()
reg=lm(happiness~income+factor(gender))
summary(reg)
Compute coefficient estimates by hand
x=cbind(income,gender)
y=happiness
z=as.matrix(cbind(rep(1,100),x))
beta=solve(t(z)%*%z)%*%t(z)%*%y
Compare estimates
cbind(reg$coef,beta) ##fine so far, they both look the same
reg$coef[1]-beta[1]
reg$coef[2]-beta[2]
reg$coef[3]-beta[3] ##differences are too small to cause a 1%
difference
Check predicted values
estimates=c(beta[2],beta[3])
predicted=estimates%*%t(x)
predicted=as.vector(t(as.double(predicted+beta[1])))
cbind(reg$fitted,predicted) ##inspect fitted values
as.vector(reg$fitted-predicted) ##differences are marginal
Compute errors
e=NA
e2=NA
for(i in 1:length(happiness)){
e[i]=y[i]-predicted[i] ##for hand-computed regression
e2[i]=y[i]-reg$fitted[i] ##for lm() regression
}
Compute standard error of the coefficients
sqrt(abs(var(e)*solve(t(z)%*%z)))##for hand-computed regression
sqrt(abs(var(e2)*solve(t(z)%*%z))) ##for lm() regression using e2 from
above
##Both are the same
Compare to lm() standard errors of the coefficients again
summary(reg)
The diagonal elements of the variance/covariance matrices should be the
standard errors of the coefficients. Both are identical when computed by
hand. However, they differ from the standard errors reported in
summary(reg). The difference of 1% seems nonmarginal. Should I have
multiplied var(e)*solve(t(z)%*%z) by n and divided by n-1? But even if I do
this, I still observe a difference. Can anybody help me out what the source
of this difference is?
Cheers,
Daniel
-
cuncta stricte discussurus
__
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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.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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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] OLS standard errors
Try multiplying var(e) by n-1 and dividing by n-3 (97 are the degrees of
freedom for the sum of squares error in your example). Then it all matches up
nicely.
Best,
--
Wolfgang Viechtbauer
Department of Methodology and Statistics
University of Maastricht, The Netherlands
http://www.wvbauer.com/
Original Message
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Daniel Malter Sent:
Tuesday, February 26, 2008 08:25 To: 'r-help'
Subject: [R] OLS standard errors
Hi,
the standard errors of the coefficients in two regressions that I
computed by hand and using lm() differ by about 1%. Can somebody help
me to identify the source of this difference? The coefficient
estimates are the same, but the standard errors differ.
Simulate data
happiness=0
income=0
gender=(rep(c(0,1,1,0),25))
for(i in 1:100){
happiness[i]=1000+i+rnorm(1,0,40)
income[i]=2*i+rnorm(1,0,40)
}
Run lm()
reg=lm(happiness~income+factor(gender))
summary(reg)
Compute coefficient estimates by hand
x=cbind(income,gender)
y=happiness
z=as.matrix(cbind(rep(1,100),x))
beta=solve(t(z)%*%z)%*%t(z)%*%y
Compare estimates
cbind(reg$coef,beta) ##fine so far, they both look the same
reg$coef[1]-beta[1]
reg$coef[2]-beta[2]
reg$coef[3]-beta[3] ##differences are too small to cause a 1%
difference
Check predicted values
estimates=c(beta[2],beta[3])
predicted=estimates%*%t(x)
predicted=as.vector(t(as.double(predicted+beta[1])))
cbind(reg$fitted,predicted) ##inspect fitted values
as.vector(reg$fitted-predicted) ##differences are marginal
Compute errors
e=NA
e2=NA
for(i in 1:length(happiness)){
e[i]=y[i]-predicted[i] ##for hand-computed regression
e2[i]=y[i]-reg$fitted[i] ##for lm() regression
}
Compute standard error of the coefficients
sqrt(abs(var(e)*solve(t(z)%*%z))) ##for hand-computed regression
sqrt(abs(var(e2)*solve(t(z)%*%z))) ##for lm() regression using e2
from
above
##Both are the same
Compare to lm() standard errors of the coefficients again
summary(reg)
The diagonal elements of the variance/covariance matrices should be
the standard errors of the coefficients. Both are identical when
computed by hand. However, they differ from the standard errors
reported in summary(reg). The difference of 1% seems nonmarginal.
Should I have multiplied var(e)*solve(t(z)%*%z) by n and divided by
n-1? But even if I do this, I still observe a difference. Can anybody
help me out what the source of this difference is?
Cheers,
Daniel
-
cuncta stricte discussurus
__
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-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] anova repeated measure
Dear R people, I'm new user of R and I'm trying to do a Anova with 3 different tests (intra subject), 6 times of measures (intra subject) and 3 groups (inter subject). I want to obtain an Huynh-Feldt epsilon on accuracy with: anova(lm(acc.t1~gr.dem),test=Spherical) for test 1 # gr.dem is my group variable anova(lm(acc.t2~gr.dem),test=Spherical) for test 2 anova(lm(acc.t3~gr.dem),test=Spherical) for test 3 acc.t1, acc.t2 and acc.t3 was data frames with 6 columns each the results was something like this: Analysis of Variance Table Greenhouse-Geisser epsilon: 0.2746 Huynh-Feldt epsilon:0.2915 Df F num Df den Df Pr(F) G-G Pr H-F Pr (Intercept) 1 7352.7017 6150 1.640e-182 6.894e-52 6.269e-55 gr.dem10.6222 61500.712300.511700.52064 Residuals25 And so what could I do with my epsilon? Previous aov() revealed me that there no effects of my groups but is my 6 times measures factor and my test factor were always significant? Guillaume [[alternative HTML version deleted]] __ 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] Split data.frames depeding values of a column
Hello to all is there a function wich splits a data.frame (column1,column2,column3,) into data1 -(column1,column3) #column2 = 1 data2 -(column1,column3) #column2 = 2 data3 -(column1,column3) #column2 = 3 ... Regards Knut __ 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] Split data.frames depeding values of a column
try split(), e.g., dat - data.frame(x = rnorm(12), y = runif(12), z = rep(1:4, 3)) dat split(dat[1:2], dat$z) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Knut Krueger [EMAIL PROTECTED] To: 'R R-help' [EMAIL PROTECTED] Sent: Tuesday, February 26, 2008 11:22 AM Subject: [R] Split data.frames depeding values of a column Hello to all is there a function wich splits a data.frame (column1,column2,column3,) into data1 -(column1,column3) #column2 = 1 data2 -(column1,column3) #column2 = 2 data3 -(column1,column3) #column2 = 3 ... Regards Knut __ 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. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ 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] How to include the documentation of a function in a Sweave document?
On 26/02/2008 5:30 AM, Thibaut Jombart wrote:
Jean lobry wrote:
Dear R-help,
I would like to include the documentation of an R function in an
*.rnw document processed by Sweave. Because I'm sharing my *.rnw
files with colleagues under Linux and Windows (I'm on Mac OS X),
I would like a pure R solution.
The naive approach doesn't work, because Sweaving this *.rnw
file:
tmp.rnw
\documentclass{article}
\begin{document}
=
?plot
@
\end{document}
tmp.rnw
yields the following LaTeX file on my platform (session info at the end):
tmp.tex
\documentclass{article}
\usepackage{/Library/Frameworks/R.framework/Resources/share/texmf/Sweave}
\begin{document}
\begin{Schunk}
\begin{Sinput}
`?`(plot)
\end{Sinput}
\end{Schunk}
\end{document}
tmp.tex ---
-
in which no Soutput has been generated. Is it possible to redirect the
help output, in a platform-independent way, so that it is included in
the Soutput environment of the LaTeX file?
Best,
Jean
sessionInfo()
R version 2.6.2 (2008-02-08)
i386-apple-darwin8.10.1
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
Maybe a clue: we can use
cat(readLines(as.character(?plot)),sep=\n)
to display the help (here, of plot) directly to the screen. So we could
use something like:
echo=TRUE,print=FALSE,eval=FALSE=
?plot
@
echo=FALSE,print=TRUE,eval=TRUE=
cat(readLines(as.character(?plot)),sep=\n)
@
But this doesn't work (latex compilation error) as weird characters
appear in the produced tex, at some places (tabulations?), like:
_T_h_e _D_e_f_a_
(not sure what it will look like in this email, but emacs reads things
like _^HT_^HH_^He...).
Maybe an encoding problem? I tried specifying different encoding to
readLines, with no luck (latin1, UTF-8). Otherwise, the help appears in
the .tex.
Those are backspaces: it's trying to underline the title. You'd get a
better display if you read the latex version instead. I think you need
to construct the path to it yourself (using system.file() etc.)
Duncan Murdoch
Cheers,
Thibaut.
sessionInfo()
R version 2.6.2 (2008-02-08)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] datasets utils stats graphics grDevices methods base
other attached packages:
[1] phylobase_0.3 nlme_3.1-87ape_2.1-1 adegenet_1.1-0
pixmap_0.4-7
[6] ade4_1.4-5 MASS_7.2-41
loaded via a namespace (and not attached):
[1] grid_2.6.2 lattice_0.17-6 rcompgen_0.1-17 tcltk_2.6.2
[5] tools_2.6.2
__
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] How to include the documentation of a function in a Sweave document?
Jean lobry wrote:
Dear R-help,
I would like to include the documentation of an R function in an
*.rnw document processed by Sweave. Because I'm sharing my *.rnw
files with colleagues under Linux and Windows (I'm on Mac OS X),
I would like a pure R solution.
The naive approach doesn't work, because Sweaving this *.rnw
file:
tmp.rnw
\documentclass{article}
\begin{document}
=
?plot
@
\end{document}
tmp.rnw
yields the following LaTeX file on my platform (session info at the end):
tmp.tex
\documentclass{article}
\usepackage{/Library/Frameworks/R.framework/Resources/share/texmf/Sweave}
\begin{document}
\begin{Schunk}
\begin{Sinput}
`?`(plot)
\end{Sinput}
\end{Schunk}
\end{document}
tmp.tex ---
-
in which no Soutput has been generated. Is it possible to redirect the
help output, in a platform-independent way, so that it is included in
the Soutput environment of the LaTeX file?
Best,
Jean
sessionInfo()
R version 2.6.2 (2008-02-08)
i386-apple-darwin8.10.1
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
Maybe a clue: we can use
cat(readLines(as.character(?plot)),sep=\n)
to display the help (here, of plot) directly to the screen. So we could
use something like:
echo=TRUE,print=FALSE,eval=FALSE=
?plot
@
echo=FALSE,print=TRUE,eval=TRUE=
cat(readLines(as.character(?plot)),sep=\n)
@
But this doesn't work (latex compilation error) as weird characters
appear in the produced tex, at some places (tabulations?), like:
_T_h_e _D_e_f_a_
(not sure what it will look like in this email, but emacs reads things
like _^HT_^HH_^He...).
Maybe an encoding problem? I tried specifying different encoding to
readLines, with no luck (latin1, UTF-8). Otherwise, the help appears in
the .tex.
Cheers,
Thibaut.
sessionInfo()
R version 2.6.2 (2008-02-08)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] datasets utils stats graphics grDevices methods base
other attached packages:
[1] phylobase_0.3 nlme_3.1-87ape_2.1-1 adegenet_1.1-0
pixmap_0.4-7
[6] ade4_1.4-5 MASS_7.2-41
loaded via a namespace (and not attached):
[1] grid_2.6.2 lattice_0.17-6 rcompgen_0.1-17 tcltk_2.6.2
[5] tools_2.6.2
--
##
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
http://adegenet.r-forge.r-project.org/
__
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.
Re: [R] Split data.frames depeding values of a column
Dimitris Rizopoulos schrieb: I hope it helps. yes, thank's a lot Knut __ 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] graphics of profile in longitudinal data
I want to obtain a tool to draw, with R, the profiles associated with longitudinal or repeated measures data. Thanks a lot, Luis Guillermo DÃaz Monroy Profesor Asociado Departamento de EstadÃstica Universidad Nacional de Colombia ¡+!: Para comodidad en la recepcion este mensaje no tiene signos de acentuac ion __ 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] Avoiding overplotting of text.
On Mon, Feb 25, 2008 at 10:36 PM, hadley wickham [EMAIL PROTECTED] wrote: I am plotting some data, and use text() to get variable names next to points on the graph. What is the best way to make sure that these text labels are readable and not overlapping when two datapoints are close? I've tried using jitter(), but the effect is random and doesn't always give a good result. Any suggestions would be most appreciated. Have a look at pointLabel in maptools - http://finzi.psych.upenn.edu/R/library/maptools/html/pointLabel.html -- http://had.co.nz/ Thank you, Hadley. That was a very good tool to find! In conjunction to the regular tricks mentioned by Rickard Cotton, and thigmophobe by Jim Lemon, the problem turned out to be fairly easy. This seem like one of those tasks that is needed fairly frequently, but which is rarely bothered with. Would it be possible to add one of these algorithms as an option to the regular text()? Regards, Gustaf -- Gustaf Rydevik, M.Sci. tel: +46(0)703 051 451 address:Essingetorget 40,112 66 Stockholm, SE skype:gustaf_rydevik __ 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] Help needed to analyse a factorial microarray experiments! Newbie Question
Dear R-users: I am using the package MAANOVA to analyze microarray data and have encountered problems when trying to get interactions. I am a newbie in both, R and maanova, and I do not have good knowledge in statistical methods. I have four effects: Effects Levels Var 2 Ind 2 Trat 2 Time 4 Sample 3 -- biological replicate Spot 4 -- technical replicate I had fitted a model to got all interactions with Samples in random effect (mixed). But, I got an error when I include the Var:ind:Trat and Var:ind:Time in the fitted model. May be I didn't had degree of freedom enough. Then I did an analyses without those interactions (Var:ind:Trat and Var:ind:Time ). Now, I would like to known if are possible to get the interactions with three factors and interactions with four factors. I am interested in known which genes are differentially expressed in Var 1, Ind 2, Trat 1 , Time 3, for example. Could you address me how do I could do that? If I include the technical replicate in the model, can I get those interactions? If you had analysed a experiment like this, could you share your script? Does anyone have experience using MAANOVA commands and is willing to help? Any comments are very welcome! Thank you very much. Leonardo __ 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] How to include the documentation of a function in a Sweave document?
Duncan Murdoch wrote:
Maybe a clue: we can use
cat(readLines(as.character(?plot)),sep=\n)
to display the help (here, of plot) directly to the screen. So we could
use something like:
echo=TRUE,print=FALSE,eval=FALSE=
?plot
@
echo=FALSE,print=TRUE,eval=TRUE=
cat(readLines(as.character(?plot)),sep=\n)
@
But this doesn't work (latex compilation error) as weird characters
appear in the produced tex, at some places (tabulations?), like:
_T_h_e _D_e_f_a_
(not sure what it will look like in this email, but emacs reads things
like _^HT_^HH_^He...).
Maybe an encoding problem? I tried specifying different encoding to
readLines, with no luck (latin1, UTF-8). Otherwise, the help appears
in the .tex.
Those are backspaces: it's trying to underline the title. You'd get
a better display if you read the latex version instead. I think you
need to construct the path to it yourself (using system.file() etc.)
Duncan Murdoch
Thanks for the hint !
So, the code below roughly works:
###
\documentclass{article}
\usepackage{verbatim}
\begin{document}
echo=TRUE,print=FALSE,eval=FALSE=
?plot
@
echo=FALSE,print=FALSE,results=tex=
path - sub(help,latex,as.character(?plot))
path - paste(path,'tex',sep=.)
cat(readLines(path),sep=\n)
@
\end{document}
###
The document compiles with pdflatex but still complains about a bunch of
unknown latex instructions (like \HeaderA, used at the begining of the
included (plot.tex) tex file. The resulting pdf indeed looks a bit nasty.
What command shall we include in the header to have it work?
Best,
Thibaut.
--
##
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
http://adegenet.r-forge.r-project.org/
__
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] Generalized additive model regression with lag
Hi everyone I'm trying to do a semiparametric regression using generalized additive models (mgcv) with lags of the parameter. Does any of you know a package or a methodology for introducing the lags into the model? Thank you very much Sergio Ibarra Espinosa National Center of Environment Technological Metropolitan University Santiago - Chile __ ¿Con Mascota por primera vez? Sé un mejor Amigo. Entra en Yahoo! Respuestas http://es.answers.yahoo.com/info/welcome [[alternative HTML version deleted]] __ 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] AIC and anova, lme
Dear listers, Here we have a strange result we can hardly cope with. We want to compare a null mixed model with a mixed model with one independent variable. lmmedt1-lme(mediane~1, random=~1|site, na.action=na.omit, data=bdd2) lmmedt9-lme(mediane~log(0.0001+transat), random=~1|site, na.action=na.omit, data=bdd2) Using the Akaike Criterion and selMod of the package pgirmess gives the following output: selMod(list(lmmedt1,lmmedt9)) model LL K N2K AIC deltAIC w_i AICc deltAICc w_ic 2 log(1e-04 + transat) 44.63758 4 7.5 -81.27516 0.00 0.65 -79.67516 0.00 0.57 11 43.02205 3 10.0 -80.04410 1.231069 0.35 -79.12102 0.554146 0.43 The usual conclusion would be that the two models are equivalent and to keep the null model for parsimony (!). However, an anova shows that the variable 'log(1e-04 + transat)' is significantly different from 0 in model 2 (lmmedt9) anova(lmmedt9) numDF denDF F-value p-value (Intercept) 120 289.43109 .0001 log(1e-04 + transat) 120 31.18446 .0001 Has anyone an opinion about what looks like a paradox here ? Patrick __ 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] Combining series of variables using identifier
R users, I have df like this a - data.frame(indx =1:20, var1 =rep(c(I20, I40, A50, B60), each=5), var1_lab= rep(c(cat, dog, mouse, horse), each=5), var2 =rep(c(B20, X40, D50, G60), each=5), var2_lab= rep(c(car, bicycle, train, bus), each=5)) str(a) I'd like to create new variables by combining varX and varX_lab like this: a$var1_new - factor(paste(a$var1, a$var1_lab, sep=: )) a$var2_new - factor(paste(a$var2, a$var2_lab, sep=: )) a But, in the real world, I have multiple df:s and many of variables named by the same manner. Is there a possibility to create a function which combines these variables and creates new ones into the same df using varX as an identifier? Many thanks, Lauri __ 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] AIC and anova, lme
Patrick, The likelihoods of two models fitted using REML cannot be compared unless the fixed effects are the same in the two models. On Tue, 2008-02-26 at 14:38 +0100, Patrick Giraudoux wrote: Dear listers, Here we have a strange result we can hardly cope with. We want to compare a null mixed model with a mixed model with one independent variable. lmmedt1-lme(mediane~1, random=~1|site, na.action=na.omit, data=bdd2) lmmedt9-lme(mediane~log(0.0001+transat), random=~1|site, na.action=na.omit, data=bdd2) Using the Akaike Criterion and selMod of the package pgirmess gives the following output: selMod(list(lmmedt1,lmmedt9)) model LL K N2K AIC deltAIC w_i AICc deltAICc w_ic 2 log(1e-04 + transat) 44.63758 4 7.5 -81.27516 0.00 0.65 -79.67516 0.00 0.57 11 43.02205 3 10.0 -80.04410 1.231069 0.35 -79.12102 0.554146 0.43 The usual conclusion would be that the two models are equivalent and to keep the null model for parsimony (!). However, an anova shows that the variable 'log(1e-04 + transat)' is significantly different from 0 in model 2 (lmmedt9) anova(lmmedt9) numDF denDF F-value p-value (Intercept) 120 289.43109 .0001 log(1e-04 + transat) 120 31.18446 .0001 Has anyone an opinion about what looks like a paradox here ? Patrick __ 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-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] How to include the documentation of a function in a Sweave document?
You can use '\include' also:
\documentclass{article}
\begin{document}
\include{/usr/local/lib/R/library/graphics/latex/plot}
%file.path(system.file(package=graphics), latex, plot)
\end{document}
I don't know if there is a way of input file.path in include by Sweave.
On 25/02/2008, Jean lobry [EMAIL PROTECTED] wrote:
Dear R-help,
I would like to include the documentation of an R function in an
*.rnw document processed by Sweave. Because I'm sharing my *.rnw
files with colleagues under Linux and Windows (I'm on Mac OS X),
I would like a pure R solution.
The naive approach doesn't work, because Sweaving this *.rnw
file:
tmp.rnw
\documentclass{article}
\begin{document}
=
?plot
@
\end{document}
tmp.rnw
yields the following LaTeX file on my platform (session info at the end):
tmp.tex
\documentclass{article}
\usepackage{/Library/Frameworks/R.framework/Resources/share/texmf/Sweave}
\begin{document}
\begin{Schunk}
\begin{Sinput}
`?`(plot)
\end{Sinput}
\end{Schunk}
\end{document}
tmp.tex
in which no Soutput has been generated. Is it possible to redirect the
help output, in a platform-independent way, so that it is included in
the Soutput environment of the LaTeX file?
Best,
Jean
sessionInfo()
R version 2.6.2 (2008-02-08)
i386-apple-darwin8.10.1
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
--
Jean R. Lobry([EMAIL PROTECTED])
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo : +33 472 43 27 56 fax: +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/
__
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.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
__
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.
Re: [R] AIC and anova, lme
ian white a écrit : Patrick, The likelihoods of two models fitted using REML cannot be compared unless the fixed effects are the same in the two models. Many thanks for this reminder. Shame on me: it recalls me that this subject may have been already largely discussed on this list. Now, I can search the archives specifically with the REML issue... All the best, Patrick On Tue, 2008-02-26 at 14:38 +0100, Patrick Giraudoux wrote: Dear listers, Here we have a strange result we can hardly cope with. We want to compare a null mixed model with a mixed model with one independent variable. lmmedt1-lme(mediane~1, random=~1|site, na.action=na.omit, data=bdd2) lmmedt9-lme(mediane~log(0.0001+transat), random=~1|site, na.action=na.omit, data=bdd2) Using the Akaike Criterion and selMod of the package pgirmess gives the following output: selMod(list(lmmedt1,lmmedt9)) model LL K N2K AIC deltAIC w_i AICc deltAICc w_ic 2 log(1e-04 + transat) 44.63758 4 7.5 -81.27516 0.00 0.65 -79.67516 0.00 0.57 11 43.02205 3 10.0 -80.04410 1.231069 0.35 -79.12102 0.554146 0.43 The usual conclusion would be that the two models are equivalent and to keep the null model for parsimony (!). However, an anova shows that the variable 'log(1e-04 + transat)' is significantly different from 0 in model 2 (lmmedt9) anova(lmmedt9) numDF denDF F-value p-value (Intercept) 120 289.43109 .0001 log(1e-04 + transat) 120 31.18446 .0001 Has anyone an opinion about what looks like a paradox here ? Patrick __ 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-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] AIC and anova, lme
Patrick Giraudoux patrick.giraudoux at univ-fcomte.fr writes: Dear listers, Here we have a strange result we can hardly cope with. We want to compare a null mixed model with a mixed model with one independent variable. lmmedt1-lme(mediane~1, random=~1|site, na.action=na.omit, data=bdd2) lmmedt9-lme(mediane~log(0.0001+transat), random=~1|site, na.action=na.omit, data=bdd2) ... The usual conclusion would be that the two models are equivalent and to keep the null model for parsimony (!). However, an anova shows that the variable 'log(1e-04 + transat)' is significantly different from 0 in model 2 (lmmedt9) anova(lmmedt9) numDF denDF F-value p-value (Intercept) 120 289.43109 .0001 log(1e-04 + transat) 120 31.18446 .0001 Ask the author of pgirmess to add some checks for the model as anova and stepAIC do: Dieter - library(MASS) library(nlme) fm1 - lme(distance ~ age, data = Orthodont) fm2 - lme(distance ~ age + Sex, data = Orthodont, random = ~ 1) In anova.lme(fm1, fm2) : Fitted objects with different fixed effects. REML comparisons are not meaningful. stepAIC(fm2) Error in extractAIC.lme(fit, scale, k = k, ...) : AIC undefined for REML fit __ 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] predict.rpart question
Dear All, I have a question regarding predict.rpart. I use rpart to build classification and regression trees and I deal with data with relatively large number of input variables (predictors). For example, I build an rpart model like this rpartModel - rpart(Y ~ X, method=class, minsplit =1, minbucket=nMinBucket,cp=nCp); and get predictors used in building the model like this colnamesUsed-unique(rownames(rpartModel$splits)); When later I apply the rpart model to predict the new data I strip the input data from unneccessary columns and only use X columns that exist in colnamesUsed. Unfortunately I get error message like this Error: variable 'X' was fitted with type nmatrix.3522 but type nmatrix.19 was supplied The error message is correct. In the documentation it clearly specifies that the predictors referred to in the right side of formula (object) must be present by name in newdata, but I wonder why, if they are not used? Thanks DK _ Who's friends with who and co-starred in what? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining series of variables using identifier
Hi, if the columns always follow the same order (indx,var#, var#_lab ...), then You could use the column numbers and do the following: 1) CN-colnames(df)[#] (#=colnum of 'var#') 2) df$NEW-(here the expression to create the new variable) 3) colnames(df)[ncol(df)]-c(paste(CN,new,sep=_)) This can easily be built in a loop. Hope this helps, Kimmo Lauri Nikkinen kirjoitti viestissään (26.02.2008): R users, I have df like this a - data.frame(indx =1:20, var1 =rep(c(I20, I40, A50, B60), each=5), var1_lab= rep(c(cat, dog, mouse, horse), each=5), var2 =rep(c(B20, X40, D50, G60), each=5), var2_lab= rep(c(car, bicycle, train, bus), each=5)) str(a) I'd like to create new variables by combining varX and varX_lab like this: a$var1_new - factor(paste(a$var1, a$var1_lab, sep=: )) a$var2_new - factor(paste(a$var2, a$var2_lab, sep=: )) a But, in the real world, I have multiple df:s and many of variables named by the same manner. Is there a possibility to create a function which combines these variables and creates new ones into the same df using varX as an identifier? Many thanks, Lauri __ 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-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] combine vector and data frame on field?
I have managed to create a data frame like this: tsus_same_mean[1:10,] PIDGrpDist PercAlnPercId 1 12638 Acidobacteria 0.0 1.000 1.000 2 87 Actinobacteria 0.0 0.970 0.970 3 92 Actinobacteria 0.008902000 1.000 0.991 4 94 Actinobacteria 0.0 1.000 1.000 5189 Actinobacteria 0.005876733 0.973 0.9676667 6242 Actinobacteria 0.001734200 0.973 0.9715333 7305 Actinobacteria 0.0 0.970 0.970 8307 Actinobacteria 0.0 0.970 0.970 9328 Actinobacteria 0.0 1.000 1.000 10 10689 Actinobacteria 0.0 1.000 1.000 and what I think is a factor like this: tsuPIDCount[1:10] 3 4 5 8 9 12 13 15 18 19 2 2 2 3 4 7 4 2 2 3 Now, I'd like to combine the two. The factor levels in tsuPIDCount corresponds to the field called PID in the data frame. Any hints on how to do this? cbind just adds the vector onto the end, and I couldn't quite figure out if I could somehow say that the level should correspond to the PID. Thanks a lot for your helpin advance:) Karin -- Karin Lagesen, PhD student [EMAIL PROTECTED] http://folk.uio.no/karinlag __ 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] Rcmdr importing excel files
I am using R 2.6.2 on Mac OS X 10.4.9- I would like to import excel files into R with Rcmdr, but This option does not present itself in the file menu. Any help would be greatly appreciated. Stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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] predict.rpart question
Dear All, I have a question regarding predict.rpart. I use rpart to build classification and regression trees and I deal with data with relatively large number of input variables (predictors). For example, I build an rpart model like this rpartModel - rpart(Y ~ X, method=class, minsplit =1, minbucket=nMinBucket,cp=nCp); and get predictors used in building the model like this colnamesUsed-unique(rownames(rpartModel$splits)); When later I apply the rpart model to predict the new data I strip the input data from unneccessary columns and only use X columns that exist in colnamesUsed. Unfortunately I get error message like this Error: variable 'X' was fitted with type nmatrix.3522 but type nmatrix.19 was supplied The error message is correct. In the documentation it clearly specifies that the predictors referred to in the right side of formula (object) must be present by name in newdata, but I wonder why, if they are not used? Thanks DK _ Share what Santa brought you __ 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] combine vector and data frame on field?
Try this: merge(tsus_same_mean, as.data.frame(tsuPIDCount), by.x=PID, by.y=0) On 26/02/2008, Karin Lagesen [EMAIL PROTECTED] wrote: I have managed to create a data frame like this: tsus_same_mean[1:10,] PIDGrpDist PercAlnPercId 1 12638 Acidobacteria 0.0 1.000 1.000 2 87 Actinobacteria 0.0 0.970 0.970 3 92 Actinobacteria 0.008902000 1.000 0.991 4 94 Actinobacteria 0.0 1.000 1.000 5189 Actinobacteria 0.005876733 0.973 0.9676667 6242 Actinobacteria 0.001734200 0.973 0.9715333 7305 Actinobacteria 0.0 0.970 0.970 8307 Actinobacteria 0.0 0.970 0.970 9328 Actinobacteria 0.0 1.000 1.000 10 10689 Actinobacteria 0.0 1.000 1.000 and what I think is a factor like this: tsuPIDCount[1:10] 3 4 5 8 9 12 13 15 18 19 2 2 2 3 4 7 4 2 2 3 Now, I'd like to combine the two. The factor levels in tsuPIDCount corresponds to the field called PID in the data frame. Any hints on how to do this? cbind just adds the vector onto the end, and I couldn't quite figure out if I could somehow say that the level should correspond to the PID. Thanks a lot for your helpin advance:) Karin -- Karin Lagesen, PhD student [EMAIL PROTECTED] http://folk.uio.no/karinlag __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] action executing twice while loading tiles
*hi I aam facing following problem my action executing twice when i try to load the tileslayout page as actionforward success * [[alternative HTML version deleted]] __ 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] R package to perform Horn's parallel analysis
I am seeking information on whether anyone has written code to perform Horn's parallel analysis (a procedure that informs the selection of the proper number of components in PCA) in R. Thank you in advance for any help you can provide. Please respond off-list at the email address below. Karen Douglas *** Karen Douglas, PhD Status of Reading Instruction Institute Associate Director, Research and Policy International Reading Association 444 North Capitol St. NW Suite 524 Washington, DC 20001 [EMAIL PROTECTED] Phone: 202-624-8473 Fax: 202-624-8826 [[alternative HTML version deleted]] __ 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] R package to perform Horn's parallel analysis
Dear Karen, You should find the code you want in the package paran: http://cran.r-project.org/web/packages/paran/index.html And you may be interested in looking at the Multivariate Cran Task view which attempts to catalogue these kinds of things: http://cran.r-project.org/web/views/Multivariate.html Best Paul -=-=-=-=-=-=-=-=-=-=-=-= Paul Hewson Lecturer in Statistics School of Mathematics and Statistics University of Plymouth Drake Circus Plymouth PL4 8AA tel (01752) 232778 (Campus) tel (01752) 764437 (Tamar Science Park) fax (01752) 232780 email: [EMAIL PROTECTED] web: http://www.plymouth.ac.uk/staff/phewson -=-=-=-=-=-=-=-=-=-=-=-= -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Karen Douglas Sent: 26 February 2008 15:28 To: R-help@r-project.org Subject: [R] R package to perform Horn's parallel analysis I am seeking information on whether anyone has written code to perform Horn's parallel analysis (a procedure that informs the selection of the proper number of components in PCA) in R. Thank you in advance for any help you can provide. Please respond off-list at the email address below. Karen Douglas *** Karen Douglas, PhD Status of Reading Instruction Institute Associate Director, Research and Policy International Reading Association 444 North Capitol St. NW Suite 524 Washington, DC 20001 [EMAIL PROTECTED] Phone: 202-624-8473 Fax: 202-624-8826 [[alternative HTML version deleted]] __ 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-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] R package to perform Horn's parallel analysis
ade4 has the testdim function which implements the method proposed in: *S. Dray*. On the number of principal components: A test of dimensionality based on measurements of similarity between matrices. /Computational Statistics and Data Analysis/, 52:2228-2237, 2008. Cheers, Karen Douglas wrote: I am seeking information on whether anyone has written code to perform Horn's parallel analysis (a procedure that informs the selection of the proper number of components in PCA) in R. Thank you in advance for any help you can provide. Please respond off-list at the email address below. Karen Douglas *** Karen Douglas, PhD Status of Reading Instruction Institute Associate Director, Research and Policy International Reading Association 444 North Capitol St. NW Suite 524 Washington, DC 20001 [EMAIL PROTECTED] Phone: 202-624-8473 Fax: 202-624-8826 [[alternative HTML version deleted]] __ 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. -- Stéphane DRAY ([EMAIL PROTECTED] ) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I 43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France Tel: 33 4 72 43 27 57 Fax: 33 4 72 43 13 88 http://biomserv.univ-lyon1.fr/~dray/ __ 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] R package to perform Horn's parallel analysis
see fa.parallel in the psych package At 7:27 AM -0800 2/26/08, Karen Douglas wrote: I am seeking information on whether anyone has written code to perform Horn's parallel analysis (a procedure that informs the selection of the proper number of components in PCA) in R. Thank you in advance for any help you can provide. Please respond off-list at the email address below. Karen Douglas *** Karen Douglas, PhD Status of Reading Instruction Institute Associate Director, Research and Policy International Reading Association 444 North Capitol St. NW Suite 524 Washington, DC 20001 [EMAIL PROTECTED] Phone: 202-624-8473 Fax: 202-624-8826 [[alternative HTML version deleted]] __ 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. -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for statistics: http://personality-project.org/r __ 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] Getting Stangle to tangle Sexpr expressions
Is there a way to get Stangle to print out Sexpr expressions as well as code chunks? I am using weaver and when trying to debug Sweave files, it is sometimes difficult to figure out where the error is. The errors are hardest to find when they are in Sexpr expressions because stepping through the output produced by Stangle reveals nothing. That said, any other suggestions on debugging Sweave would be welcome. __ 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] Custom LaTeX tables
Hello, I am very happy that I have Sweave and R to write my papers. But I still have to do some tables by hand since I have not found out how I can customize the latex tables produced by R further (I mainly use xtable()). Like for instance, I have a table which needs an extra row every few rows as a group header and sometimes I want some extra horizontal lines in the table and also a multicolumn heading. How do you guys cope with such cases, do you set the table by hand in the end or have you found a neat way to deal with this? Many thanks and regards, Werner __ 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] Custom LaTeX tables
Werner Wernersen pensterfuzzer at yahoo.de writes: I am very happy that I have Sweave and R to write my papers. But I still have to do some tables by hand since I have not found out how I can customize the latex tables produced by R further (I mainly use xtable()). Like for instance, I have a table which needs an extra row every few rows as a group header and sometimes I want some extra horizontal lines in the table and also a multicolumn heading. Use latex in package Hmisc, it is very powerful and has options to do what you need. And if something is missing, you can plug in your own table handling such as I did quick and very dirty for ftable: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/115684.html Dieter __ 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] projection.matrix() {popbio} for more than one matrix
Hello,
I am trying to use the projection.matrix( ) function and am following the
example given. I have my data formatted very similar to the test.census
example.
str(AsMi05mat)
`data.frame': 1854 obs. of 6 variables:
$ Tag : num 501 502 503 504 505 506 507 508 509 510 ...
$ Year : int 1995 1995 1995 1995 1995 1995 1995 1995 1995 1995 ...
$ Length : num 34 37 11 24 7 44 4 7 12 20 ...
$ Flowering: int 1 1 0 1 0 1 0 0 0 1 ...
$ Fruits : int 22 22 0 89 0 15 0 0 0 0 ...
$ Stage: Factor w/ 5 levels ,Dead,Dormant,..: 4 4 5 4 5 4 5 5 5 4
...
The example data includes three years but only shows how to create a matrix
from year 1 to 2. I have 13 years of data and would like to automate creating
all matrices for each pair of years.
My code is the following:
AsMi05mat - read.csv(C:/AsMi05mat.csv)
library(popbio)
library(base)
##for(i in 1995:2005){
##AsMitrans.i - subset(merge(AsMi05mat, AsMi05mat, by = Tag, sort =
FALSE),
##Year.x == i Year.y == (i+1) )
##}
AsMi05trans - subset(merge(AsMi05mat, AsMi05mat, by = Tag, sort = FALSE),
Year.x == 1995 Year.y == 1996 )
stages - c(Vegetative, Reproductive, Dead, Dormant)
projection.matrix(AsMi05trans, stage=Stage.x, fate=Stage.y,
sort=stages, TF=TRUE)
I tried a for( ) loop but don't know how to assign new names for each matrix
so end up with only the final comparison (2005 to 2006). I assume an apply( )
function is the way to go but can't see how to do it.
Thanks for any help!
Michelle
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[R] GLM
Hello, I am trying to perform a glm analysis on a 68x13113 matrix (named data.spect). The first column corresponds to the predictor (data.spect[,1]) and the rest to the response variables (data.spect[,2:13113]). When I try this code glmObject - glm(data.spect[,2:13113]~data.spect[,1]) I get the following error: Error: (subscript) logical subscript too long Could anyone help me on solving this problem? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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] wrapper for save function
Of course the second this showed up on R-help, I got rid of the formal
argument 'mydata' and just used ..., which seems to have solved the problem.
Erik
Erik Iverson wrote:
Hello -
I would like to create a wrapper to the 'save' function in the base
package, but have a small problem with the name of the object that is
getting saved in the file. Below is a simple example illustrating my
problem.
## BEGIN SAMPLE R CODE
##
## Here is the wrapper for the save function
##
wrapsave - function(mydata, ...) {
save(mydata, ...)
}
##
## Create a test data.frame and save it
##
testdf - data.frame(a = rnorm(10), b = rnorm(10))
wrapsave(testdf, file = ~/test.Rdata)
##
## remove test data.frame and try to load it
##
rm(testdf)
load(file = ~/test.Rdata)
## END SAMPLE R CODE
After the load function is called, an object called 'testdf' does not
exist in the global environment, but an object called 'mydata' does. I
understand why, but I'd like 'wrapsave' to save the object passed to it
with the name of the object it was called with, in this case 'testdf'.
Is this possible?
Thank you,
Erik Iverson
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[R] using eval-parse-paste in a loop
R-helpers
I have 120 small Excel sheets to read and I am using
library(xlsReadWrite): one example below.
I had hoped to read sheets by looping over a list of numbers in their
name (eg Book1.xls, Book2.xls, etc).
I thought I had seen examples which used eval-parse-paste in this way.
However, I have not been able to get it to work..
1. is this a feasible approach?
2. if not advice would be welcome.
3. Equally, advice about a better approach would also be v. welcome.
I haven't included the data because my failed attempt is
data-independent (and probably more basic).
Michael Anyadike-Danes
# show that read.xls works
test - read.xls(Book1.xls,sheet=1,from=4,colClasses=numeric)
str(test)
'data.frame': 23 obs. of 13 variables:
$ Off.Flows..Thousands.: num 117.19NaN NA 1.43 2.26 ...
$ Off.Flows..Thousands.: num 8.42 NaN NA 0.08 0.11 0.01 0.11 1.59 0.16
0.04 ...
$ Off.Flows..Thousands.: num 20 NaN NA 0.2 0.3 0.02 0.32 4.39 0.41
0.11 ...
$ Off.Flows..Thousands.: num 12.36 NaNNA 0.14 0.27 ...
$ Off.Flows..Thousands.: num 7.59 NaN NA 0.11 0.18 0.01 0.14 1.46 0.23
0.06 ...
$ Off.Flows..Thousands.: num 10.31 NaNNA 0.12 0.23 ...
$ Off.Flows..Thousands.: num 7.55 NaN NA 0.08 0.2 0.01 0.11 1.6 0.23
0.05 ...
$ Off.Flows..Thousands.: num 10.57 NaNNA 0.19 0.21 ...
$ Off.Flows..Thousands.: num 9.36 NaN NA 0.13 0.26 0.02 0.13 2.12 0.27
0.07 ...
$ Off.Flows..Thousands.: num 8.21 NaN NA 0.1 0.19 0.01 0.1 1.9 0.23
0.06 ...
$ Off.Flows..Thousands.: num 9.04 NaN NA 0.13 0.11 0.01 0.17 1.54 0.17
0.05 ...
$ Off.Flows..Thousands.: num 13.42 NaNNA 0.14 0.19 ...
$ Off.Flows..Thousands.: num 0.37 NaN NA NaN 0.01 NaN 0.01 0.05 0.02
NaN ...
### simple minded attempt substituting eval-parse-paste
nam - 1
test -
eval(parse(paste('read.xls(Book',nam,'.xls,sheet=1,from=4,colClasses=
numeric)',sep='')))
Error in file(file, r) : unable to open connection
In addition: Warning message:
In file(file, r) :
cannot open file
'read.xls(Book1.xls,sheet=1,from=4,colClasses=numeric)', reason
'Invalid argument'
### stripping off eval, looking for clues
parse(paste('read.xls(Book',nam,'.xls,sheet=1,from=4,colClasses=numer
ic)',sep=''))
Error in file(file, r) : unable to open connection
In addition: Warning message:
In file(file, r) :
cannot open file
'read.xls(Book1.xls,sheet=1,from=4,colClasses=numeric)', reason
'Invalid argument'
### stripping off parse, still looking for clues
paste('read.xls(Book',nam,'.xls,sheet=1,from=4,colClasses=numeric)',
sep='')
[1] read.xls(\Book1.xls\,sheet=1,from=4,colClasses=\numeric\)
Economic Research Institute of Northern Ireland
Floral Buildings
2-14 East Bridge Street
Belfast BT1 3NQ
Tel: (028) 90727362
Fax: (028) 90319003
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Re: [R] R package to perform Horn's parallel analysis
And also scree.plot psy package. Bruno Falissard INSERM U669, PSIGIAM Paris Sud Innovation Group in Adolescent Mental Health Maison de Solenn 97 Boulevard de Port Royal 75679 Paris cedex 14, France tel : (+33) 6 81 82 70 76 fax : (+33) 1 58 41 28 43 web site : http://perso.wanadoo.fr/bruno.falissard/ -Message d'origine- De : [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] De la part de William Revelle Envoyé : mardi 26 février 2008 16:44 À : Karen Douglas; R-help@r-project.org Objet : Re: [R] R package to perform Horn's parallel analysis see fa.parallel in the psych package At 7:27 AM -0800 2/26/08, Karen Douglas wrote: I am seeking information on whether anyone has written code to perform Horn's parallel analysis (a procedure that informs the selection of the proper number of components in PCA) in R. Thank you in advance for any help you can provide. Please respond off-list at the email address below. Karen Douglas *** Karen Douglas, PhD Status of Reading Instruction Institute Associate Director, Research and Policy International Reading Association 444 North Capitol St. NW Suite 524 Washington, DC 20001 [EMAIL PROTECTED] Phone: 202-624-8473 Fax: 202-624-8826 [[alternative HTML version deleted]] __ 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. -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for statistics: http://personality-project.org/r __ 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-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] using eval-parse-paste in a loop
As Thomas Lumley has frequently noted, eval(parse...)) should generally be
avoided.
You probably want do.call(), as in
## warning: UNTESTED
lapply(numbs,
function(n)do.call(read.xls,list(file=paste(Book,n,.xls,sep=),sheet=1,
...))) ## ... contains the other explicitly names arguments
Note that this would automatically create your list for you.
Cheers,
Bert Gunter
Genentech Nonclinical Statistics
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Erik Iverson
Sent: Tuesday, February 26, 2008 9:29 AM
To: Michael Anyadike-Danes
Cc: r-help@r-project.org
Subject: Re: [R] using eval-parse-paste in a loop
### stripping off eval, looking for clues
parse(paste('read.xls(Book',nam,'.xls,sheet=1,from=4,colClasses=numer
ic)',sep=''))
Error in file(file, r) : unable to open connection
In addition: Warning message:
In file(file, r) :
cannot open file
'read.xls(Book1.xls,sheet=1,from=4,colClasses=numeric)', reason
'Invalid argument'
Your clue is that it looks like parseis unsuccessfully trying to open a
file. Look at ?parse and note the first argument, which you are using
because of positional matching.
You want eval(parse(text = paste(...)))
Best,
Erik Iverson
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[R] Kalman Filter
Hi My name is Vladimir Samaj. I am a student of Univerzity of Zilina. I am trying to implement Kalman Filter into my school work. I have some problems with understanding of R version of Kalman Filter in package stats( functions KalmanLike, KalmanRun, KalmanSmooth,KalmanForecast). 1) Can you tell me how are you seting the initial values of state vector in Kalman Filter? Are you using some method? 2) I have fond function StructTS in stats package. I dont understand, how exactly, are you computing(what method are you using) fitted values which are the output of this function( $fitted ) . In description od this function is that it fit a structural model for a time series by maximum likehood. Does it means, that the fitted values are fit by maximum likehood? If so how does look the likehood function? 3)Finaly, I dont understand smooting problem. What I know is that, if I have t observations of some time serie, I can use function KalmanRun to get estimates of state vector. And if I gain aditional observations of time serie( T t ), I shoud use KalmanSmooth function to smooth estimates of state vector. I dont understand, that how shoud I tell to KalmanSmooth funtion that I allready did filtering and it shoud use the values from filtering to smoothing. I will be glad if you help me. I hope that my folmulations were correct. Thank you very much. [[alternative HTML version deleted]] __ 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] Reading a file created with Fortran
Dennis Fisher fisher at plessthan.com writes: Colleagues, I am trying to read a file written by Fortran. Several lines of the file are pasted below: Perhaps read.fwf is what you want? (fwf stands for fixed width format). You would have to work out the field widths, but it would seem to be pretty straightforward). [A little bit of extra verbiage will make gmane happier ...] Ben Bolker __ 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] Kenward-Roger correction in lme
On Mon, Feb 25, 2008 at 1:46 PM, Peter Dalgaard [EMAIL PROTECTED] wrote: Ben Bolker wrote: stian at mail.rockefeller.edu stian at mail.rockefeller.edu writes: Hi,I am wondering how to conduct Kenward-Roger correction in the linear mixed model using R. Any idea? Thanks a lot, Suyan Not really possible, I'm afraid. Having already invested a huge amount of time in making lme4 available (and this is the cutting-edge version of linear mixed models for R), Doug Bates has declined to spend effort implementing K-R because (1) he's not convinced of the appropriateness of adjusting F-distribution degrees of freedom in this way, (2) he doesn't think that the K-R algorithm will be feasible for the sorts of large-data problems he's interested in, (3) [can't find the reference] he finds the correspondence between K-R's notation and his difficult. Regarding (2), it is more an issue of the structure of the model than of the size of the data set. One of the big differences between the lme4 package and the nlme package, or other software for fitting linear mixed models, is that lme4 is designed to handle models with non-nested random effects. The random effects can be completely crossed, such as in an experiment where a sample of subjects are each exposed to the same selection of items and the model incorporates random effects for both subject and item, or partially crossed where annual test scores may be associated with both the student taking the test and the teacher for the student that year. It has been a while since I looked at the Kenward-Roger formulation but my recollection is that it would be difficult to extend the calculations to models with non-nested random effects. I am not opposed to the method in principle - it's just that I am not about to have the time to work on it myself in the foreseeable future. If someone else wants to work it out then I say go for it. The last one could be due to me rather than Doug, and certainly, it is just an obstacle rather than anything prohibitive in itself. I tend to think that (2) is nontrivial rather than infeasible, but it is true that the K-R formulas depend on items like the covariance matrix (say, Sigma) for the entire data set, which is at best implicitly available in large-data problems. Whether or not it would be possible to work with implicit representations of Sigma is what is difficult to see because of the notational differences (it's been a while, but my recollection is that Doug uses Sigma for a different purpose, and there are a couple of similarly confusing notational switches). Beyond notation there is a question of emphasis in the formulation of the model. Most of the theory of linear mixed models focuses on the marginal distribution of the response random variable. I have found it more useful to consider the distribution of the random effects, conditional on the observed values of the response. My latest attempts to explain the computational methods (slides at http://www.stat.wisc.edu/~bates/2008-02-22-Emory.pdf) examine the conditional distribution of the random effects - in particular, the unnormalized conditional density of the random effects. In the case of a linear mixed model the logarithm of this density is a quadratic form. For a generalized linear mixed model or a nonlinear mixed model or a generalized nonlinear mixed model the conditional density can be optimized via a penalized IRLS or penalized NLS algorithm to obtain the conditional means and the conditional variance-covariance matrix. I consider a linear transformation, U, of the random effects, B, for which Var(U) = sigma^2 I. By transforming to U I can incorporate the effect of the variance component parameters into a (sparse) model matrix A rather than into the variance-covariance matrix. The linear predictor that was expressed as eta = X beta + Z b is now X beta + A' u where A is the transpose of a sparse model matrix that is derived from Z. Evaluation of the deviance and related quantities hinges on calculating the sparse Cholesky factor L that satisfies LL' = AA' + I. (There is also a fixed permutation matrix. P, involved in that expression but it doesn't have any effect on the theory - although it can have a tremendous effect on the speed of the calculation.) One reason for expressing the model in this way is because it is exactly the way that the calculations are carried out. There are slots named X, Zt (for Z-transpose), A and L in the object returned by lmer and they have exactly the meanings shown above. It is possible to get an expression for the marginal variance-covariance of the response vector but it will be an n by n matrix and will only have nice sparsity patterns for models with nested random effects. For models with non-nested random effects this is potentially a dense n by n matrix and you really don't want to try working with that for large data sets. It may be
[R] Subsetting within xyplot()
All, I'm having problems w/ a simple attempt to subset an xyplot. The first plot below is a plot of y versus x for certain values of a third categorical variable z. Now I'd like to further restrict this to certain values of variable y. Neither of the two attempts below work. Any suggestions much appreciated. (note: I don't want to merely use ylim since I have a loess plot and I want this to be calculated w/ the restricted values). Thanks, David y = c( 0.4, 0.6, -0.1, 0.3, 0.3, -0.2, 0.7, 0.7, 0.2, 0.0, 0.9, -0.1, 0.6, -1.1, 0.8, -1.0, 0.4, 0.1, 0.7, -0.2, -0.1, -0.1, 2.2, 0.7, 1.1, 0.2, -0.2, -0.9, 0.4, 0.1, -0.3, -0.4) x = c(4.1000, 4.9600, 1.2000, 3.9000, 3.1875, 1.9000, 1.8625, 0.7650, 1.5750, 2.4700, 1.6250, 1.5500, 2.3125, 1.3125, 1.0600, -0.5500, 1.1000, 0.0200, -0.0375, 3.4600, 2.5250, 2.0950, 0.8000, 1.6050, -0.4150, -0.7300, 1.1550, 1.4850, 2.2000, 2.2500, 0.6000, 2.1000) junk.frm = data.frame(x, y, z = rep(c(D, P), 16)) xyplot(y ~ x , data = junk.frm[junk.frm$z ==D,], type = c(g, p, smooth), pch = 20) xyplot(y ~ x , data = junk.frm[junk.frm$z ==D,], type = c(g, p, smooth), pch = 20, , subset = junk.frm[junk.frm$y 2, ]) Error in tmp[subset] : invalid subscript type 'list' xyplot(y ~ x , data = junk.frm[junk.frm$z ==D,], type = c(g, p, smooth), pch = 20, data = junk.frm[junk.frm$y 2 junk.frm$z ==D, ]) Error in xyplot(y ~ x, data = junk.frm[junk.frm$z == D, ], type = c(g, : formal argument data matched by multiple actual arguments __ 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] Subsetting within xyplot()
Try this: xyplot(y ~ x , data = junk.frm, type = c(g, p,smooth), pch=20, subset=z==D y 2) On 26/02/2008, David Afshartous [EMAIL PROTECTED] wrote: All, I'm having problems w/ a simple attempt to subset an xyplot. The first plot below is a plot of y versus x for certain values of a third categorical variable z. Now I'd like to further restrict this to certain values of variable y. Neither of the two attempts below work. Any suggestions much appreciated. (note: I don't want to merely use ylim since I have a loess plot and I want this to be calculated w/ the restricted values). Thanks, David y = c( 0.4, 0.6, -0.1, 0.3, 0.3, -0.2, 0.7, 0.7, 0.2, 0.0, 0.9, -0.1, 0.6, -1.1, 0.8, -1.0, 0.4, 0.1, 0.7, -0.2, -0.1, -0.1, 2.2, 0.7, 1.1, 0.2, -0.2, -0.9, 0.4, 0.1, -0.3, -0.4) x = c(4.1000, 4.9600, 1.2000, 3.9000, 3.1875, 1.9000, 1.8625, 0.7650, 1.5750, 2.4700, 1.6250, 1.5500, 2.3125, 1.3125, 1.0600, -0.5500, 1.1000, 0.0200, -0.0375, 3.4600, 2.5250, 2.0950, 0.8000, 1.6050, -0.4150, -0.7300, 1.1550, 1.4850, 2.2000, 2.2500, 0.6000, 2.1000) junk.frm = data.frame(x, y, z = rep(c(D, P), 16)) xyplot(y ~ x , data = junk.frm[junk.frm$z ==D,], type = c(g, p, smooth), pch = 20) xyplot(y ~ x , data = junk.frm[junk.frm$z ==D,], type = c(g, p, smooth), pch = 20, , subset = junk.frm[junk.frm$y 2, ]) Error in tmp[subset] : invalid subscript type 'list' xyplot(y ~ x , data = junk.frm[junk.frm$z ==D,], type = c(g, p, smooth), pch = 20, data = junk.frm[junk.frm$y 2 junk.frm$z ==D, ]) Error in xyplot(y ~ x, data = junk.frm[junk.frm$z == D, ], type = c(g, : formal argument data matched by multiple actual arguments __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] combining 40,000 with 40,000 data frame (different tact)
I have not been able to find anything to do what I want, so I am going to tact to the left. I have twp continuous time series for two years with the same fourteen variables. I would like to simply append the second year to the first. They both have the same column headings etc. Just like tapping two pieces of paper together for a long number series. Thanks Stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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] Summing up diagonals w/o for-loop
Dear R-users,
is there any way to sum up the elements of the diagonals of a matrix
without using a for-loop? While there is a simple way over rows and
columns, I don't see a straightforward multiplication for the diagonals,
am I too demanding? Or, more likely, I'm lack some algebra trick? Is
there any R-function that can deal with this problem w/o loop?
Actually I would need to sum up just the upper diagonals.
Here a simple, but general, example for presenting the problem.
Thanks in advance for any help,
Carlo Giovanni Camarda
m - 7
n - 5
mat - matrix(1:35, n, m)
ones.r - rep(1,n)
ones.c - rep(1,m)
# sum over the rows
sum.r - mat%*%ones.c
# sum over the cols
sum.c - t(mat)%*%ones.r
# sum over the diags
sum.d - numeric(m+n-1)
sum.d[1] - mat[n,1]
sum.d[m+n-1] - mat[1,m]
for(i in 2:n){
sum.d[i] - sum(diag(mat[(n+1-i):n,1:i]))
}
for(i in 2:(m-1)){
sum.d[i+n-1] - sum(diag(mat[,i:m]))
}
--
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[R] Cryptic error message using RuleFit
Hello LIST, In using Rulefit I;ve bee nabel to fit a model using rulefit without incident. However, when trying to use intnull and interact things go astray. rf=rulefit(x,N, cat.vars=H, not.used=c(G,T),huber=0.9,path.speed=1); [snip] RuleFit model 2/26/2008 2:17p ave(abs(error)) terms path steps 84.16 110 8301 null.mod - intnull() [snip building trees and fitting rules] Warning messages: 1: In system(mv -f rulefit.mod mod.sv) : mv not found 2: In system(mv -f rulefit.sum sum.sv) : mv not found 3: In system(mv -f rfout out.sv) : mv not found 4: In system(mv -f train.y train.sv) : mv not found 5: In system(mv -f mod.sv rulefit.mod) : mv not found 6: In system(mv -f sum.sv rulefit.sum) : mv not found 7: In system(mv -f train.sv train.y) : mv not found 8: In system(mv -f out.sv rfout) : mv not found int = interact(c(A, M, H, P), null.mod) Error in interact(c(A, M, H, P), null.mod) : input null.mods inconsistent with RuleFit home directory model. Something is amiss with the directory but it looks fine (the files from rf are present and where they should be based on the installation notes) and I can not figure out what the missing piece here is. Any insight appreciated. Thanks, Christopher __ 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] How to include the documentation of a function in a Sweave document?
Dear all,
thanks for your suggestions. I like the idea of including directly
the LaTeX file corresponding to the targeted topic, however, my
understanding from the reading of ?help is that these LaTeX files
are not always available, depending on the build of R.
I found a solution that works well enough for me by removing
the backslashes from the help file this way:
tmp.rnw
\documentclass{article}
\begin{document}
mypager,echo=F,eval=T=
mypager - function(..., header = rep(, nfiles),
title = R Information, delete.file = FALSE){
args - list(...)
sanitize - function(strings){
f - function(x){
x.raw - charToRaw(x)
backspaces - which(x.raw == charToRaw('\b'))
if(length(backspaces) 0){
x.raw - x.raw[-c(backspaces, backspaces - 1)] # remove _\b
}
rawToChar(x.raw[x.raw = as.raw(20)]) # remove non-printable ASCII
}
res - sapply(strings, f)
names(res) - NULL
return(res)
}
help.out - lapply(args[[1]], readLines)
help.out - lapply(help.out, sanitize)
lapply(help.out, cat, sep = \n)
}
@
echo=T,print=F,eval=F, keep.source=T=
?plot
@
echo=F,print=T,eval=T=
help(plot, chmhelp = FALSE, htmlhelp = FALSE, pager = mypager)
@
\end{document}
tmp.rnw
This works well for me when I'm Sweaving the file from an R
session in the CLI interface in a terminal, but not when I'm
Sweaving the file from the R GUI for the Mac (the function
mypager is not called despite pager = mypager when calling
the help function, don't understand why).
The PDF looks like this:
http://pbil.univ-lyon1.fr/members/lobry/tmp/tmp.pdf
Thanks again for your help,
Best,
Jean
--
Jean R. Lobry([EMAIL PROTECTED])
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo : +33 472 43 27 56 fax: +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/
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[R] Obtaining values from adfstat objects
Hi, I'm using the ADF.test function in the uroot package to obtain an adfstat-class object. I'm wondering how I can extract the values (test statistic, p value, etc.) from this class, since it doesn't seem to have usual values. I get the following summary, but I'm not sure how to do anything with these values -- how can I put the number into another variable? - -- - -- Augmented Dickey Fuller test - -- - -- Null hypothesis: Unit root. Alternative hypothesis: Stationarity. ADF statistic: Estimate Std. Error t value Pr(|t|) adf.reg -0.997 0.123 -8.074 0.01 Lag orders: Number of available observations: 67 Warning message: In interpolpval(code = code, stat = adfreg[, 3], N = N) : p-value is smaller than printed p-value Thanks. -- View this message in context: http://www.nabble.com/Obtaining-values-from-adfstat-objects-tp15699940p15699940.html Sent from the R help mailing list archive at Nabble.com. __ 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] Obtaining values from adfstat objects
Try str(yourobject) to see the structure of the object. If there were a value called, say, p.value, you could then do: myvar - yourobject$p.value This is just general advice, I don't know the specifics of the package you mention, but try this first. Best, Erik Iverson Matt33 wrote: Hi, I'm using the ADF.test function in the uroot package to obtain an adfstat-class object. I'm wondering how I can extract the values (test statistic, p value, etc.) from this class, since it doesn't seem to have usual values. I get the following summary, but I'm not sure how to do anything with these values -- how can I put the number into another variable? - -- - -- Augmented Dickey Fuller test - -- - -- Null hypothesis: Unit root. Alternative hypothesis: Stationarity. ADF statistic: Estimate Std. Error t value Pr(|t|) adf.reg -0.997 0.123 -8.074 0.01 Lag orders: Number of available observations: 67 Warning message: In interpolpval(code = code, stat = adfreg[, 3], N = N) : p-value is smaller than printed p-value Thanks. __ 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] Obtaining values from adfstat objects
Thanks for the tip, Erik. I did check, but didn't see any $... elements to choose from. For comparison, I checked another object class (lm) with the str function, and it clearly showed $coefficients, $residuals, etc.. So it would seem that the usual approach doesn't work with adfstat objects... -- View this message in context: http://www.nabble.com/Obtaining-values-from-adfstat-objects-tp15699940p15700174.html Sent from the R help mailing list archive at Nabble.com. __ 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] Summing up diagonals w/o for-loop
Camarda, Carlo Giovanni wrote:
Dear R-users,
is there any way to sum up the elements of the diagonals of a matrix
without using a for-loop? While there is a simple way over rows and
columns, I don't see a straightforward multiplication for the diagonals,
am I too demanding? Or, more likely, I'm lack some algebra trick? Is
there any R-function that can deal with this problem w/o loop?
Actually I would need to sum up just the upper diagonals.
Here a simple, but general, example for presenting the problem.
Thanks in advance for any help,
Carlo Giovanni Camarda
m- 7
n- 5
mat- matrix(1:35, n, m)
ones.r- rep(1,n)
ones.c- rep(1,m)
# sum over the rows
sum.r- mat%*%ones.c
# sum over the cols
sum.c- t(mat)%*%ones.r
# sum over the diags
sum.d- numeric(m+n-1)
sum.d[1]- mat[n,1]
sum.d[m+n-1]- mat[1,m]
for(i in 2:n){
sum.d[i]- sum(diag(mat[(n+1-i):n,1:i]))
}
for(i in 2:(m-1)){
sum.d[i+n-1]- sum(diag(mat[,i:m]))
}
If we have 'mat':
mat
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,]16 11 16 21 26 31
[2,]27 12 17 22 27 32
[3,]38 13 18 23 28 33
[4,]49 14 19 24 29 34
[5,]5 10 15 20 25 30 35
You can use:
rowSums(mat)
[1] 112 119 126 133 140
and:
colSums(mat)
[1] 15 40 65 90 115 140 165
for your initial steps, rather than the matrix multiplication. See
?colSums for more information.
There may be a better way than this, but one approach for the diagonals
in the order you want is to split() the matrix into it's constituent
diagonals based upon subsetting using the row() and col() values. This
yields a list:
split(mat, col(mat) - row(mat))
$`-4`
[1] 5
$`-3`
[1] 4 10
$`-2`
[1] 3 9 15
$`-1`
[1] 2 8 14 20
$`0`
[1] 1 7 13 19 25
$`1`
[1] 6 12 18 24 30
$`2`
[1] 11 17 23 29 35
$`3`
[1] 16 22 28 34
$`4`
[1] 21 27 33
$`5`
[1] 26 32
$`6`
[1] 31
Then we can use sapply() to sum() over the list elements:
sum.d
[1] 5 14 27 44 65 90 115 100 81 58 31
sapply(split(mat, col(mat) - row(mat)), sum)
-4 -3 -2 -1 0 1 2 3 4 5 6
5 14 27 44 65 90 115 100 81 58 31
If you want to sum the diagonals the other way replace the '-' in the
second argument in split() with a '+'.
See ?split, ?sapply, ?row and ?col for more information.
HTH,
Marc Schwartz
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[R] numeric format
Hi! I'm an R newbie and this should be a trivial problem, but I can't make it work and cannot find what I'm doing wrong in the literature. I entered the the command: table-data.frame(x, scientific=F, digits=4) table This prints a column of x with 16 useless decimal places after the decimal point. Also, it prints an unwanted index number (1-20) in the left column. How do I get rid of the index column and how do I control the number of decimal places? Thanks in advance. CHV -- View this message in context: http://www.nabble.com/numeric-format-tp15700452p15700452.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lrm error message
I'm trying to learn how to use the lrm() function by simulating data using an old dataset but it's giving me an error I don't understand: (nst$regular already exists) nst$regular-as.ordered(nst$regular) nst$age-rnorm(n=942,mean=43.20488,sd=17.03) nst$age-round(age,digits=0) regform-regular~age reglrm-lrm(regform,nst) summary(reglrm) Error in summary.Design(reglrm) : adjustment values not defined here or with datadist for age ive looked at the help file for lrm and thought it was simple enough but apparently not. any help would be greatly appreciated. [[alternative HTML version deleted]] __ 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] combining 40,000 with 40,000 data frame (different tact)
stephen sefick schreef: I have not been able to find anything to do what I want, so I am going to tact to the left. I have twp continuous time series for two years with the same fourteen variables. I would like to simply append the second year to the first. They both have the same column headings etc. Just like tapping two pieces of paper together for a long number series. Thanks Stephen ?rbind cheers, Paul -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +31302535773 Fax:+31302531145 http://intamap.geo.uu.nl/~paul __ 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] combining 40,000 with 40,000 data frame (different tact)
?rbind On 2/26/08, stephen sefick [EMAIL PROTECTED] wrote: I have not been able to find anything to do what I want, so I am going to tact to the left. I have twp continuous time series for two years with the same fourteen variables. I would like to simply append the second year to the first. They both have the same column headings etc. Just like tapping two pieces of paper together for a long number series. Thanks Stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? Tell me what you want to do, not how you want to do it. __ 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] Set without argument
Hi Martin
What do you think of the following code ?
A - 1
imputeMyObj - function(x){
xImp - 3 #Calcul for Imputation of x
nam-deparse(substitute(x))
assign(nam,xImp,envir=parent.frame())
}
imputeMyObj(A)
A
I guess it is not usual, but do you think it is 'bad' programming or
will have side effect that I do not see ?
Christophe
Christophe Genolini [EMAIL PROTECTED] writes:
Hi the list,
I am defining S4 objet. Is it possbile to define a method that change
the slot of an object without using - ?
My object contain a numeric and a matrix. At some point, I would like to
impute the missing value in the matrix. So I would like to use something
like :
-
setClass(MyObj,representation(time=numeric,traj=matrix))
a - new(MyObj,time=3,traj=matrix(c(1:6,NA,8:12),ncol=3))
imputeMyObj(a)
-
Hi Christophe --
The 'usual' way to write the above code is
a - imputeMyObj(a)
with imputeMyObj designed to take a 'MyObj' as it's argument, and
return a modified 'MyObj' (that the user can assign to 'a', if they
like). Inside imputeMyObj, the developer would, in the end, write
something like
impuateMyObj - function(obj) {
# calculate imputed values 'imp'
slot(obj, traj) - imp
obj
}
A better design would have a 'setter' method, minimally
setGeneric(traj-,
+function(object, ..., value) standardGeneric(traj-))
[1] traj-
setReplaceMethod(traj,
+ signature=signature(
+object=MyObj,
+value=matrix),
+ function(object, ..., value) {
+ slot(object, traj) - value
+ object
+ })
[1] traj-
and then the impute code would have
impuateMyObj - function(obj) {
# calculate imputed values 'imp'
traj(obj) - imp
obj
}
It's possible to design 'MyObj' so that it can be modified in-place
(e.g., storing data in a slot of class 'environment', which has
reference-like behavior) but this will probably surprise both you and
the user.
Martin
I find 'setTime-' to change le slot time, but it can not work in the
case of imputeMyObs since this mehod does not need a value...
Any solution ?
Thanks
Christophe
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Re: [R] numeric format
Without knowing what your 'x' is, it's hard to see what is happening that you don't like. Your data.frame function creates a data.frame containing columns scientific and digits, equal to FALSE and 4 for all rows, respectively. Is that what you want? cvandy wrote: Hi! I'm an R newbie and this should be a trivial problem, but I can't make it work and cannot find what I'm doing wrong in the literature. I entered the the command: table-data.frame(x, scientific=F, digits=4) table This prints a column of x with 16 useless decimal places after the decimal point. Also, it prints an unwanted index number (1-20) in the left column. How do I get rid of the index column and how do I control the number of decimal places? Thanks in advance. CHV __ 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] Plot Principal component analysis
If your samples are in the specified order (i.e. first 100 from group A and remaining from group B) you can try the following in your plot call: plot(..., col=c(red, blue)[c(rep(100, 1), rep(15, 2))]) -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of SNN Sent: Tuesday, February 26, 2008 4:11 PM To: r-help@r-project.org Subject: [R] Plot Principal component analysis Hi, I have matrix of 300,000*115 (snps*individual). I ran the PCA on the covariance matrix which has a dimention oof 115*115. I have the first 100 individuals from group A and the rest of 15 individuals from group B. I need to plot the data in two and 3 dimentions with respect to PC1 and PC2 and (in 3D with respect to PC1, PC2 and PC3). I do not know how to have the plot ploting the first 100 points corresponding to group A in red (for example) and the rest of the 15 points in Blue? i.e I want the each group in a diffrent color in the same plot. I appreciate if someone can help. Thanks, -- View this message in context: http://www.nabble.com/Plot-Principal-component-analysis-tp1570 0123p15700123.html Sent from the R help mailing list archive at Nabble.com. __ 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-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] numeric format
Those are parameter to 'print'; what you want is something like: x - data.frame(a=runif(10)) print(x) a 1 0.713705394 2 0.715496609 3 0.629578524 4 0.184360667 5 0.456639418 6 0.008667156 7 0.260985437 8 0.270915631 9 0.689128652 10 0.302484280 print(x,scientific=F, digits=4) a 1 0.713705 2 0.715497 3 0.629579 4 0.184361 5 0.456639 6 0.008667 7 0.260985 8 0.270916 9 0.689129 10 0.302484 On 2/26/08, cvandy [EMAIL PROTECTED] wrote: Hi! I'm an R newbie and this should be a trivial problem, but I can't make it work and cannot find what I'm doing wrong in the literature. I entered the the command: table-data.frame(x, scientific=F, digits=4) table This prints a column of x with 16 useless decimal places after the decimal point. Also, it prints an unwanted index number (1-20) in the left column. How do I get rid of the index column and how do I control the number of decimal places? Thanks in advance. CHV -- View this message in context: http://www.nabble.com/numeric-format-tp15700452p15700452.html Sent from the R help mailing list archive at Nabble.com. __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? Tell me what you want to do, not how you want to do it. __ 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] Multiple lines with a different color assigned to each line
I am not sure if I completely understand but would
something like this work? (not tested)
points( col=i)
lines ( col=i=1)
--- Judith Flores [EMAIL PROTECTED] wrote:
Dear R-experts,
I want to assign different colors to groups of
points, lines and segments in a plot.
I have a vector(dat$tx) that is going to have a
different number of levels every time the user wants
to plot a set of data. The number of lines is going
to
be equal to the number of levels of the vector
mentioned.
What I have so far is this:
plot(1,1,type=n)
for (i in dat$tx) {
points(summ$timep[summ$tx==i],summ$mn[summ$tx==i])
lines(summ$timep[summ$tx==i],summ$mn[summ$tx==i])
}
How can I assign different colors to the points and
lines?
Thank you in advance for any help,
Judith
Be a better friend, newshound, and
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[[elided Yahoo spam]]
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Re: [R] Plot Principal component analysis
Sorry, it should have been: col = c(red, blue)[c(rep(1, 100), rep(2, 15))] -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Christos Hatzis Sent: Tuesday, February 26, 2008 4:46 PM To: 'SNN'; r-help@r-project.org Subject: Re: [R] Plot Principal component analysis If your samples are in the specified order (i.e. first 100 from group A and remaining from group B) you can try the following in your plot call: plot(..., col=c(red, blue)[c(rep(100, 1), rep(15, 2))]) -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of SNN Sent: Tuesday, February 26, 2008 4:11 PM To: r-help@r-project.org Subject: [R] Plot Principal component analysis Hi, I have matrix of 300,000*115 (snps*individual). I ran the PCA on the covariance matrix which has a dimention oof 115*115. I have the first 100 individuals from group A and the rest of 15 individuals from group B. I need to plot the data in two and 3 dimentions with respect to PC1 and PC2 and (in 3D with respect to PC1, PC2 and PC3). I do not know how to have the plot ploting the first 100 points corresponding to group A in red (for example) and the rest of the 15 points in Blue? i.e I want the each group in a diffrent color in the same plot. I appreciate if someone can help. Thanks, -- View this message in context: http://www.nabble.com/Plot-Principal-component-analysis-tp1570 0123p15700123.html Sent from the R help mailing list archive at Nabble.com. __ 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-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-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] numeric format
Can you give a working example of what is happening and explain what is x? With a simple x vector of x - rnorm(20, 5, 2) I don't get anything like what you seem to be getting. My code === x - rnorm(20, 5, 2) table-data.frame(x, scientific=F, digits=4) table === The numbers on the left are simply line numbers that are automatically printed when you are printing a dataframe to the screen. I don't see any way to supress them for a simple command such as your table You might want to have a look at print and print.default to address the digits problem By the way, table is a reserved word in R and probably should not be used as a name for a data.frame. --- cvandy [EMAIL PROTECTED] wrote: Hi! I'm an R newbie and this should be a trivial problem, but I can't make it work and cannot find what I'm doing wrong in the literature. I entered the the command: table-data.frame(x, scientific=F, digits=4) table This prints a column of x with 16 useless decimal places after the decimal point. Also, it prints an unwanted index number (1-20) in the left column. How do I get rid of the index column and how do I control the number of decimal places? Thanks in advance. CHV -- View this message in context: http://www.nabble.com/numeric-format-tp15700452p15700452.html Sent from the R help mailing list archive at Nabble.com. __ 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-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] Raw histogram plots
Hello I need to plot a histogram, but insted of using bars, I'd like to plot the data points. I've been doing it like this so far: h - hist(x, plot = F) plot(y = x$counts / sum(x$counts), x = x$breaks[2:length(x$breaks)], type = p, log = xy) Sometimes I want to have a look at the raw data (avoiding any kind of binning). When x only contains integers, it's easy to just use bins of size 1 when generating h with breaks = seq(0, max(x)). Is there any way to do something similar when x consists of fractional data? What I'm doing is setting a small bin length (for example, breaks = seq(0, 1, by = 1e-6), but there's still a chance that points will be grouped in a single bin. Is there a better way to do this kind of raw histogram plotting? Thanks, Andre __ 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] Raw histogram plots
take a look at ?stem There is still a place for handtools in the age of integrated circuits. Of course, avoiding binning isn't really desirable. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Feb 26, 2008, at 4:10 PM, Andre Nathan wrote: Hello I need to plot a histogram, but insted of using bars, I'd like to plot the data points. I've been doing it like this so far: h - hist(x, plot = F) plot(y = x$counts / sum(x$counts), x = x$breaks[2:length(x$breaks)], type = p, log = xy) Sometimes I want to have a look at the raw data (avoiding any kind of binning). When x only contains integers, it's easy to just use bins of size 1 when generating h with breaks = seq(0, max(x)). Is there any way to do something similar when x consists of fractional data? What I'm doing is setting a small bin length (for example, breaks = seq(0, 1, by = 1e-6), but there's still a chance that points will be grouped in a single bin. Is there a better way to do this kind of raw histogram plotting? Thanks, Andre __ 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-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] numeric format
On 27/02/2008, at 11:01 AM, John Kane wrote:
Can you give a working example of what is happening
and explain what is x?
With a simple x vector of x - rnorm(20, 5, 2)
I don't get anything like what you seem to be getting.
My code
===
x - rnorm(20, 5, 2)
table-data.frame(x, scientific=F, digits=4)
table
===
The numbers on the left are simply line numbers that
are automatically printed when you are printing a
dataframe to the screen. I don't see any way to
supress them for a simple command such as your
table
You might want to have a look at print and
print.default to address the digits problem
snip
I have often wanted to suppress these row numbers and for that purpose
wrote the following version of print.data.frame() which I keep in a
local package (that I have set up to be loaded automatically on startup)
which masks the system version of print.data.frame():
print.data.frame - function (x, ..., digits = NULL, quote = FALSE,
right = TRUE, srn = FALSE)
{
if (length(x) == 0) {
cat(NULL data frame with, length(row.names(x)), rows\n)
}
else if (length(row.names(x)) == 0) {
print.default(names(x), quote = FALSE)
cat(0 rows (or 0-length row.names)\n)
}
else {
if (!is.null(digits)) {
op - options(digits = digits)
on.exit(options(op))
}
rowlab - if (srn)
rep(, nrow(x))
else row.names(x)
prmatrix(format(x), rowlab = rowlab, ..., quote = quote,
right = right)
}
invisible(x)
}
The ``srn'' argument means ``suppress row numbers''; it defaults to
FALSE so by default
the behaviour of my print.data.frame() is the same as that of the
system print.data.frame().
To suppress the row numbers you can say, e.g.
print(junk,srn=TRUE)
Note to Young Players --- you need only type ``print'' in the above,
r.t. ``print.data.frame'',
since print.data.frame() is a ``method'' for print().
I once suggested to an R Core person that my version of
print.data.frame() be adopted as the
system version, but was politely declined.
cheers,
Rolf Turner
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[R] Multiple lines with a different color assigned to each line (corrected code)
Sorry, I just realized I didn't type in the correct
names of the variables I am working with, this is how
it should be:
plot(1,1,type=n)
for (i in summ$tx) {
points(summ$timep[summ$tx==i],summ$mn[summ$tx==i])
lines(summ$timep[summ$tx==i],summ$mn[summ$tx==i])
}
Thank you,
Judith
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Re: [R] Rcmdr importing excel files
I'm on Windows XP R 2.6.2 The command Data Import From Excel, Access etc Supply data.frame name Select xls file and then select the sheet seem to work for me What is not showing? --- stephen sefick [EMAIL PROTECTED] wrote: I am using R 2.6.2 on Mac OS X 10.4.9- I would like to import excel files into R with Rcmdr, but This option does not present itself in the file menu. Any help would be greatly appreciated. Stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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-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] RSPerl on OS X Server 10.4.11
Hello, I tried the R-Sig-Mac list with this query, but had no takers. I hope that the following isn't too far off the mark for this list. Many thanks in advance if someone can help me out! Quick summary: I can't get RSPerl working on a PPC G5 with the pre-compiled binary for Mac OS X, but it does work if I compile R from source with the --enable-R-shlib flag. If I need to compile from source...what other options are recommended? More details... I'm having some trouble getting RSPerl working on an XServe cluster. Using: perl v5.8.6 R v2.6.2 (installed from binaries from CRAN) RSPerl v0.92-1 OS X Server 10.4.11, PowerPC G5 I'm installing RSPerl with: R CMD INSTALL -c -l '/home/gdowns/R' --configure-args='--with-in-perl' RSPerl_0.92-1.tar.gz but when I try to load the library I get: library(RSPerl) Error in dyn.load(file, ...) : unable to load shared library '/home/gdowns/R/RSPerl/libs/ppc/RSPerl.so': dlopen(/home/gdowns/R/RSPerl/libs/ppc/RSPerl.so, 6): Symbol not found: _boot_R Referenced from: /home/gdowns/R/RSPerl/libs/ppc/RSPerl.so Expected in: dynamic lookup Error: package/namespace load failed for 'RSPerl' So, I tried building R from scratch, using: ./configure --prefix=/tmp/R/ --enable-R-shlib I then repeated the install of RSPerl with this special version of R: /tmp/R/R.framework/Resources/bin/R CMD INSTALL -c -l '/home/gdowns/R' --configure-args='--with-in-perl' RSPerl_0.92-1.tar.gz RSPerl *does* work with this version of R. I'm confused because question 1.3 of the RMacOSX-FAQ says: Note that the CRAN binary includes R shared library, so there is no need to re-compile R with --enable-R-shlib. I also note that when installing RSPerl with the binary distribution of R, the R CMD INSTALL process does not generate the perl modules (in the RSPerl/perl directory). They do get created with the compiled-from-source version of R (which is, I suspect, why it works!). I'm not sure where I'm going wrong with this. I'd highly prefer to stick with the pre-compiled binary to make upgrading easier. Plus I'm sure that the version I built today is not as well optimized as the binary distribution! If I really do need to compile R from scratch, can anyone recommend the appropriate configure flags? many thanks and best regards, Greg. -- Gregory Downs CRSC Room 219/414 Department of Plant Agriculture University of Guelph Guelph, Ontario, Canada, N1G 2W1 519-824-4120 x58164 __ 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] Rcmdr importing excel files
Dear John and Stephen, As I recall, importing from Excel, Access, or dBase files works properly only under Windows, and consequently the menu item appears only in Windows systems. I frankly don't recall why this is the case, since the RODBC package is used. The code for reading these kinds of files was contributed by Matthieu Lesnoff, to whom I'm copying this response. Maybe he'll have a more complete answer. Regards, John John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] project.org] On Behalf Of John Kane Sent: February-26-08 5:27 PM To: stephen sefick; r-help@r-project.org Subject: Re: [R] Rcmdr importing excel files I'm on Windows XP R 2.6.2 The command Data Import From Excel, Access etc Supply data.frame name Select xls file and then select the sheet seem to work for me What is not showing? --- stephen sefick [EMAIL PROTECTED] wrote: I am using R 2.6.2 on Mac OS X 10.4.9- I would like to import excel files into R with Rcmdr, but This option does not present itself in the file menu. Any help would be greatly appreciated. Stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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-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-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] Rcmdr importing excel files
Thanks very much. --- John Fox [EMAIL PROTECTED] wrote: Dear John and Stephen, As I recall, importing from Excel, Access, or dBase files works properly only under Windows, and consequently the menu item appears only in Windows systems. I frankly don't recall why this is the case, since the RODBC package is used. The code for reading these kinds of files was contributed by Matthieu Lesnoff, to whom I'm copying this response. Maybe he'll have a more complete answer. Regards, John John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] project.org] On Behalf Of John Kane Sent: February-26-08 5:27 PM To: stephen sefick; r-help@r-project.org Subject: Re: [R] Rcmdr importing excel files I'm on Windows XP R 2.6.2 The command Data Import From Excel, Access etc Supply data.frame name Select xls file and then select the sheet seem to work for me What is not showing? --- stephen sefick [EMAIL PROTECTED] wrote: I am using R 2.6.2 on Mac OS X 10.4.9- I would like to import excel files into R with Rcmdr, but This option does not present itself in the file menu. Any help would be greatly appreciated. Stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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-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-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] lasso with Cox regression
Rob Tibshirani propose to use lasso with Cox regression for variable selection in his 1997 paper The lasso method for variable selection in the Cox model published in Statistics In Medicine 16:385. I understand the lars() function in lars package implemented lasso, but it does not do lasso with Cox model, does anyone know of any R package/function that does lasso with a Cox model? Thanks John Zhang Looking for last minute shopping deals? __ 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] Raw histogram plots
On Tue, Feb 26, 2008 at 4:10 PM, Andre Nathan [EMAIL PROTECTED] wrote: Hello I need to plot a histogram, but insted of using bars, I'd like to plot the data points. I've been doing it like this so far: h - hist(x, plot = F) plot(y = x$counts / sum(x$counts), x = x$breaks[2:length(x$breaks)], type = p, log = xy) Another approach would be to use ggplot2, where all statistical transformations can be performed separately from their traditional appearance: install.packages(ggplot2) qplot(x, stat=bin, geom=bar) qplot(x, stat=bin) Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple lines with a different color assigned to each line (corrected code)
It's hard to provide a useful answer without know what your data looks
like, but maybe something like:
library(ggplot2)
qplot(timep, mn, data=summ, geom=line, colour = tx)
Hadley
On Tue, Feb 26, 2008 at 4:24 PM, Judith Flores [EMAIL PROTECTED] wrote:
Sorry, I just realized I didn't type in the correct
names of the variables I am working with, this is how
it should be:
plot(1,1,type=n)
for (i in summ$tx) {
points(summ$timep[summ$tx==i],summ$mn[summ$tx==i])
lines(summ$timep[summ$tx==i],summ$mn[summ$tx==i])
}
Thank you,
Judith
Be a better friend, newshound, and
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Re: [R] Rcmdr importing excel files
On Tue, 26 Feb 2008, John Fox wrote: Dear John and Stephen, As I recall, importing from Excel, Access, or dBase files works properly only under Windows, and consequently the menu item appears only in Windows systems. I frankly don't recall why this is the case, since the RODBC package is used. The code for reading these kinds of files was contributed by Matthieu Lesnoff, to whom I'm copying this response. Maybe he'll have a more complete answer. You don't just need the RODBC package, but also the MS ODBC drivers. I'd be surprised if such drivers existed anywhere else, as they rely on Windows internals. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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] GLM
Just a couple of notes. * What you are attempting to fit here is a linear model, or, more precisely 13112 simple linear regressions. Why not just use 'lm'? 'glm' is for fitting generalized linear models and using it for this special case is going to be computationally costly. [NB the concept of a 'general' linear model is foreign to R.] * If ever you do manage to fit you 13112 simple linear regressions, what then? * Since thery really are separate models, why not try doing it in smaller batches, the first 1000, the next 1000, and so on? Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dani Valverde Sent: Wednesday, 27 February 2008 3:11 AM To: R Help Subject: [R] GLM Hello, I am trying to perform a glm analysis on a 68x13113 matrix (named data.spect). The first column corresponds to the predictor (data.spect[,1]) and the rest to the response variables (data.spect[,2:13113]). When I try this code glmObject - glm(data.spect[,2:13113]~data.spect[,1]) I get the following error: Error: (subscript) logical subscript too long Could anyone help me on solving this problem? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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-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] numeric format
Thanks, Erik,
This is a partial copy of my code. I want to get rid of the left column of
integers and I want to control the number of decimal places after the
decimal point.
j-0.4
for(i in 1:20){
+ j=j+0.1;cp[i]-pnorm(-j*3)*10^6;ratio[i]-j}
table-data.frame(ratio,cp)
table
ratio cp
10.5 66807.201268858
20.6 35930.3191129258
30.7 17864.4205628166
40.8 8197.53592459613
50.9 3466.97380304067
6
CHV
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[R] multdrc error---Error in mdrcOpt(opfct, startVec, optMethod, derFlag, constrained, warnVal
Hi,
I am newbie of R. I a currently using multdrc object to generate fitting
curve and IC50. My 384 well format raw data contains multi dose response
curves. My script goes through set of data then produce curve and ic50.
Here is my sudo code:
For (plateid in platelist)
{
Input data (plateid) as matrix
Curve fitting
model4logistic - multdrc(rdata ~ ld, logDose=10)
}
The first 3 plates are ok, 4th plate has following error
Error in mdrcOpt(opfct, startVec, optMethod, derFlag, constrained,
warnVal, :
Convergence failed
I know the expected fitting is ugly, is it the reason to produce the
error?
Thanks you in advance for your help,
Xin Gong
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[R] Multiple linear regression with for loop
Hi everyone!
I have an array containing the following fields for over hundred compounds:
cpd, activity, fixterm, energy1, energy2, energy3, ...
I want to run a multiple linear regression on all entries of an array.
Therefore I tried to do this with a for loop. (Maybe there is a direct way of
calculating it using apply, but I don't know that either.)
Actually i tried the following code:
...
attach(data)
for(i in 1:length(cpd)) {
fitted.model - lm(activity ~ fixterm + i)
coef(fitted.model)
}
...
Unfortunatly this loop doesn't give the intended correlation coefficients of
each regression. If I insert a line print(i) into the loop the desired values
for i are printed correctly. Only the coefficient outputs are missing.
Probably the solution is very near, but I just can't see it.
Many thanks in advance,
Markus
-
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and provide commented, minimal, self-contained, reproducible code.
[R] NLS -- multiplicative errors and group comparison
Hello, I am attempting to fit a non-linear model (Von Bertalanffy growth model) to fish length-at-age data with the purpose of determining if any of the three parameters differ between male and female fish. I believe that I can successfully accomplish this goal assuming an additive error structure (illustrated in section 1 below). My trouble begins when I attempt this analysis using a model with a multiplicative error structure. I believe that I can fit the multiplicative error model to data without attempting to test between males and females (section 2 below), but I am not sure how to declare the model formula if I want to test between males and females (section 3 below). In addition, I assumed what I did in section 2 was correct, separated the data into a dataframe of males and a dataframe of females, and then attempted to fit separate models to each group (Section 4). This was successful for males but not for females. The problem with the female group appears to be that my logging creates NaN cells. When I put a trace on the nls function it appears to do one iteration and then fails. My assumption is that the nls function must be attempting different parameter estimates that return a NaN but I cannot test this as I'm not sure how to see the new parameters that it is trying. [I tried different starting values but did not find any that corrected this problem.] So (1) how do I declare the model formula for using multiplicative errors (i.e., is what I did in Section 2 correct), (2) how do I declare the model formula for comparing two groups and using multiplicative errors, and (3) any suggestions for how to find the issue leading to the error for just the female model in section 4. Sys.info information is in Section 4 and I am using R 2.6.1. I have not included the data as it is a rather large file. Thank you very much for reading this long message and for any help that you can offer. ### Section 1 ### library(xlsReadWrite) fwd - read.xls(FWDrum_SDF.xls,sheet=1) fwd$Gm - fwd$Gf - rep(0,length(fwd$age)) fwd$Gf[fwd$sex==female] - 1 fwd$Gm[fwd$sex==male] - 1 str(fwd) 'data.frame': 719 obs. of 5 variables: $ age: num 1.27 2.25 2.25 2.25 2.25 ... $ tl : num 226 208 226 226 234 ... $ sex: Factor w/ 2 levels female,male: 1 1 1 1 1 1 1 1 1 1 ... $ Gf : num 1 1 1 1 1 1 1 1 1 1 ... $ Gm : num 0 0 0 0 0 0 0 0 0 0 ... # starting values sLinf - 405 sK - 0.11 sto - -5.2 svb - list(Linf=sLinf,K=sK,to=sto) # Fit the additive error structure model to both groups combined vbla - nls(tl~Linf*(1-exp(-K*(age-to))),start=svb,data=fwd) summary(vbl1) Formula: tl ~ Linf * (1 - exp(-K * (age - to))) Parameters: Estimate Std. Error t value Pr(|t|) Linf 520.751048 19.560552 26.623 2e-16 *** K 0.061097 0.008506 7.183 1.72e-12 *** to-6.950346 1.112839 -6.246 7.24e-10 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 83.75 on 716 degrees of freedom Number of iterations to convergence: 9 Achieved convergence tolerance: 7.525e-06 # Fit the additive error structure model to the separate groups # compare this to vbla to see if any parameters differ (fit other models to see which parameter) vbla.gen- nls(tl~Gf*Linff*(1-exp(-Kf*(age-tof))) + Gm*Linfm*(1-exp(-Km*(age-tom))), + start=list(Linff=sLinf,Kf=sK,tof=sto,Linfm=sLinf,Km=sK,tom=sto),data=fwd ) summary(vbla.gen) Formula: tl ~ Gf * Linff * (1 - exp(-Kf * (age - tof))) + Gm * Linfm * (1 - exp(-Km * (age - tom))) Parameters: Estimate Std. Error t value Pr(|t|) Linff 692.719734 47.191732 14.679 2e-16 *** Kf 0.038532 0.006469 5.957 4.04e-09 *** tof-7.589941 1.235644 -6.142 1.35e-09 *** Linfm 372.224132 13.268491 28.053 2e-16 *** Km 0.095814 0.024983 3.835 0.000137 *** tom-8.058334 2.445654 -3.295 0.001033 ** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 68.15 on 713 degrees of freedom Number of iterations to convergence: 8 Achieved convergence tolerance: 6.589e-06 ### Section 2 ### vblm - nls(log(tl)~log(Linf*(1-exp(-K*(age-to,start=svb,data=fwd) summary(vblm) Formula: log(tl) ~ log(Linf * (1 - exp(-K * (age - to Parameters: Estimate Std. Error t value Pr(|t|) Linf 515.414166 21.239627 24.267 2e-16 *** K 0.055431 0.007486 7.404 3.71e-13 *** to-8.289902 1.002402 -8.270 6.51e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.1907 on 716 degrees of freedom Number of iterations to convergence: 8 Achieved convergence tolerance: 2.236e-06 ### Section 3 ### # FIRST TRY -- Fit the multiplicative error structure model to the separate groups vblm.gen1- nls(log(tl)~log(Gf*Linff*(1-exp(-Kf*(age-tof))) + Gm*Linfm*(1-exp(-Km*(age-tom,
[R] score test statistic in logistic regression
Hi, looking for a function or syntax to estimate the score test in logistic regression for the null hypothesis b1=0 in the model logit(p)=b0+ b1*x +b2*z. Data comes from the binomial distribution (n,p). Thanks, ben __ 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] Add a rectangle behind a plot
Hi there, I found one reference to add a reactangle behind a plot using plot(...,add=T), I tried this but didn't obtain the desired result. If a I have the following code: plot(x,y) rect(xleft, ybottom, xright,ytop,col='green) The rectangle appear on top of the plot. Any help will be greatly appreciated, Judith Never miss a thing. Make Yahoo your home page. __ 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] Highlighting different series with colors
Valentin == Valentin Bellassen [EMAIL PROTECTED] writes: Hello, I have a data frame with 3 vectors $x, $y, and $type. I would like to plot $x~$y and having different colors for the corresponding points, one for each level of $type. Would someone know how to do that? Is it possible to then generate a legend automatically? If type is a factor, you can use it as.numeric: plot(x ~ y, data, col=as.numeric(type)) legend(..., col=as.numeric(data$type)) Mike __ 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] Raw histogram plots
I know about stem, but the data set has 1 million points, so it's not very useful here. I want to avoid binning just to have an idea about the shape of the distribution, before deciding how I'll bin it. Andre On Tue, 2008-02-26 at 16:20 -0600, roger koenker wrote: take a look at ?stem There is still a place for handtools in the age of integrated circuits. Of course, avoiding binning isn't really desirable. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Feb 26, 2008, at 4:10 PM, Andre Nathan wrote: Hello I need to plot a histogram, but insted of using bars, I'd like to plot the data points. I've been doing it like this so far: h - hist(x, plot = F) plot(y = x$counts / sum(x$counts), x = x$breaks[2:length(x$breaks)], type = p, log = xy) Sometimes I want to have a look at the raw data (avoiding any kind of binning). When x only contains integers, it's easy to just use bins of size 1 when generating h with breaks = seq(0, max(x)). Is there any way to do something similar when x consists of fractional data? What I'm doing is setting a small bin length (for example, breaks = seq(0, 1, by = 1e-6), but there's still a chance that points will be grouped in a single bin. Is there a better way to do this kind of raw histogram plotting? Thanks, Andre __ 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-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] missing packages from install
Hi,
When I install new packages from CRAN, I frequently
find that some packages were missing from the download
queue. For example, on one of my computer with R2.6.2,
I can not find package glmpath from the download
queue. On my other computer with R2.5.1, I could still
find that particular package. What could be the reason
for this? Is this computer related or R version
related?
I downloaded the gz file for package glmpath into my
local drive (Windows XP), how can I install it? I
tried:
install.packages('H:\\R\\glmpath_0.94.tar.gz')
but got error message:
Warning message:
package 'H:\rw1070\glmpath_0.94.tar.gz' is not
available
Thanks
John Zhang
Looking for last minute shopping deals?
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[R] Hmisc xYplot won't do conditioning on factors?
Hi,
I am trying to replace (lattice) standard xyplot with xYplot variant from
Hmisc package to be able to add error bars to my plots. However, this does
not work, e.g:
library(lattice)
d - data.frame(
SKU=gl(3, 1, 21, labels=c(a, b, c)),
Weekday=gl(7, 3, 21),
QCRate=runif(21))
xyplot(QCRate ~ Weekday | SKU, data=d)
(this plots nice 3 panels as per a,b,c conditionals)
library(Hmisc)
xYplot(QCRate ~ Weekday | SKU, data=d)
Error in Summary.factor(1:7, na.rm = TRUE) :
range not meaningful for factors
Is there a workaround?
Thanks,
Ivan
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Re: [R] Raw histogram plots
Andre If I understand you correctly, you could try a barplot() on the result of table(). HTH .. Peter Alspach -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Andre Nathan Sent: Wednesday, 27 February 2008 1:34 p.m. To: roger koenker Cc: r-help Subject: Re: [R] Raw histogram plots I know about stem, but the data set has 1 million points, so it's not very useful here. I want to avoid binning just to have an idea about the shape of the distribution, before deciding how I'll bin it. Andre On Tue, 2008-02-26 at 16:20 -0600, roger koenker wrote: take a look at ?stem There is still a place for handtools in the age of integrated circuits. Of course, avoiding binning isn't really desirable. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Feb 26, 2008, at 4:10 PM, Andre Nathan wrote: Hello I need to plot a histogram, but insted of using bars, I'd like to plot the data points. I've been doing it like this so far: h - hist(x, plot = F) plot(y = x$counts / sum(x$counts), x = x$breaks[2:length(x$breaks)], type = p, log = xy) Sometimes I want to have a look at the raw data (avoiding any kind of binning). When x only contains integers, it's easy to just use bins of size 1 when generating h with breaks = seq(0, max(x)). Is there any way to do something similar when x consists of fractional data? What I'm doing is setting a small bin length (for example, breaks = seq(0, 1, by = 1e-6), but there's still a chance that points will be grouped in a single bin. Is there a better way to do this kind of raw histogram plotting? Thanks, Andre __ 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-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. The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. __ 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] 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:
fig=TRUE=
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
fig=TRUE=
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):
fig=TRUE=
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 at 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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Re: [R] How to include the documentation of a function in a Sweave document?
Thibaut Jombart wrote:
Duncan Murdoch wrote:
Maybe a clue: we can use
cat(readLines(as.character(?plot)),sep=\n)
to display the help (here, of plot) directly to the screen. So we could
use something like:
echo=TRUE,print=FALSE,eval=FALSE=
?plot
@
echo=FALSE,print=TRUE,eval=TRUE=
cat(readLines(as.character(?plot)),sep=\n)
@
But this doesn't work (latex compilation error) as weird characters
appear in the produced tex, at some places (tabulations?), like:
_T_h_e _D_e_f_a_
(not sure what it will look like in this email, but emacs reads things
like _^HT_^HH_^He...).
Maybe an encoding problem? I tried specifying different encoding to
readLines, with no luck (latin1, UTF-8). Otherwise, the help appears
in the .tex.
Those are backspaces: it's trying to underline the title. You'd get
a better display if you read the latex version instead. I think you
need to construct the path to it yourself (using system.file() etc.)
Duncan Murdoch
Thanks for the hint !
So, the code below roughly works:
###
\documentclass{article}
\usepackage{verbatim}
\begin{document}
echo=TRUE,print=FALSE,eval=FALSE=
?plot
@
echo=FALSE,print=FALSE,results=tex=
path - sub(help,latex,as.character(?plot))
path - paste(path,'tex',sep=.)
cat(readLines(path),sep=\n)
@
\end{document}
###
The document compiles with pdflatex but still complains about a bunch of
unknown latex instructions (like \HeaderA, used at the begining of the
included (plot.tex) tex file. The resulting pdf indeed looks a bit nasty.
What command shall we include in the header to have it work?
The refman.tex file starts like this:
\documentclass[a4paper]{book}
\usepackage[times,hyper]{Rd}
\usepackage[latin1]{inputenc}
\usepackage{makeidx}
Those packages should do it. (Rd.sty is in R_HOME/share/texmf).
Duncan Murdoch
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Re: [R] Add a rectangle behind a plot
Just replot the points over it again: points(x, y) Also there is an example using lattice graphics in the Example section of: library(zoo) ?xyplot.zoo On Tue, Feb 26, 2008 at 7:16 PM, Judith Flores [EMAIL PROTECTED] wrote: Hi there, I found one reference to add a reactangle behind a plot using plot(...,add=T), I tried this but didn't obtain the desired result. If a I have the following code: plot(x,y) rect(xleft, ybottom, xright,ytop,col='green) The rectangle appear on top of the plot. Any help will be greatly appreciated, Judith Never miss a thing. Make Yahoo your home page. __ 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-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] Kalman Filter
Have you looked at the 'dlm' package? It has a vignette to help
you learn to use it. Also, I've heard that a book about that package is
scheduled to appear in the next few months.
I have looked at the Kalman functions in the 'stats' package but
have not found documentation that seemed sufficient to get me started
using it.
RSiteSearch('Kalman', 'fun') produced 48 hits for me just now. If
you don't find what you want with 'dlm' (and maybe even if you do), you
may wish to examine that list, if you haven't already.
Hope this helps.
Spencer
Vladimír Šamaj wrote:
Hi
My name is Vladimir Samaj. I am a student of Univerzity of Zilina. I am
trying to implement Kalman Filter into my school work. I have some problems
with understanding of R version of Kalman Filter in package stats( functions
KalmanLike, KalmanRun, KalmanSmooth,KalmanForecast).
1) Can you tell me how are you seting the initial values of state vector in
Kalman Filter? Are you using some method?
2) I have fond function StructTS in stats package. I dont understand, how
exactly, are you computing(what method are you using) fitted values which
are the output of this function( $fitted ) . In description od this function
is that it fit a structural model for a time series by maximum likehood.
Does it means, that the fitted values are fit by maximum likehood? If so how
does look the likehood function?
3)Finaly, I dont understand smooting problem. What I know is that, if I
have t observations of some time serie, I can use function KalmanRun to get
estimates of state vector. And if I gain aditional observations of time
serie( T t ), I shoud use KalmanSmooth function to smooth estimates of
state vector. I dont understand, that how shoud I tell to KalmanSmooth
funtion that I allready did filtering and it shoud use the values from
filtering to smoothing.
I will be glad if you help me. I hope that my folmulations were correct.
Thank you very much.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding LaTeX cross-references into Sweave plots
Peter Dunn wrote:
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:
fig=TRUE=
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
fig=TRUE=
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):
fig=TRUE=
plot( c(-1,1), c(-1,1), type=n,
main=Graph of Eq (\label{EQ:equation}))
abline(-1, 3)
@
Thanks as always.
I don't think there's a reasonable way to do this. If you want to be
unreasonable, you could execute R code to read the .aux file produced
from a previous LaTeX run (which is how LaTeX handles references). I'd
say a better approach is just not to use a main title, use the figure
caption to include the equation number.
Duncan Murdoch
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[R] Backwards Lasso
Has anyone computed a Backwards lasso with positive coefficients? I would like the R commands or guidance on fitting such a model. The backwards lasso and positively constrained lasso are both described in Least Angle Regression, Efron etal 2002. __ 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] Raw histogram plots
If the goal is to get a sense of the 'shape' of the overall distribution of 'x', then why not use: plot(density(x)) ? HTH, Marc Schwartz Peter Alspach wrote: Andre If I understand you correctly, you could try a barplot() on the result of table(). HTH .. Peter Alspach -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Andre Nathan Sent: Wednesday, 27 February 2008 1:34 p.m. To: roger koenker Cc: r-help Subject: Re: [R] Raw histogram plots I know about stem, but the data set has 1 million points, so it's not very useful here. I want to avoid binning just to have an idea about the shape of the distribution, before deciding how I'll bin it. Andre On Tue, 2008-02-26 at 16:20 -0600, roger koenker wrote: take a look at ?stem There is still a place for handtools in the age of integrated circuits. Of course, avoiding binning isn't really desirable. On Feb 26, 2008, at 4:10 PM, Andre Nathan wrote: Hello I need to plot a histogram, but insted of using bars, I'd like to plot the data points. I've been doing it like this so far: h- hist(x, plot = F) plot(y = x$counts / sum(x$counts), x = x$breaks[2:length(x$breaks)], type = p, log = xy) Sometimes I want to have a look at the raw data (avoiding any kind of binning). When x only contains integers, it's easy to just use bins of size 1 when generating h with breaks = seq(0, max(x)). Is there any way to do something similar when x consists of fractional data? What I'm doing is setting a small bin length (for example, breaks = seq(0, 1, by = 1e-6), but there's still a chance that points will be grouped in a single bin. Is there a better way to do this kind of raw histogram plotting? Thanks, Andre __ 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] multdrc error
Dear Sir/Madam:
I am newbie of R. I a currently using multdrc object to generate fitting curve
and IC50. My 384 well format raw data contains multi dose response curves. My
script goes through sets of data then produce curve and ic50.
Here is my sudo code:
For (plateid in platelist)
{
Input data (plateid) as matrix
Curve fitting
model4logistic - multdrc(rdata ~ ld, logDose=10)
}
The first 3 plates are ok, 4th plate has following error
Error in mdrcOpt(opfct, startVec, optMethod, derFlag, constrained, warnVal, :
Convergence failed
I know the expected fitting is ugly, is it the reason to produce the error?
Any clue about this error message?
Thanks you in advance for your help,
Xin Gong
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Re: [R] numeric format
While we're at it, and since you're new...
Your example will be much easier for r-help folks to read if you do
it like this:
j - 0.4
for(i in 1:20) {
j=j+0.1
cp[i] - pnorm(-j*3)*10^6
ratio[i] - j
}
table - data.frame(ratio,cp)
table
But the loop is unnecessary. Try
j - seq(0.5, by=0.1, length=20)
tbl - data.frame(ratio=j, cp= pnorm(-3*j)*10^6)
Also, the formatting you are getting is not, I don't think, the default. I get:
j - seq(0.5, by=0.1, length=20)
tbl - data.frame(ratio=j, cp= pnorm(-3*j)*10^6)
head(tbl)
ratiocp
1 0.5 66807.201
2 0.6 35930.319
3 0.7 17864.421
4 0.8 8197.536
5 0.9 3466.974
6 1.0 1349.898
Note that they are aligned to all have 3 places after the decimal point.
Do you want the actual cp values to be adjusted to have some other
number of decimal places, or do you just want the format changed?
For the former, use, for example, round(cp,1).
For the latter, it kind of depends on your ultimate goal. If you want
to control the number of decimal places, because you're going to move
it into a report, for example, you might try looking into the
formatC() and use something like
formatC(tbl$cp,digits=1,format='f')
As in,
tbl$cp - formatC(tbl$cp,digits=1,format='f')
head(tbl)
ratio cp
1 0.5 66807.2
2 0.6 35930.3
3 0.7 17864.4
4 0.8 8197.5
5 0.9 3467.0
6 1.0 1349.9
To get rid of the row labels, you will have to use Rolf's suggestion,
or perhaps delve into the write.table function.
-Don
At 3:41 PM -0800 2/26/08, cvandy wrote:
Thanks, Erik,
This is a partial copy of my code. I want to get rid of the left column of
integers and I want to control the number of decimal places after the
decimal point.
j-0.4
for(i in 1:20){
+ j=j+0.1;cp[i]-pnorm(-j*3)*10^6;ratio[i]-j}
table-data.frame(ratio,cp)
table
ratio cp
10.5 66807.201268858
20.6 35930.3191129258
30.7 17864.4205628166
40.8 8197.53592459613
50.9 3466.97380304067
6
CHV
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Don MacQueen
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925-423-1062
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[R] Loading user defined functions autometically each time I start R
Hi all, I wrote some user defined function for my own. Now I want to get a mechanism so that every time I start R, those function will automatically be loaded in R without manually copying pasting. Can gurus here pls tell me how to do that? Or I have to build my own packages bundled with those functions. However I am not familiar in writing R package yet. Regards, [[alternative HTML version deleted]] __ 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] Add a rectangle behind a plot
On Tue, 26 Feb 2008, Judith Flores wrote: Hi there, I found one reference to add a reactangle behind a plot using plot(...,add=T), I tried this but didn't obtain the desired result. If a I have the following code: plot(x,y) rect(xleft, ybottom, xright,ytop,col='green) The rectangle appear on top of the plot. That's what you asked for by plotting it second. Try something like plot(x, y, type=n) rect(xleft, ybottom, xright,ytop,col='green') points(x, y) Any help will be greatly appreciated, Judith -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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] Raw histogram plots
On Tue, 26 Feb 2008, Andre Nathan wrote: I know about stem, but the data set has 1 million points, so it's not very useful here. I want to avoid binning just to have an idea about the shape of the distribution, before deciding how I'll bin it. Ideas: 1) use a much smaller sample of the data (1000 should suffice) 2) use a density plot (see ?density), perhaps on a sub-sample (although as that will bin the data on a fine grid, this does not matter much). Andre On Tue, 2008-02-26 at 16:20 -0600, roger koenker wrote: take a look at ?stem There is still a place for handtools in the age of integrated circuits. Of course, avoiding binning isn't really desirable. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Feb 26, 2008, at 4:10 PM, Andre Nathan wrote: Hello I need to plot a histogram, but insted of using bars, I'd like to plot the data points. I've been doing it like this so far: h - hist(x, plot = F) plot(y = x$counts / sum(x$counts), x = x$breaks[2:length(x$breaks)], type = p, log = xy) Sometimes I want to have a look at the raw data (avoiding any kind of binning). When x only contains integers, it's easy to just use bins of size 1 when generating h with breaks = seq(0, max(x)). Is there any way to do something similar when x consists of fractional data? What I'm doing is setting a small bin length (for example, breaks = seq(0, 1, by = 1e-6), but there's still a chance that points will be grouped in a single bin. Is there a better way to do this kind of raw histogram plotting? Thanks, Andre __ 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-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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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] Loading user defined functions autometically each time I start R
I am using R 2.6.2. under windows On Wed, Feb 27, 2008 at 12:43 PM, [EMAIL PROTECTED] wrote: From: Arun Kumar Saha [EMAIL PROTECTED] Date: 2008/02/27 Wed AM 01:03:26 CST To: [EMAIL PROTECTED] [EMAIL PROTECTED] Subject: [R] Loading user defined functions autometically each time I start R i'm on linux so if you are not it's probably slightly different on windows but not much. I just put my .Rprofile file ( you need the . in front but I had to take it off when I sent you ) in my /opt/mark ( hiome dorectory on linux ) directory. generally speaking, when you ask questions like that, be sure to specify your OS or people ( not me ) will get annoyed. i you start up R, the .Rprofile should get called and the functions in your arun.R file should be available to you. good luck. I';m no expert so hopefully someone else will reply also ( that's why i emailed privately ). Hi all, I wrote some user defined function for my own. Now I want to get a mechanism so that every time I start R, those function will automatically be loaded in R without manually copying pasting. Can gurus here pls tell me how to do that? Or I have to build my own packages bundled with those functions. However I am not familiar in writing R package yet. Regards, [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- -- Arun Kumar Saha, M.Sc. Statistical Arbitrage Quant RISK MANAGEMENT DIVISION Transgraph Consulting [www.transgraph.com] Hyderabad, INDIA Contact # Home: (91-033) 25558038 [CALCUTTA] Home: (91-040) 40033010 [HYDERABAD] Office: (91-040) 30685012 Ext. 17 [email preferred] FAX: (91-040) 55755003 [if absolutely necessary] Mobile: 919989122010 E-Mail: [EMAIL PROTECTED] [EMAIL PROTECTED] -- [[alternative HTML version deleted]] __ 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.
