Re: [R] Latex and r (using summary from RMS)
Dear all,
After spending all day and most of the night on this I did a new R-installation
and it works. The question now is - upon running this code (from the Hmisc
library-latex function) I believe the call to summary.formula is allright, but
the latex command results in a totally different table where all the numbers
and test columns are wrong are wrong. Is this still a matter for the
installation or is there something in the latex syntax I havent grasped?
//M
library(Hmisc)
options(digits=3)
set.seed(173)
sex <- factor(sample(c("m","f"), 500, rep=TRUE))
age <- rnorm(500, 50, 5)
treatment <- factor(sample(c("Drug","Placebo"), 500, rep=TRUE))
symp <- c('Headache','Stomach Ache','Hangnail',
'Muscle Ache','Depressed')
symptom1 <- sample(symp, 500,TRUE)
symptom2 <- sample(symp, 500,TRUE)
symptom3 <- sample(symp, 500,TRUE)
Symptoms <- mChoice(symptom1, symptom2, symptom3, label='Primary Symptoms')
table (Symptoms)
table(symptom1,symptom2)
f <- summary(treatment ~ age + sex + Symptoms, method="reverse", test=TRUE)
g <- summary(treatment ~ age + sex + symptom1, method="reverse", test=TRUE)
latex(g)
Produces nice tables-but the numbers are all wrong as you can see below from
the latex file...
> latex(g,file="")
% latex.default(cstats, title = title, caption = caption, rowlabel = rowlabel,
col.just = col.just, numeric.dollar = FALSE, insert.bottom = legend,
rowname = lab, dcolumn = dcolumn, extracolheads = extracolheads,
extracolsize = Nsize, ...)
%
\begin{table}[!tbp]
\caption{Descriptive Statistics by treatment\label{g}}
\begin{center}
\begin{tabular}{lccc}\hline\hline
\multicolumn{1}{l}{}&\multicolumn{1}{c}{Drug}&\multicolumn{1}{c}{Placebo}&\multicolumn{1}{c}{Test
Statistic}\tabularnewline
&\multicolumn{1}{c}{{\scriptsize $N=263$}}&\multicolumn{1}{c}{{\scriptsize
$N=237$}}&\tabularnewline
\hline
age&1&1&4\tabularnewline
sex~:~m&6&7&2\tabularnewline
symptom1~:~Depressed&4&3&3\tabularnewline
Hangnail&5&6&1\tabularnewline
Headache&4&2&1\tabularnewline
Muscle~Ache&3&5&1\tabularnewline
Stomach~Ache&2&4&1\tabularnewline
\hline
\end{tabular}
\end{center}
\noindent {\scriptsize $a$\ }{$b$\ }{\scriptsize $c$\ } represent the lower
quartile $a$, the median $b$, and the upper quartile $c$\ for continuous
variables.\\Numbers after percents are frequencies.\\\indent Tests
used:\\\textsuperscript{\normalfont 1}Wilcoxon test;
\textsuperscript{\normalfont 2}Pearson test
\end{table}
Then I did another example from Harrell´s "statistical tables and plots"
rm(list=ls())
library(Hmisc)
getHdata(prostate)
# Variables in prostate had units in ( ) inside variable labels. Move
# these units of measurements to separate units attributes
# wt is an exception. It has ( ) in its label but this does not denote units
# Also make hg have a legal R plotmath expression
prostate<-upData(prostate, moveUnits=TRUE,units=c(wt="",
hg="g/100*ml"),labels=c(wt="Weight Index = wt(kg)-ht(cm)+200"))
attach(prostate)
stage<- factor(stage, 3:4, c("Stage 3","Stage 4"))
s6<-summary(stage~rx+age+wt+pf+hx+sbp+dbp+ekg+hg+sz+sg+ap+bm,method="reverse",
overall=TRUE, test=TRUE)
options(digits=2)
w<-latex(s6, size="smaller[3]", outer.size="smaller",
Nsize="smaller",long=TRUE, prmsd=TRUE, msdsize="smaller",middle.bold=TRUE,
ctable=TRUE)
This refused to run ( as long as the ctable=T was included), but without it
latex (s6)
I do get a nicely formated table, but again the numbers are all wrong... Also
latex(s6, long=TRUE, prmsd=TRUE, msdsize="smaller",middle.bold=TRUE)
makes no difference from latex(s6) alone with regards to formatting...
Quite frustrating-Any suggestions??
//M
On 16. juni 2010, at 20.10, Kevin E. Thorpe wrote:
> moleps wrote:
>> Dear R´ers I´m trying to get a summary table using latex and summary in the
>> rms package to no avail. I´m running R 2.10.1, Mac OS X snow leopard and I
>> have the mactex 2009 distribution installed. Any obvious things I´m missing?
>> //M
>> options(digits=3)
>> set.seed(173)
>> sex <- factor(sample(c("m","f"), 500, rep=TRUE))
>> age <- rnorm(500, 50, 5)
>> treatment <- factor(sample(c("Drug","Placebo"), 500, rep=TRUE))
>> f <- summary(treatment ~ age + sex + Symptoms, method="reverse", test=TRUE)
>> latex(f)
>> results in the following:
>> This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009)
>> entering extended mode
>> (/var/folders/q9/q9COp2FREsikCyHB7w+OxE+++TI/-Tmp-//RtmpVIk0iB/file587f83cb.tex
>> LaTeX2e <2009/09/24>
>> Babel and hyphenation patterns for english, usenglishmax, dumylang,
>> noh
>> yphenation, german-x-2009-06-19, ngerman-x-2009-06-19, ancientgreek, ibycus,
>> ar
>> abic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish,
>> dutc
>> h, esperanto, estonian, farsi, finnish, french, galician, german, ngerman,
>> mono
>> greek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian,
>> ku
>> rmanji, latin, latvian, lithuanian, mongolian, mongolian2a, bokmal, n
Re: [R] Latex and r
xdvi is installed in the same location as yours. I even did a reinstallment of mactex. Still doesnt work. But since I´m now convinced its related to my latex distribution I´ll take the problem elsewhere.. Regards, //M On 16. juni 2010, at 17.19, Prof Brian Ripley wrote: > On Wed, 16 Jun 2010, Erik Iverson wrote: > >> >> >> moleps wrote: >>> Dear R´ers >>> I´m trying to get a summary table using latex and summary in the rms >>> package to no avail. I´m running R 2.10.1, Mac OS X snow leopard and >>> I have the mactex 2009 distribution installed. Any obvious things I´m >>> missing? >> >>> file587f83cb.log. sh: xdvi: command not found >> >> You apparently don't have xdvi installed, which is used to view the resulting > > xdvi is part of MacTeX 2009. So the latter may be installed, but it is not > in the path or incomplete or I have > > tystie% which xdvi > /usr/texbin/xdvi > > >> document. How you get that installed on your OS, I don't know. Depending on >> what you're doing, you might want to use the "file" argument of latex >> function to output a latex file, and then do further processing. Also, >> assigning the latex function call to a variable, x <- latex(...) will >> suppress printing of the object, which is ultimately what is trying to use >> xdvi. >> >> __ >> 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, rip...@stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, 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] Latex and r
moleps writes:
Apparently you don't have xdvi installed on your system.
HTH
Georg
> Dear R´ers
>
> I´m trying to get a summary table using latex and summary in the rms package
> to no avail. I´m running R 2.10.1, Mac OS X snow leopard and I have the
> mactex 2009 distribution installed. Any obvious things I´m missing?
>
> //M
>
>
>
> options(digits=3)
> set.seed(173)
> sex <- factor(sample(c("m","f"), 500, rep=TRUE))
> age <- rnorm(500, 50, 5)
> treatment <- factor(sample(c("Drug","Placebo"), 500, rep=TRUE))
> f <- summary(treatment ~ age + sex + Symptoms, method="reverse", test=TRUE)
>
> latex(f)
>
> results in the following:
>
>
> This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009)
> entering extended mode
>
> (/var/folders/q9/q9COp2FREsikCyHB7w+OxE+++TI/-Tmp-//RtmpVIk0iB/file587f83cb.tex
> LaTeX2e <2009/09/24>
> Babel and hyphenation patterns for english, usenglishmax, dumylang,
> noh
> yphenation, german-x-2009-06-19, ngerman-x-2009-06-19, ancientgreek, ibycus,
> ar
> abic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish,
> dutc
> h, esperanto, estonian, farsi, finnish, french, galician, german, ngerman,
> mono
> greek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian,
> ku
> rmanji, latin, latvian, lithuanian, mongolian, mongolian2a, bokmal, nynorsk,
> po
> lish, portuguese, romanian, russian, sanskrit, serbian, slovak, slovenian,
> span
> ish, swedish, turkish, ukenglish, ukrainian, uppersorbian, welsh, loaded.
> (/usr/local/texlive/2009/texmf-dist/tex/latex/base/report.cls
> Document Class: report 2007/10/19 v1.4h Standard LaTeX document class
> (/usr/local/texlive/2009/texmf-dist/tex/latex/base/size10.clo))
> (/usr/local/texlive/2009/texmf-dist/tex/latex/geometry/geometry.sty
> (/usr/local/texlive/2009/texmf-dist/tex/latex/graphics/keyval.sty)
> (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
> (/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
> (/usr/local/texlive/2009/texmf-dist/tex/xelatex/xetexconfig/geometry.cfg))
> No file file587f83cb.aux.
> *geometry auto-detecting driver*
> *geometry detected driver: dvips*
>
> Overfull \hbox (1.14412pt too wide) in paragraph at lines 9--23
> []
> [1] (./file587f83cb.aux)
>
> LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
>
> )
> (see the transcript file for additional information)
> Output written on file587f83cb.dvi (1 page, 1620 bytes).
> Transcript written on file587f83cb.log.
> sh: xdvi: command not found
__
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] Latex and r
moleps wrote:
Dear R´ers
I´m trying to get a summary table using latex and summary in the rms package
to no avail. I´m running R 2.10.1, Mac OS X snow leopard and I have the mactex
2009 distribution installed. Any obvious things I´m missing?
//M
options(digits=3)
set.seed(173)
sex <- factor(sample(c("m","f"), 500, rep=TRUE))
age <- rnorm(500, 50, 5)
treatment <- factor(sample(c("Drug","Placebo"), 500, rep=TRUE))
f <- summary(treatment ~ age + sex + Symptoms, method="reverse", test=TRUE)
latex(f)
results in the following:
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009)
entering extended mode
(/var/folders/q9/q9COp2FREsikCyHB7w+OxE+++TI/-Tmp-//RtmpVIk0iB/file587f83cb.tex
LaTeX2e <2009/09/24>
Babel and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, german-x-2009-06-19, ngerman-x-2009-06-19, ancientgreek, ibycus, ar
abic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutc
h, esperanto, estonian, farsi, finnish, french, galician, german, ngerman, mono
greek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian, ku
rmanji, latin, latvian, lithuanian, mongolian, mongolian2a, bokmal, nynorsk, po
lish, portuguese, romanian, russian, sanskrit, serbian, slovak, slovenian, span
ish, swedish, turkish, ukenglish, ukrainian, uppersorbian, welsh, loaded.
(/usr/local/texlive/2009/texmf-dist/tex/latex/base/report.cls
Document Class: report 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2009/texmf-dist/tex/latex/base/size10.clo))
(/usr/local/texlive/2009/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/local/texlive/2009/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/local/texlive/2009/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/local/texlive/2009/texmf-dist/tex/xelatex/xetexconfig/geometry.cfg))
No file file587f83cb.aux.
*geometry auto-detecting driver*
*geometry detected driver: dvips*
Overfull \hbox (1.14412pt too wide) in paragraph at lines 9--23
[]
[1] (./file587f83cb.aux)
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
(see the transcript file for additional information)
Output written on file587f83cb.dvi (1 page, 1620 bytes).
Transcript written on file587f83cb.log.
sh: xdvi: command not found
I believe there is something in the latex help page in the rms package
that talks about preview difficulties on MAC.
--
Kevin E. Thorpe
Biostatistician/Trialist, Knowledge Translation Program
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: kevin.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
__
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] Latex and r
moleps wrote: xdvi is installed in the same location as yours. I even did a reinstallment of mactex. Still doesnt work. But since I´m now convinced its related to my latex distribution I´ll take the problem elsewhere.. And the directory that xdvi is located in is in your path? __ 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] Latex and r
moleps wrote: Dear R´ers I´m trying to get a summary table using latex and summary in the rms package to no avail. I´m running R 2.10.1, Mac OS X snow leopard and I have the mactex 2009 distribution installed. Any obvious things I´m missing? file587f83cb.log. sh: xdvi: command not found You apparently don't have xdvi installed, which is used to view the resulting document. How you get that installed on your OS, I don't know. Depending on what you're doing, you might want to use the "file" argument of latex function to output a latex file, and then do further processing. Also, assigning the latex function call to a variable, x <- latex(...) will suppress printing of the object, which is ultimately what is trying to use xdvi. __ 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] LaTeX and R-scripts/-results
Hello Thomas (and all), Zitat von Thomas Petzoldt <[EMAIL PROTECTED]>: > Oliver Bandel wrote: > > Hello, > > > > at some places I read about good interaction of > > LaTeX and R. > > > > Can you give me a starting point, where I can find > > information about it? > > > > Are there special LaTeX-packages for the support, > > or does R have packages for support of LaTeX? > > Or will an external Code-Generator be used? > > > > TIA, > >Oliver > > > Hi Oliver, > > you are right, LaTeX and R are perfect companions. Look for > "Sweave"(*). > You find an introduction of Fritz Leisch in R-News 2002, Vol 2/3: > > http://cran.r-project.org/doc/Rnews/Rnews_2002-3.pdf [...] OK, really wonderful tool! This is something, I'm looking for since many years... ... maybe about a decade ... R as graphical pre-processor and data-analyser for LaTeX, and LaTeX as a tool to write papers with analysed data imported into the papers. This noweb-based approach (literate programming is so wunderful) is so much better than the many workarounds with so many other tools. When I remember -- for example -- metapost and the problem of not being able to name the outputs arbitrarily (using numbers for the figures is the only possibility), and hand made inserting the results with \includegraphics, this is so much better! Maybe noweb can also be used to insert not only R-stuff but also creations from metapost, dia, dot (graphviz) and other tools into a LaTeX-document. This is the right way to make documents and research clean and handy. :) Ciao, Oliver __ 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] LaTeX and R-scripts/-results
On Wed, Nov 26, 2008 at 08:50:33AM +0100, Oliver Bandel wrote: > at some places I read about good interaction of > LaTeX and R. > > Can you give me a starting point, where I can find > information about it? Have a look at these: Sweave() xtable()(xtable) latex() (Hmisc) cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ 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] LaTeX and R-scripts/-results
Oliver Bandel wrote: Hello, at some places I read about good interaction of LaTeX and R. Can you give me a starting point, where I can find information about it? Are there special LaTeX-packages for the support, or does R have packages for support of LaTeX? Or will an external Code-Generator be used? TIA, Oliver Hi Oliver, you are right, LaTeX and R are perfect companions. Look for "Sweave"(*). You find an introduction of Fritz Leisch in R-News 2002, Vol 2/3: http://cran.r-project.org/doc/Rnews/Rnews_2002-3.pdf and an entire homepage about it: http://www.statistik.lmu.de/~leisch/Sweave/ HTH Thomas P. (*) Many thanks to Friedrich Leisch for this great peace of software! __ 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.
