[R] Latex and r (using summary from RMS)

[moleps]

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 <v3.8l> 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.thorpe at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016