[R] Latex problem in Hmisc (3.8-1) and Mac Os X with R 2.11.1

From: moleps islon <moleps2_at_gmail.com>
Date: Fri, 18 Jun 2010 07:32:52 +0200


Dear all,

I did post this more or less identical mail in a follow up to another question I posted, but under another heading. I try again, but now under the correct header.

upon running this code (from the Hmisc library-latex function) I believe the call to summary.formula is allright and produces wonderful tables, but the latex command results in a correct formatted table but where all the numbers and the test columns are wrong. I've pasted in both the R code and the resulting latex code annotated with comments from the run. Does the same code produce correct cell-entries in other installation ?

//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)

> 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 Harrellīs "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



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