moleps islon
2010-Jun-18 05:32 UTC
[R] Latex problem in Hmisc (3.8-1) and Mac Os X with R 2.11.1
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 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
Frank E Harrell Jr
2010-Jun-18 13:19 UTC
[R] Latex problem in Hmisc (3.8-1) and Mac Os X with R 2.11.1
On 06/18/2010 12:32 AM, moleps islon wrote:> 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 ? > > //MI could reproduce your problem. We'll get to work on it. Frank> > > > 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 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 > > ______________________________________________ > R-help at 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. >-- Frank E Harrell Jr Professor and Chairman School of Medicine Department of Biostatistics Vanderbilt University