Conflict between xtable and Hmisc when using Sweave?

From: Of Sander Oom

Dear David,

I would like to use summarize(Hmisc) and print.xtable(xtable) in a 
single Sweave document, but a conflict with the 'label' function 
prohibits this at the moment!

Would you be able to correct the conflicting code? I will gladly test 
the new package!

I have tried latex(Hmisc) to export the anova table, but 
results are not 
promising! I prefer xtable!!

Thanks,

Sander.

Frank E Harrell Jr wrote:

Sander Oom wrote:

Dear Frank,

I have a Sweave document in which I export anova (aov) 

tables to Latex 

and calculate some summary statistics with summarize{Hmisc} for a 
graph (as in the example below).

I currently use the following code for the aov tables:
<<results=tex>>=
  tmp <- datGrassHC[datGrassHC$Loc > 0 & datGrassHC$Loc < 9 ,]
  tmpAov <- aov(Height~Geology*Altitude*Origin*BinInOut , data=tmp)
  tmpTable <- xtable (tmpAov ,
    caption="ANOVA table for vegetation height.",
    label="tab:AnovaHeight"
    )
  print.xtable(tmpTable, type="latex", floating=TRUE,
    table.placement="ht", caption.placement="top",
    latex.environments=c("center"))
    )
@

I used xtables, because it has a working aov example. I 

would be happy 

to use an alternative if I knew how! Would you have sample code to 
illustrate how to export an aov table to Latex using latex{Hmisc}.

Thanks very much for your help,

Sander.

Frank E Harrell Jr wrote:

Sander Oom wrote:

Dear R users,

The Sweave code below runs fine, as it is. However, an 

error occurs 

when the line 'library(xtable)' is uncommented:
Error:  chunk 1
Error in "label<-"(`*tmp*`, value = "month") :
        no applicable method for "label<-"

Is anybody aware of this and knows a workaround?

Thanks,

Sander.

*******************

\documentclass[a4paper]{article}
\title{Sweave Test for summarize}
\author{Sander Oom}

\usepackage{a4wide}

\begin{document}

\maketitle

\begin{figure}[ht]
\begin{center}
<<fig=TRUE,echo=FALSE>>=
  # library(xtable)
  library(Hmisc)
  set.seed(111)
  dfr <- expand.grid(month=1:12, year=c(1997,1998), reps=1:100)
  month <- dfr$month
  year <- dfr$year
  y <- abs(month-6.5) + 2*runif(length(month)) + year-1997
  s <- summarize(y, llist(month,year), smedian.hilow, 

conf.int=.5)

  print(xYplot(Cbind(y,Lower,Upper) ~ month, groups=year, data=s,
        keys='lines', method='alt', type='b'))
@
\end{center}
\end{figure}

\end{document}

************************

 > version

         _
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    2
minor    1.0
year     2005
month    04
day      18
language R

I feel this is an xtable problem because Hmisc has being 

using label 

and label<- since 1991.

Frank

There are ways to make functions from one area override those from 
another, but the real solution is to ask the xtable author 

not to have 

functions that conflict with the (older) Hmisc package.  -Frank

-- 
--------------------------------------------
Dr Sander P. Oom
Animal, Plant and Environmental Sciences,
University of the Witwatersrand
Private Bag 3, Wits 2050, South Africa
Tel (work)      +27 (0)11 717 64 04
Tel (home)      +27 (0)18 297 44 51
Fax             +27 (0)18 299 24 64
Email   sander at oomvanlieshout.net
Web     www.oomvanlieshout.net/sander