Re: [R] Conflict between xtable and Hmisc when using Sweave?

From: Sander Oom <slist_at_oomvanlieshout.net>
Date: Mon 16 May 2005 - 20:23:12 EST

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@oomvanlieshout.net
Web     www.oomvanlieshout.net/sander

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Received on Mon May 16 20:45:57 2005

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