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

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Mon 16 May 2005 - 23:21:11 EST

Even without a namespace one could explicitly reference the label in xtable via:

xtable.label <- get("label", "package:xtable")

On 5/16/05, Liaw, Andy <andy_liaw@merck.com> wrote:
> One possible solution without renaming the functions is to add namespace to
> either xtable or Hmisc. Given the size of Hmisc, it probably would be much
> easier to do that with xtable.
>
> With namespace in xtable, you can do xtable:::label() to refer to the
> label() in xtable specifically.
>
> Andy
>
> > 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@oomvanlieshout.net
> > Web www.oomvanlieshout.net/sander
> >
> > ______________________________________________
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> > http://www.R-project.org/posting-guide.html
> >
> >
> >
>
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R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon May 16 23:26:53 2005

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