I am resending this since I sent it about an hour ago and still have
not seen it appear on R-help. I assume it never went out but sorry
if it did and you get it twice.
On 5/16/05, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> Using label as an lvalue (i.e. on the left hand side of the assignment)
> causes it to refer to a different function, not label itself.
>
> Any any rate, looking at your example,
> it seems that you don't actually need to use Hmisc and xtable at the same time
> so just make sure that whichever you want at a particular point
> in your code is the only one of the two loaded:
>
> library(Hmisc)
> ...code that involves Hmisc but not xtable...
> detach("package:Hmisc")
> library(xtable)
> ...code that involves xtable but not Hmisc...
>
> On 5/16/05, Sander Oom <[EMAIL PROTECTED]> wrote:
> > I tried to follow your suggestions, but without success:
> >
> > Error: couldn't find function "xtable.mylabel<-"
> >
> > ... resulting from the code below.
> >
> > Any suggestions?
> >
> > Thanks,
> >
> > Sander.
> >
> > library(xtable)
> > xtable.mylabel <- get("label", "package:xtable")
> > library(Hmisc) # provides summarize
> >
> > set.seed(1)
> > temperature <- rnorm(300, 70, 10)
> > month <- sample(1:12, 300, TRUE)
> > year <- sample(2000:2001, 300, TRUE)
> > g <- function(x)c(Mean=mean(x,na.rm=TRUE),Median=median(x,na.rm=TRUE))
> > summarize(temperature, month, g)
> >
> > ## From Venables and Ripley (2002) p.165.
> > N <- c(0,1,0,1,1,1,0,0,0,1,1,0,1,1,0,0,1,0,1,0,1,1,0,0)
> > P <- c(1,1,0,0,0,1,0,1,1,1,0,0,0,1,0,1,1,0,0,1,0,1,1,0)
> > K <- c(1,0,0,1,0,1,1,0,0,1,0,1,0,1,1,0,0,0,1,1,1,0,1,0)
> > yield <-c(49.5,62.8,46.8,57.0,59.8,58.5,55.5,56.0,
> > 62.8,55.8,69.5,55.0,
> > 62.0,48.8,45.5,44.2,52.0,
> > 51.5,49.8,48.8,57.2,59.0,53.2,56.0)
> > npk <- data.frame(block=gl(6,4), N=factor(N), P=factor(P),
> > K=factor(K), yield=yield)
> > ## to show the effects of re-ordering terms contrast the two fits
> > tmpAov <- aov(yield ~ block + N * P + K, npk)
> > tmpTable <- xtable (tmpAov ,
> > caption="ANOVA table for vegetation height.")
> > xtable.mylabel(tmpTable) <- paste("tab:AnovaHeight")
> > print.xtable(tmpTable, type="latex", floating=TRUE,
> > table.placement="h", caption.placement="top",
> > latex.environments=c("center"),
> > title=first.word(deparse(substitute(object))),
> > append=FALSE
> > )
> >
> >
> > Liaw, Andy wrote:
> > > You need to add the namespace to the source package, by adding a NAMESPACE
> > > file. There's an R News article by Prof. Tierney on how to do this. Also
> > > see the `Writing R Extensions' manual. You should get the package
> > > maintainer to do that, as that constitute a change in the package source
> > > code.
> > >
> > > Short of that, you should make sure that Hmisc is loaded later than
> > > xtable,
> > > and use something like what Gabor suggested to access label() in xtable.
> > > (I
> > > would use some other name, though: label() in xtable is already an S3
> > > generic).
> > >
> > > Andy
> > >
> > >>From: Sander Oom
> > >>
> > >>Hi Andy and Gabor,
> > >>
> > >>Thanks for your help so far! I am discovering another R dimension.
> > >>
> > >>Trying to put my head around all this....the conflict
> > >>actually exposes
> > >>itself when calling summarize(Hmisc). Summarize(Hmisc) calls label
> > >>internally, so I can not call it explicitly. Simply calling
> > >>label(xtable) explicitly will not solve the problem with
> > >>summarize(Hmisc).
> > >>
> > >>Thus, I should use namespaces as Andy is suggesting. Now I
> > >>just need to
> > >>know how I 'add namespace' to a library? Does 'loadNamespace' have
> > >>something to do with it?
> > >>
> > >>Thanks very much for your help!
> > >>
> > >>Sander.
> > >>
> > >>
> > >>## From Venables and Ripley (2002) p.165.
> > >>N <- c(0,1,0,1,1,1,0,0,0,1,1,0,1,1,0,0,1,0,1,0,1,1,0,0)
> > >>P <- c(1,1,0,0,0,1,0,1,1,1,0,0,0,1,0,1,1,0,0,1,0,1,1,0)
> > >>K <- c(1,0,0,1,0,1,1,0,0,1,0,1,0,1,1,0,0,0,1,1,1,0,1,0)
> > >>yield <-c(49.5,62.8,46.8,57.0,59.8,58.5,55.5,56.0,
> > >> 62.8,55.8,69.5,55.0,
> > >> 62.0,48.8,45.5,44.2,52.0,
> > >> 51.5,49.8,48.8,57.2,59.0,53.2,56.0)
> > >>npk <- data.frame(block=gl(6,4), N=factor(N), P=factor(P),
> > >> K=factor(K), yield=yield)
> > >>## to show the effects of re-ordering terms contrast the two fits
> > >>tmpAov <- aov(yield ~ block + N * P + K, npk)
> > >>tmpTable <- xtable(tmpAov , caption="Test export of ANOVA table.",
> > >> label="tab:Anova")
> > >>print.xtable(tmpTable, type="latex", floating=TRUE,
> > >> table.placement="h", caption.placement="top",
> > >> latex.environments=c("center"))
> > >>
> > >>Alternatively, using namespace for xtable:
> > >>
> > >>tmpTable <- xtable(tmpAov , caption="Test export of ANOVA table.")
> > >>xtable:::label(tmpTable) <- paste("tab:Anova")
> > >>print.xtable(tmpTable, type="latex", floating=TRUE,
> > >> table.placement="ht", caption.placement="top",
> > >> latex.environments=c("center"))
> > >>
> > >>
> > >>
> > >>Gabor Grothendieck wrote:
> > >>>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 <[EMAIL PROTECTED]> 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 [EMAIL PROTECTED]
> > >>>>>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
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>______________________________________________
> > >>>>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
> > >>--
> > >>
> > >>--------------------------------------------
> > >>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 [EMAIL PROTECTED]
> > >>Web www.oomvanlieshout.net/sander
> > >>---------------------------------------------
> > >>
> > >>
> > >>
> > >
> > >
> > >
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