[R] Conflict between xtable and Hmisc when using Sweave?
Sander Oom
slist at oomvanlieshout.net
Mon May 16 17:49:55 CEST 2005
I did receive it in good order, but the threading on this discussion is
a bit messy!
I have used your suggestion to temporarily 'attach' and detach Hmisc,
while I am awaiting a more permanent solution to the conflict.
Thanks,
Sander.
Gabor Grothendieck wrote:
> 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 <ggrothendieck at gmail.com> 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 <sander at oomvanlieshout.net> 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 <andy_liaw at 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 at oomvanlieshout.net
>>>>>>>>Web www.oomvanlieshout.net/sander
>>>>>>>>
>>>>>>>>______________________________________________
>>>>>>>>R-help at 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 at 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 sander at oomvanlieshout.net
>>>>>Web www.oomvanlieshout.net/sander
>>>>>---------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>
>>>>
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--
--------------------------------------------
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
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