Sander,
Thanks for pointing out the conflict between Hmisc and xtable. I am not sure I have a good solution.
My understand of the namespace solution is that packages can specify which variables to export for use by the package users. The label function is not an internal function, rather one what is intended for the user.
Renaming the label() would resolve the conflict with the Hmisc package, but make xtable not compatible with previous versions.
As noted by Andy, label() in xtable is an S3 generic with an implementation label.xtable() specific to the xtable package. Perhaps Frank of Hmisc might be willing to make his follow the S3 generic naming convention?
I am open to suggestions and, more especially, code. Thanks for using xtable.
-- David
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:
add namespace toEven 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
probably would be mucheither xtable or Hmisc. Given the size of Hmisc, it
refer to theeasier to do that with xtable.
With namespace in xtable, you can do xtable:::label() to
gladly testlabel() 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
, data=tmp)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:tables to Latex
Dear Frank,
I have a Sweave document in which I export anova (aov)
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
sample code towould be happytmpTable <- 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
to use an alternative if I knew how! Would you have
latex{Hmisc}.illustrate how to export an aov table to Latex using
groups=year, data=s,error occursThanks 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
conf.int=.5)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,
print(xYplot(Cbind(y,Lower,Upper) ~ month,
http://www.R-project.org/posting-guide.html______________________________________________using labelI feel this is an xtable problem because Hmisc has beingkeys='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
not to haveThere are ways to make functions from one area override those fromand label<- since 1991.
Frank
another, but the real solution is to ask the xtable author
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
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