Conflict between xtable and Hmisc when using Sweave?

From: Sander Oom 

Hi David,

Thanks for creating and supporting xtable. Glad I can contribute by 
pointing out problems!

An earlier response from Frank Harrell Jr. suggests that the 
responsibility to resolve the conflict lies primarily with 
you, as Hmisc 
'was there first'.

Not sure how disputes over package conflicts are generally resolved!?

I'll await a final decision!

Thanks again,

Sander.


David B. Dahl wrote:

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:
  

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

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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
---------------------------------------------