Conflict between xtable and Hmisc when using Sweave?

4 messages · Liaw, Andy, Sander Oom, Gabor Grothendieck

Original

1

4

Liaw, Andy

Mon, May 16, 2005 5:46 AM #

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

Gabor Grothendieck

Mon, May 16, 2005 6:21 AM #

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

Sander Oom

Mon, May 16, 2005 6:35 AM #

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

Gabor Grothendieck

Mon, May 16, 2005 6:46 AM #

Do you need label in both xtable and Hmisc?  If you only need
it in Hmisc and not in xtable then just be sure you have loaded
xtable first and Hmisc second.  This:

search()

will give you the search path.  It will find the first one on the
search path so if Hmisc is before xtable (which would occur
if you loaded Hmisc last) then it would find that one.

If you have already loaded them in the wrong order then just
detach Hmisc and load it again:

detach("package:Hmisc")
library(Hmisc)

On 5/16/05, Sander Oom <slist at oomvanlieshout.net> wrote:

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