Conflict between xtable and Hmisc when using Sweave?

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

------------------------------------------------------------------------------
Notice:  This e-mail message, together with any attachment...{{dropped}}

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

------------------------------------------------------------------------------
Notice:  This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message.  If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
------------------------------------------------------------------------------
 

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

------------------------------------------------------------------------------
Notice:  This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message.  If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
------------------------------------------------------------------------------

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

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

Notice:  This e-mail message, together with any attachments, contains 
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, 
New Jersey, USA 08889), and/or its affiliates (which may be known 
outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD 
and in Japan, as Banyu) that may be confidential, proprietary 
copyrighted and/or legally privileged. It is intended solely for the 
use of the individual or entity named on this message.  If you are not 
the intended recipient, and have received this message in error, 
please notify us immediately by reply e-mail and then delete it from 
your system.
------------------------------------------------------------------------------ 

 

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

------------------------------------------------------------------------------
Notice:  This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message.  If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
------------------------------------------------------------------------------

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

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