Hmisc-xtable label

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Hmisc-xtable label

Felipe Carrillo
Dear all:
Does anybody know about label conflicts between xtable and Hmisc? I found a couple of e-mails similar to this problem but is not clear to me how to get around the label problem.
The first table(longtable below) is generated with the latex function from Hmisc but for some reason when I try to hyperlink to it,it takes me to the top of the document. The second table created with the xtable package(bottom of document)hyperlinks OK, but if I would create the bottom table first using xtable and then create the longtable using Hmisc then the hyperlink works OK on the longtable but not on the other one.  Thanks
I'am using Sweave and Miktex, windows XP,R-2.8.1 to generate the document below:



\documentclass[11pt]{article}

\usepackage{amsmath}
\usepackage{floatflt,graphicx,times}
\usepackage[usenames,dvipsnames]{color}
\usepackage{longtable,pdflscape}
\usepackage{rotating}
\usepackage{verbatim}
\usepackage[ps2pdf,
bookmarks=true,
bookmarksnumbered=false,
bookmarksopen=false,
colorlinks=true,
linkcolor=webblue]{hyperref}

\definecolor{webgreen}{rgb}{0, 0.5, 0} % less intense green
\definecolor{webblue}{rgb}{0, 0, 0.5} % less intense blue
\definecolor{webred}{rgb}{0.5, 0, 0} % less intense red

\usepackage[all]{hypcap}
\pdfbookmark[1]{Contents}{table}
\title{BROOD-YEAR 2007 WINTER CHINOOK JUVENILE PRODUCTION}
\author{Felipe D. Carrillo}
\date{January 5, 2009}
\pagestyle{headings}
\parskip 7.2pt  
\begin{document}
\setkeys{Gin}{width=1.1\textwidth}
\maketitle

\tableofcontents
The hyperlink of table 1 doesn't work!!!! but the hyperlink of table 2 works OK
\newpage
\listoftables
\listoffigures
\section{Introduction}
\label{sec:introduction}
Winter-run Chinook salmon is one of four distinct "runs" of Chinook salmon (Oncorhynchus tshawytscha)....
\section{Study Area}
The Sacramento River is the largest river system in California, flowing south through 600 kilometers (km)...
\section{Methods}
\subsection{Sampling gear}
Sampling was conducted along a transect using four 2.4 m diameter rotary-screw traps.........
\subsection{Sampling regimes}
In general, rotary traps sampled continuously throughout 24-hour periods and were serviced once daily.  
\subsection{Data collection}
All fish captured were anesthetized, identified to species......

The first table(longtable below) is generated with the latex function from Hmisc but for some reason when I try to hyperlink to it
takes me to the top of the document. The second table created with the xtable package(bottom of document)hyperlinks OK, but
 If I would create the bottom table first using xtable and then create the longtable using Hmisc then the hyperlink works OK on the
 longtable but not on the other one. Does anybody know about conflicts between these two packages? I found a couple of e-mails similar to
 this problem but is not clear to me how to get around the label problem. Thanks
\newpage  
<<tab.R,echo=FALSE,results=tex>>=
library(Hmisc)
x <- matrix(rnorm(1000), ncol = 10)
x.big <- data.frame(x)
latex(x.big,"",label="tab:nice",file="",longtable=TRUE, dec=2,landscape=TRUE,
caption='longtable generated with Hmisc.')
@

\section{Results}
\subsection{Sampling effort}
Weekly sampling effort throughout the 2006 brood-year emigration period was highly variable and ranged
from 0.21 to 1.00 (0 = 0.74, N = 52 weeks; Table 1).  Weekly sampling effort ranged from 0.21 to 1.00 (0 = 0.73, N = 26 weeks)
between July and December, the period of greatest juvenile winter Chinook emigration, and 0.21 to 1.00 (0 = 0.75, N = 26 weeks)
during the latter half of the emigration period (Table 1).\\
\subsection{Trap efficiency trials}
Eight mark-recapture trials were conducted using naturally produced fall run fry sized Chinook

<<tab.RR,echo=F,results=tex>>=
library(xtable)
x <- matrix(rnorm(100), ncol = 10)
ci.table <- data.frame(x)
ci.table <- xtable(x,label='tab:mytable',align="ccccccccccc",caption='Table created with xtable',digits=0)
print(ci.table,tabular.environment='longtable',include.rownames=FALSE,floating=FALSE)
@
\end{document}


Felipe D. Carrillo  
Supervisory Fishery Biologist  
Department of the Interior  
US Fish & Wildlife Service  
California, USA

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Hmisc-xtable label (Solved)

Felipe Carrillo
As soon as I sent the e-mail I found a solution to the hyperlink problem.
I removed the squared brackets and the number 1 from the line below. I don't know why I had the number there in the first place.
\pdfbookmark[1]{Contents}{table}

--- On Sat, 1/10/09, Felipe Carrillo <[hidden email]> wrote:

> From: Felipe Carrillo <[hidden email]>
> Subject: [R] Hmisc-xtable label
> To: [hidden email]
> Date: Saturday, January 10, 2009, 1:36 PM
> Dear all:
> Does anybody know about label conflicts between xtable and
> Hmisc? I found a couple of e-mails similar to this problem
> but is not clear to me how to get around the label problem.
> The first table(longtable below) is generated with the
> latex function from Hmisc but for some reason when I try to
> hyperlink to it,it takes me to the top of the document. The
> second table created with the xtable package(bottom of
> document)hyperlinks OK, but if I would create the bottom
> table first using xtable and then create the longtable using
> Hmisc then the hyperlink works OK on the longtable but not
> on the other one.  Thanks
> I'am using Sweave and Miktex, windows XP,R-2.8.1 to
> generate the document below:
>
>
>
> \documentclass[11pt]{article}
>
> \usepackage{amsmath}
> \usepackage{floatflt,graphicx,times}
> \usepackage[usenames,dvipsnames]{color}
> \usepackage{longtable,pdflscape}
> \usepackage{rotating}
> \usepackage{verbatim}
> \usepackage[ps2pdf,
> bookmarks=true,
> bookmarksnumbered=false,
> bookmarksopen=false,
> colorlinks=true,
> linkcolor=webblue]{hyperref}
>
> \definecolor{webgreen}{rgb}{0, 0.5, 0} % less intense
> green
> \definecolor{webblue}{rgb}{0, 0, 0.5} % less intense
> blue
> \definecolor{webred}{rgb}{0.5, 0, 0} % less intense red
>
> \usepackage[all]{hypcap}
> \pdfbookmark[1]{Contents}{table}
> \title{BROOD-YEAR 2007 WINTER CHINOOK JUVENILE
> PRODUCTION}
> \author{Felipe D. Carrillo}
> \date{January 5, 2009}
> \pagestyle{headings}
> \parskip 7.2pt  
> \begin{document}
> \setkeys{Gin}{width=1.1\textwidth}
> \maketitle
>
> \tableofcontents
> The hyperlink of table 1 doesn't work!!!! but the
> hyperlink of table 2 works OK
> \newpage
> \listoftables
> \listoffigures
> \section{Introduction}
> \label{sec:introduction}
> Winter-run Chinook salmon is one of four distinct
> "runs" of Chinook salmon (Oncorhynchus
> tshawytscha)....
> \section{Study Area}
> The Sacramento River is the largest river system in
> California, flowing south through 600 kilometers (km)...
> \section{Methods}
> \subsection{Sampling gear}
> Sampling was conducted along a transect using four 2.4 m
> diameter rotary-screw traps.........
> \subsection{Sampling regimes}
> In general, rotary traps sampled continuously throughout
> 24-hour periods and were serviced once daily.  
> \subsection{Data collection}
> All fish captured were anesthetized, identified to
> species......
>
> The first table(longtable below) is generated with the
> latex function from Hmisc but for some reason when I try to
> hyperlink to it
> takes me to the top of the document. The second table
> created with the xtable package(bottom of
> document)hyperlinks OK, but
>  If I would create the bottom table first using xtable and
> then create the longtable using Hmisc then the hyperlink
> works OK on the
>  longtable but not on the other one. Does anybody know
> about conflicts between these two packages? I found a couple
> of e-mails similar to
>  this problem but is not clear to me how to get around the
> label problem. Thanks
> \newpage  
> <<tab.R,echo=FALSE,results=tex>>=
> library(Hmisc)
> x <- matrix(rnorm(1000), ncol = 10)
> x.big <- data.frame(x)
> latex(x.big,"",label="tab:nice",file="",longtable=TRUE,
> dec=2,landscape=TRUE,
> caption='longtable generated with Hmisc.')
> @
>
> \section{Results}
> \subsection{Sampling effort}
> Weekly sampling effort throughout the 2006 brood-year
> emigration period was highly variable and ranged
> from 0.21 to 1.00 (0 = 0.74, N = 52 weeks; Table 1).
> Weekly sampling effort ranged from 0.21 to 1.00 (0 = 0.73, N
> = 26 weeks)
> between July and December, the period of greatest juvenile
> winter Chinook emigration, and 0.21 to 1.00 (0 = 0.75, N =
> 26 weeks)
> during the latter half of the emigration period (Table
> 1).\\
> \subsection{Trap efficiency trials}
> Eight mark-recapture trials were conducted using naturally
> produced fall run fry sized Chinook
>
> <<tab.RR,echo=F,results=tex>>=
> library(xtable)
> x <- matrix(rnorm(100), ncol = 10)
> ci.table <- data.frame(x)
> ci.table <-
> xtable(x,label='tab:mytable',align="ccccccccccc",caption='Table
> created with xtable',digits=0)
> print(ci.table,tabular.environment='longtable',include.rownames=FALSE,floating=FALSE)
> @
> \end{document}
>
>
> Felipe D. Carrillo  
> Supervisory Fishery Biologist  
> Department of the Interior  
> US Fish & Wildlife Service  
> California, USA
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained,
> reproducible code.

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.