[Genabel-commits] r1154 - tutorials/GenABEL_general

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-03-16 13:48:32 +0100 (Sat, 16 Mar 2013)
New Revision: 1154

Modified:
   tutorials/GenABEL_general/GenABEL-tutorial.Rnw
   tutorials/GenABEL_general/introR.Rnw
Log:
- IntroR.Rnw: fix \ref to figure
- GenABEL-tutorial.Rnw: coloured hyperlinks instead of boxes, finetuned the PDF experience (e.g. added metadata). Changed from the color package to the xcolor package.


Modified: tutorials/GenABEL_general/GenABEL-tutorial.Rnw
===================================================================
--- tutorials/GenABEL_general/GenABEL-tutorial.Rnw	2013-03-16 12:33:49 UTC (rev 1153)
+++ tutorials/GenABEL_general/GenABEL-tutorial.Rnw	2013-03-16 12:48:32 UTC (rev 1154)
@@ -2,13 +2,40 @@
 
 \usepackage{Sweave}
 \usepackage{amsmath}
-\usepackage{color,framed}
+\usepackage{framed}
 \usepackage{titleref}
 \usepackage{nameref}
 \usepackage{verbatim}
 \usepackage{makeidx}
 \usepackage[answerdelayed,lastexercise]{exercise}
-\usepackage{hyperref}
+
+\usepackage[dvipsnames]{xcolor}
+\definecolor{webgreen}{rgb}{0,.5,0}
+
+\usepackage[pdftex,pdfpagelabels]{hyperref}
+\pdfcompresslevel=9
+\pdfadjustspacing=1
+ % get the links to the figures and tables right:
+\usepackage[all]{hypcap} % to be loaded after hyperref package
+\hypersetup{%
+  linktocpage=false, % If true the page numbers in the toc are links
+	 	     % instead of the section headings.
+  pdfstartview=FitH, % pdfstartpage=3,
+  breaklinks=true, pageanchor=true, %
+  pdfpagemode=UseOutlines, plainpages=false, bookmarksnumbered, %
+  bookmarksopen=true, bookmarksopenlevel=1, hypertexnames=true, %
+  pdfhighlight=/O, %hyperfootnotes=true,%nesting=true,%frenchlinks,%
+  pdfauthor={\textcopyright\ Y.S. Aulchenko},
+  pdftitle={GenABEL tutorial},
+  pdfkeywords={GenABEL, ProbABEL, MixABEL, DatABEL, tutorial, R, statistics, 
+    genetics}
+}
+
+% Coloured hyperlinks instead of boxes
+\hypersetup{%
+  colorlinks=true, urlcolor=MidnightBlue, linkcolor=blue, %
+  citecolor=webgreen}
+
 \usepackage{cite}
 \usepackage{natbib}
 \usepackage{xspace}

Modified: tutorials/GenABEL_general/introR.Rnw
===================================================================
--- tutorials/GenABEL_general/introR.Rnw	2013-03-16 12:33:49 UTC (rev 1153)
+++ tutorials/GenABEL_general/introR.Rnw	2013-03-16 12:48:32 UTC (rev 1154)
@@ -1323,7 +1323,7 @@
 <<>>=
 check.trait( c("sex", "age", "qt3"), phdata(srdta) )
 @
-The corresponding graph is shown in figure \ref{qcgra}.
+The corresponding graph is shown in figure \ref{fig:qcgra}.
 \begin{figure}[t]
 \centering
 <<fig=true,echo=false>>=