[Genabel-commits] r1163 - tutorials/GenABEL_general

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

Author: yurii
Date: 2013-03-19 20:42:37 +0100 (Tue, 19 Mar 2013)
New Revision: 1163

Modified:
   tutorials/GenABEL_general/GenABEL-tutorial.Rnw
   tutorials/GenABEL_general/introR.Rnw
Log:
small changes to allow conversion to HTML

Modified: tutorials/GenABEL_general/GenABEL-tutorial.Rnw
===================================================================
--- tutorials/GenABEL_general/GenABEL-tutorial.Rnw	2013-03-19 19:26:22 UTC (rev 1162)
+++ tutorials/GenABEL_general/GenABEL-tutorial.Rnw	2013-03-19 19:42:37 UTC (rev 1163)
@@ -8,10 +8,13 @@
 \usepackage{verbatim}
 \usepackage{makeidx}
 \usepackage[answerdelayed,lastexercise]{exercise}
+\usepackage{ifpdf}
 
 \usepackage[dvipsnames]{xcolor}
 \definecolor{webgreen}{rgb}{0,.5,0}
 
+\ifpdf 
+
 \usepackage[pdfpagelabels]{hyperref}
 \pdfcompresslevel=9
 \pdfadjustspacing=1
@@ -36,6 +39,8 @@
   colorlinks=true, urlcolor=MidnightBlue, linkcolor=blue, %
   citecolor=webgreen}
 
+\fi
+
 \usepackage{cite}
 \usepackage{natbib}
 \usepackage{xspace}

Modified: tutorials/GenABEL_general/introR.Rnw
===================================================================
--- tutorials/GenABEL_general/introR.Rnw	2013-03-19 19:26:22 UTC (rev 1162)
+++ tutorials/GenABEL_general/introR.Rnw	2013-03-19 19:42:37 UTC (rev 1163)
@@ -584,12 +584,12 @@
 \texttt{map(srdta)}. Explore these vectors and answer 
 the questions.
 \Question What is the ID and sex of the first person in the data set? 
-\Question Of the $22^\text{nd}$ person? 
+\Question Of the $22^{\text{nd}}$ person? 
 \Question How many males are observed among the first hundred subjects? 
-\Question How many FEMALES are among the $4^\text{th}$ hundred?
+\Question How many FEMALES are among the $4^{\text{th}}$ hundred?
 \Question What is the male proportion in the first 1000 people?
 \Question What is the FEMALE proportion in second 1000 (1001:2000) people?
-\Question What is name, chromosome and map position of 33$^\text{rd}$ marker? 
+\Question What is name, chromosome and map position of 33$^{\text{rd}}$ marker? 
 \Question What is distance between markers 25 and 26?
 \end{Exercise}
 \begin{Answer}
@@ -599,7 +599,7 @@
 idnames(srdta)[1]
 male(srdta)[1]
 @
-The id for the 22$^\text{nd}$ person is "\Sexpr{idnames(srdta)[22]}" and 
+The id for the 22$^{\text{nd}}$ person is "\Sexpr{idnames(srdta)[22]}" and 
 sex code is \Sexpr{male(srdta)[22]}:
 <<>>=
 idnames(srdta)[22]
@@ -610,7 +610,7 @@
 <<>>=
 sum(male(srdta)[1:100])
 @
-Among the 4$^\text{th}$ hundred subjects there are 
+Among the 4$^{\text{th}}$ hundred subjects there are 
 \Sexpr{sum(male(srdta)[301:400]==0)} females:
 <<>>=
 100 - sum(male(srdta)[301:400])
@@ -623,7 +623,7 @@
 <<>>=
 1 - mean(male(srdta)[1001:2000])
 @
-Name, chromosome and map position of the 33$^\text{rd}$ marker are:
+Name, chromosome and map position of the 33$^{\text{rd}}$ marker are:
 <<>>=
 snpnames(srdta)[33]
 chromosome(srdta)[33]
@@ -930,7 +930,7 @@
 with phenotypes. This data frame may be accessed through 
 \texttt{phdata(srdta)}. Explore this data frame and 
 answer the questions
-\Question What is the value of the $4^\text{th}$ variable for subject 
+\Question What is the value of the $4^{\text{th}}$ variable for subject 
 number 75? 
 \Question What is the value of variable 1 for person 75? Check the value 
 of this variable for the first ten people.
@@ -945,7 +945,7 @@
 data(srdta)
 phdata(srdta)[1:5, ]
 @
-The value of the $4^\text{th}$ variable of person 75:
+The value of the $4^{\text{th}}$ variable of person 75:
 <<>>=
 phdata(srdta)[75, 4]
 @