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CHAPTER2. L
A
T
E
X
13
$\beta_{1}$ is the coefficient of $X_{1}$; $F_{1,11}=1.2$.
results in
β
1
is the cofﬁcient of
X
1
;
F
1,11
=1.2
.
·
Online help resources at
biostat.virginia.edu/latex/
2.1.1 Commonly Used L
A
T
E
XCommands
TypedbyUser
Result
\textbf{this}
thisisboldface
\emph{this}
thisisemphasized
$whatever$
Typeset
whatever
inmathmode
$\chi \tau \gamma \sigma \alpha$
χτγσα
$\hat{Y} \neq 2 \times X\hat{\beta}$
ˆ
Y =2×X
ˆ
β
$a \leq X \leq b, W < c, Z \geq a$
a≤X ≤b,W <c,Z ≥a
$\chi^2$
χ
2
$X^{i+j}$
X
i+j
tocontrolwhichtextis superscripted
$X_3$
X
3
subscriptonlyoneletter/number
$X_{i+1}$
X
i+1
controlwhatissubscripted
$\bar{X} = \sum_{i=1}^{n} X_{i}$
¯
X=
n
i=1
X
i
\$100$100use\$withoutmeaningmathmode
\& \% \# \{ \}
&%#
{}
otherspecialcharacter escapes
\begin{enumerate} ... \end{enumerate}
sequentiallynumberedlist
\begin{itemize} ... \end{itemize}
bulletlist
\item text
...
entriesfornumberedor bulletitems
~
forceablank character
\\
forceanewline
\newpage
forceanewpage
\section{text}
startanewsection,withtitle
2.1.2 Using L
A
T
E
Xand
PSTricks
forDrawing Diagrams
·
Section 1.3 showedhow a powerful standalonecommandlanguage
graphviz
can produce complex diagrams
·
L
A
T
E
X has a number of macro packages for composing special diagrams,
including electronic circuits and music [1]
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CHAPTER2. L
A
T
E
X
14
·
L
A
T
E
Xcan be faster to use than drawing programs in many cases, with easier
alignment of elements of a diagram, by thinking of the diagram as a matrix
·
Example: The
PSTricks
L
A
T
E
Xpackage
\usepackage{pstricks,pst-node}
% Define shorthand for a 20 character-wide centered-text parbox
% This automatically formats multi-line boxes of text
\newcommand{\pb}[1]{\parbox[c]{20ex}{#1}}
\centerline{\begin{psmatrix}
[name=A]\psframebox{This is a box of text}
&
[name=C]And some more text \\
\psovalbox{This is yet another bunch of text} &
[name=B]\psframebox{\pb{Hello there and how are you today?}} \\
\pscirclebox{A single line} &
\psovalbox{Another single line} \\
\psovalbox{\pb{A lot of text that does not mean very much, but I am
putting it here anyway}} &
[name=E]\psframebox{\pb{
\begin{itemize}
\item Point one
\item Point two
\end{itemize}}}
\psset{arrows=->}
\ncline{A}{B}
\ncline{C}{B}
\nccurve{C}{E}
\end{psmatrix}}
·
See Figure 2.1
2.1.3 Beneﬁts ofL
A
T
E
Xfor Statistical Reports
·
Automatic symbolic cross-referencing
\section{Introduction}
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CHAPTER2. L
A
T
E
X
15
Thisisaboxoftext
Andsomemoretext
Thisisyetanotherbunchof text
Hellothereandhow
areyoutoday?
Asingleline
Another singleline
A lot of text that
does notmeanvery
much, but I am
puttingithereany-
way
• Pointone
• Pointtwo
1
Figure2.1:
Adiagramproduced by
PSTricks
The theory behind this project can be summarized in the equation
e = m c^{2}
\label{mc2}
\section{Results} \label{results}
....
\section{Conclusion}
As seen in Section \ref{results}, Equation \ref{mc2} has
far-reaching implications. Figure \ref{myfigure} shows an example.
·
The
\input{filename}
and
\includegraphics{filename}
commandsinL
A
T
E
X
can insert tables and graphs created by statistical programs.
·
Adobe PostScript format is recommended for creating graphics ﬁles; L
A
T
E
X
renders these much better than Word renders Microsoft format graphics
·
Entire document can be regenerated (with pages and section numbers re-
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CHAPTER2. L
A
T
E
X
16
computed) using latest versions of tables and graphs
·
There are functions in S-P
LUS
and R for automatically creating L
A
T
E
Xcode
for complex tables
·
There is an option to make all references within the document clickable hy-
perlinks in the ﬁnal
pdf
ﬁle; these can be driven by automatically created
tables of contents, ﬁgures, and tables, which is ideal for navigating long sta-
tistical reports
b
·
Excellent facility for handling bibliographic database and citing references in
various styles
·
Typical sequence:
– RunS-P
LUS
to create or recreate tables and graphics ﬁles
– Runthe
latex
system command on the L
A
T
E
Xmaster document to com-
pile it
– Printtheresultorcreatea
pdf
ﬁle from it
– Nomanualoperationssuchasmenuselectionsforimportingﬁlesintoa
Word document
·
Can construct batch programs for executing dataset operations, statistical
analysis, and report building to make report reproducible when any compo-
nent data change
·
See
hesweb1.med.virginia.edu/biostat/s/doc/summary.pdf
fora detailed
how-to document
b
Suchhyperlinked
pdf
reportsarepreferredbyFDAreviewersofNewDrugApplications.
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CHAPTER2. L
A
T
E
X
17
2.2 Biostatistics L
A
T
E
XWeb Server
·
You can install L
A
T
E
Xyourself but requires some effort and requires 100MB
of disk space
·
Can execute L
A
T
E
Xon a Linux server that has all the tools installed, including
Ghostscript to convert to Adobe Acrobat Portable Document Format (PDF),
anearly-universal format for transmitting electronic documents
·
The server can accept S-P
LUS
output with text to be sent to L
A
T
E
Xspeciﬁed
as S-P
LUS
comment lines. The server runs a reformatting program to create
the L
A
T
E
Xsource code for a report.
·
Access the server at
biostat.virginia.edu/latex
or through the course
web page
·
In-class exercise:
– Rightclickonthe“BarebonesL
A
T
E
Xexample”on the
latex
web page
and save it to a temporary directory (in Wilson 308 a good area to use
is
\temp
on
C:
)under any name you wish
c
– Clickonthelinktotheserverandhit
Browse
to ﬁnd the ﬁle you saved.
Right click on this ﬁle to rename it to have a sufﬁx of
.tex
. Get under
Browse
again to select this ﬁle to upload it for processing.
NOTE:ForallL
A
T
E
Xapplications after this exercise and after Homework 1,
you willnotneed to rename the ﬁle to upload to have a sufﬁx of
.tex
.You
only need to use this sufﬁx to tell the server that you have a plain L
A
T
E
X
ﬁle. Ordinarily you will be uploading S-P
LUS
output, which can have any
ﬁle extension other than
.tex
.
– WhenL
A
T
E
Xcompilation ﬁnishes, left click on the resulting
pdf
ﬁle to view
it
c
AproblemwithMicrosoftWindowspreventsyoufromsavingitwiththeextensionthatisreallyneeded,
.tex
.
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CHAPTER2. L
A
T
E
X
18
– Rightclickonthe
pdf
ﬁle and save it to a temporary area , then invoke
Acrobat Reader
manually and look at this ﬁle (this method sometimes
ﬁxes problems with printing
pdf
documents)
Chapter 3
Introduction to S
3.1 Statistical Languages and Packages
·
Procedure-oriented statistical packages
– SAS,SPSS
– Lackofgoodinteractivegraphics
– Difﬁculttoimplementnewmethods
– Closedsource—sometimescan’tﬁndouthowcalculationsdone
·
Statistical language
– S—objectoriented
– PerlDataLanguage,MATLAB,Gauss
– Interactivegraphics
19
CHAPTER3. INTRODUCTION TOS
20
– Easytoimplementnewmethodsanddistributetoothers
– AnopensourceversionofSexists:R
3.2 Why S?
AH1.1
·
S: a language for interactive data analysis and graphics
·
Early on S was planned to be extendible
– UserswritenewfunctionsintheSlanguage,sameasdevelopers
– Documentationforaddingfunctionstothesystemisexcellent
– User-addedfunctionsareinvokedinsamewayasbuilt-ins
– Userscancreatetheirowndatatypesandaddattributessuchascom-
ments to any piece of data in S
– MostusersaddingtoaproceduralsystemsuchasSASwriteinalan-
guage (SAS macro or IML language) not used by SAS developers
– VeryhardtowritenewSASprocedures
·
Sdata elements may be complex and asymmetric (e.g., trees)
·
Huge international community of users adding new capabilities to S
·
High-level language: a few commands do a lot of work
CHAPTER3. INTRODUCTION TOS
21
·
Unlike macros, language is “live”, i.e., connected to the data while com-
mands are running
if(is.category(x) | is.character(x) |
(is.numeric(x) & length(unique(x)) < 20))
table(x) else quantile(x)
Computes quantiles of a variable
x
if
x
is numeric and fairly continuous (at
least 20 unique values), frequency tabulation otherwise
·
Object orientation means fewer commands to learn
·
Second-order analyses easy; e.g. repeat a multi-step analysis multiple times
perturbing the data slightly to see if results are unstable
·
Best scientiﬁc graphics available
SAS graphics are ugly, inﬂexible, have poor defaults, difﬁcult to program
3.3 History and Background of S-P
LUS
KOpp.1-4
·
Slanguage developed at AT&T–Bell Labs, where C and UNIX were devel-
oped
·
Initial version 1976
·
Usage increased rapidly after John Tukey’s book on exploratory data analy-
sis published
·
S-P
LUS
acommercial version of S, began 1987, popularity increased dra-
matically after 1990
·
S-P
LUS
runs on Microsoft Windows, UNIX, Linux