Cleaned up
This commit is contained in:
parent
33865bb899
commit
822737bc69
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homan@homan-Lenovo-YOGA-710-11IKB.3240:1522929731
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\begin{Verbatim}[commandchars=\\\{\}]
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\PYG{k+kp}{set.seed}\PYG{p}{(}\PYG{l+m}{20180402}\PYG{p}{)}
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x1 \PYG{o}{\PYGZlt{}\PYGZhy{}} rnorm\PYG{p}{(}\PYG{l+m}{100}\PYG{p}{,} \PYG{l+m}{0}\PYG{p}{,} \PYG{l+m}{1}\PYG{p}{)}
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x2 \PYG{o}{\PYGZlt{}\PYGZhy{}} rnorm\PYG{p}{(}\PYG{l+m}{100}\PYG{p}{,} \PYG{l+m}{0.5}\PYG{p}{,} \PYG{l+m}{1}\PYG{p}{)}
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hist\PYG{p}{(}x1\PYG{p}{,} col\PYG{o}{=}\PYG{l+s}{\PYGZdq{}red\PYGZdq{}}\PYG{p}{)}
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hist\PYG{p}{(}x2\PYG{p}{,} col\PYG{o}{=}\PYG{l+s}{\PYGZdq{}blue\PYGZdq{}}\PYG{p}{,} add\PYG{o}{=}\PYG{k+kc}{TRUE}\PYG{p}{)}
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\end{Verbatim}
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\begin{Verbatim}[commandchars=\\\{\}]
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\PYG{c+c1}{\PYGZsh{} Download emacs icon from gnu.org}
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curl \PYGZhy{}0 https://www.gnu.org/software/emacs/images/emacs.png
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\end{Verbatim}
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\begin{Verbatim}[commandchars=\\\{\}]
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\PYG{k+kn}{library}\PYG{p}{(}broom\PYG{p}{)}
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\PYG{k+kn}{library}\PYG{p}{(}dplyr\PYG{p}{)}
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t1 \PYG{o}{\PYGZlt{}\PYGZhy{}} tidy\PYG{p}{(}\PYG{k+kp}{round}\PYG{p}{(}\PYG{k+kp}{summary}\PYG{p}{(}x1\PYG{p}{),} \PYG{l+m}{2}\PYG{p}{))}
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t2 \PYG{o}{\PYGZlt{}\PYGZhy{}} tidy\PYG{p}{(}\PYG{k+kp}{round}\PYG{p}{(}\PYG{k+kp}{summary}\PYG{p}{(}x2\PYG{p}{),} \PYG{l+m}{2}\PYG{p}{))}
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\PYG{c+c1}{\PYGZsh{} This will export as a table}
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\PYG{k+kp}{rbind}\PYG{p}{(}t1\PYG{p}{,} t2\PYG{p}{)} \PYG{o}{\PYGZpc{}\PYGZgt{}\PYGZpc{}}
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mutate\PYG{p}{(}name\PYG{o}{=}\PYG{k+kt}{c}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}x1\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}x2\PYGZdq{}}\PYG{p}{))}
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\end{Verbatim}
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@ -1,101 +0,0 @@
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\makeatletter
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\def\PYG@reset{\let\PYG@it=\relax \let\PYG@bf=\relax%
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\let\PYG@ul=\relax \let\PYG@tc=\relax%
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\let\PYG@bc=\relax \let\PYG@ff=\relax}
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\def\PYG@tok#1{\csname PYG@tok@#1\endcsname}
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\def\PYG@toks#1+{\ifx\relax#1\empty\else%
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\PYG@tok{#1}\expandafter\PYG@toks\fi}
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\def\PYG@do#1{\PYG@bc{\PYG@tc{\PYG@ul{%
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\PYG@it{\PYG@bf{\PYG@ff{#1}}}}}}}
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\def\PYG#1#2{\PYG@reset\PYG@toks#1+\relax+\PYG@do{#2}}
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\expandafter\def\csname PYG@tok@gd\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.63,0.00,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@gu\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.50,0.00,0.50}{##1}}}
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\expandafter\def\csname PYG@tok@gt\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.27,0.87}{##1}}}
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\expandafter\def\csname PYG@tok@gs\endcsname{\let\PYG@bf=\textbf}
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\expandafter\def\csname PYG@tok@gr\endcsname{\def\PYG@tc##1{\textcolor[rgb]{1.00,0.00,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@cm\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PYG@tok@vg\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYG@tok@vi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYG@tok@vm\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYG@tok@mh\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYG@tok@cs\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PYG@tok@ge\endcsname{\let\PYG@it=\textit}
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\expandafter\def\csname PYG@tok@vc\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYG@tok@il\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYG@tok@go\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.53,0.53,0.53}{##1}}}
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\expandafter\def\csname PYG@tok@cp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.74,0.48,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@gi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.63,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@gh\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
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\expandafter\def\csname PYG@tok@ni\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.60,0.60,0.60}{##1}}}
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\expandafter\def\csname PYG@tok@nl\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.63,0.63,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@nn\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PYG@tok@no\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.53,0.00,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@na\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.49,0.56,0.16}{##1}}}
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\expandafter\def\csname PYG@tok@nb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@nc\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PYG@tok@nd\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}}
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\expandafter\def\csname PYG@tok@ne\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.82,0.25,0.23}{##1}}}
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\expandafter\def\csname PYG@tok@nf\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PYG@tok@si\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}}
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\expandafter\def\csname PYG@tok@s2\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PYG@tok@nt\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@nv\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYG@tok@s1\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PYG@tok@dl\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PYG@tok@ch\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PYG@tok@m\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYG@tok@gp\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
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\expandafter\def\csname PYG@tok@sh\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PYG@tok@ow\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}}
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\expandafter\def\csname PYG@tok@sx\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@bp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@c1\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PYG@tok@fm\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PYG@tok@o\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYG@tok@kc\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@c\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PYG@tok@mf\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYG@tok@err\endcsname{\def\PYG@bc##1{\setlength{\fboxsep}{0pt}\fcolorbox[rgb]{1.00,0.00,0.00}{1,1,1}{\strut ##1}}}
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\expandafter\def\csname PYG@tok@mb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYG@tok@ss\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYG@tok@sr\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}}
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\expandafter\def\csname PYG@tok@mo\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYG@tok@kd\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@mi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYG@tok@kn\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@cpf\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PYG@tok@kr\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@s\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PYG@tok@kp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@w\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}}
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\expandafter\def\csname PYG@tok@kt\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.69,0.00,0.25}{##1}}}
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\expandafter\def\csname PYG@tok@sc\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PYG@tok@sb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PYG@tok@sa\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PYG@tok@k\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYG@tok@se\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.73,0.40,0.13}{##1}}}
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\expandafter\def\csname PYG@tok@sd\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\def\PYGZbs{\char`\\}
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\def\PYGZus{\char`\_}
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\def\PYGZob{\char`\{}
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\def\PYGZcb{\char`\}}
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\def\PYGZca{\char`\^}
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\def\PYGZam{\char`\&}
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\def\PYGZlt{\char`\<}
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\def\PYGZgt{\char`\>}
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\def\PYGZsh{\char`\#}
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\def\PYGZpc{\char`\%}
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\def\PYGZdl{\char`\$}
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\def\PYGZhy{\char`\-}
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\def\PYGZsq{\char`\'}
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\def\PYGZdq{\char`\"}
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\def\PYGZti{\char`\~}
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% for compatibility with earlier versions
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\def\PYGZat{@}
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\def\PYGZlb{[}
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\def\PYGZrb{]}
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\makeatother
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@ -1,101 +0,0 @@
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\makeatletter
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\def\PYGdefault@reset{\let\PYGdefault@it=\relax \let\PYGdefault@bf=\relax%
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\let\PYGdefault@ul=\relax \let\PYGdefault@tc=\relax%
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\let\PYGdefault@bc=\relax \let\PYGdefault@ff=\relax}
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\def\PYGdefault@tok#1{\csname PYGdefault@tok@#1\endcsname}
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\def\PYGdefault@toks#1+{\ifx\relax#1\empty\else%
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\PYGdefault@tok{#1}\expandafter\PYGdefault@toks\fi}
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\def\PYGdefault@do#1{\PYGdefault@bc{\PYGdefault@tc{\PYGdefault@ul{%
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\PYGdefault@it{\PYGdefault@bf{\PYGdefault@ff{#1}}}}}}}
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\def\PYGdefault#1#2{\PYGdefault@reset\PYGdefault@toks#1+\relax+\PYGdefault@do{#2}}
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\expandafter\def\csname PYGdefault@tok@gd\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.63,0.00,0.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@gu\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.50,0.00,0.50}{##1}}}
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\expandafter\def\csname PYGdefault@tok@gt\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.27,0.87}{##1}}}
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\expandafter\def\csname PYGdefault@tok@gs\endcsname{\let\PYGdefault@bf=\textbf}
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\expandafter\def\csname PYGdefault@tok@gr\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{1.00,0.00,0.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@cm\endcsname{\let\PYGdefault@it=\textit\def\PYGdefault@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PYGdefault@tok@vg\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYGdefault@tok@vi\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYGdefault@tok@vm\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYGdefault@tok@mh\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYGdefault@tok@cs\endcsname{\let\PYGdefault@it=\textit\def\PYGdefault@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PYGdefault@tok@ge\endcsname{\let\PYGdefault@it=\textit}
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\expandafter\def\csname PYGdefault@tok@vc\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
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\expandafter\def\csname PYGdefault@tok@il\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PYGdefault@tok@go\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.53,0.53,0.53}{##1}}}
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\expandafter\def\csname PYGdefault@tok@cp\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.74,0.48,0.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@gi\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.63,0.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@gh\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
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\expandafter\def\csname PYGdefault@tok@ni\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.60,0.60,0.60}{##1}}}
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\expandafter\def\csname PYGdefault@tok@nl\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.63,0.63,0.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@nn\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@no\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.53,0.00,0.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@na\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.49,0.56,0.16}{##1}}}
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\expandafter\def\csname PYGdefault@tok@nb\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@nc\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@nd\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@ne\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.82,0.25,0.23}{##1}}}
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\expandafter\def\csname PYGdefault@tok@nf\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PYGdefault@tok@si\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}}
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\expandafter\def\csname PYGdefault@tok@s2\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@nt\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@nv\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@s1\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@dl\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@ch\endcsname{\let\PYGdefault@it=\textit\def\PYGdefault@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@m\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@gp\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@sh\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@ow\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@sx\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@bp\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@c1\endcsname{\let\PYGdefault@it=\textit\def\PYGdefault@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@fm\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@o\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@kc\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@c\endcsname{\let\PYGdefault@it=\textit\def\PYGdefault@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@mf\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@err\endcsname{\def\PYGdefault@bc##1{\setlength{\fboxsep}{0pt}\fcolorbox[rgb]{1.00,0.00,0.00}{1,1,1}{\strut ##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@mb\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@ss\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@sr\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@mo\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@kd\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@mi\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@kn\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@cpf\endcsname{\let\PYGdefault@it=\textit\def\PYGdefault@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@kr\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@s\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@kp\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@w\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@kt\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.69,0.00,0.25}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@sc\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@sb\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@sa\endcsname{\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@k\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@se\endcsname{\let\PYGdefault@bf=\textbf\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.40,0.13}{##1}}}
|
||||
\expandafter\def\csname PYGdefault@tok@sd\endcsname{\let\PYGdefault@it=\textit\def\PYGdefault@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
|
||||
|
||||
\def\PYGdefaultZbs{\char`\\}
|
||||
\def\PYGdefaultZus{\char`\_}
|
||||
\def\PYGdefaultZob{\char`\{}
|
||||
\def\PYGdefaultZcb{\char`\}}
|
||||
\def\PYGdefaultZca{\char`\^}
|
||||
\def\PYGdefaultZam{\char`\&}
|
||||
\def\PYGdefaultZlt{\char`\<}
|
||||
\def\PYGdefaultZgt{\char`\>}
|
||||
\def\PYGdefaultZsh{\char`\#}
|
||||
\def\PYGdefaultZpc{\char`\%}
|
||||
\def\PYGdefaultZdl{\char`\$}
|
||||
\def\PYGdefaultZhy{\char`\-}
|
||||
\def\PYGdefaultZsq{\char`\'}
|
||||
\def\PYGdefaultZdq{\char`\"}
|
||||
\def\PYGdefaultZti{\char`\~}
|
||||
% for compatibility with earlier versions
|
||||
\def\PYGdefaultZat{@}
|
||||
\def\PYGdefaultZlb{[}
|
||||
\def\PYGdefaultZrb{]}
|
||||
\makeatother
|
||||
|
|
@ -1,173 +0,0 @@
|
|||
\frametitle{}
|
||||
\begin{columns}
|
||||
\begin{column}[t]{0.45\columnwidth}
|
||||
\begin{block}{Background}
|
||||
\begin{itemize}
|
||||
\item Here we show how org-mode (version
|
||||
9.1.7) and emacs (version
|
||||
25.2.2) can be used to make decent looking scientific
|
||||
posters
|
||||
\item With org-mode we can populate the poster with code, graphs and numbers
|
||||
from inline code in languages such as R, python, Matlab and even shell
|
||||
scripting
|
||||
\item For example, this poster was created on 2018-04-05 15:59 on
|
||||
Ubuntu 17.10.
|
||||
\item Inline code could look like this (which will produce a graph;
|
||||
Fig. \ref{fig:orgd999323}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.68\columnwidth}
|
||||
\begin{minted}[linenos=true,bgcolor=lightgray]{r}
|
||||
set.seed(20180402)
|
||||
x1 <- rnorm(100, 0, 1)
|
||||
x2 <- rnorm(100, 0.5, 1)
|
||||
hist(x1, col="red")
|
||||
hist(x2, col="blue", add=TRUE)
|
||||
\end{minted}
|
||||
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{3.png}
|
||||
\caption{\label{fig:orgd999323}
|
||||
This is the output.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
|
||||
\begin{block}{Inline code and tables}
|
||||
\begin{itemize}
|
||||
\item In addition to inline code, we can also produce tables
|
||||
\item Tables are very powerful in org-mode, they even include spreadsheet
|
||||
capabilities
|
||||
\item Some code to process the first vector from above to make a table out
|
||||
of its summary could look like this, which would result in a little
|
||||
table (Table \ref{tab:org3b1c59c}) :
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.78\columnwidth}
|
||||
\begin{minted}[linenos=true,bgcolor=lightgray]{r}
|
||||
library(broom)
|
||||
library(dplyr)
|
||||
t1 <- tidy(round(summary(x1), 2))
|
||||
t2 <- tidy(round(summary(x2), 2))
|
||||
|
||||
# This will export as a table
|
||||
rbind(t1, t2) %>%
|
||||
mutate(name=c("x1", "x2"))
|
||||
\end{minted}
|
||||
|
||||
\vspace{2cm}
|
||||
|
||||
\begin{table}[htbp]
|
||||
\caption{\label{tab:org3b1c59c}
|
||||
A table summarizing the two distributions.}
|
||||
\centering
|
||||
\begin{tabular}{rrrrrrl}
|
||||
\hline
|
||||
minimum & q1 & median & mean & q3 & maximum & name\\
|
||||
\hline
|
||||
-2.29 & -0.49 & 0.11 & 0.14 & 0.8 & 2.47 & x1\\
|
||||
-2.17 & -0.45 & 0.07 & 0.13 & 0.85 & 2.23 & x2\\
|
||||
\hline
|
||||
\end{tabular}
|
||||
\end{table}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
\end{column}
|
||||
|
||||
\begin{column}[t]{0.45\columnwidth}
|
||||
\begin{block}{Graphics}
|
||||
\begin{itemize}
|
||||
\item We can use shell scripting to grab an image with curl from the
|
||||
internet (Fig. \ref{fig:org5db1ca6}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.78\columnwidth}
|
||||
\footnotesize
|
||||
\begin{minted}[linenos=true,bgcolor=lightgray]{bash}
|
||||
# Download emacs icon from gnu.org
|
||||
curl -0 https://www.gnu.org/software/emacs/images/emacs.png
|
||||
\end{minted}
|
||||
\normalsize
|
||||
|
||||
\vspace{2cm}
|
||||
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[page=9,width=0.2\textwidth]{emacs.png}
|
||||
\caption{\label{fig:org5db1ca6}
|
||||
This is the downloaded image.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
|
||||
\begin{block}{Math}
|
||||
\begin{itemize}
|
||||
\item We can easily include math
|
||||
\item For example, let's describe how to compute the distance between the
|
||||
two simulated distributions \(x1\) and \(x2\) from before:
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.78\columnwidth}
|
||||
The Kullback-Leibler (KL) divergence measures the difference between two
|
||||
probability distributions (i.e., the loss of information when one
|
||||
distribution is used to approximate another). The KL divergence is thus
|
||||
defined as
|
||||
|
||||
\begin{align}
|
||||
\label{eq:KL}
|
||||
\DKLPQ{P}{Q}{\|} = \sumin \Xoi{P} \log \frakPQ{P}{Q}
|
||||
\end{align}
|
||||
|
||||
with \(P\) and \(Q\) being two probability distribution functions and \(n\)
|
||||
the number of sample points. Since \(\DKLPQ{P}{Q}{\|}\) is not equal to
|
||||
\(\DKLPQ{Q}{P}{\|}\), a symmetric variation of the KL divergence can be
|
||||
derived as follows:
|
||||
|
||||
\begin{align}
|
||||
\label{eq:KL2}
|
||||
\DKLPQ{P}{Q}{,} = \sumin \Big(\Xoi{P} \log \frakPQ{P}{Q} + \Xoi{Q} \log \frakPQ{Q}{P} \Big).
|
||||
\end{align}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
|
||||
\begin{block}{Columns}
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.48\columnwidth}
|
||||
\captionsetup{justification=justified,width=.85\linewidth}
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4l.png}
|
||||
\caption{\label{fig:org4d1aa8d}
|
||||
This is the left figure of a two-column block, showing the density of \(x1\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
||||
\begin{column}[T]{0.48\columnwidth}
|
||||
\captionsetup{justification=justified,width=.85\linewidth}
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4r.png}
|
||||
\caption{\label{fig:org46ae343}
|
||||
This is the right figure. It shows the density of \(x2\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
|
||||
\begin{block}{Conclusions}
|
||||
\begin{itemize}
|
||||
\item This little example is meant to show how versatile org-mode is
|
||||
\item Scientific posters can be produced with a simple text editor
|
||||
\end{itemize}
|
||||
\end{block}
|
||||
\end{column}
|
||||
\end{columns}
|
|
@ -1,51 +0,0 @@
|
|||
\relax
|
||||
\providecommand\hyper@newdestlabel[2]{}
|
||||
\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
|
||||
\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
|
||||
\global\let\oldcontentsline\contentsline
|
||||
\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
|
||||
\global\let\oldnewlabel\newlabel
|
||||
\gdef\newlabel#1#2{\newlabelxx{#1}#2}
|
||||
\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
|
||||
\AtEndDocument{\ifx\hyper@anchor\@undefined
|
||||
\let\contentsline\oldcontentsline
|
||||
\let\newlabel\oldnewlabel
|
||||
\fi}
|
||||
\fi}
|
||||
\global\let\hyper@last\relax
|
||||
\gdef\HyperFirstAtBeginDocument#1{#1}
|
||||
\providecommand*\HyPL@Entry[1]{}
|
||||
\HyPL@Entry{0<</P(1)>>}
|
||||
\providecommand \oddpage@label [2]{}
|
||||
\newlabel{sec:orgf567eda<1>}{{1}{1}{}{Doc-Start}{}}
|
||||
\@writefile{snm}{\beamer@slide {sec:orgf567eda<1>}{1}}
|
||||
\newlabel{sec:orgf567eda}{{1}{1}{}{Doc-Start}{}}
|
||||
\@writefile{snm}{\beamer@slide {sec:orgf567eda}{1}}
|
||||
\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
|
||||
\newlabel{fig:orgd999323}{{1}{1}{This is the output.\relax }{Doc-Start}{}}
|
||||
\@writefile{snm}{\beamer@slide {fig:orgd999323}{1}}
|
||||
\newlabel{tab:org3b1c59c}{{1}{1}{A table summarizing the two distributions.\relax }{Doc-Start}{}}
|
||||
\@writefile{snm}{\beamer@slide {tab:org3b1c59c}{1}}
|
||||
\newlabel{fig:org5db1ca6}{{2}{1}{This is the downloaded image.\relax }{Doc-Start}{}}
|
||||
\@writefile{snm}{\beamer@slide {fig:org5db1ca6}{1}}
|
||||
\@writefile{snm}{\beamer@slide {eq:KL}{1}}
|
||||
\newlabel{eq:KL}{{1}{1}{}{Doc-Start}{}}
|
||||
\@writefile{snm}{\beamer@slide {eq:KL2}{1}}
|
||||
\newlabel{eq:KL2}{{2}{1}{}{Doc-Start}{}}
|
||||
\newlabel{fig:org4d1aa8d}{{3}{1}{This is the left figure of a two-column block, showing the density of \(x1\).\relax }{Doc-Start}{}}
|
||||
\@writefile{snm}{\beamer@slide {fig:org4d1aa8d}{1}}
|
||||
\newlabel{fig:org46ae343}{{4}{1}{This is the right figure. It shows the density of \(x2\).\relax }{Doc-Start}{}}
|
||||
\@writefile{snm}{\beamer@slide {fig:org46ae343}{1}}
|
||||
\@writefile{nav}{\headcommand {\slideentry {0}{0}{1}{1/1}{}{0}}}
|
||||
\@writefile{nav}{\headcommand {\beamer@framepages {1}{1}}}
|
||||
\@writefile{nav}{\headcommand {\beamer@partpages {1}{1}}}
|
||||
\@writefile{nav}{\headcommand {\beamer@subsectionpages {1}{1}}}
|
||||
\@writefile{nav}{\headcommand {\beamer@sectionpages {1}{1}}}
|
||||
\@writefile{nav}{\headcommand {\beamer@documentpages {1}}}
|
||||
\@writefile{nav}{\headcommand {\def \inserttotalframenumber {1}}}
|
||||
\gdef\minted@oldcachelist{,
|
||||
default-pyg-prefix.pygstyle,
|
||||
default.pygstyle,
|
||||
4F50C45CD1733808924D80824FB708527206BDF2FB9743A1FCD8E321435A60EC.pygtex,
|
||||
F870F16C680A2900730ED6B4821BCFEC7206BDF2FB9743A1FCD8E321435A60EC.pygtex,
|
||||
960F98AC4966D313135E43FDA8CBB8AD7ECE1161BED6D70335945ACD46C35809.pygtex}
|
|
@ -1,48 +0,0 @@
|
|||
This is BibTeX, Version 0.99d (TeX Live 2017/Debian)
|
||||
Capacity: max_strings=100000, hash_size=100000, hash_prime=85009
|
||||
The top-level auxiliary file: src/org-mode-poster_poster.aux
|
||||
I found no \citation commands---while reading file src/org-mode-poster_poster.aux
|
||||
I found no \bibdata command---while reading file src/org-mode-poster_poster.aux
|
||||
I found no \bibstyle command---while reading file src/org-mode-poster_poster.aux
|
||||
You've used 0 entries,
|
||||
0 wiz_defined-function locations,
|
||||
83 strings with 526 characters,
|
||||
and the built_in function-call counts, 0 in all, are:
|
||||
= -- 0
|
||||
> -- 0
|
||||
< -- 0
|
||||
+ -- 0
|
||||
- -- 0
|
||||
* -- 0
|
||||
:= -- 0
|
||||
add.period$ -- 0
|
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call.type$ -- 0
|
||||
change.case$ -- 0
|
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chr.to.int$ -- 0
|
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|
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|
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empty$ -- 0
|
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format.name$ -- 0
|
||||
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|
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int.to.chr$ -- 0
|
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int.to.str$ -- 0
|
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missing$ -- 0
|
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newline$ -- 0
|
||||
num.names$ -- 0
|
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pop$ -- 0
|
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purify$ -- 0
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|
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|
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|
||||
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|
||||
warning$ -- 0
|
||||
while$ -- 0
|
||||
width$ -- 0
|
||||
write$ -- 0
|
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(There were 3 error messages)
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INPUT org-mode-poster_poster.aux
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INPUT org-mode-poster_poster.aux
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OUTPUT org-mode-poster_poster.aux
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INPUT org-mode-poster_poster.out
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INPUT org-mode-poster_poster.out
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INPUT org-mode-poster_poster.out
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OUTPUT org-mode-poster_poster.out
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-basic-dictionary/translator-basic-dictionary-English.dict
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-bibliography-dictionary/translator-bibliography-dictionary-English.dict
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-environment-dictionary/translator-environment-dictionary-English.dict
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-environment-dictionary/translator-environment-dictionary-English.dict
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-months-dictionary/translator-months-dictionary-English.dict
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-months-dictionary/translator-months-dictionary-English.dict
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-numbers-dictionary/translator-numbers-dictionary-English.dict
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-numbers-dictionary/translator-numbers-dictionary-English.dict
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-theorem-dictionary/translator-theorem-dictionary-English.dict
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INPUT /usr/share/texlive/texmf-dist/tex/latex/beamer/translator/dicts/translator-theorem-dictionary/translator-theorem-dictionary-English.dict
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INPUT org-mode-poster_poster.nav
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INPUT org-mode-poster_poster.nav
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INPUT ../lib/logo_feinstein.pdf
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmss17.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmss17.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmss17.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmmi12.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmex10.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmex10.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm10.tfm
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INPUT ../lib/twitter.pdf
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INPUT ../lib/github.pdf
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm10.tfm
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INPUT ../lib/logo.pdf
|
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OUTPUT org-mode-poster_poster.1.vrb
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INPUT org-mode-poster_poster.1.vrb
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INPUT org-mode-poster_poster.1.vrb
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OUTPUT org-mode-poster_poster.pyg
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INPUT _minted-org-mode-poster_poster/default.pygstyle
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INPUT ./org-mode-poster_poster.pyg
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INPUT _minted-org-mode-poster_poster/4F50C45CD1733808924D80824FB708527206BDF2FB9743A1FCD8E321435A60EC.pygtex
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INPUT 3.png
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OUTPUT org-mode-poster_poster.pyg
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INPUT ./org-mode-poster_poster.pyg
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INPUT _minted-org-mode-poster_poster/F870F16C680A2900730ED6B4821BCFEC7206BDF2FB9743A1FCD8E321435A60EC.pygtex
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OUTPUT org-mode-poster_poster.pyg
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INPUT ./org-mode-poster_poster.pyg
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INPUT emacs.png
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INPUT 4l.png
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INPUT 4r.png
|
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INPUT ../lib/logo.pdf
|
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INPUT ../lib/logo_feinstein.pdf
|
||||
INPUT ../lib/twitter.pdf
|
||||
INPUT ../lib/github.pdf
|
||||
OUTPUT org-mode-poster_poster.nav
|
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OUTPUT org-mode-poster_poster.toc
|
||||
OUTPUT org-mode-poster_poster.snm
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INPUT org-mode-poster_poster.aux
|
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INPUT org-mode-poster_poster.pyg
|
File diff suppressed because it is too large
Load Diff
|
@ -1,7 +0,0 @@
|
|||
\headcommand {\slideentry {0}{0}{1}{1/1}{}{0}}
|
||||
\headcommand {\beamer@framepages {1}{1}}
|
||||
\headcommand {\beamer@partpages {1}{1}}
|
||||
\headcommand {\beamer@subsectionpages {1}{1}}
|
||||
\headcommand {\beamer@sectionpages {1}{1}}
|
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\headcommand {\beamer@documentpages {1}}
|
||||
\headcommand {\def \inserttotalframenumber {1}}
|
|
@ -371,3 +371,4 @@ plot(d2, col="blue", lwd=3)
|
|||
- This little example is meant to show how versatile org-mode is
|
||||
- Scientific posters can be produced with a simple text editor
|
||||
|
||||
|
||||
|
|
|
@ -1,433 +0,0 @@
|
|||
#+startup: beamer
|
||||
#+TITLE: Structural similarity networks predict
|
||||
#+TITLE: clinical outcome in early-phase schizophrenia
|
||||
* Preamble :ignore:
|
||||
** General comments :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
# - Turn on synonyms by starting synosaurus-mode
|
||||
# - Look up words using C-c sr
|
||||
# - Turn on dictionary by starting flyspell-mode
|
||||
# - Count words by section using org-wc-display
|
||||
# ----------------------------------------------------------------------
|
||||
** Specific comments for this manuscript :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
** org specific settings :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
#+OPTIONS: email:nil toc:nil num:nil author:nil date:t tex:t title:nil
|
||||
#+STARTUP: align fold
|
||||
#+SEQ_TODO: TODO(t) | DONE(d)
|
||||
#+TAGS: figure(f) check(c) noexport(n) ignore(i)
|
||||
#+LANGUAGE: en
|
||||
#+EXCLUDE_TAGS: noexport TODO
|
||||
#+DATE: {{{time(%Y-%m-%d %H:%M)}}}
|
||||
# ----------------------------------------------------------------------
|
||||
** Latex header :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
#+LATEX_CLASS: mybeamerposter
|
||||
#+LATEX_HEADER: \setlength{\paperwidth}{36in}
|
||||
#+LATEX_HEADER: \setlength{\paperheight}{48in}
|
||||
#+LATEX_HEADER: \setlength{\textwidth}{0.98\paperwidth}
|
||||
#+LATEX_HEADER: \setlength{\textheight}{0.98\paperheight}
|
||||
# LATEX_HEADER: \usepackage[absolute,overlay]{textpos}
|
||||
#+LATEX_HEADER: \graphicspath{{../output/figures/}{../lib/}}
|
||||
#+LATEX_HEADER: \usepackage[export]{adjustbox}
|
||||
#+LATEX_HEADER: \usepackage{graphicx,caption}
|
||||
#+LATEX_HEADER: \usepackage{eurosym}
|
||||
#+LATEX_HEADER: \usepackage{textcomp}
|
||||
#+LATEX_HEADER: \usepackage{bibentry}
|
||||
# LATEX_HEADER: \setlength{\TPVertModule}{1cm}
|
||||
# LATEX_HEADER: \setlength{\oddsidemargin}{0.1in}
|
||||
# LATEX_HEADER: \title{The demise of the spotted swamp frog}
|
||||
# LATEX_HEADER: \author{Rob J Hyndman}
|
||||
# LATEX_HEADER: \footer{
|
||||
# LATEX_HEADER: \textbf{Philipp Homan, MD, PhD}\\
|
||||
# LATEX_HEADER: phoman1@northwell.edu\\
|
||||
# LATEX_HEADER: github.com/philipphoman}
|
||||
#+LATEX_HEADER: \date{}
|
||||
# ----------------------------------------------------------------------
|
||||
** Authors and affiliations :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
#+LATEX_HEADER: \author{
|
||||
#+LATEX_HEADER: Philipp Homan$^{1}$,
|
||||
#+LATEX_HEADER: Miklos Argyelan$^{1}$,
|
||||
#+LATEX_HEADER: Pamela DeRosse$^{1}$,
|
||||
#+LATEX_HEADER: Delbert Robinson$^{1}$,
|
||||
#+LATEX_HEADER: John M. Kane$^{1}$,
|
||||
#+LATEX_HEADER: Todd Lencz$^{1}$,
|
||||
#+LATEX_HEADER: Anil K. Malhotra$^{1}$
|
||||
#+LATEX_HEADER: \\
|
||||
#+LATEX_HEADER: \normalsize{$^{1}$Department of Psychiatry,}
|
||||
#+LATEX_HEADER: \normalsize{The Donald and Barbara Zucker}
|
||||
#+LATEX_HEADER: \normalsize{School of Medicine at Northwell/Hofstra,}
|
||||
#+LATEX_HEADER: \normalsize{Hempstead, NY}\\
|
||||
#+LATEX_HEADER: }
|
||||
# ----------------------------------------------------------------------
|
||||
** Buffer-wide source code blocks :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
# Set elisp variables need for nice formatting We want no new lines in
|
||||
# inline results and a paragraph size of 80 characters Important: this
|
||||
# has to be evaluated witch C-c C-c in order to work in the current
|
||||
# buffer
|
||||
#+BEGIN_SRC emacs-lisp :exports none :results silent
|
||||
|
||||
; set timestamp format
|
||||
;(setq org-export-date-timestamp-format "%FT%T%z")
|
||||
(require 'org-wc)
|
||||
(flyspell-mode t)
|
||||
;(evil-declare-change-repeat 'company-complete)
|
||||
(setq synosaurus-choose-method 'popup)
|
||||
(synosaurus-mode t)
|
||||
(auto-complete-mode t)
|
||||
;(ac-config-default)
|
||||
;(add-to-list 'ac-modes 'org-mode)
|
||||
(linum-mode t)
|
||||
(whitespace-mode t)
|
||||
(setq org-babel-inline-result-wrap "%s")
|
||||
(setq org-export-with-broken-links "mark")
|
||||
(setq fill-column 72)
|
||||
(setq whitespace-line-column 72)
|
||||
;(setq org-latex-caption-above '(table image))
|
||||
(setq org-latex-caption-above nil)
|
||||
(org-toggle-link-display)
|
||||
; don't remove logfiles at export
|
||||
(setq org-latex-remove-logfiles nil)
|
||||
|
||||
; Keybindings
|
||||
; (global-set-key (kbd "<f7> c") "#+CAPTION: ")
|
||||
(defun setfillcolumn72 ()
|
||||
(interactive)
|
||||
(setq fill-column 72)
|
||||
)
|
||||
|
||||
(defun setfillcolumn42 ()
|
||||
(interactive)
|
||||
(setq fill-column 42)
|
||||
)
|
||||
(define-key org-mode-map (kbd "C-c c #") "#+CAPTION: ")
|
||||
(define-key org-mode-map (kbd "C-c l #") "#+LATEX_HEADER: ")
|
||||
(define-key org-mode-map (kbd "C-c f c 4 2") 'setfillcolumn42)
|
||||
(define-key org-mode-map (kbd "C-c f c 7 2") 'setfillcolumn72)
|
||||
|
||||
(setq org-odt-category-map-alist
|
||||
'(("__Figure__" "*Figure*" "value" "Figure" org-odt--enumerable-image-p)))
|
||||
|
||||
|
||||
; let ess not ask for starting directory
|
||||
(setq ess-ask-for-ess-directory nil)
|
||||
|
||||
;(setq org-latex-pdf-process '("latexmk -pdflatex='xelatex
|
||||
;-output-directory=../output/tex/ -interaction nonstopmode' -pdf
|
||||
;-bibtex -f %f"))
|
||||
(setq org-latex-logfiles-extensions
|
||||
(quote("bcf" "blg" "fdb_latexmk" "fls"
|
||||
"figlist" "idx" "log" "nav" "out" "ptc"
|
||||
"run.xml" "snm" "toc" "vrb" "xdv")))
|
||||
|
||||
; deactivate link resolving
|
||||
(setq org-activate-links nil)
|
||||
|
||||
|
||||
#+END_SRC
|
||||
#
|
||||
#
|
||||
#
|
||||
# ----------------------------------------------------------------------
|
||||
** End preamble :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
|
||||
* References :ignore:
|
||||
\bibliographystyle{nature}
|
||||
\nobibliography{master}
|
||||
* The poster
|
||||
:PROPERTIES:
|
||||
:BEGIN:
|
||||
:BEAMER_env: fullframe
|
||||
:END:
|
||||
|
||||
** Code :ignore:
|
||||
# First, make sure all variables are availabe
|
||||
#+HEADER: :exports none
|
||||
#+BEGIN_SRC R :results silent :session
|
||||
source("../src/fe_func.R")
|
||||
source("../src/fe_load.R")
|
||||
|
||||
fef <- read.csv("../data/fe_cidar.csv")
|
||||
feo <- read.csv("../data/fe_omega3.csv")
|
||||
hca <- read.csv("../data/fe_hcm.csv")
|
||||
|
||||
# Load necessary results tables
|
||||
roistab <- read.csv("../output/tables/fe_freesurfer_roinames.csv")
|
||||
roitvalstab <- read.csv("../output/tables/fe_freesurfer_roitvals.csv")
|
||||
permuttab <- read.csv("../output/tables/fe_msn_permut_rsq.csv")
|
||||
bootstraptab <- read.csv("../output/tables/fe_msn_bootstrap_rsq.csv")
|
||||
crossvaltab <- read.csv("../output/tables/fe_msn_crossvalidation.csv")
|
||||
graphsumtab <- read.csv("../output/tables/fe_freesurfer_graphsum.csv")
|
||||
plsrtab <- read.csv("../output/tables/fe_msn_plsscore_rs.csv")
|
||||
deltadegreestab <- read.csv("../output/tables/fe_freesurfer_deltadegrees.csv")
|
||||
|
||||
|
||||
# Custom functions
|
||||
pvalstr <- function(pval) {
|
||||
if (pval < 0.001) {
|
||||
return("< 0.001")
|
||||
} else {
|
||||
return(paste("=", round(pval, 3)))
|
||||
}
|
||||
}
|
||||
|
||||
#+END_SRC
|
||||
|
||||
#+HEADER: :exports none
|
||||
#+BEGIN_SRC R :results silent :session :cache yes
|
||||
# Merge data sets and keep only interesting variables
|
||||
# Rename variables for later
|
||||
fefa <- fef %>% dplyr::filter(day==0&included16w==1) %>%
|
||||
dplyr::mutate(study="CIDAR", group="SZ") %>%
|
||||
dplyr::select(dup, iq, mccb, bprs, bprs_td, bprs_tdbl,
|
||||
age, sex, race, hasmri, study, group,
|
||||
education,
|
||||
bmi, class, alcohol, drugs)
|
||||
|
||||
feoa <- feo %>% dplyr::filter(day==0&included16w==1) %>%
|
||||
dplyr::mutate(study="Omega3", group="SZ") %>%
|
||||
dplyr::select(dup, iq, mccb, bprs, bprs_td, bprs_tdbl,
|
||||
age, sex, race, hasmri, study, group,
|
||||
education,
|
||||
bmi, class, alcohol, drugs)
|
||||
|
||||
|
||||
#hca$male[hca$sex==1] <- 1
|
||||
#hca$female[hca$sex==2] <- 1
|
||||
hcab <- hca %>% dplyr::rename(age=age) %>%
|
||||
filter(age<50) %>%
|
||||
dplyr::select(sex, age, education, iq) %>%
|
||||
dplyr::mutate(study="HC",
|
||||
group="HC")
|
||||
hcmeanage <- round(mean(hcab$age), 1)
|
||||
hcsdage <- round(sd(hcab$age), 1)
|
||||
hcmales <- sum(hcab$sex==1, na.rm=TRUE)
|
||||
hcfemales <- sum(hcab$sex==2, na.rm=TRUE)
|
||||
feffeo <- rbind(fefa, feoa) %>% filter(hasmri==1)
|
||||
|
||||
# Custom function
|
||||
parse_agesex <- function() {
|
||||
print(paste("(", n_females, " females; mean age [SD] = ",
|
||||
meanage, " [", sdage, "])", sep=""))
|
||||
}
|
||||
|
||||
parse_n <- function(group) {
|
||||
switch(group,
|
||||
sz={
|
||||
print(paste("(/N/ = ", n_partic, ")", sep=""))
|
||||
},
|
||||
hc={
|
||||
print(paste("(/N/ = ", n_partic_hc, ")", sep=""))
|
||||
})
|
||||
}
|
||||
|
||||
# R version
|
||||
rvers <- version$version.string
|
||||
|
||||
# Python version
|
||||
# pyvers <- system("python --version")
|
||||
# pysurfvers <- system("pip freeze | grep pysurf")
|
||||
#pyvers <- "2.7.13"
|
||||
#pysurfvers <- "0.7"
|
||||
pyplusvers <- system("pyv=$(python -V 2>&1); echo $pyv", intern=TRUE)
|
||||
pysurfplusvers <- system("pip list | grep pysurf", intern=TRUE)
|
||||
|
||||
# Custom variables
|
||||
n_nodes <- 2 * nlevels(roistab$name)
|
||||
n_partic <- nrow(feffeo)
|
||||
n_partic_hc <- nrow(hcab)
|
||||
n_partic_full_bothsamples <- nrow(rbind(fef %>% filter(day==0),
|
||||
feo %>% filter(day==0)))
|
||||
n_females <- sum(feffeo$sex==1)
|
||||
n_males <- sum(feffeo$sex==2)
|
||||
meanage <- round(mean(feffeo$age, na.rm=TRUE), 1)
|
||||
sdage <- round(sd(feffeo$age, na.rm=TRUE), 1)
|
||||
|
||||
# Cross validation values
|
||||
cvkfold_k <- crossvaltab$k
|
||||
cvrsq_mean <- crossvaltab$mean
|
||||
cvrsq_sd <- crossvaltab$sd
|
||||
|
||||
# Permutation and bootstrap values
|
||||
rsqorig <- unique(permuttab$rsq_orig)
|
||||
npermut <- unique(permuttab$niter)
|
||||
prsq_pval <- unique(permuttab$prsq_pva)
|
||||
|
||||
# PLS correlation values
|
||||
pls1r <- plsrtab$r[plsrtab$component=="PLS1"]
|
||||
pls1rpval <- plsrtab$pval[plsrtab$component=="PLS1"]
|
||||
pls2r <- plsrtab$r[plsrtab$component=="PLS2"]
|
||||
pls2rpval <- plsrtab$pval[plsrtab$component=="PLS2"]
|
||||
|
||||
# Graph summary, drop Cp and keep transitivity
|
||||
# as the two are essential equal
|
||||
graphsumtab <- graphsumtab %>% filter(metric!="Cp") %>%
|
||||
mutate(metric=recode(metric,
|
||||
transitivity="Cluster coef.",
|
||||
diameter="Diameter",
|
||||
E.global="Global efficiency",
|
||||
E.local="Local efficiency",
|
||||
num.hubs="Number of hubs",
|
||||
richclub="Rich club coef.",
|
||||
vulnerability="Vulnerability"))
|
||||
|
||||
#+END_SRC
|
||||
|
||||
** Left column :BMCOL:
|
||||
:PROPERTIES:
|
||||
:BEAMER_col: 0.45\textwidth
|
||||
:BEAMER_opt: [t]
|
||||
:END:
|
||||
*** Background :B_block:
|
||||
:PROPERTIES:
|
||||
:BEAMER_env: block
|
||||
:END:
|
||||
- Schizophrenia has long been considered a disorder of dysconnectivity
|
||||
in the brain
|
||||
- Using graph theory, we computed statistical similarity networks for
|
||||
each individual (Fig [[figflowchart]], [[figshrinkage]]) in two
|
||||
early-phase schizophrenia cohorts src_R[:session]{parse_n("sz")}
|
||||
{{{results((/N/ = 82))}}} and in healthy controls
|
||||
src_R[:session]{parse_n("hc")} {{{results((/N/ = 77))}}} and tested
|
||||
whether network architecture predicted treatment response
|
||||
|
||||
*** Methods: Structural similarity networks :B_block:
|
||||
:PROPERTIES:
|
||||
:BEAMER_env: block
|
||||
:END:
|
||||
|
||||
\captionsetup{justification=justified,width=.85\linewidth}
|
||||
#+NAME: figflowchart
|
||||
#+CAPTION: *Analysis flow chart.*
|
||||
#+CAPTION: The similarity between any pair of region was
|
||||
#+CAPTION: estimated by calculating the
|
||||
#+CAPTION: Kullback-Leibler (KL) divergence of their
|
||||
#+CAPTION: probability distributions, resulting in
|
||||
#+CAPTION: a similarity matrix.
|
||||
#+CAPTION: The similarity matrix
|
||||
#+CAPTION: was then thresholded into a binary matrix to
|
||||
#+CAPTION: create a network graph. Graph-based
|
||||
#+CAPTION: degree (or hubness) for each node was then
|
||||
#+CAPTION: calculated for each individual participant.
|
||||
#+CAPTION: Nodal degrees were then entered as
|
||||
#+CAPTION: predictors into a partial
|
||||
#+CAPTION: least squares regression, using individual
|
||||
#+CAPTION: treatment response slopes as outcome
|
||||
#+CAPTION: measure.
|
||||
#+ATTR_LATEX: :width 0.85\textwidth
|
||||
[[file:fe_freesurfer_flowchart.pdf]]
|
||||
|
||||
*** Methods: Individual treatment response :B_block:
|
||||
:PROPERTIES:
|
||||
:BEAMER_env: block
|
||||
:END:
|
||||
|
||||
\captionsetup{justification=justified,width=.85\linewidth}
|
||||
#+NAME: figshrinkage
|
||||
#+CAPTION: *Partial pooling to regularize individual response slopes.*
|
||||
#+CAPTION: *A.* *Individual time courses for all participants*
|
||||
#+CAPTION: *from the first schizophrenia cohort.*
|
||||
#+CAPTION: Partial pooling regularized
|
||||
#+CAPTION: the individual slopes, i.e., the influence
|
||||
#+CAPTION: of outliers with only few assessments was attenuated.
|
||||
#+CAPTION: *B.* *The partial pooling effect*
|
||||
#+CAPTION: *is demonstrated by the individual responses being*
|
||||
#+CAPTION: *pulled toward the average treatment effect.*
|
||||
#+CAPTION: As a consequence, outliers are less influential.
|
||||
#+CAPTION: *C, D.* The same is shown for the second schizophrenia
|
||||
#+CAPTION: cohort.
|
||||
#+CAPTION: Dotted ellipses indicate confidence regions for the
|
||||
#+CAPTION: average treatment effect.
|
||||
#+ATTR_LATEX: :width 0.85\textwidth
|
||||
[[file:fe_freesurfer_shrinkage.pdf]]
|
||||
|
||||
** Right column :BMCOL:
|
||||
:PROPERTIES:
|
||||
:BEAMER_col: 0.45\textwidth
|
||||
:BEAMER_opt: [t]
|
||||
:END:
|
||||
*** Results: Partial least squares regression :B_block:
|
||||
:PROPERTIES:
|
||||
:BEAMER_env: block
|
||||
:END:
|
||||
|
||||
- Individual differences in the configuration of structural similarity
|
||||
networks explained a significant proportion of variance in treatment
|
||||
response (Fig. [[figplsbrains]])
|
||||
- Exploratory analysis: increased clustering and decreased network
|
||||
integration in patients compared to controls (Fig. [[figge]],
|
||||
[[figclus]])
|
||||
|
||||
\captionsetup{justification=justified,width=.8\linewidth}
|
||||
#+NAME: figplsbrains
|
||||
#+CAPTION: *PLS scores with individual treatment*
|
||||
#+CAPTION: *response and contribution of cortical nodes*
|
||||
#+CAPTION: *in the schizophrenia cohort*
|
||||
#+CAPTION: Nodal degree for each of
|
||||
#+CAPTION: the src_R[:session]{n_nodes} {{{results(68)}}}
|
||||
#+CAPTION: was entered into a partial least squares (PLS)
|
||||
#+CAPTION: regression, with individual treatment response
|
||||
#+CAPTION: slopes as outcome measure. The first two
|
||||
#+CAPTION: PLS components explained a significant proportion
|
||||
#+CAPTION: of variance in treatment response. *A, B.* The first
|
||||
#+CAPTION: PLS component correlated most strongly with
|
||||
#+CAPTION: nodal degree of orbito- and prefrontal cortices
|
||||
#+CAPTION: and posterior cingulate cortex. Note that
|
||||
#+CAPTION: more negative slopes meant better
|
||||
#+CAPTION: treatment response.
|
||||
#+CAPTION: *B, C.* The second PLS component correlated most
|
||||
#+CAPTION: most strongly with superior temporal, precentral,
|
||||
#+CAPTION: and middle cingulate brain areas.
|
||||
#+ATTR_LATEX: :width 0.8\textwidth
|
||||
[[file:fe_freesurfer_plsbrains.pdf]]
|
||||
|
||||
*** Results: Increased clustering in patients :B_block:
|
||||
:PROPERTIES:
|
||||
:BEAMER_env: block
|
||||
:END:
|
||||
|
||||
**** Left
|
||||
:PROPERTIES:
|
||||
:BEAMER_col: 0.48
|
||||
:BEAMER_opt: [T]
|
||||
:END:
|
||||
|
||||
\captionsetup{justification=justified,width=.8\linewidth}
|
||||
#+NAME: figge
|
||||
#+CAPTION: *Decreased network integration in*
|
||||
#+CAPTION: *schizophrenia patients compared to controls.*
|
||||
#+CAPTION: Means with error bands
|
||||
#+CAPTION: are shown.
|
||||
#+CAPTION: Non-overlapping error bands
|
||||
#+CAPTION: indicate significant group differences (/P/ < 0.05).
|
||||
#+ATTR_LATEX: :width 0.9\textwidth :options page=3
|
||||
[[file:fe_freesurfer_graphsum_individual.pdf]]
|
||||
|
||||
**** Right
|
||||
:PROPERTIES:
|
||||
:BEAMER_col: 0.48
|
||||
:BEAMER_opt: [T]
|
||||
:END:
|
||||
|
||||
\captionsetup{justification=justified,width=.8\linewidth}
|
||||
#+NAME: figclus
|
||||
#+CAPTION: *Increased clustering in schizophrenia patients*
|
||||
#+CAPTION: *compared to controls.*
|
||||
#+CAPTION: Means with error bands are shown.
|
||||
#+CAPTION: Non-overlapping error bands
|
||||
#+CAPTION: indicate significant group differences (/P/ < 0.05).
|
||||
#+ATTR_LATEX: :width 0.9\textwidth :options page=9
|
||||
[[file:fe_freesurfer_graphsum_individual.pdf]]
|
||||
|
||||
*** Conclusions :B_block:
|
||||
:PROPERTIES:
|
||||
:BEAMER_env: block
|
||||
:END:
|
||||
- These data suggest a potential link between brain network morphology
|
||||
and clinical outcome in early-phase schizophrenia
|
||||
|
||||
|
Binary file not shown.
|
@ -1,9 +0,0 @@
|
|||
\beamer@slide {sec:orgf567eda<1>}{1}
|
||||
\beamer@slide {sec:orgf567eda}{1}
|
||||
\beamer@slide {fig:orgd999323}{1}
|
||||
\beamer@slide {tab:org3b1c59c}{1}
|
||||
\beamer@slide {fig:org5db1ca6}{1}
|
||||
\beamer@slide {eq:KL}{1}
|
||||
\beamer@slide {eq:KL2}{1}
|
||||
\beamer@slide {fig:org4d1aa8d}{1}
|
||||
\beamer@slide {fig:org46ae343}{1}
|
|
@ -1,4 +1,4 @@
|
|||
% Created 2018-04-05 Thu 15:59
|
||||
% Created 2018-04-05 Thu 16:07
|
||||
% Intended LaTeX compiler: pdflatex
|
||||
\documentclass[final]{beamer}
|
||||
\usetheme{ph}
|
||||
|
@ -37,11 +37,11 @@ Philipp Homan$^{1}$
|
|||
\normalsize{Hempstead, NY}
|
||||
}
|
||||
\usetheme{default}
|
||||
\date{2018-04-05 15:59}
|
||||
\date{2018-04-05 16:07}
|
||||
\title{Using org-mode for scientific posters}
|
||||
\begin{document}
|
||||
|
||||
\begin{frame}[fragile,label={sec:orgf567eda}]{}
|
||||
\begin{frame}[fragile,label={sec:org7ec99ec}]{}
|
||||
\begin{columns}
|
||||
\begin{column}[t]{0.45\columnwidth}
|
||||
\begin{block}{Background}
|
||||
|
@ -53,10 +53,10 @@ posters
|
|||
\item With org-mode we can populate the poster with code, graphs and numbers
|
||||
from inline code in languages such as R, python, Matlab and even shell
|
||||
scripting
|
||||
\item For example, this poster was created on 2018-04-05 15:59 on
|
||||
\item For example, this poster was created on 2018-04-05 16:07 on
|
||||
Ubuntu 17.10.
|
||||
\item Inline code could look like this (which will produce a graph;
|
||||
Fig. \ref{fig:orgd999323}):
|
||||
Fig. \ref{fig:org9802921}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
|
@ -72,7 +72,7 @@ hist(x2, col="blue", add=TRUE)
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{3.png}
|
||||
\caption{\label{fig:orgd999323}
|
||||
\caption{\label{fig:org9802921}
|
||||
This is the output.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -86,7 +86,7 @@ This is the output.}
|
|||
capabilities
|
||||
\item Some code to process the first vector from above to make a table out
|
||||
of its summary could look like this, which would result in a little
|
||||
table (Table \ref{tab:org3b1c59c}) :
|
||||
table (Table \ref{tab:orgd48ea4b}) :
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
|
@ -105,7 +105,7 @@ mutate(name=c("x1", "x2"))
|
|||
\vspace{2cm}
|
||||
|
||||
\begin{table}[htbp]
|
||||
\caption{\label{tab:org3b1c59c}
|
||||
\caption{\label{tab:orgd48ea4b}
|
||||
A table summarizing the two distributions.}
|
||||
\centering
|
||||
\begin{tabular}{rrrrrrl}
|
||||
|
@ -126,7 +126,7 @@ minimum & q1 & median & mean & q3 & maximum & name\\
|
|||
\begin{block}{Graphics}
|
||||
\begin{itemize}
|
||||
\item We can use shell scripting to grab an image with curl from the
|
||||
internet (Fig. \ref{fig:org5db1ca6}):
|
||||
internet (Fig. \ref{fig:orge74f4ee}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
|
@ -143,7 +143,7 @@ curl -0 https://www.gnu.org/software/emacs/images/emacs.png
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[page=9,width=0.2\textwidth]{emacs.png}
|
||||
\caption{\label{fig:org5db1ca6}
|
||||
\caption{\label{fig:orge74f4ee}
|
||||
This is the downloaded image.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -189,7 +189,7 @@ derived as follows:
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4l.png}
|
||||
\caption{\label{fig:org4d1aa8d}
|
||||
\caption{\label{fig:org16d62b9}
|
||||
This is the left figure of a two-column block, showing the density of \(x1\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -199,7 +199,7 @@ This is the left figure of a two-column block, showing the density of \(x1\).}
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4r.png}
|
||||
\caption{\label{fig:org46ae343}
|
||||
\caption{\label{fig:orgf50bc84}
|
||||
This is the right figure. It shows the density of \(x2\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
|
|
@ -1,218 +0,0 @@
|
|||
% Created 2018-04-04 Wed 12:21
|
||||
% Intended LaTeX compiler: pdflatex
|
||||
\documentclass[final]{beamer}
|
||||
\usetheme{ph}
|
||||
\usepackage[orientation=portrait,size=a0,scale=1.4]{beamerposter}
|
||||
\usepackage[absolute,overlay]{textpos}
|
||||
\usepackage[authoryear]{natbib}
|
||||
|
||||
|
||||
\setlength{\paperwidth}{36in}
|
||||
\setlength{\paperheight}{48in}
|
||||
\setlength{\textwidth}{0.98\paperwidth}
|
||||
\setlength{\textheight}{0.98\paperheight}
|
||||
\graphicspath{{../output/figures/}{../lib/}}
|
||||
\usepackage[export]{adjustbox}
|
||||
\usepackage{graphicx,caption}
|
||||
\usepackage{minted}
|
||||
\usepackage{eurosym}
|
||||
\usepackage{listings}
|
||||
\usepackage{textcomp}
|
||||
\usepackage{bibentry}
|
||||
\newcommand\sumin{\sum_{i=1}^{n}}
|
||||
\newcommand{\Xoi}[1]{#1(i)}
|
||||
\newcommand{\frakPQ}[2]{\frac{\Xoi{#1}}{\Xoi{#2}}}
|
||||
\newcommand{\DKLPQ}[3]{D_{\mathrm{KL}}(#1 #3 #2)}
|
||||
\date{}
|
||||
\newcommand{\auth}{Philipp Homan, MD, PhD}
|
||||
\newcommand{\authemail}{phoman1@northwell.edu}
|
||||
\newcommand{\authtwitter}{@philipphoman}
|
||||
\newcommand{\authgithub}{github.com/philipphoman}
|
||||
\author{
|
||||
Philipp Homan$^{1}$
|
||||
\\
|
||||
\normalsize{$^{1}$Department of Psychiatry,}
|
||||
\normalsize{The Donald and Barbara Zucker}
|
||||
\normalsize{School of Medicine at Northwell/Hofstra,}
|
||||
\normalsize{Hempstead, NY}
|
||||
}
|
||||
\usetheme{default}
|
||||
\date{2018-04-04 12:21}
|
||||
\title{Using org-mode for scientific posters}
|
||||
\begin{document}
|
||||
|
||||
\begin{frame}[fragile,label={sec:org954d466}]{}
|
||||
\begin{columns}
|
||||
\begin{column}[t]{0.45\columnwidth}
|
||||
\begin{block}{Background}
|
||||
\begin{itemize}
|
||||
\item Here we show how org-mode (version
|
||||
9.1.7) and emacs (version
|
||||
25.2.2) can be used to make decent looking scientific
|
||||
posters
|
||||
\item With org-mode we can populate the poster with code, graphs and numbers
|
||||
from inline code in languages such as R, python, Matlab and even shell
|
||||
scripting
|
||||
\item For example, this poster was created on 2018-04-04 12:21 on
|
||||
Ubuntu 17.10.
|
||||
\item Inline code could look like this (which will produce a graph;
|
||||
Fig. \ref{fig:org8e3f41e}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.68\columnwidth}
|
||||
\begin{minted}[linenos=true,bgcolor=lightgray]{r}
|
||||
set.seed(20180402)
|
||||
x1 <- rnorm(100, 0, 1)
|
||||
x2 <- rnorm(100, 0.5, 1)
|
||||
hist(x1, col="red")
|
||||
hist(x2, col="blue", add=TRUE)
|
||||
\end{minted}
|
||||
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{3.png}
|
||||
\caption{\label{fig:org8e3f41e}
|
||||
This is the output.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
|
||||
\begin{block}{Inline code and tables}
|
||||
\begin{itemize}
|
||||
\item In addition to inline code, we can also produce tables
|
||||
\item Tables are very powerful in org-mode, they even include spreadsheet
|
||||
capabilities
|
||||
\item Some code to process the first vector from above to make a table out
|
||||
of its summary could look like this, which would result in a little
|
||||
table (Table \ref{tab:orgd66dcb7}) :
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.78\columnwidth}
|
||||
\begin{minted}[linenos=true,bgcolor=lightgray]{r}
|
||||
library(broom)
|
||||
library(dplyr)
|
||||
t1 <- tidy(round(summary(x1), 2))
|
||||
t2 <- tidy(round(summary(x2), 2))
|
||||
|
||||
# This will export as a table
|
||||
rbind(t1, t2) %>%
|
||||
mutate(name=c("x1", "x2"))
|
||||
\end{minted}
|
||||
|
||||
\vspace{2cm}
|
||||
|
||||
\begin{table}[htbp]
|
||||
\caption{\label{tab:orgd66dcb7}
|
||||
A table summarizing the two distributions.}
|
||||
\centering
|
||||
\begin{tabular}{rrrrrrl}
|
||||
\hline
|
||||
minimum & q1 & median & mean & q3 & maximum & name\\
|
||||
\hline
|
||||
-2.29 & -0.49 & 0.11 & 0.14 & 0.8 & 2.47 & x1\\
|
||||
-2.17 & -0.45 & 0.07 & 0.13 & 0.85 & 2.23 & x2\\
|
||||
\hline
|
||||
\end{tabular}
|
||||
\end{table}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
\end{column}
|
||||
|
||||
\begin{column}[t]{0.45\columnwidth}
|
||||
\begin{block}{Graphics}
|
||||
\begin{itemize}
|
||||
\item We can use shell scripting to grab an image with curl from the
|
||||
internet (Fig. \ref{fig:orga7f94bb}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.78\columnwidth}
|
||||
\footnotesize
|
||||
\begin{minted}[linenos=true,bgcolor=lightgray]{bash}
|
||||
# Download emacs icon from gnu.org
|
||||
curl -0 https://www.gnu.org/software/emacs/images/emacs.png
|
||||
\end{minted}
|
||||
\normalsize
|
||||
|
||||
\vspace{2cm}
|
||||
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[page=9,width=0.2\textwidth]{emacs.png}
|
||||
\caption{\label{fig:orga7f94bb}
|
||||
This is the downloaded image.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
|
||||
\begin{block}{Math}
|
||||
\begin{itemize}
|
||||
\item We can easily include math
|
||||
\item For example, let's describe how to compute the distance between the
|
||||
two simulated distributions \(x1\) and \(x2\) from before:
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.78\columnwidth}
|
||||
The Kullback-Leibler (KL) divergence measures the difference between two
|
||||
probability distributions (i.e., the loss of information when one
|
||||
distribution is used to approximate another). The KL divergence is thus
|
||||
defined as
|
||||
|
||||
\begin{align}
|
||||
\label{eq:KL}
|
||||
\DKLPQ{P}{Q}{\|} = \sumin \Xoi{P} \log \frakPQ{P}{Q}
|
||||
\end{align}
|
||||
|
||||
with \(P\) and \(Q\) being two probability distribution functions and \(n\)
|
||||
the number of sample points. Since \(\DKLPQ{P}{Q}{\|}\) is not equal to
|
||||
\(\DKLPQ{Q}{P}{\|}\), a symmetric variation of the KL divergence can be
|
||||
derived as follows:
|
||||
|
||||
\begin{align}
|
||||
\label{eq:KL2}
|
||||
\DKLPQ{P}{Q}{,} = \sumin \Big(\Xoi{P} \log \frakPQ{P}{Q} + \Xoi{Q} \log \frakPQ{Q}{P} \Big).
|
||||
\end{align}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
|
||||
\begin{block}{Columns}
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.48\columnwidth}
|
||||
\captionsetup{justification=justified,width=.85\linewidth}
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4l.png}
|
||||
\caption{\label{fig:org0b56e4b}
|
||||
This is the left figure of a two-column block, showing the density of \(x1\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
||||
\begin{column}[T]{0.48\columnwidth}
|
||||
\captionsetup{justification=justified,width=.85\linewidth}
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4r.png}
|
||||
\caption{\label{fig:org5983ee2}
|
||||
This is the right figure. It shows the density of \(x2\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
|
||||
\begin{block}{Conclusions}
|
||||
\begin{itemize}
|
||||
\item This little example is meant to show how versatile org-mode is
|
||||
\item Scientific posters can be produced with a simple text editor
|
||||
\end{itemize}
|
||||
\end{block}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{frame}
|
||||
\end{document}
|
|
@ -1,77 +0,0 @@
|
|||
,label={sec:org42c14b4}]{Left column}
|
||||
\begin{block}{Background}
|
||||
\begin{itemize}
|
||||
\item Org-mode is not only useful for producing blog posts and even
|
||||
scientific manuscripts; it is also perfectly suitable to make
|
||||
decent looking scientific posters
|
||||
\item We combine a relatively simple custom \LaTeX style file and common
|
||||
org-mode syntax
|
||||
\item The nice thing about org-mode is that we can populate the poster with
|
||||
code, graphs and numbers from inline code in languages such as R,
|
||||
python, Matlab and even shell scripting
|
||||
\item Inline code would look like this, which will produce a graph
|
||||
(Fig. \ref{fig:orgb6e58a4}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.68\columnwidth}
|
||||
\begin{minted}[linenos=true,bgcolor=lightgray]{r}
|
||||
set.seed(20180402)
|
||||
x1 <- rnorm(100, 0, 1)
|
||||
x2 <- rnorm(100, 0.5, 1)
|
||||
hist(x1, col="red")
|
||||
hist(x2, col="blue", add=TRUE)
|
||||
\end{minted}
|
||||
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{3.png}
|
||||
\caption{\label{fig:orgb6e58a4}
|
||||
This is the output.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
||||
|
||||
\begin{block}{Inline code and tables}
|
||||
\begin{itemize}
|
||||
\item In addition to inline code, we can also produce tables
|
||||
\item Tables are very powerful in org-mode, they even include spreadsheet
|
||||
capabilities
|
||||
\item Some code to process the first vector from above to make a table out
|
||||
of its summary could look like this, which would result in a little
|
||||
table (Table \ref{tab:org4e98e45}) :
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
\begin{column}[T]{0.78\columnwidth}
|
||||
\begin{minted}[linenos=true,bgcolor=lightgray]{r}
|
||||
library(broom)
|
||||
library(dplyr)
|
||||
t1 <- tidy(round(summary(x1), 2))
|
||||
t2 <- tidy(round(summary(x2), 2))
|
||||
|
||||
# This will export as a table
|
||||
rbind(t1, t2) %>%
|
||||
mutate(name=c("x1", "x2"))
|
||||
\end{minted}
|
||||
|
||||
\vspace{2cm}
|
||||
|
||||
\begin{table}[htbp]
|
||||
\centering
|
||||
\begin{tabular}{rrrrrrl}
|
||||
\hline
|
||||
minimum & q1 & median & mean & q3 & maximum & name\\
|
||||
\hline
|
||||
-2.29 & -0.49 & 0.11 & 0.14 & 0.8 & 2.47 & x1\\
|
||||
-2.17 & -0.45 & 0.07 & 0.13 & 0.85 & 2.23 & x2\\
|
||||
\hline
|
||||
\end{tabular}
|
||||
\caption{\label{tab:org4e98e45}
|
||||
A table summarizing the two distributions.}
|
||||
|
||||
\end{table}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
\end{block}
|
Loading…
Reference in New Issue