375 lines
12 KiB
Org Mode
375 lines
12 KiB
Org Mode
#+startup: beamer
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#+TITLE: Using org-mode for scientific posters
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* Preamble :ignore:
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** General comments :ignore:
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# ----------------------------------------------------------------------
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# - Turn on synonyms by starting synosaurus-mode
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# - Look up words using C-c sr
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# - Turn on dictionary by starting flyspell-mode
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# - Count words by section using org-wc-display
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# ----------------------------------------------------------------------
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** Specific comments for this manuscript :ignore:
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# ----------------------------------------------------------------------
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# This is a comment
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# ----------------------------------------------------------------------
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** org specific settings :ignore:
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# ----------------------------------------------------------------------
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#+OPTIONS: email:nil toc:nil num:nil author:nil date:t tex:t title:nil
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#+STARTUP: align fold
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#+SEQ_TODO: TODO(t) | DONE(d)
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#+TAGS: figure(f) check(c) noexport(n) ignore(i)
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#+LANGUAGE: en
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#+EXCLUDE_TAGS: noexport TODO
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#+DATE: {{{time(%Y-%m-%d %H:%M)}}}
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# ----------------------------------------------------------------------
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** Latex header :ignore:
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# ----------------------------------------------------------------------
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#+LATEX_CLASS: mybeamerposter
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#+LATEX_HEADER: \setlength{\paperwidth}{36in}
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#+LATEX_HEADER: \setlength{\paperheight}{48in}
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#+LATEX_HEADER: \setlength{\textwidth}{0.98\paperwidth}
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#+LATEX_HEADER: \setlength{\textheight}{0.98\paperheight}
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#+LATEX_HEADER: \graphicspath{{../output/figures/}{../lib/}}
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#+LATEX_HEADER: \usepackage[export]{adjustbox}
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#+LATEX_HEADER: \usepackage{graphicx,caption}
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#+LATEX_HEADER: \usepackage{minted}
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#+LATEX_HEADER: \usepackage{eurosym}
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#+LATEX_HEADER: \usepackage{listings}
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#+LATEX_HEADER: \usepackage{textcomp}
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#+LATEX_HEADER: \usepackage{bibentry}
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#+LATEX_HEADER: \newcommand\sumin{\sum_{i=1}^{n}}
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#+LATEX_HEADER: \newcommand{\Xoi}[1]{#1(i)}
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#+LATEX_HEADER: \newcommand{\frakPQ}[2]{\frac{\Xoi{#1}}{\Xoi{#2}}}
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#+LATEX_HEADER: \newcommand{\DKLPQ}[3]{D_{\mathrm{KL}}(#1 #3 #2)}
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#+LATEX_HEADER: \date{}
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# ----------------------------------------------------------------------
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** Latex macros :ignore:
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# ----------------------------------------------------------------------
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#+LATEX_HEADER: \newcommand{\auth}{Philipp Homan, MD, PhD}
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#+LATEX_HEADER: \newcommand{\authemail}{phoman1@northwell.edu}
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#+LATEX_HEADER: \newcommand{\authtwitter}{@philipphoman}
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#+LATEX_HEADER: \newcommand{\authgithub}{github.com/philipphoman}
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# ----------------------------------------------------------------------
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** Authors and affiliations :ignore:
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# ----------------------------------------------------------------------
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#+LATEX_HEADER: \author{
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#+LATEX_HEADER: Philipp Homan$^{1}$
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#+LATEX_HEADER: \\
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#+LATEX_HEADER: \normalsize{$^{1}$Department of Psychiatry,}
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#+LATEX_HEADER: \normalsize{The Donald and Barbara Zucker}
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#+LATEX_HEADER: \normalsize{School of Medicine at Northwell/Hofstra,}
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#+LATEX_HEADER: \normalsize{Hempstead, NY}
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#+LATEX_HEADER: }
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# ----------------------------------------------------------------------
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** Buffer-wide source code blocks :ignore:
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# ----------------------------------------------------------------------
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# Set elisp variables need for nice formatting We want no new lines in
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# inline results and a paragraph size of 80 characters Important: this
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# has to be evaluated witch C-c C-c in order to work in the current
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# buffer
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#+BEGIN_SRC emacs-lisp :exports none :results silent
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; Nicer formatting for code
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(setq org-latex-listings t)
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(setq org-latex-listings 'minted)
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'(org-export-latex-listings-langs
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(quote ((emacs-lisp "Lisp")
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(lisp "Lisp")
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(clojure "Lisp")
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(c "C")
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(cc "C++")
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(fortran "fortran")
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(perl "Perl")
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(cperl "Perl")
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(python "Python")
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(ruby "Ruby")
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(html "HTML")
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(xml "XML")
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(tex "TeX")
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(latex "TeX")
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(shell-script "bash")
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(gnuplot "Gnuplot")
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(ocaml "Caml")
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(caml "Caml")
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(sql "SQL")
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(sqlite "sql")
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(R-mode "R"))))
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(setq org-latex-minted-options
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'(("linenos=true") ("bgcolor=lightgray")))
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; set timestamp format
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;(setq org-export-date-timestamp-format "%FT%T%z")
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(require 'org-wc)
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(flyspell-mode t)
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;(evil-declare-change-repeat 'company-complete)
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(setq synosaurus-choose-method 'popup)
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(synosaurus-mode t)
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(auto-complete-mode t)
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;(ac-config-default)
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;(add-to-list 'ac-modes 'org-mode)
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(linum-mode t)
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(whitespace-mode t)
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(setq org-babel-inline-result-wrap "%s")
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(setq org-export-with-broken-links "mark")
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(setq fill-column 72)
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(setq whitespace-line-column 72)
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;(setq org-latex-caption-above '(table image))
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(setq org-latex-caption-above nil)
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(org-toggle-link-display)
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; don't remove logfiles at export
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(setq org-latex-remove-logfiles nil)
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; Keybindings
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; (global-set-key (kbd "<f7> c") "#+CAPTION: ")
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(defun setfillcolumn72 ()
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(interactive)
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(setq fill-column 72)
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)
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(defun setfillcolumn42 ()
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(interactive)
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(setq fill-column 42)
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)
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(define-key org-mode-map (kbd "C-c c #") "#+CAPTION: ")
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(define-key org-mode-map (kbd "C-c l #") "#+LATEX_HEADER: ")
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(define-key org-mode-map (kbd "C-c f c 4 2") 'setfillcolumn42)
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(define-key org-mode-map (kbd "C-c f c 7 2") 'setfillcolumn72)
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(setq org-odt-category-map-alist
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'(("__Figure__" "*Figure*" "value" "Figure" org-odt--enumerable-image-p)))
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; let ess not ask for starting directory
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(setq ess-ask-for-ess-directory nil)
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;(setq org-latex-pdf-process '("latexmk -pdflatex='xelatex
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;-output-directory=../output/tex/ -interaction nonstopmode' -pdf
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;-bibtex -f %f"))
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(setq org-latex-logfiles-extensions
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(quote("bcf" "blg" "fdb_latexmk" "fls"
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"figlist" "idx" "log" "nav" "out" "ptc"
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"run.xml" "snm" "toc" "vrb" "xdv")))
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; deactivate link resolving
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(setq org-activate-links nil)
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#+END_SRC
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#
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#
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#
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# ----------------------------------------------------------------------
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** End preamble :ignore:
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# ----------------------------------------------------------------------
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* The poster
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:PROPERTIES:
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:BEGIN:
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:BEAMER_env: fullframe
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:END:
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** Code :ignore:
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# Babel code can go here to populate the poster with dynamic output
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** Left column :BMCOL:
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:PROPERTIES:
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:BEAMER_col: 0.45
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:BEAMER_opt: [t]
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:END:
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*** Background :B_block:
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:PROPERTIES:
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:BEAMER_env: block
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:END:
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- Here we show how org-mode (version src_elisp{org-version}
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{{{results(9.1.7)}}}) and emacs (version src_elisp{emacs-version}
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{{{results(25.2.2)}}}) can be used to make decent looking scientific
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posters
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- With org-mode we can populate the poster with code, graphs and numbers
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from inline code in languages such as R, python, Matlab and even shell
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scripting
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- For example, this poster was created on {{{time(%Y-%m-%d %H:%M)}}} on
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src_bash{lsb_release -sd} {{{results(Ubuntu 17.10)}}}.
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- Inline code could look like this (which will produce a graph;
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Fig. [[figcode1]]):
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**** Block
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:PROPERTIES:
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:BEAMER_col: 0.68
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:BEAMER_opt: [T]
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:END:
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#+NAME: code1
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#+BEGIN_SRC R :file 3.png :session :exports both :results graphics
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set.seed(20180402)
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x1 <- rnorm(100, 0, 1)
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x2 <- rnorm(100, 0.5, 1)
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hist(x1, col="red")
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hist(x2, col="blue", add=TRUE)
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#+END_SRC
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#+NAME: figcode1
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#+CAPTION: This is the output.
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#+RESULTS: code1
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[[file:3.png]]
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*** Inline code and tables :B_block:
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:PROPERTIES:
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:BEAMER_env: block
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:END:
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- Tables are powerful in org-mode and even include spreadsheet
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capabilities
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- Some code to process the first vector from above to make a table out
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of its summary could look like this, which would result in a little
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table (Table [[tabcode2]]) :
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**** Block
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:PROPERTIES:
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:BEAMER_col: 0.78
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:BEAMER_opt: [T]
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:END:
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#+NAME: code2
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#+BEGIN_SRC R :session :exports both :results value :colnames yes :cache yes
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library(broom)
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library(dplyr)
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t1 <- tidy(round(summary(x1), 2))
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t2 <- tidy(round(summary(x2), 2))
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# This will export as a table
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rbind(t1, t2) %>%
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mutate(name=c("x1", "x2"))
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#+END_SRC
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\vspace{2cm}
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\small
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#+CAPTION: A table summarizing the two distributions.
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#+NAME: tabcode2
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#+RESULTS[9d0ec7348265a5cb6de39440ff06a8dbb8e5ecf1]: code2
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|---------+-------+--------+------+------+---------+------|
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| minimum | q1 | median | mean | q3 | maximum | name |
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|---------+-------+--------+------+------+---------+------|
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| -2.29 | -0.49 | 0.11 | 0.14 | 0.8 | 2.47 | x1 |
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| -2.17 | -0.45 | 0.07 | 0.13 | 0.85 | 2.23 | x2 |
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|---------+-------+--------+------+------+---------+------|
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** Right column :BMCOL:
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:PROPERTIES:
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:BEAMER_col: 0.45
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:BEAMER_opt: [t]
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:END:
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*** Graphics :B_block:
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:PROPERTIES:
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:BEAMER_env: block
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:END:
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- We can use shell scripting to grab an image with curl from the
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internet (Fig. [[figcode3]]):
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**** Block
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:PROPERTIES:
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:BEAMER_col: 0.78
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:BEAMER_opt: [T]
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:END:
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\footnotesize
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#+NAME: code3
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#+BEGIN_SRC bash :exports both :file emacs.png
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# Download emacs icon from gnu.org
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curl -0 https://www.gnu.org/software/emacs/images/emacs.png
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#+END_SRC
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\normalsize
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\vspace{2cm}
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#+ATTR_LATEX: :width 0.2\textwidth :options page=9
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#+NAME: figcode3
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#+CAPTION: This is the downloaded image.
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#+RESULTS: code3
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[[file:emacs.png]]
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*** Math :B_block:
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:PROPERTIES:
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:BEAMER_env: block
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:END:
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- Let's describe how to compute the distance between the
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two simulated distributions $x1$ and $x2$ from before:
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**** Block
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:PROPERTIES:
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:BEAMER_col: 0.78
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:BEAMER_opt: [T]
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:END:
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\small
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The Kullback-Leibler (KL) divergence measures the difference between two
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probability distributions (i.e., the loss of information when one
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distribution is used to approximate another). The KL divergence is thus
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defined as
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#
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\begin{align}
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\label{eq:KL}
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\DKLPQ{P}{Q}{\|} = \sumin \Xoi{P} \log \frakPQ{P}{Q}
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\end{align}
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#
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with $P$ and $Q$ being two probability distribution functions and $n$
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the number of sample points. Since $\DKLPQ{P}{Q}{\|}$ is not equal to
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$\DKLPQ{Q}{P}{\|}$, a symmetric variation of the KL divergence can be
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derived as follows:
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#
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\small
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\begin{align}
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\label{eq:KL2}
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\DKLPQ{P}{Q}{,} = \sumin \Big(\Xoi{P} \log \frakPQ{P}{Q} + \Xoi{Q} \log \frakPQ{Q}{P} \Big).
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\end{align}
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*** Columns :B_block:
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:PROPERTIES:
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:BEAMER_env: block
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:END:
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**** Left
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:PROPERTIES:
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:BEAMER_col: 0.48
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:BEAMER_opt: [T]
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:END:
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#+NAME: codeleft
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#+BEGIN_SRC R :file 4l.png :session :exports results :results graphics
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d1 <- density(x1)
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plot(d1, col="red", lwd=3)
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#+END_SRC
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\captionsetup{justification=justified,width=.85\linewidth}
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#+NAME: figcodeleft
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#+CAPTION: This is the left figure of a two-column block, showing
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#+CAPTION: the density of $x1$.
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#+RESULTS: codeleft
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[[file:4l.png]]
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**** Right
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:PROPERTIES:
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:BEAMER_col: 0.48
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:BEAMER_opt: [T]
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:END:
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#+NAME: coderight
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#+BEGIN_SRC R :file 4r.png :session :exports results :results graphics
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d2 <- density(x2)
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plot(d2, col="blue", lwd=3)
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#+END_SRC
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\captionsetup{justification=justified,width=.85\linewidth}
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#+NAME: figcoderight
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#+CAPTION: This is the right figure. It shows the density of $x2$.
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#+RESULTS: coderight
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[[file:4r.png]]
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*** Conclusions :B_block:
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:PROPERTIES:
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:BEAMER_env: block
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:END:
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- This example is meant to show how versatile org-mode is
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- Scientific posters can be produced with a simple text editor
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