initial commit

.gitignore

+.juliahistory
+*~
+ols.jl
+winston-examples.jl

ob-julia-beamer.org

+#+TITLE:     julia-beamer.org
+#+AUTHOR:    G. Jay Kerns
+#+EMAIL:     jay@gandalfrodo.no-ip.org
+#+DATE:      2013-02-25 Mon
+#+OPTIONS:   H:2 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t
+#+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
+#+LaTeX_CLASS: beamer
+#+LaTeX_CLASS_OPTIONS: [presentation, bigger]
+#+BEAMER_THEME: default
+#+COLUMNS: %45ITEM %10BEAMER_env(Env) %10BEAMER_act(Act) %4BEAMER_col(Col) %8BEAMER_opt(Opt)
+#+PROPERTY: BEAMER_col_ALL 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.0 :ETC
+#+PROPERTY: exports both
+#+PROPERTY: results output
+#+PROPERTY: session *julia*
+#+PROPERTY: tangle yes
+
+
+* Getting started
+
+#+BEGIN_SRC emacs-lisp :results silent :eval no-export
+(load "~/gitm/projects/ob-julia.el")
+(org-babel-julia-initiate-session "*julia*" nil)
+#+END_SRC
+
+Read the following links.
+- http://orgmode.org/worg/exporters/beamer/tutorial.html
+- http://orgmode.org/worg/exporters/beamer/ox-beamer.html
+- http://orgmode.org/manual/Beamer-class-export.html#Beamer-class-export
+
+Add the following to =.emacs=
+
+#+BEGIN_SRC emacs-lisp :eval never
+(require 'ox-beamer)
+#+END_SRC
+
+You also need to add the LaTeX class.
+
+#+BEGIN_SRC emacs-lisp :eval never
+(add-to-list 'org-latex-classes
+                '("beamer"
+                  "\\documentclass[presentation]{beamer}
+\[DEFAULT-PACKAGES]
+\[PACKAGES]
+\[EXTRA]"
+                  ("\\section{%s}" . "\\section*{%s}")
+                  ("\\subsection{%s}" . "\\subsection*{%s}")
+                  ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
+#+END_SRC
+
+** Exported title
+   :PROPERTIES:
+  :EXPORT_LaTeX_CLASS: beamer
+  :EXPORT_LaTeX_CLASS_OPTIONS: [presentation,smaller]
+  :EXPORT_BEAMER_THEME: default
+  :EXPORT_FILE_NAME: presentation.pdf
+  :END:
+- amsdk
+- kdsalk
+- adkfa
+- jlksa
+
+* This is the first structural section
+     
+** Frame 1
+#+BEAMER: \framesubtitle{with a subtitle}
+
+*** Thanks to Eric Fraga
+    :PROPERTIES:
+    :BEAMER_env: block
+    :BEAMER_envargs: C[t]
+    :BEAMER_col: 0.5
+    :END:
+	 for the first viable beamer setup in Org
+
+*** Thanks to everyone else
+    :PROPERTIES:
+    :BEAMER_col: 0.5
+    :BEAMER_env: block
+    :BEAMER_envargs: <2->
+    :END:
+	 for contributing to the discussion
+**** This will be formatted as a beamer note
+     :PROPERTIES:
+     :BEAMER_col: 0.5
+     :BEAMER_env: note
+     :BEAMER_envargs: <2->
+     :END:
+
+** Frame 2
+#+BEAMER: \framesubtitle{where we will not use columns}
+*** Request
+    Please test this stuff!
+    :PROPERTIES:
+    :BEAMER_env: block
+    :END:
+
+** Here is a graph
+#+BEGIN_SRC julia :exports results :results graphics :file example1.pdf :eval no-export
+using Winston
+x = linspace(0, 3pi, 100)
+c = cos(x)
+s = sin(x)
+p = FramedPlot();
+setattr(p, "title", "title!")
+setattr(p, "xlabel", L"\Sigma x^2_i")
+setattr(p, "ylabel", L"\Theta_i")
+add(p, FillBetween(x, c, x, s) )
+add(p, Curve(x, c, "color", "red") )
+add(p, Curve(x, s, "color", "blue") )
+file(p, "example1.pdf")
+#+END_SRC
+
+#+ATTR_LaTeX: :options "width=0.80\\textwidth"
+#+RESULTS:
+[[file:example1.pdf]]
+

ob-julia-beamer.tex

+% Created 2013-02-25 Mon 23:30
+\documentclass[presentation, bigger]{beamer}
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{fixltx2e}
+\usepackage{graphicx}
+\usepackage{longtable}
+\usepackage{float}
+\usepackage{wrapfig}
+\usepackage{soul}
+\usepackage{textcomp}
+\usepackage{marvosym}
+\usepackage{wasysym}
+\usepackage{latexsym}
+\usepackage{amssymb}
+\usepackage{hyperref}
+\tolerance=1000
+\usetheme{default}
+\author{G. Jay Kerns}
+\date{2013-02-25 Mon}
+\title{julia-beamer.org}
+\hypersetup{
+  pdfkeywords={},
+  pdfsubject={},
+  pdfcreator={Generated by Org mode 7.9.3f in Emacs 24.3.50.1.}}
+\begin{document}
+
+\maketitle
+\begin{frame}{Outline}
+\tableofcontents
+\end{frame}
+
+
+
+\section[Getting started]{Getting started}
+\label{sec-1}
+
+\begin{verbatim}
+(load "~/gitm/projects/ob-julia.el")
+(org-babel-julia-initiate-session "*julia*" nil)
+\end{verbatim}
+
+Read the following links.
+\begin{itemize}
+\item \url{http://orgmode.org/worg/exporters/beamer/tutorial.html}
+\item \url{http://orgmode.org/worg/exporters/beamer/ox-beamer.html}
+\item \url{http://orgmode.org/manual/Beamer-class-export.html#Beamer-class-export}
+\end{itemize}
+
+Add the following to \texttt{.emacs}
+
+\begin{verbatim}
+(require 'ox-beamer)
+\end{verbatim}
+
+You also need to add the \LaTeX{} class.
+
+\begin{verbatim}
+(add-to-list 'org-latex-classes
+                '("beamer"
+                  "\\documentclass[presentation]{beamer}
+\[DEFAULT-PACKAGES]
+\[PACKAGES]
+\[EXTRA]"
+                  ("\\section{%s}" . "\\section*{%s}")
+                  ("\\subsection{%s}" . "\\subsection*{%s}")
+                  ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
+\end{verbatim}
+
+\begin{frame}[label=sec-1-1]{Exported title}
+\begin{itemize}
+\item amsdk
+\item kdsalk
+\item adkfa
+\item jlksa
+\end{itemize}
+\end{frame}
+\section[This is the first structural section]{This is the first structural section}
+\label{sec-2}
+
+\begin{frame}[label=sec-2-1]{Frame 1}
+\framesubtitle{with a subtitle}
+
+\begin{columns}
+\begin{column}{0.5\textwidth}
+\begin{block}{Thanks to Eric Fraga}
+for the first viable beamer setup in Org
+\end{block}
+\end{column}
+
+\begin{column}{0.5\textwidth}
+\begin{block}{Thanks to everyone else}
+for contributing to the discussion
+\note{This will be formatted as a beamer note
+}
+\end{block}
+\end{column}
+\end{columns}
+\end{frame}
+\begin{frame}[label=sec-2-2]{Frame 2}
+\framesubtitle{where we will not use columns}
+\begin{block}{Request}
+Please test this stuff!
+\end{block}
+\end{frame}
+\begin{frame}[label=sec-2-3]{Here is a graph}
+\includegraphics[width=0.80\textwidth]{example1.pdf}
+\end{frame}
+% Generated by Org mode 7.9.3f in Emacs 24.3.50.1.
+\end{document}
\ No newline at end of file

ob-julia-doc.org

+#+TITLE:    Org-mode and julia: an introduction
+#+AUTHOR:   G. Jay Kerns
+#+EMAIL:    gkerns@ysu.edu
+#+PROPERTY: exports both
+#+PROPERTY: results output
+#+PROPERTY: session *julia*
+#+PROPERTY: tangle yes
+
+* What you need to get started
+
+This document assumes you have at least a passing familiarity with Org-mode and Emacs keybindings.  
+
+#+BEGIN_SRC emacs-lisp :results silent :eval no-export
+(load "~/gitm/projects/ob-julia.el")
+(org-babel-julia-initiate-session "*julia*" nil)
+#+END_SRC
+
+** Julia
+- First install takes the longest, later updates not so bad.
+- all the dependencies
+
+** Add on packages
+
+Based on [[http://www.johnmyleswhite.com/notebook/2012/12/02/the-state-of-statistics-in-julia/][The State of Statistics in Julia]] by John Myles White.
+
+#+BEGIN_SRC julia :eval never
+Pkg.add("DataFrames", "Distributions", "GLM", "MCMC", "Optim", "NHST", "Clustering")
+#+END_SRC
+
+#+BEGIN_SRC julia :eval never
+Pkg.add("RDatasets")
+#+END_SRC
+
+
+*** Winston
+
+The =Winston= package at the time of this writing appears to be the most stable and fully featured of the =julia= graphics packages, among alternatives including =Gadfly=.
+
+#+BEGIN_SRC julia :eval never
+Pkg.add("Winston")
+#+END_SRC
+
+The Winston package has lots of dependencies and many of them must be built from source (on Ubuntu).
+
+*** Gadfly
+
+#+BEGIN_SRC julia :eval never
+Pkg.add("Gadfly")
+#+END_SRC
+
+- packages take a lot longer to load than R
+
+
+** Org-mode
+
+We are assuming that you have a passing familiarity with org-mode, so that you likely have something like the following already in your =.emacs=
+
+#+BEGIN_SRC emacs-lisp :eval never
+(require 'org)
+#+END_SRC
+
+Another handy setting to have is
+
+#+BEGIN_SRC emacs-lisp
+(setq org-confirm-babel-evaluate nil)
+#+END_SRC
+
+In order to run this org file you will need to load the following code which .
+
+#+BEGIN_SRC emacs-lisp :results silent :eval never
+(load "~/gitm/projects/ob-julia.el")
+(org-babel-julia-initiate-session "*julia*" nil)
+#+END_SRC
+
+Or you can copy =ob-julia.el= to your =/path/to/org-mode/lisp= folder and put the following in your =.emacs=.
+
+#+BEGIN_SRC emacs-lisp :eval never
+(org-babel-do-load-languages
+ 'org-babel-load-languages
+ '((emacs-lisp . t)
+   (julia . t)))
+#+END_SRC
+
+The following lines (either here or in your =.emacs=) allow for inline image display in the Emacs buffer.
+
+#+BEGIN_SRC emacs-lisp :eval never
+(add-hook 'org-babel-after-execute-hook 'org-display-inline-images)   
+(add-hook 'org-mode-hook 'org-display-inline-images)
+#+END_SRC
+
+If you'd like to do LaTeX export then put the following in your emacs.
+
+#+BEGIN_SRC emacs-lisp :eval never
+(require 'ox-latex)
+(require 'ox-beamer)
+#+END_SRC
+
+
+
+** ESS
+
+The place to get the latest version of ESS is [[http://stat.ethz.ch/ESS/index.php?Section=download][here]].  
+
+#+BEGIN_SRC emacs-lisp :eval never
+(add-to-list 'load-path "~/path/to/ESS/lisp")
+(require 'ess-site)
+#+END_SRC
+
+#+BEGIN_SRC emacs-lisp :eval never
+(setq  inferior-julia-program-name "~/path/to/julia-release-basic")
+#+END_SRC
+
+* Getting started with julia
+
+#+BEGIN_SRC julia :results value
+rand(2,3)
+#+END_SRC
+
+#+BEGIN_SRC julia :results output
+print("hello")
+#+END_SRC
+
+#+BEGIN_SRC julia
+[3:50]
+x = [3:6]
+y = [5:11]
+z = [4:7]
+x + z
+ans
+sum(x)
+mean(x)
+exp(x)
+log(x)
+sort(x)
+sqrt(x)
+diff(x)
+x[3]
+y[2:4]
+typeof(x)
+1.0
+1.
+Inf
+-Inf
+NaN
+1 + 2im
+#+END_SRC
+
+* Plotting with Winston
+
+#+BEGIN_SRC julia :results graphics :file example1.png
+using Winston
+x = linspace( 0, 3pi, 100 )
+c = cos(x)
+s = sin(x)
+p = FramedPlot();
+setattr(p, "title", "title!")
+setattr(p, "xlabel", L"\Sigma x^2_i")
+setattr(p, "ylabel", L"\Theta_i")
+add(p, FillBetween(x, c, x, s) )
+add(p, Curve(x, c, "color", "red") )
+add(p, Curve(x, s, "color", "blue") )
+file(p, "example1.png")
+#+END_SRC
+
+#+RESULTS:
+[[file:example1.png]]
+
+* Plotting with Gadfly
+
+#+BEGIN_SRC julia :results graphics :file iris_plot.svg :eval never
+using RDatasets
+using Gadfly
+using Compose
+iris = data("datasets", "iris")
+p = plot(iris, {:x => "Sepal.Length", :y => "Sepal.Width"}, Geom.point);
+SVG("iris_plot.svg", 6inch, 4inch)
+#+END_SRC
+
+
+* Fitting (generalized) linear models
+
+#+BEGIN_SRC julia :eval never
+using RDatasets, DataFrames, Distributions, GLM
+trees = data("datasets", "trees");
+treeslm = lm(:(Girth ~ Height + Volume), trees);
+coef(treeslm)
+confint(treeslm)
+#+END_SRC

ob-julia-doc.tex

+% Created 2013-02-24 Sun 20:30
+\documentclass[11pt]{article}
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{fixltx2e}
+\usepackage{graphicx}
+\usepackage{longtable}
+\usepackage{float}
+\usepackage{wrapfig}
+\usepackage{soul}
+\usepackage{textcomp}
+\usepackage{marvosym}
+\usepackage{wasysym}
+\usepackage{latexsym}
+\usepackage{amssymb}
+\usepackage{hyperref}
+\tolerance=1000
+\author{G. Jay Kerns}
+\date{\today}
+\title{Org-mode and julia: an introduction}
+\hypersetup{
+  pdfkeywords={},
+  pdfsubject={},
+  pdfcreator={Generated by Org mode 7.9.3f in Emacs 24.3.50.1.}}
+\begin{document}
+
+\maketitle
+\tableofcontents
+
+
+\section[What you need to get started]{What you need to get started}
+\label{sec-1}
+
+\begin{verbatim}
+(load "~/gitm/projects/ob-julia.el")
+(org-babel-julia-initiate-session "*julia*" nil)
+\end{verbatim}
+
+\begin{verbatim}
+rand(9)
+\end{verbatim}
+
+\begin{verbatim}
+9-element Float64 Array:
+ 0.627821
+ 0.786056
+ 0.851449
+ 0.447721
+ 0.722442
+ 0.447876
+ 0.578059
+ 0.132425
+ 0.338724
+\end{verbatim}
+
+\subsection[Julia]{Julia}
+\label{sec-1-1}
+\begin{itemize}
+\item First install takes the longest, later updates not so bad.
+\item all the dependencies
+\end{itemize}
+\subsection[Add on packages]{Add on packages}
+\label{sec-1-2}
+
+Based on \href{http://www.johnmyleswhite.com/notebook/2012/12/02/the-state-of-statistics-in-julia/}{The State of Statistics in Julia} by John Myles White.
+
+\begin{verbatim}
+Pkg.add("DataFrames", "Distributions", "MCMC", "Optim", "NHST", "Clustering")
+\end{verbatim}
+
+\begin{verbatim}
+Pkg.add("RDatasets")
+\end{verbatim}
+
+This one is pretty big.
+
+\subsubsection[Winston]{Winston}
+\label{sec-1-2-1}
+
+\begin{verbatim}
+Pkg.add("Winston")
+\end{verbatim}
+
+This one has lots of dependencies.
+\subsubsection[Gadfly]{Gadfly}
+\label{sec-1-2-2}
+
+
+\begin{verbatim}
+Pkg.add("Gadfly")
+\end{verbatim}
+
+\begin{itemize}
+\item packages take a lot longer to load than R
+\end{itemize}
+\subsection[ESS]{ESS}
+\label{sec-1-3}
+\url{http://stat.ethz.ch/ESS/index.php?Section=download}
+
+\begin{verbatim}
+rand(9)
+print("hello")
+\end{verbatim}
+
+\begin{verbatim}
+9-element Float64 Array:
+ 0.294536 
+ 0.292205 
+ 0.0626337
+ 0.435547 
+ 0.830883 
+ 0.298874 
+ 0.286572 
+ 0.539265 
+ 0.855514
+hello
+\end{verbatim}
+
+\begin{verbatim}
+(add-to-list 'load-path "~/path/to/ESS/lisp")
+(require 'ess-site)
+\end{verbatim}
+\subsection[Org-mode]{Org-mode}
+\label{sec-1-4}
+
+\begin{verbatim}
+(setq  inferior-julia-program-name "~/path/to/julia-release-basic")
+\end{verbatim}
+
+\begin{verbatim}
+(org-babel-do-load-languages
+ 'org-babel-load-languages
+ '((emacs-lisp . t)
+   (julia . t)))
+\end{verbatim}
+
+
+For inline image display
+
+\begin{verbatim}
+(add-hook 'org-babel-after-execute-hook 'org-display-inline-images)   
+(add-hook 'org-mode-hook 'org-display-inline-images)
+\end{verbatim}
+\section[Getting started]{Getting started}
+\label{sec-2}
+
+\begin{verbatim}
+[3:50]
+x = [3:6]
+y = [5:11]
+z = [4:7]
+x + z
+ans
+sum(x)
+mean(x)
+exp(x)
+log(x)
+sort(x)
+sqrt(x)
+diff(x)
+x[3]
+y[2:4]
+typeof(x)
+1.0
+1.
+Inf
+-Inf
+NaN
+true
+false
+1 + 2im
+\end{verbatim}
+\section[Plotting with Winston]{Plotting with Winston}
+\label{sec-3}
+
+\begin{verbatim}
+using Winston
+x = linspace( 0, 3pi, 100 )
+c = cos(x)
+s = sin(x)
+p = FramedPlot();
+setattr(p, "title", "title!")
+setattr(p, "xlabel", L"\Sigma x^2_i")
+setattr(p, "ylabel", L"\Theta_i")
+add(p, FillBetween(x, c, x, s) )
+add(p, Curve(x, c, "color", "red") )
+add(p, Curve(x, s, "color", "blue") )
+file(p, "blah2.png")
+\end{verbatim}
+
+\includegraphics[width=.9\linewidth]{blah2.png}
+\section[Plotting with Gadfly]{Plotting with Gadfly}
+\label{sec-4}
+
+\begin{verbatim}
+using RDatasets
+using Gadfly
+using Compose
+iris = data("datasets", "iris")
+p = plot(iris, {:x => "Sepal.Length", :y => "Sepal.Width"}, Geom.point);
+SVG("iris_plot.svg", 6inch, 4inch)
+\end{verbatim}
+
+\section[Fitting linear models]{Fitting linear models}
+\label{sec-5}
+% Generated by Org mode 7.9.3f in Emacs 24.3.50.1.
+\end{document}
\ No newline at end of file