flesh out ob-doc

ob-julia-doc.tex

+% Created 2013-02-27 Wed 22:41
+\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
+\DeclareUnicodeCharacter{22EE}{⋮}
+\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
+
+One of the reasons for this document is that I wanted to make it easier to get acquainted with \texttt{julia}.  
+
+\section[What you need to get started]{What you need to get started}
+\label{sec-1}
+
+This document assumes you have at least a passing familiarity with Org-mode and Emacs keybindings.  
+
+\begin{verbatim}
+(load "/path/to/ob-julia.el")
+(org-babel-julia-initiate-session "*julia*" nil)
+\end{verbatim}
+
+\begin{description}
+\item[Note:] a lot of the code blocks below have the header argument \texttt{:eval no-export} which means that the code block can be evaluated interactively in this session by \texttt{C-c C-c} with point in the code block but will \emph{not} be evaluated during export.  The reason is that those blocks have settings which conflict with my current setup but would be useful for others going through this document.
+\end{description}
+
+\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", "GLM", "MCMC", "Optim", 
+        "NHST", "Clustering")
+\end{verbatim}
+
+\begin{verbatim}
+Pkg.add("RDatasets")
+\end{verbatim}
+
+
+\begin{enumerate}
+\item Winston
+\label{sec-1-2-1}
+
+The most stable and fully featured of the \texttt{julia} graphics packages at the time of this writing appears to be the \texttt{Winston} package, among alternatives including \texttt{Gadfly}.
+
+\begin{verbatim}
+Pkg.add("Winston")
+\end{verbatim}
+
+The Winston package has lots of dependencies and many of them must be built from source (on Ubuntu).
+\item 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}
+\end{enumerate}
+\subsection[Org-mode]{Org-mode}
+\label{sec-1-3}
+
+This document assumes that you have at least a passing familiarity with org-mode such that you likely have something like the following already in your \texttt{.emacs}:
+
+\begin{verbatim}
+(require 'org)
+\end{verbatim}
+
+Another handy setting to have is
+
+\begin{verbatim}
+(setq org-confirm-babel-evaluate nil)
+\end{verbatim}
+
+In order to run this org file you will need to load \texttt{ob-julia.el} at some point. One way is to edit the following code block and then \texttt{C-c C-c} with point inside the block:
+
+\begin{verbatim}
+(load "/path/to/ob-julia.el")
+(org-babel-julia-initiate-session "*julia*" nil)
+\end{verbatim}
+
+The first command loads the \texttt{ob-julia.el} file and the second initiates a \texttt{julia} session in a buffer called \texttt{*julia*}.  An alternative method is to put the following in your \texttt{.emacs} (these should go below the \texttt{(require 'org)} line):
+
+\begin{verbatim}
+(add-to-list 'load-path "/path/to/ob-julia.el")
+(org-babel-do-load-languages
+ 'org-babel-load-languages
+ '((emacs-lisp . t)
+   (julia . t)))
+\end{verbatim}
+
+The following lines (either here or in your \texttt{.emacs}) allow for inline image display in the Emacs buffer.
+
+\begin{verbatim}
+(add-hook 'org-babel-after-execute-hook 'org-display-inline-images)   
+(add-hook 'org-mode-hook 'org-display-inline-images)
+\end{verbatim}
+
+If you'd like to do \LaTeX{} export then put the following in your emacs.
+
+\begin{verbatim}
+(require 'ox-latex)
+(require 'ox-beamer)
+\end{verbatim}
+\subsection[ESS - Emacs Speaks Statistics]{ESS - Emacs Speaks Statistics}
+\label{sec-1-4}
+
+The place to get the latest version of ESS is \href{http://stat.ethz.ch/ESS/index.php?Section=download}{here}.  
+
+\begin{verbatim}
+(add-to-list 'load-path "/path/to/ESS/lisp")
+(require 'ess-site)
+\end{verbatim}
+
+\begin{verbatim}
+(setq  inferior-julia-program-name "/path/to/julia-release-basic")
+\end{verbatim}
+\section[Fitting (generalized) linear models]{Fitting (generalized) linear models}
+\label{sec-2}
+
+\begin{verbatim}
+using RDatasets, DataFrames, Distributions, GLM
+trees = data("datasets", "trees");
+treeslm = lm(:(Girth ~ Height + Volume), trees);
+coef(treeslm)
+coeftable(treeslm)
+\end{verbatim}
+
+\begin{verbatim}
+Warning: New definition show(Any,LmMod) is ambiguous with show(IO,ANY) at show.jl:6.
+         Make sure show(IO,LmMod) is defined first.
+Warning: New definition show(Any,GlmMod) is ambiguous with show(IO,ANY) at show.jl:6.
+         Make sure show(IO,GlmMod) is defined first.
+WARNING: strcat is deprecated, use string instead.
+WARNING: qrd is deprecated, use qrfact instead.
+3-element Float64 Array:
+ 10.8164   
+ -0.0454835
+  0.19518
+3x4 DataFrame:
+          Estimate Std.Error  t value   Pr(>|t|)
+[1,]       10.8164    1.9732  5.48165 7.44691e-6
+[2,]    -0.0454835 0.0282621 -1.60935   0.118759
+[3,]       0.19518 0.0109553  17.8161 8.2233e-17
+\end{verbatim}
+
+
+\section[Installation prerequisites]{Installation prerequisites}
+\label{sec-3}
+
+\subsection[Org-mode]{Org-mode}
+\label{sec-3-1}
+
+\subsection[ESS]{ESS}
+\label{sec-3-2}
+
+\subsection[julia]{julia}
+\label{sec-3-3}
+\section[Interactive session evaluation]{Interactive session evaluation}
+\label{sec-4}
+
+This is about ESS.
+\section[Evaluation inside the Org buffer]{Evaluation inside the Org buffer}
+\label{sec-5}
+
+\subsection[:results value]{:results value}
+\label{sec-5-1}
+
+\subsection[:results output]{:results output}
+\label{sec-5-2}
+\section[Graphics]{Graphics}
+\label{sec-6}
+
+\subsection[Plotting with Winston]{Plotting with Winston}
+\label{sec-6-1}
+
+\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, "example1.png")
+\end{verbatim}
+
+\includegraphics[width=.9\linewidth]{example1.png}
+
+\subsection[Plotting with Gadfly]{Plotting with Gadfly}
+\label{sec-6-2}
+
+\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[Exporting to other formats]{Exporting to other formats}
+\label{sec-7}
+
+\subsection[\LaTeX{}]{\LaTeX{}}
+\label{sec-7-1}
+
+\subsection[HTML]{HTML}
+\label{sec-7-2}
+
+\subsection[Beamer]{Beamer}
+\label{sec-7-3}
+\section[Other things]{Other things}
+\label{sec-8}
+
+\begin{itemize}
+\item empty lines in output for semicoloned lines
+\item need to start session first
+\item when :results value be careful because of readcsv
+\begin{itemize}
+\item characters
+\item 1x1 matrix
+\end{itemize}
+\end{itemize}
+% Generated by Org mode 7.9.3f in Emacs 24.3.50.1.
+\end{document}
\ No newline at end of file