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Weaving Markdown Documents with Julia
Pedro Henrique Pereira Braga
ph.pereirabraga@gmail.com
January 26th, 2019

Welcome! I built this tutorial because I have been interested in using Julia to perform some of the analyses related to my doctorate thesis. When learning new R routines and functions, I have always found it easier to write RMarkdown documents and tutorials as a way of learning. Do not hesitate to give your feedback or your contributions to this document. Enjoy!

Best regards,

Pedro H. P. Braga

Introduction

This document gives a brief illustration on how to create a scientific report document using Julia and its Weave.jl package. The Weave.jl package was built by Matti Pastell, and it allows the "writing of text, mathematics and code in a single document which can be run capturing results into a rich report". Visit Weave.jl's documentation and publication for further information.

For this, you will need to install the Weave.jl package:


using Pkg; Pkg.add.("Weave")

Getting started

The YAML header

Julia's markdown documents hold the extension .jmd and are built using markup language. To learn more on Markdown, visit this website or access this cheatsheet.

As I start point, I suggest that you create a .jmd document, so your Julia IDE can properly highlight your markdown syntax (currently available within Atom through the language-weave extension). Once created, you will need to start your document with an YMAL header, as in the example below:


---
title: Creating Scientific Reports with Julia
author: Pedro Henrique Pereira Braga
date: January 26th, 2019
---

As seen in the beginning of this document, the above YAML allows Julia to add a title, an author name and a date to your document.

You can then begin writing your text below the ---. Following the Markdown language, you can indicate titles and subtitles with # and ##, ### (and other variants), respectively.


# Section Header One

Hi! My name is **Pedro**!

## Section Header Two

As in Markdown, you can use many in-line elements, such as the *single-asterisks*
to make things in *italic*, or the **double-asterisks** to make your text in
**bold**. You can also create [hyperlinks](http://www.julialang.org).

### Section Header Three
#### Section Header Four
##### Section Header Five
###### Section Header Six

In-line code and code chunks

You can write in-line code using one backtick `, or define code chunks using three consecutive backticks ```.

You can create a code block without an specified-language, but if you write julia right after the code block delimiter ( ```julia ) or `j` after your in-line backtick ( ``j` ), Weave will know that you want to run julia-language commands:

A code block without a "language":

function func(x)
    # ...
end


# This code block is in Julia code

function func(x)
    # ...
end

If nothing else is written after the backticks, code and output are captured following the default parameter of code chunks:

# Loading packages
using Phylo
using DataFrames

# Creating species
species = ["Dog", "Cat", "Human", "Monkey", "Alien"];

# Creating communities
communities = DataFrame(Dog = [1, 1, 1],
                        Cat = [0, 1, 1],
                        Human = [1, 0, 0],
                        Monkey = [1, 0, 1],
                        Alien = [0, 0, 1])

nt = rand(Nonultrametric(species))
nt #the output comes right below

BinaryTree{DataFrame,Dict{String,Any}} with 5 tips, 9 nodes and 8 branches.
Leaf names are Dog, Cat, Human, Monkey and Alien

By defining chunk parameters (separated by ;), you can, for example: hide the code (echo = FALSE); provide figure captions (fig_cap="A random walk."); define a label (label="random"); and, delimit the figure width and height (fig_width=7; fig_height=4). See below an example of a figure generated using the same above-mentioned chunk options:

Plot{Plots.PlotlyBackend() n=1}

Access Weave.jl's chunk options documentation to see the currently supported chunk defining arguments.

Quotes

You can also quote from external sources, such as books, websites or articles using > following by a single-space before your text. See the following example and its consecutive effect:

Here's a quote:
> Julia is a high-level, high-performance dynamic programming language for
> technical computing, with syntax that is familiar to users of other
> technical computing environments.

>> You can also set another level or `inline` parameters by adding `>>` and
>> a space before your "sub-quote".

Here's a quote:

Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments.

You can also set another level or inline parameters by adding >> and a space before your "sub-quote".

Ordered and Unordered Lists

Unordered lists can be written with either *, +, or -. Note that an space following the list-delimiter is always needed:

An unordered list:
  * *Italic item*
  * **Bold item**
    ```
    f(x) = x # Your favorite functions
    ```
  * And a sublist:
      + Sub-item one
      + Sub-item two

An unordered list:

  • Italic item
  • Bold item 
    f(x) = x # Your favorite functions
  • And a sublist:
    • Sub-item one
    • Sub-item two

Ordered lists are written by replacing the "bullet" character, either *, +, or -, with a positive integer followed by either . or ).

One ordered list starting from 1. to 3.:
 1. Item one
 2. Item two
 3. Item three

You can also create another list starting from numbers 5. to 7.:
 5) Item five
 6) Item six
 7) Item seven

One ordered list starting from 1. to 3.:

  1. Item one
  2. Item two
  3. Item three

You can also create another list starting from numbers 5. to 7.: 5) Item five 6) Item six 7) Item seven

Footnotes

You can also use footnotes to add numbered [^1] or named footnotes [^named] to paragraphs. For this, you can add [^number] or [^text] after a desired text, and then append it to your desired place in the text by writing the following syntax:

[^1]: Numbered footnote text.

[^named]:
    Named footnote text containing several toplevel elements.
      * item one
      * item two
      * item three

    ```julia
    function func(x)
        # ...
    end
    ```

Weaving the document

When you are finally done with your document, you can save it to your preferred directory and then Weave it. You can do this with the help of the weave function. Type and run ?weave to learn about the function's arguments or access the documentation. Run list_out_formats() to see supported output formats. Below, you can see examples showing how to weave this document to Markdown, HTML and PDF.


# Output it to Markdown
weave(joinpath("", "WeavingDocumentsJl.jmd"),
      informat="markdown",
      out_path = :pwd, # This outputs the document to your current working directory
      doctype = "pandoc")

# to HTML
weave(joinpath("", "WeavingDocumentsJl.jmd"),
      informat="markdown",
      out_path = :pwd,
      doctype = "md2html")

# to PDF
weave(joinpath("", "WeavingDocumentsJl.jmd"),
      informat="markdown",
      out_path = joinpath("", "pdf"),
      doctype = "pandoc2pdf")


# Remember that you can set your working directory with cd. Here is an example:
cd("C:\\Users\\phper\\Documents\\GitHub\\pedrohbraga\\WeavingDocumentsInJulia")

Learn more

Read the Weave.jl documentation

Read the julia Markdown documentation

References

  1. Pastell, Matti. 2017. Weave.jl: Scientific Reports Using Julia. The Journal of Open Source Software. http://dx.doi.org/10.21105/joss.00204
  2. Bezanson, Jeff, Alan Edelman, Stefan Karpinski, and Viral B. Shah. 2017. “Julia: A Fresh Approach to Numerical Computing.” SIAM Review 59 (1): 65–98. doi:10.1137/141000671.
  3. Xie, Yihui. 2015. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. http://yihui.name/knitr/.