# Make LaTeX easier with custom commands

LaTeX is a powerful tool for creating professional looking documents. Its ability to easily format mathematical equations, citations and complex figures makes LaTeX especially useful for developing peer-reviewed journal articles and scientific reports. LaTeX is highly customizable, which allows you to create documents that are not carbon copies of generic Microsoft Word templates.

Using LaTeX does have it’s drawbacks- instead of simply typing on a page, you construct the document by writing LaTeX code. Once you’ve written your code, a compiler translates it into a finished and formatted document. This can sometimes result in high overhead time for fixing bugs and managing format. But coding a document also has advantages, in addition to the vast array of existing LaTeX libraries and commands, you can create your own custom commands that speed up the writing and formatting process. Below I’ll overview the basics of creating custom LaTeX commands and provide some illustrative examples.

## Commands with no arguments

If you have an equation or a complex sequence of text that you know you’ll be repeating, you can create a custom command to produce it. For example, if I’m constantly referencing the equation for an Ordinary Least Squares (OLS) estimator, I can make a new command that produces it:

\newcommand{\OLS}{$\hat{\beta}=(X^TX)^{-1}X^Ty$}


There are three parts to defining this command, as shown in the figure below:

1. Tell LaTex you are defining a new command by specifying “\newcommand”
2. name the command (make sure to include the backslash)
3. Specify the output of the new command

Example LaTex code that calls the OLS command:

I can store complex terms using a predefined command: \OLS


Compiled output:

## Commands with basic arguments

### Single argument

You can also define commands that accept arguments. For example, if you want to make commands to assist tracking changes in a document, you can create a command that formats a section of added text so it has the color blue and is bolded:

\newcommand{\addtxt}[1]{{\color{blue} \textbf{#1}}} % Highlight text that has been added



The command defined above accepts one argument (shown as the “[1]”) and calls that argument using “#1”, as highlighted in the figure below:

Example Latex code using my command:

Demonstrating my custom commands with arguments:\addtxt{This text has be inserted into this sentence}


Example compiled output:

### Multiple arguments

You can also define commands with multiple arguments, for example, you can create a template sentence that provides an update the timing of a project:

\newcommand{\projReportA}[2]{The project was planned to finish on \textbf{#1}after reviewing current progress we have determined that it will likely finish on \textbf{#2}} % insert a date for when a project was planned to be completed and when a project is likely to be completed


Here, argument #1 is the date when the project was planned on being completed, and argument #2 is the date that the project will likely be completed.

Example use of this function:

Another way you can use an argument:\\ \\
\projReportA{September $9^{th}$}{October $1^{st}$}


Example compiled output:

## Commands with optional arguments

The project report command above can be modified to accept a default completion date with an option to include an updated date.

\newcommand{\progReportB}[2][September 9th]{The project was planned to finish on \textbf{#2}, after reviewing current progress, we have determined that it will likely finish on \textbf{#1}}


To create an optional argument, specify the default value of the first argument in a new set of brackets. Note that for basic Latex this only works for a single default argument, for more defaults you can use a package such as xparse.

Here’s an example using this new command with the default argument:

Here I'll will use the command without the optional argument, so it will print the default: \\
\\
\progReportB{September $9^{th}$}


This will compile to:

Here’s an example with the optional argument specified

Now I'll add the optional argument, which will be added in place of the default: \\ \\
\progReportB[October $1^{st}$]{September $9^{th}$}


This will compile to:

### Concluding thoughts

These simple examples only scratch the surface of what you can do with LaTex commands. I should also note that while custom commands are useful, LaTex also contains a large suite of packages with predefined commands that can be easily imported into your document.

# R-Markdown

## What Is R-Markdown? Why We Are Interested in It?

A few years ago, a very dear friend of mine told me about R-Markdown. I was working on a report, and he said that I should try this very cool tool. I did so but not immediately. I started with an “if it ain’t broke, don’t fix it” attitude. However, I quickly realized that R-Markdown really is helpful—well, at least in many situations.

What is R-Markdown? It is a script-based text-development platform for preparing high-quality papers and reports. This strong tool is effective for use on complicated documents that have various types of diagrams and tables. R-Markdown is a distribution of Markdown language for R. More information about Markdown can be found here.
Personally, I’ve found R-Markdown to be a powerful tool for creating tutorial documents that include figures, tables, blocks of code, and more. R-Markdown can also be very helpful for working on papers; you can have everything in the same place. For example, as you will see in this tutorial, you can generate your figures and tables within documents. Because it is script-based, R-Markdown is reproducible; you will always get the same text format and figure quality. Therefore, if you want to have a professional-looking CV or are working on a paper or report, I suggest giving R-Markdown a try. The tool might become your new best friend.

## install R Markdown

There are two steps to install R-Markdown:

1- Install R Markdown


# 1- Install R Markdown

install.packages("rmarkdown")
library(rmarkdown)



2- You also need to install “tinytex”. You can use the following command to install and load “tinytex”

tinytex::install_tinytex()
library(tinytex)


## Create an R-Markdown Document

To create your first R-Markdown document, start by installing R-Markdown. Then, open the “File” menu, and click on “New File.” From the dropdown menu, select “R-Markdown.” Doing so will open an R-Markdown file in your RStudio. The file comes with very simple and informative instructions.

On a side note, I use RStudio, which is a popular and user-friendly integrated development environment (IDE) for R. You can find more information about it (here).

The final format of your output document can be pdf, html, or word. To select your favorite output and generate your final document, click on “Knit,” which opens a dropdown menu. Select the output format—for example, pdf—and it will generate your document.

## Components of an R-Markdown Code

R-Markdown documents usually include meta-data, text, and code chunks. The following sections briefly describe the components, and more information can be found on R-Markdown’s website.

### Meta-Data

When generating documents, R-Markdown requires some initial information and instructions. These can include general data about the documents—for example, date, title, output format, and author’s name.

Text parts in R-Markdown follow the tradition of other document-markup languages such as LaTex (see here). However, R-Markdown is easier than LaTex. Basically, authors can use scripts to adjust document formatting. Many details can be listed about R-Markdown’s text-formatting commands, but I am not going to explain them in this short tutorial. These cheat sheets here and here provide enough information to get you started on writing an R-Markdown document. A few examples: #header creates headers, ‘[]()’ creates a hyperlink. You can use $to insert equations (e.g.$y=ax^{2}+ bx +c$). ### Code Chunks Different types of code chunks can be used in R-Markdown; the types depend on application of the code. You might want to show your code when you develop an instruction. You can also write a code solely for generating a figure, but you may not want to show the code itself. The following is a generated timeline figure of Michael Jackson’s life; you can see the code. #You need to uncomment  lines #{r timeline} # This code chunck generates a timeline of Michael Jackson life. library(timelineS) timelineS(mj_life, main = "Life of Michael Jackson",label.cex = 0.7) #  ### Adding Tables There are different libraries available in R for generating nice-looking tables. Here I use knitr. #You need to uncomment  lines #{r table} library(ggplot2) library(knitr) kable(mpg[1:8,]) #  ## Adding Figures to Your Document R-Markdown allows you to generate plots in your documents. For example, you can use ggplot, which is a powerful figure-creation library in R, to create and insert a plot into your document. See the following. If you include echo = FALSE to the header of your code chunk, the code would disappear on your final pdf file. #You need to uncomment  lines #{r ggplot} library(ggplot2) # MPG dataset is already available in ggplot2, I use it to generate the following figure ggplot(mpg, aes(x=cyl, y=cty)) + geom_boxplot(aes(fill=factor(cyl))) + labs(title="Mileage vs Number of Cylinders", x="Number of Cylinders", y="City Mileage", fill="City Mileage") #  # Embedding figure text into a Latex document Often times we have to create plots and schematic drawings for our publications. These figures are then included in the final document either as bitmaps (png, jpeg, bmp) or as vectorized images (ps, eps, pdf). Some inconveniences that arise due to this process and are noticed in the final document are: • Loss of image quality due to resizing the figure (bitmaps only) • Different font type and size from the rest of the text • Limited resizing possibility due to text readability • No straight-forward method to add equations to the figure If the document is being created in LaTeX, it is possible to overcome all these inconveniences by exporting your figure into either svg or postscript formats and converting it into pdf+Latex format with Inkscape. This format allows the LaTeX engine to understand and treat figure text as any other text in the document and the lines and curves as a vectorized image. EXPORTING FIGURE The process for creating of a PDF+LaTeX figure is described below: 1 – Create your figure and save it in either svg or postscript format. Inkscape, Matlab, GNUPlot, and Python are examples of software that can export at least one of these formats. If your figure has any equations, remember to type them in LaTeX format in the figure. 2 – Open your figure with Inkscape, edit it as you see necessary (figure may need to be ungrouped), and save it. 3.0 – If you are comfortable with using a terminal and the figure does not need editing, open a terminal pointing to the folder where the figure is and type the following the command (no$). If this works, you can skip steps 3 and 4 and go straight to step 5.

$inkscape fig1.svg --export-pdf fig1.pdf --export-latex  3 – Click on File -> Save As…, select “Portable Document Format (*.pdf)” as the file format, and click on Save. 4 – On the Portable Document Format window that will open, check the option “PDF+LaTeX: Omit text in PDF, and create LaTeX file” and click on OK. Inkscape will then export two files, both with the same name but one with pdf and the other with pdf_tex extension. The pdf file contains all the drawing, while the pdf_tex contains all the text of the figure and calls the pdf file. 5 – On your latex document, include package graphicx with the command \usepackage{graphicx}. 6 – To include the figure in your document, use \input{your_figure.pdf_tex}. Do not use the conventional \includegraphics command otherwise you will end up with an error or with a figure with no text. If you want to scale the figure, type \def\svgwidth{240bp} (240 is the size of your figure in pixels) in the line before the \input command. Do not use the conventional [scale=0.5] command, which would cause an error. Some instructions are available at the first lines of the pdf_tex file, which can be opened with a regular text editor such as notepad. Below is a comparison of how the same figure would look like in the document if exported in PDF+LaTeX and png formats. It can be seen that the figure created following the procedure above looks smoother and its text style matches that of the paragraphs above and below, which is more pleasant to the eyes. Also, the text can be marked and searched with any pdf viewer. However, the user should be aware that, since text font size is not affected by the scaling of the figure, some text may end up bigger than boxes that are supposed to contain it, as well as too close or to far from lines and curves. The former can be clearly seen in the figure below. This, however, can be easily fixed with software such as Inkscape and/or with the editing tips described in the following section. TIPS FOR TEXT MANIPULATION AFTER FIGURE IS EXPORTED If you noticed a typo of a poorly positioned text in the figure after the figure has been exported and inserted in your document, there is a easier way of fixing it other than exporting the figure again. If you open the pdf_tex file (your_figure.pdf_tex) with a text editor such as notepad, you can change any text and its position by changing the parameters of the \put commands inside the \begin{picture}\end{picture} LaTeX environment. For example, it would be better if the value 1 in the y and x axes of the figures above would show as 1.0, so that its precision is consistent with that of the other values. The same applies to 2 vs. 2.0 in the x axis. This can be fixed by opening file fig1.pdf_tex and replacing lines: \put(0.106,0.76466667){\makebox(0,0)[rb]{\smash{1}}}% \put(0.53916667,0.0585){\makebox(0,0)[b]{\smash{1}}}% \put(0.95833333,0.0585){\makebox(0,0)[b]{\smash{2}}}%  by: \put(0.106,0.76466667){\makebox(0,0)[rb]{\smash{1.0}}}% \put(0.53916667,0.0585){\makebox(0,0)[b]{\smash{1.0}}}% \put(0.95833333,0.0585){\makebox(0,0)[b]{\smash{2.0}}}%  Also, one may think that the labels of both axes are too close to the axes. This can be fixed by replacing lines: \put(0.02933333,0.434){\rotatebox{90}{\makebox(0,0)[b]{\smash{$x\cdot e^{-x+1}$}}}}% \put(0.539,0.0135){\makebox(0,0)[b]{\smash{x}}}%  by: \put(0.0,0.434){\rotatebox{90}{\makebox(0,0)[b]{\smash{$x\cdot e^{-x+1}\$}}}}%
\put(0.0,0.0135){\makebox(0,0)[b]{\smash{x}}}%
`

With the modifications described above and resizing the legend box with Inkscape, the figure now would look like this:

Don’t forget to explore all the editing features of inkscape. If you export a figure form GNUPlot or Matlab and ungroup it with Inkscape into small pieces, Inkscape would give you freedom to rearrange and fine tune your plot.