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<title>R for reproducible scientific analysis</title>
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<a href="index.html"><h1 class="title">R for reproducible scientific analysis</h1></a>
<h2 class="subtitle">Reference</h2>
<h2 id="introduction-to-r-and-rstudio"><a href="01-rstudio-intro.html">Introduction to R and RStudio</a></h2>
<ul>
<li>Use the escape key to cancel incomplete commands or running code (Ctrl+C) if you’re using R from the shell.</li>
<li>Basic arithmetic operations follow standard order of precedence:</li>
<li>Brackets: <code>(</code>, <code>)</code></li>
<li>Exponents: <code>^</code> or <code>**</code></li>
<li>Divide: <code>/</code></li>
<li>Multiply: <code>*</code></li>
<li>Add: <code>+</code></li>
<li>Subtract: <code>-</code></li>
<li>Scientific notation is available, e.g: <code>2e-3</code></li>
<li>Anything to the right of a <code>#</code> is a comment, R will ignore this!</li>
<li>Functions are denoted by <code>function_name()</code>. Expressions inside the brackets are evaluated before being passed to the function, and functions can be nested.</li>
<li>Mathematical functions: <code>exp</code>, <code>sin</code>, <code>log</code>, <code>log10</code>, <code>log2</code> etc.</li>
<li>Comparison operators: <code><</code>, <code><=</code>, <code>></code>, <code>>=</code>, <code>==</code>, <code>!=</code></li>
<li>Use <code>all.equal</code> to compare numbers!</li>
<li><code><-</code> is the assignment operator. Anything to the right is evaluate, then stored in a variable named to the left.</li>
<li><code>ls</code> lists all variables and functions you’ve created</li>
<li><code>rm</code> can be used to remove them</li>
<li>When assigning values to function arguments, you <em>must</em> use <code>=</code>.</li>
</ul>
<h2 id="project-management-with-rstudio"><a href="02-project-intro.html">Project management with RStudio</a></h2>
<ul>
<li>To create a new project, go to File -> New Project</li>
<li>Install the <code>packrat</code> package to create self-contained projects</li>
<li><code>install.packages</code> to install packages from CRAN</li>
<li><code>library</code> to load a package into R</li>
<li><code>packrat::status</code> to check whether all packages referenced in your scripts have been installed.</li>
</ul>
<h2 id="seeking-help"><a href="03-seeking-help.html">Seeking help</a></h2>
<ul>
<li>To access help for a function type <code>?function_name</code> or <code>help(function_name)</code></li>
<li>Use quotes for special operators e.g. <code>?"+"</code></li>
<li>Use fuzzy search if you can’t remember a name ‘??search_term’</li>
<li><a href="http://cran.at.r-project.org/web/views">CRAN task views</a> are a good starting point.</li>
<li><a href="http://stackoverflow.com/">Stack Overflow</a> is a good place to get help with your code.
<ul>
<li><code>?dput</code> will dump data you are working from so others can load it easily.</li>
<li><code>sessionInfo()</code> will give details of your setup that others may need for debugging.</li>
</ul></li>
</ul>
<h2 id="data-structures"><a href="04-data-structures-part1.html">Data structures</a></h2>
<p>Individual values in R must be one of 5 <strong>data types</strong>, multiple values can be grouped in <strong>data structures</strong>.</p>
<p><strong>Data types</strong></p>
<ul>
<li><code>typeof(object)</code> gives information about an items data type.</li>
<li>There are 5 main data types:
<ul>
<li><code>?numeric</code> real (decimal) numbers</li>
<li><code>?integer</code> whole numbers only</li>
<li><code>?character</code> text</li>
<li><code>?complex</code> complex numbers</li>
<li><code>?logical</code> TRUE or FALSE values</li>
</ul>
<p><strong>Special types:</strong></p>
<ul>
<li><code>?NA</code> missing values</li>
<li><code>?NaN</code> “not a number” for undefined values (e.g. <code>0/0</code>).</li>
<li><code>?Inf</code>, <code>-Inf</code> infinity.</li>
<li><code>?NULL</code> a data structure that doesn’t exist</li>
</ul>
<p><code>NA</code> can occur in any atomic vector. <code>NaN</code>, and <code>Inf</code> can only occur in complex, integer or numeric type vectors. Atomic vectors are the building blocks for all other data structures. A <code>NULL</code> value will occur in place of an entire data structure (but can occur as list elements).</p></li>
</ul>
<p><strong>Basic data structures in R:</strong> - atomic <code>?vector</code> (can only contain one type) - <code>?list</code> (containers for other objects) - <code>?data.frame</code> two dimensional objects whose columns can contain different types of data - <code>?matrix</code> two dimensional objects that can contain only one type of data. - <code>?factor</code> vectors that contain predefined categorical data. - <code>?array</code> multi-dimensional objects that can only contain one type of data</p>
<p>Remember that matrices are really atomic vectors underneath the hood, and that data.frames are really lists underneath the hood (this explains some of the weirder behaviour of R).</p>
<p><strong><a href="04-data-structures-part1.html">Vectors</a></strong> - <code>?vector()</code> All items in a vector must be the same type. - Items can be converted from one type to another using <em>coercion</em>. - The concatenate function ‘c()’ will append items to a vector. - <code>seq(from=0, to=1, by=1)</code> will create a sequence of numbers. - Items in a vector can be named using the <code>names()</code> function.</p>
<p><strong><a href="04-data-structures-part1.html">Factors</a></strong> - <code>?factor()</code> Factors are a data structure designed to store categorical data. - <code>levels()</code> shows the valid values that can be stored in a vector of type factor.</p>
<p><strong><a href="04-data-structures-part1.html">Lists</a></strong> - <code>?list()</code> Lists are a data structure designed to store data of different types.</p>
<p><strong><a href="04-data-structures-part1.html">Matrices</a></strong> - <code>?matrix()</code> Matrices are a data structure designed to store 2-dimensional data.</p>
<p><strong><a href="05-data-structures-part2.html">Data Frames</a></strong> - <code>?data.frame</code> is a key data structure. It is a <code>list</code> of <code>vectors</code>. - <code>cbind()</code> will add a column (vector) to a data.frame. - <code>rbind()</code> will add a row (list) to a data.frame.</p>
<p><strong>Useful functions for querying data structures:</strong> - <code>?str</code> structure, prints out a summary of the whole data structure - <code>?typeof</code> tells you the type inside an atomic vector - <code>?class</code> what is the data structure? - <code>?head</code> print the first <code>n</code> elements (rows for two-dimensional objects) - <code>?tail</code> print the last <code>n</code> elements (rows for two-dimensional objects) - <code>?rownames</code>, <code>?colnames</code>, <code>?dimnames</code> retrieve or modify the row names and column names of an object. - <code>?names</code> retrieve or modify the names of an atomic vector or list (or columns of a data.frame). - <code>?length</code> get the number of elements in an atomic vector - <code>?nrow</code>, <code>?ncol</code>, <code>?dim</code> get the dimensions of a n-dimensional object (Won’t work on atomic vectors or lists).</p>
<h2 id="reading-data"><a href="05-data-structures-part2.html">Reading data</a></h2>
<ul>
<li><code>read.csv</code> to read in data in a regular structure</li>
<li><code>sep</code> argument to specify the separator
<ul>
<li>“,” for comma separated</li>
<li>“” for tab separated</li>
</ul></li>
<li>Other arguments:
<ul>
<li><code>header=TRUE</code> if there is a header row</li>
</ul></li>
</ul>
<h2 id="subsetting-data"><a href="06-data-subsetting.html">Subsetting data</a></h2>
<ul>
<li>Elements can be accessed by:</li>
<li>Index</li>
<li>Name</li>
<li><p>Logical vectors</p></li>
<li><code>[</code> single square brackets:</li>
<li><em>extract</em> single elements or <em>subset</em> vectors
<ul>
<li>e.g.<code>x[1]</code> extracts the first item from vector x.</li>
</ul></li>
<li><em>extract</em> single elements of a list. The returned value will be another <code>list()</code>.</li>
<li><em>extract</em> columns from a data.frame</li>
<li><code>[</code> with two arguments to:</li>
<li><em>extract</em> rows and/or columns of
<ul>
<li>matrices</li>
<li>data.frames</li>
<li>e.g. <code>x[1,2]</code> will extract the value in row 1, column 2.</li>
<li>e.g. <code>x[2,:]</code> will extract the entire second column of values.</li>
</ul></li>
<li><code>[[</code> double square brackets to extract items from lists.</li>
<li><code>$</code> to access columns or list elements by name</li>
<li><p>negative indices skip elements</p></li>
</ul>
<h2 id="functions"><a href="07-functions.html">Functions</a></h2>
<ul>
<li><code>?"function"</code></li>
<li>Put code whose parameters change frequently in a function, then call it with different parameter values to customize its behavior.</li>
<li>The last line of a function is returned, or you can use <code>return</code> explictly</li>
<li>Any code written in the body of the function will preferably look for variables defined inside the function.</li>
<li>Document Why, then What, then lastly How (if the code isn’t self explanatory)</li>
</ul>
<h2 id="creating-graphics"><a href="08-plot-ggplot2.html">Creating graphics</a></h2>
<ul>
<li>figures can be created with the grammar of graphics:</li>
<li><code>library(ggplot2)</code></li>
<li><code>ggplot</code> to create the base figure</li>
<li><code>aes</code>thetics specify the data axes, shape, color, and data size</li>
<li><code>geom</code>etry functions specify the type of plot, e.g. <code>point</code>, <code>line</code>, <code>density</code>, <code>box</code></li>
<li><code>geom</code>etry functions also add statistical transforms, e.g. <code>geom_smooth</code></li>
<li><code>scale</code> functions change the mapping from data to aesthetics</li>
<li><code>facet</code> functions stratify the figure into panels</li>
<li><code>aes</code>thetics apply to individual layers, or can be set for the whole plot inside <code>ggplot</code>.</li>
<li><code>theme</code> functions change the overall look of the plot</li>
<li>order of layers matters!</li>
<li><code>ggsave</code> to save a figure.</li>
</ul>
<h2 id="vectorisation"><a href="09-vectorisation.html">Vectorisation</a></h2>
<ul>
<li>Most functions and operations apply to each element of a vector</li>
<li><code>*</code> applies element-wise to matrices</li>
<li><code>%*%</code> for true matrix multiplication</li>
<li><code>any()</code> will return <code>TRUE</code> if any element of a vector is <code>TRUE</code></li>
<li><code>all()</code> will return <code>TRUE</code> if <em>all</em> elements of a vector are <code>TRUE</code></li>
</ul>
<h2 id="control-flow"><a href="10-control-flow.html">Control flow</a></h2>
<ul>
<li>Use <code>if</code> condition to start a conditional statement, <code>else if</code> condition to provide additional tests, and <code>else</code> to provide a default</li>
<li>The bodies of the branches of conditional statements must be indented.</li>
<li>Use <code>==</code> to test for equality.</li>
<li><code>X && Y</code> is only true if both X and Y are <code>TRUE</code>.</li>
<li><code>X || Y</code> is true if either X or Y, or both, are <code>TRUE</code>.</li>
<li>Zero is considered <code>FALSE</code>; all other numbers are considered <code>TRUE</code></li>
<li>Nest loops to operate on multi-dimensional data.</li>
</ul>
<h2 id="writing-data"><a href="11-writing-data.html">Writing data</a></h2>
<ul>
<li><code>write.table</code> to write out objects in regular format</li>
<li>set <code>quote=FALSE</code> so that text isn’t wrapped in <code>"</code> marks</li>
</ul>
<h2 id="split-apply-combine"><a href="12-plyr.html">Split-apply-combine</a></h2>
<ul>
<li>Use the <code>xxply</code> family of functions to apply functions to groups within some data.</li>
<li>the first letter, <code>a</code>rray , <code>d</code>ata.frame or <code>l</code>ist corresponds to the input data</li>
<li>the second letter denotes the output data structure</li>
<li>Anonymous functions (those not assigned a name) are used inside the <code>plyr</code> family of functions on groups within data.</li>
</ul>
<h2 id="dataframe-manipulation-with-dplyr"><a href="13-dplyr.html">Dataframe manipulation with dplyr</a></h2>
<ul>
<li><code>library(dplyr)</code></li>
<li><code>?select</code> to extract variables by name.</li>
<li><code>?filter</code> return rows with matching conditions.</li>
<li><code>?group_by</code> group data by one of more variables.</li>
<li><code>?summarize</code> summarise multiple values to a single value.</li>
<li><code>?mutate</code> add new variables to a data.frame.</li>
<li>Combine operations using the <code>?"%>%"</code> pipe operator.</li>
</ul>
<h2 id="dataframe-manipulation-with-tidyr"><a href="14-tidyr.html">Dataframe manipulation with tidyr</a></h2>
<ul>
<li><code>library(tidyr)</code></li>
<li>‘?gather’ convert data from <em>wide</em> to <em>long</em> format.</li>
<li>‘?spread’ convert data from <em>long</em> to <em>wide</em> format.</li>
<li>‘?seprarate’ split a single value into multiple values.</li>
<li>‘?unite’ merge multipe values into a single value.</li>
</ul>
<h2 id="defensive-programming"><a href="15-wrap-up.html">Defensive Programming</a></h2>
<ul>
<li>Program defensively, i.e., assume that errors are going to arise, and write code to detect them when they do.</li>
<li>Write tests before writing code in order to help determine exactly what that code is supposed to do.</li>
<li>Know what code is supposed to do before trying to debug it.</li>
<li>Make it fail every time.</li>
<li>Make it fail fast.</li>
<li>Change one thing at a time, and for a reason.</li>
<li>Keep track of what you’ve done.</li>
<li>Be humble</li>
</ul>
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