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<a href="02-starting-with-data.html">Starting with data</a>
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<h1 class="title toc-ignore">Starting with data</h1>
<h4 class="author"><em>Data Carpentry contributors</em></h4>
</div>
<hr />
<blockquote>
<h3 id="learning-objectives">Learning Objectives</h3>
<ul>
<li>Describe what a data frame is.</li>
<li>Summarize the contents of a data frame in R.</li>
<li>Load external data from a .csv file into R.</li>
<li>Manipulate categorical data in R</li>
<li>Read data from a file into a data.frame.</li>
<li>Change how character strings are handled in a data.frame.</li>
</ul>
</blockquote>
<hr />
<div id="presentation-of-the-survey-data" class="section level2">
<h2>Presentation of the Survey Data</h2>
<p>We are studying the species and weight of animals caught in plots in our study area. The dataset is stored as a comma separated value (CSV) file. Each row holds information for a single animal, and the columns represent:</p>
<table>
<thead>
<tr class="header">
<th>Column</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>record_id</td>
<td>Unique id for the observation</td>
</tr>
<tr class="even">
<td>month</td>
<td>month of observation</td>
</tr>
<tr class="odd">
<td>day</td>
<td>day of observation</td>
</tr>
<tr class="even">
<td>year</td>
<td>year of observation</td>
</tr>
<tr class="odd">
<td>plot_id</td>
<td>ID of a particular plot</td>
</tr>
<tr class="even">
<td>species_id</td>
<td>2-letter code</td>
</tr>
<tr class="odd">
<td>sex</td>
<td>sex of animal (“M”, “F”)</td>
</tr>
<tr class="even">
<td>hindfoot_length</td>
<td>length of the hindfoot in mm</td>
</tr>
<tr class="odd">
<td>weight</td>
<td>weight of the animal in grams</td>
</tr>
<tr class="even">
<td>genus</td>
<td>genus of animal</td>
</tr>
<tr class="odd">
<td>species</td>
<td>species of animal</td>
</tr>
<tr class="even">
<td>taxa</td>
<td>e.g. Rodent, Reptile, Bird, Rabbit</td>
</tr>
<tr class="odd">
<td>plot_type</td>
<td>type of plot</td>
</tr>
</tbody>
</table>
<p>We are going to use the R function <code>download.file()</code> to download the CSV file that contains the survey data from figshare, and we will use <code>read.csv()</code> to load into memory the content of the CSV file as an object of class <code>data.frame</code>.</p>
<p>To download the data into the <code>data/</code> subdirectory, run the following:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">download.file</span>(<span class="st">"https://ndownloader.figshare.com/files/2292169"</span>,
<span class="st">"data/portal_data_joined.csv"</span>)</code></pre></div>
<p>You are now ready to load the data:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">surveys <-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">'data/portal_data_joined.csv'</span>)</code></pre></div>
<p>This statement doesn’t produce any output because, as you might recall, assignments don’t display anything. If we want to check that our data has been loaded, we can print the variable’s value: <code>surveys</code>.</p>
<p>Wow… that was a lot of output. At least it means the data loaded properly. Let’s check the top (the first 6 lines) of this data frame using the function <code>head()</code>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">head</span>(surveys)</code></pre></div>
<pre><code>#> record_id month day year plot_id species_id sex hindfoot_length weight
#> 1 1 7 16 1977 2 NL M 32 NA
#> 2 72 8 19 1977 2 NL M 31 NA
#> 3 224 9 13 1977 2 NL NA NA
#> 4 266 10 16 1977 2 NL NA NA
#> 5 349 11 12 1977 2 NL NA NA
#> 6 363 11 12 1977 2 NL NA NA
#> genus species taxa plot_type
#> 1 Neotoma albigula Rodent Control
#> 2 Neotoma albigula Rodent Control
#> 3 Neotoma albigula Rodent Control
#> 4 Neotoma albigula Rodent Control
#> 5 Neotoma albigula Rodent Control
#> 6 Neotoma albigula Rodent Control</code></pre>
</div>
<div id="what-are-data-frames" class="section level2">
<h2>What are data frames?</h2>
<p>Data frames are the <em>de facto</em> data structure for most tabular data, and what we use for statistics and plotting.</p>
<p>A data frame can be created by hand, but most commonly they are generated by the functions <code>read.csv()</code> or <code>read.table()</code>; in other words, when importing spreadsheets from your hard drive (or the web).</p>
<p>A <code>data.frame</code> is the representation of data in the format of a table where the columns are vectors that all have the same length. Because the column are vectors, they all contain the same type of data (e.g., characters, integers, factors). We can see this when inspecting the <b>str</b>ucture of a <code>data.frame</code> with the function <code>str()</code>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">str</span>(surveys)</code></pre></div>
</div>
<div id="inspecting-data.frame-objects" class="section level2">
<h2>Inspecting <code>data.frame</code> Objects</h2>
<p>We already saw how the functions <code>head()</code> and <code>str()</code> can be useful to check the content and the structure of a <code>data.frame</code>. Here is a non-exhaustive list of functions to get a sense of the content/structure of the data. Let’s try them out!</p>
<ul>
<li>Size:
<ul>
<li><code>dim(surveys)</code> - returns a vector with the number of rows in the first element, and the number of columns as the second element (the <strong>dim</strong>ensions of the object)</li>
<li><code>nrow(surveys)</code> - returns the number of rows</li>
<li><code>ncol(surveys)</code> - returns the number of columns</li>
</ul></li>
<li>Content:
<ul>
<li><code>head(surveys)</code> - shows the first 6 rows</li>
<li><code>tail(surveys)</code> - shows the last 6 rows</li>
</ul></li>
<li>Names:
<ul>
<li><code>names(surveys)</code> - returns the column names (synonym of <code>colnames()</code> for <code>data.frame</code> objects)</li>
<li><code>rownames(surveys)</code> - returns the row names</li>
</ul></li>
<li>Summary:
<ul>
<li><code>str(surveys)</code> - structure of the object and information about the class, length and content of each column</li>
<li><code>summary(surveys)</code> - summary statistics for each column</li>
</ul></li>
</ul>
<p>Note: most of these functions are “generic”, they can be used on other types of objects besides <code>data.frame</code>.</p>
<blockquote>
<h3 id="challenge">Challenge</h3>
<p>Based on the output of <code>str(surveys)</code>, can you answer the following questions?</p>
<ul>
<li>What is the class of the object <code>surveys</code>?</li>
<li>How many rows and how many columns are in this object?</li>
<li>How many species have been recorded during these surveys?</li>
</ul>
</blockquote>
<!---
--->
</div>
<div id="indexing-and-subsetting-data-frames" class="section level2">
<h2>Indexing and subsetting data frames</h2>
<p>Our survey data frame has rows and columns (it has 2 dimensions), if we want to extract some specific data from it, we need to specify the “coordinates” we want from it. Row numbers come first, followed by column numbers. However, note that different ways of specifying these coordinates lead to results with different classes.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">surveys[<span class="dv">1</span>] <span class="co"># first column in the data frame (as a data.frame)</span>
surveys[, <span class="dv">1</span>] <span class="co"># first column in the data frame (as a vector)</span>
surveys[<span class="dv">1</span>, <span class="dv">1</span>] <span class="co"># first element in the first column of the data frame (as a vector)</span>
surveys[<span class="dv">1</span>, <span class="dv">6</span>] <span class="co"># first element in the 6th column (as a vector)</span>
surveys[<span class="dv">1</span>:<span class="dv">3</span>, <span class="dv">7</span>] <span class="co"># first three elements in the 7th column (as a vector)</span>
surveys[<span class="dv">3</span>, ] <span class="co"># the 3rd element for all columns (as a data.frame)</span>
head_surveys <-<span class="st"> </span>surveys[<span class="dv">1</span>:<span class="dv">6</span>, ] <span class="co"># equivalent to head(surveys)</span></code></pre></div>
<p><code>:</code> is a special function that creates numeric vectors of integers in increasing or decreasing order, test <code>1:10</code> and <code>10:1</code> for instance.</p>
<p>You can also exclude certain parts of a data frame using the “<code>-</code>” sign:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">surveys[,-<span class="dv">1</span>] <span class="co">#The whole data frame, except the first column</span>
surveys[-<span class="kw">c</span>(<span class="dv">7</span>:<span class="dv">34786</span>),] <span class="co">#equivalent to head(surveys)</span></code></pre></div>
<p>As well as using numeric values to subset a <code>data.frame</code> (or <code>matrix</code>), columns can be called by name, using one of the four following notations:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">surveys[<span class="st">"species_id"</span>] <span class="co"># Result is a data.frame</span>
surveys[, <span class="st">"species_id"</span>] <span class="co"># Result is a vector</span>
surveys[[<span class="st">"species_id"</span>]] <span class="co"># Result is a vector</span>
surveys$species_id <span class="co"># Result is a vector</span></code></pre></div>
<p>For our purposes, the last three notations are equivalent. RStudio knows about the columns in your data frame, so you can take advantage of the autocompetion feature to get the full and correct column name.</p>
<blockquote>
<h3 id="challenge-1">Challenge</h3>
<ol style="list-style-type: decimal">
<li><p>Create a <code>data.frame</code> (<code>surveys_200</code>) containing only the observations from row 200 of the <code>surveys</code> dataset.</p></li>
<li><p>Notice how <code>nrow()</code> gave you the number of rows in a <code>data.frame</code>?</p>
<ul>
<li>Use that number to pull out just that last row in the data frame</li>
<li>Compare that with what you see as the last row using <code>tail()</code> to make sure it’s meeting expectations.</li>
<li>Pull out that last row using <code>nrow()</code> instead of the row number</li>
<li>Create a new data frame object (<code>surveys_last</code>) from that last row></li>
</ul></li>
<li><p>Use <code>nrow()</code> in conjunction with the <code>:</code> function to create a new data frame called <code>surveys_last_100</code> that includes the 100 rows of the <code>surveys</code> data frame.</p></li>
<li><p>Combine <code>nrow()</code> with the <code>-</code> notation above to reproduce the behavior of <code>head(surveys)</code> keeping just the first through 7th rows of the surveys dataset.</p></li>
</ol>
</blockquote>
<!---
```r
## Answers
surveys_200 <- surveys[200, ]
surveys_last <- surveys[nrow(surveys), ]
surveys_last_100 <- surveys[(nrow(surveys)-99):nrow(surveys), ]
surveys_head <- surveys[-c(7:nrow(surveys)),]
```
--->
</div>
<div id="factors" class="section level2">
<h2>Factors</h2>
<p>When we did <code>str(surveys)</code> we saw that several of the columns consist of integers, however, the columns <code>genus</code>, <code>species</code>, <code>sex</code>, <code>plot_type</code>, … are of a special class called a <code>factor</code>. Factors are very useful and are actually something that make R particularly well suited to working with data, so we’re going to spend a little time introducing them.</p>
<p>Factors are used to represent categorical data. Factors can be ordered or unordered, and understanding them is necessary for statistical analysis and for plotting.</p>
<p>Factors are stored as integers, and have labels (text) associated with these unique integers. While factors look (and often behave) like character vectors, they are actually integers under the hood, and you need to be careful when treating them like strings.</p>
<p>Once created, factors can only contain a pre-defined set of values, known as <em>levels</em>. By default, R always sorts <em>levels</em> in alphabetical order. For instance, if you have a factor with 2 levels:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sex <-<span class="st"> </span><span class="kw">factor</span>(<span class="kw">c</span>(<span class="st">"male"</span>, <span class="st">"female"</span>, <span class="st">"female"</span>, <span class="st">"male"</span>))</code></pre></div>
<p>R will assign <code>1</code> to the level <code>"female"</code> and <code>2</code> to the level <code>"male"</code> (because <code>f</code> comes before <code>m</code>, even though the first element in this vector is <code>"male"</code>). You can check this by using the function <code>levels()</code>, and check the number of levels using <code>nlevels()</code>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">levels</span>(sex)
<span class="kw">nlevels</span>(sex)</code></pre></div>
<p>Sometimes, the order of the factors does not matter, other times you might want to specify the order because it is meaningful (e.g., “low”, “medium”, “high”), it improves your visualization, or it is required by a particular type of analysis. Here, one way to reorder our levels in the <code>sex</code> vector would be:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sex <span class="co"># current order</span></code></pre></div>
<pre><code>#> [1] male female female male
#> Levels: female male</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sex <-<span class="st"> </span><span class="kw">factor</span>(sex, <span class="dt">levels =</span> <span class="kw">c</span>(<span class="st">"male"</span>, <span class="st">"female"</span>))
sex <span class="co"># after re-ordering</span></code></pre></div>
<pre><code>#> [1] male female female male
#> Levels: male female</code></pre>
<p>In R’s memory, these factors are represented by integers (1, 2, 3), but are more informative than integers because factors are self describing: <code>"female"</code>, <code>"male"</code> is more descriptive than <code>1</code>, <code>2</code>. Which one is “male”? You wouldn’t be able to tell just from the integer data. Factors, on the other hand, have this information built in. It is particularly helpful when there are many levels (like the species names in our example data set).</p>
<div id="converting-factors" class="section level3">
<h3>Converting factors</h3>
<p>If you need to convert a factor to a character vector, you use <code>as.character(x)</code>.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">as.character</span>(sex)</code></pre></div>
<p>Converting factors where the levels appear as numbers (such as concentration levels, or years) to a numeric vector is a little trickier. One method is to convert factors to characters and then numbers. Another method is to use the <code>levels()</code> function. Compare:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">f <-<span class="st"> </span><span class="kw">factor</span>(<span class="kw">c</span>(<span class="dv">1990</span>, <span class="dv">1983</span>, <span class="dv">1977</span>, <span class="dv">1998</span>, <span class="dv">1990</span>))
<span class="kw">as.numeric</span>(f) <span class="co"># wrong! and there is no warning...</span>
<span class="kw">as.numeric</span>(<span class="kw">as.character</span>(f)) <span class="co"># works...</span>
<span class="kw">as.numeric</span>(<span class="kw">levels</span>(f))[f] <span class="co"># The recommended way.</span></code></pre></div>
<p>Notice that in the <code>levels()</code> approach, three important steps occur:</p>
<ul>
<li>We obtain all the factor levels using <code>levels(f)</code></li>
<li>We convert these levels to numeric values using <code>as.numeric(levels(f))</code></li>
<li>We then access these numeric values using the underlying integers of the vector <code>f</code> inside the square brackets</li>
</ul>
</div>
<div id="renaming-factors" class="section level3">
<h3>Renaming factors</h3>
<p>When your data is stored as a factor, you can use the <code>plot()</code> function to get a quick glance at the number of observations represented by each factor level. Let’s look at the number of males and females captured over the course of the experiment:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">## bar plot of the number of females and males captured during the experiment:
<span class="kw">plot</span>(surveys$sex)</code></pre></div>
<p><img src="img/R-ecology-unnamed-chunk-21-1.png" width="672" /></p>
<p>In addition of males and females, there are about 1700 individuals for which the sex information hasn’t been recorded. Additionally, for the these individuals, there is no label to indicate that the information is missing. Let’s rename this label to something more meaningful. Before doing that, we’re going to pull out the data on sex and work with that data, so we’re not modifying the working copy of the data frame:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sex <-<span class="st"> </span>surveys$sex
<span class="kw">head</span>(sex)</code></pre></div>
<pre><code>#> [1] M M
#> Levels: F M</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">levels</span>(sex)</code></pre></div>
<pre><code>#> [1] "" "F" "M"</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">levels</span>(sex)[<span class="dv">1</span>] <-<span class="st"> "missing"</span>
<span class="kw">levels</span>(sex)</code></pre></div>
<pre><code>#> [1] "missing" "F" "M"</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">head</span>(sex)</code></pre></div>
<pre><code>#> [1] M M missing missing missing missing
#> Levels: missing F M</code></pre>
<blockquote>
<h3 id="challenge-2">Challenge</h3>
<ul>
<li>Rename “F” and “M” to “female” and “male” respectively.</li>
<li>Now that we have renamed the factor level to “missing”, can you recreate the barplot such that “missing” is last (after “male”)</li>
</ul>
</blockquote>
<!---
```r
## Answers
levels(sex)[2:3] <- c("female", "male")
sex <- factor(sex, levels = c("female", "male", "missing"))
plot(sex)
```
<img src="img/R-ecology-correct-order-1.png" width="672" />
--->
</div>
<div id="using-stringsasfactorsfalse" class="section level3">
<h3>Using <code>stringsAsFactors=FALSE</code></h3>
<p>By default, when building or importing a data frame, the columns that contain characters (i.e., text) are coerced (=converted) into the <code>factor</code> data type. Depending on what you want to do with the data, you may want to keep these columns as <code>character</code>. To do so, <code>read.csv()</code> and <code>read.table()</code> have an argument called <code>stringsAsFactors</code> which can be set to <code>FALSE</code>.</p>
<p>In most cases, it’s preferrable to set <code>stringsAsFactors = FALSE</code> when importing your data, and converting as a factor only the columns that require this data type.</p>
<p>Compare the output of <code>str(surveys)</code> when setting <code>stringsAsFactors = TRUE</code> (default) and <code>stringsAsFactors = FALSE</code>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">## Compare the difference between when the data are being read as
## `factor`, and when they are being read as `character`.
surveys <-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">"data/portal_data_joined.csv"</span>, <span class="dt">stringsAsFactors =</span> <span class="ot">TRUE</span>)
<span class="kw">str</span>(surveys)
surveys <-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">"data/portal_data_joined.csv"</span>, <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)
<span class="kw">str</span>(surveys)
## Convert the column "plot_type" into a factor
surveys$plot_type <-<span class="st"> </span><span class="kw">factor</span>(surveys$plot_type)</code></pre></div>
<blockquote>
<h3 id="challenge-3">Challenge</h3>
<ol style="list-style-type: decimal">
<li><p>We have seen how data frames are created when using the <code>read.csv()</code>, but they can also be created by hand with the <code>data.frame()</code> function. There are a few mistakes in this hand-crafted <code>data.frame</code>, can you spot and fix them? Don’t hesitate to experiment!</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">animal_data <-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">animal=</span><span class="kw">c</span>(<span class="st">"dog"</span>, <span class="st">"cat"</span>, <span class="st">"sea cucumber"</span>, <span class="st">"sea urchin"</span>),
<span class="dt">feel=</span><span class="kw">c</span>(<span class="st">"furry"</span>, <span class="st">"squishy"</span>, <span class="st">"spiny"</span>),
<span class="dt">weight=</span><span class="kw">c</span>(<span class="dv">45</span>, <span class="dv">8</span> <span class="fl">1.1</span>, <span class="fl">0.8</span>))</code></pre></div></li>
<li>Can you predict the class for each of the columns in the following example? Check your guesses using <code>str(country_climate)</code>:
<ul>
<li>Are they what you expected? Why? Why not?</li>
<li>What would have been different if we had added <code>stringsAsFactors = FALSE</code> to this call?</li>
<li>What would you need to change to ensure that each column had the accurate data type?</li>
</ul>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">country_climate <-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">country=</span><span class="kw">c</span>(<span class="st">"Canada"</span>, <span class="st">"Panama"</span>, <span class="st">"South Africa"</span>, <span class="st">"Australia"</span>),
<span class="dt">climate=</span><span class="kw">c</span>(<span class="st">"cold"</span>, <span class="st">"hot"</span>, <span class="st">"temperate"</span>, <span class="st">"hot/temperate"</span>),
<span class="dt">temperature=</span><span class="kw">c</span>(<span class="dv">10</span>, <span class="dv">30</span>, <span class="dv">18</span>, <span class="st">"15"</span>),
<span class="dt">northern_hemisphere=</span><span class="kw">c</span>(<span class="ot">TRUE</span>, <span class="ot">TRUE</span>, <span class="ot">FALSE</span>, <span class="st">"FALSE"</span>),
<span class="dt">has_kangaroo=</span><span class="kw">c</span>(<span class="ot">FALSE</span>, <span class="ot">FALSE</span>, <span class="ot">FALSE</span>, <span class="dv">1</span>))</code></pre></div></li>
</ol>
<p><!--- Answers
--></p>
</blockquote>
<p>The automatic conversion of data type is sometimes a blessing, sometimes an annoyance. Be aware that it exists, learn the rules, and double check that data you import in R are of the correct type within your data frame. If not, use it to your advantage to detect mistakes that might have been introduced during data entry (a letter in a column that should only contain numbers for instance.).</p>
</div>
</div>
<hr/>
<p><a href="http://datacarpentry.org/">Data Carpentry</a>, 2017. <br/>
<a href="LICENSE.html">License</a>. Questions? Feedback?
Please <a href="https://github.com/datacarpentry/R-ecology-lesson/issues/new">file
an issue on GitHub</a>. <br/>
On Twitter: <a href="https://twitter.com/datacarpentry">@datacarpentry</a></p>
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