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<li><a href="#common-issues"><strong>Common Issues</strong></a>
<ul>
<li><a href="#im-getting-an-error-related-to-something-called-rtools"><strong>I’m getting an error related to something called Rtools</strong></a></li>
<li><a href="#what-packages-are-part-of-the-tidyverse"><strong>What packages are part of the Tidyverse</strong>?</a></li>
<li><a href="#why-are-my-changes-not-taking-effect-its-making-my-results-look-weird"><strong>Why are my changes not taking effect? It’s making my results look weird!</strong></a></li>
<li><a href="#why-do-i-have-a-sign-instead-of-the-cursor-in-the-console"><strong>Why do I have a <code>+</code> sign instead of the cursor <code>></code> in the console?</strong></a></li>
<li><a href="#when-should-i-use-quotes-or-backticks"><strong>When should I use quotes (““) or backticks (``)?</strong></a></li>
<li><a href="#how-do-i-know-when-to-use-the-pull-function-instead-of-just-using-select"><strong>How do I know when to use the <code>pull()</code> function, instead of just using <code>select()</code>?</strong></a></li>
</ul></li>
<li><a href="#common-errors"><strong>Common Errors</strong></a>
<ul>
<li><a href="#error-in-x-could-not-find-function-y"><strong>Error in x : could not find function “y”</strong></a></li>
<li><a href="#error-object-x-not-found"><strong>Error: object ‘X’ not found</strong></a></li>
<li><a href="#error-unexpected-in-error-unexpected-in-error-unexpected-x-in"><strong>Error: unexpected ‘,’ in … / Error: unexpected ‘)’ in … / Error: unexpected ‘X’ in …</strong></a></li>
<li><a href="#error-unexpected-symbol-in-x"><strong>Error: unexpected symbol in “x”</strong></a></li>
<li><a href="#error-unexpected-input-in-x"><strong>Error: unexpected input in “x”</strong></a></li>
<li><a href="#error-mapping-must-be-created-by-aes-ℹ-did-you-use-or-instead-of"><strong>Error: <code>mapping</code> must be created by <code>aes()</code> / <code>ℹ</code> Did you use ‘%>%’ or ‘|>’ instead of ‘+’?</strong></a></li>
<li><a href="#error-in-.gg-ℹ-did-you-accidentally-put-on-a-new-line"><strong>Error in +.gg: <code>ℹ</code> Did you accidentally put ‘+’ on a new line?</strong></a></li>
</ul></li>
<li><a href="#preference-changes"><strong>Preference Changes</strong></a>
<ul>
<li><a href="#how-do-i-get-output-to-stop-printing-inside-the-rmarkdown-and-only-show-it-in-the-console-how-ava-has-her-setup"><strong>How do I get output to stop printing inside the Rmarkdown and only show it in the console? (How Ava has her setup?)</strong></a></li>
<li><a href="#how-do-i-change-the-color-theme"><strong>How do I change the color / theme?</strong></a></li>
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<div id="common-issues" class="section level1">
<h1><strong>Common Issues</strong></h1>
<hr />
<div id="im-getting-an-error-related-to-something-called-rtools" class="section level2">
<h2><strong>I’m getting an error related to something called Rtools</strong></h2>
<p>You probably need some add-on software for a Windows machine. Note that this is <em>not</em> an additional R package to install. Here is a quick guide to installing Rtools: <a href="https://docs.google.com/viewer?url=https://raw.githubusercontent.com/jhudsl/intro_to_r/main/resources/rtools_windows.pdf">link</a>.</p>
<hr />
</div>
<div id="what-packages-are-part-of-the-tidyverse" class="section level2">
<h2><strong>What packages are part of the Tidyverse</strong>?</h2>
<p>If you need to check what packages are part of the <code>tidyverse</code>, you can do so at this <a href="https://www.tidyverse.org/packages/">link</a>.</p>
<hr />
</div>
<div id="why-are-my-changes-not-taking-effect-its-making-my-results-look-weird" class="section level2">
<h2><strong>Why are my changes not taking effect? It’s making my results look weird!</strong></h2>
<p><strong>Forgetting to assign your data to an object</strong></p>
<p>Often we are just printing our data and not either reassigning an existing object or creating a new object.</p>
<p>Here we are creating a new object from an existing one:</p>
<pre class="r"><code>new_rivers <- sample(rivers, 5)
new_rivers</code></pre>
<pre><code>## [1] 630 230 338 500 1306</code></pre>
<p>Using just this will only print the result and not actually change <code>new_rivers</code>:</p>
<pre class="r"><code>new_rivers + 1</code></pre>
<pre><code>## [1] 631 231 339 501 1307</code></pre>
<p>If we want to modify <code>new_rivers</code> and save that modified version, then we need to reassign <code>new_rivers</code> like so:</p>
<pre class="r"><code>new_rivers <- new_rivers + 1
new_rivers</code></pre>
<pre><code>## [1] 631 231 339 501 1307</code></pre>
<p>If we forget to reassign this can cause subsequent steps to not work as expected because we will not be working with the data that has been modified.</p>
<hr />
</div>
<div id="why-do-i-have-a-sign-instead-of-the-cursor-in-the-console" class="section level2">
<h2><strong>Why do I have a <code>+</code> sign instead of the cursor <code>></code> in the console?</strong></h2>
<p><strong>Trouble with parentheses</strong></p>
<p>You may get a <code>+</code> sign instead of the cursor <code>></code> in the console suggesting that you have not closed an open parentheses. Each instance of <code>(</code> should be followed by <code>)</code>.</p>
<p>Hit the “esc” key to restore your <code>></code>, then fix/rerun your code.</p>
<hr />
</div>
<div id="when-should-i-use-quotes-or-backticks" class="section level2">
<h2><strong>When should I use quotes (““) or backticks (``)?</strong></h2>
<p>Check out our <a href="https://daseh.org/resources/quotes_vs_backticks.html">Guide on when to use quotes or backticks</a>.</p>
<hr />
</div>
<div id="how-do-i-know-when-to-use-the-pull-function-instead-of-just-using-select" class="section level2">
<h2><strong>How do I know when to use the <code>pull()</code> function, instead of just using <code>select()</code>?</strong></h2>
<p>Check out our <a href="https://daseh.org/resources/functions_for_vectors.html">Guide on what functions require pulling values out first</a>.</p>
<p><br><br><br></p>
</div>
</div>
<div id="common-errors" class="section level1">
<h1><strong>Common Errors</strong></h1>
<hr />
<div id="error-in-x-could-not-find-function-y" class="section level2">
<h2><strong>Error in x : could not find function “y”</strong></h2>
<p><strong>Forgetting to load a library or misspelling a function or package</strong></p>
<p>For example, we forgot <code>library(tidyverse)</code> below:</p>
<pre class="r"><code>iris %>% pull(Species) </code></pre>
<pre class="bg-error"><code>## Error in iris %>% pull(Species): could not find function "%>%"</code></pre>
<p>Below will not work because <code>str_detect</code> is missing a <code>t</code> at the end:</p>
<pre class="r"><code>library(tidyverse) # need this! This can be at the top of your file
iris %>% pull(Species) %>% str_detec("setosa")</code></pre>
<pre class="bg-error"><code>## Error in str_detec(., "setosa"): could not find function "str_detec"</code></pre>
<p>This will not work because <code>library()</code> is misspelled:</p>
<pre class="r"><code>libary(tidyverse)</code></pre>
<pre class="bg-error"><code>## Error in libary(tidyverse): could not find function "libary"</code></pre>
<hr />
</div>
<div id="error-object-x-not-found" class="section level2">
<h2><strong>Error: object ‘X’ not found</strong></h2>
<p><strong>Forgetting to assign an object to start with</strong></p>
<p>This error is usually caused by forgetting to assign an object to start with, or not running the piece of code that assigns an object. If you never created <code>rivers2</code> and try to modify it like so:</p>
<pre class="r"><code>rivers2 + 1</code></pre>
<pre class="bg-error"><code>## Error in eval(expr, envir, enclos): object 'rivers2' not found</code></pre>
<p>Make sure you run something like this, with the <code><-</code> operator:</p>
<pre class="r"><code>rivers2 <- new_rivers + 1
rivers2</code></pre>
<pre><code>## [1] 632 232 340 502 1308</code></pre>
<hr />
</div>
<div id="error-unexpected-in-error-unexpected-in-error-unexpected-x-in" class="section level2">
<h2><strong>Error: unexpected ‘,’ in … / Error: unexpected ‘)’ in … / Error: unexpected ‘X’ in …</strong></h2>
<p><strong>Trouble with parentheses</strong></p>
<p>This error can be caused by missing parentheses. Such as:</p>
<pre class="r"><code>library(dplyr)
all.equal((rivers+1, rivers)</code></pre>
<pre class="bg-error"><code>## Error: <text>:2:20: unexpected ','
## 1: library(dplyr)
## 2: all.equal((rivers+1,
## ^</code></pre>
<p>It should be:</p>
<pre class="r"><code>all.equal((rivers+1), rivers)</code></pre>
<pre><code>## [1] "Mean relative difference: 0.001688663"</code></pre>
<p>You will also often get this error if you have the correct number of parentheses but wrong placement:</p>
<pre class="r"><code>all.equal((rivers+1, rivers))</code></pre>
<pre class="bg-error"><code>## Error: <text>:1:20: unexpected ','
## 1: all.equal((rivers+1,
## ^</code></pre>
<p>If you have too many parentheses like this (the last one is extra)… you will get this error:</p>
<pre class="r"><code>all_equal((rivers+1), rivers))</code></pre>
<pre class="bg-error"><code>## Error: <text>:1:30: unexpected ')'
## 1: all_equal((rivers+1), rivers))
## ^</code></pre>
<hr />
</div>
<div id="error-unexpected-symbol-in-x" class="section level2">
<h2><strong>Error: unexpected symbol in “x”</strong></h2>
<p><strong>Not using quotes or backticks when needed</strong></p>
<p>You will need to use quotes for variable names that have spaces or unusual punctuation. It is best to avoid these and rename variables if a variable name has spaces.</p>
<pre class="r"><code>df_quotes</code></pre>
<pre><code>## # A tibble: 3 × 2
## `The Values` names
## <dbl> <chr>
## 1 1 A
## 2 2 B
## 3 3 C</code></pre>
<p>If we want to specifically pull out the column with the variable named <code>The Values</code> we need to use quotes or back ticks.</p>
<pre class="r"><code>df_quotes %>% pull(names) # this works fine! no spaces in `names`</code></pre>
<pre><code>## [1] "A" "B" "C"</code></pre>
<pre class="r"><code>df_quotes %>% pull("The Values") # this works</code></pre>
<pre><code>## [1] 1 2 3</code></pre>
<pre class="r"><code>df_quotes %>% pull(`The Values`) # this works</code></pre>
<pre><code>## [1] 1 2 3</code></pre>
<pre class="r"><code>df_quotes %>% pull(The Values) # this does not work!</code></pre>
<pre class="bg-error"><code>## Error: <text>:1:24: unexpected symbol
## 1: df_quotes %>% pull(The Values
## ^</code></pre>
<hr />
</div>
<div id="error-unexpected-input-in-x" class="section level2">
<h2><strong>Error: unexpected input in “x”</strong></h2>
<p><strong>Copy+pasting quotation marks</strong></p>
<p>If you copy paste code form somewhere with curly quotation marks, it will not work.</p>
<pre class="r"><code>df_quotes %>% pull("The Values") # this works</code></pre>
<pre><code>## [1] 1 2 3</code></pre>
<pre class="r"><code>df_quotes %>% pull(“The Values”) # this doesn't work</code></pre>
<pre class="bg-error"><code>## Error: <text>:1:20: unexpected invalid token
## 1: df_quotes %>% pull(“
## ^</code></pre>
<hr />
</div>
<div id="error-mapping-must-be-created-by-aes-ℹ-did-you-use-or-instead-of" class="section level2">
<h2><strong>Error: <code>mapping</code> must be created by <code>aes()</code> / <code>ℹ</code> Did you use ‘%>%’ or ‘|>’ instead of ‘+’?</strong></h2>
<p><strong>Forgetting to use <code>+</code> to add <code>ggplot2</code> layers</strong></p>
<p>This will not work:</p>
<pre class="r"><code>ggplot(data = iris, aes(x = Species, y = Petal.Length)) %>%
geom_boxplot()</code></pre>
<pre class="bg-error"><code>## Error in `geom_boxplot()`:
## ! `mapping` must be created by `aes()`.
## ℹ Did you use `%>%` or `|>` instead of `+`?</code></pre>
<p>This will work:</p>
<pre class="r"><code>ggplot(data = iris, aes(x = Species, y = Petal.Length)) +
geom_boxplot()</code></pre>
<p><img src="help_files/figure-html/unnamed-chunk-24-1.png" width="30%" /></p>
<hr />
</div>
<div id="error-in-.gg-ℹ-did-you-accidentally-put-on-a-new-line" class="section level2">
<h2><strong>Error in +.gg: <code>ℹ</code> Did you accidentally put ‘+’ on a new line?</strong></h2>
<p>This will not work:</p>
<pre class="r"><code>ggplot(data = iris, aes(x = Species, y = Petal.Length))</code></pre>
<p><img src="help_files/figure-html/unnamed-chunk-25-1.png" width="30%" /></p>
<pre class="r"><code> + geom_boxplot()</code></pre>
<pre class="bg-error"><code>## Error:
## ! Cannot use `+` with a single argument.
## ℹ Did you accidentally put `+` on a new line?</code></pre>
<p>This will work:</p>
<pre class="r"><code>ggplot(data = iris, aes(x = Species, y = Petal.Length)) +
geom_boxplot()</code></pre>
<p><img src="help_files/figure-html/unnamed-chunk-26-1.png" width="30%" /></p>
</div>
</div>
<div id="preference-changes" class="section level1">
<h1><strong>Preference Changes</strong></h1>
<hr />
<div id="how-do-i-get-output-to-stop-printing-inside-the-rmarkdown-and-only-show-it-in-the-console-how-ava-has-her-setup" class="section level2">
<h2><strong>How do I get output to stop printing inside the Rmarkdown and only show it in the console? (How Ava has her setup?)</strong></h2>
<p><strong>To change this, you will need to adjust the RStudio Settings.</strong></p>
<div class="figure">
<img src="images/console_output1.jpg" alt="" />
<p class="caption">Click the gear icon beside the knit button to expand the options menu. Select “Chunk Output in Console”.</p>
</div>
<div class="figure">
<img src="images/console_output2.jpg" alt="" />
<p class="caption">You can select Remove Output. You should now see output in the console.</p>
</div>
<p><br> <br></p>
<hr />
</div>
<div id="how-do-i-change-the-color-theme" class="section level2">
<h2><strong>How do I change the color / theme?</strong></h2>
<p>Go to the menu Tools > Global Options > Appearance. Choose a theme and apply!</p>
<p><br> <br></p>
</div>
</div>
<p style="text-align:center;"> <small> This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>. </small></p>
<p style="text-align:center;"><img src="images/logo_icon_highres.png" height="20"/><small>DaSEH is funded by the National Institute of Environmental Health Sciences <a href="https://reporter.nih.gov/search/cMEAgQFeo025gUX1DDzH9g/project-details/10746327">1R25ES035590-01.</a> </p></small>
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