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    <p>I think the way to think about the difference between <code>labels</code> and <code>levels</code> (ignoring the <code>labels()</code> function that Tommy describes in his answer) is that <code>levels</code> is intended to tell R which values to look for in the input (<code>x</code>) and what order to use in the levels of the resulting <code>factor</code> object, and <code>labels</code> is to change the <em>values</em> of the levels after the input has been coded as a factor ... as suggested by Tommy's answer, there is no part of the <code>factor</code> object returned by <code>factor()</code> that is called <code>labels</code> ... just the levels, which have been adjusted by the <code>labels</code> argument ... (clear as mud).</p> <p>For example:</p> <pre><code>&gt; f &lt;- factor(x=c("a","b","c"),levels=c("c","d","e")) &gt; f [1] &lt;NA&gt; &lt;NA&gt; c Levels: c d e &gt; str(f) Factor w/ 3 levels "c","d","e": NA NA 1 </code></pre> <p>Because the first two elements of <code>x</code> were not found in <code>levels</code>, the first two elements of <code>f</code> are <code>NA</code>. Because <code>"d"</code> and <code>"e"</code> were included in <code>levels</code>, they show up in the levels of <code>f</code> even though they did not occur in <code>x</code>.</p> <p>Now with <code>labels</code>:</p> <pre><code>&gt; f &lt;- factor(c("a","b","c"),levels=c("c","d","e"),labels=c("C","D","E")) &gt; f [1] &lt;NA&gt; &lt;NA&gt; C Levels: C D E </code></pre> <p>After R figures out what should be in the factor, it re-codes the levels. One can of course use this to do brain-frying things such as:</p> <pre><code>&gt; f &lt;- factor(c("a","b","c"),levels=c("c","d","e"),labels=c("a","b","c")) &gt; f [1] &lt;NA&gt; &lt;NA&gt; a Levels: a b c </code></pre> <p>Another way to think about <code>levels</code> is that <code>factor(x,levels=L1,labels=L2)</code> is equivalent to</p> <pre><code>f &lt;- factor(x,levels=L1) levels(f) &lt;- L2 </code></pre> <p>I think an appropriately phrased version of this example might be nice for Pat Burns's <a href="http://www.burns-stat.com/pages/Tutor/R_inferno.pdf" rel="noreferrer">R inferno</a> -- there are plenty of factor puzzles in section 8.2, but not this particular one ...</p>
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    1. POWhy is the terminology of labels and levels in factors so weird?
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    1. POWhy is the terminology of labels and levels in factors so weird?
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    1. COYou sound more sympathetic to my take that this is as 'clear as mud'. I do not understand the phrase " `levels` is intended to tell R which levels to look for in the input (x) ". Nor is there any function `labels<-` that would as you say "change the names of the levels after the input has been coded". They aren't names (in the R sense), anyway. They are values in an attribute.
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    2. COI agree that the terminology is confusing. Does my updated answer help?
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    3. COIt does. Especially the clarification about input and output. Kind of like <gasp> SAS's informat and format.
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