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returned by spread_draws()), compare the value of a variable in those draws
across different paired combinations of levels of a factor."><meta property="og:image" content="https://mjskay.github.io/tidybayes/logo.svg"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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    <h1>Compare the value of draws of some variable from a Bayesian model for different levels of a factor</h1>
    <small class="dont-index">Source: <a href="https://github.com/mjskay/tidybayes/blob/HEAD/R/compare_levels.R" class="external-link"><code>R/compare_levels.R</code></a></small>
    <div class="hidden name"><code>compare_levels.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Given posterior draws from a Bayesian model in long format (e.g. as
returned by <code><a href="spread_draws.html">spread_draws()</a></code>), compare the value of a variable in those draws
across different paired combinations of levels of a factor.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">compare_levels</span><span class="op">(</span></span>
<span>  <span class="va">data</span>,</span>
<span>  <span class="va">variable</span>,</span>
<span>  <span class="va">by</span>,</span>
<span>  fun <span class="op">=</span> <span class="va">`-`</span>,</span>
<span>  comparison <span class="op">=</span> <span class="st">"default"</span>,</span>
<span>  draw_indices <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">".chain"</span>, <span class="st">".iteration"</span>, <span class="st">".draw"</span><span class="op">)</span>,</span>
<span>  ignore_groups <span class="op">=</span> <span class="st">".row"</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>


<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>Long-format <code>data.frame</code> of draws such as returned by
<code><a href="spread_draws.html">spread_draws()</a></code> or <code><a href="spread_draws.html">gather_draws()</a></code>. If <code>data</code>
is a grouped data frame, comparisons will be made within groups (if
one of the groups in the data frame is the <code>by</code> column, that specific
group will be ignored, as it is not possible to make comparisons both
within some variable and across it simultaneously).</p></dd>


<dt id="arg-variable">variable<a class="anchor" aria-label="anchor" href="#arg-variable"></a></dt>
<dd><p>Bare (unquoted) name of a column in data representing the
variable to compare across levels. Can be a numeric variable (as in
long-data-frame-of-draws format) or a <code><a href="https://mc-stan.org/posterior/reference/rvar.html" class="external-link">posterior::rvar</a></code>.</p></dd>


<dt id="arg-by">by<a class="anchor" aria-label="anchor" href="#arg-by"></a></dt>
<dd><p>Bare (unquoted) name of a column in data that is a
<code>factor</code> or <code>ordered</code>. The value of <code>variable</code> will be
compared across pairs of levels of this <code>factor</code>.</p></dd>


<dt id="arg-fun">fun<a class="anchor" aria-label="anchor" href="#arg-fun"></a></dt>
<dd><p>Binary function to use for comparison. For each pair of levels of
<code>by</code> we are comparing (as determined by <code>comparison</code>), compute the
result of this function.</p></dd>


<dt id="arg-comparison">comparison<a class="anchor" aria-label="anchor" href="#arg-comparison"></a></dt>
<dd><p>One of (a) the comparison types <code>ordered</code>,
<code>control</code>, <code>pairwise</code>, or <code>default</code> (may also be given as
strings, e.g. <code>"ordered"</code>), see <em>Details</em>; (b) a user-specified
function that takes a <code>factor</code> and returns a list of pairs of names of
levels to compare (as strings) and/or unevaluated expressions containing
representing the comparisons to make; or (c) a list of pairs of names of
levels to compare (as strings) and/or unevaluated expressions representing
the comparisons to make, e.g.: <code>list(c("a", "b"), c("b", "c"))</code> or
<code>exprs(a - b, b - c)</code>, both of which would compare level <code>"a"</code> against
<code>"b"</code> and level <code>"b"</code> against <code>"c"</code>. Note that the
unevaluated expression syntax ignores the <code>fun</code> argument, can include
any other functions desired (e.g. variable transformations), and can even
include more than two levels or other columns in <code>data</code>. Types (b) and
(c) may use named lists, in which case the provided names are used
in the output <code>variable</code> column instead converting the unevaluated
expression to a string. You can also use <code><a href="emmeans_comparison.html">emmeans_comparison()</a></code> to generate
a comparison function based on contrast methods from the <code>emmeans</code> package.</p></dd>


<dt id="arg-draw-indices">draw_indices<a class="anchor" aria-label="anchor" href="#arg-draw-indices"></a></dt>
<dd><p>Character vector of column names that should be treated
as indices of draws. Operations are done within combinations of these values.
The default is <code>c(".chain", ".iteration", ".draw")</code>, which is the same names
used for chain, iteration, and draw indices returned by <code><a href="tidy_draws.html">tidy_draws()</a></code>.
Names in <code>draw_indices</code> that are not found in the data are ignored.</p></dd>


<dt id="arg-ignore-groups">ignore_groups<a class="anchor" aria-label="anchor" href="#arg-ignore-groups"></a></dt>
<dd><p>character vector of names of groups to ignore by
default in the input grouping. This is primarily provided to make it
easier to pipe output of <code><a href="add_predicted_draws.html">add_epred_draws()</a></code> into this function,
as that function provides a <code>".row"</code> output column that is grouped,
but which is virtually never desired to group by when using <code>compare_levels</code>.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    <p>A <code>data.frame</code> with the same columns as <code>data</code>, except
that the <code>by</code> column contains a symbolic representation of the
comparison of pairs of levels of <code>by</code> in <code>data</code>, and
<code>variable</code> contains the result of that comparison.</p>
    </div>
    <div id="details">
    <h2>Details</h2>
    <p>This function simplifies conducting comparisons across levels of some
variable in a tidy data frame of draws. It applies <code>fun</code> to all
values of <code>variable</code> for each pair of levels of <code>by</code> as selected
by <code>comparison</code>. By default, all pairwise comparisons are generated if
<code>by</code> is an unordered <code>factor</code> and ordered comparisons are made if
<code>by</code> is <code>ordered</code>.</p>
<p>The included <code>comparison</code> types are:</p><ul><li><p><code>ordered</code>:
compare each level <code>i</code> with level <code>i - 1</code>; e.g. <code>fun(i, i - 1)</code></p></li>
<li><p><code>pairwise</code>: compare each level of <code>by</code> with every other
level.</p></li>
<li><p><code>control</code>: compare each level of <code>by</code> with the first
level of <code>by</code>.  If you wish to compare with a different level, you can
first apply <code><a href="https://rdrr.io/r/stats/relevel.html" class="external-link">relevel()</a></code> to <code>by</code> to set the control
(reference) level.</p></li>
<li><p><code>default</code>: use <code>ordered</code> if
<code>is.ordered(by)</code> and <code>pairwise</code> otherwise.</p></li>
</ul></div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><code><a href="emmeans_comparison.html">emmeans_comparison()</a></code> to use <code>emmeans</code>-style contrast methods with
<code>compare_levels()</code>.</p></div>
    </div>
    <div id="author">
    <h2>Author</h2>
    <p>Matthew Kay</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">RankCorr</span>, package <span class="op">=</span> <span class="st">"ggdist"</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Let's do all pairwise comparisons of b[i,1]:</span></span></span>
<span class="r-in"><span><span class="va">RankCorr</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="spread_draws.html">spread_draws</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="va">i</span>,<span class="va">j</span><span class="op">]</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">j</span> <span class="op">==</span> <span class="fl">1</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu">compare_levels</span><span class="op">(</span><span class="va">b</span>, by <span class="op">=</span> <span class="va">i</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="http://mjskay.github.io/ggdist/reference/point_interval.html" class="external-link">median_qi</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   i         j     b   .lower .upper .width .point .interval</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2 - 1     1 0.343 -<span style="color: #BB0000;">0.009</span><span style="color: #BB0000; text-decoration: underline;">37</span>  0.684   0.95 median qi       </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 3 - 1     1 0.734  0.416    1.08    0.95 median qi       </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 3 - 2     1 0.402 -<span style="color: #BB0000;">0.013</span><span style="color: #BB0000; text-decoration: underline;">3</span>   0.791   0.95 median qi       </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Or let's plot all comparisons against the first level (control):</span></span></span>
<span class="r-in"><span><span class="va">RankCorr</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="spread_draws.html">spread_draws</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="va">i</span>,<span class="va">j</span><span class="op">]</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">j</span> <span class="op">==</span> <span class="fl">1</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu">compare_levels</span><span class="op">(</span><span class="va">b</span>, by <span class="op">=</span> <span class="va">i</span>, comparison <span class="op">=</span> <span class="va">control</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">b</span>, y <span class="op">=</span> <span class="va">i</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="http://mjskay.github.io/ggdist/reference/stat_halfeye.html" class="external-link">stat_halfeye</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="compare_levels-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Or let's plot comparisons of all levels of j within</span></span></span>
<span class="r-in"><span><span class="co"># all levels of i</span></span></span>
<span class="r-in"><span><span class="va">RankCorr</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="spread_draws.html">spread_draws</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="va">i</span>,<span class="va">j</span><span class="op">]</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu">compare_levels</span><span class="op">(</span><span class="va">b</span>, by <span class="op">=</span> <span class="va">j</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">b</span>, y <span class="op">=</span> <span class="va">j</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="http://mjskay.github.io/ggdist/reference/stat_halfeye.html" class="external-link">stat_halfeye</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/facet_grid.html" class="external-link">facet_grid</a></span><span class="op">(</span>cols <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="compare_levels-2.png" alt="" width="700" height="433"></span>
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</code></pre></div>
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