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technical details (e.g., cores used, duration of the fitting process, number
of specifications), a descriptive analysis of the overall specification curve,
a descriptive summary of the resulting sample sizes, and a head of the results.'><!-- 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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    <div class="page-header">
    <h1>Summarizing the Specification Curve Analysis</h1>
    <small class="dont-index">Source: <a href="https://github.com/masurp/specr/blob/HEAD/R/generics.r" class="external-link"><code>R/generics.r</code></a></small>
    <div class="hidden name"><code>summary.specr.object.Rd</code></div>
    </div>

    <div class="ref-description">
    <p><code>summary</code> method for class "specr". It provides a printed output including
technical details (e.g., cores used, duration of the fitting process, number
of specifications), a descriptive analysis of the overall specification curve,
a descriptive summary of the resulting sample sizes, and a head of the results.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for specr.object</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span></span>
<span>  <span class="va">object</span>,</span>
<span>  type <span class="op">=</span> <span class="st">"default"</span>,</span>
<span>  group <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  var <span class="op">=</span> <span class="va">.data</span><span class="op">$</span><span class="va">estimate</span>,</span>
<span>  stats <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>median <span class="op">=</span> <span class="va">median</span>, mad <span class="op">=</span> <span class="va">mad</span>, min <span class="op">=</span> <span class="va">min</span>, max <span class="op">=</span> <span class="va">max</span>, q25 <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
<span>    <span class="fu"><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">quantile</a></span><span class="op">(</span><span class="va">x</span>, prob <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span>, q75 <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/stats/quantile.html" class="external-link">quantile</a></span><span class="op">(</span><span class="va">x</span>, prob <span class="op">=</span> <span class="fl">0.75</span><span class="op">)</span><span class="op">)</span>,</span>
<span>  digits <span class="op">=</span> <span class="fl">2</span>,</span>
<span>  rows <span class="op">=</span> <span class="fl">6</span>,</span>
<span>  <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>object</dt>
<dd><p>An object of class "specr", usually resulting of a call to <code>specr</code>.</p></dd>


<dt>type</dt>
<dd><p>Different aspects can be summarized and printed. See details for alternative summaries</p></dd>


<dt>group</dt>
<dd><p>In combination with <code>what = "curve"</code>, provide a vector of one or more variables (e.g., subsets, controls,...) that denote the available analytic choices to group summary of the estimate.</p></dd>


<dt>var</dt>
<dd><p>In combination with <code>what = "curve"</code>, unquoted name of parameter to be summarized. Defaults to estimate.</p></dd>


<dt>stats</dt>
<dd><p>Named vector or named list of summary functions (individually defined summary functions can included). If it is not named, placeholders (e.g., "fn1") will be used as column names.</p></dd>


<dt>digits</dt>
<dd><p>The number of digits to use when printing the specification table.</p></dd>


<dt>rows</dt>
<dd><p>The number of rows of the specification tibble that should be printed.</p></dd>


<dt>...</dt>
<dd><p>further arguments passed to or from other methods (currently ignored).</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>A printed summary of an object of class <code>specr.object</code>.</p>
    </div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p>The function used to create the "specr.setup" object: <code>setup</code>.</p></div>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Setup up specifications (returns object of class "specr.setup")</span></span></span>
<span class="r-in"><span><span class="va">specs</span> <span class="op">&lt;-</span> <span class="fu"><a href="setup.html">setup</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">example_data</span>,</span></span>
<span class="r-in"><span>   y <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">"y1"</span>, <span class="st">"y2"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>   x <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">"x1"</span>, <span class="st">"x2"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>   model <span class="op">=</span> <span class="st">"lm"</span>,</span></span>
<span class="r-in"><span>   controls <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">"c1"</span>, <span class="st">"c2"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>   subsets <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>group1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/unique.html" class="external-link">unique</a></span><span class="op">(</span><span class="va">example_data</span><span class="op">$</span><span class="va">group1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Run analysis (returns object of class "specr.object")</span></span></span>
<span class="r-in"><span><span class="va">results</span> <span class="op">&lt;-</span> <span class="fu"><a href="specr.html">specr</a></span><span class="op">(</span><span class="va">specs</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Default summary of the "specr.object"</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">results</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Results of the specification curve analysis</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> -------------------</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Technical details:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   Class:                          specr.object -- version: 1.0.1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   Cores used:                     1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   Duration of fitting process:    0.495 sec elapsed </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   Number of specifications:       64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Descriptive summary of the specification curve:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  median  mad   min  max   q25  q75</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    0.13 0.41 -0.39 0.66 -0.14 0.39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Descriptive summary of sample sizes: </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  median min  max</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   338.5 323 1000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Head of the specification results (first 6 rows): </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6 × 25</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   x     y     model controls subsets group1 formula estimate std.error statistic</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;chr&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 style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;glue&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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> x1    y1    lm    no cova… middle  middle y1 ~ x…     0.61      0.07      9.28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> x1    y1    lm    no cova… old     old    y1 ~ x…     0.66      0.06     10.4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> x1    y1    lm    no cova… young   young  y1 ~ x…     0.57      0.06     10.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> x1    y1    lm    no cova… all     <span style="color: #BB0000;">NA</span>     y1 ~ x…     0.62      0.04     16.4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> x1    y1    lm    c1       middle  middle y1 ~ x…     0.6       0.07      8.81</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> x1    y1    lm    c1       old     old    y1 ~ x…     0.64      0.06      9.81</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 15 more variables: p.value &lt;dbl&gt;, conf.low &lt;dbl&gt;, conf.high &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   fit_r.squared &lt;dbl&gt;, fit_adj.r.squared &lt;dbl&gt;, fit_sigma &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   fit_statistic &lt;dbl&gt;, fit_p.value &lt;dbl&gt;, fit_df &lt;dbl&gt;, fit_logLik &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   fit_AIC &lt;dbl&gt;, fit_BIC &lt;dbl&gt;, fit_deviance &lt;dbl&gt;, fit_df.residual &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   fit_nobs &lt;dbl&gt;</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Summarize the specification curve descriptively</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">results</span>, type <span class="op">=</span> <span class="st">"curve"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   median   mad    min   max    q25   q75   obs</span>
<span class="r-out co"><span class="r-pr">#&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;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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span>  0.126 0.412 -<span style="color: #BB0000;">0.387</span> 0.662 -<span style="color: #BB0000;">0.139</span> 0.395  338.</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Grouping for certain analytical decisions</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">results</span>,</span></span>
<span class="r-in"><span>       type <span class="op">=</span> <span class="st">"curve"</span>,</span></span>
<span class="r-in"><span>       group <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">"x"</span>, <span class="st">"y"</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: 4 × 9</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   x [2]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   x     y      median    mad    min     max     q25     q75   obs</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;chr&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;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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> x1    y1     0.601  0.038<span style="text-decoration: underline;">8</span>  0.541  0.662   0.577   0.623   338.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> x1    y2    -<span style="color: #BB0000;">0.258</span>  0.078<span style="text-decoration: underline;">4</span> -<span style="color: #BB0000;">0.387</span> -<span style="color: #BB0000;">0.178</span>  -<span style="color: #BB0000;">0.314</span>  -<span style="color: #BB0000;">0.211</span>   338.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> x2    y1     0.232  0.057<span style="text-decoration: underline;">3</span>  0.159  0.346   0.200   0.283   338.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> x2    y2    -<span style="color: #BB0000;">0.021</span><span style="color: #BB0000; text-decoration: underline;">1</span> 0.115  -<span style="color: #BB0000;">0.127</span>  0.091<span style="text-decoration: underline;">7</span> -<span style="color: #BB0000;">0.088</span><span style="color: #BB0000; text-decoration: underline;">2</span>  0.057<span style="text-decoration: underline;">2</span>  338.</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Using customized functions</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">results</span>,</span></span>
<span class="r-in"><span>        type <span class="op">=</span> <span class="st">"curve"</span>,</span></span>
<span class="r-in"><span>       group <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">"x"</span>, <span class="st">"group1"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>       stats <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>median <span class="op">=</span> <span class="va">median</span>,</span></span>
<span class="r-in"><span>                    min <span class="op">=</span> <span class="va">min</span>,</span></span>
<span class="r-in"><span>                    max <span class="op">=</span> <span class="va">max</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: 8 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   x [2]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   x     group1 median     min   max   obs</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;fct&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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> x1    middle  0.178 -<span style="color: #BB0000;">0.387</span>  0.613   331</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> x1    old     0.221 -<span style="color: #BB0000;">0.304</span>  0.662   323</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> x1    young   0.182 -<span style="color: #BB0000;">0.310</span>  0.567   346</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> x1    <span style="color: #BB0000;">NA</span>      0.195 -<span style="color: #BB0000;">0.339</span>  0.620  <span style="text-decoration: underline;">1</span>000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> x2    middle  0.130 -<span style="color: #BB0000;">0.069</span><span style="color: #BB0000; text-decoration: underline;">3</span> 0.228   331</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> x2    old     0.204 -<span style="color: #BB0000;">0.083</span><span style="color: #BB0000; text-decoration: underline;">6</span> 0.346   323</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> x2    young   0.101 -<span style="color: #BB0000;">0.127</span>  0.202   346</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">8</span> x2    <span style="color: #BB0000;">NA</span>      0.144 -<span style="color: #BB0000;">0.107</span>  0.272  <span style="text-decoration: underline;">1</span>000</span>
</code></pre></div>
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