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updated docs for 1.2.5
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rmflight committed Oct 16, 2024
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<h1 id="icikendalltau">ICIKendallTau</h1>
<!-- badges: start -->

<p><a href="https://moseleybioinformaticslab.r-universe.dev"><img role="img" aria-label="ICIKendallTau status badge" src="data:image/svg+xml; charset=utf-8;base64,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" alt="ICIKendallTau status badge" /></a></p>
<p><a href="https://moseleybioinformaticslab.r-universe.dev"><img role="img" aria-label="ICIKendallTau status badge" src="data:image/svg+xml; charset=utf-8;base64,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" alt="ICIKendallTau status badge" /></a></p>
<!-- badges: end -->

<p>You can see the pkgdown site <a href="https://moseleybioinformaticslab.github.io/ICIKendallTau/">here</a>.</p>
Expand Down Expand Up @@ -728,13 +728,13 @@ <h2 id="is-it-fast">Is It Fast?</h2>
<span id="cb5-13"><a href="#cb5-13" tabindex="-1"></a>)</span>
<span id="cb5-14"><a href="#cb5-14" tabindex="-1"></a><span class="co">#&gt; Unit: microseconds</span></span>
<span id="cb5-15"><a href="#cb5-15" tabindex="-1"></a><span class="co">#&gt; expr min lq mean median</span></span>
<span id="cb5-16"><a href="#cb5-16" tabindex="-1"></a><span class="co">#&gt; cor(x, y, method = &quot;kendall&quot;) 13191.399 13608.067 13688.8872 13773.376</span></span>
<span id="cb5-17"><a href="#cb5-17" tabindex="-1"></a><span class="co">#&gt; ici_kt(x, y, &quot;global&quot;) 337.849 367.467 426.3204 375.616</span></span>
<span id="cb5-18"><a href="#cb5-18" tabindex="-1"></a><span class="co">#&gt; ici_kt(x2, y2, &quot;global&quot;) 20221.147 21001.428 21366.2374 21186.299</span></span>
<span id="cb5-16"><a href="#cb5-16" tabindex="-1"></a><span class="co">#&gt; cor(x, y, method = &quot;kendall&quot;) 12299.117 12617.607 13300.3072 13214.135</span></span>
<span id="cb5-17"><a href="#cb5-17" tabindex="-1"></a><span class="co">#&gt; ici_kt(x, y, &quot;global&quot;) 366.796 370.173 530.6206 401.068</span></span>
<span id="cb5-18"><a href="#cb5-18" tabindex="-1"></a><span class="co">#&gt; ici_kt(x2, y2, &quot;global&quot;) 19343.691 19680.732 20578.4926 19799.741</span></span>
<span id="cb5-19"><a href="#cb5-19" tabindex="-1"></a><span class="co">#&gt; uq max neval</span></span>
<span id="cb5-20"><a href="#cb5-20" tabindex="-1"></a><span class="co">#&gt; 13895.864 13975.730 5</span></span>
<span id="cb5-21"><a href="#cb5-21" tabindex="-1"></a><span class="co">#&gt; 390.208 660.462 5</span></span>
<span id="cb5-22"><a href="#cb5-22" tabindex="-1"></a><span class="co">#&gt; 21580.156 22842.157 5</span></span></code></pre></div>
<span id="cb5-20"><a href="#cb5-20" tabindex="-1"></a><span class="co">#&gt; 13767.479 14603.198 5</span></span>
<span id="cb5-21"><a href="#cb5-21" tabindex="-1"></a><span class="co">#&gt; 405.009 1110.057 5</span></span>
<span id="cb5-22"><a href="#cb5-22" tabindex="-1"></a><span class="co">#&gt; 20533.946 23534.353 5</span></span></code></pre></div>
<p>In the case of 40,000 features, the average time on a modern CPU is
14 milliseconds.</p>
<p>Of course, if you want to use it to calculate Kendall-tau-b without
Expand All @@ -758,7 +758,7 @@ <h2 id="is-it-fast">Is It Fast?</h2>
<span id="cb7-11"><a href="#cb7-11" tabindex="-1"></a><span class="co">#&gt; y 0.8716723 0.0000000</span></span>
<span id="cb7-12"><a href="#cb7-12" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb7-13"><a href="#cb7-13" tabindex="-1"></a><span class="co">#&gt; $run_time</span></span>
<span id="cb7-14"><a href="#cb7-14" tabindex="-1"></a><span class="co">#&gt; [1] 0.02046323</span></span></code></pre></div>
<span id="cb7-14"><a href="#cb7-14" tabindex="-1"></a><span class="co">#&gt; [1] 0.02207708</span></span></code></pre></div>
<h2 id="p-values">P-Values</h2>
<p>ICI-Kt functions only calculates the tau-b variant that handles ties.
P-value calculations use the asymptotic approximation in all cases, and
Expand Down Expand Up @@ -792,7 +792,7 @@ <h2 id="many-many-comparisons">Many Many Comparisons</h2>
<span id="cb9-7"><a href="#cb9-7" tabindex="-1"></a><span class="co">#&gt; 3 s4 s4 0 1.0000000 0 1.000000 0.950 1.0000000</span></span>
<span id="cb9-8"><a href="#cb9-8" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb9-9"><a href="#cb9-9" tabindex="-1"></a><span class="co">#&gt; $run_time</span></span>
<span id="cb9-10"><a href="#cb9-10" tabindex="-1"></a><span class="co">#&gt; [1] 0.01763749</span></span></code></pre></div>
<span id="cb9-10"><a href="#cb9-10" tabindex="-1"></a><span class="co">#&gt; [1] 0.02029967</span></span></code></pre></div>
<h2 id="other-correlations">Other Correlations</h2>
<p><code>ici_kendalltau</code> and <code>ici_kt</code> calculate the
p-value of the correlation as part of the overall calculation.
Expand All @@ -816,7 +816,7 @@ <h2 id="other-correlations">Other Correlations</h2>
<span id="cb10-11"><a href="#cb10-11" tabindex="-1"></a><span class="co">#&gt; y 0.8199608 0.0000000</span></span>
<span id="cb10-12"><a href="#cb10-12" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb10-13"><a href="#cb10-13" tabindex="-1"></a><span class="co">#&gt; $run_time</span></span>
<span id="cb10-14"><a href="#cb10-14" tabindex="-1"></a><span class="co">#&gt; [1] 0.02564859</span></span></code></pre></div>
<span id="cb10-14"><a href="#cb10-14" tabindex="-1"></a><span class="co">#&gt; [1] 0.02324367</span></span></code></pre></div>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a>m_3 <span class="ot">=</span> <span class="fu">cbind</span>(x, y, x)</span>
<span id="cb11-2"><a href="#cb11-2" tabindex="-1"></a><span class="fu">colnames</span>(m_3) <span class="ot">=</span> <span class="fu">c</span>(<span class="st">&quot;s1&quot;</span>, <span class="st">&quot;s2&quot;</span>, <span class="st">&quot;s3&quot;</span>)</span>
<span id="cb11-3"><a href="#cb11-3" tabindex="-1"></a>r_6 <span class="ot">=</span> <span class="fu">cor_fast</span>(m_3)</span>
Expand All @@ -834,7 +834,7 @@ <h2 id="other-correlations">Other Correlations</h2>
<span id="cb11-15"><a href="#cb11-15" tabindex="-1"></a><span class="co">#&gt; s3 0.0000000 0.8199608 0.0000000</span></span>
<span id="cb11-16"><a href="#cb11-16" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb11-17"><a href="#cb11-17" tabindex="-1"></a><span class="co">#&gt; $run_time</span></span>
<span id="cb11-18"><a href="#cb11-18" tabindex="-1"></a><span class="co">#&gt; [1] 0.02596617</span></span></code></pre></div>
<span id="cb11-18"><a href="#cb11-18" tabindex="-1"></a><span class="co">#&gt; [1] 0.0229435</span></span></code></pre></div>
<h2 id="code-of-conduct">Code of Conduct</h2>
<p>Please note that the ICIKendallTau project is released with a <a href="https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html">Contributor
Code of Conduct</a>. By contributing to this project, you agree to abide
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Expand Up @@ -144,13 +144,13 @@ microbenchmark(
)
#> Unit: microseconds
#> expr min lq mean median
#> cor(x, y, method = "kendall") 13191.399 13608.067 13688.8872 13773.376
#> ici_kt(x, y, "global") 337.849 367.467 426.3204 375.616
#> ici_kt(x2, y2, "global") 20221.147 21001.428 21366.2374 21186.299
#> cor(x, y, method = "kendall") 12299.117 12617.607 13300.3072 13214.135
#> ici_kt(x, y, "global") 366.796 370.173 530.6206 401.068
#> ici_kt(x2, y2, "global") 19343.691 19680.732 20578.4926 19799.741
#> uq max neval
#> 13895.864 13975.730 5
#> 390.208 660.462 5
#> 21580.156 22842.157 5
#> 13767.479 14603.198 5
#> 405.009 1110.057 5
#> 20533.946 23534.353 5
```

In the case of 40,000 features, the average time on a modern CPU is 14
Expand Down Expand Up @@ -182,7 +182,7 @@ k_tau_fast
#> y 0.8716723 0.0000000
#>
#> $run_time
#> [1] 0.02046323
#> [1] 0.02207708
```

## P-Values
Expand Down Expand Up @@ -227,7 +227,7 @@ r_4
#> 3 s4 s4 0 1.0000000 0 1.000000 0.950 1.0000000
#>
#> $run_time
#> [1] 0.01763749
#> [1] 0.02029967
```

## Other Correlations
Expand Down Expand Up @@ -255,7 +255,7 @@ r_5
#> y 0.8199608 0.0000000
#>
#> $run_time
#> [1] 0.02564859
#> [1] 0.02324367
```

``` r
Expand All @@ -276,7 +276,7 @@ r_6
#> s3 0.0000000 0.8199608 0.0000000
#>
#> $run_time
#> [1] 0.02596617
#> [1] 0.0229435
```

## Code of Conduct
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