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-rw-r--r--docs/articles/web_only/FOCUS_Z.html42
1 files changed, 21 insertions, 21 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 9602adb5..4cda45e3 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -33,7 +33,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span>
</span>
</div>
@@ -134,7 +134,7 @@
Ranke</h4>
<h4 data-toc-skip class="date">Last change 16 January 2018
-(rebuilt 2023-04-20)</h4>
+(rebuilt 2023-05-19)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_Z.rmd</code></div>
@@ -189,7 +189,7 @@ pathway from parent directly to sink included (default in mkin).</p>
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></span></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
<pre><code><span><span class="co">## Estimate se_notrans t value Pr(&gt;t) Lower Upper</span></span>
<span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span>
<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span>
@@ -217,7 +217,7 @@ the model formulation:</p>
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></span></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
<pre><code><span><span class="co">## Estimate se_notrans t value Pr(&gt;t) Lower Upper</span></span>
<span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span>
<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span>
@@ -247,7 +247,7 @@ previous fit when adding a further metabolite.</p>
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></span></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p>
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
<pre><code><span><span class="co">## Estimate se_notrans t value Pr(&gt;t) Lower Upper</span></span>
<span><span class="co">## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538</span></span>
<span><span class="co">## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593</span></span>
@@ -299,27 +299,27 @@ accelerate the optimization.</p>
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p>
<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div>
<pre><code><span><span class="co">## Estimate se_notrans t value Pr(&gt;t) Lower Upper</span></span>
-<span><span class="co">## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664</span></span>
-<span><span class="co">## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989</span></span>
-<span><span class="co">## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666</span></span>
-<span><span class="co">## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872</span></span>
-<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965</span></span>
-<span><span class="co">## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274</span></span>
-<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></span></code></pre>
+<span><span class="co">## Z0_0 96.842440 1.994291 48.5598 4.0226e-42 92.830421 100.854459</span></span>
+<span><span class="co">## k_Z0 2.215425 0.118457 18.7023 1.0404e-23 1.989490 2.467019</span></span>
+<span><span class="co">## k_Z1 0.478307 0.028257 16.9272 6.2332e-22 0.424709 0.538669</span></span>
+<span><span class="co">## k_Z2 0.451642 0.042139 10.7178 1.6304e-14 0.374348 0.544894</span></span>
+<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034804 0.098975</span></span>
+<span><span class="co">## f_Z2_to_Z3 0.471483 0.058348 8.0806 9.6585e-11 0.357720 0.588287</span></span>
+<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5576e-14 3.213126 4.755737</span></span></code></pre>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div>
<pre><code><span><span class="co">## $ff</span></span>
<span><span class="co">## Z2_Z3 Z2_sink </span></span>
-<span><span class="co">## 0.4715 0.5285 </span></span>
+<span><span class="co">## 0.47148 0.52852 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## $distimes</span></span>
<span><span class="co">## DT50 DT90</span></span>
-<span><span class="co">## Z0 0.31288 1.0394</span></span>
-<span><span class="co">## Z1 1.44917 4.8141</span></span>
-<span><span class="co">## Z2 1.53478 5.0984</span></span>
-<span><span class="co">## Z3 11.80986 39.2315</span></span></code></pre>
+<span><span class="co">## Z0 0.31287 1.0393</span></span>
+<span><span class="co">## Z1 1.44917 4.8140</span></span>
+<span><span class="co">## Z2 1.53473 5.0983</span></span>
+<span><span class="co">## Z3 11.80991 39.2317</span></span></code></pre>
<p>This fit corresponds to the final result chosen in Appendix 7 of the
FOCUS report. Confidence intervals returned by mkin are based on
internally transformed parameters, however.</p>
@@ -350,7 +350,7 @@ improved. However, the covariance matrix is not returned.</p>
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></span></code></pre></div>
<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></span></code></pre></div>
<pre><code><span><span class="co">## NULL</span></span></code></pre>
<p>Therefore, a further stepwise model building is performed starting
from the stage of parent and two metabolites, starting from the
@@ -442,11 +442,11 @@ obtained.</p>
<span><span class="co">## </span></span>
<span><span class="co">## $SFORB</span></span>
<span><span class="co">## Z0_b1 Z0_b2 Z0_g Z3_b1 Z3_b2 Z3_g </span></span>
-<span><span class="co">## 2.4471322 0.0075125 0.9519862 0.0800069 0.0000000 0.9347820 </span></span>
+<span><span class="co">## 2.4471342 0.0075124 0.9519866 0.0800071 0.0000000 0.9347816 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## $distimes</span></span>
<span><span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span></span>
-<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA</span></span>
+<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.267 NA NA</span></span>
<span><span class="co">## Z1 1.5148 5.0320 NA NA NA NA NA</span></span>
<span><span class="co">## Z2 1.6414 5.4526 NA NA NA NA NA</span></span>
<span><span class="co">## Z3 NA NA NA NA NA 8.6636 Inf</span></span></code></pre>

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