From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 17 Nov 2022 14:54:20 +0100
Subject: Complete update of online docs for v1.2.0
---
docs/reference/index.html | 68 ++++++++++++++++++++++++++++++++++++-----------
1 file changed, 53 insertions(+), 15 deletions(-)
(limited to 'docs/reference/index.html')
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 956648d2..665912f7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
</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">1.1.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
</span>
</div>
@@ -44,11 +44,14 @@
<a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
</li>
<li>
<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
<li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
@@ -56,7 +59,10 @@
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
<li>
- <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
</li>
</ul></li>
<li>
@@ -107,11 +113,15 @@ degradation models and one or more error models</p></td>
<p class="section-desc"></p><p>Generic functions introduced by the package</p>
</th>
</tr></tbody><tbody><tr><td>
- <p><code><a href="convergence.html">convergence()</a></code> <code><a href="convergence.html">print(<i><convergence.mmkin></i>)</a></code> </p>
+ <p><code><a href="parms.html">parms()</a></code> </p>
+ </td>
+ <td><p>Extract model parameters</p></td>
+ </tr><tr><td>
+ <p><code><a href="status.html">status()</a></code> <code><a href="status.html">print(<i><status.mmkin></i>)</a></code> <code><a href="status.html">print(<i><status.mhmkin></i>)</a></code> </p>
</td>
- <td><p>Method to get convergence information</p></td>
+ <td><p>Method to get status information for fit array objects</p></td>
</tr><tr><td>
- <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> </p>
+ <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mkinfit></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.saem.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> </p>
</td>
<td><p>Method to get the names of ill-defined parameters</p></td>
</tr><tr><td>
@@ -119,6 +129,10 @@ degradation models and one or more error models</p></td>
</td>
<td><p>Function to calculate endpoints for further use from kinetic models fitted
with mkinfit</p></td>
+ </tr><tr><td>
+ <p><code><a href="aw.html">aw()</a></code> </p>
+ </td>
+ <td><p>Calculate Akaike weights for model averaging</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="show-results">Show results <a href="#show-results" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Functions working with mkinfit objects</p>
@@ -131,10 +145,6 @@ with mkinfit</p></td>
<p><code><a href="summary.mkinfit.html">summary(<i><mkinfit></i>)</a></code> <code><a href="summary.mkinfit.html">print(<i><summary.mkinfit></i>)</a></code> </p>
</td>
<td><p>Summary method for class "mkinfit"</p></td>
- </tr><tr><td>
- <p><code><a href="parms.html">parms()</a></code> </p>
- </td>
- <td><p>Extract model parameters from mkinfit models</p></td>
</tr><tr><td>
<p><code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> </p>
</td>
@@ -155,10 +165,6 @@ with mkinfit</p></td>
<p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p>
</td>
<td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
- </tr><tr><td>
- <p><code><a href="aw.html">aw()</a></code> </p>
- </td>
- <td><p>Calculate Akaike weights for model averaging</p></td>
</tr><tr><td>
<p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p>
</td>
@@ -189,11 +195,15 @@ of an mmkin object</p></td>
<p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p>
</th>
</tr></tbody><tbody><tr><td>
+ <p><code><a href="read_spreadsheet.html">read_spreadsheet()</a></code> </p>
+ </td>
+ <td><p>Read datasets and relevant meta information from a spreadsheet file</p></td>
+ </tr><tr><td>
<p><code><a href="nlme.mmkin.html">nlme(<i><mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">print(<i><nlme.mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">update(<i><nlme.mmkin></i>)</a></code> </p>
</td>
<td><p>Create an nlme model for an mmkin row object</p></td>
</tr><tr><td>
- <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p>
+ <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> <code><a href="saem.html">parms(<i><saem.mmkin></i>)</a></code> </p>
</td>
<td><p>Fit nonlinear mixed models with SAEM</p></td>
</tr><tr><td>
@@ -213,6 +223,14 @@ degradation models and one or more error models</p></td>
<p><code><a href="summary.saem.mmkin.html">summary(<i><saem.mmkin></i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i><summary.saem.mmkin></i>)</a></code> </p>
</td>
<td><p>Summary method for class "saem.mmkin"</p></td>
+ </tr><tr><td>
+ <p><code><a href="anova.saem.mmkin.html">anova(<i><saem.mmkin></i>)</a></code> </p>
+ </td>
+ <td><p>Anova method for saem.mmkin objects</p></td>
+ </tr><tr><td>
+ <p><code><a href="logLik.saem.mmkin.html">logLik(<i><saem.mmkin></i>)</a></code> </p>
+ </td>
+ <td><p>logLik method for saem.mmkin objects</p></td>
</tr><tr><td>
<p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p>
</td>
@@ -233,6 +251,18 @@ degradation models and one or more error models</p></td>
<p><code><a href="intervals.saem.mmkin.html">intervals(<i><saem.mmkin></i>)</a></code> </p>
</td>
<td><p>Confidence intervals for parameters in saem.mmkin objects</p></td>
+ </tr><tr><td>
+ <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i><multistart></i>)</a></code> <code><a href="multistart.html">best()</a></code> <code><a href="multistart.html">which.best()</a></code> </p>
+ </td>
+ <td><p>Perform a hierarchical model fit with multiple starting values</p></td>
+ </tr><tr><td>
+ <p><code><a href="llhist.html">llhist()</a></code> </p>
+ </td>
+ <td><p>Plot the distribution of log likelihoods from multistart objects</p></td>
+ </tr><tr><td>
+ <p><code><a href="parplot.html">parplot()</a></code> </p>
+ </td>
+ <td><p>Plot parameter variability of multistart objects</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="datasets-and-known-results">Datasets and known results <a href="#datasets-and-known-results" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p>
@@ -322,9 +352,17 @@ degradation models and one or more error models</p></td>
<p class="section-desc"></p>
</th>
</tr></tbody><tbody><tr><td>
+ <p><code><a href="tex_listing.html">tex_listing()</a></code> </p>
+ </td>
+ <td><p>Wrap the output of a summary function in tex listing environment</p></td>
+ </tr><tr><td>
<p><code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> </p>
</td>
<td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td>
+ </tr><tr><td>
+ <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p>
+ </td>
+ <td><p>Set non-detects and unquantified values in residue series without replicates</p></td>
</tr><tr><td>
<p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> </p>
</td>
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