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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-03 16:41:31 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-03 18:18:19 +0100
commitf0ef23a7598e5d19648ae4edc2b74e0fba27a41c (patch)
tree03af20e730330e148acf3a7c008d82387dbe52eb /docs/reference/index.html
parent82814b17ec182467c25325d747fffa8ffbe4bb33 (diff)
Prepare for v1.0.0v1.0.0
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
Diffstat (limited to 'docs/reference/index.html')
-rw-r--r--docs/reference/index.html97
1 files changed, 70 insertions, 27 deletions
diff --git a/docs/reference/index.html b/docs/reference/index.html
index e0d34e8f..c9f66992 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
</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">0.9.50.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span>
</span>
</div>
@@ -120,7 +120,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -163,7 +163,7 @@
<tr>
<td>
- <p><code><a href="mkinmod.html">mkinmod()</a></code> </p>
+ <p><code><a href="mkinmod.html">mkinmod()</a></code> <code><a href="mkinmod.html">print(<i>&lt;mkinmod&gt;</i>)</a></code> <code><a href="mkinmod.html">mkinsub()</a></code> </p>
</td>
<td><p>Function to set up a kinetic model with one or more state variables</p></td>
</tr><tr>
@@ -297,12 +297,18 @@ of an mmkin object</p></td>
<p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
</td>
<td><p>Calculate the AIC for a column of an mmkin object</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="print.mmkin.html">print(<i>&lt;mmkin&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Print method for mmkin objects</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-mixed-models" class="hasAnchor"><a href="#section-mixed-models" class="anchor"></a>Mixed models</h2>
- <p class="section-desc"><p>Create and work with nonlinear mixed models</p></p>
+ <p class="section-desc"><p>Create and work with nonlinear mixed effects models</p></p>
</th>
</tr>
@@ -319,9 +325,15 @@ of an mmkin object</p></td>
</tr><tr>
<td>
- <p><code><a href="plot.nlme.mmkin.html">plot(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
+ <p><code><a href="plot.mixed.mmkin.html">plot(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="summary.nlme.mmkin.html">summary(<i>&lt;nlme.mmkin&gt;</i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i>&lt;summary.nlme.mmkin&gt;</i>)</a></code> </p>
</td>
- <td><p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
+ <td><p>Summary method for class "nlme.mmkin"</p></td>
</tr><tr>
<td>
@@ -334,6 +346,12 @@ of an mmkin object</p></td>
<p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p>
</td>
<td><p>Retrieve a degradation function from the mmkin namespace</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="mixed.html">mixed()</a></code> <code><a href="mixed.html">print(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Create a mixed effects model from an mmkin row object</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -350,6 +368,24 @@ of an mmkin object</p></td>
<tr>
<td>
+ <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p>
+ </td>
+ <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="D24_2014.html">D24_2014</a></code> </p>
+ </td>
+ <td><p>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="dimethenamid_2018.html">dimethenamid_2018</a></code> </p>
+ </td>
+ <td><p>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</p></td>
+ </tr><tr>
+
+ <td>
<p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code> </p>
</td>
<td><p>Datasets A to F from the FOCUS Kinetics report from 2006</p></td>
@@ -422,15 +458,15 @@ of an mmkin object</p></td>
</tr><tr>
<td>
- <p><code><a href="mkinds.html">mkinds</a></code> </p>
+ <p><code><a href="mkinds.html">print(<i>&lt;mkinds&gt;</i>)</a></code> </p>
</td>
<td><p>A dataset class for mkin</p></td>
</tr><tr>
<td>
- <p><code><a href="print.mkinds.html">print(<i>&lt;mkinds&gt;</i>)</a></code> </p>
+ <p><code><a href="mkindsg.html">print(<i>&lt;mkindsg&gt;</i>)</a></code> </p>
</td>
- <td><p>Print mkinds objects</p></td>
+ <td><p>A class for dataset groups for mkin</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -460,7 +496,7 @@ of an mmkin object</p></td>
</tbody><tbody>
<tr>
<th colspan="2">
- <h2 id="section-helper-functions-mainly-used-internally" class="hasAnchor"><a href="#section-helper-functions-mainly-used-internally" class="anchor"></a>Helper functions mainly used internally</h2>
+ <h2 id="section-utility-functions" class="hasAnchor"><a href="#section-utility-functions" class="anchor"></a>Utility functions</h2>
<p class="section-desc"></p>
</th>
</tr>
@@ -472,9 +508,9 @@ of an mmkin object</p></td>
<tr>
<td>
- <p><code><a href="mkinsub.html">mkinsub()</a></code> </p>
+ <p><code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> </p>
</td>
- <td><p>Function to set up a kinetic submodel for one state variable</p></td>
+ <td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td>
</tr><tr>
<td>
@@ -485,12 +521,6 @@ kinetic models fitted with mkinfit</p></td>
</tr><tr>
<td>
- <p><code><a href="mkinpredict.html">mkinpredict()</a></code> </p>
- </td>
- <td><p>Produce predictions from a kinetic model using specific parameters</p></td>
- </tr><tr>
-
- <td>
<p><code><a href="mkin_wide_to_long.html">mkin_wide_to_long()</a></code> </p>
</td>
<td><p>Convert a dataframe with observations over time into long format</p></td>
@@ -500,12 +530,25 @@ kinetic models fitted with mkinfit</p></td>
<p><code><a href="mkin_long_to_wide.html">mkin_long_to_wide()</a></code> </p>
</td>
<td><p>Convert a dataframe from long to wide format</p></td>
- </tr><tr>
+ </tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-helper-functions-mainly-used-internally" class="hasAnchor"><a href="#section-helper-functions-mainly-used-internally" class="anchor"></a>Helper functions mainly used internally</h2>
+ <p class="section-desc"></p>
+ </th>
+ </tr>
+
+
+ </tbody><tbody>
+
+
+ <tr>
<td>
- <p><code><a href="print.mkinmod.html">print(<i>&lt;mkinmod&gt;</i>)</a></code> </p>
+ <p><code><a href="mkinpredict.html">mkinpredict()</a></code> </p>
</td>
- <td><p>Print mkinmod objects</p></td>
+ <td><p>Produce predictions from a kinetic model using specific parameters</p></td>
</tr><tr>
<td>
@@ -521,12 +564,6 @@ kinetic models fitted with mkinfit</p></td>
</tr><tr>
<td>
- <p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p>
- </td>
- <td><p>Two-component error model</p></td>
- </tr><tr>
-
- <td>
<p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
</td>
<td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
@@ -640,6 +677,12 @@ kinetic models fitted with mkinfit</p></td>
<p><code><a href="add_err.html">add_err()</a></code> </p>
</td>
<td><p>Add normally distributed errors to simulated kinetic degradation data</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p>
+ </td>
+ <td><p>Two-component error model</p></td>
</tr>
</tbody><tbody>
<tr>

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