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Diffstat (limited to 'docs/reference/index.html')
| -rw-r--r-- | docs/reference/index.html | 97 |
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><mkinmod></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><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></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><mmkin></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><nlme.mmkin></i>)</a></code> </p> + <p><code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></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><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></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><mixed.mmkin></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><mkinds></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><mkinds></i>)</a></code> </p> + <p><code><a href="mkindsg.html">print(<i><mkindsg></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><mkinmod></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><mkinfit></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> |