diff options
Diffstat (limited to 'docs/dev/reference/index.html')
| -rw-r--r-- | docs/dev/reference/index.html | 104 |
1 files changed, 70 insertions, 34 deletions
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index afd3692d..0fac6842 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> </span> </div> @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -41,12 +41,18 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <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/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> <li> @@ -95,9 +101,35 @@ <td><p>Fit one or more kinetic models with one or more state variables to one or more datasets</p></td> </tr><tr><td> - <p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i><nafta></i>)</a></code> </p> + <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> </p> </td> - <td><p>Evaluate parent kinetics using the NAFTA guidance</p></td> + <td><p>Fit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models</p></td> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="generics">Generics <a href="#generics" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>Generic functions introduced by the package</p> + </th> + </tr></tbody><tbody><tr><td> + <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 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> + </td> + <td><p>Method to get the names of ill-defined parameters</p></td> + </tr><tr><td> + <p><code><a href="endpoints.html">endpoints()</a></code> </p> + </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> @@ -111,10 +143,6 @@ more datasets</p></td> </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> <td><p>Confidence intervals for parameters of mkinfit objects</p></td> @@ -135,15 +163,6 @@ more datasets</p></td> </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="endpoints.html">endpoints()</a></code> </p> - </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><tr><td> <p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p> </td> <td><p>Export a list of datasets format to a CAKE study file</p></td> @@ -164,22 +183,27 @@ 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="summary.mmkin.html">summary(<i><mmkin></i>)</a></code> <code><a href="summary.mmkin.html">print(<i><summary.mmkin></i>)</a></code> </p> + </td> + <td><p>Summary method for class "mmkin"</p></td> </tr></tbody><tbody><tr><th colspan="2"> <h2 id="mixed-models">Mixed models <a href="#mixed-models" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Create and work with nonlinear mixed effects models</p> + <p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p> </th> </tr></tbody><tbody><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> - <p><code><a href="nlmixr.mmkin.html">nlmixr(<i><mmkin></i>)</a></code> <code><a href="nlmixr.mmkin.html">print(<i><nlmixr.mmkin></i>)</a></code> <code><a href="nlmixr.mmkin.html">nlmixr_model()</a></code> <code><a href="nlmixr.mmkin.html">nlmixr_data()</a></code> </p> + <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> </p> </td> - <td><p>Fit nonlinear mixed models using nlmixr</p></td> + <td><p>Fit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models</p></td> </tr><tr><td> <p><code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></i>)</a></code> </p> </td> @@ -189,14 +213,18 @@ of an mmkin object</p></td> </td> <td><p>Summary method for class "nlme.mmkin"</p></td> </tr><tr><td> - <p><code><a href="summary.nlmixr.mmkin.html">summary(<i><nlmixr.mmkin></i>)</a></code> <code><a href="summary.nlmixr.mmkin.html">print(<i><summary.nlmixr.mmkin></i>)</a></code> </p> - </td> - <td><p>Summary method for class "nlmixr.mmkin"</p></td> - </tr><tr><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> <td><p>Helper functions to create nlme models from mmkin row objects</p></td> @@ -209,7 +237,7 @@ of an mmkin object</p></td> </td> <td><p>Create a mixed effects model from an mmkin row object</p></td> </tr><tr><td> - <p><code><a href="reexports.html">reexports</a></code> </p> + <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">intervals</a></code> <code><a href="reexports.html">lrtest</a></code> <code><a href="reexports.html">nlme</a></code> </p> </td> <td><p>Objects exported from other packages</p></td> </tr><tr><td> @@ -217,9 +245,17 @@ of an mmkin object</p></td> </td> <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td> </tr><tr><td> - <p><code><a href="intervals.nlmixr.mmkin.html">intervals(<i><nlmixr.mmkin></i>)</a></code> </p> + <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>Confidence intervals for parameters in nlmixr.mmkin objects</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> @@ -313,6 +349,10 @@ of an mmkin object</p></td> </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> <td><p>Function to calculate maximum time weighted average concentrations from @@ -342,10 +382,6 @@ kinetic models fitted with mkinfit</p></td> </td> <td><p>Function to perform isometric log-ratio transformation</p></td> </tr><tr><td> - <p><code><a href="tffm0.html">tffm0()</a></code> <code><a href="tffm0.html">invtffm0()</a></code> </p> - </td> - <td><p>Transform formation fractions as in the first published mkin version</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> @@ -442,7 +478,7 @@ kinetic models fitted with mkinfit</p></td> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> |