diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-06 18:30:32 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-06 18:30:32 +0100 |
| commit | 48c463680b51fa767b4cd7bd62865f192d0354ac (patch) | |
| tree | 5b66eb08a7fd5e29fb7e6d3a9a8258ccdcaea73e /docs | |
| parent | 2ee20b257e34210e2d1f044431f3bfe059c9c5e7 (diff) | |
Reintroduce interface to saemix
Also after the upgrade from buster to bullseye of my local system, some
test results for saemix have changed.
Diffstat (limited to 'docs')
36 files changed, 559 insertions, 511 deletions
diff --git a/docs/dev/404.html b/docs/dev/404.html index bea38406..5f29faf2 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 6daa6960..441d49c0 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> diff --git a/docs/dev/authors.html b/docs/dev/authors.html index d592b39f..9641eec0 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -71,7 +71,7 @@ </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -147,15 +147,15 @@ </li> <li> <p><strong>Katrin Lindenberger</strong>. Contributor. - </p> + <br /><small>contributed to mkinresplot()</small></p> </li> <li> <p><strong>René Lehmann</strong>. Contributor. - </p> + <br /><small>ilr() and invilr()</small></p> </li> <li> <p><strong>Eurofins Regulatory AG</strong>. Copyright holder. - </p> + <br /><small>copyright for some of the contributions of JR 2012-2014</small></p> </li> </ul> diff --git a/docs/dev/index.html b/docs/dev/index.html index a4399963..8888633d 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -38,7 +38,7 @@ </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -147,7 +147,7 @@ <li>Three different error models can be selected using the argument <code>error_model</code> to the <a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html"><code>mkinfit</code></a> function.</li> <li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) should now be specified as <code>error_model = "obs"</code>.</li> <li>A two-component error model similar to the one proposed by <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">Rocke and Lorenzato</a> can be selected using the argument <code>error_model = "tc"</code>.</li> -<li>Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> method.</li> +<li>Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> method. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils).</li> </ul> </div> <div id="gui" class="section level2"> diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index c3597efe..998917f2 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -141,13 +141,36 @@ <small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small> </div> - <div id="mkin-0-9-50-4-unreleased" class="section level1"> -<h1 class="page-header" data-toc-text="0.9.50.4"> -<a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small> + <div id="mkin-1019000" class="section level1"> +<h1 class="page-header" data-toc-text="1.0.1.9000"> +<a href="#mkin-1019000" class="anchor"></a>mkin 1.0.1.9000<small> Unreleased </small> </h1> -<div id="general-new-features" class="section level2"> +<ul> +<li><p>Switch to a versioning scheme where the fourth version component indicates development versions</p></li> +<li><p>Reintroduce the interface to the current development version of saemix, in particular:</p></li> +<li><p>‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects</p></li> +<li><p>‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods</p></li> +</ul> +</div> + <div id="mkin-101" class="section level1"> +<h1 class="page-header" data-toc-text="1.0.1"> +<a href="#mkin-101" class="anchor"></a>mkin 1.0.1<small> Unreleased </small> +</h1> +<ul> +<li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li> +<li><p>‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax</p></li> +<li><p>‘mkinresplot’: Re-add Katrin Lindenberger as coauthor who was accidentally removed long ago</p></li> +<li><p>Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset as this is platform dependent (revealed by the new additional tests on CRAN, thanks!)</p></li> +<li><p>Increase test tolerance for some parameter comparisons that also proved to be platform dependent</p></li> +</ul> +</div> + <div id="mkin-100" class="section level1"> +<h1 class="page-header" data-toc-text="1.0.0"> +<a href="#mkin-100" class="anchor"></a>mkin 1.0.0<small> 2021-02-03 </small> +</h1> +<div id="general" class="section level2"> <h2 class="hasAnchor"> -<a href="#general-new-features" class="anchor"></a>General new features</h2> +<a href="#general" class="anchor"></a>General</h2> <ul> <li><p>‘mkinmod’ models gain arguments ‘name’ and ‘dll_dir’ which, in conjunction with a current version of the ‘inline’ package, make it possible to still use the DLL used for fast ODE solutions with ‘deSolve’ after saving and restoring the ‘mkinmod’ object.</p></li> <li><p>‘mkindsg’ R6 class for groups of ‘mkinds’ datasets with metadata</p></li> @@ -156,6 +179,8 @@ <li><p>‘focus_soil_moisture’ FOCUS default soil moisture data</p></li> <li><p>‘update’ method for ‘mmkin’ objects</p></li> <li><p>‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable</p></li> +<li><p>‘plot.mmkin’: Add a ylab argument, making it possible to customize the y axis label of the panels on the left without affecting the residual plots. Reduce legend size and vertical distance between panels</p></li> +<li><p>‘plot.mkinfit’: Change default ylab from “Observed” to “Residue”. Pass xlab to residual plot if show_residuals is TRUE.</p></li> </ul> </div> <div id="mixed-effects-models" class="section level2"> @@ -163,18 +188,14 @@ <a href="#mixed-effects-models" class="anchor"></a>Mixed-effects models</h2> <ul> <li><p>‘mixed.mmkin’ New container for mmkin objects for plotting with the ‘plot.mixed.mmkin’ method</p></li> -<li><p>‘plot.mixed.mmkin’ method used for ‘nlme.mmkin’ and ‘saem.mmkin’, both inheriting from ‘mixed.mmkin’ (currently virtual)</p></li> +<li><p>‘plot.mixed.mmkin’ method used for ‘nlme.mmkin’ inheriting from ‘mixed.mmkin’ (currently virtual)</p></li> <li><p>‘plot’, ‘summary’ and ‘print’ methods for ‘nlme.mmkin’ objects</p></li> -<li><p>Add the current development version of the saemix package as a second, optional backend for mixed-effects models</p></li> -<li><p>DESCRIPTION: Additional_repositories entry pointing to my drat repository on github for a suitable saemix version</p></li> -<li><p>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects.</p></li> -<li><p>‘saem’ generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods</p></li> </ul> </div> </div> - <div id="mkin-0-9-50-3-2020-10-08" class="section level1"> + <div id="mkin-09503-2020-10-08" class="section level1"> <h1 class="page-header" data-toc-text="0.9.50.3"> -<a href="#mkin-0-9-50-3-2020-10-08" class="anchor"></a>mkin 0.9.50.3 (2020-10-08)<small> 2020-10-08 </small> +<a href="#mkin-09503-2020-10-08" class="anchor"></a>mkin 0.9.50.3 (2020-10-08)<small> 2020-10-08 </small> </h1> <ul> <li><p>‘parms’: Add a method for mmkin objects</p></li> @@ -188,18 +209,18 @@ <li><p>‘endpoints’: Back-calculate DT50 value from DT90 also for the biphasic models DFOP, HS and SFORB</p></li> </ul> </div> - <div id="mkin-0-9-50-2-2020-05-12" class="section level1"> + <div id="mkin-09502-2020-05-12" class="section level1"> <h1 class="page-header" data-toc-text="0.9.50.2"> -<a href="#mkin-0-9-50-2-2020-05-12" class="anchor"></a>mkin 0.9.50.2 (2020-05-12)<small> 2020-05-12 </small> +<a href="#mkin-09502-2020-05-12" class="anchor"></a>mkin 0.9.50.2 (2020-05-12)<small> 2020-05-12 </small> </h1> <ul> <li><p>Increase tolerance for a platform specific test results on the Solaris test machine on CRAN</p></li> <li><p>Updates and corrections (using the spelling package) to the documentation</p></li> </ul> </div> - <div id="mkin-0-9-50-1-2020-05-11" class="section level1"> + <div id="mkin-09501-2020-05-11" class="section level1"> <h1 class="page-header" data-toc-text="0.9.50.1"> -<a href="#mkin-0-9-50-1-2020-05-11" class="anchor"></a>mkin 0.9.50.1 (2020-05-11)<small> 2020-05-11 </small> +<a href="#mkin-09501-2020-05-11" class="anchor"></a>mkin 0.9.50.1 (2020-05-11)<small> 2020-05-11 </small> </h1> <ul> <li><p>Support SFORB with formation fractions</p></li> @@ -207,17 +228,17 @@ <li><p>Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO</p></li> </ul> </div> - <div id="mkin-0-9-49-11-2020-04-20" class="section level1"> + <div id="mkin-094911-2020-04-20" class="section level1"> <h1 class="page-header" data-toc-text="0.9.49.11"> -<a href="#mkin-0-9-49-11-2020-04-20" class="anchor"></a>mkin 0.9.49.11 (2020-04-20)<small> 2020-04-20 </small> +<a href="#mkin-094911-2020-04-20" class="anchor"></a>mkin 0.9.49.11 (2020-04-20)<small> 2020-04-20 </small> </h1> <ul> <li>Increase a test tolerance to make it pass on all CRAN check machines</li> </ul> </div> - <div id="mkin-0-9-49-10-2020-04-18" class="section level1"> + <div id="mkin-094910-2020-04-18" class="section level1"> <h1 class="page-header" data-toc-text="0.9.49.10"> -<a href="#mkin-0-9-49-10-2020-04-18" class="anchor"></a>mkin 0.9.49.10 (2020-04-18)<small> 2020-04-18 </small> +<a href="#mkin-094910-2020-04-18" class="anchor"></a>mkin 0.9.49.10 (2020-04-18)<small> 2020-04-18 </small> </h1> <ul> <li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods</p></li> @@ -228,18 +249,18 @@ <li><p>‘summary.mkinfit’: Add AIC, BIC and log likelihood to the summary</p></li> </ul> </div> - <div id="mkin-0-9-49-9-2020-03-31" class="section level1"> + <div id="mkin-09499-2020-03-31" class="section level1"> <h1 class="page-header" data-toc-text="0.9.49.9"> -<a href="#mkin-0-9-49-9-2020-03-31" class="anchor"></a>mkin 0.9.49.9 (2020-03-31)<small> 2020-03-31 </small> +<a href="#mkin-09499-2020-03-31" class="anchor"></a>mkin 0.9.49.9 (2020-03-31)<small> 2020-03-31 </small> </h1> <ul> <li><p>‘mkinmod’: Use pkgbuild::has_compiler instead of Sys.which(‘gcc’), as the latter will often fail even if Rtools are installed</p></li> <li><p>‘mkinds’: Use roxygen for documenting fields and methods of this R6 class</p></li> </ul> </div> - <div id="mkin-0-9-49-8-2020-01-09" class="section level1"> + <div id="mkin-09498-2020-01-09" class="section level1"> <h1 class="page-header" data-toc-text="0.9.49.8"> -<a href="#mkin-0-9-49-8-2020-01-09" class="anchor"></a>mkin 0.9.49.8 (2020-01-09)<small> 2020-01-09 </small> +<a href="#mkin-09498-2020-01-09" class="anchor"></a>mkin 0.9.49.8 (2020-01-09)<small> 2020-01-09 </small> </h1> <ul> <li><p>‘aw’: Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns</p></li> @@ -249,18 +270,18 @@ <li><p>‘confint.mkinfit’: Make the quadratic approximation the default, as the likelihood profiling takes a lot of time, especially if the fit has more than three parameters</p></li> </ul> </div> - <div id="mkin-0-9-49-7-2019-11-01" class="section level1"> + <div id="mkin-09497-2019-11-01" class="section level1"> <h1 class="page-header" data-toc-text="0.9.49.7"> -<a href="#mkin-0-9-49-7-2019-11-01" class="anchor"></a>mkin 0.9.49.7 (2019-11-01)<small> 2019-11-02 </small> +<a href="#mkin-09497-2019-11-01" class="anchor"></a>mkin 0.9.49.7 (2019-11-01)<small> 2019-11-02 </small> </h1> <ul> <li><p>Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation</p></li> <li><p>Add a ‘nobs’ method for mkinfit objects, enabling the default ‘BIC’ method from the stats package. Also, add a ‘BIC’ method for mmkin column objects.</p></li> </ul> </div> - <div id="mkin-0-9-49-6-2019-10-31" class="section level1"> + <div id="mkin-09496-2019-10-31" class="section level1"> <h1 class="page-header" data-toc-text="0.9.49.6"> -<a href="#mkin-0-9-49-6-2019-10-31" class="anchor"></a>mkin 0.9.49.6 (2019-10-31)<small> 2019-10-31 </small> +<a href="#mkin-09496-2019-10-31" class="anchor"></a>mkin 0.9.49.6 (2019-10-31)<small> 2019-10-31 </small> </h1> <ul> <li><p>Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package</p></li> @@ -278,9 +299,9 @@ <li><p>Support summarizing ‘mkinfit’ objects generated with versions < 0.9.49.5</p></li> </ul> </div> - <div id="mkin-0-9-49-5-2019-07-04" class="section level1"> + <div id="mkin-09495-2019-07-04" class="section level1"> <h1 class="page-header" data-toc-text="0.9.49.5"> -<a href="#mkin-0-9-49-5-2019-07-04" class="anchor"></a>mkin 0.9.49.5 (2019-07-04)<small> 2019-07-04 </small> +<a href="#mkin-09495-2019-07-04" class="anchor"></a>mkin 0.9.49.5 (2019-07-04)<small> 2019-07-04 </small> </h1> <ul> <li><p>Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm ‘d_3’ tries direct minimization and a three-step procedure, and returns the model with the highest likelihood.</p></li> @@ -297,9 +318,9 @@ <li><p>Add example datasets obtained from risk assessment reports published by the European Food Safety Agency.</p></li> </ul> </div> - <div id="mkin-0-9-48-1-2019-03-04" class="section level1"> + <div id="mkin-09481-2019-03-04" class="section level1"> <h1 class="page-header" data-toc-text="0.9.48.1"> -<a href="#mkin-0-9-48-1-2019-03-04" class="anchor"></a>mkin 0.9.48.1 (2019-03-04)<small> 2019-03-04 </small> +<a href="#mkin-09481-2019-03-04" class="anchor"></a>mkin 0.9.48.1 (2019-03-04)<small> 2019-03-04 </small> </h1> <ul> <li><p>Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects</p></li> @@ -314,9 +335,9 @@ <li><p>‘nafta’: Add evaluations according to the NAFTA guidance</p></li> </ul> </div> - <div id="mkin-0-9-47-5-2018-09-14" class="section level1"> + <div id="mkin-09475-2018-09-14" class="section level1"> <h1 class="page-header" data-toc-text="0.9.47.5"> -<a href="#mkin-0-9-47-5-2018-09-14" class="anchor"></a>mkin 0.9.47.5 (2018-09-14)<small> 2018-09-14 </small> +<a href="#mkin-09475-2018-09-14" class="anchor"></a>mkin 0.9.47.5 (2018-09-14)<small> 2018-09-14 </small> </h1> <ul> <li><p>Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows</p></li> @@ -324,27 +345,27 @@ <li><p>Exclude more example code from testing on CRAN to avoid NOTES from long execution times</p></li> </ul> </div> - <div id="mkin-0-9-47-3" class="section level1"> + <div id="mkin-09473" class="section level1"> <h1 class="page-header" data-toc-text="0.9.47.3"> -<a href="#mkin-0-9-47-3" class="anchor"></a>mkin 0.9.47.3<small> Unreleased </small> +<a href="#mkin-09473" class="anchor"></a>mkin 0.9.47.3<small> Unreleased </small> </h1> <ul> <li><p>‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’</p></li> <li><p>Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’</p></li> </ul> </div> - <div id="mkin-0-9-47-2-2018-07-19" class="section level1"> + <div id="mkin-09472-2018-07-19" class="section level1"> <h1 class="page-header" data-toc-text="0.9.47.2"> -<a href="#mkin-0-9-47-2-2018-07-19" class="anchor"></a>mkin 0.9.47.2 (2018-07-19)<small> 2018-07-19 </small> +<a href="#mkin-09472-2018-07-19" class="anchor"></a>mkin 0.9.47.2 (2018-07-19)<small> 2018-07-19 </small> </h1> <ul> <li><p>‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.</p></li> <li><p>‘mkinfit’: Use 1.1 as starting value for N parameter of IORE models to obtain convergence in more difficult cases. Show parameter names when ‘trace_parms’ is ‘TRUE’.</p></li> </ul> </div> - <div id="mkin-0-9-47-1-2018-02-06" class="section level1"> + <div id="mkin-09471-2018-02-06" class="section level1"> <h1 class="page-header" data-toc-text="0.9.47.1"> -<a href="#mkin-0-9-47-1-2018-02-06" class="anchor"></a>mkin 0.9.47.1 (2018-02-06)<small> 2018-02-06 </small> +<a href="#mkin-09471-2018-02-06" class="anchor"></a>mkin 0.9.47.1 (2018-02-06)<small> 2018-02-06 </small> </h1> <ul> <li><p>Skip some tests on CRAN and winbuilder to avoid timeouts</p></li> @@ -355,27 +376,27 @@ <li><p>‘summary.mkinfit’: Show versions of mkin and R used for fitting (not the ones used for the summary) if the fit was generated with mkin >= 0.9.47.1</p></li> </ul> </div> - <div id="mkin-0-9-46-3-2017-11-16" class="section level1"> + <div id="mkin-09463-2017-11-16" class="section level1"> <h1 class="page-header" data-toc-text="0.9.46.3"> -<a href="#mkin-0-9-46-3-2017-11-16" class="anchor"></a>mkin 0.9.46.3 (2017-11-16)<small> 2017-11-16 </small> +<a href="#mkin-09463-2017-11-16" class="anchor"></a>mkin 0.9.46.3 (2017-11-16)<small> 2017-11-16 </small> </h1> <ul> <li><p><code>README.md</code>, <code>vignettes/mkin.Rmd</code>: URLs were updated</p></li> <li><p><code>synthetic_data_for_UBA</code>: Add the code used to generate the data in the interest of reproducibility</p></li> </ul> </div> - <div id="mkin-0-9-46-2-2017-10-10" class="section level1"> + <div id="mkin-09462-2017-10-10" class="section level1"> <h1 class="page-header" data-toc-text="0.9.46.2"> -<a href="#mkin-0-9-46-2-2017-10-10" class="anchor"></a>mkin 0.9.46.2 (2017-10-10)<small> 2017-10-10 </small> +<a href="#mkin-09462-2017-10-10" class="anchor"></a>mkin 0.9.46.2 (2017-10-10)<small> 2017-10-10 </small> </h1> <ul> <li><p>Converted the vignette FOCUS_Z from tex/pdf to markdown/html</p></li> <li><p><code>DESCRIPTION</code>: Add ORCID</p></li> </ul> </div> - <div id="mkin-0-9-46-1-2017-09-14" class="section level1"> + <div id="mkin-09461-2017-09-14" class="section level1"> <h1 class="page-header" data-toc-text="0.9.46.1"> -<a href="#mkin-0-9-46-1-2017-09-14" class="anchor"></a>mkin 0.9.46.1 (2017-09-14)<small> 2017-09-14 </small> +<a href="#mkin-09461-2017-09-14" class="anchor"></a>mkin 0.9.46.1 (2017-09-14)<small> 2017-09-14 </small> </h1> <ul> <li><p><code>plot.mkinfit</code>: Fix scaling of residual plots for the case of separate plots for each observed variable</p></li> @@ -383,17 +404,17 @@ <li><p>Documentation updates</p></li> </ul> </div> - <div id="mkin-0-9-46-2017-07-24" class="section level1"> + <div id="mkin-0946-2017-07-24" class="section level1"> <h1 class="page-header" data-toc-text="0.9.46"> -<a href="#mkin-0-9-46-2017-07-24" class="anchor"></a>mkin 0.9.46 (2017-07-24)<small> 2017-07-29 </small> +<a href="#mkin-0946-2017-07-24" class="anchor"></a>mkin 0.9.46 (2017-07-24)<small> 2017-07-29 </small> </h1> <ul> <li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li> </ul> </div> - <div id="mkin-0-9-45-2-2017-07-24" class="section level1"> + <div id="mkin-09452-2017-07-24" class="section level1"> <h1 class="page-header" data-toc-text="0.9.45.2"> -<a href="#mkin-0-9-45-2-2017-07-24" class="anchor"></a>mkin 0.9.45.2 (2017-07-24)<small> 2017-07-22 </small> +<a href="#mkin-09452-2017-07-24" class="anchor"></a>mkin 0.9.45.2 (2017-07-24)<small> 2017-07-22 </small> </h1> <ul> <li><p>Rename <code>twa</code> to <code>max_twa_parent</code> to avoid conflict with <code>twa</code> from my <code>pfm</code> package</p></li> @@ -402,9 +423,9 @@ <li><p>Switch from <code>microbenchmark</code> to <code>rbenchmark</code> as the former is not supported on all platforms</p></li> </ul> </div> - <div id="mkin-0-9-45-1-2016-12-20" class="section level1"> + <div id="mkin-09451-2016-12-20" class="section level1"> <h1 class="page-header" data-toc-text="0.9.45.1"> -<a href="#mkin-0-9-45-1-2016-12-20" class="anchor"></a>mkin 0.9.45.1 (2016-12-20)<small> Unreleased </small> +<a href="#mkin-09451-2016-12-20" class="anchor"></a>mkin 0.9.45.1 (2016-12-20)<small> Unreleased </small> </h1> <div id="new-features" class="section level2"> <h2 class="hasAnchor"> @@ -414,9 +435,9 @@ </ul> </div> </div> - <div id="mkin-0-9-45-2016-12-08" class="section level1"> + <div id="mkin-0945-2016-12-08" class="section level1"> <h1 class="page-header" data-toc-text="0.9.45"> -<a href="#mkin-0-9-45-2016-12-08" class="anchor"></a>mkin 0.9.45 (2016-12-08)<small> 2016-12-08 </small> +<a href="#mkin-0945-2016-12-08" class="anchor"></a>mkin 0.9.45 (2016-12-08)<small> 2016-12-08 </small> </h1> <div id="minor-changes" class="section level2"> <h2 class="hasAnchor"> @@ -428,9 +449,9 @@ </ul> </div> </div> - <div id="mkin-0-9-44-2016-06-29" class="section level1"> + <div id="mkin-0944-2016-06-29" class="section level1"> <h1 class="page-header" data-toc-text="0.9.44"> -<a href="#mkin-0-9-44-2016-06-29" class="anchor"></a>mkin 0.9.44 (2016-06-29)<small> 2016-06-29 </small> +<a href="#mkin-0944-2016-06-29" class="anchor"></a>mkin 0.9.44 (2016-06-29)<small> 2016-06-29 </small> </h1> <div id="bug-fixes" class="section level2"> <h2 class="hasAnchor"> @@ -440,9 +461,9 @@ </ul> </div> </div> - <div id="mkin-0-9-43-2016-06-28" class="section level1"> + <div id="mkin-0943-2016-06-28" class="section level1"> <h1 class="page-header" data-toc-text="0.9.43"> -<a href="#mkin-0-9-43-2016-06-28" class="anchor"></a>mkin 0.9.43 (2016-06-28)<small> 2016-06-28 </small> +<a href="#mkin-0943-2016-06-28" class="anchor"></a>mkin 0.9.43 (2016-06-28)<small> 2016-06-28 </small> </h1> <div id="major-changes" class="section level2"> <h2 class="hasAnchor"> @@ -479,9 +500,9 @@ </ul> </div> </div> - <div id="mkin-0-9-42-2016-03-25" class="section level1"> + <div id="mkin-0942-2016-03-25" class="section level1"> <h1 class="page-header" data-toc-text="0.9.42"> -<a href="#mkin-0-9-42-2016-03-25" class="anchor"></a>mkin 0.9.42 (2016-03-25)<small> 2016-03-25 </small> +<a href="#mkin-0942-2016-03-25" class="anchor"></a>mkin 0.9.42 (2016-03-25)<small> 2016-03-25 </small> </h1> <div id="major-changes-1" class="section level2"> <h2 class="hasAnchor"> @@ -500,9 +521,9 @@ </ul> </div> </div> - <div id="mkin-0-9-41-2015-11-09" class="section level1"> + <div id="mkin-09-41-2015-11-09" class="section level1"> <h1 class="page-header" data-toc-text="0.9-41"> -<a href="#mkin-0-9-41-2015-11-09" class="anchor"></a>mkin 0.9-41 (2015-11-09)<small> 2015-11-09 </small> +<a href="#mkin-09-41-2015-11-09" class="anchor"></a>mkin 0.9-41 (2015-11-09)<small> 2015-11-09 </small> </h1> <div id="minor-changes-3" class="section level2"> <h2 class="hasAnchor"> @@ -523,9 +544,9 @@ </ul> </div> </div> - <div id="mkin-0-9-40-2015-07-21" class="section level1"> + <div id="mkin-09-40-2015-07-21" class="section level1"> <h1 class="page-header" data-toc-text="0.9-40"> -<a href="#mkin-0-9-40-2015-07-21" class="anchor"></a>mkin 0.9-40 (2015-07-21)<small> 2015-07-21 </small> +<a href="#mkin-09-40-2015-07-21" class="anchor"></a>mkin 0.9-40 (2015-07-21)<small> 2015-07-21 </small> </h1> <div id="bug-fixes-3" class="section level2"> <h2 class="hasAnchor"> @@ -544,9 +565,9 @@ </ul> </div> </div> - <div id="mkin-0-9-39-2015-06-26" class="section level1"> + <div id="mkin-09-39-2015-06-26" class="section level1"> <h1 class="page-header" data-toc-text="0.9-39"> -<a href="#mkin-0-9-39-2015-06-26" class="anchor"></a>mkin 0.9-39 (2015-06-26)<small> 2015-06-26 </small> +<a href="#mkin-09-39-2015-06-26" class="anchor"></a>mkin 0.9-39 (2015-06-26)<small> 2015-06-26 </small> </h1> <div id="major-changes-2" class="section level2"> <h2 class="hasAnchor"> @@ -565,9 +586,9 @@ </ul> </div> </div> - <div id="mkin-0-9-38-2015-06-24" class="section level1"> + <div id="mkin-09-38-2015-06-24" class="section level1"> <h1 class="page-header" data-toc-text="0.9-38"> -<a href="#mkin-0-9-38-2015-06-24" class="anchor"></a>mkin 0.9-38 (2015-06-24)<small> 2015-06-23 </small> +<a href="#mkin-09-38-2015-06-24" class="anchor"></a>mkin 0.9-38 (2015-06-24)<small> 2015-06-23 </small> </h1> <div id="minor-changes-4" class="section level2"> <h2 class="hasAnchor"> @@ -586,9 +607,9 @@ </ul> </div> </div> - <div id="mkin-0-9-36-2015-06-21" class="section level1"> + <div id="mkin-09-36-2015-06-21" class="section level1"> <h1 class="page-header" data-toc-text="0.9-36"> -<a href="#mkin-0-9-36-2015-06-21" class="anchor"></a>mkin 0.9-36 (2015-06-21)<small> 2015-06-21 </small> +<a href="#mkin-09-36-2015-06-21" class="anchor"></a>mkin 0.9-36 (2015-06-21)<small> 2015-06-21 </small> </h1> <div id="major-changes-3" class="section level2"> <h2 class="hasAnchor"> @@ -608,9 +629,9 @@ </ul> </div> </div> - <div id="mkin-0-9-35-2015-05-15" class="section level1"> + <div id="mkin-09-35-2015-05-15" class="section level1"> <h1 class="page-header" data-toc-text="0.9-35"> -<a href="#mkin-0-9-35-2015-05-15" class="anchor"></a>mkin 0.9-35 (2015-05-15)<small> 2015-05-15 </small> +<a href="#mkin-09-35-2015-05-15" class="anchor"></a>mkin 0.9-35 (2015-05-15)<small> 2015-05-15 </small> </h1> <div id="major-changes-4" class="section level2"> <h2 class="hasAnchor"> @@ -640,9 +661,9 @@ </ul> </div> </div> - <div id="mkin-0-9-34-2014-11-22" class="section level1"> + <div id="mkin-09-34-2014-11-22" class="section level1"> <h1 class="page-header" data-toc-text="0.9-34"> -<a href="#mkin-0-9-34-2014-11-22" class="anchor"></a>mkin 0.9-34 (2014-11-22)<small> 2014-11-22 </small> +<a href="#mkin-09-34-2014-11-22" class="anchor"></a>mkin 0.9-34 (2014-11-22)<small> 2014-11-22 </small> </h1> <div id="new-features-2" class="section level2"> <h2 class="hasAnchor"> @@ -662,9 +683,9 @@ </ul> </div> </div> - <div id="mkin-0-9-33-2014-10-22" class="section level1"> + <div id="mkin-09-33-2014-10-22" class="section level1"> <h1 class="page-header" data-toc-text="0.9-33"> -<a href="#mkin-0-9-33-2014-10-22" class="anchor"></a>mkin 0.9-33 (2014-10-22)<small> 2014-10-12 </small> +<a href="#mkin-09-33-2014-10-22" class="anchor"></a>mkin 0.9-33 (2014-10-22)<small> 2014-10-12 </small> </h1> <div id="new-features-3" class="section level2"> <h2 class="hasAnchor"> @@ -695,9 +716,9 @@ </ul> </div> </div> - <div id="mkin-0-9-32-2014-07-24" class="section level1"> + <div id="mkin-09-32-2014-07-24" class="section level1"> <h1 class="page-header" data-toc-text="0.9-32"> -<a href="#mkin-0-9-32-2014-07-24" class="anchor"></a>mkin 0.9-32 (2014-07-24)<small> 2014-07-24 </small> +<a href="#mkin-09-32-2014-07-24" class="anchor"></a>mkin 0.9-32 (2014-07-24)<small> 2014-07-24 </small> </h1> <div id="new-features-4" class="section level2"> <h2 class="hasAnchor"> @@ -705,7 +726,7 @@ <ul> <li><p>The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.</p></li> <li><p>The default for the initial value for the first state value is now taken from the mean of the observations at time zero, if available.</p></li> -<li><p>The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. <code>SFO</code>, or <code>DFOP</code>.</p></li> +<li><p>The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. <code>SFO</code>, or <code>DFOP</code>.</p></li> <li><p>Optimisation method, number of model evaluations and time elapsed during optimisation are given in the summary of mkinfit objects.</p></li> <li><p>The maximum number of iterations in the optimisation algorithm can be specified using the argument <code>maxit.modFit</code> to the mkinfit function.</p></li> <li><p>mkinfit gives a warning when the fit does not converge (does not apply to SANN method). This warning is included in the summary.</p></li> @@ -732,9 +753,9 @@ </ul> </div> </div> - <div id="mkin-0-9-31-2014-07-14" class="section level1"> + <div id="mkin-09-31-2014-07-14" class="section level1"> <h1 class="page-header" data-toc-text="0.9-31"> -<a href="#mkin-0-9-31-2014-07-14" class="anchor"></a>mkin 0.9-31 (2014-07-14)<small> 2014-07-14 </small> +<a href="#mkin-09-31-2014-07-14" class="anchor"></a>mkin 0.9-31 (2014-07-14)<small> 2014-07-14 </small> </h1> <div id="bug-fixes-9" class="section level2"> <h2 class="hasAnchor"> @@ -744,9 +765,9 @@ </ul> </div> </div> - <div id="mkin-0-9-30-2014-07-11" class="section level1"> + <div id="mkin-09-30-2014-07-11" class="section level1"> <h1 class="page-header" data-toc-text="0.9-30"> -<a href="#mkin-0-9-30-2014-07-11" class="anchor"></a>mkin 0.9-30 (2014-07-11)<small> 2014-07-11 </small> +<a href="#mkin-09-30-2014-07-11" class="anchor"></a>mkin 0.9-30 (2014-07-11)<small> 2014-07-11 </small> </h1> <div id="new-features-5" class="section level2"> <h2 class="hasAnchor"> @@ -759,7 +780,7 @@ <h2 class="hasAnchor"> <a href="#major-changes-5" class="anchor"></a>Major changes</h2> <ul> -<li><p>The original and the transformed parameters now have different names (e.g. <code>k_parent</code> and <code>log_k_parent</code>. They also differ in how many they are when we have formation fractions but no pathway to sink.</p></li> +<li><p>The original and the transformed parameters now have different names (e.g. <code>k_parent</code> and <code>log_k_parent</code>. They also differ in how many they are when we have formation fractions but no pathway to sink.</p></li> <li><p>The order of some of the information blocks in <code>print.summary.mkinfit.R()</code> has been ordered in a more logical way.</p></li> </ul> </div> @@ -776,9 +797,9 @@ </ul> </div> </div> - <div id="mkin-0-9-29-2014-06-27" class="section level1"> + <div id="mkin-09-29-2014-06-27" class="section level1"> <h1 class="page-header" data-toc-text="0.9-29"> -<a href="#mkin-0-9-29-2014-06-27" class="anchor"></a>mkin 0.9-29 (2014-06-27)<small> 2014-06-27 </small> +<a href="#mkin-09-29-2014-06-27" class="anchor"></a>mkin 0.9-29 (2014-06-27)<small> 2014-06-27 </small> </h1> <ul> <li><p>R/mkinresplot.R: Make it possible to specify <code>xlim</code></p></li> @@ -786,9 +807,9 @@ <li><p>R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted</p></li> </ul> </div> - <div id="mkin-0-9-28-2014-05-20" class="section level1"> + <div id="mkin-09-28-2014-05-20" class="section level1"> <h1 class="page-header" data-toc-text="0.9-28"> -<a href="#mkin-0-9-28-2014-05-20" class="anchor"></a>mkin 0.9-28 (2014-05-20)<small> 2014-05-20 </small> +<a href="#mkin-09-28-2014-05-20" class="anchor"></a>mkin 0.9-28 (2014-05-20)<small> 2014-05-20 </small> </h1> <ul> <li><p>Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set</p></li> @@ -796,9 +817,9 @@ <li><p>Correct ‘isotropic’ into ‘isometric’ for the ilr transformation</p></li> </ul> </div> - <div id="mkin-0-9-27-2014-05-10" class="section level1"> + <div id="mkin-09-27-2014-05-10" class="section level1"> <h1 class="page-header" data-toc-text="0.9-27"> -<a href="#mkin-0-9-27-2014-05-10" class="anchor"></a>mkin 0.9-27 (2014-05-10)<small> 2014-05-10 </small> +<a href="#mkin-09-27-2014-05-10" class="anchor"></a>mkin 0.9-27 (2014-05-10)<small> 2014-05-10 </small> </h1> <ul> <li><p>Fork the GUI into a separate package <a href="https://github.com/jranke/gmkin">gmkin</a></p></li> @@ -820,9 +841,9 @@ <li><p>Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin</p></li> </ul> </div> - <div id="mkin-0-9-24-2013-11-06" class="section level1"> + <div id="mkin-09-24-2013-11-06" class="section level1"> <h1 class="page-header" data-toc-text="0.9-24"> -<a href="#mkin-0-9-24-2013-11-06" class="anchor"></a>mkin 0.9-24 (2013-11-06)<small> 2013-11-06 </small> +<a href="#mkin-09-24-2013-11-06" class="anchor"></a>mkin 0.9-24 (2013-11-06)<small> 2013-11-06 </small> </h1> <ul> <li><p>Bugfix re-enabling the fixing of any combination of initial values for state variables</p></li> @@ -830,9 +851,9 @@ <li><p>Backtransform fixed ODE parameters for the summary</p></li> </ul> </div> - <div id="mkin-0-9-22-2013-10-26" class="section level1"> + <div id="mkin-09-22-2013-10-26" class="section level1"> <h1 class="page-header" data-toc-text="0.9-22"> -<a href="#mkin-0-9-22-2013-10-26" class="anchor"></a>mkin 0.9-22 (2013-10-26)<small> 2013-10-26 </small> +<a href="#mkin-09-22-2013-10-26" class="anchor"></a>mkin 0.9-22 (2013-10-26)<small> 2013-10-26 </small> </h1> <ul> <li><p>Get rid of the optimisation step in <code>mkinerrmin</code> - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally</p></li> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 2963e810..f9b16e29 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.2.1 +pandoc: 2.9.2.1 pkgdown: 1.6.1 pkgdown_sha: ~ articles: @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-01-25T13:41Z +last_built: 2021-02-06T17:26Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex bca41e2c..17a35806 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png Binary files differindex ff6bc722..2b011ec1 100644 --- a/docs/dev/reference/Rplot003.png +++ b/docs/dev/reference/Rplot003.png diff --git a/docs/dev/reference/Rplot005.png b/docs/dev/reference/Rplot005.png Binary files differindex 5e675828..8c91d61e 100644 --- a/docs/dev/reference/Rplot005.png +++ b/docs/dev/reference/Rplot005.png diff --git a/docs/dev/reference/Rplot006.png b/docs/dev/reference/Rplot006.png Binary files differindex da52f580..730a7481 100644 --- a/docs/dev/reference/Rplot006.png +++ b/docs/dev/reference/Rplot006.png diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html index 515a7c9e..89bb3d89 100644 --- a/docs/dev/reference/confint.mkinfit.html +++ b/docs/dev/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." /> </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -128,7 +128,7 @@ method of Venzon and Moolgavkar (1988)." /> <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> @@ -273,68 +273,69 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"NOT_CRAN"</span><span class='op'>)</span>, <span class='st'>"true"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>1</span> <span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span> - <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fl'>1</span> + <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fl'>1</span> <span class='op'>}</span> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>!=</span> <span class='st'>""</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span> -<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, + use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>SFO_SFO.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_d_1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> user system elapsed -#> 3.900 0.929 3.548 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> +#> 4.258 0.916 3.889 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> <span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span> -<span class='co'># minor interest), we get a nice performance improvement from about 50</span> -<span class='co'># seconds to about 12 seconds if we use at least four cores</span> +<span class='co'># minor interest), we get a nice performance improvement if we use at least 4 cores</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> <span class='warning'>Warning: scheduled cores 3, 2, 1 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#> <span class='error'>Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.009 0.034 0.257</span></div><div class='input'><span class='va'>ci_profile</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.456003640 1.027703e+02 -#> k_parent 0.090911032 1.071578e-01 -#> k_m1 0.003892606 6.702775e-03 -#> f_parent_to_m1 0.471328495 5.611550e-01 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> user system elapsed +#> 1.459 0.088 0.907 </div><div class='input'><span class='va'>ci_profile</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.456003640 1.027703e+02 +#> k_parent_sink 0.040762501 5.549764e-02 +#> k_parent_m1 0.046786482 5.500879e-02 +#> k_m1_sink 0.003892605 6.702778e-03 +#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> <span class='va'>ci_quadratic_transformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833585 102.79311650 -#> k_parent 0.090823771 0.10725430 -#> k_m1 0.004012219 0.00689755 -#> f_parent_to_m1 0.469118824 0.55959615 -#> sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403841640 1.027931e+02 +#> k_parent_sink 0.041033378 5.596269e-02 +#> k_parent_m1 0.046777902 5.511931e-02 +#> k_m1_sink 0.004012217 6.897547e-03 +#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> <span class='va'>ci_quadratic_untransformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833589 1.027931e+02 -#> k_parent 0.090491913 1.069035e-01 -#> k_m1 0.003835485 6.685823e-03 -#> f_parent_to_m1 0.469113477 5.598387e-01 -#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403841645 102.79312449 +#> k_parent_sink 0.040485331 0.05535491 +#> k_parent_m1 0.046611582 0.05494364 +#> k_m1_sink 0.003835483 0.00668582 +#> sigma 2.396089689 3.85491806</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span> <span class='co'># intervals based on the internal parameter transformation are less</span> <span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span> <span class='co'># interval based on the untransformed fit for k_m1_sink</span> <span class='va'>rel_diffs_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_transformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span> <span class='va'>rel_diffs_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_untransformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span> <span class='va'>rel_diffs_transformed</span> <span class='op'><</span> <span class='va'>rel_diffs_untransformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 FALSE FALSE -#> k_parent TRUE TRUE -#> k_m1 FALSE FALSE -#> f_parent_to_m1 TRUE FALSE -#> sigma TRUE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent 0.000960 0.000900 -#> k_m1 0.030700 0.029100 -#> f_parent_to_m1 0.004690 0.002780 -#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent 0.004610 0.002370 -#> k_m1 0.014700 0.002530 -#> f_parent_to_m1 0.004700 0.002350 -#> sigma 0.055000 0.032700</div><div class='input'> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 FALSE FALSE +#> k_parent_sink TRUE FALSE +#> k_parent_m1 TRUE FALSE +#> k_m1_sink FALSE FALSE +#> sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.000541 0.000222 +#> k_parent_sink 0.006650 0.008380 +#> k_parent_m1 0.000183 0.002010 +#> k_m1_sink 0.030700 0.029100 +#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.000541 0.000222 +#> k_parent_sink 0.006800 0.002570 +#> k_parent_m1 0.003740 0.001180 +#> k_m1_sink 0.014700 0.002530 +#> sigma 0.055000 0.032700</div><div class='input'> <span class='co'># Investigate a case with formation fractions</span> <span class='va'>f_d_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> @@ -348,14 +349,14 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> <span class='va'>ci_quadratic_transformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833585 102.79311650 +#> parent_0 96.403833578 102.79311649 #> k_parent 0.090823771 0.10725430 #> k_m1 0.004012219 0.00689755 #> f_parent_to_m1 0.469118824 0.55959615 #> sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> <span class='va'>ci_quadratic_untransformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833589 1.027931e+02 +#> parent_0 96.403833583 1.027931e+02 #> k_parent 0.090491913 1.069035e-01 #> k_m1 0.003835485 6.685823e-03 #> f_parent_to_m1 0.469113477 5.598387e-01 @@ -373,15 +374,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> f_parent_to_m1 TRUE FALSE #> sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217234 +#> parent_0 0.0005408690 0.0002217233 #> k_parent 0.0009598532 0.0009001864 -#> k_m1 0.0307283044 0.0290588365 -#> f_parent_to_m1 0.0046881768 0.0027780063 +#> k_m1 0.0307283041 0.0290588361 +#> f_parent_to_m1 0.0046881769 0.0027780063 #> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217233 -#> k_parent 0.0046102155 0.0023732281 -#> k_m1 0.0146740688 0.0025291817 +#> parent_0 0.0005408689 0.0002217232 +#> k_parent 0.0046102156 0.0023732281 +#> k_m1 0.0146740690 0.0025291820 #> f_parent_to_m1 0.0046995211 0.0023457712 #> sigma 0.0550252516 0.0327066836</div><div class='input'> <span class='co'># The profiling for the following fit does not finish in a reasonable time,</span> @@ -395,18 +396,18 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, error_model_algorithm <span class='op'>=</span> <span class='st'>"direct"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.596126334 106.19944007 -#> k_M1 0.037605408 0.04490759 -#> k_M2 0.008568739 0.01087675 -#> f_parent_to_M1 0.021463787 0.62023881 -#> f_parent_to_M2 0.015166531 0.37975349 -#> k1 0.273897467 0.33388084 -#> k2 0.018614555 0.02250379 -#> g 0.671943606 0.73583278 -#> sigma_low 0.251283766 0.83992113 -#> rsd_high 0.040411014 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> +#> parent_0 94.596039609 106.19954892 +#> k_M1 0.037605368 0.04490762 +#> k_M2 0.008568731 0.01087676 +#> f_parent_to_M1 0.021462489 0.62023882 +#> f_parent_to_M2 0.015165617 0.37975348 +#> k1 0.273897348 0.33388101 +#> k2 0.018614554 0.02250378 +#> g 0.671943411 0.73583305 +#> sigma_low 0.251283495 0.83992077 +#> rsd_high 0.040411024 0.07662008</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59613 106.1994</div><div class='input'><span class='co'># }</span> +#> parent_0 94.59604 106.1995</div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index db702c2e..a13e11a7 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -127,7 +127,7 @@ advantage that the SFORB model can also be used for metabolites." /> <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> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index e038ef5c..7e98aa50 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -175,7 +175,7 @@ </tr><tr> <td> - <p><code><a href="mmkin.html">mmkin()</a></code> </p> + <p><code><a href="mmkin.html">mmkin()</a></code> <code><a href="mmkin.html">print(<i><mmkin></i>)</a></code> </p> </td> <td><p>Fit one or more kinetic models with one or more state variables to one or more datasets</p></td> @@ -297,12 +297,6 @@ 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> diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html index 66539dbd..82c0654f 100644 --- a/docs/dev/reference/logLik.mkinfit.html +++ b/docs/dev/reference/logLik.mkinfit.html @@ -76,7 +76,7 @@ the error model." /> </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -125,7 +125,7 @@ the error model." /> <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> @@ -196,11 +196,11 @@ and the fitted error model parameters.</p> parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span> <span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'><-</span> <span class='va'>FOCUS_2006_D</span> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='va'>f_nw</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># no weighting (weights are unity)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='va'>f_obs</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='va'>f_tc</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nw</span>, <span class='va'>f_obs</span>, <span class='va'>f_tc</span><span class='op'>)</span> + <span class='va'>f_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> + <span class='va'>f_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> + <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nw</span>, <span class='va'>f_obs</span>, <span class='va'>f_tc</span><span class='op'>)</span> </div><div class='output co'>#> df AIC #> f_nw 5 204.4486 #> f_obs 6 205.8727 diff --git a/docs/dev/reference/mkinresplot.html b/docs/dev/reference/mkinresplot.html index 4b2f6bea..2e10d5f6 100644 --- a/docs/dev/reference/mkinresplot.html +++ b/docs/dev/reference/mkinresplot.html @@ -75,7 +75,7 @@ argument show_residuals = TRUE." /> </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -124,7 +124,7 @@ argument show_residuals = TRUE." /> <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> @@ -242,7 +242,7 @@ lines of the mkinfit object, and <code><a href='plot.mkinfit.html'>plot_res</a>< combining the plot of the fit and the residual plot.</p></div> <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - <p>Johannes Ranke</p> + <p>Johannes Ranke and Katrin Lindenberger</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> diff --git a/docs/dev/reference/mmkin-1.png b/docs/dev/reference/mmkin-1.png Binary files differindex 7b7da90a..0db3379f 100644 --- a/docs/dev/reference/mmkin-1.png +++ b/docs/dev/reference/mmkin-1.png diff --git a/docs/dev/reference/mmkin-2.png b/docs/dev/reference/mmkin-2.png Binary files differindex ce2b2af4..024a9892 100644 --- a/docs/dev/reference/mmkin-2.png +++ b/docs/dev/reference/mmkin-2.png diff --git a/docs/dev/reference/mmkin-3.png b/docs/dev/reference/mmkin-3.png Binary files differindex bb96f1b2..a23d7cb9 100644 --- a/docs/dev/reference/mmkin-3.png +++ b/docs/dev/reference/mmkin-3.png diff --git a/docs/dev/reference/mmkin-4.png b/docs/dev/reference/mmkin-4.png Binary files differindex 351b21aa..89975db5 100644 --- a/docs/dev/reference/mmkin-4.png +++ b/docs/dev/reference/mmkin-4.png diff --git a/docs/dev/reference/mmkin-5.png b/docs/dev/reference/mmkin-5.png Binary files differindex c1c05eea..a2f34983 100644 --- a/docs/dev/reference/mmkin-5.png +++ b/docs/dev/reference/mmkin-5.png diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index 651eb9a6..65c91adf 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -75,7 +75,7 @@ datasets specified in its first two arguments." /> </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -124,7 +124,7 @@ datasets specified in its first two arguments." /> <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> @@ -158,7 +158,10 @@ datasets specified in its first two arguments.</p> cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>, cluster <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span> -<span class='op'>)</span></pre> +<span class='op'>)</span> + +<span class='co'># S3 method for mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -189,7 +192,11 @@ for parallel execution.</p></td> </tr> <tr> <th>...</th> - <td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> + <td><p>Not used.</p></td> + </tr> + <tr> + <th>x</th> + <td><p>An mmkin object.</p></td> </tr> </table> @@ -227,19 +234,19 @@ plotting.</p></div> <span class='va'>time_default</span> </div><div class='output co'>#> user system elapsed -#> 4.968 0.427 1.342 </div><div class='input'><span class='va'>time_1</span> +#> 4.438 0.334 1.640 </div><div class='input'><span class='va'>time_1</span> </div><div class='output co'>#> user system elapsed -#> 5.365 0.000 5.368 </div><div class='input'> +#> 5.535 0.004 5.539 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340478 0.2659522 0.7505687 0.2494313 +#> 0.7340481 0.2659519 0.7505683 0.2494317 #> #> $distimes #> DT50 DT90 #> parent 0.877769 2.915885 -#> M1 2.325746 7.725960 -#> M2 33.720083 112.015691 +#> M1 2.325744 7.725956 +#> M2 33.720100 112.015749 #> </div><div class='input'> <span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span><span class='op'>)</span> @@ -266,12 +273,10 @@ plotting.</p></div> #> dataset #> model A B C D #> SFO OK OK OK OK -#> FOMC C OK OK OK +#> FOMC OK OK OK OK #> DFOP OK OK OK OK #> -#> OK: No warnings -#> C: Optimisation did not converge: -#> false convergence (8)</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> +#> OK: No warnings</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> <span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span> <span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span> <span class='co'># }</span> diff --git a/docs/dev/reference/nlme.mmkin-1.png b/docs/dev/reference/nlme.mmkin-1.png Binary files differindex 25bebeca..9186c135 100644 --- a/docs/dev/reference/nlme.mmkin-1.png +++ b/docs/dev/reference/nlme.mmkin-1.png diff --git a/docs/dev/reference/nlme.mmkin-2.png b/docs/dev/reference/nlme.mmkin-2.png Binary files differindex c314c149..d395fe02 100644 --- a/docs/dev/reference/nlme.mmkin-2.png +++ b/docs/dev/reference/nlme.mmkin-2.png diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png Binary files differindex a40b7cad..40518a59 100644 --- a/docs/dev/reference/nlme.mmkin-3.png +++ b/docs/dev/reference/nlme.mmkin-3.png diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index a4d7070a..2649c111 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." /> </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -123,7 +123,7 @@ have been obtained by fitting the same model to a list of datasets." /> <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> @@ -262,6 +262,12 @@ parameters taken from the mmkin object are used</p></td> <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object with additional elements. It also inherits from 'mixed.mmkin'.</p> + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>Note that the convergence of the nlme algorithms depends on the quality +of the data. In degradation kinetics, we often only have few datasets +(e.g. data for few soils) and complicated degradation models, which may +make it impossible to obtain convergence with nlme.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of @@ -284,7 +290,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value #> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 -#> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> +#> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: @@ -312,7 +318,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as </div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 10.79857 100.7937 30.34192 4.193937 43.85442 +#> parent 10.79857 100.7937 30.34193 4.193938 43.85443 #> </div><div class='input'> <span class='va'>ds_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span> @@ -335,16 +341,17 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class='co'># f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])</span> <span class='co'>#plot(f_nlme_sfo_sfo_ff)</span> - <span class='co'># With the log-Cholesky parameterization, this converges in 11</span> - <span class='co'># iterations and around 100 seconds, but without tweaking control</span> - <span class='co'># parameters (with pdDiag, increasing the tolerance and pnlsMaxIter was</span> - <span class='co'># necessary)</span> - <span class='va'>f_nlme_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in nlme.formula(model = value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_A1, f_parent_qlogis, log_k1, log_k2, g_qlogis), data = structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L ), .Label = c("1", "2", "3", "4", "5"), class = c("ordered", "factor")), name = c("parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0, 0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2, 96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18, 10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 4.3, 4.6, 7, 7.2, 8.2, 8, 11, 13.7, 11.5, 12.7, 14.9, 14.5, 12.1, 12.3, 9.9, 10.2, 8.8, 7.8, 93.6, 92.3, 87, 82.2, 74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1, 29, 26.5, 27.6, 3.9, 3.1, 6.9, 6.6, 10.4, 8.3, 14.4, 13.7, 22.1, 22.3, 27.5, 25.4, 28, 26.6, 25.8, 25.3, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1, 10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 9.6, 7.7, 15, 15.1, 21.2, 21.1, 19.7, 18.9, 17.5, 15.9, 9.5, 9.8, 6.2, 6.1, 99.8, 98.3, 77.1, 77.2, 59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3, 2.9, 2, 1.8, 2, 2.2, 4.2, 3.9, 7.4, 7.9, 14.5, 13.7, 14.2, 12.2, 13.7, 13.2, 13.6, 15.4, 10.4, 11.6, 10, 9.5, 9.1, 9, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6, 65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3, 3.3, 3.4, 3.9, 2.9, 6.4, 7.2, 9.1, 8.5, 11.7, 12, 13.3, 13.2, 14.3, 12.1)), row.names = c(NA, -170L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = value ~ time | ds, FUN = function (x) max(x, na.rm = TRUE), order.groups = FALSE), start = list( fixed = c(parent_0 = 93.8101519326534, log_k_A1 = -9.76474551635931, f_parent_qlogis = -0.971114801595408, log_k1 = -1.87993711571859, log_k2 = -4.27081421366622, g_qlogis = 0.135644115277507 ), random = list(ds = structure(c(2.56569977430371, -3.49441920289139, -3.32614443321494, 4.35347873814922, -0.0986148763466161, 4.65850590018027, 1.8618544764481, 6.12693257601545, 4.91792724701579, -17.5652201996596, -0.466203822618637, 0.746660653597927, 0.282193987271096, -0.42053488943072, -0.142115928819667, 0.369240076779088, -1.38985563501659, 1.02592753494098, 0.73090914081534, -0.736221117518819, 0.768170629350299, -1.89347658079869, 1.72168783460352, 0.844607177798114, -1.44098906095325, -0.377731855445672, 0.168180098477565, 0.469683412912104, 0.500717664434525, -0.760849320378522), .Dim = 5:6, .Dimnames = list(c("1", "2", "3", "4", "5"), c("parent_0", "log_k_A1", "f_parent_qlogis", "log_k1", "log_k2", "g_qlogis"))))), fixed = list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = structure(list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), class = "listForm"), Dimnames = list(NULL, NULL))): maximum number of iterations (maxIter = 50) reached without convergence</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 49.95 16.5 44.08</span></div><div class='input'> + <span class='co'># For the following, we need to increase pnlsMaxIter and the tolerance</span> + <span class='co'># to get convergence</span> + <span class='va'>f_nlme_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, + control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span><span class='op'>)</span> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in plot(f_nlme_dfop_sfo): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'> +</div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'> +</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value +#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 +#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3273 <.0001</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_sink parent_A1 A1_sink @@ -355,7 +362,15 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> parent 19.13518 63.5657 #> A1 66.02155 219.3189 #> </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in endpoints(f_nlme_dfop_sfo): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'> +</div><div class='output co'>#> $ff +#> parent_A1 parent_sink +#> 0.2768575 0.7231425 +#> +#> $distimes +#> DT50 DT90 DT50back DT50_k1 DT50_k2 +#> parent 11.07091 104.6320 31.49737 4.462384 46.20825 +#> A1 162.30492 539.1653 NA NA NA +#> </div><div class='input'> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span> <span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span> <span class='co'># but need tweeking of control values and sometimes do not converge</span> @@ -381,7 +396,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Fixed effects: #> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> parent_0 log_k1 log_k2 g_qlogis -#> 94.04775 -1.82340 -4.16715 0.05685 +#> 94.04774 -1.82340 -4.16716 0.05686 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) @@ -395,10 +410,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 2.23224114 0.01262341 </div><div class='input'> - <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>, - <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, - <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> +#> 2.23223147 0.01262395 </div><div class='input'> + <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> <span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood @@ -429,18 +442,21 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Formula: ~1 | name #> Parameter estimates: #> parent A1 -#> 1.0000000 0.2050003 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in nlme.formula(model = value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_A1, f_parent_qlogis, log_k1, log_k2, g_qlogis), data = structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L ), .Label = c("1", "2", "3", "4", "5"), class = c("ordered", "factor")), name = c("parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0, 0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2, 96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18, 10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 4.3, 4.6, 7, 7.2, 8.2, 8, 11, 13.7, 11.5, 12.7, 14.9, 14.5, 12.1, 12.3, 9.9, 10.2, 8.8, 7.8, 93.6, 92.3, 87, 82.2, 74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1, 29, 26.5, 27.6, 3.9, 3.1, 6.9, 6.6, 10.4, 8.3, 14.4, 13.7, 22.1, 22.3, 27.5, 25.4, 28, 26.6, 25.8, 25.3, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1, 10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 9.6, 7.7, 15, 15.1, 21.2, 21.1, 19.7, 18.9, 17.5, 15.9, 9.5, 9.8, 6.2, 6.1, 99.8, 98.3, 77.1, 77.2, 59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3, 2.9, 2, 1.8, 2, 2.2, 4.2, 3.9, 7.4, 7.9, 14.5, 13.7, 14.2, 12.2, 13.7, 13.2, 13.6, 15.4, 10.4, 11.6, 10, 9.5, 9.1, 9, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6, 65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3, 3.3, 3.4, 3.9, 2.9, 6.4, 7.2, 9.1, 8.5, 11.7, 12, 13.3, 13.2, 14.3, 12.1)), row.names = c(NA, -170L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = value ~ time | ds, FUN = function (x) max(x, na.rm = TRUE), order.groups = FALSE), start = list( fixed = c(parent_0 = 93.4272167134207, log_k_A1 = -9.71590717106959, f_parent_qlogis = -0.953712099744438, log_k1 = -1.95256957646888, log_k2 = -4.42919226610318, g_qlogis = 0.193023137298073 ), random = list(ds = structure(c(2.85557330683041, -3.87630303729395, -2.78062140212751, 4.82042042600536, -1.01906929341432, 4.613992019697, 2.05871276943309, 6.0766404049189, 4.86471337131288, -17.6140585653619, -0.480721175257541, 0.773079218835614, 0.260464433006093, -0.440615012802434, -0.112207463781733, 0.445812953745225, -1.49588630006094, 1.13602040717272, 0.801850880762046, -0.887797941619048, 0.936480292463262, -2.43093808171905, 1.91256225793793, 0.984827519864443, -1.40293198854659, -0.455176326336681, 0.376355651864385, 0.343919720700401, 0.46329187713133, -0.728390923359434 ), .Dim = 5:6, .Dimnames = list(c("1", "2", "3", "4", "5"), c("parent_0", "log_k_A1", "f_parent_qlogis", "log_k1", "log_k2", "g_qlogis"))))), fixed = list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = structure(list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), class = "listForm"), Dimnames = list(NULL, NULL)), weights = structure(numeric(0), formula = ~1 | name, class = c("varIdent", "varFunc"))): maximum number of iterations (maxIter = 50) reached without convergence</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 59.38 16.5 53.5</span></div><div class='input'> - <span class='va'>f_2_tc</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>, - <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, - <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> - <span class='co'># f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # stops with error message</span> - <span class='va'>f_nlme_dfop_sfo_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#> <span class='error'>Error in X[, fmap[[nm]]] <- gradnm: number of items to replace is not a multiple of replacement length</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 6.363 2.688 5.469</span></div><div class='input'> <span class='co'># We get warnings about false convergence in the LME step in several iterations</span> - <span class='co'># but as the last such warning occurs in iteration 25 and we have 28 iterations</span> - <span class='co'># we can ignore these</span> - <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_dfop_sfo_obs</span>, <span class='va'>f_nlme_dfop_sfo_tc</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs, f_nlme_dfop_sfo_tc): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'> +#> 1.0000000 0.2049995 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, + control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span><span class='op'>)</span> + + <span class='va'>f_2_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> + <span class='co'># f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</span> + <span class='co'># f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],</span> + <span class='co'># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</span> + + <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_dfop_sfo_obs</span><span class='op'>)</span> +</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio +#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 +#> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093 +#> p-value +#> f_nlme_dfop_sfo +#> f_nlme_dfop_sfo_obs <.0001</div><div class='input'> <span class='co'># }</span> </div></pre> </div> diff --git a/docs/dev/reference/plot.mixed.mmkin-1.png b/docs/dev/reference/plot.mixed.mmkin-1.png Binary files differindex 5cb33214..9c9a2211 100644 --- a/docs/dev/reference/plot.mixed.mmkin-1.png +++ b/docs/dev/reference/plot.mixed.mmkin-1.png diff --git a/docs/dev/reference/plot.mixed.mmkin-2.png b/docs/dev/reference/plot.mixed.mmkin-2.png Binary files differindex c0d67204..0f66ff0f 100644 --- a/docs/dev/reference/plot.mixed.mmkin-2.png +++ b/docs/dev/reference/plot.mixed.mmkin-2.png diff --git a/docs/dev/reference/plot.mixed.mmkin-3.png b/docs/dev/reference/plot.mixed.mmkin-3.png Binary files differindex 5e00afe6..34212f1c 100644 --- a/docs/dev/reference/plot.mixed.mmkin-3.png +++ b/docs/dev/reference/plot.mixed.mmkin-3.png diff --git a/docs/dev/reference/plot.mixed.mmkin-4.png b/docs/dev/reference/plot.mixed.mmkin-4.png Binary files differindex 6a5f3b9c..c1450d24 100644 --- a/docs/dev/reference/plot.mixed.mmkin-4.png +++ b/docs/dev/reference/plot.mixed.mmkin-4.png diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 55c411e7..601e1554 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -161,7 +161,7 @@ maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'><=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'><=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>, nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>, - rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>, + rel.height.legend <span class='op'>=</span> <span class='fl'>0.02</span> <span class='op'>+</span> <span class='fl'>0.07</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>, rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>, pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>, col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>, @@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.</p></td> </div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='va'>f_saem</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span>, transformations <span class='op'>=</span> <span class='st'>"saemix"</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Dec 21 05:58:23 2020" +#> [1] "Sat Feb 6 18:29:17 2021" #> .... #> Minimisation finished -#> [1] "Mon Dec 21 05:58:30 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span> +#> [1] "Sat Feb 6 18:29:23 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span> </div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># We can overlay the two variants if we generate predictions</span> <span class='va'>pred_nlme</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>, diff --git a/docs/dev/reference/saem-3.png b/docs/dev/reference/saem-3.png Binary files differindex 6a32cda1..4474b1f1 100644 --- a/docs/dev/reference/saem-3.png +++ b/docs/dev/reference/saem-3.png diff --git a/docs/dev/reference/saem-5.png b/docs/dev/reference/saem-5.png Binary files differindex 6e6e0f91..27ed3f8f 100644 --- a/docs/dev/reference/saem-5.png +++ b/docs/dev/reference/saem-5.png diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 59589378..4578db2a 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." /> </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -261,27 +261,27 @@ using <a href='mmkin.html'>mmkin</a>.</p> state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 25 14:41:42 2021" +#> [1] "Sat Feb 6 18:29:26 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 25 14:41:43 2021"</div><div class='input'> +#> [1] "Sat Feb 6 18:29:27 2021"</div><div class='input'> <span class='va'>f_mmkin_parent</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 25 14:41:45 2021" +#> [1] "Sat Feb 6 18:29:28 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 25 14:41:46 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Sat Feb 6 18:29:30 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 25 14:41:47 2021" +#> [1] "Sat Feb 6 18:29:30 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 25 14:41:49 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Sat Feb 6 18:29:32 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 25 14:41:49 2021" +#> [1] "Sat Feb 6 18:29:32 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 25 14:41:52 2021"</div><div class='input'> +#> [1] "Sat Feb 6 18:29:35 2021"</div><div class='input'> <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span> <span class='co'># functions from saemix</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span> @@ -324,10 +324,10 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='va'>f_mmkin_parent_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>f_saem_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 25 14:41:55 2021" +#> [1] "Sat Feb 6 18:29:37 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 25 14:42:00 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +#> [1] "Sat Feb 6 18:29:42 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> <span class='error'>Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'> <span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> @@ -346,15 +346,15 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='co'># four minutes</span> <span class='va'>f_saem_sfo_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 25 14:42:02 2021" +#> [1] "Sat Feb 6 18:29:44 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 25 14:42:07 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Sat Feb 6 18:29:48 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 25 14:42:08 2021" +#> [1] "Sat Feb 6 18:29:49 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 25 14:42:17 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [1] "Sat Feb 6 18:29:57 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -395,10 +395,10 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> SD.g_qlogis 0.44771 -0.86417 1.7596</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span> </div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 0.9.50.4 +#> mkin version used for pre-fitting: 1.0.1.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Jan 25 14:42:18 2021 -#> Date of summary: Mon Jan 25 14:42:18 2021 +#> Date of fit: Sat Feb 6 18:29:57 2021 +#> Date of summary: Sat Feb 6 18:29:58 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -413,7 +413,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.954 s using 300, 100 iterations +#> Fitted in 8.539 s using 300, 100 iterations #> #> Variance model: Constant variance #> @@ -489,12 +489,12 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> Dataset 6 parent 3 69.2 71.32042 2.12042 1.883 1.125873 #> Dataset 6 parent 6 58.1 56.45256 -1.64744 1.883 -0.874739 #> Dataset 6 parent 6 56.6 56.45256 -0.14744 1.883 -0.078288 -#> Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045256 +#> Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045257 #> Dataset 6 parent 10 43.4 44.48523 1.08523 1.883 0.576224 #> Dataset 6 parent 20 33.3 29.75774 -3.54226 1.883 -1.880826 #> Dataset 6 parent 20 29.2 29.75774 0.55774 1.883 0.296141 #> Dataset 6 parent 34 17.6 19.35710 1.75710 1.883 0.932966 -#> Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720578 +#> Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720579 #> Dataset 6 parent 55 10.5 10.48443 -0.01557 1.883 -0.008266 #> Dataset 6 parent 55 9.3 10.48443 1.18443 1.883 0.628895 #> Dataset 6 parent 90 4.5 3.78622 -0.71378 1.883 -0.378995 @@ -560,9 +560,9 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> Dataset 8 parent 1 64.9 67.73197 2.83197 1.883 1.503686 #> Dataset 8 parent 1 66.2 67.73197 1.53197 1.883 0.813428 #> Dataset 8 parent 3 43.5 41.58448 -1.91552 1.883 -1.017081 -#> Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335661 +#> Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335662 #> Dataset 8 parent 8 18.3 19.62286 1.32286 1.883 0.702395 -#> Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808589 +#> Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808588 #> Dataset 8 parent 14 10.2 10.77819 0.57819 1.883 0.306999 #> Dataset 8 parent 14 10.8 10.77819 -0.02181 1.883 -0.011582 #> Dataset 8 parent 27 4.9 3.26977 -1.63023 1.883 -0.865599 @@ -575,13 +575,13 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> Dataset 8 A1 1 7.7 7.61539 -0.08461 1.883 -0.044923 #> Dataset 8 A1 3 15.0 15.47954 0.47954 1.883 0.254622 #> Dataset 8 A1 3 15.1 15.47954 0.37954 1.883 0.201525 -#> Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517076 +#> Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517075 #> Dataset 8 A1 8 21.1 20.22616 -0.87384 1.883 -0.463979 #> Dataset 8 A1 14 19.7 20.00067 0.30067 1.883 0.159645 #> Dataset 8 A1 14 18.9 20.00067 1.10067 1.883 0.584419 -#> Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593929 -#> Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255619 -#> Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400123 +#> Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593928 +#> Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255620 +#> Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400124 #> Dataset 8 A1 48 9.8 10.25357 0.45357 1.883 0.240833 #> Dataset 8 A1 70 6.2 5.95728 -0.24272 1.883 -0.128878 #> Dataset 8 A1 70 6.1 5.95728 -0.14272 1.883 -0.075781 @@ -622,7 +622,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> Dataset 9 A1 91 10.0 10.09177 0.09177 1.883 0.048727 #> Dataset 9 A1 91 9.5 10.09177 0.59177 1.883 0.314211 #> Dataset 9 A1 120 9.1 7.91379 -1.18621 1.883 -0.629841 -#> Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576745 +#> Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576744 #> Dataset 10 parent 0 96.1 93.65257 -2.44743 1.883 -1.299505 #> Dataset 10 parent 0 94.3 93.65257 -0.64743 1.883 -0.343763 #> Dataset 10 parent 8 73.9 77.85906 3.95906 1.883 2.102132 diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 722415fb..93e1365d 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.</p> quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span> <span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:40 2021" +#> [1] "Sat Feb 6 18:30:00 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:53 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +#> [1] "Sat Feb 6 18:30:11 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 0.9.50.4 +#> mkin version used for pre-fitting: 1.0.1.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Jan 11 12:42:54 2021 -#> Date of summary: Mon Jan 11 12:42:54 2021 +#> Date of fit: Sat Feb 6 18:30:12 2021 +#> Date of summary: Sat Feb 6 18:30:12 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 13.298 s using 300, 100 iterations +#> Fitted in 11.769 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> @@ -291,7 +291,7 @@ saemix authors for the parts inherited from saemix.</p> #> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 #> 101.65645 -4.05368 -0.94311 -2.35943 -4.07006 #> g_qlogis -#> -0.01133 +#> -0.01132 #> #> Fixed degradation parameter values: #> None @@ -299,232 +299,232 @@ saemix authors for the parts inherited from saemix.</p> #> Results: #> #> Likelihood computed by importance sampling -#> AIC BIC logLik -#> 830 824.5 -401 +#> AIC BIC logLik +#> 829.3 823.9 -400.7 #> #> Optimised parameters: -#> est. lower upper -#> parent_0 101.4423 97.862 105.0224 -#> log_k_m1 -4.0703 -4.191 -3.9495 -#> f_parent_qlogis -0.9539 -1.313 -0.5949 -#> log_k1 -2.9724 -3.811 -2.1342 -#> log_k2 -3.4977 -4.206 -2.7895 -#> g_qlogis -0.0449 -1.116 1.0262 +#> est. lower upper +#> parent_0 101.29457 97.855 104.7344 +#> log_k_m1 -4.06337 -4.182 -3.9445 +#> f_parent_qlogis -0.94546 -1.307 -0.5841 +#> log_k1 -2.98794 -3.844 -2.1321 +#> log_k2 -3.47891 -4.253 -2.7050 +#> g_qlogis -0.03211 -1.157 1.0931 #> #> Correlation: #> prnt_0 lg_k_1 f_prn_ log_k1 log_k2 -#> log_k_m1 -0.207 -#> f_parent_qlogis -0.148 0.202 -#> log_k1 0.040 -0.038 -0.022 -#> log_k2 0.022 -0.015 -0.009 0.001 -#> g_qlogis -0.012 0.005 0.011 -0.173 -0.130 +#> log_k_m1 -0.202 +#> f_parent_qlogis -0.145 0.195 +#> log_k1 0.094 -0.099 -0.049 +#> log_k2 -0.042 0.056 0.024 -0.097 +#> g_qlogis -0.005 0.000 0.007 -0.160 -0.113 #> #> Random effects: -#> est. lower upper -#> SD.parent_0 2.88564 -0.5163 6.2876 -#> SD.log_k_m1 0.08502 -0.0427 0.2127 -#> SD.f_parent_qlogis 0.38857 0.1350 0.6421 -#> SD.log_k1 0.92338 0.3296 1.5172 -#> SD.log_k2 0.78644 0.2817 1.2912 -#> SD.g_qlogis 0.34614 -0.8727 1.5650 +#> est. lower upper +#> SD.parent_0 2.70085 -0.64980 6.0515 +#> SD.log_k_m1 0.08408 -0.04023 0.2084 +#> SD.f_parent_qlogis 0.39215 0.13695 0.6473 +#> SD.log_k1 0.89280 0.27466 1.5109 +#> SD.log_k2 0.82387 0.26388 1.3838 +#> SD.g_qlogis 0.36468 -0.86978 1.5991 #> #> Variance model: #> est. lower upper -#> a.1 0.65859 0.49250 0.82469 -#> b.1 0.06411 0.05006 0.07817 +#> a.1 0.65724 0.49361 0.82086 +#> b.1 0.06434 0.05034 0.07835 #> #> Backtransformed parameters: #> est. lower upper -#> parent_0 101.44231 97.86220 105.02241 -#> k_m1 0.01707 0.01513 0.01926 -#> f_parent_to_m1 0.27811 0.21201 0.35551 -#> k1 0.05118 0.02213 0.11834 -#> k2 0.03027 0.01491 0.06145 -#> g 0.48878 0.24675 0.73618 +#> parent_0 101.29457 97.85477 104.73437 +#> k_m1 0.01719 0.01526 0.01936 +#> f_parent_to_m1 0.27980 0.21302 0.35798 +#> k1 0.05039 0.02141 0.11859 +#> k2 0.03084 0.01422 0.06687 +#> g 0.49197 0.23916 0.74896 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.2781 -#> parent_sink 0.7219 +#> parent_m1 0.2798 +#> parent_sink 0.7202 #> #> Estimated disappearance times: #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 17.53 61.64 18.55 13.54 22.9 -#> m1 40.60 134.88 NA NA NA +#> parent 17.49 61.05 18.38 13.76 22.47 +#> m1 40.32 133.94 NA NA NA #> #> Data: -#> ds name time observed predicted residual std standardized -#> ds 1 parent 0 89.8 9.869e+01 8.894553 6.3618 1.398124 -#> ds 1 parent 0 104.1 9.869e+01 -5.405447 6.3618 -0.849676 -#> ds 1 parent 1 88.7 9.413e+01 5.426448 6.0706 0.893897 -#> ds 1 parent 1 95.5 9.413e+01 -1.373552 6.0706 -0.226265 -#> ds 1 parent 3 81.8 8.576e+01 3.961821 5.5377 0.715422 -#> ds 1 parent 3 94.5 8.576e+01 -8.738179 5.5377 -1.577932 -#> ds 1 parent 7 71.5 7.168e+01 0.184828 4.6429 0.039809 -#> ds 1 parent 7 70.3 7.168e+01 1.384828 4.6429 0.298270 -#> ds 1 parent 14 54.2 5.351e+01 -0.688235 3.4934 -0.197008 -#> ds 1 parent 14 49.6 5.351e+01 3.911765 3.4934 1.119747 -#> ds 1 parent 28 31.5 3.209e+01 0.590445 2.1603 0.273322 -#> ds 1 parent 28 28.8 3.209e+01 3.290445 2.1603 1.523177 -#> ds 1 parent 60 12.1 1.272e+01 0.618158 1.0481 0.589761 -#> ds 1 parent 60 13.6 1.272e+01 -0.881842 1.0481 -0.841332 -#> ds 1 parent 90 6.2 6.085e+00 -0.115212 0.7655 -0.150512 -#> ds 1 parent 90 8.3 6.085e+00 -2.215212 0.7655 -2.893953 -#> ds 1 parent 120 2.2 3.009e+00 0.809439 0.6863 1.179470 -#> ds 1 parent 120 2.4 3.009e+00 0.609439 0.6863 0.888041 -#> ds 1 m1 1 0.3 1.129e+00 0.828817 0.6626 1.250938 -#> ds 1 m1 1 0.2 1.129e+00 0.928817 0.6626 1.401869 -#> ds 1 m1 3 2.2 3.141e+00 0.940880 0.6887 1.366187 -#> ds 1 m1 3 3.0 3.141e+00 0.140880 0.6887 0.204562 -#> ds 1 m1 7 6.5 6.326e+00 -0.174162 0.7735 -0.225175 -#> ds 1 m1 7 5.0 6.326e+00 1.325838 0.7735 1.714181 -#> ds 1 m1 14 10.2 9.883e+00 -0.317417 0.9139 -0.347326 -#> ds 1 m1 14 9.5 9.883e+00 0.382583 0.9139 0.418631 -#> ds 1 m1 28 12.2 1.251e+01 0.309856 1.0378 0.298572 -#> ds 1 m1 28 13.4 1.251e+01 -0.890144 1.0378 -0.857726 -#> ds 1 m1 60 11.8 1.086e+01 -0.940009 0.9584 -0.980812 -#> ds 1 m1 60 13.2 1.086e+01 -2.340009 0.9584 -2.441581 -#> ds 1 m1 90 6.6 7.823e+00 1.222977 0.8278 1.477332 -#> ds 1 m1 90 9.3 7.823e+00 -1.477023 0.8278 -1.784214 -#> ds 1 m1 120 3.5 5.315e+00 1.815201 0.7415 2.447906 -#> ds 1 m1 120 5.4 5.315e+00 -0.084799 0.7415 -0.114356 -#> ds 2 parent 0 118.0 1.031e+02 -14.876736 6.6443 -2.239038 -#> ds 2 parent 0 99.8 1.031e+02 3.323264 6.6443 0.500171 -#> ds 2 parent 1 90.2 9.757e+01 7.371379 6.2902 1.171891 -#> ds 2 parent 1 94.6 9.757e+01 2.971379 6.2902 0.472386 -#> ds 2 parent 3 96.1 8.788e+01 -8.222746 5.6724 -1.449599 -#> ds 2 parent 3 78.4 8.788e+01 9.477254 5.6724 1.670758 -#> ds 2 parent 7 77.9 7.293e+01 -4.972272 4.7218 -1.053054 -#> ds 2 parent 7 77.7 7.293e+01 -4.772272 4.7218 -1.010697 -#> ds 2 parent 14 56.0 5.602e+01 0.016773 3.6513 0.004594 -#> ds 2 parent 14 54.7 5.602e+01 1.316773 3.6513 0.360633 -#> ds 2 parent 28 36.6 3.855e+01 1.945779 2.5575 0.760803 -#> ds 2 parent 28 36.8 3.855e+01 1.745779 2.5575 0.682603 -#> ds 2 parent 60 22.1 2.101e+01 -1.086693 1.4996 -0.724663 -#> ds 2 parent 60 24.7 2.101e+01 -3.686693 1.4996 -2.458475 -#> ds 2 parent 90 12.4 1.246e+01 0.058759 1.0353 0.056757 -#> ds 2 parent 90 10.8 1.246e+01 1.658759 1.0353 1.602256 -#> ds 2 parent 120 6.8 7.406e+00 0.606226 0.8119 0.746659 -#> ds 2 parent 120 7.9 7.406e+00 -0.493774 0.8119 -0.608157 -#> ds 2 m1 1 1.3 1.438e+00 0.138236 0.6650 0.207869 -#> ds 2 m1 3 3.7 3.879e+00 0.178617 0.7040 0.253726 -#> ds 2 m1 3 4.7 3.879e+00 -0.821383 0.7040 -1.166780 -#> ds 2 m1 7 8.1 7.389e+00 -0.710951 0.8113 -0.876337 -#> ds 2 m1 7 7.9 7.389e+00 -0.510951 0.8113 -0.629812 -#> ds 2 m1 14 10.1 1.069e+01 0.593533 0.9507 0.624328 -#> ds 2 m1 14 10.3 1.069e+01 0.393533 0.9507 0.413951 -#> ds 2 m1 28 10.7 1.240e+01 1.703647 1.0325 1.649956 -#> ds 2 m1 28 12.2 1.240e+01 0.203647 1.0325 0.197229 -#> ds 2 m1 60 10.7 1.055e+01 -0.147672 0.9442 -0.156405 -#> ds 2 m1 60 12.5 1.055e+01 -1.947672 0.9442 -2.062848 -#> ds 2 m1 90 9.1 8.010e+00 -1.090041 0.8351 -1.305210 -#> ds 2 m1 90 7.4 8.010e+00 0.609959 0.8351 0.730362 -#> ds 2 m1 120 6.1 5.793e+00 -0.306797 0.7561 -0.405759 -#> ds 2 m1 120 4.5 5.793e+00 1.293203 0.7561 1.710347 -#> ds 3 parent 0 106.2 1.035e+02 -2.712344 6.6675 -0.406801 -#> ds 3 parent 0 106.9 1.035e+02 -3.412344 6.6675 -0.511788 -#> ds 3 parent 1 107.4 9.548e+01 -11.924044 6.1566 -1.936801 -#> ds 3 parent 1 96.1 9.548e+01 -0.624044 6.1566 -0.101362 -#> ds 3 parent 3 79.4 8.246e+01 3.056105 5.3274 0.573662 -#> ds 3 parent 3 82.6 8.246e+01 -0.143895 5.3274 -0.027010 -#> ds 3 parent 7 63.9 6.489e+01 0.991141 4.2122 0.235304 -#> ds 3 parent 7 62.4 6.489e+01 2.491141 4.2122 0.591416 -#> ds 3 parent 14 51.0 4.869e+01 -2.306824 3.1906 -0.723013 -#> ds 3 parent 14 47.1 4.869e+01 1.593176 3.1906 0.499338 -#> ds 3 parent 28 36.1 3.480e+01 -1.304261 2.3260 -0.560722 -#> ds 3 parent 28 36.6 3.480e+01 -1.804261 2.3260 -0.775679 -#> ds 3 parent 60 20.1 1.988e+01 -0.221952 1.4346 -0.154719 -#> ds 3 parent 60 19.8 1.988e+01 0.078048 1.4346 0.054406 -#> ds 3 parent 90 11.3 1.194e+01 0.642458 1.0099 0.636132 -#> ds 3 parent 90 10.7 1.194e+01 1.242458 1.0099 1.230224 -#> ds 3 parent 120 8.2 7.176e+00 -1.023847 0.8034 -1.274423 -#> ds 3 parent 120 7.3 7.176e+00 -0.123847 0.8034 -0.154158 -#> ds 3 m1 0 0.8 8.527e-13 -0.800000 0.6586 -1.214712 -#> ds 3 m1 1 1.8 1.856e+00 0.055925 0.6693 0.083562 -#> ds 3 m1 1 2.3 1.856e+00 -0.444075 0.6693 -0.663537 -#> ds 3 m1 3 4.2 4.780e+00 0.580164 0.7264 0.798676 -#> ds 3 m1 3 4.1 4.780e+00 0.680164 0.7264 0.936340 -#> ds 3 m1 7 6.8 8.410e+00 1.609920 0.8512 1.891455 -#> ds 3 m1 7 10.1 8.410e+00 -1.690080 0.8512 -1.985633 -#> ds 3 m1 14 11.4 1.098e+01 -0.424444 0.9638 -0.440389 -#> ds 3 m1 14 12.8 1.098e+01 -1.824444 0.9638 -1.892979 -#> ds 3 m1 28 11.5 1.142e+01 -0.079336 0.9848 -0.080558 -#> ds 3 m1 28 10.6 1.142e+01 0.820664 0.9848 0.833311 -#> ds 3 m1 60 7.5 9.110e+00 1.610231 0.8803 1.829222 -#> ds 3 m1 60 8.6 9.110e+00 0.510231 0.8803 0.579622 -#> ds 3 m1 90 7.3 6.799e+00 -0.501085 0.7898 -0.634463 -#> ds 3 m1 90 8.1 6.799e+00 -1.301085 0.7898 -1.647404 -#> ds 3 m1 120 5.3 4.868e+00 -0.431505 0.7288 -0.592064 -#> ds 3 m1 120 3.8 4.868e+00 1.068495 0.7288 1.466073 -#> ds 4 parent 0 104.7 9.926e+01 -5.444622 6.3975 -0.851049 -#> ds 4 parent 0 88.3 9.926e+01 10.955378 6.3975 1.712436 -#> ds 4 parent 1 94.2 9.618e+01 1.978413 6.2013 0.319030 -#> ds 4 parent 1 94.6 9.618e+01 1.578413 6.2013 0.254527 -#> ds 4 parent 3 78.1 9.037e+01 12.268550 5.8311 2.103985 -#> ds 4 parent 3 96.5 9.037e+01 -6.131450 5.8311 -1.051508 -#> ds 4 parent 7 76.2 7.999e+01 3.794958 5.1708 0.733918 -#> ds 4 parent 7 77.8 7.999e+01 2.194958 5.1708 0.424489 -#> ds 4 parent 14 70.8 6.518e+01 -5.624996 4.2301 -1.329742 -#> ds 4 parent 14 67.3 6.518e+01 -2.124996 4.2301 -0.502346 -#> ds 4 parent 28 43.1 4.462e+01 1.517860 2.9354 0.517085 -#> ds 4 parent 28 45.1 4.462e+01 -0.482140 2.9354 -0.164249 -#> ds 4 parent 60 21.3 2.130e+01 -0.003305 1.5159 -0.002180 -#> ds 4 parent 60 23.5 2.130e+01 -2.203305 1.5159 -1.453435 -#> ds 4 parent 90 11.8 1.180e+01 0.002834 1.0032 0.002825 -#> ds 4 parent 90 12.1 1.180e+01 -0.297166 1.0032 -0.296226 -#> ds 4 parent 120 7.0 6.868e+00 -0.132251 0.7922 -0.166937 -#> ds 4 parent 120 6.2 6.868e+00 0.667749 0.7922 0.842879 -#> ds 4 m1 0 1.6 0.000e+00 -1.600000 0.6586 -2.429424 -#> ds 4 m1 1 0.9 6.826e-01 -0.217363 0.6600 -0.329315 -#> ds 4 m1 3 3.7 1.935e+00 -1.765082 0.6702 -2.633768 -#> ds 4 m1 3 2.0 1.935e+00 -0.065082 0.6702 -0.097112 -#> ds 4 m1 7 3.6 4.035e+00 0.434805 0.7076 0.614501 -#> ds 4 m1 7 3.8 4.035e+00 0.234805 0.7076 0.331845 -#> ds 4 m1 14 7.1 6.652e+00 -0.448187 0.7846 -0.571220 -#> ds 4 m1 14 6.6 6.652e+00 0.051813 0.7846 0.066036 -#> ds 4 m1 28 9.5 9.156e+00 -0.343805 0.8822 -0.389696 -#> ds 4 m1 28 9.3 9.156e+00 -0.143805 0.8822 -0.163000 -#> ds 4 m1 60 8.3 8.848e+00 0.547762 0.8692 0.630185 -#> ds 4 m1 60 9.0 8.848e+00 -0.152238 0.8692 -0.175146 -#> ds 4 m1 90 6.6 6.674e+00 0.073979 0.7854 0.094194 -#> ds 4 m1 90 7.7 6.674e+00 -1.026021 0.7854 -1.306390 -#> ds 4 m1 120 3.7 4.668e+00 0.967537 0.7234 1.337503 -#> ds 4 m1 120 3.5 4.668e+00 1.167537 0.7234 1.613979 -#> ds 5 parent 0 110.4 1.022e+02 -8.170986 6.5872 -1.240433 -#> ds 5 parent 0 112.1 1.022e+02 -9.870986 6.5872 -1.498509 -#> ds 5 parent 1 93.5 9.513e+01 1.630764 6.1346 0.265832 -#> ds 5 parent 1 91.0 9.513e+01 4.130764 6.1346 0.673359 -#> ds 5 parent 3 71.0 8.296e+01 11.964279 5.3597 2.232268 -#> ds 5 parent 3 89.7 8.296e+01 -6.735721 5.3597 -1.256735 -#> ds 5 parent 7 60.4 6.495e+01 4.547441 4.2157 1.078684 -#> ds 5 parent 7 59.1 6.495e+01 5.847441 4.2157 1.387053 -#> ds 5 parent 14 56.5 4.626e+01 -10.241319 3.0380 -3.371047 -#> ds 5 parent 14 47.0 4.626e+01 -0.741319 3.0380 -0.244014 -#> ds 5 parent 28 30.2 3.026e+01 0.058478 2.0487 0.028544 -#> ds 5 parent 28 23.9 3.026e+01 6.358478 2.0487 3.103661 -#> ds 5 parent 60 17.0 1.792e+01 0.919046 1.3242 0.694024 -#> ds 5 parent 60 18.7 1.792e+01 -0.780954 1.3242 -0.589742 -#> ds 5 parent 90 11.3 1.187e+01 0.573917 1.0066 0.570144 -#> ds 5 parent 90 11.9 1.187e+01 -0.026083 1.0066 -0.025912 -#> ds 5 parent 120 9.0 7.898e+00 -1.102089 0.8307 -1.326622 -#> ds 5 parent 120 8.1 7.898e+00 -0.202089 0.8307 -0.243261 -#> ds 5 m1 0 0.7 -1.421e-14 -0.700000 0.6586 -1.062873 -#> ds 5 m1 1 3.0 3.144e+00 0.143526 0.6887 0.208390 -#> ds 5 m1 1 2.6 3.144e+00 0.543526 0.6887 0.789161 -#> ds 5 m1 3 5.1 8.390e+00 3.290265 0.8504 3.869277 -#> ds 5 m1 3 7.5 8.390e+00 0.890265 0.8504 1.046932 -#> ds 5 m1 7 16.5 1.566e+01 -0.841368 1.2007 -0.700751 -#> ds 5 m1 7 19.0 1.566e+01 -3.341368 1.2007 -2.782928 -#> ds 5 m1 14 22.9 2.188e+01 -1.017753 1.5498 -0.656687 -#> ds 5 m1 14 23.2 2.188e+01 -1.317753 1.5498 -0.850257 -#> ds 5 m1 28 22.2 2.386e+01 1.655914 1.6652 0.994399 -#> ds 5 m1 28 24.4 2.386e+01 -0.544086 1.6652 -0.326731 -#> ds 5 m1 60 15.5 1.859e+01 3.091124 1.3618 2.269915 -#> ds 5 m1 60 19.8 1.859e+01 -1.208876 1.3618 -0.887718 -#> ds 5 m1 90 14.9 1.372e+01 -1.176815 1.0990 -1.070784 -#> ds 5 m1 90 14.2 1.372e+01 -0.476815 1.0990 -0.433854 -#> ds 5 m1 120 10.9 9.961e+00 -0.938796 0.9174 -1.023332 -#> ds 5 m1 120 10.4 9.961e+00 -0.438796 0.9174 -0.478308</div><div class='input'><span class='co'># }</span> +#> ds name time observed predicted residual std standardized +#> ds 1 parent 0 89.8 9.878e+01 8.98039 6.3899 1.40541 +#> ds 1 parent 0 104.1 9.878e+01 -5.31961 6.3899 -0.83251 +#> ds 1 parent 1 88.7 9.422e+01 5.52084 6.0981 0.90533 +#> ds 1 parent 1 95.5 9.422e+01 -1.27916 6.0981 -0.20976 +#> ds 1 parent 3 81.8 8.587e+01 4.06752 5.5641 0.73103 +#> ds 1 parent 3 94.5 8.587e+01 -8.63248 5.5641 -1.55147 +#> ds 1 parent 7 71.5 7.180e+01 0.29615 4.6662 0.06347 +#> ds 1 parent 7 70.3 7.180e+01 1.49615 4.6662 0.32063 +#> ds 1 parent 14 54.2 5.360e+01 -0.59602 3.5112 -0.16975 +#> ds 1 parent 14 49.6 5.360e+01 4.00398 3.5112 1.14035 +#> ds 1 parent 28 31.5 3.213e+01 0.62529 2.1691 0.28828 +#> ds 1 parent 28 28.8 3.213e+01 3.32529 2.1691 1.53306 +#> ds 1 parent 60 12.1 1.271e+01 0.60718 1.0490 0.57879 +#> ds 1 parent 60 13.6 1.271e+01 -0.89282 1.0490 -0.85108 +#> ds 1 parent 90 6.2 6.080e+00 -0.12020 0.7649 -0.15716 +#> ds 1 parent 90 8.3 6.080e+00 -2.22020 0.7649 -2.90279 +#> ds 1 parent 120 2.2 3.011e+00 0.81059 0.6852 1.18302 +#> ds 1 parent 120 2.4 3.011e+00 0.61059 0.6852 0.89113 +#> ds 1 m1 1 0.3 1.131e+00 0.83071 0.6613 1.25628 +#> ds 1 m1 1 0.2 1.131e+00 0.93071 0.6613 1.40750 +#> ds 1 m1 3 2.2 3.147e+00 0.94691 0.6877 1.37688 +#> ds 1 m1 3 3.0 3.147e+00 0.14691 0.6877 0.21361 +#> ds 1 m1 7 6.5 6.341e+00 -0.15949 0.7736 -0.20618 +#> ds 1 m1 7 5.0 6.341e+00 1.34051 0.7736 1.73290 +#> ds 1 m1 14 10.2 9.910e+00 -0.28991 0.9157 -0.31659 +#> ds 1 m1 14 9.5 9.910e+00 0.41009 0.9157 0.44783 +#> ds 1 m1 28 12.2 1.255e+01 0.34690 1.0410 0.33323 +#> ds 1 m1 28 13.4 1.255e+01 -0.85310 1.0410 -0.81949 +#> ds 1 m1 60 11.8 1.087e+01 -0.92713 0.9599 -0.96586 +#> ds 1 m1 60 13.2 1.087e+01 -2.32713 0.9599 -2.42434 +#> ds 1 m1 90 6.6 7.813e+00 1.21254 0.8274 1.46541 +#> ds 1 m1 90 9.3 7.813e+00 -1.48746 0.8274 -1.79766 +#> ds 1 m1 120 3.5 5.295e+00 1.79489 0.7403 2.42457 +#> ds 1 m1 120 5.4 5.295e+00 -0.10511 0.7403 -0.14198 +#> ds 2 parent 0 118.0 1.074e+02 -10.63436 6.9396 -1.53242 +#> ds 2 parent 0 99.8 1.074e+02 7.56564 6.9396 1.09021 +#> ds 2 parent 1 90.2 1.012e+02 10.96486 6.5425 1.67594 +#> ds 2 parent 1 94.6 1.012e+02 6.56486 6.5425 1.00342 +#> ds 2 parent 3 96.1 9.054e+01 -5.56014 5.8627 -0.94839 +#> ds 2 parent 3 78.4 9.054e+01 12.13986 5.8627 2.07069 +#> ds 2 parent 7 77.9 7.468e+01 -3.21805 4.8501 -0.66350 +#> ds 2 parent 7 77.7 7.468e+01 -3.01805 4.8501 -0.62226 +#> ds 2 parent 14 56.0 5.748e+01 1.47774 3.7563 0.39340 +#> ds 2 parent 14 54.7 5.748e+01 2.77774 3.7563 0.73948 +#> ds 2 parent 28 36.6 3.996e+01 3.36317 2.6541 1.26717 +#> ds 2 parent 28 36.8 3.996e+01 3.16317 2.6541 1.19182 +#> ds 2 parent 60 22.1 2.132e+01 -0.78225 1.5210 -0.51430 +#> ds 2 parent 60 24.7 2.132e+01 -3.38225 1.5210 -2.22369 +#> ds 2 parent 90 12.4 1.215e+01 -0.25010 1.0213 -0.24487 +#> ds 2 parent 90 10.8 1.215e+01 1.34990 1.0213 1.32169 +#> ds 2 parent 120 6.8 6.931e+00 0.13105 0.7943 0.16500 +#> ds 2 parent 120 7.9 6.931e+00 -0.96895 0.7943 -1.21994 +#> ds 2 m1 1 1.3 1.519e+00 0.21924 0.6645 0.32995 +#> ds 2 m1 3 3.7 4.049e+00 0.34891 0.7070 0.49351 +#> ds 2 m1 3 4.7 4.049e+00 -0.65109 0.7070 -0.92094 +#> ds 2 m1 7 8.1 7.565e+00 -0.53526 0.8179 -0.65448 +#> ds 2 m1 7 7.9 7.565e+00 -0.33526 0.8179 -0.40993 +#> ds 2 m1 14 10.1 1.071e+01 0.60614 0.9521 0.63663 +#> ds 2 m1 14 10.3 1.071e+01 0.40614 0.9521 0.42657 +#> ds 2 m1 28 10.7 1.224e+01 1.54440 1.0260 1.50526 +#> ds 2 m1 28 12.2 1.224e+01 0.04440 1.0260 0.04327 +#> ds 2 m1 60 10.7 1.056e+01 -0.14005 0.9453 -0.14815 +#> ds 2 m1 60 12.5 1.056e+01 -1.94005 0.9453 -2.05226 +#> ds 2 m1 90 9.1 8.089e+00 -1.01088 0.8384 -1.20577 +#> ds 2 m1 90 7.4 8.089e+00 0.68912 0.8384 0.82197 +#> ds 2 m1 120 6.1 5.855e+00 -0.24463 0.7576 -0.32292 +#> ds 2 m1 120 4.5 5.855e+00 1.35537 0.7576 1.78911 +#> ds 3 parent 0 106.2 1.095e+02 3.30335 7.0765 0.46680 +#> ds 3 parent 0 106.9 1.095e+02 2.60335 7.0765 0.36788 +#> ds 3 parent 1 107.4 9.939e+01 -8.01282 6.4287 -1.24641 +#> ds 3 parent 1 96.1 9.939e+01 3.28718 6.4287 0.51133 +#> ds 3 parent 3 79.4 8.365e+01 4.24698 5.4222 0.78326 +#> ds 3 parent 3 82.6 8.365e+01 1.04698 5.4222 0.19309 +#> ds 3 parent 7 63.9 6.405e+01 0.14704 4.1732 0.03523 +#> ds 3 parent 7 62.4 6.405e+01 1.64704 4.1732 0.39467 +#> ds 3 parent 14 51.0 4.795e+01 -3.04985 3.1546 -0.96681 +#> ds 3 parent 14 47.1 4.795e+01 0.85015 3.1546 0.26950 +#> ds 3 parent 28 36.1 3.501e+01 -1.09227 2.3465 -0.46549 +#> ds 3 parent 28 36.6 3.501e+01 -1.59227 2.3465 -0.67858 +#> ds 3 parent 60 20.1 2.012e+01 0.02116 1.4520 0.01457 +#> ds 3 parent 60 19.8 2.012e+01 0.32116 1.4520 0.22119 +#> ds 3 parent 90 11.3 1.206e+01 0.76096 1.0170 0.74826 +#> ds 3 parent 90 10.7 1.206e+01 1.36096 1.0170 1.33825 +#> ds 3 parent 120 8.2 7.230e+00 -0.97022 0.8052 -1.20493 +#> ds 3 parent 120 7.3 7.230e+00 -0.07022 0.8052 -0.08721 +#> ds 3 m1 0 0.8 -5.684e-13 -0.80000 0.6572 -1.21722 +#> ds 3 m1 1 1.8 2.045e+00 0.24538 0.6703 0.36608 +#> ds 3 m1 1 2.3 2.045e+00 -0.25462 0.6703 -0.37987 +#> ds 3 m1 3 4.2 5.136e+00 0.93594 0.7356 1.27228 +#> ds 3 m1 3 4.1 5.136e+00 1.03594 0.7356 1.40822 +#> ds 3 m1 7 6.8 8.674e+00 1.87438 0.8623 2.17381 +#> ds 3 m1 7 10.1 8.674e+00 -1.42562 0.8623 -1.65335 +#> ds 3 m1 14 11.4 1.083e+01 -0.56746 0.9580 -0.59233 +#> ds 3 m1 14 12.8 1.083e+01 -1.96746 0.9580 -2.05369 +#> ds 3 m1 28 11.5 1.098e+01 -0.51762 0.9651 -0.53637 +#> ds 3 m1 28 10.6 1.098e+01 0.38238 0.9651 0.39623 +#> ds 3 m1 60 7.5 8.889e+00 1.38911 0.8713 1.59436 +#> ds 3 m1 60 8.6 8.889e+00 0.28911 0.8713 0.33183 +#> ds 3 m1 90 7.3 6.774e+00 -0.52608 0.7886 -0.66708 +#> ds 3 m1 90 8.1 6.774e+00 -1.32608 0.7886 -1.68150 +#> ds 3 m1 120 5.3 4.954e+00 -0.34584 0.7305 -0.47345 +#> ds 3 m1 120 3.8 4.954e+00 1.15416 0.7305 1.58004 +#> ds 4 parent 0 104.7 9.957e+01 -5.13169 6.4403 -0.79681 +#> ds 4 parent 0 88.3 9.957e+01 11.26831 6.4403 1.74966 +#> ds 4 parent 1 94.2 9.644e+01 2.23888 6.2400 0.35879 +#> ds 4 parent 1 94.6 9.644e+01 1.83888 6.2400 0.29469 +#> ds 4 parent 3 78.1 9.054e+01 12.43946 5.8627 2.12180 +#> ds 4 parent 3 96.5 9.054e+01 -5.96054 5.8627 -1.01669 +#> ds 4 parent 7 76.2 8.004e+01 3.83771 5.1918 0.73919 +#> ds 4 parent 7 77.8 8.004e+01 2.23771 5.1918 0.43101 +#> ds 4 parent 14 70.8 6.511e+01 -5.69246 4.2406 -1.34238 +#> ds 4 parent 14 67.3 6.511e+01 -2.19246 4.2406 -0.51702 +#> ds 4 parent 28 43.1 4.454e+01 1.43744 2.9401 0.48890 +#> ds 4 parent 28 45.1 4.454e+01 -0.56256 2.9401 -0.19134 +#> ds 4 parent 60 21.3 2.132e+01 0.02005 1.5211 0.01318 +#> ds 4 parent 60 23.5 2.132e+01 -2.17995 1.5211 -1.43310 +#> ds 4 parent 90 11.8 1.182e+01 0.02167 1.0053 0.02156 +#> ds 4 parent 90 12.1 1.182e+01 -0.27833 1.0053 -0.27687 +#> ds 4 parent 120 7.0 6.852e+00 -0.14780 0.7914 -0.18675 +#> ds 4 parent 120 6.2 6.852e+00 0.65220 0.7914 0.82408 +#> ds 4 m1 0 1.6 -5.684e-14 -1.60000 0.6572 -2.43444 +#> ds 4 m1 1 0.9 6.918e-01 -0.20821 0.6587 -0.31607 +#> ds 4 m1 3 3.7 1.959e+00 -1.74131 0.6692 -2.60204 +#> ds 4 m1 3 2.0 1.959e+00 -0.04131 0.6692 -0.06173 +#> ds 4 m1 7 3.6 4.076e+00 0.47590 0.7076 0.67252 +#> ds 4 m1 7 3.8 4.076e+00 0.27590 0.7076 0.38989 +#> ds 4 m1 14 7.1 6.698e+00 -0.40189 0.7859 -0.51135 +#> ds 4 m1 14 6.6 6.698e+00 0.09811 0.7859 0.12483 +#> ds 4 m1 28 9.5 9.175e+00 -0.32492 0.8835 -0.36779 +#> ds 4 m1 28 9.3 9.175e+00 -0.12492 0.8835 -0.14141 +#> ds 4 m1 60 8.3 8.818e+00 0.51810 0.8683 0.59671 +#> ds 4 m1 60 9.0 8.818e+00 -0.18190 0.8683 -0.20949 +#> ds 4 m1 90 6.6 6.645e+00 0.04480 0.7841 0.05713 +#> ds 4 m1 90 7.7 6.645e+00 -1.05520 0.7841 -1.34581 +#> ds 4 m1 120 3.7 4.648e+00 0.94805 0.7221 1.31293 +#> ds 4 m1 120 3.5 4.648e+00 1.14805 0.7221 1.58991 +#> ds 5 parent 0 110.4 1.026e+02 -7.81752 6.6333 -1.17853 +#> ds 5 parent 0 112.1 1.026e+02 -9.51752 6.6333 -1.43482 +#> ds 5 parent 1 93.5 9.560e+01 2.10274 6.1865 0.33989 +#> ds 5 parent 1 91.0 9.560e+01 4.60274 6.1865 0.74399 +#> ds 5 parent 3 71.0 8.356e+01 12.55799 5.4165 2.31846 +#> ds 5 parent 3 89.7 8.356e+01 -6.14201 5.4165 -1.13394 +#> ds 5 parent 7 60.4 6.550e+01 5.09732 4.2653 1.19506 +#> ds 5 parent 7 59.1 6.550e+01 6.39732 4.2653 1.49984 +#> ds 5 parent 14 56.5 4.641e+01 -10.09145 3.0576 -3.30044 +#> ds 5 parent 14 47.0 4.641e+01 -0.59145 3.0576 -0.19344 +#> ds 5 parent 28 30.2 2.982e+01 -0.37647 2.0284 -0.18560 +#> ds 5 parent 28 23.9 2.982e+01 5.92353 2.0284 2.92028 +#> ds 5 parent 60 17.0 1.754e+01 0.53981 1.3060 0.41332 +#> ds 5 parent 60 18.7 1.754e+01 -1.16019 1.3060 -0.88834 +#> ds 5 parent 90 11.3 1.175e+01 0.45050 1.0018 0.44969 +#> ds 5 parent 90 11.9 1.175e+01 -0.14950 1.0018 -0.14923 +#> ds 5 parent 120 9.0 7.915e+00 -1.08476 0.8315 -1.30462 +#> ds 5 parent 120 8.1 7.915e+00 -0.18476 0.8315 -0.22220 +#> ds 5 m1 0 0.7 0.000e+00 -0.70000 0.6572 -1.06507 +#> ds 5 m1 1 3.0 3.062e+00 0.06170 0.6861 0.08992 +#> ds 5 m1 1 2.6 3.062e+00 0.46170 0.6861 0.67290 +#> ds 5 m1 3 5.1 8.209e+00 3.10938 0.8432 3.68760 +#> ds 5 m1 3 7.5 8.209e+00 0.70938 0.8432 0.84130 +#> ds 5 m1 7 16.5 1.544e+01 -1.05567 1.1914 -0.88605 +#> ds 5 m1 7 19.0 1.544e+01 -3.55567 1.1914 -2.98436 +#> ds 5 m1 14 22.9 2.181e+01 -1.08765 1.5498 -0.70181 +#> ds 5 m1 14 23.2 2.181e+01 -1.38765 1.5498 -0.89539 +#> ds 5 m1 28 22.2 2.404e+01 1.83624 1.6805 1.09270 +#> ds 5 m1 28 24.4 2.404e+01 -0.36376 1.6805 -0.21647 +#> ds 5 m1 60 15.5 1.875e+01 3.25390 1.3741 2.36805 +#> ds 5 m1 60 19.8 1.875e+01 -1.04610 1.3741 -0.76131 +#> ds 5 m1 90 14.9 1.380e+01 -1.09507 1.1050 -0.99102 +#> ds 5 m1 90 14.2 1.380e+01 -0.39507 1.1050 -0.35753 +#> ds 5 m1 120 10.9 1.002e+01 -0.88429 0.9205 -0.96069 +#> ds 5 m1 120 10.4 1.002e+01 -0.38429 0.9205 -0.41749</div><div class='input'><span class='co'># }</span> </div></pre> </div> diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html index 46b66073..6e19505f 100644 --- a/docs/dev/reference/transform_odeparms.html +++ b/docs/dev/reference/transform_odeparms.html @@ -77,7 +77,7 @@ the ilr transformation is used." /> </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">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> </span> </div> @@ -126,7 +126,7 @@ the ilr transformation is used." /> <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> @@ -231,50 +231,64 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</ <pre class="examples"><div class='input'> <span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> + m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> +<span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='va'>FOCUS_D</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># remove zero values to avoid warning</span> +<span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>fit.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> <span class='co'># Transformed and backtransformed parameters</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.5985 1.5702 96.404 102.79 -#> log_k_parent -2.3157 0.0409 -2.399 -2.23 -#> log_k_m1 -5.2475 0.1332 -5.518 -4.98 -#> f_parent_qlogis 0.0579 0.0893 -0.124 0.24 -#> sigma 3.1255 0.3585 2.396 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931 -#> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 -#> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> +</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.60 1.5702 96.40 102.79 +#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 +#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 +#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 +#> sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 +#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 +#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 +#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> <span class='co'># \dontrun{</span> -<span class='co'># Compare to the version without transforming rate parameters</span> -<span class='va'>fit.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.006 0 0.005</span></div><div class='input'><span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'fit.2' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span> +<span class='co'># Compare to the version without transforming rate parameters (does not work</span> +<span class='co'># with analytical solution, we get NA values for m1 in predictions)</span> +<span class='va'>fit.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>, + solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.59848 1.57022 96.40384 1.03e+02 +#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 +#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 +#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 +#> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 +#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 +#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 +#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'><span class='co'># }</span> <span class='va'>initials</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>$</span><span class='va'>value</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>initials</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>)</span> <span class='va'>transformed</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>$</span><span class='va'>value</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>transformed</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>)</span> <span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 log_k_parent log_k_m1 f_parent_qlogis -#> 100.750000 -2.302585 -2.301586 0.000000 </div><div class='input'><span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 -#> 100.7500 0.1000 0.1001 0.5000 </div><div class='input'> +</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> +</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> <span class='co'># \dontrun{</span> -<span class='co'># The case of formation fractions</span> +<span class='co'># The case of formation fractions (this is now the default)</span> <span class='va'>SFO_SFO.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>fit.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span> +<span class='va'>fit.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>fit.ff.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> Estimate Std. Error Lower Upper #> parent_0 99.5985 1.5702 96.404 102.79 @@ -299,8 +313,8 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</ use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>fit.ff.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span> +<span class='va'>fit.ff.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>fit.ff.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> Estimate Std. Error Lower Upper #> parent_0 84.79 3.012 78.67 90.91 diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index ecf68e50..27f0e392 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -175,9 +175,6 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html</loc> </url> <url> - <loc>https://pkgdown.jrwb.de/mkin/reference/print.mmkin.html</loc> - </url> - <url> <loc>https://pkgdown.jrwb.de/mkin/reference/reexports.html</loc> </url> <url> |
