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-rw-r--r--docs/dev/404.html2
-rw-r--r--docs/dev/articles/index.html2
-rw-r--r--docs/dev/authors.html8
-rw-r--r--docs/dev/index.html4
-rw-r--r--docs/dev/news/index.html211
-rw-r--r--docs/dev/pkgdown.yml4
-rw-r--r--docs/dev/reference/Rplot001.pngbin19395 -> 1011 bytes
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-rw-r--r--docs/dev/reference/confint.mkinfit.html127
-rw-r--r--docs/dev/reference/endpoints.html4
-rw-r--r--docs/dev/reference/index.html10
-rw-r--r--docs/dev/reference/logLik.mkinfit.html12
-rw-r--r--docs/dev/reference/mkinresplot.html6
-rw-r--r--docs/dev/reference/mmkin-1.pngbin114048 -> 110459 bytes
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-rw-r--r--docs/dev/reference/mmkin.html31
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-rw-r--r--docs/dev/reference/saem.html56
-rw-r--r--docs/dev/reference/summary.saem.mmkin.html426
-rw-r--r--docs/dev/reference/transform_odeparms.html80
-rw-r--r--docs/dev/sitemap.xml3
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 &lt; 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 &gt;= 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
index bca41e2c..17a35806 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
Binary files differ
diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png
index ff6bc722..2b011ec1 100644
--- a/docs/dev/reference/Rplot003.png
+++ b/docs/dev/reference/Rplot003.png
Binary files differ
diff --git a/docs/dev/reference/Rplot005.png b/docs/dev/reference/Rplot005.png
index 5e675828..8c91d61e 100644
--- a/docs/dev/reference/Rplot005.png
+++ b/docs/dev/reference/Rplot005.png
Binary files differ
diff --git a/docs/dev/reference/Rplot006.png b/docs/dev/reference/Rplot006.png
index da52f580..730a7481 100644
--- a/docs/dev/reference/Rplot006.png
+++ b/docs/dev/reference/Rplot006.png
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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'>&lt;-</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'>&lt;-</span> <span class='fl'>1</span>
+ <span class='va'>n_cores</span> <span class='op'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>#&gt; user system elapsed
-#&gt; 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>
+#&gt; 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'>&lt;-</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'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; <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'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <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'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.456003640 1.027703e+02
-#&gt; k_parent 0.090911032 1.071578e-01
-#&gt; k_m1 0.003892606 6.702775e-03
-#&gt; f_parent_to_m1 0.471328495 5.611550e-01
-#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'>&lt;-</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'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 1.459 0.088 0.907 </div><div class='input'><span class='va'>ci_profile</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.456003640 1.027703e+02
+#&gt; k_parent_sink 0.040762501 5.549764e-02
+#&gt; k_parent_m1 0.046786482 5.500879e-02
+#&gt; k_m1_sink 0.003892605 6.702778e-03
+#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'>&lt;-</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'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833585 102.79311650
-#&gt; k_parent 0.090823771 0.10725430
-#&gt; k_m1 0.004012219 0.00689755
-#&gt; f_parent_to_m1 0.469118824 0.55959615
-#&gt; sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'>&lt;-</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'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.403841640 1.027931e+02
+#&gt; k_parent_sink 0.041033378 5.596269e-02
+#&gt; k_parent_m1 0.046777902 5.511931e-02
+#&gt; k_m1_sink 0.004012217 6.897547e-03
+#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'>&lt;-</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'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833589 1.027931e+02
-#&gt; k_parent 0.090491913 1.069035e-01
-#&gt; k_m1 0.003835485 6.685823e-03
-#&gt; f_parent_to_m1 0.469113477 5.598387e-01
-#&gt; 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'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.403841645 102.79312449
+#&gt; k_parent_sink 0.040485331 0.05535491
+#&gt; k_parent_m1 0.046611582 0.05494364
+#&gt; k_m1_sink 0.003835483 0.00668582
+#&gt; 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'>&lt;-</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'>&lt;-</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'>&lt;</span> <span class='va'>rel_diffs_untransformed</span>
-</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 FALSE FALSE
-#&gt; k_parent TRUE TRUE
-#&gt; k_m1 FALSE FALSE
-#&gt; f_parent_to_m1 TRUE FALSE
-#&gt; 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'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.000541 0.000222
-#&gt; k_parent 0.000960 0.000900
-#&gt; k_m1 0.030700 0.029100
-#&gt; f_parent_to_m1 0.004690 0.002780
-#&gt; 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'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.000541 0.000222
-#&gt; k_parent 0.004610 0.002370
-#&gt; k_m1 0.014700 0.002530
-#&gt; f_parent_to_m1 0.004700 0.002350
-#&gt; sigma 0.055000 0.032700</div><div class='input'>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 FALSE FALSE
+#&gt; k_parent_sink TRUE FALSE
+#&gt; k_parent_m1 TRUE FALSE
+#&gt; k_m1_sink FALSE FALSE
+#&gt; 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'>#&gt; 2.5% 97.5%
+#&gt; parent_0 0.000541 0.000222
+#&gt; k_parent_sink 0.006650 0.008380
+#&gt; k_parent_m1 0.000183 0.002010
+#&gt; k_m1_sink 0.030700 0.029100
+#&gt; 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'>#&gt; 2.5% 97.5%
+#&gt; parent_0 0.000541 0.000222
+#&gt; k_parent_sink 0.006800 0.002570
+#&gt; k_parent_m1 0.003740 0.001180
+#&gt; k_m1_sink 0.014700 0.002530
+#&gt; 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'>&lt;-</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,
#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'>&lt;-</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'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833585 102.79311650
+#&gt; parent_0 96.403833578 102.79311649
#&gt; k_parent 0.090823771 0.10725430
#&gt; k_m1 0.004012219 0.00689755
#&gt; f_parent_to_m1 0.469118824 0.55959615
#&gt; sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'>&lt;-</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'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833589 1.027931e+02
+#&gt; parent_0 96.403833583 1.027931e+02
#&gt; k_parent 0.090491913 1.069035e-01
#&gt; k_m1 0.003835485 6.685823e-03
#&gt; f_parent_to_m1 0.469113477 5.598387e-01
@@ -373,15 +374,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
#&gt; f_parent_to_m1 TRUE FALSE
#&gt; sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408689 0.0002217234
+#&gt; parent_0 0.0005408690 0.0002217233
#&gt; k_parent 0.0009598532 0.0009001864
-#&gt; k_m1 0.0307283044 0.0290588365
-#&gt; f_parent_to_m1 0.0046881768 0.0027780063
+#&gt; k_m1 0.0307283041 0.0290588361
+#&gt; f_parent_to_m1 0.0046881769 0.0027780063
#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408689 0.0002217233
-#&gt; k_parent 0.0046102155 0.0023732281
-#&gt; k_m1 0.0146740688 0.0025291817
+#&gt; parent_0 0.0005408689 0.0002217232
+#&gt; k_parent 0.0046102156 0.0023732281
+#&gt; k_m1 0.0146740690 0.0025291820
#&gt; f_parent_to_m1 0.0046995211 0.0023457712
#&gt; 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'>#&gt; 2.5% 97.5%
-#&gt; parent_0 94.596126334 106.19944007
-#&gt; k_M1 0.037605408 0.04490759
-#&gt; k_M2 0.008568739 0.01087675
-#&gt; f_parent_to_M1 0.021463787 0.62023881
-#&gt; f_parent_to_M2 0.015166531 0.37975349
-#&gt; k1 0.273897467 0.33388084
-#&gt; k2 0.018614555 0.02250379
-#&gt; g 0.671943606 0.73583278
-#&gt; sigma_low 0.251283766 0.83992113
-#&gt; 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>
+#&gt; parent_0 94.596039609 106.19954892
+#&gt; k_M1 0.037605368 0.04490762
+#&gt; k_M2 0.008568731 0.01087676
+#&gt; f_parent_to_M1 0.021462489 0.62023882
+#&gt; f_parent_to_M2 0.015165617 0.37975348
+#&gt; k1 0.273897348 0.33388101
+#&gt; k2 0.018614554 0.02250378
+#&gt; g 0.671943411 0.73583305
+#&gt; sigma_low 0.251283495 0.83992077
+#&gt; 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'>#&gt; 2.5% 97.5%
-#&gt; parent_0 94.59613 106.1994</div><div class='input'><span class='co'># }</span>
+#&gt; 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>&lt;mmkin&gt;</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>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
</td>
<td><p>Calculate the AIC for a column of an mmkin object</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="print.mmkin.html">print(<i>&lt;mmkin&gt;</i>)</a></code> </p>
- </td>
- <td><p>Print method for mmkin objects</p></td>
</tr>
</tbody><tbody>
<tr>
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'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'>&lt;-</span> <span class='va'>FOCUS_2006_D</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'>&lt;-</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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>&lt;-</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'>#&gt; df AIC
#&gt; f_nw 5 204.4486
#&gt; 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
index 7b7da90a..0db3379f 100644
--- a/docs/dev/reference/mmkin-1.png
+++ b/docs/dev/reference/mmkin-1.png
Binary files differ
diff --git a/docs/dev/reference/mmkin-2.png b/docs/dev/reference/mmkin-2.png
index ce2b2af4..024a9892 100644
--- a/docs/dev/reference/mmkin-2.png
+++ b/docs/dev/reference/mmkin-2.png
Binary files differ
diff --git a/docs/dev/reference/mmkin-3.png b/docs/dev/reference/mmkin-3.png
index bb96f1b2..a23d7cb9 100644
--- a/docs/dev/reference/mmkin-3.png
+++ b/docs/dev/reference/mmkin-3.png
Binary files differ
diff --git a/docs/dev/reference/mmkin-4.png b/docs/dev/reference/mmkin-4.png
index 351b21aa..89975db5 100644
--- a/docs/dev/reference/mmkin-4.png
+++ b/docs/dev/reference/mmkin-4.png
Binary files differ
diff --git a/docs/dev/reference/mmkin-5.png b/docs/dev/reference/mmkin-5.png
index c1c05eea..a2f34983 100644
--- a/docs/dev/reference/mmkin-5.png
+++ b/docs/dev/reference/mmkin-5.png
Binary files differ
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'>#&gt; user system elapsed
-#&gt; 4.968 0.427 1.342 </div><div class='input'><span class='va'>time_1</span>
+#&gt; 4.438 0.334 1.640 </div><div class='input'><span class='va'>time_1</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 5.365 0.000 5.368 </div><div class='input'>
+#&gt; 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'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
-#&gt; 0.7340478 0.2659522 0.7505687 0.2494313
+#&gt; 0.7340481 0.2659519 0.7505683 0.2494317
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 0.877769 2.915885
-#&gt; M1 2.325746 7.725960
-#&gt; M2 33.720083 112.015691
+#&gt; M1 2.325744 7.725956
+#&gt; M2 33.720100 112.015749
#&gt; </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>
#&gt; dataset
#&gt; model A B C D
#&gt; SFO OK OK OK OK
-#&gt; FOMC C OK OK OK
+#&gt; FOMC OK OK OK OK
#&gt; DFOP OK OK OK OK
#&gt;
-#&gt; OK: No warnings
-#&gt; C: Optimisation did not converge:
-#&gt; 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>
+#&gt; 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
index 25bebeca..9186c135 100644
--- a/docs/dev/reference/nlme.mmkin-1.png
+++ b/docs/dev/reference/nlme.mmkin-1.png
Binary files differ
diff --git a/docs/dev/reference/nlme.mmkin-2.png b/docs/dev/reference/nlme.mmkin-2.png
index c314c149..d395fe02 100644
--- a/docs/dev/reference/nlme.mmkin-2.png
+++ b/docs/dev/reference/nlme.mmkin-2.png
Binary files differ
diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png
index a40b7cad..40518a59 100644
--- a/docs/dev/reference/nlme.mmkin-3.png
+++ b/docs/dev/reference/nlme.mmkin-3.png
Binary files differ
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'>#&gt; Model df AIC BIC logLik Test L.Ratio p-value
#&gt; f_nlme_sfo 1 5 625.0539 637.5529 -307.5269
-#&gt; f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 &lt;.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>
+#&gt; f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 &lt;.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'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
#&gt;
#&gt; 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'>#&gt; $distimes
#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
-#&gt; parent 10.79857 100.7937 30.34192 4.193937 43.85442
+#&gt; parent 10.79857 100.7937 30.34193 4.193938 43.85443
#&gt; </div><div class='input'>
<span class='va'>ds_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
<span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</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 &lt;- 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'>&lt;-</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'>#&gt; <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'>#&gt; <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'>&lt;-</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'>#&gt; <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'>#&gt; <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'>#&gt; Model df AIC BIC logLik Test L.Ratio p-value
+#&gt; f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274
+#&gt; f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3273 &lt;.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'>#&gt; $ff
#&gt; parent_sink parent_A1 A1_sink
@@ -355,7 +362,15 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
#&gt; parent 19.13518 63.5657
#&gt; A1 66.02155 219.3189
#&gt; </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'>#&gt; <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'>#&gt; $ff
+#&gt; parent_A1 parent_sink
+#&gt; 0.2768575 0.7231425
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
+#&gt; parent 11.07091 104.6320 31.49737 4.462384 46.20825
+#&gt; A1 162.30492 539.1653 NA NA NA
+#&gt; </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'>&gt;</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
#&gt; Fixed effects:
#&gt; list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
#&gt; parent_0 log_k1 log_k2 g_qlogis
-#&gt; 94.04775 -1.82340 -4.16715 0.05685
+#&gt; 94.04774 -1.82340 -4.16716 0.05686
#&gt;
#&gt; Random effects:
#&gt; 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
#&gt; Formula: ~fitted(.)
#&gt; Parameter estimates:
#&gt; const prop
-#&gt; 2.23224114 0.01262341 </div><div class='input'>
- <span class='va'>f_2_obs</span> <span class='op'>&lt;-</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>
+#&gt; 2.23223147 0.01262395 </div><div class='input'>
+ <span class='va'>f_2_obs</span> <span class='op'>&lt;-</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'>&lt;-</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'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
@@ -429,18 +442,21 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
#&gt; Formula: ~1 | name
#&gt; Parameter estimates:
#&gt; parent A1
-#&gt; 1.0000000 0.2050003 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'>&lt;-</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'>#&gt; <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'>#&gt; <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'>&lt;-</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 &lt;- nlme(f_2_tc["SFO-SFO", ]) # stops with error message</span>
- <span class='va'>f_nlme_dfop_sfo_tc</span> <span class='op'>&lt;-</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'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='error'>Error in X[, fmap[[nm]]] &lt;- gradnm: number of items to replace is not a multiple of replacement length</span></div><div class='output co'>#&gt; <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'>#&gt; <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'>
+#&gt; 1.0000000 0.2049995 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'>&lt;-</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'>&lt;-</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 &lt;- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</span>
+ <span class='co'># f_nlme_dfop_sfo_tc &lt;- nlme(f_2_tc["DFOP-SFO", ],</span>
+ <span class='co'># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] &lt;- 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'>#&gt; Model df AIC BIC logLik Test L.Ratio
+#&gt; f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274
+#&gt; f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093
+#&gt; p-value
+#&gt; f_nlme_dfop_sfo
+#&gt; f_nlme_dfop_sfo_obs &lt;.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
index 5cb33214..9c9a2211 100644
--- a/docs/dev/reference/plot.mixed.mmkin-1.png
+++ b/docs/dev/reference/plot.mixed.mmkin-1.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-2.png b/docs/dev/reference/plot.mixed.mmkin-2.png
index c0d67204..0f66ff0f 100644
--- a/docs/dev/reference/plot.mixed.mmkin-2.png
+++ b/docs/dev/reference/plot.mixed.mmkin-2.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-3.png b/docs/dev/reference/plot.mixed.mmkin-3.png
index 5e00afe6..34212f1c 100644
--- a/docs/dev/reference/plot.mixed.mmkin-3.png
+++ b/docs/dev/reference/plot.mixed.mmkin-3.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-4.png b/docs/dev/reference/plot.mixed.mmkin-4.png
index 6a5f3b9c..c1450d24 100644
--- a/docs/dev/reference/plot.mixed.mmkin-4.png
+++ b/docs/dev/reference/plot.mixed.mmkin-4.png
Binary files differ
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'>&lt;=</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'>&lt;=</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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Dec 21 05:58:23 2020"
+#&gt; [1] "Sat Feb 6 18:29:17 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [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>
+#&gt; [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'>&lt;-</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
index 6a32cda1..4474b1f1 100644
--- a/docs/dev/reference/saem-3.png
+++ b/docs/dev/reference/saem-3.png
Binary files differ
diff --git a/docs/dev/reference/saem-5.png b/docs/dev/reference/saem-5.png
index 6e6e0f91..27ed3f8f 100644
--- a/docs/dev/reference/saem-5.png
+++ b/docs/dev/reference/saem-5.png
Binary files differ
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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:42 2021"
+#&gt; [1] "Sat Feb 6 18:29:26 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:43 2021"</div><div class='input'>
+#&gt; [1] "Sat Feb 6 18:29:27 2021"</div><div class='input'>
<span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:45 2021"
+#&gt; [1] "Sat Feb 6 18:29:28 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:46 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</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>
+#&gt; [1] "Sat Feb 6 18:29:30 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:47 2021"
+#&gt; [1] "Sat Feb 6 18:29:30 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:49 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</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>
+#&gt; [1] "Sat Feb 6 18:29:32 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:49 2021"
+#&gt; [1] "Sat Feb 6 18:29:32 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:52 2021"</div><div class='input'>
+#&gt; [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'>&lt;-</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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:55 2021"
+#&gt; [1] "Sat Feb 6 18:29:37 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [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'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Sat Feb 6 18:29:42 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(list(f_saem_fomc$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'>&lt;-</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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:42:02 2021"
+#&gt; [1] "Sat Feb 6 18:29:44 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:42:07 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</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>
+#&gt; [1] "Sat Feb 6 18:29:48 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:42:08 2021"
+#&gt; [1] "Sat Feb 6 18:29:49 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [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>
+#&gt; [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'>#&gt; Kinetic nonlinear mixed-effects model fit by SAEM
#&gt; Structural model:
@@ -395,10 +395,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; 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'>#&gt; saemix version used for fitting: 3.1.9000
-#&gt; mkin version used for pre-fitting: 0.9.50.4
+#&gt; mkin version used for pre-fitting: 1.0.1.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Jan 25 14:42:18 2021
-#&gt; Date of summary: Mon Jan 25 14:42:18 2021
+#&gt; Date of fit: Sat Feb 6 18:29:57 2021
+#&gt; Date of summary: Sat Feb 6 18:29:58 2021
#&gt;
#&gt; Equations:
#&gt; 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>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 9.954 s using 300, 100 iterations
+#&gt; Fitted in 8.539 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;
@@ -489,12 +489,12 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Dataset 6 parent 3 69.2 71.32042 2.12042 1.883 1.125873
#&gt; Dataset 6 parent 6 58.1 56.45256 -1.64744 1.883 -0.874739
#&gt; Dataset 6 parent 6 56.6 56.45256 -0.14744 1.883 -0.078288
-#&gt; Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045256
+#&gt; Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045257
#&gt; Dataset 6 parent 10 43.4 44.48523 1.08523 1.883 0.576224
#&gt; Dataset 6 parent 20 33.3 29.75774 -3.54226 1.883 -1.880826
#&gt; Dataset 6 parent 20 29.2 29.75774 0.55774 1.883 0.296141
#&gt; Dataset 6 parent 34 17.6 19.35710 1.75710 1.883 0.932966
-#&gt; Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720578
+#&gt; Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720579
#&gt; Dataset 6 parent 55 10.5 10.48443 -0.01557 1.883 -0.008266
#&gt; Dataset 6 parent 55 9.3 10.48443 1.18443 1.883 0.628895
#&gt; 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>
#&gt; Dataset 8 parent 1 64.9 67.73197 2.83197 1.883 1.503686
#&gt; Dataset 8 parent 1 66.2 67.73197 1.53197 1.883 0.813428
#&gt; Dataset 8 parent 3 43.5 41.58448 -1.91552 1.883 -1.017081
-#&gt; Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335661
+#&gt; Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335662
#&gt; Dataset 8 parent 8 18.3 19.62286 1.32286 1.883 0.702395
-#&gt; Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808589
+#&gt; Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808588
#&gt; Dataset 8 parent 14 10.2 10.77819 0.57819 1.883 0.306999
#&gt; Dataset 8 parent 14 10.8 10.77819 -0.02181 1.883 -0.011582
#&gt; 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>
#&gt; Dataset 8 A1 1 7.7 7.61539 -0.08461 1.883 -0.044923
#&gt; Dataset 8 A1 3 15.0 15.47954 0.47954 1.883 0.254622
#&gt; Dataset 8 A1 3 15.1 15.47954 0.37954 1.883 0.201525
-#&gt; Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517076
+#&gt; Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517075
#&gt; Dataset 8 A1 8 21.1 20.22616 -0.87384 1.883 -0.463979
#&gt; Dataset 8 A1 14 19.7 20.00067 0.30067 1.883 0.159645
#&gt; Dataset 8 A1 14 18.9 20.00067 1.10067 1.883 0.584419
-#&gt; Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593929
-#&gt; Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255619
-#&gt; Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400123
+#&gt; Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593928
+#&gt; Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255620
+#&gt; Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400124
#&gt; Dataset 8 A1 48 9.8 10.25357 0.45357 1.883 0.240833
#&gt; Dataset 8 A1 70 6.2 5.95728 -0.24272 1.883 -0.128878
#&gt; 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>
#&gt; Dataset 9 A1 91 10.0 10.09177 0.09177 1.883 0.048727
#&gt; Dataset 9 A1 91 9.5 10.09177 0.59177 1.883 0.314211
#&gt; Dataset 9 A1 120 9.1 7.91379 -1.18621 1.883 -0.629841
-#&gt; Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576745
+#&gt; Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576744
#&gt; Dataset 10 parent 0 96.1 93.65257 -2.44743 1.883 -1.299505
#&gt; Dataset 10 parent 0 94.3 93.65257 -0.64743 1.883 -0.343763
#&gt; 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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 11 12:42:40 2021"
+#&gt; [1] "Sat Feb 6 18:30:00 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [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>
+#&gt; [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'>#&gt; saemix version used for fitting: 3.1.9000
-#&gt; mkin version used for pre-fitting: 0.9.50.4
+#&gt; mkin version used for pre-fitting: 1.0.1.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Jan 11 12:42:54 2021
-#&gt; Date of summary: Mon Jan 11 12:42:54 2021
+#&gt; Date of fit: Sat Feb 6 18:30:12 2021
+#&gt; Date of summary: Sat Feb 6 18:30:12 2021
#&gt;
#&gt; Equations:
#&gt; 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>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 13.298 s using 300, 100 iterations
+#&gt; Fitted in 11.769 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Two-component variance function
#&gt;
@@ -291,7 +291,7 @@ saemix authors for the parts inherited from saemix.</p>
#&gt; parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2
#&gt; 101.65645 -4.05368 -0.94311 -2.35943 -4.07006
#&gt; g_qlogis
-#&gt; -0.01133
+#&gt; -0.01132
#&gt;
#&gt; Fixed degradation parameter values:
#&gt; None
@@ -299,232 +299,232 @@ saemix authors for the parts inherited from saemix.</p>
#&gt; Results:
#&gt;
#&gt; Likelihood computed by importance sampling
-#&gt; AIC BIC logLik
-#&gt; 830 824.5 -401
+#&gt; AIC BIC logLik
+#&gt; 829.3 823.9 -400.7
#&gt;
#&gt; Optimised parameters:
-#&gt; est. lower upper
-#&gt; parent_0 101.4423 97.862 105.0224
-#&gt; log_k_m1 -4.0703 -4.191 -3.9495
-#&gt; f_parent_qlogis -0.9539 -1.313 -0.5949
-#&gt; log_k1 -2.9724 -3.811 -2.1342
-#&gt; log_k2 -3.4977 -4.206 -2.7895
-#&gt; g_qlogis -0.0449 -1.116 1.0262
+#&gt; est. lower upper
+#&gt; parent_0 101.29457 97.855 104.7344
+#&gt; log_k_m1 -4.06337 -4.182 -3.9445
+#&gt; f_parent_qlogis -0.94546 -1.307 -0.5841
+#&gt; log_k1 -2.98794 -3.844 -2.1321
+#&gt; log_k2 -3.47891 -4.253 -2.7050
+#&gt; g_qlogis -0.03211 -1.157 1.0931
#&gt;
#&gt; Correlation:
#&gt; prnt_0 lg_k_1 f_prn_ log_k1 log_k2
-#&gt; log_k_m1 -0.207
-#&gt; f_parent_qlogis -0.148 0.202
-#&gt; log_k1 0.040 -0.038 -0.022
-#&gt; log_k2 0.022 -0.015 -0.009 0.001
-#&gt; g_qlogis -0.012 0.005 0.011 -0.173 -0.130
+#&gt; log_k_m1 -0.202
+#&gt; f_parent_qlogis -0.145 0.195
+#&gt; log_k1 0.094 -0.099 -0.049
+#&gt; log_k2 -0.042 0.056 0.024 -0.097
+#&gt; g_qlogis -0.005 0.000 0.007 -0.160 -0.113
#&gt;
#&gt; Random effects:
-#&gt; est. lower upper
-#&gt; SD.parent_0 2.88564 -0.5163 6.2876
-#&gt; SD.log_k_m1 0.08502 -0.0427 0.2127
-#&gt; SD.f_parent_qlogis 0.38857 0.1350 0.6421
-#&gt; SD.log_k1 0.92338 0.3296 1.5172
-#&gt; SD.log_k2 0.78644 0.2817 1.2912
-#&gt; SD.g_qlogis 0.34614 -0.8727 1.5650
+#&gt; est. lower upper
+#&gt; SD.parent_0 2.70085 -0.64980 6.0515
+#&gt; SD.log_k_m1 0.08408 -0.04023 0.2084
+#&gt; SD.f_parent_qlogis 0.39215 0.13695 0.6473
+#&gt; SD.log_k1 0.89280 0.27466 1.5109
+#&gt; SD.log_k2 0.82387 0.26388 1.3838
+#&gt; SD.g_qlogis 0.36468 -0.86978 1.5991
#&gt;
#&gt; Variance model:
#&gt; est. lower upper
-#&gt; a.1 0.65859 0.49250 0.82469
-#&gt; b.1 0.06411 0.05006 0.07817
+#&gt; a.1 0.65724 0.49361 0.82086
+#&gt; b.1 0.06434 0.05034 0.07835
#&gt;
#&gt; Backtransformed parameters:
#&gt; est. lower upper
-#&gt; parent_0 101.44231 97.86220 105.02241
-#&gt; k_m1 0.01707 0.01513 0.01926
-#&gt; f_parent_to_m1 0.27811 0.21201 0.35551
-#&gt; k1 0.05118 0.02213 0.11834
-#&gt; k2 0.03027 0.01491 0.06145
-#&gt; g 0.48878 0.24675 0.73618
+#&gt; parent_0 101.29457 97.85477 104.73437
+#&gt; k_m1 0.01719 0.01526 0.01936
+#&gt; f_parent_to_m1 0.27980 0.21302 0.35798
+#&gt; k1 0.05039 0.02141 0.11859
+#&gt; k2 0.03084 0.01422 0.06687
+#&gt; g 0.49197 0.23916 0.74896
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
-#&gt; parent_m1 0.2781
-#&gt; parent_sink 0.7219
+#&gt; parent_m1 0.2798
+#&gt; parent_sink 0.7202
#&gt;
#&gt; Estimated disappearance times:
#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
-#&gt; parent 17.53 61.64 18.55 13.54 22.9
-#&gt; m1 40.60 134.88 NA NA NA
+#&gt; parent 17.49 61.05 18.38 13.76 22.47
+#&gt; m1 40.32 133.94 NA NA NA
#&gt;
#&gt; Data:
-#&gt; ds name time observed predicted residual std standardized
-#&gt; ds 1 parent 0 89.8 9.869e+01 8.894553 6.3618 1.398124
-#&gt; ds 1 parent 0 104.1 9.869e+01 -5.405447 6.3618 -0.849676
-#&gt; ds 1 parent 1 88.7 9.413e+01 5.426448 6.0706 0.893897
-#&gt; ds 1 parent 1 95.5 9.413e+01 -1.373552 6.0706 -0.226265
-#&gt; ds 1 parent 3 81.8 8.576e+01 3.961821 5.5377 0.715422
-#&gt; ds 1 parent 3 94.5 8.576e+01 -8.738179 5.5377 -1.577932
-#&gt; ds 1 parent 7 71.5 7.168e+01 0.184828 4.6429 0.039809
-#&gt; ds 1 parent 7 70.3 7.168e+01 1.384828 4.6429 0.298270
-#&gt; ds 1 parent 14 54.2 5.351e+01 -0.688235 3.4934 -0.197008
-#&gt; ds 1 parent 14 49.6 5.351e+01 3.911765 3.4934 1.119747
-#&gt; ds 1 parent 28 31.5 3.209e+01 0.590445 2.1603 0.273322
-#&gt; ds 1 parent 28 28.8 3.209e+01 3.290445 2.1603 1.523177
-#&gt; ds 1 parent 60 12.1 1.272e+01 0.618158 1.0481 0.589761
-#&gt; ds 1 parent 60 13.6 1.272e+01 -0.881842 1.0481 -0.841332
-#&gt; ds 1 parent 90 6.2 6.085e+00 -0.115212 0.7655 -0.150512
-#&gt; ds 1 parent 90 8.3 6.085e+00 -2.215212 0.7655 -2.893953
-#&gt; ds 1 parent 120 2.2 3.009e+00 0.809439 0.6863 1.179470
-#&gt; ds 1 parent 120 2.4 3.009e+00 0.609439 0.6863 0.888041
-#&gt; ds 1 m1 1 0.3 1.129e+00 0.828817 0.6626 1.250938
-#&gt; ds 1 m1 1 0.2 1.129e+00 0.928817 0.6626 1.401869
-#&gt; ds 1 m1 3 2.2 3.141e+00 0.940880 0.6887 1.366187
-#&gt; ds 1 m1 3 3.0 3.141e+00 0.140880 0.6887 0.204562
-#&gt; ds 1 m1 7 6.5 6.326e+00 -0.174162 0.7735 -0.225175
-#&gt; ds 1 m1 7 5.0 6.326e+00 1.325838 0.7735 1.714181
-#&gt; ds 1 m1 14 10.2 9.883e+00 -0.317417 0.9139 -0.347326
-#&gt; ds 1 m1 14 9.5 9.883e+00 0.382583 0.9139 0.418631
-#&gt; ds 1 m1 28 12.2 1.251e+01 0.309856 1.0378 0.298572
-#&gt; ds 1 m1 28 13.4 1.251e+01 -0.890144 1.0378 -0.857726
-#&gt; ds 1 m1 60 11.8 1.086e+01 -0.940009 0.9584 -0.980812
-#&gt; ds 1 m1 60 13.2 1.086e+01 -2.340009 0.9584 -2.441581
-#&gt; ds 1 m1 90 6.6 7.823e+00 1.222977 0.8278 1.477332
-#&gt; ds 1 m1 90 9.3 7.823e+00 -1.477023 0.8278 -1.784214
-#&gt; ds 1 m1 120 3.5 5.315e+00 1.815201 0.7415 2.447906
-#&gt; ds 1 m1 120 5.4 5.315e+00 -0.084799 0.7415 -0.114356
-#&gt; ds 2 parent 0 118.0 1.031e+02 -14.876736 6.6443 -2.239038
-#&gt; ds 2 parent 0 99.8 1.031e+02 3.323264 6.6443 0.500171
-#&gt; ds 2 parent 1 90.2 9.757e+01 7.371379 6.2902 1.171891
-#&gt; ds 2 parent 1 94.6 9.757e+01 2.971379 6.2902 0.472386
-#&gt; ds 2 parent 3 96.1 8.788e+01 -8.222746 5.6724 -1.449599
-#&gt; ds 2 parent 3 78.4 8.788e+01 9.477254 5.6724 1.670758
-#&gt; ds 2 parent 7 77.9 7.293e+01 -4.972272 4.7218 -1.053054
-#&gt; ds 2 parent 7 77.7 7.293e+01 -4.772272 4.7218 -1.010697
-#&gt; ds 2 parent 14 56.0 5.602e+01 0.016773 3.6513 0.004594
-#&gt; ds 2 parent 14 54.7 5.602e+01 1.316773 3.6513 0.360633
-#&gt; ds 2 parent 28 36.6 3.855e+01 1.945779 2.5575 0.760803
-#&gt; ds 2 parent 28 36.8 3.855e+01 1.745779 2.5575 0.682603
-#&gt; ds 2 parent 60 22.1 2.101e+01 -1.086693 1.4996 -0.724663
-#&gt; ds 2 parent 60 24.7 2.101e+01 -3.686693 1.4996 -2.458475
-#&gt; ds 2 parent 90 12.4 1.246e+01 0.058759 1.0353 0.056757
-#&gt; ds 2 parent 90 10.8 1.246e+01 1.658759 1.0353 1.602256
-#&gt; ds 2 parent 120 6.8 7.406e+00 0.606226 0.8119 0.746659
-#&gt; ds 2 parent 120 7.9 7.406e+00 -0.493774 0.8119 -0.608157
-#&gt; ds 2 m1 1 1.3 1.438e+00 0.138236 0.6650 0.207869
-#&gt; ds 2 m1 3 3.7 3.879e+00 0.178617 0.7040 0.253726
-#&gt; ds 2 m1 3 4.7 3.879e+00 -0.821383 0.7040 -1.166780
-#&gt; ds 2 m1 7 8.1 7.389e+00 -0.710951 0.8113 -0.876337
-#&gt; ds 2 m1 7 7.9 7.389e+00 -0.510951 0.8113 -0.629812
-#&gt; ds 2 m1 14 10.1 1.069e+01 0.593533 0.9507 0.624328
-#&gt; ds 2 m1 14 10.3 1.069e+01 0.393533 0.9507 0.413951
-#&gt; ds 2 m1 28 10.7 1.240e+01 1.703647 1.0325 1.649956
-#&gt; ds 2 m1 28 12.2 1.240e+01 0.203647 1.0325 0.197229
-#&gt; ds 2 m1 60 10.7 1.055e+01 -0.147672 0.9442 -0.156405
-#&gt; ds 2 m1 60 12.5 1.055e+01 -1.947672 0.9442 -2.062848
-#&gt; ds 2 m1 90 9.1 8.010e+00 -1.090041 0.8351 -1.305210
-#&gt; ds 2 m1 90 7.4 8.010e+00 0.609959 0.8351 0.730362
-#&gt; ds 2 m1 120 6.1 5.793e+00 -0.306797 0.7561 -0.405759
-#&gt; ds 2 m1 120 4.5 5.793e+00 1.293203 0.7561 1.710347
-#&gt; ds 3 parent 0 106.2 1.035e+02 -2.712344 6.6675 -0.406801
-#&gt; ds 3 parent 0 106.9 1.035e+02 -3.412344 6.6675 -0.511788
-#&gt; ds 3 parent 1 107.4 9.548e+01 -11.924044 6.1566 -1.936801
-#&gt; ds 3 parent 1 96.1 9.548e+01 -0.624044 6.1566 -0.101362
-#&gt; ds 3 parent 3 79.4 8.246e+01 3.056105 5.3274 0.573662
-#&gt; ds 3 parent 3 82.6 8.246e+01 -0.143895 5.3274 -0.027010
-#&gt; ds 3 parent 7 63.9 6.489e+01 0.991141 4.2122 0.235304
-#&gt; ds 3 parent 7 62.4 6.489e+01 2.491141 4.2122 0.591416
-#&gt; ds 3 parent 14 51.0 4.869e+01 -2.306824 3.1906 -0.723013
-#&gt; ds 3 parent 14 47.1 4.869e+01 1.593176 3.1906 0.499338
-#&gt; ds 3 parent 28 36.1 3.480e+01 -1.304261 2.3260 -0.560722
-#&gt; ds 3 parent 28 36.6 3.480e+01 -1.804261 2.3260 -0.775679
-#&gt; ds 3 parent 60 20.1 1.988e+01 -0.221952 1.4346 -0.154719
-#&gt; ds 3 parent 60 19.8 1.988e+01 0.078048 1.4346 0.054406
-#&gt; ds 3 parent 90 11.3 1.194e+01 0.642458 1.0099 0.636132
-#&gt; ds 3 parent 90 10.7 1.194e+01 1.242458 1.0099 1.230224
-#&gt; ds 3 parent 120 8.2 7.176e+00 -1.023847 0.8034 -1.274423
-#&gt; ds 3 parent 120 7.3 7.176e+00 -0.123847 0.8034 -0.154158
-#&gt; ds 3 m1 0 0.8 8.527e-13 -0.800000 0.6586 -1.214712
-#&gt; ds 3 m1 1 1.8 1.856e+00 0.055925 0.6693 0.083562
-#&gt; ds 3 m1 1 2.3 1.856e+00 -0.444075 0.6693 -0.663537
-#&gt; ds 3 m1 3 4.2 4.780e+00 0.580164 0.7264 0.798676
-#&gt; ds 3 m1 3 4.1 4.780e+00 0.680164 0.7264 0.936340
-#&gt; ds 3 m1 7 6.8 8.410e+00 1.609920 0.8512 1.891455
-#&gt; ds 3 m1 7 10.1 8.410e+00 -1.690080 0.8512 -1.985633
-#&gt; ds 3 m1 14 11.4 1.098e+01 -0.424444 0.9638 -0.440389
-#&gt; ds 3 m1 14 12.8 1.098e+01 -1.824444 0.9638 -1.892979
-#&gt; ds 3 m1 28 11.5 1.142e+01 -0.079336 0.9848 -0.080558
-#&gt; ds 3 m1 28 10.6 1.142e+01 0.820664 0.9848 0.833311
-#&gt; ds 3 m1 60 7.5 9.110e+00 1.610231 0.8803 1.829222
-#&gt; ds 3 m1 60 8.6 9.110e+00 0.510231 0.8803 0.579622
-#&gt; ds 3 m1 90 7.3 6.799e+00 -0.501085 0.7898 -0.634463
-#&gt; ds 3 m1 90 8.1 6.799e+00 -1.301085 0.7898 -1.647404
-#&gt; ds 3 m1 120 5.3 4.868e+00 -0.431505 0.7288 -0.592064
-#&gt; ds 3 m1 120 3.8 4.868e+00 1.068495 0.7288 1.466073
-#&gt; ds 4 parent 0 104.7 9.926e+01 -5.444622 6.3975 -0.851049
-#&gt; ds 4 parent 0 88.3 9.926e+01 10.955378 6.3975 1.712436
-#&gt; ds 4 parent 1 94.2 9.618e+01 1.978413 6.2013 0.319030
-#&gt; ds 4 parent 1 94.6 9.618e+01 1.578413 6.2013 0.254527
-#&gt; ds 4 parent 3 78.1 9.037e+01 12.268550 5.8311 2.103985
-#&gt; ds 4 parent 3 96.5 9.037e+01 -6.131450 5.8311 -1.051508
-#&gt; ds 4 parent 7 76.2 7.999e+01 3.794958 5.1708 0.733918
-#&gt; ds 4 parent 7 77.8 7.999e+01 2.194958 5.1708 0.424489
-#&gt; ds 4 parent 14 70.8 6.518e+01 -5.624996 4.2301 -1.329742
-#&gt; ds 4 parent 14 67.3 6.518e+01 -2.124996 4.2301 -0.502346
-#&gt; ds 4 parent 28 43.1 4.462e+01 1.517860 2.9354 0.517085
-#&gt; ds 4 parent 28 45.1 4.462e+01 -0.482140 2.9354 -0.164249
-#&gt; ds 4 parent 60 21.3 2.130e+01 -0.003305 1.5159 -0.002180
-#&gt; ds 4 parent 60 23.5 2.130e+01 -2.203305 1.5159 -1.453435
-#&gt; ds 4 parent 90 11.8 1.180e+01 0.002834 1.0032 0.002825
-#&gt; ds 4 parent 90 12.1 1.180e+01 -0.297166 1.0032 -0.296226
-#&gt; ds 4 parent 120 7.0 6.868e+00 -0.132251 0.7922 -0.166937
-#&gt; ds 4 parent 120 6.2 6.868e+00 0.667749 0.7922 0.842879
-#&gt; ds 4 m1 0 1.6 0.000e+00 -1.600000 0.6586 -2.429424
-#&gt; ds 4 m1 1 0.9 6.826e-01 -0.217363 0.6600 -0.329315
-#&gt; ds 4 m1 3 3.7 1.935e+00 -1.765082 0.6702 -2.633768
-#&gt; ds 4 m1 3 2.0 1.935e+00 -0.065082 0.6702 -0.097112
-#&gt; ds 4 m1 7 3.6 4.035e+00 0.434805 0.7076 0.614501
-#&gt; ds 4 m1 7 3.8 4.035e+00 0.234805 0.7076 0.331845
-#&gt; ds 4 m1 14 7.1 6.652e+00 -0.448187 0.7846 -0.571220
-#&gt; ds 4 m1 14 6.6 6.652e+00 0.051813 0.7846 0.066036
-#&gt; ds 4 m1 28 9.5 9.156e+00 -0.343805 0.8822 -0.389696
-#&gt; ds 4 m1 28 9.3 9.156e+00 -0.143805 0.8822 -0.163000
-#&gt; ds 4 m1 60 8.3 8.848e+00 0.547762 0.8692 0.630185
-#&gt; ds 4 m1 60 9.0 8.848e+00 -0.152238 0.8692 -0.175146
-#&gt; ds 4 m1 90 6.6 6.674e+00 0.073979 0.7854 0.094194
-#&gt; ds 4 m1 90 7.7 6.674e+00 -1.026021 0.7854 -1.306390
-#&gt; ds 4 m1 120 3.7 4.668e+00 0.967537 0.7234 1.337503
-#&gt; ds 4 m1 120 3.5 4.668e+00 1.167537 0.7234 1.613979
-#&gt; ds 5 parent 0 110.4 1.022e+02 -8.170986 6.5872 -1.240433
-#&gt; ds 5 parent 0 112.1 1.022e+02 -9.870986 6.5872 -1.498509
-#&gt; ds 5 parent 1 93.5 9.513e+01 1.630764 6.1346 0.265832
-#&gt; ds 5 parent 1 91.0 9.513e+01 4.130764 6.1346 0.673359
-#&gt; ds 5 parent 3 71.0 8.296e+01 11.964279 5.3597 2.232268
-#&gt; ds 5 parent 3 89.7 8.296e+01 -6.735721 5.3597 -1.256735
-#&gt; ds 5 parent 7 60.4 6.495e+01 4.547441 4.2157 1.078684
-#&gt; ds 5 parent 7 59.1 6.495e+01 5.847441 4.2157 1.387053
-#&gt; ds 5 parent 14 56.5 4.626e+01 -10.241319 3.0380 -3.371047
-#&gt; ds 5 parent 14 47.0 4.626e+01 -0.741319 3.0380 -0.244014
-#&gt; ds 5 parent 28 30.2 3.026e+01 0.058478 2.0487 0.028544
-#&gt; ds 5 parent 28 23.9 3.026e+01 6.358478 2.0487 3.103661
-#&gt; ds 5 parent 60 17.0 1.792e+01 0.919046 1.3242 0.694024
-#&gt; ds 5 parent 60 18.7 1.792e+01 -0.780954 1.3242 -0.589742
-#&gt; ds 5 parent 90 11.3 1.187e+01 0.573917 1.0066 0.570144
-#&gt; ds 5 parent 90 11.9 1.187e+01 -0.026083 1.0066 -0.025912
-#&gt; ds 5 parent 120 9.0 7.898e+00 -1.102089 0.8307 -1.326622
-#&gt; ds 5 parent 120 8.1 7.898e+00 -0.202089 0.8307 -0.243261
-#&gt; ds 5 m1 0 0.7 -1.421e-14 -0.700000 0.6586 -1.062873
-#&gt; ds 5 m1 1 3.0 3.144e+00 0.143526 0.6887 0.208390
-#&gt; ds 5 m1 1 2.6 3.144e+00 0.543526 0.6887 0.789161
-#&gt; ds 5 m1 3 5.1 8.390e+00 3.290265 0.8504 3.869277
-#&gt; ds 5 m1 3 7.5 8.390e+00 0.890265 0.8504 1.046932
-#&gt; ds 5 m1 7 16.5 1.566e+01 -0.841368 1.2007 -0.700751
-#&gt; ds 5 m1 7 19.0 1.566e+01 -3.341368 1.2007 -2.782928
-#&gt; ds 5 m1 14 22.9 2.188e+01 -1.017753 1.5498 -0.656687
-#&gt; ds 5 m1 14 23.2 2.188e+01 -1.317753 1.5498 -0.850257
-#&gt; ds 5 m1 28 22.2 2.386e+01 1.655914 1.6652 0.994399
-#&gt; ds 5 m1 28 24.4 2.386e+01 -0.544086 1.6652 -0.326731
-#&gt; ds 5 m1 60 15.5 1.859e+01 3.091124 1.3618 2.269915
-#&gt; ds 5 m1 60 19.8 1.859e+01 -1.208876 1.3618 -0.887718
-#&gt; ds 5 m1 90 14.9 1.372e+01 -1.176815 1.0990 -1.070784
-#&gt; ds 5 m1 90 14.2 1.372e+01 -0.476815 1.0990 -0.433854
-#&gt; ds 5 m1 120 10.9 9.961e+00 -0.938796 0.9174 -1.023332
-#&gt; ds 5 m1 120 10.4 9.961e+00 -0.438796 0.9174 -0.478308</div><div class='input'><span class='co'># }</span>
+#&gt; ds name time observed predicted residual std standardized
+#&gt; ds 1 parent 0 89.8 9.878e+01 8.98039 6.3899 1.40541
+#&gt; ds 1 parent 0 104.1 9.878e+01 -5.31961 6.3899 -0.83251
+#&gt; ds 1 parent 1 88.7 9.422e+01 5.52084 6.0981 0.90533
+#&gt; ds 1 parent 1 95.5 9.422e+01 -1.27916 6.0981 -0.20976
+#&gt; ds 1 parent 3 81.8 8.587e+01 4.06752 5.5641 0.73103
+#&gt; ds 1 parent 3 94.5 8.587e+01 -8.63248 5.5641 -1.55147
+#&gt; ds 1 parent 7 71.5 7.180e+01 0.29615 4.6662 0.06347
+#&gt; ds 1 parent 7 70.3 7.180e+01 1.49615 4.6662 0.32063
+#&gt; ds 1 parent 14 54.2 5.360e+01 -0.59602 3.5112 -0.16975
+#&gt; ds 1 parent 14 49.6 5.360e+01 4.00398 3.5112 1.14035
+#&gt; ds 1 parent 28 31.5 3.213e+01 0.62529 2.1691 0.28828
+#&gt; ds 1 parent 28 28.8 3.213e+01 3.32529 2.1691 1.53306
+#&gt; ds 1 parent 60 12.1 1.271e+01 0.60718 1.0490 0.57879
+#&gt; ds 1 parent 60 13.6 1.271e+01 -0.89282 1.0490 -0.85108
+#&gt; ds 1 parent 90 6.2 6.080e+00 -0.12020 0.7649 -0.15716
+#&gt; ds 1 parent 90 8.3 6.080e+00 -2.22020 0.7649 -2.90279
+#&gt; ds 1 parent 120 2.2 3.011e+00 0.81059 0.6852 1.18302
+#&gt; ds 1 parent 120 2.4 3.011e+00 0.61059 0.6852 0.89113
+#&gt; ds 1 m1 1 0.3 1.131e+00 0.83071 0.6613 1.25628
+#&gt; ds 1 m1 1 0.2 1.131e+00 0.93071 0.6613 1.40750
+#&gt; ds 1 m1 3 2.2 3.147e+00 0.94691 0.6877 1.37688
+#&gt; ds 1 m1 3 3.0 3.147e+00 0.14691 0.6877 0.21361
+#&gt; ds 1 m1 7 6.5 6.341e+00 -0.15949 0.7736 -0.20618
+#&gt; ds 1 m1 7 5.0 6.341e+00 1.34051 0.7736 1.73290
+#&gt; ds 1 m1 14 10.2 9.910e+00 -0.28991 0.9157 -0.31659
+#&gt; ds 1 m1 14 9.5 9.910e+00 0.41009 0.9157 0.44783
+#&gt; ds 1 m1 28 12.2 1.255e+01 0.34690 1.0410 0.33323
+#&gt; ds 1 m1 28 13.4 1.255e+01 -0.85310 1.0410 -0.81949
+#&gt; ds 1 m1 60 11.8 1.087e+01 -0.92713 0.9599 -0.96586
+#&gt; ds 1 m1 60 13.2 1.087e+01 -2.32713 0.9599 -2.42434
+#&gt; ds 1 m1 90 6.6 7.813e+00 1.21254 0.8274 1.46541
+#&gt; ds 1 m1 90 9.3 7.813e+00 -1.48746 0.8274 -1.79766
+#&gt; ds 1 m1 120 3.5 5.295e+00 1.79489 0.7403 2.42457
+#&gt; ds 1 m1 120 5.4 5.295e+00 -0.10511 0.7403 -0.14198
+#&gt; ds 2 parent 0 118.0 1.074e+02 -10.63436 6.9396 -1.53242
+#&gt; ds 2 parent 0 99.8 1.074e+02 7.56564 6.9396 1.09021
+#&gt; ds 2 parent 1 90.2 1.012e+02 10.96486 6.5425 1.67594
+#&gt; ds 2 parent 1 94.6 1.012e+02 6.56486 6.5425 1.00342
+#&gt; ds 2 parent 3 96.1 9.054e+01 -5.56014 5.8627 -0.94839
+#&gt; ds 2 parent 3 78.4 9.054e+01 12.13986 5.8627 2.07069
+#&gt; ds 2 parent 7 77.9 7.468e+01 -3.21805 4.8501 -0.66350
+#&gt; ds 2 parent 7 77.7 7.468e+01 -3.01805 4.8501 -0.62226
+#&gt; ds 2 parent 14 56.0 5.748e+01 1.47774 3.7563 0.39340
+#&gt; ds 2 parent 14 54.7 5.748e+01 2.77774 3.7563 0.73948
+#&gt; ds 2 parent 28 36.6 3.996e+01 3.36317 2.6541 1.26717
+#&gt; ds 2 parent 28 36.8 3.996e+01 3.16317 2.6541 1.19182
+#&gt; ds 2 parent 60 22.1 2.132e+01 -0.78225 1.5210 -0.51430
+#&gt; ds 2 parent 60 24.7 2.132e+01 -3.38225 1.5210 -2.22369
+#&gt; ds 2 parent 90 12.4 1.215e+01 -0.25010 1.0213 -0.24487
+#&gt; ds 2 parent 90 10.8 1.215e+01 1.34990 1.0213 1.32169
+#&gt; ds 2 parent 120 6.8 6.931e+00 0.13105 0.7943 0.16500
+#&gt; ds 2 parent 120 7.9 6.931e+00 -0.96895 0.7943 -1.21994
+#&gt; ds 2 m1 1 1.3 1.519e+00 0.21924 0.6645 0.32995
+#&gt; ds 2 m1 3 3.7 4.049e+00 0.34891 0.7070 0.49351
+#&gt; ds 2 m1 3 4.7 4.049e+00 -0.65109 0.7070 -0.92094
+#&gt; ds 2 m1 7 8.1 7.565e+00 -0.53526 0.8179 -0.65448
+#&gt; ds 2 m1 7 7.9 7.565e+00 -0.33526 0.8179 -0.40993
+#&gt; ds 2 m1 14 10.1 1.071e+01 0.60614 0.9521 0.63663
+#&gt; ds 2 m1 14 10.3 1.071e+01 0.40614 0.9521 0.42657
+#&gt; ds 2 m1 28 10.7 1.224e+01 1.54440 1.0260 1.50526
+#&gt; ds 2 m1 28 12.2 1.224e+01 0.04440 1.0260 0.04327
+#&gt; ds 2 m1 60 10.7 1.056e+01 -0.14005 0.9453 -0.14815
+#&gt; ds 2 m1 60 12.5 1.056e+01 -1.94005 0.9453 -2.05226
+#&gt; ds 2 m1 90 9.1 8.089e+00 -1.01088 0.8384 -1.20577
+#&gt; ds 2 m1 90 7.4 8.089e+00 0.68912 0.8384 0.82197
+#&gt; ds 2 m1 120 6.1 5.855e+00 -0.24463 0.7576 -0.32292
+#&gt; ds 2 m1 120 4.5 5.855e+00 1.35537 0.7576 1.78911
+#&gt; ds 3 parent 0 106.2 1.095e+02 3.30335 7.0765 0.46680
+#&gt; ds 3 parent 0 106.9 1.095e+02 2.60335 7.0765 0.36788
+#&gt; ds 3 parent 1 107.4 9.939e+01 -8.01282 6.4287 -1.24641
+#&gt; ds 3 parent 1 96.1 9.939e+01 3.28718 6.4287 0.51133
+#&gt; ds 3 parent 3 79.4 8.365e+01 4.24698 5.4222 0.78326
+#&gt; ds 3 parent 3 82.6 8.365e+01 1.04698 5.4222 0.19309
+#&gt; ds 3 parent 7 63.9 6.405e+01 0.14704 4.1732 0.03523
+#&gt; ds 3 parent 7 62.4 6.405e+01 1.64704 4.1732 0.39467
+#&gt; ds 3 parent 14 51.0 4.795e+01 -3.04985 3.1546 -0.96681
+#&gt; ds 3 parent 14 47.1 4.795e+01 0.85015 3.1546 0.26950
+#&gt; ds 3 parent 28 36.1 3.501e+01 -1.09227 2.3465 -0.46549
+#&gt; ds 3 parent 28 36.6 3.501e+01 -1.59227 2.3465 -0.67858
+#&gt; ds 3 parent 60 20.1 2.012e+01 0.02116 1.4520 0.01457
+#&gt; ds 3 parent 60 19.8 2.012e+01 0.32116 1.4520 0.22119
+#&gt; ds 3 parent 90 11.3 1.206e+01 0.76096 1.0170 0.74826
+#&gt; ds 3 parent 90 10.7 1.206e+01 1.36096 1.0170 1.33825
+#&gt; ds 3 parent 120 8.2 7.230e+00 -0.97022 0.8052 -1.20493
+#&gt; ds 3 parent 120 7.3 7.230e+00 -0.07022 0.8052 -0.08721
+#&gt; ds 3 m1 0 0.8 -5.684e-13 -0.80000 0.6572 -1.21722
+#&gt; ds 3 m1 1 1.8 2.045e+00 0.24538 0.6703 0.36608
+#&gt; ds 3 m1 1 2.3 2.045e+00 -0.25462 0.6703 -0.37987
+#&gt; ds 3 m1 3 4.2 5.136e+00 0.93594 0.7356 1.27228
+#&gt; ds 3 m1 3 4.1 5.136e+00 1.03594 0.7356 1.40822
+#&gt; ds 3 m1 7 6.8 8.674e+00 1.87438 0.8623 2.17381
+#&gt; ds 3 m1 7 10.1 8.674e+00 -1.42562 0.8623 -1.65335
+#&gt; ds 3 m1 14 11.4 1.083e+01 -0.56746 0.9580 -0.59233
+#&gt; ds 3 m1 14 12.8 1.083e+01 -1.96746 0.9580 -2.05369
+#&gt; ds 3 m1 28 11.5 1.098e+01 -0.51762 0.9651 -0.53637
+#&gt; ds 3 m1 28 10.6 1.098e+01 0.38238 0.9651 0.39623
+#&gt; ds 3 m1 60 7.5 8.889e+00 1.38911 0.8713 1.59436
+#&gt; ds 3 m1 60 8.6 8.889e+00 0.28911 0.8713 0.33183
+#&gt; ds 3 m1 90 7.3 6.774e+00 -0.52608 0.7886 -0.66708
+#&gt; ds 3 m1 90 8.1 6.774e+00 -1.32608 0.7886 -1.68150
+#&gt; ds 3 m1 120 5.3 4.954e+00 -0.34584 0.7305 -0.47345
+#&gt; ds 3 m1 120 3.8 4.954e+00 1.15416 0.7305 1.58004
+#&gt; ds 4 parent 0 104.7 9.957e+01 -5.13169 6.4403 -0.79681
+#&gt; ds 4 parent 0 88.3 9.957e+01 11.26831 6.4403 1.74966
+#&gt; ds 4 parent 1 94.2 9.644e+01 2.23888 6.2400 0.35879
+#&gt; ds 4 parent 1 94.6 9.644e+01 1.83888 6.2400 0.29469
+#&gt; ds 4 parent 3 78.1 9.054e+01 12.43946 5.8627 2.12180
+#&gt; ds 4 parent 3 96.5 9.054e+01 -5.96054 5.8627 -1.01669
+#&gt; ds 4 parent 7 76.2 8.004e+01 3.83771 5.1918 0.73919
+#&gt; ds 4 parent 7 77.8 8.004e+01 2.23771 5.1918 0.43101
+#&gt; ds 4 parent 14 70.8 6.511e+01 -5.69246 4.2406 -1.34238
+#&gt; ds 4 parent 14 67.3 6.511e+01 -2.19246 4.2406 -0.51702
+#&gt; ds 4 parent 28 43.1 4.454e+01 1.43744 2.9401 0.48890
+#&gt; ds 4 parent 28 45.1 4.454e+01 -0.56256 2.9401 -0.19134
+#&gt; ds 4 parent 60 21.3 2.132e+01 0.02005 1.5211 0.01318
+#&gt; ds 4 parent 60 23.5 2.132e+01 -2.17995 1.5211 -1.43310
+#&gt; ds 4 parent 90 11.8 1.182e+01 0.02167 1.0053 0.02156
+#&gt; ds 4 parent 90 12.1 1.182e+01 -0.27833 1.0053 -0.27687
+#&gt; ds 4 parent 120 7.0 6.852e+00 -0.14780 0.7914 -0.18675
+#&gt; ds 4 parent 120 6.2 6.852e+00 0.65220 0.7914 0.82408
+#&gt; ds 4 m1 0 1.6 -5.684e-14 -1.60000 0.6572 -2.43444
+#&gt; ds 4 m1 1 0.9 6.918e-01 -0.20821 0.6587 -0.31607
+#&gt; ds 4 m1 3 3.7 1.959e+00 -1.74131 0.6692 -2.60204
+#&gt; ds 4 m1 3 2.0 1.959e+00 -0.04131 0.6692 -0.06173
+#&gt; ds 4 m1 7 3.6 4.076e+00 0.47590 0.7076 0.67252
+#&gt; ds 4 m1 7 3.8 4.076e+00 0.27590 0.7076 0.38989
+#&gt; ds 4 m1 14 7.1 6.698e+00 -0.40189 0.7859 -0.51135
+#&gt; ds 4 m1 14 6.6 6.698e+00 0.09811 0.7859 0.12483
+#&gt; ds 4 m1 28 9.5 9.175e+00 -0.32492 0.8835 -0.36779
+#&gt; ds 4 m1 28 9.3 9.175e+00 -0.12492 0.8835 -0.14141
+#&gt; ds 4 m1 60 8.3 8.818e+00 0.51810 0.8683 0.59671
+#&gt; ds 4 m1 60 9.0 8.818e+00 -0.18190 0.8683 -0.20949
+#&gt; ds 4 m1 90 6.6 6.645e+00 0.04480 0.7841 0.05713
+#&gt; ds 4 m1 90 7.7 6.645e+00 -1.05520 0.7841 -1.34581
+#&gt; ds 4 m1 120 3.7 4.648e+00 0.94805 0.7221 1.31293
+#&gt; ds 4 m1 120 3.5 4.648e+00 1.14805 0.7221 1.58991
+#&gt; ds 5 parent 0 110.4 1.026e+02 -7.81752 6.6333 -1.17853
+#&gt; ds 5 parent 0 112.1 1.026e+02 -9.51752 6.6333 -1.43482
+#&gt; ds 5 parent 1 93.5 9.560e+01 2.10274 6.1865 0.33989
+#&gt; ds 5 parent 1 91.0 9.560e+01 4.60274 6.1865 0.74399
+#&gt; ds 5 parent 3 71.0 8.356e+01 12.55799 5.4165 2.31846
+#&gt; ds 5 parent 3 89.7 8.356e+01 -6.14201 5.4165 -1.13394
+#&gt; ds 5 parent 7 60.4 6.550e+01 5.09732 4.2653 1.19506
+#&gt; ds 5 parent 7 59.1 6.550e+01 6.39732 4.2653 1.49984
+#&gt; ds 5 parent 14 56.5 4.641e+01 -10.09145 3.0576 -3.30044
+#&gt; ds 5 parent 14 47.0 4.641e+01 -0.59145 3.0576 -0.19344
+#&gt; ds 5 parent 28 30.2 2.982e+01 -0.37647 2.0284 -0.18560
+#&gt; ds 5 parent 28 23.9 2.982e+01 5.92353 2.0284 2.92028
+#&gt; ds 5 parent 60 17.0 1.754e+01 0.53981 1.3060 0.41332
+#&gt; ds 5 parent 60 18.7 1.754e+01 -1.16019 1.3060 -0.88834
+#&gt; ds 5 parent 90 11.3 1.175e+01 0.45050 1.0018 0.44969
+#&gt; ds 5 parent 90 11.9 1.175e+01 -0.14950 1.0018 -0.14923
+#&gt; ds 5 parent 120 9.0 7.915e+00 -1.08476 0.8315 -1.30462
+#&gt; ds 5 parent 120 8.1 7.915e+00 -0.18476 0.8315 -0.22220
+#&gt; ds 5 m1 0 0.7 0.000e+00 -0.70000 0.6572 -1.06507
+#&gt; ds 5 m1 1 3.0 3.062e+00 0.06170 0.6861 0.08992
+#&gt; ds 5 m1 1 2.6 3.062e+00 0.46170 0.6861 0.67290
+#&gt; ds 5 m1 3 5.1 8.209e+00 3.10938 0.8432 3.68760
+#&gt; ds 5 m1 3 7.5 8.209e+00 0.70938 0.8432 0.84130
+#&gt; ds 5 m1 7 16.5 1.544e+01 -1.05567 1.1914 -0.88605
+#&gt; ds 5 m1 7 19.0 1.544e+01 -3.55567 1.1914 -2.98436
+#&gt; ds 5 m1 14 22.9 2.181e+01 -1.08765 1.5498 -0.70181
+#&gt; ds 5 m1 14 23.2 2.181e+01 -1.38765 1.5498 -0.89539
+#&gt; ds 5 m1 28 22.2 2.404e+01 1.83624 1.6805 1.09270
+#&gt; ds 5 m1 28 24.4 2.404e+01 -0.36376 1.6805 -0.21647
+#&gt; ds 5 m1 60 15.5 1.875e+01 3.25390 1.3741 2.36805
+#&gt; ds 5 m1 60 19.8 1.875e+01 -1.04610 1.3741 -0.76131
+#&gt; ds 5 m1 90 14.9 1.380e+01 -1.09507 1.1050 -0.99102
+#&gt; ds 5 m1 90 14.2 1.380e+01 -0.39507 1.1050 -0.35753
+#&gt; ds 5 m1 120 10.9 1.002e+01 -0.88429 0.9205 -0.96069
+#&gt; 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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.5985 1.5702 96.404 102.79
-#&gt; log_k_parent -2.3157 0.0409 -2.399 -2.23
-#&gt; log_k_m1 -5.2475 0.1332 -5.518 -4.98
-#&gt; f_parent_qlogis 0.0579 0.0893 -0.124 0.24
-#&gt; 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'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931
-#&gt; k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073
-#&gt; k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
-#&gt; f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596
-#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'>
+</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60 1.5702 96.40 102.79
+#&gt; log_k_parent_sink -3.04 0.0763 -3.19 -2.88
+#&gt; log_k_parent_m1 -2.98 0.0403 -3.06 -2.90
+#&gt; log_k_m1_sink -5.25 0.1332 -5.52 -4.98
+#&gt; sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931
+#&gt; k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560
+#&gt; k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551
+#&gt; k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
+#&gt; 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'>&lt;-</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'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='error'>Error in if (cost &lt; 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'>#&gt; <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'>&lt;-</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'>#&gt; <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'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <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'>&lt;-</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'>&lt;-</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'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.59848 1.57022 96.40384 1.03e+02
+#&gt; k_parent_sink 0.04792 0.00365 0.04049 5.54e-02
+#&gt; k_parent_m1 0.05078 0.00205 0.04661 5.49e-02
+#&gt; k_m1_sink 0.00526 0.00070 0.00384 6.69e-03
+#&gt; sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02
+#&gt; k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02
+#&gt; k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02
+#&gt; k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03
+#&gt; 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'>&lt;-</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'>&lt;-</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'>$</span><span class='va'>start</span><span class='op'>)</span>
<span class='va'>transformed</span> <span class='op'>&lt;-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>$</span><span class='va'>value</span>
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>transformed</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</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'>#&gt; parent_0 log_k_parent log_k_m1 f_parent_qlogis
-#&gt; 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'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1
-#&gt; 100.7500 0.1000 0.1001 0.5000 </div><div class='input'>
+</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 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'>#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
+#&gt; 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'>&lt;-</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'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
-<span class='va'>fit.ff</span> <span class='op'>&lt;-</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'>#&gt; <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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
#&gt; parent_0 99.5985 1.5702 96.404 102.79
@@ -299,8 +313,8 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</
use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
-<span class='va'>fit.ff.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.2.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span>
+<span class='va'>fit.ff.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>fit.ff.2.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
#&gt; 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>

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