Update docs

14 files changed, 279 insertions, 18 deletions

diff --git a/docs/404.html b/docs/404.html
index 36135992..8e7e8f45 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -32,7 +32,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
       </span>
     </div>
 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 292a72a4..f4f6d557 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
       </span>
     </div>
 
diff --git a/docs/authors.html b/docs/authors.html
index 6560ab17..7afe3000 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
       </span>
     </div>
 
@@ -115,13 +115,13 @@
 
     <p>Ranke J (2022).
 <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>.
-R package version 1.2.0, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. 
+R package version 1.2.1, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. 
 </p>
     <pre>@Manual{,
   title = {mkin: Kinetic Evaluation of Chemical Degradation Data},
   author = {Johannes Ranke},
   year = {2022},
-  note = {R package version 1.2.0},
+  note = {R package version 1.2.1},
   url = {https://pkgdown.jrwb.de/mkin/},
 }</pre>
 
diff --git a/docs/index.html b/docs/index.html
index 9048bc38..bb14906d 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
       </span>
     </div>
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 90768141..6b9a7d51 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
       </span>
     </div>
 
@@ -88,6 +88,14 @@
     </div>
 
     <div class="section level2">
+<h2 class="page-header" data-toc-text="1.2.1" id="mkin-121-unreleased">mkin 1.2.1 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-121-unreleased"></a></h2>
+<ul><li><p>‘tests/testthat/setup_script.R’: Excluded another ill-defined random effect for the DFOP fit with ‘saem’, in an attempt to avoid a platform dependence that surfaced on Fedora systems on the CRAN check farm</p></li>
+<li><p>‘tests/testthat/test_mixed.R’: Round parameters found by saemix to two significant digits before printing, to also help to avoid platform dependence of tests</p></li>
+<li><p>‘R/saem.R’: Fix a bug that prevented that ‘error.ini’ is passed to ‘saemix_model’, and set default to c(1, 1) to avoid changing test results</p></li>
+<li><p>‘R/parplot.R’: Show initial values for error model parameters</p></li>
+<li><p>‘R/loglik.mkinfit.R’: Add ‘nobs’ attribute to the resulting ‘logLik’ object, in order to make test_AIC.R succeed on current R-devel</p></li>
+</ul></div>
+    <div class="section level2">
 <h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-2022-11-17">mkin 1.2.0 (2022-11-17)<a class="anchor" aria-label="anchor" href="#mkin-120-2022-11-17"></a></h2>
 <ul><li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li>
 <li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 14c22439..b6c8f1cc 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -13,7 +13,7 @@ articles:
   dimethenamid_2018: web_only/dimethenamid_2018.html
   multistart: web_only/multistart.html
   saem_benchmarks: web_only/saem_benchmarks.html
-last_built: 2022-11-17T13:56Z
+last_built: 2022-11-18T18:18Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index ca982688..b3448db0 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index de2d61aa..27feab09 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
diff --git a/docs/reference/ds_mixed-1.png b/docs/reference/ds_mixed-1.png
new file mode 100644
index 00000000..a7f5c395
--- /dev/null
+++ b/docs/reference/ds_mixed-1.png
diff --git a/docs/reference/ds_mixed.html b/docs/reference/ds_mixed.html
new file mode 100644
index 00000000..64b02749
--- /dev/null
+++ b/docs/reference/ds_mixed.html
@@ -0,0 +1,240 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Synthetic data for hierarchical kinetic degradation models — ds_mixed • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Synthetic data for hierarchical kinetic degradation models — ds_mixed"><meta property="og:description" content="The R code used to create this data object is installed with this package in
+the 'dataset_generation' directory."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-reference-topic">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">mkin</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="../articles/mkin.html">Introduction to mkin</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">News</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/mkin/" class="external-link">
+    <span class="fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Synthetic data for hierarchical kinetic degradation models</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ds_mixed.R" class="external-link"><code>R/ds_mixed.R</code></a></small>
+    <div class="hidden name"><code>ds_mixed.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>The R code used to create this data object is installed with this package in
+the 'dataset_generation' directory.</p>
+    </div>
+
+
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span>  <span class="va">sfo_mmkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo</span>, 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">15</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">sfo_saem</span> <span class="op">&lt;-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">sfo_mmkin</span>, no_random_effect <span class="op">=</span> <span class="st">"parent_0"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sfo_saem</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="ds_mixed-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># This is the code used to generate the datasets</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/cat.html" class="external-link">cat</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"dataset_generation/ds_mixed.R"</span>, package <span class="op">=</span> <span class="st">"mkin"</span><span class="op">)</span><span class="op">)</span>, sep <span class="op">=</span> <span class="st">"\n"</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> # Synthetic data for hierarchical kinetic models</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> # Refactored version of the code previously in tests/testthat/setup_script.R</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> # The number of datasets was 3 for FOMC, and 10 for HS in that script, now it</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> # is always 15 for consistency</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> library(mkin)  # We use mkinmod and mkinpredict</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> n &lt;- 15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_sd &lt;- 0.3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> err_1 = list(const = 1, prop = 0.05)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> tc &lt;- function(value) sigma_twocomp(value, err_1$const, err_1$prop)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> const &lt;- function(value) 2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO &lt;- mkinmod(parent = mkinsub("SFO"))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sfo_pop &lt;- list(parent_0 = 100, k_parent = 0.03)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sfo_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     k_parent = rlnorm(n, log(sfo_pop$k_parent), log_sd)))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_sfo &lt;- lapply(1:n, function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   ds_mean &lt;- mkinpredict(SFO, sfo_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     c(parent = sfo_pop$parent_0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   add_err(ds_mean, tc, n = 1)[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_sfo, "pop") &lt;- sfo_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_sfo, "parms") &lt;- sfo_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC &lt;- mkinmod(parent = mkinsub("FOMC"))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> fomc_pop &lt;- list(parent_0 = 100, alpha = 2, beta = 8)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> fomc_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     alpha = rlnorm(n, log(fomc_pop$alpha), 0.4),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     beta = rlnorm(n, log(fomc_pop$beta), 0.2)))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_fomc &lt;- lapply(1:n, function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   ds_mean &lt;- mkinpredict(FOMC, fomc_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     c(parent = fomc_pop$parent_0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   add_err(ds_mean, tc, n = 1)[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_fomc, "pop") &lt;- fomc_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_fomc, "parms") &lt;- fomc_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DFOP &lt;- mkinmod(parent = mkinsub("DFOP"))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dfop_pop &lt;- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dfop_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   k1 = rlnorm(n, log(dfop_pop$k1), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   k2 = rlnorm(n, log(dfop_pop$k2), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   g = plogis(rnorm(n, qlogis(dfop_pop$g), log_sd))))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_dfop &lt;- lapply(1:n, function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   ds_mean &lt;- mkinpredict(DFOP, dfop_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     c(parent = dfop_pop$parent_0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   add_err(ds_mean, tc, n = 1)[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_dfop, "pop") &lt;- dfop_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_dfop, "parms") &lt;- dfop_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> HS &lt;- mkinmod(parent = mkinsub("HS"))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> hs_pop &lt;- list(parent_0 = 100, k1 = 0.08, k2 = 0.01, tb = 15)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> hs_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   k1 = rlnorm(n, log(hs_pop$k1), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   k2 = rlnorm(n, log(hs_pop$k2), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   tb = rlnorm(n, log(hs_pop$tb), 0.1)))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_hs &lt;- lapply(1:n, function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   ds_mean &lt;- mkinpredict(HS, hs_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     c(parent = hs_pop$parent_0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   add_err(ds_mean, const, n = 1)[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_hs, "pop") &lt;- hs_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_hs, "parms") &lt;- hs_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DFOP_SFO &lt;- mkinmod(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   parent = mkinsub("DFOP", "m1"),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   m1 = mkinsub("SFO"),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   quiet = TRUE)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dfop_sfo_pop &lt;- list(parent_0 = 100,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   k_m1 = 0.007, f_parent_to_m1 = 0.5,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   k1 = 0.1, k2 = 0.02, g = 0.5)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dfop_sfo_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   k1 = rlnorm(n, log(dfop_sfo_pop$k1), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   k2 = rlnorm(n, log(dfop_sfo_pop$k2), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   g = plogis(rnorm(n, qlogis(dfop_sfo_pop$g), log_sd)),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   f_parent_to_m1 = plogis(rnorm(n,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       qlogis(dfop_sfo_pop$f_parent_to_m1), log_sd)),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   k_m1 = rlnorm(n, log(dfop_sfo_pop$k_m1), log_sd)))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_dfop_sfo_mean &lt;- lapply(1:n,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     mkinpredict(DFOP_SFO, dfop_sfo_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       c(parent = dfop_sfo_pop$parent_0, m1 = 0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   }</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> )</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_dfop_sfo &lt;- lapply(ds_dfop_sfo_mean, function(ds) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   add_err(ds,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     n = 1, secondary = "m1")[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_dfop_sfo, "pop") &lt;- dfop_sfo_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_dfop_sfo, "parms") &lt;- dfop_sfo_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> #save(ds_sfo, ds_fomc, ds_dfop, ds_hs, ds_dfop_sfo, file = "data/ds_mixed.rda", version = 2)</span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 665912f7..9fddf541 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
       </span>
     </div>
 
@@ -268,9 +268,9 @@ degradation models and one or more error models</p></td>
           <p class="section-desc"></p>
         </th>
       </tr></tbody><tbody><tr><td>
-          <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p>
+          <p><code><a href="ds_mixed.html">ds_mixed</a></code> <code><a href="ds_mixed.html">ds_sfo</a></code> <code><a href="ds_mixed.html">ds_fomc</a></code> <code><a href="ds_mixed.html">ds_dfop</a></code> <code><a href="ds_mixed.html">ds_hs</a></code> <code><a href="ds_mixed.html">ds_dfop_sfo</a></code> </p>
         </td>
-        <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td>
+        <td><p>Synthetic data for hierarchical kinetic degradation models</p></td>
       </tr><tr><td>
           <p><code><a href="D24_2014.html">D24_2014</a></code> </p>
         </td>
@@ -328,6 +328,10 @@ degradation models and one or more error models</p></td>
         </td>
         <td><p>Three experimental datasets from two water sediment systems and one soil</p></td>
       </tr><tr><td>
+          <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p>
+        </td>
+        <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td>
+      </tr><tr><td>
           <p><code><a href="mkinds.html">print(<i>&lt;mkinds&gt;</i>)</a></code> </p>
         </td>
         <td><p>A dataset class for mkin</p></td>
diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html
index f4f3c811..ab02cbb3 100644
--- a/docs/reference/parplot.html
+++ b/docs/reference/parplot.html
@@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
       </span>
     </div>
 
@@ -137,6 +137,12 @@ If 'median', parameters are scaled using the median parameters from all fits.</p
 <dd><p>Title of the plot</p></dd>
 
 </dl></div>
+    <div id="details">
+    <h2>Details</h2>
+    <p>Starting values of degradation model parameters and error model parameters
+are shown as green circles. The results obtained in the original run
+are shown as red circles.</p>
+    </div>
     <div id="references">
     <h2>References</h2>
     <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical
diff --git a/docs/reference/saem.html b/docs/reference/saem.html
index 5e7e0861..957c098e 100644
--- a/docs/reference/saem.html
+++ b/docs/reference/saem.html
@@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
       </span>
     </div>
 
@@ -113,7 +113,7 @@ Expectation Maximisation algorithm (SAEM).</p>
 <span>  covariates <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  error.init <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
+<span>  error.init <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span>,</span>
 <span>  nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">300</span>, <span class="fl">100</span><span class="op">)</span>,</span>
 <span>  control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,</span>
 <span>    save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
@@ -430,10 +430,10 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.0 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.1 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Nov 17 14:03:17 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 17 14:03:17 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Fri Nov 18 19:19:25 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Nov 18 19:19:25 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -448,7 +448,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 8.829 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.068 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Constant variance </span>
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 320fe932..2571bb4b 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -121,6 +121,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/dimethenamid_2018.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/ds_mixed.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/endpoints.html</loc>
   </url>
   <url>