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authorJohannes Ranke <jranke@uni-bremen.de>2019-03-04 14:09:45 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-03-04 14:09:45 +0100
commit9d6a975a0e3850a36889a18b5d9929d27b901ab3 (patch)
tree2130084703b45ba08a7f94e0d446a081a4ba2894 /docs
parentd0b124992232dde30fbff83dd4eeae8fc977d3ba (diff)
Make some example output more reproducible
In order to avoid some unnecessary documentation rebuilds
Diffstat (limited to 'docs')
-rw-r--r--docs/articles/FOCUS_D.html6
-rw-r--r--docs/articles/FOCUS_L.html36
-rw-r--r--docs/articles/web_only/NAFTA_examples.html14
-rw-r--r--docs/articles/web_only/compiled_models.html10
-rw-r--r--docs/reference/Extract.mmkin.html367
-rw-r--r--docs/reference/NAFTA_SOP_2015.html6
-rw-r--r--docs/reference/mccall81_245T.html229
-rw-r--r--docs/reference/mkinfit.html44
-rw-r--r--docs/reference/mkinmod.html2
-rw-r--r--docs/reference/mkinpredict.html2
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/nafta.html6
-rw-r--r--docs/reference/summary.mkinfit.html6
-rw-r--r--docs/reference/transform_odeparms.html330
14 files changed, 159 insertions, 903 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index fabb567a..376acee2 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -166,8 +166,8 @@
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Mar 4 10:09:33 2019
-## Date of summary: Mon Mar 4 10:09:33 2019
+## Date of fit: Mon Mar 4 14:06:39 2019
+## Date of summary: Mon Mar 4 14:06:39 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -175,7 +175,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.687 s
+## Fitted with method Port using 153 model solutions performed in 0.693 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 7157f973..5dac9999 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -114,15 +114,15 @@
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Mar 4 10:09:35 2019
-## Date of summary: Mon Mar 4 10:09:35 2019
+## Date of fit: Mon Mar 4 14:06:41 2019
+## Date of summary: Mon Mar 4 14:06:41 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.102 s
+## Fitted with method Port using 37 model solutions performed in 0.095 s
##
## Weighting: none
##
@@ -205,15 +205,15 @@
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Mar 4 10:09:36 2019
-## Date of summary: Mon Mar 4 10:09:36 2019
+## Date of fit: Mon Mar 4 14:06:43 2019
+## Date of summary: Mon Mar 4 14:06:43 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 611 model solutions performed in 1.508 s
+## Fitted with method Port using 611 model solutions performed in 1.502 s
##
## Weighting: none
##
@@ -300,8 +300,8 @@
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Mar 4 10:09:37 2019
-## Date of summary: Mon Mar 4 10:09:37 2019
+## Date of fit: Mon Mar 4 14:06:43 2019
+## Date of summary: Mon Mar 4 14:06:43 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -373,8 +373,8 @@
## covariance matrix; singular system.</code></pre>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Mar 4 10:09:38 2019
-## Date of summary: Mon Mar 4 10:09:38 2019
+## Date of fit: Mon Mar 4 14:06:44 2019
+## Date of summary: Mon Mar 4 14:06:44 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -383,7 +383,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.841 s
+## Fitted with method Port using 336 model solutions performed in 0.84 s
##
## Weighting: none
##
@@ -463,8 +463,8 @@
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Mar 4 10:09:39 2019
-## Date of summary: Mon Mar 4 10:09:39 2019
+## Date of fit: Mon Mar 4 14:06:45 2019
+## Date of summary: Mon Mar 4 14:06:46 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -564,8 +564,8 @@
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Mar 4 10:09:40 2019
-## Date of summary: Mon Mar 4 10:09:40 2019
+## Date of fit: Mon Mar 4 14:06:46 2019
+## Date of summary: Mon Mar 4 14:06:46 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -624,15 +624,15 @@
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Mar 4 10:09:40 2019
-## Date of summary: Mon Mar 4 10:09:40 2019
+## Date of fit: Mon Mar 4 14:06:46 2019
+## Date of summary: Mon Mar 4 14:06:46 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.162 s
+## Fitted with method Port using 66 model solutions performed in 0.173 s
##
## Weighting: none
##
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index db1fc478..12e5d522 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -347,7 +347,7 @@
## DT50 DT90 DT50_rep
## SFO 86.3 287 86.3
## IORE 53.4 668 201.0
-## DFOP 55.6 517 253.5
+## DFOP 55.6 517 253.0
##
## Representative half-life:
## [1] 201.0316</code></pre>
@@ -492,9 +492,9 @@
##
## DTx values:
## DT50 DT90 DT50_rep
-## SFO 14.0 46.5 13.99
+## SFO 14.0 46.5 14.00
## IORE 16.4 29.4 8.86
-## DFOP 14.0 46.5 13.99
+## DFOP 14.0 46.5 14.00
##
## Representative half-life:
## [1] 8.862193</code></pre>
@@ -644,9 +644,9 @@
##
## DTx values:
## DT50 DT90 DT50_rep
-## SFO 11.8 39.1 11.76
+## SFO 11.8 39.1 11.80
## IORE 12.9 31.4 9.46
-## DFOP 11.8 39.1 11.76
+## DFOP 11.8 39.1 11.80
##
## Representative half-life:
## [1] 9.461912</code></pre>
@@ -830,9 +830,9 @@
##
## DTx values:
## DT50 DT90 DT50_rep
-## SFO 143 474 142.7
+## SFO 143 474 143.0
## IORE 131 236 71.2
-## DFOP 143 474 142.7
+## DFOP 143 474 143.0
##
## Representative half-life:
## [1] 71.18014</code></pre>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 1d96ea76..269b1098 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -129,9 +129,9 @@
<a class="sourceLine" id="cb5-16" title="16">}</a></code></pre></div>
<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.313 1.000 2.312 0
-## 1 deSolve, not compiled 3 17.602 7.610 17.595 0
-## 2 Eigenvalue based 3 2.853 1.233 2.851 0
+## 3 deSolve, compiled 3 2.310 1.000 2.308 0
+## 1 deSolve, not compiled 3 17.509 7.580 17.500 0
+## 2 Eigenvalue based 3 2.859 1.238 2.858 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -160,8 +160,8 @@
<a class="sourceLine" id="cb8-16" title="16">}</a></code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 4.049 1.000 4.047 0
-## 1 deSolve, not compiled 3 37.135 9.171 37.119 0
+## 2 deSolve, compiled 3 4.074 1.000 4.072 0
+## 1 deSolve, not compiled 3 37.219 9.136 37.203 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 96b9f218..3567af48 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -206,373 +206,6 @@
#&gt;
#&gt; $counts
#&gt; [1] "relative convergence (4)"
-#&gt; </div><div class='input'>
- <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(
- <span class='co'># The same can be achieved by</span>
- <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]
- )</div><div class='output co'>#&gt; [[1]]
-#&gt; $par
-#&gt; parent_0 log_k_parent_sink
-#&gt; 99.174072 -2.549028
-#&gt;
-#&gt; $ssr
-#&gt; [1] 30.65564
-#&gt;
-#&gt; $convergence
-#&gt; [1] 0
-#&gt;
-#&gt; $iterations
-#&gt; [1] 5
-#&gt;
-#&gt; $evaluations
-#&gt; function gradient
-#&gt; 8 15
-#&gt;
-#&gt; $counts
-#&gt; [1] "relative convergence (4)"
-#&gt;
-#&gt; $hessian
-#&gt; parent_0 log_k_parent_sink
-#&gt; parent_0 4.163631 -94.09343
-#&gt; log_k_parent_sink -94.093431 6311.34610
-#&gt;
-#&gt; $residuals
-#&gt; parent parent parent parent parent parent
-#&gt; 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730
-#&gt; parent parent
-#&gt; -0.24260405 -0.07020339
-#&gt;
-#&gt; $ms
-#&gt; [1] 3.831956
-#&gt;
-#&gt; $var_ms
-#&gt; parent
-#&gt; 3.831956
-#&gt;
-#&gt; $var_ms_unscaled
-#&gt; parent
-#&gt; 3.831956
-#&gt;
-#&gt; $var_ms_unweighted
-#&gt; parent
-#&gt; 3.831956
-#&gt;
-#&gt; $rank
-#&gt; [1] 2
-#&gt;
-#&gt; $df.residual
-#&gt; [1] 6
-#&gt;
-#&gt; $solution_type
-#&gt; [1] "analytical"
-#&gt;
-#&gt; $transform_rates
-#&gt; [1] TRUE
-#&gt;
-#&gt; $transform_fractions
-#&gt; [1] TRUE
-#&gt;
-#&gt; $method.modFit
-#&gt; [1] "Port"
-#&gt;
-#&gt; $maxit.modFit
-#&gt; [1] "auto"
-#&gt;
-#&gt; $calls
-#&gt; [1] 29
-#&gt;
-#&gt; $time
-#&gt; User System verstrichen
-#&gt; 0.069 0.000 0.069
-#&gt;
-#&gt; $mkinmod
-#&gt; &lt;mkinmod&gt; model generated with
-#&gt; Use of formation fractions $use_of_ff: min
-#&gt; Specification $spec:
-#&gt; $parent
-#&gt; $type: SFO; $sink: TRUE
-#&gt; Coefficient matrix $coefmat available
-#&gt; Differential equations:
-#&gt; d_parent/dt = - k_parent_sink * parent
-#&gt;
-#&gt; $observed
-#&gt; name time value
-#&gt; 1 parent 0 98.62
-#&gt; 2 parent 3 81.43
-#&gt; 3 parent 7 53.18
-#&gt; 4 parent 14 34.89
-#&gt; 5 parent 30 10.09
-#&gt; 6 parent 62 1.50
-#&gt; 7 parent 90 0.33
-#&gt; 8 parent 118 0.08
-#&gt;
-#&gt; $obs_vars
-#&gt; [1] "parent"
-#&gt;
-#&gt; $predicted
-#&gt; name time value
-#&gt; 1 parent 0.000000 99.17407218
-#&gt; 2 parent 1.191919 90.35253561
-#&gt; 3 parent 2.383838 82.31567498
-#&gt; 4 parent 3.000000 78.44547872
-#&gt; 5 parent 3.575758 74.99369333
-#&gt; 6 parent 4.767677 68.32300215
-#&gt; 7 parent 5.959596 62.24566915
-#&gt; 8 parent 7.000000 57.38445742
-#&gt; 9 parent 7.151515 56.70891509
-#&gt; 10 parent 8.343434 51.66465547
-#&gt; 11 parent 9.535354 47.06908288
-#&gt; 12 parent 10.727273 42.88228661
-#&gt; 13 parent 11.919192 39.06790599
-#&gt; 14 parent 13.111111 35.59281463
-#&gt; 15 parent 14.000000 33.20400061
-#&gt; 16 parent 14.303030 32.42683275
-#&gt; 17 parent 15.494949 29.54246504
-#&gt; 18 parent 16.686869 26.91466193
-#&gt; 19 parent 17.878788 24.52060198
-#&gt; 20 parent 19.070707 22.33949373
-#&gt; 21 parent 20.262626 20.35239512
-#&gt; 22 parent 21.454545 18.54204899
-#&gt; 23 parent 22.646465 16.89273320
-#&gt; 24 parent 23.838384 15.39012410
-#&gt; 25 parent 25.030303 14.02117212
-#&gt; 26 parent 26.222222 12.77398846
-#&gt; 27 parent 27.414141 11.63774182
-#&gt; 28 parent 28.606061 10.60256435
-#&gt; 29 parent 29.797980 9.65946594
-#&gt; 30 parent 30.000000 9.50814643
-#&gt; 31 parent 30.989899 8.80025617
-#&gt; 32 parent 32.181818 8.01747313
-#&gt; 33 parent 33.373737 7.30431867
-#&gt; 34 parent 34.565657 6.65459931
-#&gt; 35 parent 35.757576 6.06267251
-#&gt; 36 parent 36.949495 5.52339762
-#&gt; 37 parent 38.141414 5.03209124
-#&gt; 38 parent 39.333333 4.58448658
-#&gt; 39 parent 40.525253 4.17669637
-#&gt; 40 parent 41.717172 3.80517911
-#&gt; 41 parent 42.909091 3.46670832
-#&gt; 42 parent 44.101010 3.15834451
-#&gt; 43 parent 45.292929 2.87740968
-#&gt; 44 parent 46.484848 2.62146400
-#&gt; 45 parent 47.676768 2.38828471
-#&gt; 46 parent 48.868687 2.17584671
-#&gt; 47 parent 50.060606 1.98230508
-#&gt; 48 parent 51.252525 1.80597899
-#&gt; 49 parent 52.444444 1.64533711
-#&gt; 50 parent 53.636364 1.49898432
-#&gt; 51 parent 54.828283 1.36564963
-#&gt; 52 parent 56.020202 1.24417505
-#&gt; 53 parent 57.212121 1.13350565
-#&gt; 54 parent 58.404040 1.03268029
-#&gt; 55 parent 59.595960 0.94082335
-#&gt; 56 parent 60.787879 0.85713708
-#&gt; 57 parent 61.979798 0.78089471
-#&gt; 58 parent 62.000000 0.77966270
-#&gt; 59 parent 63.171717 0.71143411
-#&gt; 60 parent 64.363636 0.64815202
-#&gt; 61 parent 65.555556 0.59049888
-#&gt; 62 parent 66.747475 0.53797399
-#&gt; 63 parent 67.939394 0.49012119
-#&gt; 64 parent 69.131313 0.44652489
-#&gt; 65 parent 70.323232 0.40680649
-#&gt; 66 parent 71.515152 0.37062104
-#&gt; 67 parent 72.707071 0.33765429
-#&gt; 68 parent 73.898990 0.30761993
-#&gt; 69 parent 75.090909 0.28025713
-#&gt; 70 parent 76.282828 0.25532825
-#&gt; 71 parent 77.474747 0.23261679
-#&gt; 72 parent 78.666667 0.21192552
-#&gt; 73 parent 79.858586 0.19307474
-#&gt; 74 parent 81.050505 0.17590074
-#&gt; 75 parent 82.242424 0.16025436
-#&gt; 76 parent 83.434343 0.14599973
-#&gt; 77 parent 84.626263 0.13301305
-#&gt; 78 parent 85.818182 0.12118154
-#&gt; 79 parent 87.010101 0.11040244
-#&gt; 80 parent 88.202020 0.10058214
-#&gt; 81 parent 89.393939 0.09163535
-#&gt; 82 parent 90.000000 0.08739595
-#&gt; 83 parent 90.585859 0.08348439
-#&gt; 84 parent 91.777778 0.07605845
-#&gt; 85 parent 92.969697 0.06929305
-#&gt; 86 parent 94.161616 0.06312943
-#&gt; 87 parent 95.353535 0.05751406
-#&gt; 88 parent 96.545455 0.05239819
-#&gt; 89 parent 97.737374 0.04773737
-#&gt; 90 parent 98.929293 0.04349113
-#&gt; 91 parent 100.121212 0.03962259
-#&gt; 92 parent 101.313131 0.03609816
-#&gt; 93 parent 102.505051 0.03288723
-#&gt; 94 parent 103.696970 0.02996191
-#&gt; 95 parent 104.888889 0.02729679
-#&gt; 96 parent 106.080808 0.02486874
-#&gt; 97 parent 107.272727 0.02265667
-#&gt; 98 parent 108.464646 0.02064136
-#&gt; 99 parent 109.656566 0.01880531
-#&gt; 100 parent 110.848485 0.01713257
-#&gt; 101 parent 112.040404 0.01560863
-#&gt; 102 parent 113.232323 0.01422024
-#&gt; 103 parent 114.424242 0.01295535
-#&gt; 104 parent 115.616162 0.01180297
-#&gt; 105 parent 116.808081 0.01075310
-#&gt; 106 parent 118.000000 0.00979661
-#&gt;
-#&gt; $cost
-#&gt; function (P)
-#&gt; {
-#&gt; assign("calls", calls + 1, inherits = TRUE)
-#&gt; if (trace_parms)
-#&gt; cat(P, "\n")
-#&gt; if (length(state.ini.optim) &gt; 0) {
-#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
-#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-#&gt; }
-#&gt; else {
-#&gt; odeini &lt;- state.ini.fixed
-#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
-#&gt; }
-#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
-#&gt; transparms.fixed)
-#&gt; parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
-#&gt; transform_fractions = transform_fractions)
-#&gt; out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
-#&gt; use_compiled = use_compiled, method.ode = method.ode,
-#&gt; atol = atol, rtol = rtol, ...)
-#&gt; assign("out_predicted", out, inherits = TRUE)
-#&gt; mC &lt;- modCost(out, observed, y = "value", err = err, weight = weight,
-#&gt; scaleVar = scaleVar)
-#&gt; if (mC$model &lt; cost.old) {
-#&gt; if (!quiet)
-#&gt; cat("Model cost at call ", calls, ": ", mC$model,
-#&gt; "\n")
-#&gt; if (plot) {
-#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
-#&gt; length.out = 100)
-#&gt; out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
-#&gt; solution_type = solution_type, use_compiled = use_compiled,
-#&gt; method.ode = method.ode, atol = atol, rtol = rtol,
-#&gt; ...)
-#&gt; plot(0, type = "n", xlim = range(observed$time),
-#&gt; ylim = c(0, max(observed$value, na.rm = TRUE)),
-#&gt; xlab = "Time", ylab = "Observed")
-#&gt; col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
-#&gt; lty_obs &lt;- rep(1, length(obs_vars))
-#&gt; names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
-#&gt; for (obs_var in obs_vars) {
-#&gt; points(subset(observed, name == obs_var, c(time,
-#&gt; value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
-#&gt; }
-#&gt; matlines(out_plot$time, out_plot[-1], col = col_obs,
-#&gt; lty = lty_obs)
-#&gt; legend("topright", inset = c(0.05, 0.05), legend = obs_vars,
-#&gt; col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
-#&gt; }
-#&gt; assign("cost.old", mC$model, inherits = TRUE)
-#&gt; }
-#&gt; return(mC)
-#&gt; }
-#&gt; &lt;bytecode: 0x55555c1f3208&gt;
-#&gt; &lt;environment: 0x555555c27dc0&gt;
-#&gt;
-#&gt; $cost_notrans
-#&gt; function (P)
-#&gt; {
-#&gt; if (length(state.ini.optim) &gt; 0) {
-#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
-#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-#&gt; }
-#&gt; else {
-#&gt; odeini &lt;- state.ini.fixed
-#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
-#&gt; }
-#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
-#&gt; parms.fixed)
-#&gt; out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
-#&gt; use_compiled = use_compiled, method.ode = method.ode,
-#&gt; atol = atol, rtol = rtol, ...)
-#&gt; mC &lt;- modCost(out, observed, y = "value", err = err, weight = weight,
-#&gt; scaleVar = scaleVar)
-#&gt; return(mC)
-#&gt; }
-#&gt; &lt;bytecode: 0x55555b84fce8&gt;
-#&gt; &lt;environment: 0x555555c27dc0&gt;
-#&gt;
-#&gt; $hessian_notrans
-#&gt; parent_0 k_parent_sink
-#&gt; parent_0 4.163631 -1203.894
-#&gt; k_parent_sink -1203.893702 1033188.753
-#&gt;
-#&gt; $start
-#&gt; value type
-#&gt; parent_0 98.62 state
-#&gt; k_parent_sink 0.10 deparm
-#&gt;
-#&gt; $start_transformed
-#&gt; value lower upper
-#&gt; parent_0 98.620000 -Inf Inf
-#&gt; log_k_parent_sink -2.302585 -Inf Inf
-#&gt;
-#&gt; $fixed
-#&gt; [1] value type
-#&gt; &lt;0 Zeilen&gt; (oder row.names mit Länge 0)
-#&gt;
-#&gt; $data
-#&gt; time variable observed predicted residual
-#&gt; 1 0 parent 98.62 99.17407218 -0.55407218
-#&gt; 2 3 parent 81.43 78.44547872 2.98452128
-#&gt; 3 7 parent 53.18 57.38445742 -4.20445742
-#&gt; 4 14 parent 34.89 33.20400061 1.68599939
-#&gt; 5 30 parent 10.09 9.50814643 0.58185357
-#&gt; 6 62 parent 1.50 0.77966270 0.72033730
-#&gt; 7 90 parent 0.33 0.08739595 0.24260405
-#&gt; 8 118 parent 0.08 0.00979661 0.07020339
-#&gt;
-#&gt; $atol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $rtol
-#&gt; [1] 1e-10
-#&gt;
-#&gt; $weight.ini
-#&gt; [1] "none"
-#&gt;
-#&gt; $tc.ini
-#&gt; sigma_low rsd_high
-#&gt; 0.50 0.07
-#&gt;
-#&gt; $reweight.tol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $reweight.max.iter
-#&gt; [1] 10
-#&gt;
-#&gt; $bparms.optim
-#&gt; parent_0 k_parent_sink
-#&gt; 99.17407218 0.07815759
-#&gt;
-#&gt; $bparms.fixed
-#&gt; numeric(0)
-#&gt;
-#&gt; $bparms.ode
-#&gt; k_parent_sink
-#&gt; 0.07815759
-#&gt;
-#&gt; $bparms.state
-#&gt; parent
-#&gt; 99.17407
-#&gt;
-#&gt; $date
-#&gt; [1] "Mon Mar 4 10:07:37 2019"
-#&gt;
-#&gt; $version
-#&gt; [1] "0.9.48.1"
-#&gt;
-#&gt; $Rversion
-#&gt; [1] "3.5.2"
-#&gt;
-#&gt; attr(,"class")
-#&gt; [1] "mkinfit" "modFit"
#&gt; </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html
index d56c0ca3..b2aba7ef 100644
--- a/docs/reference/NAFTA_SOP_2015.html
+++ b/docs/reference/NAFTA_SOP_2015.html
@@ -185,9 +185,9 @@
#&gt;
#&gt; DTx values:
#&gt; DT50 DT90 DT50_rep
-#&gt; SFO 407 1352 407
-#&gt; IORE 541 5192060 1562966
-#&gt; DFOP 429 2383 841
+#&gt; SFO 407 1350 407
+#&gt; IORE 541 5190000 1560000
+#&gt; DFOP 429 2380 841
#&gt;
#&gt; Representative half-life:
#&gt; [1] 841.4096</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 5fbbc962..47fa6482 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -161,189 +161,60 @@
<pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>),
<span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>),
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
-#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:00 2019
-#&gt; Date of summary: Mon Mar 4 10:08:00 2019
-#&gt;
-#&gt; Equations:
-#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
-#&gt; d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
-#&gt; k_phenol_anisole * phenol
-#&gt; d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 574 model solutions performed in 3.762 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; T245_0 100.9000 state
-#&gt; k_T245_sink 0.1000 deparm
-#&gt; k_T245_phenol 0.1001 deparm
-#&gt; k_phenol_sink 0.1002 deparm
-#&gt; k_phenol_anisole 0.1003 deparm
-#&gt; k_anisole_sink 0.1004 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; T245_0 100.900000 -Inf Inf
-#&gt; log_k_T245_sink -2.302585 -Inf Inf
-#&gt; log_k_T245_phenol -2.301586 -Inf Inf
-#&gt; log_k_phenol_sink -2.300587 -Inf Inf
-#&gt; log_k_phenol_anisole -2.299590 -Inf Inf
-#&gt; log_k_anisole_sink -2.298593 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; phenol_0 0 state
-#&gt; anisole_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; T245_0 103.9000 NA NA NA
-#&gt; log_k_T245_sink -4.1130 NA NA NA
-#&gt; log_k_T245_phenol -3.6120 NA NA NA
-#&gt; log_k_phenol_sink -25.0800 NA NA NA
-#&gt; log_k_phenol_anisole -0.9037 NA NA NA
-#&gt; log_k_anisole_sink -5.0090 NA NA NA
-#&gt;
-#&gt; Parameter correlation:
-#&gt; Could not estimate covariance matrix; singular system.
-#&gt; Residual standard error: 2.78 on 18 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA
-#&gt; k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA
-#&gt; k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA
-#&gt; k_phenol_sink 1.286e-11 4.575e-11 5.000e-01 NA NA
-#&gt; k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA
-#&gt; k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 10.070 6 16
-#&gt; T245 7.908 3 5
-#&gt; phenol 106.445 2 5
-#&gt; anisole 5.379 1 6
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; T245_sink 3.772e-01
-#&gt; T245_phenol 6.228e-01
-#&gt; phenol_sink 3.175e-11
-#&gt; phenol_anisole 1.000e+00
-#&gt; anisole_sink 1.000e+00
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; T245 15.982 53.091
-#&gt; phenol 1.711 5.685
-#&gt; anisole 103.784 344.763</div><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span>
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
+#&gt; T245_0 1.038550e+02 2.4256088519 4.281607e+01 7.235908e-20 NA
+#&gt; k_T245_sink 1.636106e-02 0.0183803090 8.901408e-01 1.925667e-01 NA
+#&gt; k_T245_phenol 2.700936e-02 0.0179604385 1.503825e+00 7.498498e-02 NA
+#&gt; k_phenol_sink 1.286034e-11 0.2810970202 4.575054e-11 5.000000e-01 NA
+#&gt; k_phenol_anisole 4.050581e-01 0.1608928349 2.517564e+00 1.075371e-02 NA
+#&gt; k_anisole_sink 6.678742e-03 0.0008199239 8.145563e+00 9.469402e-08 NA
+#&gt; Upper
+#&gt; T245_0 NA
+#&gt; k_T245_sink NA
+#&gt; k_T245_phenol NA
+#&gt; k_phenol_sink NA
+#&gt; k_phenol_anisole NA
+#&gt; k_anisole_sink NA</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
+#&gt; T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
+#&gt; 3.772401e-01 6.227599e-01 3.174937e-11 1.000000e+00 1.000000e+00
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; T245 15.982025 53.09114
+#&gt; phenol 1.711229 5.68458
+#&gt; anisole 103.784093 344.76330
+#&gt; </div><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span>
<span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
-#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:02 2019
-#&gt; Date of summary: Mon Mar 4 10:08:02 2019
-#&gt;
-#&gt; Equations:
-#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
-#&gt; d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
-#&gt; k_phenol_anisole * phenol
-#&gt; d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.598 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; T245_0 100.9000 state
-#&gt; k_T245_sink 0.1000 deparm
-#&gt; k_T245_phenol 0.1001 deparm
-#&gt; k_phenol_anisole 0.1002 deparm
-#&gt; k_anisole_sink 0.1003 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; T245_0 100.900000 -Inf Inf
-#&gt; log_k_T245_sink -2.302585 -Inf Inf
-#&gt; log_k_T245_phenol -2.301586 -Inf Inf
-#&gt; log_k_phenol_anisole -2.300587 -Inf Inf
-#&gt; log_k_anisole_sink -2.299590 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; phenol_0 0 state
-#&gt; anisole_0 0 state
-#&gt; k_phenol_sink 0 deparm
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; T245_0 103.9000 2.35200 98.930 108.8000
-#&gt; log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350
-#&gt; log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070
-#&gt; log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637
-#&gt; log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750
-#&gt;
-#&gt; Parameter correlation:
-#&gt; T245_0 log_k_T245_sink log_k_T245_phenol
-#&gt; T245_0 1.00000 0.63761 -0.1742
-#&gt; log_k_T245_sink 0.63761 1.00000 -0.3831
-#&gt; log_k_T245_phenol -0.17416 -0.38313 1.0000
-#&gt; log_k_phenol_anisole -0.05948 0.08745 -0.3047
-#&gt; log_k_anisole_sink -0.16208 -0.60469 0.5227
-#&gt; log_k_phenol_anisole log_k_anisole_sink
-#&gt; T245_0 -0.05948 -0.1621
-#&gt; log_k_T245_sink 0.08745 -0.6047
-#&gt; log_k_T245_phenol -0.30470 0.5227
-#&gt; log_k_phenol_anisole 1.00000 -0.1774
-#&gt; log_k_anisole_sink -0.17744 1.0000
-#&gt;
-#&gt; Residual standard error: 2.706 on 19 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; T245_0 1.039e+02 44.160 6.462e-21 98.930000 108.80000
-#&gt; k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159
-#&gt; k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999
-#&gt; k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820
-#&gt; k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 9.831 5 17
-#&gt; T245 7.908 3 5
-#&gt; phenol 99.808 1 6
-#&gt; anisole 5.379 1 6
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; T245_sink 0.3772
-#&gt; T245_phenol 0.6228
-#&gt; phenol_anisole 1.0000
-#&gt; phenol_sink 0.0000
-#&gt; anisole_sink 1.0000
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; T245 15.982 53.091
-#&gt; phenol 1.711 5.685
-#&gt; anisole 103.784 344.763</div><div class='input'> </div></pre>
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
+#&gt; T245_0 1.038550e+02 2.3517950656 44.159900 6.461715e-21 98.932670927
+#&gt; k_T245_sink 1.636106e-02 0.0021685502 7.544701 1.978480e-07 0.012397413
+#&gt; k_T245_phenol 2.700936e-02 0.0013511301 19.990199 1.606634e-14 0.024324422
+#&gt; k_phenol_anisole 4.050581e-01 0.1238660786 3.270129 2.013627e-03 0.213574853
+#&gt; k_anisole_sink 6.678742e-03 0.0007468908 8.942059 1.543812e-08 0.005284957
+#&gt; Upper
+#&gt; T245_0 1.087774e+02
+#&gt; k_T245_sink 2.159195e-02
+#&gt; k_T245_phenol 2.999066e-02
+#&gt; k_phenol_anisole 7.682180e-01
+#&gt; k_anisole_sink 8.440105e-03</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
+#&gt; T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
+#&gt; 3.772401e-01 6.227599e-01 3.174937e-11 1.000000e+00 1.000000e+00
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; T245 15.982025 53.09114
+#&gt; phenol 1.711229 5.68458
+#&gt; anisole 103.784093 344.76330
+#&gt; </div><div class='input'> </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index cd6ace43..df30ef09 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -441,8 +441,8 @@
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:05 2019
-#&gt; Date of summary: Mon Mar 4 10:08:05 2019
+#&gt; Date of fit: Mon Mar 4 14:05:12 2019
+#&gt; Date of summary: Mon Mar 4 14:05:12 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -518,7 +518,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.026 0.000 1.035 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 1.013 0.000 1.014 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -593,7 +593,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.814 0.008 0.830 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.821 0.000 0.822 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -631,8 +631,8 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:17 2019
-#&gt; Date of summary: Mon Mar 4 10:08:17 2019
+#&gt; Date of fit: Mon Mar 4 14:05:24 2019
+#&gt; Date of summary: Mon Mar 4 14:05:24 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -640,7 +640,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.853 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.841 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -748,8 +748,8 @@
#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:20 2019
-#&gt; Date of summary: Mon Mar 4 10:08:20 2019
+#&gt; Date of fit: Mon Mar 4 14:05:26 2019
+#&gt; Date of summary: Mon Mar 4 14:05:26 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -757,7 +757,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.525 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.517 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -870,8 +870,8 @@
#&gt; 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:21 2019
-#&gt; Date of summary: Mon Mar 4 10:08:21 2019
+#&gt; Date of fit: Mon Mar 4 14:05:27 2019
+#&gt; Date of summary: Mon Mar 4 14:05:27 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -879,7 +879,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.706 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.704 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -988,8 +988,8 @@
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:22 2019
-#&gt; Date of summary: Mon Mar 4 10:08:22 2019
+#&gt; Date of fit: Mon Mar 4 14:05:28 2019
+#&gt; Date of summary: Mon Mar 4 14:05:28 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -997,7 +997,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.875 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.866 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1108,8 +1108,8 @@
<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:23 2019
-#&gt; Date of summary: Mon Mar 4 10:08:23 2019
+#&gt; Date of fit: Mon Mar 4 14:05:30 2019
+#&gt; Date of summary: Mon Mar 4 14:05:30 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1117,7 +1117,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.279 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.23 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1226,8 +1226,8 @@
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:26 2019
-#&gt; Date of summary: Mon Mar 4 10:08:26 2019
+#&gt; Date of fit: Mon Mar 4 14:05:33 2019
+#&gt; Date of summary: Mon Mar 4 14:05:33 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1235,7 +1235,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 3.203 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.197 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index ddb695e3..37f95690 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -234,7 +234,7 @@ For the definition of model types and their parameters, the equations given
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file135d360177d0.c 2&gt; file135d360177d0.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB filef43390002d2.c 2&gt; filef43390002d2.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index a0880959..fb4afa9a 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -328,7 +328,7 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.004 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 5f82f41f..af963d13 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -194,8 +194,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_default</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.057 0.014 6.939 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 22.525 0.000 22.538 </div><div class='input'>
+#&gt; 0.049 0.025 6.950 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 22.404 0.000 22.417 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340480 0.2659520 0.7505686 0.2494314
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index 38e642df..f12e24e0 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -212,9 +212,9 @@
#&gt;
#&gt; DTx values:
#&gt; DT50 DT90 DT50_rep
-#&gt; SFO 407 1352 407
-#&gt; IORE 541 5192060 1562966
-#&gt; DFOP 429 2383 841
+#&gt; SFO 407 1350 407
+#&gt; IORE 541 5190000 1560000
+#&gt; DFOP 429 2380 841
#&gt;
#&gt; Representative half-life:
#&gt; [1] 841.4096</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div></pre>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index e2f4d2e2..f561e258 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -211,15 +211,15 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:09:19 2019
-#&gt; Date of summary: Mon Mar 4 10:09:19 2019
+#&gt; Date of fit: Mon Mar 4 14:06:25 2019
+#&gt; Date of summary: Mon Mar 4 14:06:25 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.086 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.085 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 3148f00b..fbc792f1 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -203,157 +203,29 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
-#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:09:27 2019
-#&gt; Date of summary: Mon Mar 4 10:09:27 2019
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-#&gt; d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.699 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent_sink 0.1000 deparm
-#&gt; k_parent_m1 0.1001 deparm
-#&gt; k_m1_sink 0.1002 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.750000 -Inf Inf
-#&gt; log_k_parent_sink -2.302585 -Inf Inf
-#&gt; log_k_parent_m1 -2.301586 -Inf Inf
-#&gt; log_k_m1_sink -2.300587 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.600 1.61400 96.330 102.900
-#&gt; log_k_parent_sink -3.038 0.07826 -3.197 -2.879
-#&gt; log_k_parent_m1 -2.980 0.04124 -3.064 -2.897
-#&gt; log_k_m1_sink -5.248 0.13610 -5.523 -4.972
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
-#&gt; parent_0 1.00000 0.6075 -0.06625 -0.1701
-#&gt; log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253
-#&gt; log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716
-#&gt; log_k_m1_sink -0.17006 -0.6253 0.47164 1.0000
-#&gt;
-#&gt; Residual standard error: 3.211 on 36 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
-#&gt; k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02
-#&gt; k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02
-#&gt; k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-03
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 6.398 4 15
-#&gt; parent 6.827 3 6
-#&gt; m1 4.490 1 9
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; parent_sink 0.4855
-#&gt; parent_m1 0.5145
-#&gt; m1_sink 1.0000
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 7.023 23.33
-#&gt; m1 131.761 437.70</div><div class='input'>
-</div><div class='input'><span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
-#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:09:29 2019
-#&gt; Date of summary: Mon Mar 4 10:09:29 2019
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-#&gt; d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 350 model solutions performed in 1.584 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent_sink 0.1000 deparm
-#&gt; k_parent_m1 0.1001 deparm
-#&gt; k_m1_sink 0.1002 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.7500 -Inf Inf
-#&gt; k_parent_sink 0.1000 0 Inf
-#&gt; k_parent_m1 0.1001 0 Inf
-#&gt; k_m1_sink 0.1002 0 Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.600000 1.6140000 96.330000 1.029e+02
-#&gt; k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02
-#&gt; k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02
-#&gt; k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
-#&gt; parent_0 1.00000 0.6075 -0.06625 -0.1701
-#&gt; k_parent_sink 0.60752 1.0000 -0.08740 -0.6253
-#&gt; k_parent_m1 -0.06625 -0.0874 1.00000 0.4716
-#&gt; k_m1_sink -0.17006 -0.6253 0.47164 1.0000
-#&gt;
-#&gt; Residual standard error: 3.211 on 36 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
-#&gt; k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02
-#&gt; k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02
-#&gt; k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 6.398 4 15
-#&gt; parent 6.827 3 6
-#&gt; m1 4.490 1 9
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; parent_sink 0.4855
-#&gt; parent_m1 0.5145
-#&gt; m1_sink 1.0000
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 7.023 23.33
-#&gt; m1 131.761 437.70</div><div class='input'>
+<span class='no'>fit.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)
+<span class='co'># Transformed and backtransformed parameters</span>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60 1.6137 96.33 102.87
+#&gt; log_k_parent_sink -3.04 0.0783 -3.20 -2.88
+#&gt; log_k_parent_m1 -2.98 0.0412 -3.06 -2.90
+#&gt; log_k_m1_sink -5.25 0.1361 -5.52 -4.97</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.59848 1.613712 61.72 2.02e-38 96.32572 1.03e+02
+#&gt; k_parent_sink 0.04792 0.003750 12.78 3.05e-15 0.04089 5.62e-02
+#&gt; k_parent_m1 0.05078 0.002094 24.25 3.41e-24 0.04670 5.52e-02
+#&gt; k_m1_sink 0.00526 0.000716 7.35 5.76e-09 0.00399 6.93e-03</div><div class='input'>
+</div><div class='input'><span class='co'># Compare to the version without transforming rate parameters</span>
+<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>fit.2.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.59848 1.613710 96.32573 1.03e+02
+#&gt; k_parent_sink 0.04792 0.003750 0.04031 5.55e-02
+#&gt; k_parent_m1 0.05078 0.002094 0.04653 5.50e-02
+#&gt; k_m1_sink 0.00526 0.000716 0.00381 6.71e-03</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.59848 1.613710 61.72 2.02e-38 96.32573 1.03e+02
+#&gt; k_parent_sink 0.04792 0.003750 12.78 3.05e-15 0.04031 5.55e-02
+#&gt; k_parent_m1 0.05078 0.002094 24.25 3.41e-24 0.04653 5.50e-02
+#&gt; k_m1_sink 0.00526 0.000716 7.35 5.76e-09 0.00381 6.71e-03</div><div class='input'>
<span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>initials</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>)
<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span>
@@ -367,80 +239,16 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
-#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:09:30 2019
-#&gt; Date of summary: Mon Mar 4 10:09:30 2019
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.86 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent 0.1000 deparm
-#&gt; k_m1 0.1001 deparm
-#&gt; f_parent_to_m1 0.5000 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.750000 -Inf Inf
-#&gt; log_k_parent -2.302585 -Inf Inf
-#&gt; log_k_m1 -2.301586 -Inf Inf
-#&gt; f_parent_ilr_1 0.000000 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.60000 1.61400 96.3300 102.9000
-#&gt; log_k_parent -2.31600 0.04187 -2.4010 -2.2310
-#&gt; log_k_m1 -5.24800 0.13610 -5.5230 -4.9720
-#&gt; f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
-#&gt; parent_0 1.0000 0.5178 -0.1701 -0.5489
-#&gt; log_k_parent 0.5178 1.0000 -0.3285 -0.5451
-#&gt; log_k_m1 -0.1701 -0.3285 1.0000 0.7466
-#&gt; f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000
-#&gt;
-#&gt; Residual standard error: 3.211 on 36 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
-#&gt; k_parent 0.098700 23.880 5.700e-24 0.090660 1.074e-01
-#&gt; k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03
-#&gt; f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 6.398 4 15
-#&gt; parent 6.459 2 7
-#&gt; m1 4.690 2 8
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; parent_m1 0.5145
-#&gt; parent_sink 0.4855
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 7.023 23.33
-#&gt; m1 131.761 437.70</div><div class='input'><span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
+<span class='no'>fit.ff.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>)
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.598 1.6137 96.3257 102.871
+#&gt; log_k_parent -2.316 0.0419 -2.4006 -2.231
+#&gt; log_k_m1 -5.248 0.1361 -5.5235 -4.972
+#&gt; f_parent_ilr_1 0.041 0.0648 -0.0904 0.172</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.59848 1.613712 61.72 2.02e-38 96.32574 1.03e+02
+#&gt; k_parent 0.09870 0.004132 23.88 5.70e-24 0.09066 1.07e-01
+#&gt; k_m1 0.00526 0.000716 7.35 5.76e-09 0.00399 6.93e-03
+#&gt; f_parent_to_m1 0.51448 0.022880 22.49 4.37e-23 0.46808 5.61e-01</div><div class='input'><span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>)
<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#&gt; f_parent_to_m1
#&gt; 0.5 </div><div class='input'>
@@ -451,70 +259,14 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
-#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:09:31 2019
-#&gt; Date of summary: Mon Mar 4 10:09:31 2019
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; d_m1/dt = + k_parent * parent - k_m1 * m1
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 104 model solutions performed in 0.476 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent 0.1000 deparm
-#&gt; k_m1 0.1001 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.750000 -Inf Inf
-#&gt; log_k_parent -2.302585 -Inf Inf
-#&gt; log_k_m1 -2.301586 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 84.790 2.96500 78.78 90.800
-#&gt; log_k_parent -2.756 0.08088 -2.92 -2.593
-#&gt; log_k_m1 -4.214 0.11150 -4.44 -3.988
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1
-#&gt; parent_0 1.0000 0.11058 0.46156
-#&gt; log_k_parent 0.1106 1.00000 0.06274
-#&gt; log_k_m1 0.4616 0.06274 1.00000
-#&gt;
-#&gt; Residual standard error: 8.333 on 37 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000
-#&gt; k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483
-#&gt; k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 19.66 3 16
-#&gt; parent 17.56 2 7
-#&gt; m1 18.71 1 9
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 10.91 36.25
-#&gt; m1 46.89 155.75</div></pre>
+<span class='no'>fit.ff.2.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>)
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 84.79 2.9651 78.78 90.80
+#&gt; log_k_parent -2.76 0.0809 -2.92 -2.59
+#&gt; log_k_m1 -4.21 0.1115 -4.44 -3.99</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 84.7916 2.96505 28.60 3.94e-27 78.7838 90.7994
+#&gt; k_parent 0.0635 0.00514 12.36 5.24e-15 0.0539 0.0748
+#&gt; k_m1 0.0148 0.00165 8.97 4.11e-11 0.0118 0.0185</div></pre>
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