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-rw-r--r--docs/reference/NAFTA_SOP_2015.html32
-rw-r--r--docs/reference/NAFTA_SOP_Attachment.html32
-rw-r--r--docs/reference/logLik.mkinfit.html2
-rw-r--r--docs/reference/logistic.solution.html18
-rw-r--r--docs/reference/mccall81_245T.html45
-rw-r--r--docs/reference/mkinfit.html339
-rw-r--r--docs/reference/mkinmod.html2
-rw-r--r--docs/reference/mkinparplot-1.pngbin16549 -> 17306 bytes
-rw-r--r--docs/reference/mkinparplot.html2
-rw-r--r--docs/reference/mkinpredict.html8
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/nafta.html32
-rw-r--r--docs/reference/summary.mkinfit.html30
-rw-r--r--docs/reference/test_data_from_UBA_2014.html54
-rw-r--r--docs/reference/transform_odeparms.html90
15 files changed, 300 insertions, 390 deletions
diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html
index 84341a17..9fbc71c6 100644
--- a/docs/reference/NAFTA_SOP_2015.html
+++ b/docs/reference/NAFTA_SOP_2015.html
@@ -155,7 +155,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Sums of squares:
+ <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Sums of squares:
#&gt; SFO IORE DFOP
#&gt; 1378.6832 615.7730 517.8836
#&gt;
@@ -164,25 +164,25 @@
#&gt;
#&gt; Parameters:
#&gt; $SFO
-#&gt; Estimate Pr(&gt;t) Lower Upper
-#&gt; parent_0 83.7558 1.80e-14 77.18268 90.3288
-#&gt; k_parent_sink 0.0017 7.43e-05 0.00112 0.0026
-#&gt; sigma 8.7518 1.22e-05 5.64278 11.8608
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 83.7558 NA NA NA
+#&gt; k_parent_sink 0.0017 NA NA NA
+#&gt; sigma 8.7518 NA NA NA
#&gt;
#&gt; $IORE
-#&gt; Estimate Pr(&gt;t) Lower Upper
-#&gt; parent_0 9.69e+01 NA 8.88e+01 1.05e+02
-#&gt; k__iore_parent_sink 8.40e-14 NA 1.79e-18 3.94e-09
-#&gt; N_parent 6.68e+00 NA 4.19e+00 9.17e+00
-#&gt; sigma 5.85e+00 NA 3.76e+00 7.94e+00
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.69e+01 NA NA NA
+#&gt; k__iore_parent_sink 8.40e-14 NA NA NA
+#&gt; N_parent 6.68e+00 NA NA NA
+#&gt; sigma 5.85e+00 NA NA NA
#&gt;
#&gt; $DFOP
-#&gt; Estimate Pr(&gt;t) Lower Upper
-#&gt; parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02
-#&gt; k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02
-#&gt; k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03
-#&gt; g 2.88e-01 2.47e-05 1.95e-01 4.03e-01
-#&gt; sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.76e+01 NA NA NA
+#&gt; k1 4.24e-02 NA NA NA
+#&gt; k2 8.24e-04 NA NA NA
+#&gt; g 2.88e-01 NA NA NA
+#&gt; sigma 5.36e+00 NA NA NA
#&gt;
#&gt;
#&gt; DTx values:
diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html
index 76d91c40..149b4d82 100644
--- a/docs/reference/NAFTA_SOP_Attachment.html
+++ b/docs/reference/NAFTA_SOP_Attachment.html
@@ -152,7 +152,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>nafta_att_p5a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</span>]], <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='output co'>#&gt; Sums of squares:
+ <pre class="examples"><div class='input'> <span class='no'>nafta_att_p5a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</span>]], <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='output co'>#&gt; Sums of squares:
#&gt; SFO IORE DFOP
#&gt; 465.21753 56.27506 32.06401
#&gt;
@@ -161,25 +161,25 @@
#&gt;
#&gt; Parameters:
#&gt; $SFO
-#&gt; Estimate Pr(&gt;t) Lower Upper
-#&gt; parent_0 95.8401 4.67e-21 92.245 99.4357
-#&gt; k_parent_sink 0.0102 3.92e-12 0.009 0.0117
-#&gt; sigma 4.8230 3.81e-06 3.214 6.4318
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 95.8401 NA NA NA
+#&gt; k_parent_sink 0.0102 NA NA NA
+#&gt; sigma 4.8230 NA NA NA
#&gt;
#&gt; $IORE
-#&gt; Estimate Pr(&gt;t) Lower Upper
-#&gt; parent_0 1.01e+02 NA 9.91e+01 1.02e+02
-#&gt; k__iore_parent_sink 1.54e-05 NA 4.08e-06 5.84e-05
-#&gt; N_parent 2.57e+00 NA 2.25e+00 2.89e+00
-#&gt; sigma 1.68e+00 NA 1.12e+00 2.24e+00
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 1.01e+02 NA NA NA
+#&gt; k__iore_parent_sink 1.54e-05 NA NA NA
+#&gt; N_parent 2.57e+00 NA NA NA
+#&gt; sigma 1.68e+00 NA NA NA
#&gt;
#&gt; $DFOP
-#&gt; Estimate Pr(&gt;t) Lower Upper
-#&gt; parent_0 9.99e+01 1.41e-26 98.8116 101.0810
-#&gt; k1 2.67e-02 5.05e-06 0.0243 0.0295
-#&gt; k2 2.86e-12 5.00e-01 0.0000 Inf
-#&gt; g 6.47e-01 3.67e-06 0.6248 0.6677
-#&gt; sigma 1.27e+00 8.91e-06 0.8395 1.6929
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.99e+01 NA NA NA
+#&gt; k1 2.67e-02 NA NA NA
+#&gt; k2 2.86e-12 NA NA NA
+#&gt; g 6.47e-01 NA NA NA
+#&gt; sigma 1.27e+00 NA NA NA
#&gt;
#&gt;
#&gt; DTx values:
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index f5844a8e..0184d573 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -180,7 +180,7 @@ The total number of estimated parameters returned with the value
<span class='no'>f_nw</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'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># no weighting (weights are unity)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='no'>f_obs</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'>d_t</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='no'>f_tc</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'>d_t</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>)</div><div class='output co'>#&gt; df AIC
#&gt; f_nw 5 204.4486
#&gt; f_obs 6 205.8727
-#&gt; f_tc 6 148.1802</div><div class='input'> </div></pre>
+#&gt; f_tc 6 141.9656</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/logistic.solution.html b/docs/reference/logistic.solution.html
index 3b45b14f..082cd4fb 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -205,18 +205,12 @@
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
<span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02
-#&gt; kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02
-#&gt; k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846685e-08
-#&gt; r 2.263946e-01 0.1718110773 1.317695 1.061044e-01 4.335843e-02
-#&gt; sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00
-#&gt; Upper
-#&gt; parent_0 109.9341588
-#&gt; kmax 0.1041853
-#&gt; k0 0.4448750
-#&gt; r 1.1821121
-#&gt; sigma 7.3256566</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; DT50 DT90 DT50_k0 DT50_kmax
+ <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 1.057896e+02 NA NA NA NA NA
+#&gt; kmax 6.398190e-02 NA NA NA NA NA
+#&gt; k0 1.612775e-04 NA NA NA NA NA
+#&gt; r 2.263946e-01 NA NA NA NA NA
+#&gt; sigma 5.332935e+00 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; DT50 DT90 DT50_k0 DT50_kmax
#&gt; parent 36.86533 62.41511 4297.854 10.83349</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 1db9a9d9..26bbd2ec 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -160,22 +160,14 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://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: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; T245_0 1.038550e+02 2.1508110557 48.286452 3.542232e-18 99.246062215
-#&gt; k_T245_sink 1.636106e-02 NaN NaN NaN 0.012661558
-#&gt; k_T245_phenol 2.700936e-02 NaN NaN NaN 0.024487315
-#&gt; k_phenol_sink 1.788604e-10 NaN NaN NaN 0.000000000
-#&gt; k_phenol_anisole 4.050581e-01 0.1053801116 3.843781 7.970202e-04 0.218013982
-#&gt; k_anisole_sink 6.678742e-03 0.0006205844 10.762020 9.428076e-09 0.005370739
-#&gt; sigma 2.514628e+00 0.3383670685 7.431657 1.054101e-06 1.706607296
-#&gt; Upper
-#&gt; T245_0 1.084640e+02
-#&gt; k_T245_sink 2.114150e-02
-#&gt; k_T245_phenol 2.979116e-02
-#&gt; k_phenol_sink Inf
-#&gt; k_phenol_anisole 7.525759e-01
-#&gt; k_anisole_sink 8.305299e-03
-#&gt; sigma 3.322649e+00</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; $ff
+ <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; T245_0 1.038550e+02 NA NA NA NA NA
+#&gt; k_T245_sink 1.636106e-02 NA NA NA NA NA
+#&gt; k_T245_phenol 2.700936e-02 NA NA NA NA NA
+#&gt; k_phenol_sink 1.788604e-10 NA NA NA NA NA
+#&gt; k_phenol_anisole 4.050581e-01 NA NA NA NA NA
+#&gt; k_anisole_sink 6.678742e-03 NA NA NA NA NA
+#&gt; sigma 2.514628e+00 NA NA NA NA 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; $ff
#&gt; T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
#&gt; 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00
#&gt;
@@ -190,20 +182,13 @@
#&gt; </div><div class='input'> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
- <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<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 2.1623653063 48.028441 4.993105e-19 99.271025146
-#&gt; k_T245_sink 1.636106e-02 0.0019676255 8.315130 1.673674e-07 0.012679148
-#&gt; k_T245_phenol 2.700936e-02 0.0012421966 21.743224 1.314080e-13 0.024500319
-#&gt; k_phenol_anisole 4.050581e-01 0.1177235488 3.440757 1.679237e-03 0.218746679
-#&gt; k_anisole_sink 6.678742e-03 0.0006829745 9.778904 1.872892e-08 0.005377084
-#&gt; sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655
-#&gt; Upper
-#&gt; T245_0 108.43904395
-#&gt; k_T245_sink 0.02111217
-#&gt; k_T245_phenol 0.02977535
-#&gt; k_phenol_anisole 0.75005504
-#&gt; k_anisole_sink 0.00829550
-#&gt; sigma 3.31827222</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; $ff
+ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; T245_0 1.038550e+02 NA NA NA NA NA
+#&gt; k_T245_sink 1.636106e-02 NA NA NA NA NA
+#&gt; k_T245_phenol 2.700936e-02 NA NA NA NA NA
+#&gt; k_phenol_anisole 4.050581e-01 NA NA NA NA NA
+#&gt; k_anisole_sink 6.678742e-03 NA NA NA NA NA
+#&gt; sigma 2.514628e+00 NA NA NA NA 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 4.415672e-10 1.000000e+00 1.000000e+00
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 8c14fc9d..b75b7c95 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -360,17 +360,17 @@ Per default, parameters in the kinetic models are internally transformed in
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span>
<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: 0.9.49.4
+<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; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Fri May 3 19:07:19 2019
-#&gt; Date of summary: Fri May 3 19:07:19 2019
+#&gt; Date of fit: Tue May 7 08:08:23 2019
+#&gt; Date of summary: Tue May 7 08:08:23 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 222 model solutions performed in 0.463 s
+#&gt; Fitted using 66 model solutions performed in 0.139 s
#&gt;
#&gt; Error model:
#&gt; Constant variance
@@ -393,28 +393,23 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; None
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 85.87000 1.8070 81.23000 90.5200
-#&gt; log_alpha 0.05192 0.1353 -0.29580 0.3996
-#&gt; log_beta 0.65100 0.2287 0.06315 1.2390
-#&gt; sigma 1.85700 0.4378 0.73200 2.9830
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 85.87000 NA NA NA
+#&gt; log_alpha 0.05192 NA NA NA
+#&gt; log_beta 0.65100 NA NA NA
+#&gt; sigma 1.85700 NA NA NA
#&gt;
#&gt; Parameter correlation:
-#&gt; parent_0 log_alpha log_beta sigma
-#&gt; parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08
-#&gt; log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08
-#&gt; log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08
-#&gt; sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00
-#&gt;
+#&gt; No covariance matrix
#&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 85.870 47.530 3.893e-08 81.2300 90.520
-#&gt; alpha 1.053 7.393 3.562e-04 0.7439 1.491
-#&gt; beta 1.917 4.373 3.601e-03 1.0650 3.451
-#&gt; sigma 1.857 4.243 4.074e-03 0.7320 2.983
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 85.870 NA NA NA NA
+#&gt; alpha 1.053 NA NA NA NA
+#&gt; beta 1.917 NA NA NA NA
+#&gt; sigma 1.857 NA NA NA NA
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
@@ -443,7 +438,7 @@ Per default, parameters in the kinetic models are internally transformed in
<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; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.493 0.000 1.494 </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; NULL</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; 0.637 0.000 0.640 </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; NULL</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
#&gt;
@@ -514,10 +509,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; Sum of squared residuals at call 125: 371.2134
#&gt; Sum of squared residuals at call 126: 371.2134
#&gt; Sum of squared residuals at call 135: 371.2134
-#&gt; Negative log-likelihood at call 145: 97.22429
-#&gt; Optimisation successfully terminated.
-#&gt; User System verstrichen
-#&gt; 1.082 0.000 1.083 </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; NULL</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; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 0.544 0.000 0.550 </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; NULL</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; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
@@ -547,10 +540,10 @@ Per default, parameters in the kinetic models are internally transformed in
<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>
</div><div class='input'><span class='co'># Weighted fits, including IRLS</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</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='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'>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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://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: 0.9.49.4
+ <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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Fri May 3 19:07:35 2019
-#&gt; Date of summary: Fri May 3 19:07:35 2019
+#&gt; Date of fit: Tue May 7 08:08:30 2019
+#&gt; Date of summary: Tue May 7 08:08:30 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -558,7 +551,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 421 model solutions performed in 1.099 s
+#&gt; Fitted using 185 model solutions performed in 0.499 s
#&gt;
#&gt; Error model:
#&gt; Constant variance
@@ -584,31 +577,25 @@ Per default, parameters in the kinetic models are internally transformed in
#&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 1.57000 96.40000 102.8000
-#&gt; log_k_parent -2.31600 0.04087 -2.39900 -2.2330
-#&gt; log_k_m1 -5.24800 0.13320 -5.51800 -4.9770
-#&gt; f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694
-#&gt; sigma 3.12600 0.35850 2.39600 3.8550
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60000 NA NA NA
+#&gt; log_k_parent -2.31600 NA NA NA
+#&gt; log_k_m1 -5.24800 NA NA NA
+#&gt; f_parent_ilr_1 0.04096 NA NA NA
+#&gt; sigma 3.12600 NA NA NA
#&gt;
#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma
-#&gt; parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -2.265e-07
-#&gt; log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.785e-07
-#&gt; log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.386e-07
-#&gt; f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -3.641e-08
-#&gt; sigma -2.265e-07 3.785e-07 -1.386e-07 -3.641e-08 1.000e+00
-#&gt;
+#&gt; No covariance matrix
#&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 63.430 2.298e-36 96.400000 1.028e+02
-#&gt; k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01
-#&gt; k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03
-#&gt; f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01
-#&gt; sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 NA NA NA NA
+#&gt; k_parent 0.098700 NA NA NA NA
+#&gt; k_m1 0.005261 NA NA NA NA
+#&gt; f_parent_to_m1 0.514500 NA NA NA NA
+#&gt; sigma 3.126000 NA NA NA NA
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
@@ -665,10 +652,10 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; 100 m1 31.04 31.98163 -9.416e-01
#&gt; 100 m1 33.13 31.98163 1.148e+00
#&gt; 120 m1 25.15 28.78984 -3.640e+00
-#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
+#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Fri May 3 19:07:37 2019
-#&gt; Date of summary: Fri May 3 19:07:37 2019
+#&gt; Date of fit: Tue May 7 08:08:32 2019
+#&gt; Date of summary: Tue May 7 08:08:32 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -676,7 +663,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 756 model solutions performed in 1.973 s
+#&gt; Fitted using 426 model solutions performed in 1.139 s
#&gt;
#&gt; Error model:
#&gt; Variance unique to each observed variable
@@ -704,41 +691,27 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; m1_0 0 state
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.65000 1.70200 96.19000 103.1000
-#&gt; log_k_parent -2.31300 0.04376 -2.40200 -2.2240
-#&gt; log_k_m1 -5.25000 0.12430 -5.50400 -4.9970
-#&gt; f_parent_ilr_1 0.03861 0.06171 -0.08708 0.1643
-#&gt; sigma_parent 3.40100 0.56820 2.24400 4.5590
-#&gt; sigma_m1 2.85500 0.45240 1.93400 3.7770
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.65000 NA NA NA
+#&gt; log_k_parent -2.31300 NA NA NA
+#&gt; log_k_m1 -5.25000 NA NA NA
+#&gt; f_parent_ilr_1 0.03861 NA NA NA
+#&gt; sigma_parent 3.40100 NA NA NA
+#&gt; sigma_m1 2.85500 NA NA NA
#&gt;
#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_parent
-#&gt; parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035685
-#&gt; log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069840
-#&gt; log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026160
-#&gt; f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041377
-#&gt; sigma_parent 0.03569 0.06984 -0.02616 -0.04138 1.000000
-#&gt; sigma_m1 -0.03385 -0.06626 0.02482 0.03925 -0.004628
-#&gt; sigma_m1
-#&gt; parent_0 -0.033847
-#&gt; log_k_parent -0.066264
-#&gt; log_k_m1 0.024822
-#&gt; f_parent_ilr_1 0.039254
-#&gt; sigma_parent -0.004628
-#&gt; sigma_m1 1.000000
-#&gt;
+#&gt; No covariance matrix
#&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 99.650000 58.560 2.004e-34 96.190000 1.031e+02
-#&gt; k_parent 0.098970 22.850 1.099e-21 0.090530 1.082e-01
-#&gt; k_m1 0.005245 8.046 1.732e-09 0.004072 6.756e-03
-#&gt; f_parent_to_m1 0.513600 23.560 4.352e-22 0.469300 5.578e-01
-#&gt; sigma_parent 3.401000 5.985 5.662e-07 2.244000 4.559e+00
-#&gt; sigma_m1 2.855000 6.311 2.215e-07 1.934000 3.777e+00
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.650000 NA NA NA NA
+#&gt; k_parent 0.098970 NA NA NA NA
+#&gt; k_m1 0.005245 NA NA NA NA
+#&gt; f_parent_to_m1 0.513600 NA NA NA NA
+#&gt; sigma_parent 3.401000 NA NA NA NA
+#&gt; sigma_m1 2.855000 NA NA NA NA
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
@@ -758,47 +731,47 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 99.65425 -1.942e-01
-#&gt; 0 parent 102.04 99.65425 2.386e+00
-#&gt; 1 parent 93.50 90.26338 3.237e+00
-#&gt; 1 parent 92.50 90.26338 2.237e+00
-#&gt; 3 parent 63.23 74.05309 -1.082e+01
-#&gt; 3 parent 68.99 74.05309 -5.063e+00
-#&gt; 7 parent 52.32 49.84326 2.477e+00
-#&gt; 7 parent 55.13 49.84326 5.287e+00
-#&gt; 14 parent 27.27 24.92970 2.340e+00
-#&gt; 14 parent 26.64 24.92970 1.710e+00
-#&gt; 21 parent 11.50 12.46888 -9.689e-01
-#&gt; 21 parent 11.64 12.46888 -8.289e-01
-#&gt; 35 parent 2.85 3.11924 -2.692e-01
-#&gt; 35 parent 2.91 3.11924 -2.092e-01
-#&gt; 50 parent 0.69 0.70678 -1.678e-02
-#&gt; 50 parent 0.63 0.70678 -7.678e-02
-#&gt; 75 parent 0.05 0.05952 -9.522e-03
-#&gt; 75 parent 0.06 0.05952 4.776e-04
+#&gt; 0 parent 99.46 99.65417 -1.942e-01
+#&gt; 0 parent 102.04 99.65417 2.386e+00
+#&gt; 1 parent 93.50 90.26332 3.237e+00
+#&gt; 1 parent 92.50 90.26332 2.237e+00
+#&gt; 3 parent 63.23 74.05306 -1.082e+01
+#&gt; 3 parent 68.99 74.05306 -5.063e+00
+#&gt; 7 parent 52.32 49.84325 2.477e+00
+#&gt; 7 parent 55.13 49.84325 5.287e+00
+#&gt; 14 parent 27.27 24.92971 2.340e+00
+#&gt; 14 parent 26.64 24.92971 1.710e+00
+#&gt; 21 parent 11.50 12.46890 -9.689e-01
+#&gt; 21 parent 11.64 12.46890 -8.289e-01
+#&gt; 35 parent 2.85 3.11925 -2.692e-01
+#&gt; 35 parent 2.91 3.11925 -2.092e-01
+#&gt; 50 parent 0.69 0.70679 -1.679e-02
+#&gt; 50 parent 0.63 0.70679 -7.679e-02
+#&gt; 75 parent 0.05 0.05952 -9.523e-03
+#&gt; 75 parent 0.06 0.05952 4.772e-04
#&gt; 1 m1 4.84 4.81075 2.925e-02
#&gt; 1 m1 5.64 4.81075 8.292e-01
-#&gt; 3 m1 12.91 13.04197 -1.320e-01
-#&gt; 3 m1 12.96 13.04197 -8.197e-02
-#&gt; 7 m1 22.97 25.06848 -2.098e+00
-#&gt; 7 m1 24.47 25.06848 -5.985e-01
+#&gt; 3 m1 12.91 13.04196 -1.320e-01
+#&gt; 3 m1 12.96 13.04196 -8.196e-02
+#&gt; 7 m1 22.97 25.06847 -2.098e+00
+#&gt; 7 m1 24.47 25.06847 -5.985e-01
#&gt; 14 m1 41.69 36.70308 4.987e+00
#&gt; 14 m1 33.21 36.70308 -3.493e+00
#&gt; 21 m1 44.37 41.65115 2.719e+00
#&gt; 21 m1 46.44 41.65115 4.789e+00
-#&gt; 35 m1 41.22 43.29464 -2.075e+00
-#&gt; 35 m1 37.95 43.29464 -5.345e+00
-#&gt; 50 m1 41.19 41.19947 -9.473e-03
-#&gt; 50 m1 40.01 41.19947 -1.189e+00
-#&gt; 75 m1 40.09 36.44035 3.650e+00
-#&gt; 75 m1 33.85 36.44035 -2.590e+00
-#&gt; 100 m1 31.04 31.98773 -9.477e-01
-#&gt; 100 m1 33.13 31.98773 1.142e+00
+#&gt; 35 m1 41.22 43.29465 -2.075e+00
+#&gt; 35 m1 37.95 43.29465 -5.345e+00
+#&gt; 50 m1 41.19 41.19948 -9.481e-03
+#&gt; 50 m1 40.01 41.19948 -1.189e+00
+#&gt; 75 m1 40.09 36.44036 3.650e+00
+#&gt; 75 m1 33.85 36.44036 -2.590e+00
+#&gt; 100 m1 31.04 31.98774 -9.477e-01
+#&gt; 100 m1 33.13 31.98774 1.142e+00
#&gt; 120 m1 25.15 28.80430 -3.654e+00
-#&gt; 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
+#&gt; 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Fri May 3 19:07:40 2019
-#&gt; Date of summary: Fri May 3 19:07:40 2019
+#&gt; Date of fit: Tue May 7 08:08:34 2019
+#&gt; Date of summary: Tue May 7 08:08:34 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -806,7 +779,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 888 model solutions performed in 3.579 s
+#&gt; Fitted using 489 model solutions performed in 2.013 s
#&gt;
#&gt; Error model:
#&gt; Two-component variance function
@@ -834,98 +807,84 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; m1_0 0 state
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 100.30000 3.06400 94.08000 106.60000
-#&gt; log_k_parent -2.31100 0.02913 -2.37100 -2.25200
-#&gt; log_k_m1 -5.27800 0.10890 -5.49900 -5.05600
-#&gt; f_parent_ilr_1 0.02128 0.07223 -0.12590 0.16840
-#&gt; sigma_low 0.99650 NaN NaN NaN
-#&gt; rsd_high 0.07560 0.01059 0.05402 0.09717
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 100.70000 NA NA NA
+#&gt; log_k_parent -2.29700 NA NA NA
+#&gt; log_k_m1 -5.26600 NA NA NA
+#&gt; f_parent_ilr_1 0.02374 NA NA NA
+#&gt; sigma_low 0.00305 NA NA NA
+#&gt; rsd_high 0.07928 NA NA NA
#&gt;
#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low
-#&gt; parent_0 1.00000 0.64703 -0.220160 -0.79035 NaN
-#&gt; log_k_parent 0.64703 1.00000 -0.339633 -0.67982 NaN
-#&gt; log_k_m1 -0.22016 -0.33963 1.000000 0.62815 NaN
-#&gt; f_parent_ilr_1 -0.79035 -0.67982 0.628148 1.00000 NaN
-#&gt; sigma_low NaN NaN NaN NaN 1
-#&gt; rsd_high -0.05745 -0.01123 0.003502 0.00568 NaN
-#&gt; rsd_high
-#&gt; parent_0 -0.057450
-#&gt; log_k_parent -0.011230
-#&gt; log_k_m1 0.003502
-#&gt; f_parent_ilr_1 0.005680
-#&gt; sigma_low NaN
-#&gt; rsd_high 1.000000
-#&gt;
+#&gt; No covariance matrix
#&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 1.003e+02 32.740 1.759e-26 94.080000 1.066e+02
-#&gt; k_parent 9.914e-02 34.330 4.045e-27 0.093430 1.052e-01
-#&gt; k_m1 5.105e-03 9.186 8.682e-11 0.004089 6.372e-03
-#&gt; f_parent_to_m1 5.075e-01 19.880 7.143e-20 0.455600 5.593e-01
-#&gt; sigma_low 9.965e-01 NaN NaN NaN NaN
-#&gt; rsd_high 7.560e-02 7.137 2.114e-08 0.054020 9.717e-02
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 1.007e+02 NA NA NA NA
+#&gt; k_parent 1.006e-01 NA NA NA NA
+#&gt; k_m1 5.167e-03 NA NA NA NA
+#&gt; f_parent_to_m1 5.084e-01 NA NA NA NA
+#&gt; sigma_low 3.050e-03 NA NA NA NA
+#&gt; rsd_high 7.928e-02 NA NA NA NA
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
-#&gt; All data 6.433 4 15
-#&gt; parent 6.506 2 7
-#&gt; m1 4.692 2 8
+#&gt; All data 6.475 4 15
+#&gt; parent 6.573 2 7
+#&gt; m1 4.671 2 8
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
-#&gt; parent_m1 0.5075
-#&gt; parent_sink 0.4925
+#&gt; parent_m1 0.5084
+#&gt; parent_sink 0.4916
#&gt;
#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 6.992 23.23
-#&gt; m1 135.787 451.08
+#&gt; DT50 DT90
+#&gt; parent 6.893 22.9
+#&gt; m1 134.156 445.7
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 100.32122 -0.861220
-#&gt; 0 parent 102.04 100.32122 1.718780
-#&gt; 1 parent 93.50 90.85266 2.647340
-#&gt; 1 parent 92.50 90.85266 1.647340
-#&gt; 3 parent 63.23 74.51219 -11.282190
-#&gt; 3 parent 68.99 74.51219 -5.522190
-#&gt; 7 parent 52.32 50.11950 2.200504
-#&gt; 7 parent 55.13 50.11950 5.010504
-#&gt; 14 parent 27.27 25.03921 2.230792
-#&gt; 14 parent 26.64 25.03921 1.600792
-#&gt; 21 parent 11.50 12.50934 -1.009342
-#&gt; 21 parent 11.64 12.50934 -0.869342
-#&gt; 35 parent 2.85 3.12221 -0.272211
-#&gt; 35 parent 2.91 3.12221 -0.212211
-#&gt; 50 parent 0.69 0.70572 -0.015724
-#&gt; 50 parent 0.63 0.70572 -0.075724
-#&gt; 75 parent 0.05 0.05919 -0.009191
-#&gt; 75 parent 0.06 0.05919 0.000809
-#&gt; 1 m1 4.84 4.79307 0.046928
-#&gt; 1 m1 5.64 4.79307 0.846928
-#&gt; 3 m1 12.91 12.99398 -0.083980
-#&gt; 3 m1 12.96 12.99398 -0.033980
-#&gt; 7 m1 22.97 24.97744 -2.007441
-#&gt; 7 m1 24.47 24.97744 -0.507441
-#&gt; 14 m1 41.69 36.57917 5.110827
-#&gt; 14 m1 33.21 36.57917 -3.369173
-#&gt; 21 m1 44.37 41.52931 2.840692
-#&gt; 21 m1 46.44 41.52931 4.910692
-#&gt; 35 m1 41.22 43.22614 -2.006138
-#&gt; 35 m1 37.95 43.22614 -5.276138
-#&gt; 50 m1 41.19 41.20972 -0.019717
-#&gt; 50 m1 40.01 41.20972 -1.199717
-#&gt; 75 m1 40.09 36.57312 3.516882
-#&gt; 75 m1 33.85 36.57312 -2.723118
-#&gt; 100 m1 31.04 32.21655 -1.176546
-#&gt; 100 m1 33.13 32.21655 0.913454
-#&gt; 120 m1 25.15 29.09181 -3.941814
-#&gt; 120 m1 33.31 29.09181 4.218186</div><div class='input'>
+#&gt; 0 parent 99.46 100.73433 -1.274329
+#&gt; 0 parent 102.04 100.73433 1.305671
+#&gt; 1 parent 93.50 91.09750 2.402495
+#&gt; 1 parent 92.50 91.09750 1.402495
+#&gt; 3 parent 63.23 74.50140 -11.271403
+#&gt; 3 parent 68.99 74.50140 -5.511403
+#&gt; 7 parent 52.32 49.82880 2.491205
+#&gt; 7 parent 55.13 49.82880 5.301205
+#&gt; 14 parent 27.27 24.64809 2.621909
+#&gt; 14 parent 26.64 24.64809 1.991909
+#&gt; 21 parent 11.50 12.19231 -0.692315
+#&gt; 21 parent 11.64 12.19231 -0.552315
+#&gt; 35 parent 2.85 2.98327 -0.133266
+#&gt; 35 parent 2.91 2.98327 -0.073266
+#&gt; 50 parent 0.69 0.66013 0.029874
+#&gt; 50 parent 0.63 0.66013 -0.030126
+#&gt; 75 parent 0.05 0.05344 -0.003438
+#&gt; 75 parent 0.06 0.05344 0.006562
+#&gt; 1 m1 4.84 4.88645 -0.046451
+#&gt; 1 m1 5.64 4.88645 0.753549
+#&gt; 3 m1 12.91 13.22867 -0.318668
+#&gt; 3 m1 12.96 13.22867 -0.268668
+#&gt; 7 m1 22.97 25.36416 -2.394164
+#&gt; 7 m1 24.47 25.36416 -0.894164
+#&gt; 14 m1 41.69 37.00974 4.680265
+#&gt; 14 m1 33.21 37.00974 -3.799735
+#&gt; 21 m1 44.37 41.90133 2.468670
+#&gt; 21 m1 46.44 41.90133 4.538670
+#&gt; 35 m1 41.22 43.45691 -2.236914
+#&gt; 35 m1 37.95 43.45691 -5.506914
+#&gt; 50 m1 41.19 41.34199 -0.151988
+#&gt; 50 m1 40.01 41.34199 -1.331988
+#&gt; 75 m1 40.09 36.61471 3.475290
+#&gt; 75 m1 33.85 36.61471 -2.764710
+#&gt; 100 m1 31.04 32.20083 -1.160830
+#&gt; 100 m1 33.13 32.20083 0.929170
+#&gt; 120 m1 25.15 29.04131 -3.891312
+#&gt; 120 m1 33.31 29.04131 4.268688</div><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 9ba463e3..9f417cf3 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 file2b304be466d0.c 2&gt; file2b304be466d0.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file6d1314eef3d7.c 2&gt; file6d1314eef3d7.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png
index 65918d53..d4e465d4 100644
--- a/docs/reference/mkinparplot-1.png
+++ b/docs/reference/mkinparplot-1.png
Binary files differ
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 8cfb9374..05af0f15 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -154,7 +154,7 @@
<pre class="examples"><div class='input'><span class='no'>model</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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
<span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"anisole"</span>)),
- <span class='kw'>anisole</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'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div></pre>
+ <span class='kw'>anisole</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'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 074ac3ac..8c5c50e4 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -333,12 +333,12 @@
<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
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.002 0.000 0.001 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.001 0.000 0.001 </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='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</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; 0.022 0.000 0.021 </div><div class='input'>
+#&gt; 0.021 0.000 0.022 </div><div class='input'>
</div><div class='input'> <span class='co'># Predict from a fitted model</span>
<span class='no'>f</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_C</span>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
#&gt; Sum of squared residuals at call 3: 552.5739
@@ -368,9 +368,7 @@
#&gt; Sum of squared residuals at call 59: 196.5334
#&gt; Sum of squared residuals at call 65: 196.5334
#&gt; Sum of squared residuals at call 73: 196.5334
-#&gt; Negative log-likelihood at call 75: 26.64668
-#&gt; Negative log-likelihood at call 103: 26.64668
-#&gt; Optimisation successfully terminated.</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#&gt; time parent m1
+#&gt; Negative log-likelihood at call 75: 26.64668</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#&gt; time parent m1
#&gt; 1 0.0 82.49216 0.000000
#&gt; 2 0.1 80.00563 1.179955
#&gt; 3 0.2 77.59404 2.312580
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index c730ecb0..849e619e 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; 0.042 0.028 5.095 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 19.29 0.00 19.30 </div><div class='input'>
+#&gt; 0.039 0.031 3.113 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 10.445 0.001 10.456 </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; 0.7340481 0.2659519 0.7505684 0.2494316
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index a9ee2f76..62027fab 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -182,7 +182,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'>nafta</span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Sums of squares:
+ <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'>nafta</span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Sums of squares:
#&gt; SFO IORE DFOP
#&gt; 1378.6832 615.7730 517.8836
#&gt;
@@ -191,25 +191,25 @@
#&gt;
#&gt; Parameters:
#&gt; $SFO
-#&gt; Estimate Pr(&gt;t) Lower Upper
-#&gt; parent_0 83.7558 1.80e-14 77.18268 90.3288
-#&gt; k_parent_sink 0.0017 7.43e-05 0.00112 0.0026
-#&gt; sigma 8.7518 1.22e-05 5.64278 11.8608
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 83.7558 NA NA NA
+#&gt; k_parent_sink 0.0017 NA NA NA
+#&gt; sigma 8.7518 NA NA NA
#&gt;
#&gt; $IORE
-#&gt; Estimate Pr(&gt;t) Lower Upper
-#&gt; parent_0 9.69e+01 NA 8.88e+01 1.05e+02
-#&gt; k__iore_parent_sink 8.40e-14 NA 1.79e-18 3.94e-09
-#&gt; N_parent 6.68e+00 NA 4.19e+00 9.17e+00
-#&gt; sigma 5.85e+00 NA 3.76e+00 7.94e+00
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.69e+01 NA NA NA
+#&gt; k__iore_parent_sink 8.40e-14 NA NA NA
+#&gt; N_parent 6.68e+00 NA NA NA
+#&gt; sigma 5.85e+00 NA NA NA
#&gt;
#&gt; $DFOP
-#&gt; Estimate Pr(&gt;t) Lower Upper
-#&gt; parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02
-#&gt; k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02
-#&gt; k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03
-#&gt; g 2.88e-01 2.47e-05 1.95e-01 4.03e-01
-#&gt; sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.76e+01 NA NA NA
+#&gt; k1 4.24e-02 NA NA NA
+#&gt; k2 8.24e-04 NA NA NA
+#&gt; g 2.88e-01 NA NA NA
+#&gt; sigma 5.36e+00 NA NA NA
#&gt;
#&gt;
#&gt; DTx values:
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 351d7a7e..a4f3d04f 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -209,17 +209,17 @@
<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: 0.9.49.4
+ <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; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Fri May 3 19:08:31 2019
-#&gt; Date of summary: Fri May 3 19:08:31 2019
+#&gt; Date of fit: Tue May 7 08:09:03 2019
+#&gt; Date of summary: Tue May 7 08:09:03 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 131 model solutions performed in 0.27 s
+#&gt; Fitted using 39 model solutions performed in 0.08 s
#&gt;
#&gt; Error model:
#&gt; Constant variance
@@ -240,25 +240,21 @@
#&gt; None
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 109.200 3.70400 99.630 118.700
-#&gt; log_k_parent_sink -3.291 0.09176 -3.527 -3.055
-#&gt; sigma 5.266 1.31600 1.882 8.649
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 109.200 NA NA NA
+#&gt; log_k_parent_sink -3.291 NA NA NA
+#&gt; sigma 5.266 NA NA NA
#&gt;
#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent_sink sigma
-#&gt; parent_0 1.000e+00 5.428e-01 1.648e-07
-#&gt; log_k_parent_sink 5.428e-01 1.000e+00 2.513e-07
-#&gt; sigma 1.648e-07 2.513e-07 1.000e+00
-#&gt;
+#&gt; No covariance matrix
#&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_0 109.20000 29.47 4.218e-07 99.6300 118.70000
-#&gt; k_parent_sink 0.03722 10.90 5.650e-05 0.0294 0.04712
-#&gt; sigma 5.26600 4.00 5.162e-03 1.8820 8.64900
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 109.20000 NA NA NA NA
+#&gt; k_parent_sink 0.03722 NA NA NA NA
+#&gt; sigma 5.26600 NA NA NA NA
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index bc988340..11cb6420 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -159,20 +159,13 @@
<span class='co'># model).</span>
<span class='no'>m_ws</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>),
<span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</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_river</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>
- <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t)
-#&gt; parent_w_0 9.598567e+01 2.12351789 4.520126e+01 9.476190e-18
-#&gt; k_parent_w_sink 3.603743e-01 0.03149282 1.144306e+01 4.126593e-09
-#&gt; k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04
-#&gt; k_parent_s_sink 5.108964e-11 0.09482736 5.387647e-10 5.000000e-01
-#&gt; k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01
-#&gt; sigma 2.982879e+00 0.50545649 5.901356e+00 1.454535e-05
-#&gt; Lower Upper
-#&gt; parent_w_0 91.48420503 100.4871438
-#&gt; k_parent_w_sink 0.30668904 0.4234571
-#&gt; k_parent_w_parent_s 0.03423904 0.1062455
-#&gt; k_parent_s_sink 0.00000000 Inf
-#&gt; k_parent_s_parent_w 0.02289956 0.2404043
-#&gt; sigma 2.00184022 3.9639169</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#&gt; err.min n.optim df
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_w_0 9.598567e+01 NA NA NA NA NA
+#&gt; k_parent_w_sink 3.603743e-01 NA NA NA NA NA
+#&gt; k_parent_w_parent_s 6.031371e-02 NA NA NA NA NA
+#&gt; k_parent_s_sink 5.108964e-11 NA NA NA NA NA
+#&gt; k_parent_s_parent_w 7.419672e-02 NA NA NA NA NA
+#&gt; sigma 2.982879e+00 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#&gt; err.min n.optim df
#&gt; All data 0.09246946 5 6
#&gt; parent_w 0.06377096 3 3
#&gt; parent_s 0.20882325 2 3</div><div class='input'>
@@ -183,28 +176,17 @@
<span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>),
<span class='kw'>M3</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_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; parent_0 76.55425584 0.859186619 89.1008474 1.113866e-26 74.755959756
-#&gt; k_parent 0.12081956 0.004601922 26.2541544 1.077373e-16 0.111561582
-#&gt; k_M1 0.84258649 0.806231419 1.0450926 1.545475e-01 0.113839803
-#&gt; k_M2 0.04210878 0.017083049 2.4649453 1.170195e-02 0.018013807
-#&gt; k_M3 0.01122919 0.007245890 1.5497322 6.885127e-02 0.002909463
-#&gt; f_parent_to_M1 0.32240199 0.240803555 1.3388589 9.820820e-02 NA
-#&gt; f_parent_to_M2 0.16099854 0.033691991 4.7785403 6.531224e-05 NA
-#&gt; f_M1_to_M3 0.27921501 0.269443514 1.0362655 1.565440e-01 0.022992937
-#&gt; f_M2_to_M3 0.55641331 0.595125445 0.9349513 1.807725e-01 0.008003317
-#&gt; sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778
-#&gt; Upper
-#&gt; parent_0 78.35255192
-#&gt; k_parent 0.13084582
-#&gt; k_M1 6.23641265
-#&gt; k_M2 0.09843279
-#&gt; k_M3 0.04333950
-#&gt; f_parent_to_M1 NA
-#&gt; f_parent_to_M2 NA
-#&gt; f_M1_to_M3 0.86443083
-#&gt; f_M2_to_M3 0.99489847
-#&gt; sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#&gt; err.min n.optim df
+ <span class='no'>f_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 76.55425584 NA NA NA NA NA
+#&gt; k_parent 0.12081956 NA NA NA NA NA
+#&gt; k_M1 0.84258649 NA NA NA NA NA
+#&gt; k_M2 0.04210878 NA NA NA NA NA
+#&gt; k_M3 0.01122919 NA NA NA NA NA
+#&gt; f_parent_to_M1 0.32240199 NA NA NA NA NA
+#&gt; f_parent_to_M2 0.16099854 NA NA NA NA NA
+#&gt; f_M1_to_M3 0.27921501 NA NA NA NA NA
+#&gt; f_M2_to_M3 0.55641331 NA NA NA NA NA
+#&gt; sigma 1.14005399 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#&gt; err.min n.optim df
#&gt; All data 0.09649963 9 20
#&gt; parent 0.04721283 2 6
#&gt; M1 0.26551209 2 5
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 7e05480e..c91565b9 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,32 +202,30 @@ The transformation of sets of formation fractions is fragile, as it supposes
<pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</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='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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='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>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.60 1.5702 96.40 102.79
-#&gt; log_k_parent_sink -3.04 0.0763 -3.19 -2.88
-#&gt; log_k_parent_m1 -2.98 0.0403 -3.06 -2.90
-#&gt; log_k_m1_sink -5.25 0.1332 -5.52 -4.98
-#&gt; sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<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 1.57022 63.43 2.30e-36 96.40384 102.7931
-#&gt; k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560
-#&gt; k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551
-#&gt; k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
-#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'>
+<span class='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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='input'><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>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60 NA NA NA
+#&gt; log_k_parent_sink -3.04 NA NA NA
+#&gt; log_k_parent_m1 -2.98 NA NA NA
+#&gt; log_k_m1_sink -5.25 NA NA NA
+#&gt; sigma 3.13 NA NA NA</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<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 NA NA NA NA NA
+#&gt; k_parent_sink 0.04792 NA NA NA NA NA
+#&gt; k_parent_m1 0.05078 NA NA NA NA NA
+#&gt; k_m1_sink 0.00526 NA NA NA NA NA
+#&gt; sigma 3.12550 NA NA NA NA NA</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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='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>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.59848 1.57022 96.40384 1.03e+02
-#&gt; k_parent_sink 0.04792 0.00365 0.04049 5.54e-02
-#&gt; k_parent_m1 0.05078 0.00205 0.04661 5.49e-02
-#&gt; k_m1_sink 0.00526 0.00070 0.00384 6.69e-03
-#&gt; sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<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 1.57022 63.43 2.30e-36 96.40384 1.03e+02
-#&gt; k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02
-#&gt; k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02
-#&gt; k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03
-#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'>
+<span class='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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></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>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.59848 NA NA NA
+#&gt; k_parent_sink 0.04792 NA NA NA
+#&gt; k_parent_m1 0.05078 NA NA NA
+#&gt; k_m1_sink 0.00526 NA NA NA
+#&gt; sigma 3.12550 NA NA NA</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<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 NA NA NA NA NA
+#&gt; k_parent_sink 0.04792 NA NA NA NA NA
+#&gt; k_parent_m1 0.05078 NA NA NA NA NA
+#&gt; k_m1_sink 0.00526 NA NA NA NA NA
+#&gt; sigma 3.12550 NA NA NA NA NA</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>$<span class='no'>value</span>
@@ -240,18 +238,17 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.ff.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<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 1.5702 96.4038 102.793
-#&gt; log_k_parent -2.316 0.0409 -2.3988 -2.233
-#&gt; log_k_m1 -5.248 0.1332 -5.5184 -4.977
-#&gt; f_parent_ilr_1 0.041 0.0631 -0.0875 0.169
-#&gt; sigma 3.126 0.3585 2.3961 3.855</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>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931
-#&gt; k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073
-#&gt; k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
-#&gt; f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596
-#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'><span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
+<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.ff.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.598 NA NA NA
+#&gt; log_k_parent -2.316 NA NA NA
+#&gt; log_k_m1 -5.248 NA NA NA
+#&gt; f_parent_ilr_1 0.041 NA NA NA
+#&gt; sigma 3.126 NA NA NA</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 NA NA NA NA NA
+#&gt; k_parent 0.09870 NA NA NA NA NA
+#&gt; k_m1 0.00526 NA NA NA NA NA
+#&gt; f_parent_to_m1 0.51448 NA NA NA NA NA
+#&gt; sigma 3.12550 NA NA NA NA NA</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'>
@@ -261,16 +258,15 @@ 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.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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='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 3.012 78.67 90.91
-#&gt; log_k_parent -2.76 0.082 -2.92 -2.59
-#&gt; log_k_m1 -4.21 0.123 -4.46 -3.96
-#&gt; sigma 8.22 0.943 6.31 10.14</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>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913
-#&gt; k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075
-#&gt; k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019
-#&gt; sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div></pre>
+<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.ff.2.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 84.79 NA NA NA
+#&gt; log_k_parent -2.76 NA NA NA
+#&gt; log_k_m1 -4.21 NA NA NA
+#&gt; sigma 8.22 NA NA NA</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 NA NA NA NA NA
+#&gt; k_parent 0.0635 NA NA NA NA NA
+#&gt; k_m1 0.0148 NA NA NA NA NA
+#&gt; sigma 8.2229 NA NA NA NA NA</div></pre>
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<h2>Contents</h2>

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