From c322a8102a399cbb1fe38c4c4ca4485cea8bc4e8 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 7 May 2019 08:43:12 +0200
Subject: Fix hessian calculations
Static documentation rebuilt by pkgdown
---
docs/reference/NAFTA_SOP_2015.html | 32 ++---
docs/reference/NAFTA_SOP_Attachment.html | 32 ++---
docs/reference/logistic.solution.html | 18 ++-
docs/reference/mccall81_245T.html | 45 ++++---
docs/reference/mkinfit.html | 176 ++++++++++++++++------------
docs/reference/mkinmod.html | 2 +-
docs/reference/mkinparplot-1.png | Bin 17306 -> 16549 bytes
docs/reference/mkinparplot.html | 2 +-
docs/reference/mkinpredict.html | 4 +-
docs/reference/mmkin.html | 4 +-
docs/reference/nafta.html | 32 ++---
docs/reference/summary.mkinfit.html | 30 +++--
docs/reference/test_data_from_UBA_2014.html | 54 ++++++---
docs/reference/transform_odeparms.html | 90 +++++++-------
14 files changed, 300 insertions(+), 221 deletions(-)
(limited to 'docs/reference')
diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html
index 9fbc71c6..84341a17 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'><-</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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <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'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <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'>#> Sums of squares:
+ <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</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'>#> <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'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <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'>#> Sums of squares:
#> SFO IORE DFOP
#> 1378.6832 615.7730 517.8836
#>
@@ -164,25 +164,25 @@
#>
#> Parameters:
#> $SFO
-#> Estimate Pr(>t) Lower Upper
-#> parent_0 83.7558 NA NA NA
-#> k_parent_sink 0.0017 NA NA NA
-#> sigma 8.7518 NA NA NA
+#> Estimate Pr(>t) Lower Upper
+#> parent_0 83.7558 1.80e-14 77.18268 90.3288
+#> k_parent_sink 0.0017 7.43e-05 0.00112 0.0026
+#> sigma 8.7518 1.22e-05 5.64278 11.8608
#>
#> $IORE
-#> Estimate Pr(>t) Lower Upper
-#> parent_0 9.69e+01 NA NA NA
-#> k__iore_parent_sink 8.40e-14 NA NA NA
-#> N_parent 6.68e+00 NA NA NA
-#> sigma 5.85e+00 NA NA NA
+#> Estimate Pr(>t) Lower Upper
+#> parent_0 9.69e+01 NA 8.88e+01 1.05e+02
+#> k__iore_parent_sink 8.40e-14 NA 1.79e-18 3.94e-09
+#> N_parent 6.68e+00 NA 4.19e+00 9.17e+00
+#> sigma 5.85e+00 NA 3.76e+00 7.94e+00
#>
#> $DFOP
-#> Estimate Pr(>t) Lower Upper
-#> parent_0 9.76e+01 NA NA NA
-#> k1 4.24e-02 NA NA NA
-#> k2 8.24e-04 NA NA NA
-#> g 2.88e-01 NA NA NA
-#> sigma 5.36e+00 NA NA NA
+#> Estimate Pr(>t) Lower Upper
+#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02
+#> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02
+#> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03
+#> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01
+#> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00
#>
#>
#> DTx values:
diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html
index 149b4d82..76d91c40 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'><-</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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <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'>#> <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'>#> Sums of squares:
+ <pre class="examples"><div class='input'> <span class='no'>nafta_att_p5a</span> <span class='kw'><-</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'>#> <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'>#> <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'>#> Sums of squares:
#> SFO IORE DFOP
#> 465.21753 56.27506 32.06401
#>
@@ -161,25 +161,25 @@
#>
#> Parameters:
#> $SFO
-#> Estimate Pr(>t) Lower Upper
-#> parent_0 95.8401 NA NA NA
-#> k_parent_sink 0.0102 NA NA NA
-#> sigma 4.8230 NA NA NA
+#> Estimate Pr(>t) Lower Upper
+#> parent_0 95.8401 4.67e-21 92.245 99.4357
+#> k_parent_sink 0.0102 3.92e-12 0.009 0.0117
+#> sigma 4.8230 3.81e-06 3.214 6.4318
#>
#> $IORE
-#> Estimate Pr(>t) Lower Upper
-#> parent_0 1.01e+02 NA NA NA
-#> k__iore_parent_sink 1.54e-05 NA NA NA
-#> N_parent 2.57e+00 NA NA NA
-#> sigma 1.68e+00 NA NA NA
+#> Estimate Pr(>t) Lower Upper
+#> parent_0 1.01e+02 NA 9.91e+01 1.02e+02
+#> k__iore_parent_sink 1.54e-05 NA 4.08e-06 5.84e-05
+#> N_parent 2.57e+00 NA 2.25e+00 2.89e+00
+#> sigma 1.68e+00 NA 1.12e+00 2.24e+00
#>
#> $DFOP
-#> Estimate Pr(>t) Lower Upper
-#> parent_0 9.99e+01 NA NA NA
-#> k1 2.67e-02 NA NA NA
-#> k2 2.86e-12 NA NA NA
-#> g 6.47e-01 NA NA NA
-#> sigma 1.27e+00 NA NA NA
+#> Estimate Pr(>t) Lower Upper
+#> parent_0 9.99e+01 1.41e-26 98.8116 101.0810
+#> k1 2.67e-02 5.05e-06 0.0243 0.0295
+#> k2 2.86e-12 5.00e-01 0.0000 Inf
+#> g 6.47e-01 3.67e-06 0.6248 0.6677
+#> sigma 1.27e+00 8.91e-06 0.8395 1.6929
#>
#>
#> DTx values:
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 082cd4fb..3b45b14f 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -205,12 +205,18 @@
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
<span class='no'>m</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
-#> parent_0 1.057896e+02 NA NA NA NA NA
-#> kmax 6.398190e-02 NA NA NA NA NA
-#> k0 1.612775e-04 NA NA NA NA NA
-#> r 2.263946e-01 NA NA NA NA NA
-#> 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>)$<span class='no'>distimes</span></div><div class='output co'>#> DT50 DT90 DT50_k0 DT50_kmax
+ <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower
+#> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02
+#> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02
+#> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846685e-08
+#> r 2.263946e-01 0.1718110773 1.317695 1.061044e-01 4.335843e-02
+#> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00
+#> Upper
+#> parent_0 109.9341588
+#> kmax 0.1041853
+#> k0 0.4448750
+#> r 1.1821121
+#> 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'>#> DT50 DT90 DT50_k0 DT50_kmax
#> 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 26bbd2ec..1db9a9d9 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -160,14 +160,22 @@
<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'><-</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'>#> <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'><-</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'>#> <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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
-#> T245_0 1.038550e+02 NA NA NA NA NA
-#> k_T245_sink 1.636106e-02 NA NA NA NA NA
-#> k_T245_phenol 2.700936e-02 NA NA NA NA NA
-#> k_phenol_sink 1.788604e-10 NA NA NA NA NA
-#> k_phenol_anisole 4.050581e-01 NA NA NA NA NA
-#> k_anisole_sink 6.678742e-03 NA NA NA NA NA
-#> 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'>#> $ff
+ <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower
+#> T245_0 1.038550e+02 2.1508110557 48.286452 3.542232e-18 99.246062215
+#> k_T245_sink 1.636106e-02 NaN NaN NaN 0.012661558
+#> k_T245_phenol 2.700936e-02 NaN NaN NaN 0.024487315
+#> k_phenol_sink 1.788604e-10 NaN NaN NaN 0.000000000
+#> k_phenol_anisole 4.050581e-01 0.1053801116 3.843781 7.970202e-04 0.218013982
+#> k_anisole_sink 6.678742e-03 0.0006205844 10.762020 9.428076e-09 0.005370739
+#> sigma 2.514628e+00 0.3383670685 7.431657 1.054101e-06 1.706607296
+#> Upper
+#> T245_0 1.084640e+02
+#> k_T245_sink 2.114150e-02
+#> k_T245_phenol 2.979116e-02
+#> k_phenol_sink Inf
+#> k_phenol_anisole 7.525759e-01
+#> k_anisole_sink 8.305299e-03
+#> 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'>#> $ff
#> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
#> 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00
#>
@@ -182,13 +190,20 @@
#> </div><div class='input'> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
- <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
-#> T245_0 1.038550e+02 NA NA NA NA NA
-#> k_T245_sink 1.636106e-02 NA NA NA NA NA
-#> k_T245_phenol 2.700936e-02 NA NA NA NA NA
-#> k_phenol_anisole 4.050581e-01 NA NA NA NA NA
-#> k_anisole_sink 6.678742e-03 NA NA NA NA NA
-#> 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'>#> $ff
+ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower
+#> T245_0 1.038550e+02 2.1623653063 48.028441 4.993105e-19 99.271025146
+#> k_T245_sink 1.636106e-02 0.0019676255 8.315130 1.673674e-07 0.012679148
+#> k_T245_phenol 2.700936e-02 0.0012421966 21.743224 1.314080e-13 0.024500319
+#> k_phenol_anisole 4.050581e-01 0.1177235488 3.440757 1.679237e-03 0.218746679
+#> k_anisole_sink 6.678742e-03 0.0006829745 9.778904 1.872892e-08 0.005377084
+#> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655
+#> Upper
+#> T245_0 108.43904395
+#> k_T245_sink 0.02111217
+#> k_T245_phenol 0.02977535
+#> k_phenol_anisole 0.75005504
+#> k_anisole_sink 0.00829550
+#> 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'>#> $ff
#> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
#> 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00
#>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index b75b7c95..09329a86 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'><-</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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> 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'>#> mkin version used for fitting: 0.9.49.4
#> R version used for fitting: 3.6.0
-#> Date of fit: Tue May 7 08:08:23 2019
-#> Date of summary: Tue May 7 08:08:23 2019
+#> Date of fit: Tue May 7 08:36:16 2019
+#> Date of summary: Tue May 7 08:36:16 2019
#>
#> Equations:
#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#>
#> Model predictions using solution type analytical
#>
-#> Fitted using 66 model solutions performed in 0.139 s
+#> Fitted using 222 model solutions performed in 0.89 s
#>
#> Error model:
#> Constant variance
@@ -393,23 +393,28 @@ Per default, parameters in the kinetic models are internally transformed in
#> None
#>
#> Optimised, transformed parameters with symmetric confidence intervals:
-#> Estimate Std. Error Lower Upper
-#> parent_0 85.87000 NA NA NA
-#> log_alpha 0.05192 NA NA NA
-#> log_beta 0.65100 NA NA NA
-#> sigma 1.85700 NA NA NA
+#> Estimate Std. Error Lower Upper
+#> parent_0 85.87000 1.8070 81.23000 90.5200
+#> log_alpha 0.05192 0.1353 -0.29580 0.3996
+#> log_beta 0.65100 0.2287 0.06315 1.2390
+#> sigma 1.85700 0.4378 0.73200 2.9830
#>
#> Parameter correlation:
-#> No covariance matrix
+#> parent_0 log_alpha log_beta sigma
+#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08
+#> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08
+#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08
+#> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00
+#>
#> Backtransformed parameters:
#> Confidence intervals for internally transformed parameters are asymmetric.
#> t-test (unrealistically) based on the assumption of normal distribution
#> for estimators of untransformed parameters.
-#> Estimate t value Pr(>t) Lower Upper
-#> parent_0 85.870 NA NA NA NA
-#> alpha 1.053 NA NA NA NA
-#> beta 1.917 NA NA NA NA
-#> sigma 1.857 NA NA NA NA
+#> Estimate t value Pr(>t) Lower Upper
+#> parent_0 85.870 47.530 3.893e-08 81.2300 90.520
+#> alpha 1.053 7.393 3.562e-04 0.7439 1.491
+#> beta 1.917 4.373 3.601e-03 1.0650 3.451
+#> sigma 1.857 4.243 4.074e-03 0.7320 2.983
#>
#> FOCUS Chi2 error levels in percent:
#> err.min n.optim df
@@ -438,7 +443,7 @@ 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'>#> <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'><-</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'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen
-#> 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'>#> 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'>#> $ff
+#> 2.251 0.000 2.253 </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'>#> 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'>#> $ff
#> parent_sink parent_m1 m1_sink
#> 0.485524 0.514476 1.000000
#>
@@ -510,7 +515,7 @@ Per default, parameters in the kinetic models are internally transformed in
#> Sum of squared residuals at call 126: 371.2134
#> Sum of squared residuals at call 135: 371.2134
#> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen
-#> 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'>#> 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'>#> $ff
+#> 1.151 0.000 1.152 </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'>#> 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'>#> $ff
#> parent_sink parent_m1 m1_sink
#> 0.485524 0.514476 1.000000
#>
@@ -540,10 +545,10 @@ Per default, parameters in the kinetic models are internally transformed in
<span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<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'>#> <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'><-</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'>#> <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'><-</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'>#> <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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> 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'>#> <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'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.49.4
#> R version used for fitting: 3.6.0
-#> Date of fit: Tue May 7 08:08:30 2019
-#> Date of summary: Tue May 7 08:08:30 2019
+#> Date of fit: Tue May 7 08:36:33 2019
+#> Date of summary: Tue May 7 08:36:33 2019
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
@@ -551,7 +556,7 @@ Per default, parameters in the kinetic models are internally transformed in
#>
#> Model predictions using solution type deSolve
#>
-#> Fitted using 185 model solutions performed in 0.499 s
+#> Fitted using 421 model solutions performed in 1.1 s
#>
#> Error model:
#> Constant variance
@@ -577,25 +582,31 @@ Per default, parameters in the kinetic models are internally transformed in
#> m1_0 0 state
#>
#> Optimised, transformed parameters with symmetric confidence intervals:
-#> Estimate Std. Error Lower Upper
-#> parent_0 99.60000 NA NA NA
-#> log_k_parent -2.31600 NA NA NA
-#> log_k_m1 -5.24800 NA NA NA
-#> f_parent_ilr_1 0.04096 NA NA NA
-#> sigma 3.12600 NA NA NA
+#> Estimate Std. Error Lower Upper
+#> parent_0 99.60000 1.57000 96.40000 102.8000
+#> log_k_parent -2.31600 0.04087 -2.39900 -2.2330
+#> log_k_m1 -5.24800 0.13320 -5.51800 -4.9770
+#> f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694
+#> sigma 3.12600 0.35850 2.39600 3.8550
#>
#> Parameter correlation:
-#> No covariance matrix
+#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma
+#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -2.265e-07
+#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.785e-07
+#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.386e-07
+#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -3.641e-08
+#> sigma -2.265e-07 3.785e-07 -1.386e-07 -3.641e-08 1.000e+00
+#>
#> Backtransformed parameters:
#> Confidence intervals for internally transformed parameters are asymmetric.
#> t-test (unrealistically) based on the assumption of normal distribution
#> for estimators of untransformed parameters.
-#> Estimate t value Pr(>t) Lower Upper
-#> parent_0 99.600000 NA NA NA NA
-#> k_parent 0.098700 NA NA NA NA
-#> k_m1 0.005261 NA NA NA NA
-#> f_parent_to_m1 0.514500 NA NA NA NA
-#> sigma 3.126000 NA NA NA NA
+#> Estimate t value Pr(>t) Lower Upper
+#> parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02
+#> k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01
+#> k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03
+#> f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01
+#> sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
#>
#> FOCUS Chi2 error levels in percent:
#> err.min n.optim df
@@ -652,10 +663,10 @@ Per default, parameters in the kinetic models are internally transformed in
#> 100 m1 31.04 31.98163 -9.416e-01
#> 100 m1 33.13 31.98163 1.148e+00
#> 120 m1 25.15 28.78984 -3.640e+00
-#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</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'>#> <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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> mkin version used for fitting: 0.9.49.4
+#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.49.4
#> R version used for fitting: 3.6.0
-#> Date of fit: Tue May 7 08:08:32 2019
-#> Date of summary: Tue May 7 08:08:32 2019
+#> Date of fit: Tue May 7 08:36:35 2019
+#> Date of summary: Tue May 7 08:36:35 2019
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
@@ -663,7 +674,7 @@ Per default, parameters in the kinetic models are internally transformed in
#>
#> Model predictions using solution type deSolve
#>
-#> Fitted using 426 model solutions performed in 1.139 s
+#> Fitted using 758 model solutions performed in 1.991 s
#>
#> Error model:
#> Variance unique to each observed variable
@@ -691,27 +702,41 @@ Per default, parameters in the kinetic models are internally transformed in
#> m1_0 0 state
#>
#> Optimised, transformed parameters with symmetric confidence intervals:
-#> Estimate Std. Error Lower Upper
-#> parent_0 99.65000 NA NA NA
-#> log_k_parent -2.31300 NA NA NA
-#> log_k_m1 -5.25000 NA NA NA
-#> f_parent_ilr_1 0.03861 NA NA NA
-#> sigma_parent 3.40100 NA NA NA
-#> sigma_m1 2.85500 NA NA NA
+#> Estimate Std. Error Lower Upper
+#> parent_0 99.65000 1.70200 96.19000 103.1000
+#> log_k_parent -2.31300 0.04376 -2.40200 -2.2240
+#> log_k_m1 -5.25000 0.12430 -5.50400 -4.9970
+#> f_parent_ilr_1 0.03861 0.06171 -0.08708 0.1643
+#> sigma_parent 3.40100 0.56820 2.24400 4.5590
+#> sigma_m1 2.85500 0.45240 1.93400 3.7770
#>
#> Parameter correlation:
-#> No covariance matrix
+#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_parent
+#> parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035670
+#> log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069833
+#> log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026158
+#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041368
+#> sigma_parent 0.03567 0.06983 -0.02616 -0.04137 1.000000
+#> sigma_m1 -0.03385 -0.06627 0.02482 0.03925 -0.004628
+#> sigma_m1
+#> parent_0 -0.033847
+#> log_k_parent -0.066265
+#> log_k_m1 0.024821
+#> f_parent_ilr_1 0.039255
+#> sigma_parent -0.004628
+#> sigma_m1 1.000000
+#>
#> Backtransformed parameters:
#> Confidence intervals for internally transformed parameters are asymmetric.
#> t-test (unrealistically) based on the assumption of normal distribution
#> for estimators of untransformed parameters.
-#> Estimate t value Pr(>t) Lower Upper
-#> parent_0 99.650000 NA NA NA NA
-#> k_parent 0.098970 NA NA NA NA
-#> k_m1 0.005245 NA NA NA NA
-#> f_parent_to_m1 0.513600 NA NA NA NA
-#> sigma_parent 3.401000 NA NA NA NA
-#> sigma_m1 2.855000 NA NA NA NA
+#> Estimate t value Pr(>t) Lower Upper
+#> parent_0 99.650000 58.560 2.004e-34 96.190000 1.031e+02
+#> k_parent 0.098970 22.850 1.099e-21 0.090530 1.082e-01
+#> k_m1 0.005245 8.046 1.732e-09 0.004072 6.756e-03
+#> f_parent_to_m1 0.513600 23.560 4.352e-22 0.469300 5.578e-01
+#> sigma_parent 3.401000 5.985 5.662e-07 2.244000 4.559e+00
+#> sigma_m1 2.855000 6.311 2.215e-07 1.934000 3.777e+00
#>
#> FOCUS Chi2 error levels in percent:
#> err.min n.optim df
@@ -768,10 +793,10 @@ Per default, parameters in the kinetic models are internally transformed in
#> 100 m1 31.04 31.98774 -9.477e-01
#> 100 m1 33.13 31.98774 1.142e+00
#> 120 m1 25.15 28.80430 -3.654e+00
-#> 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</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'>#> <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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> mkin version used for fitting: 0.9.49.4
+#> 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.49.4
#> R version used for fitting: 3.6.0
-#> Date of fit: Tue May 7 08:08:34 2019
-#> Date of summary: Tue May 7 08:08:34 2019
+#> Date of fit: Tue May 7 08:36:39 2019
+#> Date of summary: Tue May 7 08:36:39 2019
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
@@ -779,7 +804,7 @@ Per default, parameters in the kinetic models are internally transformed in
#>
#> Model predictions using solution type deSolve
#>
-#> Fitted using 489 model solutions performed in 2.013 s
+#> Fitted using 821 model solutions performed in 3.304 s
#>
#> Error model:
#> Two-component variance function
@@ -807,27 +832,34 @@ Per default, parameters in the kinetic models are internally transformed in
#> m1_0 0 state
#>
#> Optimised, transformed parameters with symmetric confidence intervals:
-#> Estimate Std. Error Lower Upper
-#> parent_0 100.70000 NA NA NA
-#> log_k_parent -2.29700 NA NA NA
-#> log_k_m1 -5.26600 NA NA NA
-#> f_parent_ilr_1 0.02374 NA NA NA
-#> sigma_low 0.00305 NA NA NA
-#> rsd_high 0.07928 NA NA NA
+#> Estimate Std. Error Lower Upper
+#> parent_0 100.70000 2.621000 95.400000 106.10000
+#> log_k_parent -2.29700 0.008862 -2.315000 -2.27900
+#> log_k_m1 -5.26600 0.091310 -5.452000 -5.08000
+#> f_parent_ilr_1 0.02374 0.055300 -0.088900 0.13640
+#> sigma_low 0.00305 0.004829 -0.006786 0.01289
+#> rsd_high 0.07928 0.009418 0.060100 0.09847
#>
#> Parameter correlation:
-#> No covariance matrix
+#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low rsd_high
+#> parent_0 1.00000 0.67644 -0.10215 -0.76822 0.14294 -0.08783
+#> log_k_parent 0.67644 1.00000 -0.15102 -0.59491 0.34611 -0.08125
+#> log_k_m1 -0.10215 -0.15102 1.00000 0.51808 -0.05236 0.01240
+#> f_parent_ilr_1 -0.76822 -0.59491 0.51808 1.00000 -0.13900 0.03248
+#> sigma_low 0.14294 0.34611 -0.05236 -0.13900 1.00000 -0.16546
+#> rsd_high -0.08783 -0.08125 0.01240 0.03248 -0.16546 1.00000
+#>
#> Backtransformed parameters:
#> Confidence intervals for internally transformed parameters are asymmetric.
#> t-test (unrealistically) based on the assumption of normal distribution
#> for estimators of untransformed parameters.
-#> Estimate t value Pr(>t) Lower Upper
-#> parent_0 1.007e+02 NA NA NA NA
-#> k_parent 1.006e-01 NA NA NA NA
-#> k_m1 5.167e-03 NA NA NA NA
-#> f_parent_to_m1 5.084e-01 NA NA NA NA
-#> sigma_low 3.050e-03 NA NA NA NA
-#> rsd_high 7.928e-02 NA NA NA NA
+#> Estimate t value Pr(>t) Lower Upper
+#> parent_0 1.007e+02 38.4300 1.180e-28 95.400000 1.061e+02
+#> k_parent 1.006e-01 112.8000 1.718e-43 0.098760 1.024e-01
+#> k_m1 5.167e-03 10.9500 1.172e-12 0.004290 6.223e-03
+#> f_parent_to_m1 5.084e-01 26.0100 2.146e-23 0.468600 5.481e-01
+#> sigma_low 3.050e-03 0.6314 2.661e-01 -0.006786 1.289e-02
+#> rsd_high 7.928e-02 8.4170 6.418e-10 0.060100 9.847e-02
#>
#> FOCUS Chi2 error levels in percent:
#> err.min n.optim df
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 9f417cf3..d0b2a0eb 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'><-</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'>#> Compilation argument:
-#> /usr/lib/R/bin/R CMD SHLIB file6d1314eef3d7.c 2> file6d1314eef3d7.c.err.txt
+#> /usr/lib/R/bin/R CMD SHLIB fileb5a1e31297a.c 2> fileb5a1e31297a.c.err.txt
#> Program source:
#> 1: #include <R.h>
#> 2:
diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png
index d4e465d4..65918d53 100644
Binary files a/docs/reference/mkinparplot-1.png and b/docs/reference/mkinparplot-1.png differ
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 05af0f15..8cfb9374 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'><-</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'>#> <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'><-</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'>#> <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'>#> <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>
+ <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'>#> <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'><-</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'>#> <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>
</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 8c5c50e4..522cbbfe 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -328,12 +328,12 @@
<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'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1
#> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen
-#> 0.003 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1
#> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen
-#> 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>(
+#> 0.001 0.000 0.002 </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'>#> time parent m1
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 849e619e..d0cd748c 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -194,8 +194,8 @@
<span class='no'>time_1</span> <span class='kw'><-</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'><-</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'>#> User System verstrichen
-#> 0.039 0.031 3.113 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen
-#> 10.445 0.001 10.456 </div><div class='input'>
+#> 0.047 0.033 5.463 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen
+#> 19.909 0.004 19.967 </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'>#> $ff
#> parent_M1 parent_sink M1_M2 M1_sink
#> 0.7340481 0.2659519 0.7505684 0.2494316
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index 62027fab..a9ee2f76 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'><-</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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <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'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <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'>#> Sums of squares:
+ <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</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'>#> <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'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <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'>#> Sums of squares:
#> SFO IORE DFOP
#> 1378.6832 615.7730 517.8836
#>
@@ -191,25 +191,25 @@
#>
#> Parameters:
#> $SFO
-#> Estimate Pr(>t) Lower Upper
-#> parent_0 83.7558 NA NA NA
-#> k_parent_sink 0.0017 NA NA NA
-#> sigma 8.7518 NA NA NA
+#> Estimate Pr(>t) Lower Upper
+#> parent_0 83.7558 1.80e-14 77.18268 90.3288
+#> k_parent_sink 0.0017 7.43e-05 0.00112 0.0026
+#> sigma 8.7518 1.22e-05 5.64278 11.8608
#>
#> $IORE
-#> Estimate Pr(>t) Lower Upper
-#> parent_0 9.69e+01 NA NA NA
-#> k__iore_parent_sink 8.40e-14 NA NA NA
-#> N_parent 6.68e+00 NA NA NA
-#> sigma 5.85e+00 NA NA NA
+#> Estimate Pr(>t) Lower Upper
+#> parent_0 9.69e+01 NA 8.88e+01 1.05e+02
+#> k__iore_parent_sink 8.40e-14 NA 1.79e-18 3.94e-09
+#> N_parent 6.68e+00 NA 4.19e+00 9.17e+00
+#> sigma 5.85e+00 NA 3.76e+00 7.94e+00
#>
#> $DFOP
-#> Estimate Pr(>t) Lower Upper
-#> parent_0 9.76e+01 NA NA NA
-#> k1 4.24e-02 NA NA NA
-#> k2 8.24e-04 NA NA NA
-#> g 2.88e-01 NA NA NA
-#> sigma 5.36e+00 NA NA NA
+#> Estimate Pr(>t) Lower Upper
+#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02
+#> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02
+#> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03
+#> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01
+#> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00
#>
#>
#> DTx values:
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index a4f3d04f..9c4a21a9 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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> 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'>#> mkin version used for fitting: 0.9.49.4
#> R version used for fitting: 3.6.0
-#> Date of fit: Tue May 7 08:09:03 2019
-#> Date of summary: Tue May 7 08:09:03 2019
+#> Date of fit: Tue May 7 08:37:31 2019
+#> Date of summary: Tue May 7 08:37:31 2019
#>
#> Equations:
#> d_parent/dt = - k_parent_sink * parent
#>
#> Model predictions using solution type analytical
#>
-#> Fitted using 39 model solutions performed in 0.08 s
+#> Fitted using 131 model solutions performed in 0.277 s
#>
#> Error model:
#> Constant variance
@@ -240,21 +240,25 @@
#> None
#>
#> Optimised, transformed parameters with symmetric confidence intervals:
-#> Estimate Std. Error Lower Upper
-#> parent_0 109.200 NA NA NA
-#> log_k_parent_sink -3.291 NA NA NA
-#> sigma 5.266 NA NA NA
+#> Estimate Std. Error Lower Upper
+#> parent_0 109.200 3.70400 99.630 118.700
+#> log_k_parent_sink -3.291 0.09176 -3.527 -3.055
+#> sigma 5.266 1.31600 1.882 8.649
#>
#> Parameter correlation:
-#> No covariance matrix
+#> parent_0 log_k_parent_sink sigma
+#> parent_0 1.000e+00 5.428e-01 1.648e-07
+#> log_k_parent_sink 5.428e-01 1.000e+00 2.513e-07
+#> sigma 1.648e-07 2.513e-07 1.000e+00
+#>
#> Backtransformed parameters:
#> Confidence intervals for internally transformed parameters are asymmetric.
#> t-test (unrealistically) based on the assumption of normal distribution
#> for estimators of untransformed parameters.
-#> Estimate t value Pr(>t) Lower Upper
-#> parent_0 109.20000 NA NA NA NA
-#> k_parent_sink 0.03722 NA NA NA NA
-#> sigma 5.26600 NA NA NA NA
+#> Estimate t value Pr(>t) Lower Upper
+#> parent_0 109.20000 29.47 4.218e-07 99.6300 118.70000
+#> k_parent_sink 0.03722 10.90 5.650e-05 0.0294 0.04712
+#> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900
#>
#> FOCUS Chi2 error levels in percent:
#> 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 11cb6420..bc988340 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -159,13 +159,20 @@
<span class='co'># model).</span>
<span class='no'>m_ws</span> <span class='kw'><-</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'>#> <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'><-</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'>#> <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>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
-#> parent_w_0 9.598567e+01 NA NA NA NA NA
-#> k_parent_w_sink 3.603743e-01 NA NA NA NA NA
-#> k_parent_w_parent_s 6.031371e-02 NA NA NA NA NA
-#> k_parent_s_sink 5.108964e-11 NA NA NA NA NA
-#> k_parent_s_parent_w 7.419672e-02 NA NA NA NA NA
-#> sigma 2.982879e+00 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> err.min n.optim df
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t)
+#> parent_w_0 9.598567e+01 2.12351789 4.520126e+01 9.476190e-18
+#> k_parent_w_sink 3.603743e-01 0.03149282 1.144306e+01 4.126593e-09
+#> k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04
+#> k_parent_s_sink 5.108964e-11 0.09482736 5.387647e-10 5.000000e-01
+#> k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01
+#> sigma 2.982879e+00 0.50545649 5.901356e+00 1.454535e-05
+#> Lower Upper
+#> parent_w_0 91.48420503 100.4871438
+#> k_parent_w_sink 0.30668904 0.4234571
+#> k_parent_w_parent_s 0.03423904 0.1062455
+#> k_parent_s_sink 0.00000000 Inf
+#> k_parent_s_parent_w 0.02289956 0.2404043
+#> 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'>#> err.min n.optim df
#> All data 0.09246946 5 6
#> parent_w 0.06377096 3 3
#> parent_s 0.20882325 2 3</div><div class='input'>
@@ -176,17 +183,28 @@
<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'>#> <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'><-</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>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
-#> parent_0 76.55425584 NA NA NA NA NA
-#> k_parent 0.12081956 NA NA NA NA NA
-#> k_M1 0.84258649 NA NA NA NA NA
-#> k_M2 0.04210878 NA NA NA NA NA
-#> k_M3 0.01122919 NA NA NA NA NA
-#> f_parent_to_M1 0.32240199 NA NA NA NA NA
-#> f_parent_to_M2 0.16099854 NA NA NA NA NA
-#> f_M1_to_M3 0.27921501 NA NA NA NA NA
-#> f_M2_to_M3 0.55641331 NA NA NA NA NA
-#> 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'>#> err.min n.optim df
+ <span class='no'>f_soil</span> <span class='kw'><-</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>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower
+#> parent_0 76.55425584 0.859186619 89.1008474 1.113866e-26 74.755959756
+#> k_parent 0.12081956 0.004601922 26.2541544 1.077373e-16 0.111561582
+#> k_M1 0.84258649 0.806231419 1.0450926 1.545475e-01 0.113839803
+#> k_M2 0.04210878 0.017083049 2.4649453 1.170195e-02 0.018013807
+#> k_M3 0.01122919 0.007245890 1.5497322 6.885127e-02 0.002909463
+#> f_parent_to_M1 0.32240199 0.240803555 1.3388589 9.820820e-02 NA
+#> f_parent_to_M2 0.16099854 0.033691991 4.7785403 6.531224e-05 NA
+#> f_M1_to_M3 0.27921501 0.269443514 1.0362655 1.565440e-01 0.022992937
+#> f_M2_to_M3 0.55641331 0.595125445 0.9349513 1.807725e-01 0.008003317
+#> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778
+#> Upper
+#> parent_0 78.35255192
+#> k_parent 0.13084582
+#> k_M1 6.23641265
+#> k_M2 0.09843279
+#> k_M3 0.04333950
+#> f_parent_to_M1 NA
+#> f_parent_to_M2 NA
+#> f_M1_to_M3 0.86443083
+#> f_M2_to_M3 0.99489847
+#> 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'>#> err.min n.optim df
#> All data 0.09649963 9 20
#> parent 0.04721283 2 6
#> M1 0.26551209 2 5
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index c91565b9..7e05480e 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,30 +202,32 @@ 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'><-</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'>#> <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'><-</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'>#> <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'><-</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'>#> <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>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper
-#> parent_0 99.60 NA NA NA
-#> log_k_parent_sink -3.04 NA NA NA
-#> log_k_parent_m1 -2.98 NA NA NA
-#> log_k_m1_sink -5.25 NA NA NA
-#> sigma 3.13 NA NA NA</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
-#> parent_0 99.59848 NA NA NA NA NA
-#> k_parent_sink 0.04792 NA NA NA NA NA
-#> k_parent_m1 0.05078 NA NA NA NA NA
-#> k_m1_sink 0.00526 NA NA NA NA NA
-#> sigma 3.12550 NA NA NA NA NA</div><div class='input'>
+<span class='no'>fit</span> <span class='kw'><-</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'>#> <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'><-</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>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper
+#> parent_0 99.60 1.5702 96.40 102.79
+#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88
+#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90
+#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98
+#> sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931
+#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560
+#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551
+#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
+#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'>
</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'><-</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'>#> <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'><-</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'>#> <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>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper
-#> parent_0 99.59848 NA NA NA
-#> k_parent_sink 0.04792 NA NA NA
-#> k_parent_m1 0.05078 NA NA NA
-#> k_m1_sink 0.00526 NA NA NA
-#> sigma 3.12550 NA NA NA</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
-#> parent_0 99.59848 NA NA NA NA NA
-#> k_parent_sink 0.04792 NA NA NA NA NA
-#> k_parent_m1 0.05078 NA NA NA NA NA
-#> k_m1_sink 0.00526 NA NA NA NA NA
-#> sigma 3.12550 NA NA NA NA NA</div><div class='input'>
+<span class='no'>fit.2</span> <span class='kw'><-</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'>#> <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'><-</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>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper
+#> parent_0 99.59848 1.57022 96.40384 1.03e+02
+#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02
+#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02
+#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03
+#> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02
+#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02
+#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02
+#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03
+#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'>
<span class='no'>initials</span> <span class='kw'><-</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'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>)
<span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span>
@@ -238,17 +240,18 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.ff.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>)</div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper
-#> parent_0 99.598 NA NA NA
-#> log_k_parent -2.316 NA NA NA
-#> log_k_m1 -5.248 NA NA NA
-#> f_parent_ilr_1 0.041 NA NA NA
-#> 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>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
-#> parent_0 99.59848 NA NA NA NA NA
-#> k_parent 0.09870 NA NA NA NA NA
-#> k_m1 0.00526 NA NA NA NA NA
-#> f_parent_to_m1 0.51448 NA NA NA NA NA
-#> sigma 3.12550 NA NA NA NA NA</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
+<span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.ff.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>)
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper
+#> parent_0 99.598 1.5702 96.4038 102.793
+#> log_k_parent -2.316 0.0409 -2.3988 -2.233
+#> log_k_m1 -5.248 0.1332 -5.5184 -4.977
+#> f_parent_ilr_1 0.041 0.0631 -0.0875 0.169
+#> 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'>#> Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931
+#> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073
+#> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
+#> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596
+#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</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'><-</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'>#> f_parent_to_m1
#> 0.5 </div><div class='input'>
@@ -258,15 +261,16 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <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'><-</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'>#> <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'><-</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'>#> <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'>#> Estimate Std. Error Lower Upper
-#> parent_0 84.79 NA NA NA
-#> log_k_parent -2.76 NA NA NA
-#> log_k_m1 -4.21 NA NA NA
-#> 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>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper
-#> parent_0 84.7916 NA NA NA NA NA
-#> k_parent 0.0635 NA NA NA NA NA
-#> k_m1 0.0148 NA NA NA NA NA
-#> sigma 8.2229 NA NA NA NA NA</div></pre>
+<span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.ff.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>)
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper
+#> parent_0 84.79 3.012 78.67 90.91
+#> log_k_parent -2.76 0.082 -2.92 -2.59
+#> log_k_m1 -4.21 0.123 -4.46 -3.96
+#> 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'>#> Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913
+#> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075
+#> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019
+#> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div></pre>
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