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-rw-r--r--docs/dev/reference/AIC.mmkin.html13
-rw-r--r--docs/dev/reference/CAKE_export.html4
-rw-r--r--docs/dev/reference/D24_2014.html2
-rw-r--r--docs/dev/reference/DFOP.solution.html4
-rw-r--r--docs/dev/reference/Extract.mmkin.html6
-rw-r--r--docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html4
-rw-r--r--docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html4
-rw-r--r--docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html4
-rw-r--r--docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html4
-rw-r--r--docs/dev/reference/FOCUS_2006_datasets.html4
-rw-r--r--docs/dev/reference/FOMC.solution.html4
-rw-r--r--docs/dev/reference/HS.solution.html4
-rw-r--r--docs/dev/reference/IORE.solution.html4
-rw-r--r--docs/dev/reference/NAFTA_SOP_2015-1.pngbin64838 -> 61980 bytes
-rw-r--r--docs/dev/reference/NAFTA_SOP_2015.html4
-rw-r--r--docs/dev/reference/NAFTA_SOP_Attachment-1.pngbin66148 -> 63822 bytes
-rw-r--r--docs/dev/reference/NAFTA_SOP_Attachment.html8
-rw-r--r--docs/dev/reference/Rplot001.pngbin19395 -> 1011 bytes
-rw-r--r--docs/dev/reference/Rplot002.pngbin16843 -> 16859 bytes
-rw-r--r--docs/dev/reference/Rplot003.pngbin28735 -> 28844 bytes
-rw-r--r--docs/dev/reference/Rplot004.pngbin49269 -> 49360 bytes
-rw-r--r--docs/dev/reference/Rplot005.pngbin57095 -> 59216 bytes
-rw-r--r--docs/dev/reference/Rplot006.pngbin24624 -> 24545 bytes
-rw-r--r--docs/dev/reference/Rplot007.pngbin25074 -> 24992 bytes
-rw-r--r--docs/dev/reference/SFO.solution.html4
-rw-r--r--docs/dev/reference/SFORB.solution.html4
-rw-r--r--docs/dev/reference/add_err-1.pngbin111360 -> 108676 bytes
-rw-r--r--docs/dev/reference/add_err-2.pngbin64003 -> 63336 bytes
-rw-r--r--docs/dev/reference/add_err-3.pngbin60019 -> 58909 bytes
-rw-r--r--docs/dev/reference/add_err.html4
-rw-r--r--docs/dev/reference/aw.html4
-rw-r--r--docs/dev/reference/confint.mkinfit.html127
-rw-r--r--docs/dev/reference/create_deg_func.html12
-rw-r--r--docs/dev/reference/dimethenamid_2018.html2
-rw-r--r--docs/dev/reference/endpoints.html4
-rw-r--r--docs/dev/reference/experimental_data_for_UBA-1.pngbin103559 -> 102212 bytes
-rw-r--r--docs/dev/reference/experimental_data_for_UBA.html4
-rw-r--r--docs/dev/reference/f_time_norm_focus.html2
-rw-r--r--docs/dev/reference/focus_soil_moisture.html4
-rw-r--r--docs/dev/reference/get_deg_func.html4
-rw-r--r--docs/dev/reference/ilr.html4
-rw-r--r--docs/dev/reference/index.html10
-rw-r--r--docs/dev/reference/loftest-1.pngbin41288 -> 40351 bytes
-rw-r--r--docs/dev/reference/loftest-2.pngbin40668 -> 39817 bytes
-rw-r--r--docs/dev/reference/loftest-3.pngbin78452 -> 76976 bytes
-rw-r--r--docs/dev/reference/loftest-4.pngbin76132 -> 74678 bytes
-rw-r--r--docs/dev/reference/loftest-5.pngbin74691 -> 73446 bytes
-rw-r--r--docs/dev/reference/loftest.html4
-rw-r--r--docs/dev/reference/logLik.mkinfit.html12
-rw-r--r--docs/dev/reference/logistic.solution-2.pngbin43807 -> 42118 bytes
-rw-r--r--docs/dev/reference/logistic.solution.html10
-rw-r--r--docs/dev/reference/lrtest.mkinfit.html4
-rw-r--r--docs/dev/reference/max_twa_parent.html4
-rw-r--r--docs/dev/reference/mccall81_245T-1.pngbin65341 -> 62537 bytes
-rw-r--r--docs/dev/reference/mccall81_245T.html44
-rw-r--r--docs/dev/reference/mixed-1.pngbin206373 -> 219866 bytes
-rw-r--r--docs/dev/reference/mixed.html14
-rw-r--r--docs/dev/reference/mkin_long_to_wide.html4
-rw-r--r--docs/dev/reference/mkin_wide_to_long.html4
-rw-r--r--docs/dev/reference/mkinds.html4
-rw-r--r--docs/dev/reference/mkindsg.html10
-rw-r--r--docs/dev/reference/mkinerrmin.html4
-rw-r--r--docs/dev/reference/mkinerrplot.html4
-rw-r--r--docs/dev/reference/mkinfit-1.pngbin67810 -> 65835 bytes
-rw-r--r--docs/dev/reference/mkinfit.html132
-rw-r--r--docs/dev/reference/mkinmod.html8
-rw-r--r--docs/dev/reference/mkinparplot-1.pngbin25707 -> 25702 bytes
-rw-r--r--docs/dev/reference/mkinparplot.html7
-rw-r--r--docs/dev/reference/mkinplot.html4
-rw-r--r--docs/dev/reference/mkinpredict.html10
-rw-r--r--docs/dev/reference/mkinresplot.html6
-rw-r--r--docs/dev/reference/mmkin-1.pngbin114048 -> 110459 bytes
-rw-r--r--docs/dev/reference/mmkin-2.pngbin110392 -> 107057 bytes
-rw-r--r--docs/dev/reference/mmkin-3.pngbin97556 -> 96062 bytes
-rw-r--r--docs/dev/reference/mmkin-4.pngbin70005 -> 67191 bytes
-rw-r--r--docs/dev/reference/mmkin-5.pngbin66093 -> 64880 bytes
-rw-r--r--docs/dev/reference/mmkin.html31
-rw-r--r--docs/dev/reference/nafta-1.pngbin64838 -> 61980 bytes
-rw-r--r--docs/dev/reference/nafta.html4
-rw-r--r--docs/dev/reference/nlme-1.pngbin69449 -> 68233 bytes
-rw-r--r--docs/dev/reference/nlme-2.pngbin89493 -> 90552 bytes
-rw-r--r--docs/dev/reference/nlme.html45
-rw-r--r--docs/dev/reference/nlme.mmkin-1.pngbin119655 -> 124827 bytes
-rw-r--r--docs/dev/reference/nlme.mmkin-2.pngbin159253 -> 169698 bytes
-rw-r--r--docs/dev/reference/nlme.mmkin-3.pngbin161800 -> 172809 bytes
-rw-r--r--docs/dev/reference/nlme.mmkin.html78
-rw-r--r--docs/dev/reference/nobs.mkinfit.html4
-rw-r--r--docs/dev/reference/parms.html14
-rw-r--r--docs/dev/reference/plot.mixed.mmkin-1.pngbin86076 -> 85433 bytes
-rw-r--r--docs/dev/reference/plot.mixed.mmkin-2.pngbin164488 -> 174061 bytes
-rw-r--r--docs/dev/reference/plot.mixed.mmkin-3.pngbin163536 -> 172540 bytes
-rw-r--r--docs/dev/reference/plot.mixed.mmkin-4.pngbin166687 -> 175594 bytes
-rw-r--r--docs/dev/reference/plot.mixed.mmkin.html8
-rw-r--r--docs/dev/reference/plot.mkinfit-2.pngbin73247 -> 73254 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-5.pngbin66920 -> 66560 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-6.pngbin73078 -> 72717 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit-7.pngbin73909 -> 73553 bytes
-rw-r--r--docs/dev/reference/plot.mkinfit.html2
-rw-r--r--docs/dev/reference/plot.mmkin-1.pngbin49402 -> 48997 bytes
-rw-r--r--docs/dev/reference/plot.mmkin-2.pngbin49753 -> 49376 bytes
-rw-r--r--docs/dev/reference/plot.mmkin-3.pngbin46090 -> 46202 bytes
-rw-r--r--docs/dev/reference/plot.mmkin-4.pngbin33266 -> 33057 bytes
-rw-r--r--docs/dev/reference/plot.mmkin-5.pngbin57777 -> 57372 bytes
-rw-r--r--docs/dev/reference/plot.mmkin.html2
-rw-r--r--docs/dev/reference/plot.nafta.html4
-rw-r--r--docs/dev/reference/reexports.html4
-rw-r--r--docs/dev/reference/residuals.mkinfit.html6
-rw-r--r--docs/dev/reference/saem-1.pngbin47315 -> 47342 bytes
-rw-r--r--docs/dev/reference/saem-2.pngbin48720 -> 48819 bytes
-rw-r--r--docs/dev/reference/saem-3.pngbin82102 -> 82202 bytes
-rw-r--r--docs/dev/reference/saem-4.pngbin128231 -> 128213 bytes
-rw-r--r--docs/dev/reference/saem-5.pngbin164443 -> 173665 bytes
-rw-r--r--docs/dev/reference/saem.html90
-rw-r--r--docs/dev/reference/schaefer07_complex_case-1.pngbin67659 -> 66965 bytes
-rw-r--r--docs/dev/reference/schaefer07_complex_case.html14
-rw-r--r--docs/dev/reference/sigma_twocomp-1.pngbin44554 -> 43910 bytes
-rw-r--r--docs/dev/reference/sigma_twocomp.html8
-rw-r--r--docs/dev/reference/summary.mkinfit.html12
-rw-r--r--docs/dev/reference/summary.nlme.mmkin.html226
-rw-r--r--docs/dev/reference/summary.saem.mmkin.html428
-rw-r--r--docs/dev/reference/synthetic_data_for_UBA_2014-1.pngbin70005 -> 67191 bytes
-rw-r--r--docs/dev/reference/synthetic_data_for_UBA_2014.html32
-rw-r--r--docs/dev/reference/test_data_from_UBA_2014-1.pngbin59592 -> 57395 bytes
-rw-r--r--docs/dev/reference/test_data_from_UBA_2014-2.pngbin76645 -> 72786 bytes
-rw-r--r--docs/dev/reference/test_data_from_UBA_2014.html26
-rw-r--r--docs/dev/reference/transform_odeparms.html80
-rw-r--r--docs/dev/reference/update.mkinfit-1.pngbin43366 -> 42360 bytes
-rw-r--r--docs/dev/reference/update.mkinfit-2.pngbin44304 -> 43389 bytes
-rw-r--r--docs/dev/reference/update.mkinfit.html4
129 files changed, 867 insertions, 806 deletions
diff --git a/docs/dev/reference/AIC.mmkin.html b/docs/dev/reference/AIC.mmkin.html
index b332257e..8c791755 100644
--- a/docs/dev/reference/AIC.mmkin.html
+++ b/docs/dev/reference/AIC.mmkin.html
@@ -73,7 +73,7 @@ same dataset." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ same dataset." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -187,8 +187,7 @@ dataframe if there are several fits in the column).</p>
<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>,
<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS A"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>,
<span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
-#&gt; <span class='warning'>false convergence (8)</span></div><div class='input'> <span class='co'># We get a warning because the FOMC model does not converge for the</span>
+ <span class='co'># We get a warning because the FOMC model does not converge for the</span>
<span class='co'># FOCUS A dataset, as it is well described by SFO</span>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># We get a single number for a single fit</span>
@@ -199,15 +198,15 @@ dataframe if there are several fits in the column).</p>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; df AIC
#&gt; SFO 3 55.28197
-#&gt; FOMC 4 57.28211
+#&gt; FOMC 4 57.28222
#&gt; DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span>, k <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># If we do not penalize additional parameters, we get nearly the same</span>
</div><div class='output co'>#&gt; df AIC
#&gt; SFO 3 49.28197
-#&gt; FOMC 4 49.28211
+#&gt; FOMC 4 49.28222
#&gt; DFOP 5 49.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Comparing the BIC gives a very similar picture</span>
</div><div class='output co'>#&gt; df BIC
#&gt; SFO 3 55.52030
-#&gt; FOMC 4 57.59987
+#&gt; FOMC 4 57.59999
#&gt; DFOP 5 59.67918</div><div class='input'>
<span class='co'># For FOCUS C, the more complex models fit better</span>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span>
diff --git a/docs/dev/reference/CAKE_export.html b/docs/dev/reference/CAKE_export.html
index d3f45bf0..e187772f 100644
--- a/docs/dev/reference/CAKE_export.html
+++ b/docs/dev/reference/CAKE_export.html
@@ -73,7 +73,7 @@ specified as well." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ specified as well." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html
index 2498c58e..9ecb6330 100644
--- a/docs/dev/reference/D24_2014.html
+++ b/docs/dev/reference/D24_2014.html
@@ -77,7 +77,7 @@ constrained by data protection regulations." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
diff --git a/docs/dev/reference/DFOP.solution.html b/docs/dev/reference/DFOP.solution.html
index 22b28732..3ee660f2 100644
--- a/docs/dev/reference/DFOP.solution.html
+++ b/docs/dev/reference/DFOP.solution.html
@@ -73,7 +73,7 @@ two exponential decline functions." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ two exponential decline functions." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/Extract.mmkin.html b/docs/dev/reference/Extract.mmkin.html
index 0c02355f..8381337a 100644
--- a/docs/dev/reference/Extract.mmkin.html
+++ b/docs/dev/reference/Extract.mmkin.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -220,7 +220,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></td>
<span class='op'>)</span>
</div><div class='output co'>#&gt; $par
#&gt; parent_0 log_alpha log_beta sigma
-#&gt; 99.666193 2.549849 5.050586 1.890202
+#&gt; 99.666192 2.549850 5.050586 1.890202
#&gt;
#&gt; $objective
#&gt; [1] 28.58291
diff --git a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index 16d12378..a188430d 100644
--- a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -76,7 +76,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ in this fit." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index 6b8a6119..0bee1c16 100644
--- a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -76,7 +76,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ in this fit." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html
index 076a66c6..460fdf0d 100644
--- a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -76,7 +76,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ in this fit." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html
index 08f1d416..c1a5fdff 100644
--- a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -76,7 +76,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ in this fit." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/FOCUS_2006_datasets.html b/docs/dev/reference/FOCUS_2006_datasets.html
index df4651f8..fb3a8f17 100644
--- a/docs/dev/reference/FOCUS_2006_datasets.html
+++ b/docs/dev/reference/FOCUS_2006_datasets.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/FOMC.solution.html b/docs/dev/reference/FOMC.solution.html
index ed5c4d21..1a5124e0 100644
--- a/docs/dev/reference/FOMC.solution.html
+++ b/docs/dev/reference/FOMC.solution.html
@@ -73,7 +73,7 @@ a decreasing rate constant." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ a decreasing rate constant." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/HS.solution.html b/docs/dev/reference/HS.solution.html
index 8cf5c7f9..1b79e8b6 100644
--- a/docs/dev/reference/HS.solution.html
+++ b/docs/dev/reference/HS.solution.html
@@ -73,7 +73,7 @@ between them." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ between them." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/IORE.solution.html b/docs/dev/reference/IORE.solution.html
index 29d615dc..bc17319e 100644
--- a/docs/dev/reference/IORE.solution.html
+++ b/docs/dev/reference/IORE.solution.html
@@ -73,7 +73,7 @@ a concentration dependent rate constant." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ a concentration dependent rate constant." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/NAFTA_SOP_2015-1.png b/docs/dev/reference/NAFTA_SOP_2015-1.png
index 4d823d77..4f0d7833 100644
--- a/docs/dev/reference/NAFTA_SOP_2015-1.png
+++ b/docs/dev/reference/NAFTA_SOP_2015-1.png
Binary files differ
diff --git a/docs/dev/reference/NAFTA_SOP_2015.html b/docs/dev/reference/NAFTA_SOP_2015.html
index 4243faba..fb65fec8 100644
--- a/docs/dev/reference/NAFTA_SOP_2015.html
+++ b/docs/dev/reference/NAFTA_SOP_2015.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/NAFTA_SOP_Attachment-1.png b/docs/dev/reference/NAFTA_SOP_Attachment-1.png
index 6eb10cde..9417685e 100644
--- a/docs/dev/reference/NAFTA_SOP_Attachment-1.png
+++ b/docs/dev/reference/NAFTA_SOP_Attachment-1.png
Binary files differ
diff --git a/docs/dev/reference/NAFTA_SOP_Attachment.html b/docs/dev/reference/NAFTA_SOP_Attachment.html
index de984984..311a7c61 100644
--- a/docs/dev/reference/NAFTA_SOP_Attachment.html
+++ b/docs/dev/reference/NAFTA_SOP_Attachment.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -193,7 +193,7 @@
#&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 2.42e-12 5.00e-01 0.0000 Inf
+#&gt; k2 2.26e-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;
@@ -202,7 +202,7 @@
#&gt; DT50 DT90 DT50_rep
#&gt; SFO 67.7 2.25e+02 6.77e+01
#&gt; IORE 58.2 1.07e+03 3.22e+02
-#&gt; DFOP 55.5 5.22e+11 2.86e+11
+#&gt; DFOP 55.5 5.59e+11 3.07e+11
#&gt;
#&gt; Representative half-life:
#&gt; [1] 321.51</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span>
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index bca41e2c..17a35806 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
Binary files differ
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index 9b97a634..a9a972e5 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
Binary files differ
diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png
index ff6bc722..d077f01c 100644
--- a/docs/dev/reference/Rplot003.png
+++ b/docs/dev/reference/Rplot003.png
Binary files differ
diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png
index 98dd019e..ffcd2d96 100644
--- a/docs/dev/reference/Rplot004.png
+++ b/docs/dev/reference/Rplot004.png
Binary files differ
diff --git a/docs/dev/reference/Rplot005.png b/docs/dev/reference/Rplot005.png
index 5e675828..dfb5965b 100644
--- a/docs/dev/reference/Rplot005.png
+++ b/docs/dev/reference/Rplot005.png
Binary files differ
diff --git a/docs/dev/reference/Rplot006.png b/docs/dev/reference/Rplot006.png
index da52f580..81525882 100644
--- a/docs/dev/reference/Rplot006.png
+++ b/docs/dev/reference/Rplot006.png
Binary files differ
diff --git a/docs/dev/reference/Rplot007.png b/docs/dev/reference/Rplot007.png
index fce3b6ee..10b7455a 100644
--- a/docs/dev/reference/Rplot007.png
+++ b/docs/dev/reference/Rplot007.png
Binary files differ
diff --git a/docs/dev/reference/SFO.solution.html b/docs/dev/reference/SFO.solution.html
index b3e7ef9a..43c434c6 100644
--- a/docs/dev/reference/SFO.solution.html
+++ b/docs/dev/reference/SFO.solution.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/SFORB.solution.html b/docs/dev/reference/SFORB.solution.html
index 9310212f..807fbe5c 100644
--- a/docs/dev/reference/SFORB.solution.html
+++ b/docs/dev/reference/SFORB.solution.html
@@ -76,7 +76,7 @@ and no substance in the bound fraction." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ and no substance in the bound fraction." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/add_err-1.png b/docs/dev/reference/add_err-1.png
index d2ce797f..9ba106db 100644
--- a/docs/dev/reference/add_err-1.png
+++ b/docs/dev/reference/add_err-1.png
Binary files differ
diff --git a/docs/dev/reference/add_err-2.png b/docs/dev/reference/add_err-2.png
index ac220c9e..3088c40e 100644
--- a/docs/dev/reference/add_err-2.png
+++ b/docs/dev/reference/add_err-2.png
Binary files differ
diff --git a/docs/dev/reference/add_err-3.png b/docs/dev/reference/add_err-3.png
index 40465b71..493a761a 100644
--- a/docs/dev/reference/add_err-3.png
+++ b/docs/dev/reference/add_err-3.png
Binary files differ
diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html
index 6ea30515..b94cef29 100644
--- a/docs/dev/reference/add_err.html
+++ b/docs/dev/reference/add_err.html
@@ -74,7 +74,7 @@ may depend on the predicted value and is specified as a standard deviation." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -123,7 +123,7 @@ may depend on the predicted value and is specified as a standard deviation." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html
index ef808dd8..3b06f2a6 100644
--- a/docs/dev/reference/aw.html
+++ b/docs/dev/reference/aw.html
@@ -74,7 +74,7 @@ by Burnham and Anderson (2004)." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -123,7 +123,7 @@ by Burnham and Anderson (2004)." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html
index 515a7c9e..2237a539 100644
--- a/docs/dev/reference/confint.mkinfit.html
+++ b/docs/dev/reference/confint.mkinfit.html
@@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -128,7 +128,7 @@ method of Venzon and Moolgavkar (1988)." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -273,68 +273,69 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"NOT_CRAN"</span><span class='op'>)</span>, <span class='st'>"true"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>n_cores</span> <span class='op'>&lt;-</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>1</span>
<span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span>
- <span class='va'>n_cores</span> <span class='op'>&lt;-</span> <span class='fl'>1</span>
+ <span class='va'>n_cores</span> <span class='op'>&lt;-</span> <span class='fl'>1</span>
<span class='op'>}</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>!=</span> <span class='st'>""</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span>
-<span class='va'>SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
+ use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>SFO_SFO.ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_d_1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 3.900 0.929 3.548 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
+#&gt; 4.295 1.008 3.959 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
<span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span>
-<span class='co'># minor interest), we get a nice performance improvement from about 50</span>
-<span class='co'># seconds to about 12 seconds if we use at least four cores</span>
+<span class='co'># minor interest), we get a nice performance improvement if we use at least 4 cores</span>
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>,
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; <span class='warning'>Warning: scheduled cores 3, 2, 1 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.009 0.034 0.257</span></div><div class='input'><span class='va'>ci_profile</span>
-</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.456003640 1.027703e+02
-#&gt; k_parent 0.090911032 1.071578e-01
-#&gt; k_m1 0.003892606 6.702775e-03
-#&gt; f_parent_to_m1 0.471328495 5.611550e-01
-#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 1.451 0.126 0.923 </div><div class='input'><span class='va'>ci_profile</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.456003640 1.027703e+02
+#&gt; k_parent_sink 0.040762501 5.549764e-02
+#&gt; k_parent_m1 0.046786482 5.500879e-02
+#&gt; k_m1_sink 0.003892605 6.702778e-03
+#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
<span class='va'>ci_quadratic_transformed</span>
-</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833585 102.79311650
-#&gt; k_parent 0.090823771 0.10725430
-#&gt; k_m1 0.004012219 0.00689755
-#&gt; f_parent_to_m1 0.469118824 0.55959615
-#&gt; sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.403841640 1.027931e+02
+#&gt; k_parent_sink 0.041033378 5.596269e-02
+#&gt; k_parent_m1 0.046777902 5.511931e-02
+#&gt; k_m1_sink 0.004012217 6.897547e-03
+#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='va'>ci_quadratic_untransformed</span>
-</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833589 1.027931e+02
-#&gt; k_parent 0.090491913 1.069035e-01
-#&gt; k_m1 0.003835485 6.685823e-03
-#&gt; f_parent_to_m1 0.469113477 5.598387e-01
-#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 96.403841645 102.79312449
+#&gt; k_parent_sink 0.040485331 0.05535491
+#&gt; k_parent_m1 0.046611582 0.05494364
+#&gt; k_m1_sink 0.003835483 0.00668582
+#&gt; sigma 2.396089689 3.85491806</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span>
<span class='co'># intervals based on the internal parameter transformation are less</span>
<span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span>
<span class='co'># interval based on the untransformed fit for k_m1_sink</span>
<span class='va'>rel_diffs_transformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_transformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span>
<span class='va'>rel_diffs_untransformed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_untransformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span>
<span class='va'>rel_diffs_transformed</span> <span class='op'>&lt;</span> <span class='va'>rel_diffs_untransformed</span>
-</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 FALSE FALSE
-#&gt; k_parent TRUE TRUE
-#&gt; k_m1 FALSE FALSE
-#&gt; f_parent_to_m1 TRUE FALSE
-#&gt; sigma TRUE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.000541 0.000222
-#&gt; k_parent 0.000960 0.000900
-#&gt; k_m1 0.030700 0.029100
-#&gt; f_parent_to_m1 0.004690 0.002780
-#&gt; sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.000541 0.000222
-#&gt; k_parent 0.004610 0.002370
-#&gt; k_m1 0.014700 0.002530
-#&gt; f_parent_to_m1 0.004700 0.002350
-#&gt; sigma 0.055000 0.032700</div><div class='input'>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 FALSE FALSE
+#&gt; k_parent_sink TRUE FALSE
+#&gt; k_parent_m1 TRUE FALSE
+#&gt; k_m1_sink FALSE FALSE
+#&gt; sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 0.000541 0.000222
+#&gt; k_parent_sink 0.006650 0.008380
+#&gt; k_parent_m1 0.000183 0.002010
+#&gt; k_m1_sink 0.030700 0.029100
+#&gt; sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 0.000541 0.000222
+#&gt; k_parent_sink 0.006800 0.002570
+#&gt; k_parent_m1 0.003740 0.001180
+#&gt; k_m1_sink 0.014700 0.002530
+#&gt; sigma 0.055000 0.032700</div><div class='input'>
<span class='co'># Investigate a case with formation fractions</span>
<span class='va'>f_d_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@@ -348,14 +349,14 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
<span class='va'>ci_quadratic_transformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833585 102.79311650
+#&gt; parent_0 96.403833578 102.79311649
#&gt; k_parent 0.090823771 0.10725430
#&gt; k_m1 0.004012219 0.00689755
#&gt; f_parent_to_m1 0.469118824 0.55959615
#&gt; sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='va'>ci_quadratic_untransformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833589 1.027931e+02
+#&gt; parent_0 96.403833583 1.027931e+02
#&gt; k_parent 0.090491913 1.069035e-01
#&gt; k_m1 0.003835485 6.685823e-03
#&gt; f_parent_to_m1 0.469113477 5.598387e-01
@@ -373,15 +374,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
#&gt; f_parent_to_m1 TRUE FALSE
#&gt; sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408689 0.0002217234
+#&gt; parent_0 0.0005408690 0.0002217233
#&gt; k_parent 0.0009598532 0.0009001864
-#&gt; k_m1 0.0307283044 0.0290588365
-#&gt; f_parent_to_m1 0.0046881768 0.0027780063
+#&gt; k_m1 0.0307283041 0.0290588361
+#&gt; f_parent_to_m1 0.0046881769 0.0027780063
#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408689 0.0002217233
-#&gt; k_parent 0.0046102155 0.0023732281
-#&gt; k_m1 0.0146740688 0.0025291817
+#&gt; parent_0 0.0005408689 0.0002217232
+#&gt; k_parent 0.0046102156 0.0023732281
+#&gt; k_m1 0.0146740690 0.0025291820
#&gt; f_parent_to_m1 0.0046995211 0.0023457712
#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'>
<span class='co'># The profiling for the following fit does not finish in a reasonable time,</span>
@@ -395,18 +396,18 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
error_model_algorithm <span class='op'>=</span> <span class='st'>"direct"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 94.596126334 106.19944007
-#&gt; k_M1 0.037605408 0.04490759
-#&gt; k_M2 0.008568739 0.01087675
-#&gt; f_parent_to_M1 0.021463787 0.62023881
-#&gt; f_parent_to_M2 0.015166531 0.37975349
-#&gt; k1 0.273897467 0.33388084
-#&gt; k2 0.018614555 0.02250379
-#&gt; g 0.671943606 0.73583278
-#&gt; sigma_low 0.251283766 0.83992113
-#&gt; rsd_high 0.040411014 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
+#&gt; parent_0 94.596039609 106.19954892
+#&gt; k_M1 0.037605368 0.04490762
+#&gt; k_M2 0.008568731 0.01087676
+#&gt; f_parent_to_M1 0.021462489 0.62023882
+#&gt; f_parent_to_M2 0.015165617 0.37975348
+#&gt; k1 0.273897348 0.33388101
+#&gt; k2 0.018614554 0.02250378
+#&gt; g 0.671943411 0.73583305
+#&gt; sigma_low 0.251283495 0.83992077
+#&gt; rsd_high 0.040411024 0.07662008</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 94.59613 106.1994</div><div class='input'><span class='co'># }</span>
+#&gt; parent_0 94.59604 106.1995</div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html
index 4945d157..65a682bb 100644
--- a/docs/dev/reference/create_deg_func.html
+++ b/docs/dev/reference/create_deg_func.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -181,8 +181,8 @@
deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#&gt; test replications elapsed relative user.self sys.self user.child
-#&gt; 1 analytical 2 0.396 1.000 0.395 0 0
-#&gt; 2 deSolve 2 0.694 1.753 0.693 0 0
+#&gt; 1 analytical 2 0.396 1.00 0.396 0 0
+#&gt; 2 deSolve 2 0.709 1.79 0.707 0 0
#&gt; sys.child
#&gt; 1 0
#&gt; 2 0</div><div class='input'> <span class='va'>DFOP_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
@@ -193,8 +193,8 @@
deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span>
</div><div class='output co'>#&gt; test replications elapsed relative user.self sys.self user.child
-#&gt; 1 analytical 2 0.838 1.000 0.838 0.001 0
-#&gt; 2 deSolve 2 1.573 1.877 1.572 0.000 0
+#&gt; 1 analytical 2 0.844 1.000 0.844 0 0
+#&gt; 2 deSolve 2 1.624 1.924 1.624 0 0
#&gt; sys.child
#&gt; 1 0
#&gt; 2 0</div><div class='input'><span class='co'># }</span>
diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html
index 21dea623..a06599df 100644
--- a/docs/dev/reference/dimethenamid_2018.html
+++ b/docs/dev/reference/dimethenamid_2018.html
@@ -77,7 +77,7 @@ constrained by data protection regulations." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html
index db702c2e..63bec6a8 100644
--- a/docs/dev/reference/endpoints.html
+++ b/docs/dev/reference/endpoints.html
@@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span>
</span>
</div>
@@ -127,7 +127,7 @@ advantage that the SFORB model can also be used for metabolites." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/experimental_data_for_UBA-1.png b/docs/dev/reference/experimental_data_for_UBA-1.png
index 24cb54c5..33946ded 100644
--- a/docs/dev/reference/experimental_data_for_UBA-1.png
+++ b/docs/dev/reference/experimental_data_for_UBA-1.png
Binary files differ
diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html
index 78e57fb0..9904370f 100644
--- a/docs/dev/reference/experimental_data_for_UBA.html
+++ b/docs/dev/reference/experimental_data_for_UBA.html
@@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -149,7 +149,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/f_time_norm_focus.html b/docs/dev/reference/f_time_norm_focus.html
index 3421043d..852e00a0 100644
--- a/docs/dev/reference/f_time_norm_focus.html
+++ b/docs/dev/reference/f_time_norm_focus.html
@@ -73,7 +73,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
diff --git a/docs/dev/reference/focus_soil_moisture.html b/docs/dev/reference/focus_soil_moisture.html
index c46fd69a..0e6fea28 100644
--- a/docs/dev/reference/focus_soil_moisture.html
+++ b/docs/dev/reference/focus_soil_moisture.html
@@ -73,7 +73,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/get_deg_func.html b/docs/dev/reference/get_deg_func.html
index a266bf5f..fb661085 100644
--- a/docs/dev/reference/get_deg_func.html
+++ b/docs/dev/reference/get_deg_func.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/ilr.html b/docs/dev/reference/ilr.html
index 98e51211..452647d6 100644
--- a/docs/dev/reference/ilr.html
+++ b/docs/dev/reference/ilr.html
@@ -73,7 +73,7 @@ transformations." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ transformations." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index e038ef5c..5533a01f 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span>
</span>
</div>
@@ -175,7 +175,7 @@
</tr><tr>
<td>
- <p><code><a href="mmkin.html">mmkin()</a></code> </p>
+ <p><code><a href="mmkin.html">mmkin()</a></code> <code><a href="mmkin.html">print(<i>&lt;mmkin&gt;</i>)</a></code> </p>
</td>
<td><p>Fit one or more kinetic models with one or more state variables to one or
more datasets</p></td>
@@ -297,12 +297,6 @@ of an mmkin object</p></td>
<p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
</td>
<td><p>Calculate the AIC for a column of an mmkin object</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="print.mmkin.html">print(<i>&lt;mmkin&gt;</i>)</a></code> </p>
- </td>
- <td><p>Print method for mmkin objects</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/dev/reference/loftest-1.png b/docs/dev/reference/loftest-1.png
index 6b918fec..d6006ecc 100644
--- a/docs/dev/reference/loftest-1.png
+++ b/docs/dev/reference/loftest-1.png
Binary files differ
diff --git a/docs/dev/reference/loftest-2.png b/docs/dev/reference/loftest-2.png
index 60874bd3..4d0dc551 100644
--- a/docs/dev/reference/loftest-2.png
+++ b/docs/dev/reference/loftest-2.png
Binary files differ
diff --git a/docs/dev/reference/loftest-3.png b/docs/dev/reference/loftest-3.png
index 4837e7f2..6afd084b 100644
--- a/docs/dev/reference/loftest-3.png
+++ b/docs/dev/reference/loftest-3.png
Binary files differ
diff --git a/docs/dev/reference/loftest-4.png b/docs/dev/reference/loftest-4.png
index 9c18ac30..f94eede1 100644
--- a/docs/dev/reference/loftest-4.png
+++ b/docs/dev/reference/loftest-4.png
Binary files differ
diff --git a/docs/dev/reference/loftest-5.png b/docs/dev/reference/loftest-5.png
index 11f2bda7..43460a65 100644
--- a/docs/dev/reference/loftest-5.png
+++ b/docs/dev/reference/loftest-5.png
Binary files differ
diff --git a/docs/dev/reference/loftest.html b/docs/dev/reference/loftest.html
index abbbd3b9..9dbd547d 100644
--- a/docs/dev/reference/loftest.html
+++ b/docs/dev/reference/loftest.html
@@ -75,7 +75,7 @@ lrtest.default from the lmtest package." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -124,7 +124,7 @@ lrtest.default from the lmtest package." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html
index 66539dbd..3e9452c6 100644
--- a/docs/dev/reference/logLik.mkinfit.html
+++ b/docs/dev/reference/logLik.mkinfit.html
@@ -76,7 +76,7 @@ the error model." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ the error model." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -196,11 +196,11 @@ and the fitted error model parameters.</p>
parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>
<span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'>&lt;-</span> <span class='va'>FOCUS_2006_D</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>
<span class='va'>f_nw</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># no weighting (weights are unity)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='va'>f_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='va'>f_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nw</span>, <span class='va'>f_obs</span>, <span class='va'>f_tc</span><span class='op'>)</span>
+ <span class='va'>f_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
+ <span class='va'>f_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
+ <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nw</span>, <span class='va'>f_obs</span>, <span class='va'>f_tc</span><span class='op'>)</span>
</div><div class='output co'>#&gt; df AIC
#&gt; f_nw 5 204.4486
#&gt; f_obs 6 205.8727
diff --git a/docs/dev/reference/logistic.solution-2.png b/docs/dev/reference/logistic.solution-2.png
index 764996df..73e6436d 100644
--- a/docs/dev/reference/logistic.solution-2.png
+++ b/docs/dev/reference/logistic.solution-2.png
Binary files differ
diff --git a/docs/dev/reference/logistic.solution.html b/docs/dev/reference/logistic.solution.html
index 950e8a8e..ab68c99e 100644
--- a/docs/dev/reference/logistic.solution.html
+++ b/docs/dev/reference/logistic.solution.html
@@ -73,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -240,10 +240,10 @@ Version 1.1, 18 December 2014
<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</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://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02
-#&gt; kmax 6.398190e-02 0.0143201031 4.467978 3.841829e-04 3.929235e-02
+#&gt; parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-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 5.846688e-08
-#&gt; r 2.263946e-01 0.1718110715 1.317695 1.061044e-01 4.335843e-02
+#&gt; r 2.263946e-01 0.1718110662 1.317695 1.061043e-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
diff --git a/docs/dev/reference/lrtest.mkinfit.html b/docs/dev/reference/lrtest.mkinfit.html
index b76ebc87..f2d8472e 100644
--- a/docs/dev/reference/lrtest.mkinfit.html
+++ b/docs/dev/reference/lrtest.mkinfit.html
@@ -76,7 +76,7 @@ and can be expressed by fixing the parameters of the other." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ and can be expressed by fixing the parameters of the other." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/max_twa_parent.html b/docs/dev/reference/max_twa_parent.html
index 25f745e9..a358568a 100644
--- a/docs/dev/reference/max_twa_parent.html
+++ b/docs/dev/reference/max_twa_parent.html
@@ -78,7 +78,7 @@ soil section of the FOCUS guidance." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -127,7 +127,7 @@ soil section of the FOCUS guidance." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/mccall81_245T-1.png b/docs/dev/reference/mccall81_245T-1.png
index 5daa5f18..91fe060e 100644
--- a/docs/dev/reference/mccall81_245T-1.png
+++ b/docs/dev/reference/mccall81_245T-1.png
Binary files differ
diff --git a/docs/dev/reference/mccall81_245T.html b/docs/dev/reference/mccall81_245T.html
index 7179533d..f79137be 100644
--- a/docs/dev/reference/mccall81_245T.html
+++ b/docs/dev/reference/mccall81_245T.html
@@ -74,7 +74,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -181,30 +181,30 @@
<span class='va'>fit.1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t)
-#&gt; T245_0 1.038550e+02 2.1847074888 47.537272 4.472189e-18
+#&gt; T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18
#&gt; k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13
-#&gt; k_phenol 4.050581e-01 0.2986993400 1.356073 9.756988e-02
-#&gt; k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07
-#&gt; f_T245_to_phenol 6.227599e-01 0.3985340295 1.562627 6.949412e-02
-#&gt; f_phenol_to_anisole 1.000000e+00 0.6718439378 1.488441 7.867787e-02
-#&gt; sigma 2.514628e+00 0.4907558750 5.123989 6.233156e-05
+#&gt; k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02
+#&gt; k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07
+#&gt; f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02
+#&gt; f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02
+#&gt; sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05
#&gt; Lower Upper
-#&gt; T245_0 99.246061370 1.084640e+02
+#&gt; T245_0 99.246061385 1.084640e+02
#&gt; k_T245 0.039631621 4.746194e-02
-#&gt; k_phenol 0.218013878 7.525762e-01
+#&gt; k_phenol 0.218013879 7.525762e-01
#&gt; k_anisole 0.005370739 8.305299e-03
-#&gt; f_T245_to_phenol 0.547559083 6.924813e-01
+#&gt; f_T245_to_phenol 0.547559081 6.924813e-01
#&gt; f_phenol_to_anisole 0.000000000 1.000000e+00
#&gt; sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt; T245_phenol T245_sink phenol_anisole phenol_sink
-#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11
+#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; T245 15.982025 53.09114
#&gt; phenol 1.711229 5.68458
-#&gt; anisole 103.784092 344.76329
+#&gt; anisole 103.784093 344.76329
#&gt; </div><div class='input'> <span class='co'># formation fraction from phenol to anisol is practically 1. As we cannot</span>
<span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span>
<span class='co'># the sink in the model generation</span>
@@ -215,28 +215,28 @@
quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; T245_0 1.038550e+02 2.1623653027 48.028439 4.993108e-19 99.271020526
-#&gt; k_T245 4.337042e-02 0.0018343666 23.643268 3.573555e-14 0.039650977
-#&gt; k_phenol 4.050582e-01 0.1177237248 3.440752 1.679252e-03 0.218746585
-#&gt; k_anisole 6.678741e-03 0.0006829745 9.778903 1.872894e-08 0.005377083
-#&gt; f_T245_to_phenol 6.227599e-01 0.0342197865 18.198825 2.039410e-12 0.547975628
+#&gt; T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284
+#&gt; k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976
+#&gt; k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587
+#&gt; k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083
+#&gt; f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637
#&gt; sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655
#&gt; Upper
-#&gt; T245_0 108.43904097
+#&gt; T245_0 108.43904074
#&gt; k_T245 0.04743877
-#&gt; k_phenol 0.75005577
+#&gt; k_phenol 0.75005585
#&gt; k_anisole 0.00829550
-#&gt; f_T245_to_phenol 0.69212306
+#&gt; f_T245_to_phenol 0.69212308
#&gt; sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt; T245_phenol T245_sink phenol_anisole phenol_sink
-#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11
+#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; T245 15.982025 53.09114
#&gt; phenol 1.711229 5.68458
-#&gt; anisole 103.784092 344.76329
+#&gt; anisole 103.784093 344.76329
#&gt; </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span>
</div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span>
</div></pre>
diff --git a/docs/dev/reference/mixed-1.png b/docs/dev/reference/mixed-1.png
index 3400c4aa..28a376f4 100644
--- a/docs/dev/reference/mixed-1.png
+++ b/docs/dev/reference/mixed-1.png
Binary files differ
diff --git a/docs/dev/reference/mixed.html b/docs/dev/reference/mixed.html
index 18a67af8..7bf8dd56 100644
--- a/docs/dev/reference/mixed.html
+++ b/docs/dev/reference/mixed.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -235,18 +235,16 @@
#&gt; Status of individual fits:
#&gt;
#&gt; dataset
-#&gt; model 1 2 3 4 5 6 7 8
-#&gt; DFOP-SFO OK OK OK OK OK C OK OK
+#&gt; model 1 2 3 4 5 6 7 8
+#&gt; DFOP-SFO OK OK OK OK OK OK OK OK
#&gt;
#&gt; OK: No warnings
-#&gt; C: Optimisation did not converge:
-#&gt; iteration limit reached without convergence (10)
#&gt;
#&gt; Mean fitted parameters:
#&gt; parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2
-#&gt; 100.606304 -8.759216 -0.002001 -3.350539 -3.989549
+#&gt; 100.674757 -8.761916 -0.004347 -3.348812 -3.986853
#&gt; g_qlogis
-#&gt; -0.090353 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_mixed</span><span class='op'>)</span>
+#&gt; -0.087392 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_mixed</span><span class='op'>)</span>
</div><div class='img'><img src='mixed-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
diff --git a/docs/dev/reference/mkin_long_to_wide.html b/docs/dev/reference/mkin_long_to_wide.html
index 28a37800..6246fbe2 100644
--- a/docs/dev/reference/mkin_long_to_wide.html
+++ b/docs/dev/reference/mkin_long_to_wide.html
@@ -74,7 +74,7 @@ variable and several dependent variables as columns." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -123,7 +123,7 @@ variable and several dependent variables as columns." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/mkin_wide_to_long.html b/docs/dev/reference/mkin_wide_to_long.html
index f085d162..f2bf00c1 100644
--- a/docs/dev/reference/mkin_wide_to_long.html
+++ b/docs/dev/reference/mkin_wide_to_long.html
@@ -74,7 +74,7 @@ mkinfit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -123,7 +123,7 @@ mkinfit." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/mkinds.html b/docs/dev/reference/mkinds.html
index 907f8ad3..0d1de46d 100644
--- a/docs/dev/reference/mkinds.html
+++ b/docs/dev/reference/mkinds.html
@@ -75,7 +75,7 @@ provided by this package come as mkinds objects nevertheless." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -124,7 +124,7 @@ provided by this package come as mkinds objects nevertheless." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/mkindsg.html b/docs/dev/reference/mkindsg.html
index 3e4dfb39..67c6e5df 100644
--- a/docs/dev/reference/mkindsg.html
+++ b/docs/dev/reference/mkindsg.html
@@ -75,7 +75,7 @@ dataset if no data are supplied." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -124,7 +124,7 @@ dataset if no data are supplied." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -239,12 +239,12 @@ or covariates like soil pH).</p></dd>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span><span class='op'>)</span>
</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
#&gt; Title $title: Experimental X
-#&gt; Occurrene of observed compounds $observed_n:
+#&gt; Occurrence of observed compounds $observed_n:
#&gt; parent A1
#&gt; 5 5 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
#&gt; Title $title: Experimental X
-#&gt; Occurrene of observed compounds $observed_n:
+#&gt; Occurrence of observed compounds $observed_n:
#&gt; parent A1
#&gt; 5 5
#&gt;
@@ -290,7 +290,7 @@ or covariates like soil pH).</p></dd>
#&gt; Observation unit: \%AR </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
#&gt; Title $title: Experimental X
-#&gt; Occurrene of observed compounds $observed_n:
+#&gt; Occurrence of observed compounds $observed_n:
#&gt; parent A1
#&gt; 5 5
#&gt;
diff --git a/docs/dev/reference/mkinerrmin.html b/docs/dev/reference/mkinerrmin.html
index 1cff040d..94c575cb 100644
--- a/docs/dev/reference/mkinerrmin.html
+++ b/docs/dev/reference/mkinerrmin.html
@@ -73,7 +73,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/mkinerrplot.html b/docs/dev/reference/mkinerrplot.html
index 2324b968..7f1fd048 100644
--- a/docs/dev/reference/mkinerrplot.html
+++ b/docs/dev/reference/mkinerrplot.html
@@ -76,7 +76,7 @@ using the argument show_errplot = TRUE." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ using the argument show_errplot = TRUE." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/mkinfit-1.png b/docs/dev/reference/mkinfit-1.png
index eed9064f..de2a90a9 100644
--- a/docs/dev/reference/mkinfit-1.png
+++ b/docs/dev/reference/mkinfit-1.png
Binary files differ
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index 6ae7b343..5910038f 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -80,7 +80,7 @@ likelihood function." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -431,17 +431,17 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
<span class='co'># Use shorthand notation for parent only degradation</span>
<span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.4
+</div><div class='output co'>#&gt; mkin version used for fitting: 1.0.3.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Jan 11 12:41:45 2021
-#&gt; Date of summary: Mon Jan 11 12:41:45 2021
+#&gt; Date of fit: Mon Feb 15 17:09:39 2021
+#&gt; Date of summary: Mon Feb 15 17:09:39 2021
#&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 0.046 s
+#&gt; Fitted using 222 model solutions performed in 0.045 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -476,10 +476,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&gt;
#&gt; Parameter correlation:
#&gt; parent_0 log_alpha log_beta sigma
-#&gt; parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.758e-08
-#&gt; log_alpha -1.565e-01 1.000e+00 9.564e-01 1.007e-07
-#&gt; log_beta -3.142e-01 9.564e-01 1.000e+00 8.568e-08
-#&gt; sigma 4.758e-08 1.007e-07 8.568e-08 1.000e+00
+#&gt; parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08
+#&gt; log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07
+#&gt; log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08
+#&gt; sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00
#&gt;
#&gt; Backtransformed parameters:
#&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -548,7 +548,7 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&gt; ---
#&gt; Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span>
</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1 sigma_low
-#&gt; 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049884e-03
+#&gt; 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049883e-03
#&gt; rsd_high
#&gt; 7.928118e-02 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
@@ -574,10 +574,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
analytical <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>,
solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
-</div><div class='output co'>#&gt; <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#&gt; test relative elapsed
-#&gt; 3 analytical 1.000 0.526
-#&gt; 1 deSolve_compiled 1.903 1.001
-#&gt; 2 eigen 2.308 1.214</div><div class='input'><span class='co'># }</span>
+</div><div class='output co'>#&gt; test relative elapsed
+#&gt; 3 analytical 1.000 0.563
+#&gt; 1 deSolve_compiled 1.702 0.958
+#&gt; 2 eigen 2.597 1.462</div><div class='input'><span class='co'># }</span>
<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span>
<span class='co'># \dontrun{</span>
@@ -587,22 +587,21 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit.FOMC_SFO</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='co'># Again, we get a warning and try a more sophisticated error model</span>
<span class='va'>fit.FOMC_SFO.tc</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
-#&gt; <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='co'># This model has a higher likelihood, but not significantly so</span>
+<span class='co'># This model has a higher likelihood, but not significantly so</span>
<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.tc</span>, <span class='va'>fit.FOMC_SFO.tc</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Likelihood ratio test
#&gt;
#&gt; Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0
#&gt; Model 2: SFO_SFO with error model tc and fixed parameter(s) m1_0
#&gt; #Df LogLik Df Chisq Pr(&gt;Chisq)
-#&gt; 1 7 -64.870
-#&gt; 2 6 -64.983 -1 0.2259 0.6346</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span>
+#&gt; 1 7 -64.829
+#&gt; 2 6 -64.983 -1 0.3075 0.5792</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span>
<span class='co'># and beta indicate overparameterisation</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.FOMC_SFO.tc</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</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: 0.9.50.4
+</div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</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: 1.0.3.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Jan 11 12:41:56 2021
-#&gt; Date of summary: Mon Jan 11 12:41:56 2021
+#&gt; Date of fit: Mon Feb 15 17:09:50 2021
+#&gt; Date of summary: Mon Feb 15 17:09:50 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -611,12 +610,12 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 4273 model solutions performed in 3.456 s
+#&gt; Fitted using 3729 model solutions performed in 2.815 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;
#&gt; Error model algorithm: d_3
-#&gt; Three-step fitting yielded a higher likelihood than direct fitting
+#&gt; Direct fitting and three-step fitting yield approximately the same likelihood
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -642,72 +641,67 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&gt; value type
#&gt; m1_0 0 state
#&gt;
-#&gt;
-#&gt; Warning(s):
-#&gt; Optimisation did not converge:
-#&gt; iteration limit reached without convergence (10)
-#&gt;
#&gt; Results:
#&gt;
-#&gt; AIC BIC logLik
-#&gt; 143.7396 155.2027 -64.86982
+#&gt; AIC BIC logLik
+#&gt; 143.658 155.1211 -64.82902
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 1.016e+02 1.90600 97.7400 105.5000
-#&gt; log_k_m1 -5.285e+00 0.09286 -5.4740 -5.0950
-#&gt; f_parent_qlogis 6.482e-04 0.06164 -0.1251 0.1264
-#&gt; log_alpha 5.467e+00 NaN NaN NaN
-#&gt; log_beta 7.750e+00 NaN NaN NaN
-#&gt; sigma_low 0.000e+00 NaN NaN NaN
-#&gt; rsd_high 7.989e-02 NaN NaN NaN
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 101.600000 2.6400000 96.240000 107.000000
+#&gt; log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000
+#&gt; f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800
+#&gt; log_alpha 5.522000 0.0077320 5.506000 5.538000
+#&gt; log_beta 7.806000 NaN NaN NaN
+#&gt; sigma_low 0.002488 0.0002431 0.001992 0.002984
+#&gt; rsd_high 0.079210 0.0093280 0.060180 0.098230
#&gt;
#&gt; Parameter correlation:
-#&gt; parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta
-#&gt; parent_0 1.0000000 -0.0002167 -0.6060 NaN NaN
-#&gt; log_k_m1 -0.0002167 1.0000000 0.5474 NaN NaN
-#&gt; f_parent_qlogis -0.6060320 0.5474423 1.0000 NaN NaN
-#&gt; log_alpha NaN NaN NaN 1 NaN
-#&gt; log_beta NaN NaN NaN NaN 1
-#&gt; sigma_low NaN NaN NaN NaN NaN
-#&gt; rsd_high NaN NaN NaN NaN NaN
-#&gt; sigma_low rsd_high
-#&gt; parent_0 NaN NaN
-#&gt; log_k_m1 NaN NaN
-#&gt; f_parent_qlogis NaN NaN
-#&gt; log_alpha NaN NaN
-#&gt; log_beta NaN NaN
-#&gt; sigma_low 1 NaN
-#&gt; rsd_high NaN 1
+#&gt; parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta
+#&gt; parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN
+#&gt; log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN
+#&gt; f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN
+#&gt; log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN
+#&gt; log_beta NaN NaN NaN NaN 1
+#&gt; sigma_low 0.016073 0.001586 0.01548 5.87007 NaN
+#&gt; rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN
+#&gt; sigma_low rsd_high
+#&gt; parent_0 0.016073 0.006626
+#&gt; log_k_m1 0.001586 -0.011700
+#&gt; f_parent_qlogis 0.015476 -0.053566
+#&gt; log_alpha 5.870075 0.048487
+#&gt; log_beta NaN NaN
+#&gt; sigma_low 1.000000 -0.652558
+#&gt; rsd_high -0.652558 1.000000
#&gt;
#&gt; Backtransformed parameters:
#&gt; Confidence intervals for internally transformed parameters are asymmetric.
#&gt; t-test (unrealistically) based on the assumption of normal distribution
#&gt; for estimators of untransformed parameters.
#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 1.016e+02 32.5400 7.812e-26 97.740000 1.055e+02
-#&gt; k_m1 5.069e-03 10.0400 1.448e-11 0.004194 6.126e-03
-#&gt; f_parent_to_m1 5.002e-01 20.7300 5.001e-20 0.468800 5.315e-01
-#&gt; alpha 2.367e+02 0.6205 2.697e-01 NA NA
-#&gt; beta 2.322e+03 0.6114 2.727e-01 NA NA
-#&gt; sigma_low 0.000e+00 NaN NaN NaN NaN
-#&gt; rsd_high 7.989e-02 8.6630 4.393e-10 NaN NaN
+#&gt; parent_0 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02
+#&gt; k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03
+#&gt; f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01
+#&gt; alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02
+#&gt; beta 2.455e+03 0.5549 2.915e-01 NA NA
+#&gt; sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03
+#&gt; rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
-#&gt; All data 6.782 5 14
-#&gt; parent 7.142 3 6
-#&gt; m1 4.639 2 8
+#&gt; All data 6.781 5 14
+#&gt; parent 7.141 3 6
+#&gt; m1 4.640 2 8
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
-#&gt; parent_m1 0.5002
-#&gt; parent_sink 0.4998
+#&gt; parent_m1 0.5004
+#&gt; parent_sink 0.4996
#&gt;
#&gt; Estimated disappearance times:
-#&gt; DT50 DT90 DT50back
-#&gt; parent 6.81 22.7 6.833
-#&gt; m1 136.74 454.2 NA</div><div class='input'>
+#&gt; DT50 DT90 DT50back
+#&gt; parent 6.812 22.7 6.834
+#&gt; m1 136.661 454.0 NA</div><div class='input'>
<span class='co'># We can easily use starting parameters from the parent only fit (only for illustration)</span>
<span class='va'>fit.FOMC</span> <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
<span class='va'>fit.FOMC_SFO</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>,
diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 9a7dac6f..413f0ae1 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -78,7 +78,7 @@ mkinmod." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -127,7 +127,7 @@ mkinmod." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -348,7 +348,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>,
m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span>,
name <span class='op'>=</span> <span class='st'>"SFO_SFO"</span>, dll_dir <span class='op'>=</span> <span class='va'>DLL_dir</span>, unload <span class='op'>=</span> <span class='cn'>TRUE</span>, overwrite <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/Rtmpy4eiQb/file554e573761a7.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
+</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/Rtmp92fCb2/file133ad522561845.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
<span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS</a></span><span class='op'>(</span><span class='va'>SFO_SFO.2</span>, file <span class='op'>=</span> <span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span>
<span class='co'># Terminate the R session here if you would like to check, and then do</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://pkgdown.jrwb.de/mkin/'>mkin</a></span><span class='op'>)</span>
@@ -397,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
#&gt; })
#&gt; return(predicted)
#&gt; }
-#&gt; &lt;environment: 0x55555cac8d00&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x5555572517f8&gt;</div><div class='input'>
<span class='co'># If we have several parallel metabolites</span>
<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
<span class='va'>m_synth_DFOP_par</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>
diff --git a/docs/dev/reference/mkinparplot-1.png b/docs/dev/reference/mkinparplot-1.png
index dcf3e4b5..c9ed49eb 100644
--- a/docs/dev/reference/mkinparplot-1.png
+++ b/docs/dev/reference/mkinparplot-1.png
Binary files differ
diff --git a/docs/dev/reference/mkinparplot.html b/docs/dev/reference/mkinparplot.html
index 0a989ef9..bac6e71c 100644
--- a/docs/dev/reference/mkinparplot.html
+++ b/docs/dev/reference/mkinparplot.html
@@ -73,7 +73,7 @@ mkinfit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ mkinfit." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -176,7 +176,8 @@ effect, namely to produce a plot.</p>
phenol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"anisole"</span><span class='op'>)</span><span class='op'>)</span>,
anisole <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
+#&gt; <span class='warning'>false convergence (8)</span></div><div class='input'><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
diff --git a/docs/dev/reference/mkinplot.html b/docs/dev/reference/mkinplot.html
index 417c8c73..120bddb3 100644
--- a/docs/dev/reference/mkinplot.html
+++ b/docs/dev/reference/mkinplot.html
@@ -73,7 +73,7 @@ plot.mkinfit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ plot.mkinfit." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html
index 3221fc23..1ebaecb5 100644
--- a/docs/dev/reference/mkinpredict.html
+++ b/docs/dev/reference/mkinpredict.html
@@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -123,7 +123,7 @@ kinetic parameters and initial values for the state variables." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -408,10 +408,10 @@ as these always return mapped output.</p></td>
solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span><span class='op'>)</span>
<span class='op'>}</span>
</div><div class='output co'>#&gt; test relative elapsed
+#&gt; 2 deSolve_compiled 1.0 0.005
#&gt; 4 analytical 1.0 0.005
-#&gt; 2 deSolve_compiled 1.2 0.006
-#&gt; 1 eigen 4.0 0.020
-#&gt; 3 deSolve 44.2 0.221</div><div class='input'>
+#&gt; 1 eigen 4.4 0.022
+#&gt; 3 deSolve 46.8 0.234</div><div class='input'>
<span class='co'># \dontrun{</span>
<span class='co'># Predict from a fitted model</span>
<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
diff --git a/docs/dev/reference/mkinresplot.html b/docs/dev/reference/mkinresplot.html
index 4b2f6bea..30377f2c 100644
--- a/docs/dev/reference/mkinresplot.html
+++ b/docs/dev/reference/mkinresplot.html
@@ -75,7 +75,7 @@ argument show_residuals = TRUE." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -124,7 +124,7 @@ argument show_residuals = TRUE." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -242,7 +242,7 @@ lines of the mkinfit object, and <code><a href='plot.mkinfit.html'>plot_res</a><
combining the plot of the fit and the residual plot.</p></div>
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
- <p>Johannes Ranke</p>
+ <p>Johannes Ranke and Katrin Lindenberger</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'>
diff --git a/docs/dev/reference/mmkin-1.png b/docs/dev/reference/mmkin-1.png
index 7b7da90a..0db3379f 100644
--- a/docs/dev/reference/mmkin-1.png
+++ b/docs/dev/reference/mmkin-1.png
Binary files differ
diff --git a/docs/dev/reference/mmkin-2.png b/docs/dev/reference/mmkin-2.png
index ce2b2af4..024a9892 100644
--- a/docs/dev/reference/mmkin-2.png
+++ b/docs/dev/reference/mmkin-2.png
Binary files differ
diff --git a/docs/dev/reference/mmkin-3.png b/docs/dev/reference/mmkin-3.png
index bb96f1b2..a23d7cb9 100644
--- a/docs/dev/reference/mmkin-3.png
+++ b/docs/dev/reference/mmkin-3.png
Binary files differ
diff --git a/docs/dev/reference/mmkin-4.png b/docs/dev/reference/mmkin-4.png
index 351b21aa..89975db5 100644
--- a/docs/dev/reference/mmkin-4.png
+++ b/docs/dev/reference/mmkin-4.png
Binary files differ
diff --git a/docs/dev/reference/mmkin-5.png b/docs/dev/reference/mmkin-5.png
index c1c05eea..a2f34983 100644
--- a/docs/dev/reference/mmkin-5.png
+++ b/docs/dev/reference/mmkin-5.png
Binary files differ
diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html
index 651eb9a6..5da1b1de 100644
--- a/docs/dev/reference/mmkin.html
+++ b/docs/dev/reference/mmkin.html
@@ -75,7 +75,7 @@ datasets specified in its first two arguments." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -124,7 +124,7 @@ datasets specified in its first two arguments." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -158,7 +158,10 @@ datasets specified in its first two arguments.</p>
cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>,
cluster <span class='op'>=</span> <span class='cn'>NULL</span>,
<span class='va'>...</span>
-<span class='op'>)</span></pre>
+<span class='op'>)</span>
+
+<span class='co'># S3 method for mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -189,7 +192,11 @@ for parallel execution.</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+ <td><p>Not used.</p></td>
+ </tr>
+ <tr>
+ <th>x</th>
+ <td><p>An mmkin object.</p></td>
</tr>
</table>
@@ -227,19 +234,19 @@ plotting.</p></div>
<span class='va'>time_default</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 4.968 0.427 1.342 </div><div class='input'><span class='va'>time_1</span>
+#&gt; 4.921 0.475 1.707 </div><div class='input'><span class='va'>time_1</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 5.365 0.000 5.368 </div><div class='input'>
+#&gt; 5.680 0.003 5.684 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
-#&gt; 0.7340478 0.2659522 0.7505687 0.2494313
+#&gt; 0.7340481 0.2659519 0.7505683 0.2494317
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 0.877769 2.915885
-#&gt; M1 2.325746 7.725960
-#&gt; M2 33.720083 112.015691
+#&gt; M1 2.325744 7.725956
+#&gt; M2 33.720100 112.015749
#&gt; </div><div class='input'>
<span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span><span class='op'>)</span>
@@ -266,12 +273,10 @@ plotting.</p></div>
#&gt; dataset
#&gt; model A B C D
#&gt; SFO OK OK OK OK
-#&gt; FOMC C OK OK OK
+#&gt; FOMC OK OK OK OK
#&gt; DFOP OK OK OK OK
#&gt;
-#&gt; OK: No warnings
-#&gt; C: Optimisation did not converge:
-#&gt; false convergence (8)</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span>
+#&gt; OK: No warnings</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span>
<span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span>
<span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span>
<span class='co'># }</span>
diff --git a/docs/dev/reference/nafta-1.png b/docs/dev/reference/nafta-1.png
index 4d823d77..4f0d7833 100644
--- a/docs/dev/reference/nafta-1.png
+++ b/docs/dev/reference/nafta-1.png
Binary files differ
diff --git a/docs/dev/reference/nafta.html b/docs/dev/reference/nafta.html
index bbc8797d..6fb797a5 100644
--- a/docs/dev/reference/nafta.html
+++ b/docs/dev/reference/nafta.html
@@ -76,7 +76,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/nlme-1.png b/docs/dev/reference/nlme-1.png
index 193722c7..fd68ae43 100644
--- a/docs/dev/reference/nlme-1.png
+++ b/docs/dev/reference/nlme-1.png
Binary files differ
diff --git a/docs/dev/reference/nlme-2.png b/docs/dev/reference/nlme-2.png
index c0fb6dcf..853cae40 100644
--- a/docs/dev/reference/nlme-2.png
+++ b/docs/dev/reference/nlme-2.png
Binary files differ
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index b3e88428..78d132e9 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span>
</span>
</div>
@@ -124,7 +124,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -155,7 +155,7 @@ datasets. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.m
<pre class="usage"><span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span>
-<span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>object</span>, random <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+<span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>object</span>, random <span class='op'>=</span> <span class='cn'>FALSE</span>, test_log_parms <span class='op'>=</span> <span class='cn'>FALSE</span>, conf.level <span class='op'>=</span> <span class='fl'>0.6</span><span class='op'>)</span>
<span class='fu'>nlme_data</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
@@ -170,6 +170,17 @@ datasets. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.m
<th>random</th>
<td><p>Should a list with fixed and random effects be returned?</p></td>
</tr>
+ <tr>
+ <th>test_log_parms</th>
+ <td><p>If TRUE, log parameters are only considered in
+the mean calculations if their untransformed counterparts (most likely
+rate constants) pass the t-test for significant difference from zero.</p></td>
+ </tr>
+ <tr>
+ <th>conf.level</th>
+ <td><p>Possibility to adjust the required confidence level
+for parameter that are tested if requested by 'test_log_parms'.</p></td>
+ </tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -211,7 +222,7 @@ nlme for the case of a single grouping variable ds.</p>
<span class='va'>nlme_f</span> <span class='op'>&lt;-</span> <span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
<span class='co'># These assignments are necessary for these objects to be</span>
<span class='co'># visible to nlme and augPred when evaluation is done by</span>
-<span class='co'># pkgdown to generated the html docs.</span>
+<span class='co'># pkgdown to generate the html docs.</span>
<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='st'>"nlme_f"</span>, <span class='va'>nlme_f</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='st'>"grouped_data"</span>, <span class='va'>grouped_data</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
@@ -224,37 +235,37 @@ nlme for the case of a single grouping variable ds.</p>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>m_nlme</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
#&gt; Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
-#&gt; Data: grouped_data
+#&gt; Data: grouped_data
#&gt; AIC BIC logLik
-#&gt; 252.7798 262.1358 -121.3899
+#&gt; 298.2781 307.7372 -144.1391
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#&gt; Level: ds
#&gt; Structure: Diagonal
-#&gt; parent_0 log_k_parent_sink Residual
-#&gt; StdDev: 0.0006768135 0.6800777 2.489397
+#&gt; parent_0 log_k_parent_sink Residual
+#&gt; StdDev: 0.937473 0.7098105 3.83543
#&gt;
-#&gt; Fixed effects: parent_0 + log_k_parent_sink ~ 1
-#&gt; Value Std.Error DF t-value p-value
-#&gt; parent_0 101.74884 0.6456014 44 157.60321 0
-#&gt; log_k_parent_sink -3.05575 0.4015811 44 -7.60929 0
+#&gt; Fixed effects: parent_0 + log_k_parent_sink ~ 1
+#&gt; Value Std.Error DF t-value p-value
+#&gt; parent_0 101.76838 1.1445443 45 88.91607 0
+#&gt; log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0
#&gt; Correlation:
#&gt; prnt_0
-#&gt; log_k_parent_sink 0.026
+#&gt; log_k_parent_sink 0.034
#&gt;
#&gt; Standardized Within-Group Residuals:
-#&gt; Min Q1 Med Q3 Max
-#&gt; -2.1317488 -0.6878121 0.0828385 0.8592270 2.9529864
+#&gt; Min Q1 Med Q3 Max
+#&gt; -2.61693595 -0.21853231 0.05740682 0.57209372 3.04598764
#&gt;
-#&gt; Number of Observations: 48
+#&gt; Number of Observations: 49
#&gt; Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span><span class='op'>(</span><span class='va'>m_nlme</span>, level <span class='op'>=</span> <span class='fl'>0</span><span class='op'>:</span><span class='fl'>1</span><span class='op'>)</span>, layout <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># augPred does not work on fits with more than one state</span>
<span class='co'># variable</span>
<span class='co'>#</span>
<span class='co'># The procedure is greatly simplified by the nlme.mmkin function</span>
<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
</div><div class='img'><img src='nlme-2.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/dev/reference/nlme.mmkin-1.png b/docs/dev/reference/nlme.mmkin-1.png
index 25bebeca..90ede880 100644
--- a/docs/dev/reference/nlme.mmkin-1.png
+++ b/docs/dev/reference/nlme.mmkin-1.png
Binary files differ
diff --git a/docs/dev/reference/nlme.mmkin-2.png b/docs/dev/reference/nlme.mmkin-2.png
index c314c149..0d140fd1 100644
--- a/docs/dev/reference/nlme.mmkin-2.png
+++ b/docs/dev/reference/nlme.mmkin-2.png
Binary files differ
diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png
index a40b7cad..8a60b52b 100644
--- a/docs/dev/reference/nlme.mmkin-3.png
+++ b/docs/dev/reference/nlme.mmkin-3.png
Binary files differ
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index a4d7070a..f308d8b7 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span>
</span>
</div>
@@ -123,7 +123,7 @@ have been obtained by fitting the same model to a list of datasets." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -157,7 +157,7 @@ have been obtained by fitting the same model to a list of datasets.</p>
data <span class='op'>=</span> <span class='st'>"auto"</span>,
fixed <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>as.list</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>el</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/eval.html'>eval</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/parse.html'>parse</a></span><span class='op'>(</span>text <span class='op'>=</span>
<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='va'>el</span>, <span class='fl'>1</span>, sep <span class='op'>=</span> <span class='st'>"~"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
- random <span class='op'>=</span> <span class='fu'>pdDiag</span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>,
+ random <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>,
<span class='va'>groups</span>,
start <span class='op'>=</span> <span class='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span>, random <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
correlation <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -262,6 +262,12 @@ parameters taken from the mmkin object are used</p></td>
<p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object
with additional elements. It also inherits from 'mixed.mmkin'.</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Note that the convergence of the nlme algorithms depends on the quality
+of the data. In degradation kinetics, we often only have few datasets
+(e.g. data for few soils) and complicated degradation models, which may
+make it impossible to obtain convergence with nlme.</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
<p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of
@@ -284,7 +290,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_dfop</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Model df AIC BIC logLik Test L.Ratio p-value
#&gt; f_nlme_sfo 1 5 625.0539 637.5529 -307.5269
-#&gt; f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 &lt;.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+#&gt; f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 &lt;.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
#&gt;
#&gt; Structural model:
@@ -312,7 +318,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $distimes
#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
-#&gt; parent 10.79857 100.7937 30.34192 4.193937 43.85442
+#&gt; parent 10.79857 100.7937 30.34193 4.193938 43.85443
#&gt; </div><div class='input'>
<span class='va'>ds_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
<span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
@@ -335,16 +341,17 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<span class='co'># f_nlme_sfo_sfo_ff &lt;- nlme(f_2["SFO-SFO-ff", ])</span>
<span class='co'>#plot(f_nlme_sfo_sfo_ff)</span>
- <span class='co'># With the log-Cholesky parameterization, this converges in 11</span>
- <span class='co'># iterations and around 100 seconds, but without tweaking control</span>
- <span class='co'># parameters (with pdDiag, increasing the tolerance and pnlsMaxIter was</span>
- <span class='co'># necessary)</span>
- <span class='va'>f_nlme_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in nlme.formula(model = value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_A1, f_parent_qlogis, log_k1, log_k2, g_qlogis), data = structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L ), .Label = c("1", "2", "3", "4", "5"), class = c("ordered", "factor")), name = c("parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0, 0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2, 96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18, 10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 4.3, 4.6, 7, 7.2, 8.2, 8, 11, 13.7, 11.5, 12.7, 14.9, 14.5, 12.1, 12.3, 9.9, 10.2, 8.8, 7.8, 93.6, 92.3, 87, 82.2, 74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1, 29, 26.5, 27.6, 3.9, 3.1, 6.9, 6.6, 10.4, 8.3, 14.4, 13.7, 22.1, 22.3, 27.5, 25.4, 28, 26.6, 25.8, 25.3, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1, 10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 9.6, 7.7, 15, 15.1, 21.2, 21.1, 19.7, 18.9, 17.5, 15.9, 9.5, 9.8, 6.2, 6.1, 99.8, 98.3, 77.1, 77.2, 59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3, 2.9, 2, 1.8, 2, 2.2, 4.2, 3.9, 7.4, 7.9, 14.5, 13.7, 14.2, 12.2, 13.7, 13.2, 13.6, 15.4, 10.4, 11.6, 10, 9.5, 9.1, 9, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6, 65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3, 3.3, 3.4, 3.9, 2.9, 6.4, 7.2, 9.1, 8.5, 11.7, 12, 13.3, 13.2, 14.3, 12.1)), row.names = c(NA, -170L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = value ~ time | ds, FUN = function (x) max(x, na.rm = TRUE), order.groups = FALSE), start = list( fixed = c(parent_0 = 93.8101519326534, log_k_A1 = -9.76474551635931, f_parent_qlogis = -0.971114801595408, log_k1 = -1.87993711571859, log_k2 = -4.27081421366622, g_qlogis = 0.135644115277507 ), random = list(ds = structure(c(2.56569977430371, -3.49441920289139, -3.32614443321494, 4.35347873814922, -0.0986148763466161, 4.65850590018027, 1.8618544764481, 6.12693257601545, 4.91792724701579, -17.5652201996596, -0.466203822618637, 0.746660653597927, 0.282193987271096, -0.42053488943072, -0.142115928819667, 0.369240076779088, -1.38985563501659, 1.02592753494098, 0.73090914081534, -0.736221117518819, 0.768170629350299, -1.89347658079869, 1.72168783460352, 0.844607177798114, -1.44098906095325, -0.377731855445672, 0.168180098477565, 0.469683412912104, 0.500717664434525, -0.760849320378522), .Dim = 5:6, .Dimnames = list(c("1", "2", "3", "4", "5"), c("parent_0", "log_k_A1", "f_parent_qlogis", "log_k1", "log_k2", "g_qlogis"))))), fixed = list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = structure(list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), class = "listForm"), Dimnames = list(NULL, NULL))): maximum number of iterations (maxIter = 50) reached without convergence</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 49.95 16.5 44.08</span></div><div class='input'>
+ <span class='co'># For the following, we need to increase pnlsMaxIter and the tolerance</span>
+ <span class='co'># to get convergence</span>
+ <span class='va'>f_nlme_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>,
+ control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span><span class='op'>)</span>
+
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in plot(f_nlme_dfop_sfo): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'>
+</div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'>
+</div><div class='output co'>#&gt; Model df AIC BIC logLik Test L.Ratio p-value
+#&gt; f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274
+#&gt; f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3273 &lt;.0001</div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_A1 A1_sink
@@ -355,7 +362,15 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
#&gt; parent 19.13518 63.5657
#&gt; A1 66.02155 219.3189
#&gt; </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in endpoints(f_nlme_dfop_sfo): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'>
+</div><div class='output co'>#&gt; $ff
+#&gt; parent_A1 parent_sink
+#&gt; 0.2768575 0.7231425
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
+#&gt; parent 11.07091 104.6320 31.49737 4.462384 46.20825
+#&gt; A1 162.30492 539.1653 NA NA NA
+#&gt; </div><div class='input'>
<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>&gt;</span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span>
<span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span>
<span class='co'># but need tweeking of control values and sometimes do not converge</span>
@@ -381,7 +396,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
#&gt; Fixed effects:
#&gt; list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
#&gt; parent_0 log_k1 log_k2 g_qlogis
-#&gt; 94.04775 -1.82340 -4.16715 0.05685
+#&gt; 94.04774 -1.82340 -4.16716 0.05686
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
@@ -395,10 +410,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
#&gt; Formula: ~fitted(.)
#&gt; Parameter estimates:
#&gt; const prop
-#&gt; 2.23224114 0.01262341 </div><div class='input'>
- <span class='va'>f_2_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
- <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
- <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
+#&gt; 2.23223147 0.01262395 </div><div class='input'>
+ <span class='va'>f_2_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
<span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
@@ -429,18 +442,21 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
#&gt; Formula: ~1 | name
#&gt; Parameter estimates:
#&gt; parent A1
-#&gt; 1.0000000 0.2050003 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in nlme.formula(model = value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_A1, f_parent_qlogis, log_k1, log_k2, g_qlogis), data = structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L ), .Label = c("1", "2", "3", "4", "5"), class = c("ordered", "factor")), name = c("parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1", "A1"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0, 0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2, 96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18, 10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 4.3, 4.6, 7, 7.2, 8.2, 8, 11, 13.7, 11.5, 12.7, 14.9, 14.5, 12.1, 12.3, 9.9, 10.2, 8.8, 7.8, 93.6, 92.3, 87, 82.2, 74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1, 29, 26.5, 27.6, 3.9, 3.1, 6.9, 6.6, 10.4, 8.3, 14.4, 13.7, 22.1, 22.3, 27.5, 25.4, 28, 26.6, 25.8, 25.3, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1, 10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 9.6, 7.7, 15, 15.1, 21.2, 21.1, 19.7, 18.9, 17.5, 15.9, 9.5, 9.8, 6.2, 6.1, 99.8, 98.3, 77.1, 77.2, 59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3, 2.9, 2, 1.8, 2, 2.2, 4.2, 3.9, 7.4, 7.9, 14.5, 13.7, 14.2, 12.2, 13.7, 13.2, 13.6, 15.4, 10.4, 11.6, 10, 9.5, 9.1, 9, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6, 65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3, 3.3, 3.4, 3.9, 2.9, 6.4, 7.2, 9.1, 8.5, 11.7, 12, 13.3, 13.2, 14.3, 12.1)), row.names = c(NA, -170L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = value ~ time | ds, FUN = function (x) max(x, na.rm = TRUE), order.groups = FALSE), start = list( fixed = c(parent_0 = 93.4272167134207, log_k_A1 = -9.71590717106959, f_parent_qlogis = -0.953712099744438, log_k1 = -1.95256957646888, log_k2 = -4.42919226610318, g_qlogis = 0.193023137298073 ), random = list(ds = structure(c(2.85557330683041, -3.87630303729395, -2.78062140212751, 4.82042042600536, -1.01906929341432, 4.613992019697, 2.05871276943309, 6.0766404049189, 4.86471337131288, -17.6140585653619, -0.480721175257541, 0.773079218835614, 0.260464433006093, -0.440615012802434, -0.112207463781733, 0.445812953745225, -1.49588630006094, 1.13602040717272, 0.801850880762046, -0.887797941619048, 0.936480292463262, -2.43093808171905, 1.91256225793793, 0.984827519864443, -1.40293198854659, -0.455176326336681, 0.376355651864385, 0.343919720700401, 0.46329187713133, -0.728390923359434 ), .Dim = 5:6, .Dimnames = list(c("1", "2", "3", "4", "5"), c("parent_0", "log_k_A1", "f_parent_qlogis", "log_k1", "log_k2", "g_qlogis"))))), fixed = list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = structure(list(parent_0 ~ 1, log_k_A1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1), class = "listForm"), Dimnames = list(NULL, NULL)), weights = structure(numeric(0), formula = ~1 | name, class = c("varIdent", "varFunc"))): maximum number of iterations (maxIter = 50) reached without convergence</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 59.38 16.5 53.5</span></div><div class='input'>
- <span class='va'>f_2_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
- <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
- <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
- <span class='co'># f_nlme_sfo_sfo_tc &lt;- nlme(f_2_tc["SFO-SFO", ]) # stops with error message</span>
- <span class='va'>f_nlme_dfop_sfo_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='warning'>Warning: longer object length is not a multiple of shorter object length</span></div><div class='output co'>#&gt; <span class='error'>Error in X[, fmap[[nm]]] &lt;- gradnm: number of items to replace is not a multiple of replacement length</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 6.363 2.688 5.469</span></div><div class='input'> <span class='co'># We get warnings about false convergence in the LME step in several iterations</span>
- <span class='co'># but as the last such warning occurs in iteration 25 and we have 28 iterations</span>
- <span class='co'># we can ignore these</span>
- <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_dfop_sfo_obs</span>, <span class='va'>f_nlme_dfop_sfo_tc</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs, f_nlme_dfop_sfo_tc): object 'f_nlme_dfop_sfo' not found</span></div><div class='input'>
+#&gt; 1.0000000 0.2049995 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>,
+ control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span><span class='op'>)</span>
+
+ <span class='va'>f_2_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
+ <span class='co'># f_nlme_sfo_sfo_tc &lt;- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</span>
+ <span class='co'># f_nlme_dfop_sfo_tc &lt;- nlme(f_2_tc["DFOP-SFO", ],</span>
+ <span class='co'># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] &lt;- gradnm</span>
+
+ <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_dfop_sfo_obs</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Model df AIC BIC logLik Test L.Ratio
+#&gt; f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274
+#&gt; f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093
+#&gt; p-value
+#&gt; f_nlme_dfop_sfo
+#&gt; f_nlme_dfop_sfo_obs &lt;.0001</div><div class='input'>
<span class='co'># }</span>
</div></pre>
</div>
diff --git a/docs/dev/reference/nobs.mkinfit.html b/docs/dev/reference/nobs.mkinfit.html
index 621eb622..0b6c963c 100644
--- a/docs/dev/reference/nobs.mkinfit.html
+++ b/docs/dev/reference/nobs.mkinfit.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html
index ba0e89bb..9f6f4225 100644
--- a/docs/dev/reference/parms.html
+++ b/docs/dev/reference/parms.html
@@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -123,7 +123,7 @@ considering the error structure that was assumed for the fit." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -219,10 +219,10 @@ such matrices is returned.</p>
#&gt;
#&gt; $DFOP
#&gt; Dataset 7
-#&gt; parent_0 91.058971597
+#&gt; parent_0 91.058971589
#&gt; k1 0.044946770
#&gt; k2 0.002868336
-#&gt; g 0.526942414
+#&gt; g 0.526942415
#&gt; sigma 2.221302196
#&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $SFO
@@ -233,17 +233,17 @@ such matrices is returned.</p>
#&gt;
#&gt; $FOMC
#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458
+#&gt; parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459
#&gt; alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272
#&gt; beta 13.033315 14.1451255 5.007077 4.397126 6.9052224
#&gt; sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778
#&gt;
#&gt; $DFOP
#&gt; Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
-#&gt; parent_0 96.55213663 91.058971597 90.34509493 98.14858820 94.311323733
+#&gt; parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734
#&gt; k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857
#&gt; k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417
-#&gt; g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880
+#&gt; g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880
#&gt; sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831
#&gt; </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $SFO
diff --git a/docs/dev/reference/plot.mixed.mmkin-1.png b/docs/dev/reference/plot.mixed.mmkin-1.png
index 5cb33214..2224d96e 100644
--- a/docs/dev/reference/plot.mixed.mmkin-1.png
+++ b/docs/dev/reference/plot.mixed.mmkin-1.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-2.png b/docs/dev/reference/plot.mixed.mmkin-2.png
index c0d67204..28168495 100644
--- a/docs/dev/reference/plot.mixed.mmkin-2.png
+++ b/docs/dev/reference/plot.mixed.mmkin-2.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-3.png b/docs/dev/reference/plot.mixed.mmkin-3.png
index 5e00afe6..d18275dd 100644
--- a/docs/dev/reference/plot.mixed.mmkin-3.png
+++ b/docs/dev/reference/plot.mixed.mmkin-3.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin-4.png b/docs/dev/reference/plot.mixed.mmkin-4.png
index 6a5f3b9c..2fd52425 100644
--- a/docs/dev/reference/plot.mixed.mmkin-4.png
+++ b/docs/dev/reference/plot.mixed.mmkin-4.png
Binary files differ
diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
index 55c411e7..36796580 100644
--- a/docs/dev/reference/plot.mixed.mmkin.html
+++ b/docs/dev/reference/plot.mixed.mmkin.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span>
</span>
</div>
@@ -161,7 +161,7 @@
maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
- rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
+ rel.height.legend <span class='op'>=</span> <span class='fl'>0.02</span> <span class='op'>+</span> <span class='fl'>0.07</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
@@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.</p></td>
</div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span>, transformations <span class='op'>=</span> <span class='st'>"saemix"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Dec 21 05:58:23 2020"
+#&gt; [1] "Tue Mar 9 17:34:35 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Dec 21 05:58:30 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
+#&gt; [1] "Tue Mar 9 17:34:42 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># We can overlay the two variants if we generate predictions</span>
<span class='va'>pred_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>,
diff --git a/docs/dev/reference/plot.mkinfit-2.png b/docs/dev/reference/plot.mkinfit-2.png
index 376c812f..a11d1680 100644
--- a/docs/dev/reference/plot.mkinfit-2.png
+++ b/docs/dev/reference/plot.mkinfit-2.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-5.png b/docs/dev/reference/plot.mkinfit-5.png
index bc44de88..6631aa68 100644
--- a/docs/dev/reference/plot.mkinfit-5.png
+++ b/docs/dev/reference/plot.mkinfit-5.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-6.png b/docs/dev/reference/plot.mkinfit-6.png
index eb8cbd92..946b20c5 100644
--- a/docs/dev/reference/plot.mkinfit-6.png
+++ b/docs/dev/reference/plot.mkinfit-6.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit-7.png b/docs/dev/reference/plot.mkinfit-7.png
index 92a664f4..10807ea8 100644
--- a/docs/dev/reference/plot.mkinfit-7.png
+++ b/docs/dev/reference/plot.mkinfit-7.png
Binary files differ
diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html
index c5bfb528..c5249ecd 100644
--- a/docs/dev/reference/plot.mkinfit.html
+++ b/docs/dev/reference/plot.mkinfit.html
@@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
diff --git a/docs/dev/reference/plot.mmkin-1.png b/docs/dev/reference/plot.mmkin-1.png
index f12b7907..647dfb8a 100644
--- a/docs/dev/reference/plot.mmkin-1.png
+++ b/docs/dev/reference/plot.mmkin-1.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin-2.png b/docs/dev/reference/plot.mmkin-2.png
index e3127554..1bc1c9db 100644
--- a/docs/dev/reference/plot.mmkin-2.png
+++ b/docs/dev/reference/plot.mmkin-2.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin-3.png b/docs/dev/reference/plot.mmkin-3.png
index 5448976e..50d6ffac 100644
--- a/docs/dev/reference/plot.mmkin-3.png
+++ b/docs/dev/reference/plot.mmkin-3.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin-4.png b/docs/dev/reference/plot.mmkin-4.png
index 9a25fc50..e049fa16 100644
--- a/docs/dev/reference/plot.mmkin-4.png
+++ b/docs/dev/reference/plot.mmkin-4.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin-5.png b/docs/dev/reference/plot.mmkin-5.png
index 82b422b5..2421995b 100644
--- a/docs/dev/reference/plot.mmkin-5.png
+++ b/docs/dev/reference/plot.mmkin-5.png
Binary files differ
diff --git a/docs/dev/reference/plot.mmkin.html b/docs/dev/reference/plot.mmkin.html
index ee80c6e4..9ca0df94 100644
--- a/docs/dev/reference/plot.mmkin.html
+++ b/docs/dev/reference/plot.mmkin.html
@@ -76,7 +76,7 @@ the fit of at least one model to the same dataset is shown." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
diff --git a/docs/dev/reference/plot.nafta.html b/docs/dev/reference/plot.nafta.html
index 9fc59f94..c24fba99 100644
--- a/docs/dev/reference/plot.nafta.html
+++ b/docs/dev/reference/plot.nafta.html
@@ -73,7 +73,7 @@ function (SFO, then IORE, then DFOP)." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ function (SFO, then IORE, then DFOP)." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/reexports.html b/docs/dev/reference/reexports.html
index f12a2690..371567d8 100644
--- a/docs/dev/reference/reexports.html
+++ b/docs/dev/reference/reexports.html
@@ -79,7 +79,7 @@ below to see their documentation.
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -128,7 +128,7 @@ below to see their documentation.
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
diff --git a/docs/dev/reference/residuals.mkinfit.html b/docs/dev/reference/residuals.mkinfit.html
index 95114dae..3f518ab7 100644
--- a/docs/dev/reference/residuals.mkinfit.html
+++ b/docs/dev/reference/residuals.mkinfit.html
@@ -72,7 +72,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -121,7 +121,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -175,7 +175,7 @@ standard deviation obtained from the fitted error model?</p></td>
</div><div class='output co'>#&gt; [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702
#&gt; [7] -0.03269080 1.45347823 -0.88423697</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>f</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208
-#&gt; [7] -0.04695354 2.08761977 -1.27002287</div></pre>
+#&gt; [7] -0.04695355 2.08761977 -1.27002287</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
diff --git a/docs/dev/reference/saem-1.png b/docs/dev/reference/saem-1.png
index 2df248bb..0da31388 100644
--- a/docs/dev/reference/saem-1.png
+++ b/docs/dev/reference/saem-1.png
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diff --git a/docs/dev/reference/saem-2.png b/docs/dev/reference/saem-2.png
index d4a2c1be..010950ba 100644
--- a/docs/dev/reference/saem-2.png
+++ b/docs/dev/reference/saem-2.png
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diff --git a/docs/dev/reference/saem-3.png b/docs/dev/reference/saem-3.png
index 6a32cda1..829f22bf 100644
--- a/docs/dev/reference/saem-3.png
+++ b/docs/dev/reference/saem-3.png
Binary files differ
diff --git a/docs/dev/reference/saem-4.png b/docs/dev/reference/saem-4.png
index bf24d6b0..4e976fa2 100644
--- a/docs/dev/reference/saem-4.png
+++ b/docs/dev/reference/saem-4.png
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diff --git a/docs/dev/reference/saem-5.png b/docs/dev/reference/saem-5.png
index 6e6e0f91..f50969b4 100644
--- a/docs/dev/reference/saem-5.png
+++ b/docs/dev/reference/saem-5.png
Binary files differ
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 59589378..23102df3 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span>
</span>
</div>
@@ -158,9 +158,12 @@ Expectation Maximisation algorithm (SAEM).</p>
<span class='va'>object</span>,
transformations <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"mkin"</span>, <span class='st'>"saemix"</span><span class='op'>)</span>,
degparms_start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></span><span class='op'>(</span><span class='op'>)</span>,
+ test_log_parms <span class='op'>=</span> <span class='cn'>FALSE</span>,
+ conf.level <span class='op'>=</span> <span class='fl'>0.6</span>,
solution_type <span class='op'>=</span> <span class='st'>"auto"</span>,
control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, print <span class='op'>=</span> <span class='cn'>FALSE</span>, save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span>
<span class='cn'>FALSE</span><span class='op'>)</span>,
+ fail_with_errors <span class='op'>=</span> <span class='cn'>TRUE</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
quiet <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
@@ -174,6 +177,7 @@ Expectation Maximisation algorithm (SAEM).</p>
solution_type <span class='op'>=</span> <span class='st'>"auto"</span>,
transformations <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"mkin"</span>, <span class='st'>"saemix"</span><span class='op'>)</span>,
degparms_start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></span><span class='op'>(</span><span class='op'>)</span>,
+ test_log_parms <span class='op'>=</span> <span class='cn'>FALSE</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
@@ -206,6 +210,18 @@ SFO or DFOP is used for the parent and there is either no metabolite or one.</p>
be used to override the starting values obtained from the 'mmkin' object.</p></td>
</tr>
<tr>
+ <th>test_log_parms</th>
+ <td><p>If TRUE, an attempt is made to use more robust starting
+values for population parameters fitted as log parameters in mkin (like
+rate constants) by only considering rate constants that pass the t-test
+when calculating mean degradation parameters using <a href='nlme_function.html'>mean_degparms</a>.</p></td>
+ </tr>
+ <tr>
+ <th>conf.level</th>
+ <td><p>Possibility to adjust the required confidence level
+for parameter that are tested if requested by 'test_log_parms'.</p></td>
+ </tr>
+ <tr>
<th>solution_type</th>
<td><p>Possibility to specify the solution type in case the
automatic choice is not desired</p></td>
@@ -215,6 +231,11 @@ automatic choice is not desired</p></td>
<td><p>Passed to <a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix::saemix</a></p></td>
</tr>
<tr>
+ <th>fail_with_errors</th>
+ <td><p>Should a failure to compute standard errors
+from the inverse of the Fisher Information Matrix be a failure?</p></td>
+ </tr>
+ <tr>
<th>verbose</th>
<td><p>Should we print information about created objects of
type <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> and <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a>?</p></td>
@@ -261,33 +282,36 @@ using <a href='mmkin.html'>mmkin</a>.</p>
state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:42 2021"
+#&gt; [1] "Tue Mar 9 17:34:44 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:43 2021"</div><div class='input'>
+#&gt; [1] "Tue Mar 9 17:34:45 2021"</div><div class='input'>
<span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:45 2021"
+#&gt; [1] "Tue Mar 9 17:34:46 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:46 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Tue Mar 9 17:34:48 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:47 2021"
+#&gt; [1] "Tue Mar 9 17:34:48 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:49 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Tue Mar 9 17:34:50 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:49 2021"
+#&gt; [1] "Tue Mar 9 17:34:51 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:41:52 2021"</div><div class='input'>
+#&gt; [1] "Tue Mar 9 17:34:53 2021"</div><div class='input'>
<span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span>
<span class='co'># functions from saemix</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Package saemix, version 3.1.9000</span>
-#&gt; <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_sfo</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_dfop</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
+#&gt; <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='va'>f_saem_sfo</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_dfop</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Likelihoods calculated by importance sampling</span></div><div class='output co'>#&gt; AIC BIC
+#&gt; 1 624.2484 622.2956
+#&gt; 2 467.7096 464.9757
+#&gt; 3 495.4373 491.9222</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"individual.fit"</span><span class='op'>)</span>
</div><div class='img'><img src='saem-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Plotting individual fits</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span>
</div><div class='img'><img src='saem-2.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Simulating data using nsim = 1000 simulated datasets
@@ -324,11 +348,13 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
<span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:41:55 2021"
+#&gt; [1] "Tue Mar 9 17:34:55 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:42:00 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'>
+#&gt; [1] "Tue Mar 9 17:35:00 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Likelihoods calculated by importance sampling</span></div><div class='output co'>#&gt; AIC BIC
+#&gt; 1 467.7096 464.9757
+#&gt; 2 469.6831 466.5586</div><div class='input'>
<span class='va'>sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fomc_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
@@ -346,15 +372,15 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='co'># four minutes</span>
<span class='va'>f_saem_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:42:02 2021"
+#&gt; [1] "Tue Mar 9 17:35:02 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:42:07 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Tue Mar 9 17:35:07 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 25 14:42:08 2021"
+#&gt; [1] "Tue Mar 9 17:35:07 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 25 14:42:17 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+#&gt; [1] "Tue Mar 9 17:35:15 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by SAEM
#&gt; Structural model:
@@ -395,10 +421,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; SD.g_qlogis 0.44771 -0.86417 1.7596</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
</div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
-#&gt; mkin version used for pre-fitting: 0.9.50.4
-#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Jan 25 14:42:18 2021
-#&gt; Date of summary: Mon Jan 25 14:42:18 2021
+#&gt; mkin version used for pre-fitting: 1.0.4.9000
+#&gt; R version used for fitting: 4.0.4
+#&gt; Date of fit: Tue Mar 9 17:35:16 2021
+#&gt; Date of summary: Tue Mar 9 17:35:16 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -413,7 +439,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 9.954 s using 300, 100 iterations
+#&gt; Fitted in 8.668 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;
@@ -489,12 +515,12 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Dataset 6 parent 3 69.2 71.32042 2.12042 1.883 1.125873
#&gt; Dataset 6 parent 6 58.1 56.45256 -1.64744 1.883 -0.874739
#&gt; Dataset 6 parent 6 56.6 56.45256 -0.14744 1.883 -0.078288
-#&gt; Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045256
+#&gt; Dataset 6 parent 10 44.4 44.48523 0.08523 1.883 0.045257
#&gt; Dataset 6 parent 10 43.4 44.48523 1.08523 1.883 0.576224
#&gt; Dataset 6 parent 20 33.3 29.75774 -3.54226 1.883 -1.880826
#&gt; Dataset 6 parent 20 29.2 29.75774 0.55774 1.883 0.296141
#&gt; Dataset 6 parent 34 17.6 19.35710 1.75710 1.883 0.932966
-#&gt; Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720578
+#&gt; Dataset 6 parent 34 18.0 19.35710 1.35710 1.883 0.720579
#&gt; Dataset 6 parent 55 10.5 10.48443 -0.01557 1.883 -0.008266
#&gt; Dataset 6 parent 55 9.3 10.48443 1.18443 1.883 0.628895
#&gt; Dataset 6 parent 90 4.5 3.78622 -0.71378 1.883 -0.378995
@@ -560,9 +586,9 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Dataset 8 parent 1 64.9 67.73197 2.83197 1.883 1.503686
#&gt; Dataset 8 parent 1 66.2 67.73197 1.53197 1.883 0.813428
#&gt; Dataset 8 parent 3 43.5 41.58448 -1.91552 1.883 -1.017081
-#&gt; Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335661
+#&gt; Dataset 8 parent 3 44.1 41.58448 -2.51552 1.883 -1.335662
#&gt; Dataset 8 parent 8 18.3 19.62286 1.32286 1.883 0.702395
-#&gt; Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808589
+#&gt; Dataset 8 parent 8 18.1 19.62286 1.52286 1.883 0.808588
#&gt; Dataset 8 parent 14 10.2 10.77819 0.57819 1.883 0.306999
#&gt; Dataset 8 parent 14 10.8 10.77819 -0.02181 1.883 -0.011582
#&gt; Dataset 8 parent 27 4.9 3.26977 -1.63023 1.883 -0.865599
@@ -575,13 +601,13 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Dataset 8 A1 1 7.7 7.61539 -0.08461 1.883 -0.044923
#&gt; Dataset 8 A1 3 15.0 15.47954 0.47954 1.883 0.254622
#&gt; Dataset 8 A1 3 15.1 15.47954 0.37954 1.883 0.201525
-#&gt; Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517076
+#&gt; Dataset 8 A1 8 21.2 20.22616 -0.97384 1.883 -0.517075
#&gt; Dataset 8 A1 8 21.1 20.22616 -0.87384 1.883 -0.463979
#&gt; Dataset 8 A1 14 19.7 20.00067 0.30067 1.883 0.159645
#&gt; Dataset 8 A1 14 18.9 20.00067 1.10067 1.883 0.584419
-#&gt; Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593929
-#&gt; Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255619
-#&gt; Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400123
+#&gt; Dataset 8 A1 27 17.5 16.38142 -1.11858 1.883 -0.593928
+#&gt; Dataset 8 A1 27 15.9 16.38142 0.48142 1.883 0.255620
+#&gt; Dataset 8 A1 48 9.5 10.25357 0.75357 1.883 0.400124
#&gt; Dataset 8 A1 48 9.8 10.25357 0.45357 1.883 0.240833
#&gt; Dataset 8 A1 70 6.2 5.95728 -0.24272 1.883 -0.128878
#&gt; Dataset 8 A1 70 6.1 5.95728 -0.14272 1.883 -0.075781
@@ -622,7 +648,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Dataset 9 A1 91 10.0 10.09177 0.09177 1.883 0.048727
#&gt; Dataset 9 A1 91 9.5 10.09177 0.59177 1.883 0.314211
#&gt; Dataset 9 A1 120 9.1 7.91379 -1.18621 1.883 -0.629841
-#&gt; Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576745
+#&gt; Dataset 9 A1 120 9.0 7.91379 -1.08621 1.883 -0.576744
#&gt; Dataset 10 parent 0 96.1 93.65257 -2.44743 1.883 -1.299505
#&gt; Dataset 10 parent 0 94.3 93.65257 -0.64743 1.883 -0.343763
#&gt; Dataset 10 parent 8 73.9 77.85906 3.95906 1.883 2.102132
diff --git a/docs/dev/reference/schaefer07_complex_case-1.png b/docs/dev/reference/schaefer07_complex_case-1.png
index 16e657dd..96aab2dc 100644
--- a/docs/dev/reference/schaefer07_complex_case-1.png
+++ b/docs/dev/reference/schaefer07_complex_case-1.png
Binary files differ
diff --git a/docs/dev/reference/schaefer07_complex_case.html b/docs/dev/reference/schaefer07_complex_case.html
index 83555b99..4ccad5c4 100644
--- a/docs/dev/reference/schaefer07_complex_case.html
+++ b/docs/dev/reference/schaefer07_complex_case.html
@@ -74,7 +74,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -123,7 +123,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -186,15 +186,15 @@
</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt; parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink
-#&gt; 0.3809620 0.1954665 0.4235715 0.0000000 0.4479662 0.5520338
+#&gt; 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 13.95078 46.34350
-#&gt; A1 49.75343 165.27731
-#&gt; B1 37.26912 123.80533
-#&gt; C1 11.23131 37.30959
-#&gt; A2 28.50569 94.69386
+#&gt; A1 49.75342 165.27728
+#&gt; B1 37.26908 123.80520
+#&gt; C1 11.23131 37.30961
+#&gt; A2 28.50624 94.69567
#&gt; </div><div class='input'> <span class='co'># }</span>
<span class='co'># Compare with the results obtained in the original publication</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_results</span><span class='op'>)</span>
diff --git a/docs/dev/reference/sigma_twocomp-1.png b/docs/dev/reference/sigma_twocomp-1.png
index 21db3145..6e61684e 100644
--- a/docs/dev/reference/sigma_twocomp-1.png
+++ b/docs/dev/reference/sigma_twocomp-1.png
Binary files differ
diff --git a/docs/dev/reference/sigma_twocomp.html b/docs/dev/reference/sigma_twocomp.html
index 8212e480..b7d295b2 100644
--- a/docs/dev/reference/sigma_twocomp.html
+++ b/docs/dev/reference/sigma_twocomp.html
@@ -73,7 +73,7 @@ dependence of the measured value \(y\):" />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@ dependence of the measured value \(y\):" />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -188,6 +188,10 @@ Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry
24(11), 1895-1898.</p>
<p>Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for
measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p>
+<p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical
+Degradation Data. <em>Environments</em> 6(12) 124
+doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6120124</a>
+.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='va'>times</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html
index f314dfa8..494731e9 100644
--- a/docs/dev/reference/summary.mkinfit.html
+++ b/docs/dev/reference/summary.mkinfit.html
@@ -76,7 +76,7 @@ values." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ values." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -236,17 +236,17 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<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://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>FOCUS_2006_A</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.4
+</div><div class='output co'>#&gt; mkin version used for fitting: 1.0.3.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Nov 30 16:01:20 2020
-#&gt; Date of summary: Mon Nov 30 16:01:20 2020
+#&gt; Date of fit: Mon Feb 15 17:13:09 2021
+#&gt; Date of summary: Mon Feb 15 17:13:09 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 131 model solutions performed in 0.028 s
+#&gt; Fitted using 131 model solutions performed in 0.027 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html
index 2aeadc46..b2f6624a 100644
--- a/docs/dev/reference/summary.nlme.mmkin.html
+++ b/docs/dev/reference/summary.nlme.mmkin.html
@@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -125,7 +125,7 @@ endpoints such as formation fractions and DT50 values. Optionally
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -263,12 +263,12 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
<span class='va'>f_mmkin</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
#&gt; <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; nlme version used for fitting: 3.1.150.1
-#&gt; mkin version used for pre-fitting: 0.9.50.4
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; nlme version used for fitting: 3.1.152
+#&gt; mkin version used for pre-fitting: 1.0.3.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Nov 30 16:01:23 2020
-#&gt; Date of summary: Mon Nov 30 16:01:23 2020
+#&gt; Date of fit: Mon Feb 15 17:13:12 2021
+#&gt; Date of summary: Mon Feb 15 17:13:12 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -278,148 +278,146 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 0.996 s using 6 iterations
+#&gt; Fitted in 0.544 s using 4 iterations
#&gt;
#&gt; Variance model: Two-component variance function
#&gt;
#&gt; Mean of starting values for individual parameters:
#&gt; parent_0 log_k_parent
-#&gt; 101.568773 -4.454103
+#&gt; 101.569 -4.454
#&gt;
#&gt; Fixed degradation parameter values:
#&gt; None
#&gt;
#&gt; Results:
#&gt;
-#&gt; AIC BIC logLik
-#&gt; 586.4159 603.9145 -286.2079
+#&gt; AIC BIC logLik
+#&gt; 584.5 599.5 -286.2
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
#&gt; lower est. upper
-#&gt; parent_0 99.360 101.593 103.825
-#&gt; log_k_parent -4.979 -4.451 -3.924
+#&gt; parent_0 99.371 101.592 103.814
+#&gt; log_k_parent -4.973 -4.449 -3.926
#&gt;
#&gt; Correlation:
#&gt; prnt_0
-#&gt; log_k_parent 0.155
+#&gt; log_k_parent 0.051
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k_parent ~ 1)
#&gt; Level: ds
-#&gt; Structure: General positive-definite, Log-Cholesky parametrization
-#&gt; StdDev Corr
-#&gt; parent_0 0.2624248 prnt_0
-#&gt; log_k_parent 0.5907146 0.999
-#&gt; Residual 1.0000000
+#&gt; Structure: Diagonal
+#&gt; parent_0 log_k_parent Residual
+#&gt; StdDev: 6.924e-05 0.5863 1
#&gt;
#&gt; Variance function:
#&gt; Structure: Constant plus proportion of variance covariate
#&gt; Formula: ~fitted(.)
#&gt; Parameter estimates:
-#&gt; const prop
-#&gt; 6.56706e-24 7.89583e-02
+#&gt; const prop
+#&gt; 0.0001208853 0.0789968036
#&gt;
#&gt; Backtransformed parameters with asymmetric confidence intervals:
#&gt; lower est. upper
-#&gt; parent_0 99.360213 101.59280 103.82539
-#&gt; k_parent 0.006883 0.01166 0.01976
+#&gt; parent_0 99.370882 101.59243 103.81398
+#&gt; k_parent 0.006923 0.01168 0.01972
#&gt;
#&gt; Estimated disappearance times:
#&gt; DT50 DT90
-#&gt; parent 59.44 197.4
+#&gt; parent 59.32 197.1
#&gt;
#&gt; Data:
#&gt; ds name time observed predicted residual std standardized
-#&gt; ds 1 parent 0 104.1 101.417 2.68283 8.0077 0.335030
-#&gt; ds 1 parent 0 105.0 101.417 3.58283 8.0077 0.447422
-#&gt; ds 1 parent 1 98.5 100.624 -2.12400 7.9451 -0.267334
-#&gt; ds 1 parent 1 96.1 100.624 -4.52400 7.9451 -0.569407
-#&gt; ds 1 parent 3 101.9 99.056 2.84379 7.8213 0.363595
-#&gt; ds 1 parent 3 85.2 99.056 -13.85621 7.8213 -1.771597
-#&gt; ds 1 parent 7 99.1 95.994 3.10646 7.5795 0.409850
-#&gt; ds 1 parent 7 93.0 95.994 -2.99354 7.5795 -0.394953
-#&gt; ds 1 parent 14 88.1 90.860 -2.75997 7.1741 -0.384710
-#&gt; ds 1 parent 14 84.1 90.860 -6.75997 7.1741 -0.942268
-#&gt; ds 1 parent 28 80.2 81.402 -1.20174 6.4273 -0.186973
-#&gt; ds 1 parent 28 91.3 81.402 9.89826 6.4273 1.540024
-#&gt; ds 1 parent 60 65.1 63.316 1.78361 4.9994 0.356767
-#&gt; ds 1 parent 60 65.8 63.316 2.48361 4.9994 0.496785
-#&gt; ds 1 parent 90 47.8 50.029 -2.22862 3.9502 -0.564182
-#&gt; ds 1 parent 90 53.5 50.029 3.47138 3.9502 0.878792
-#&gt; ds 1 parent 120 37.6 39.529 -1.92946 3.1212 -0.618182
-#&gt; ds 1 parent 120 39.3 39.529 -0.22946 3.1212 -0.073516
-#&gt; ds 2 parent 0 107.9 101.711 6.18875 8.0309 0.770613
-#&gt; ds 2 parent 0 102.1 101.711 0.38875 8.0309 0.048406
-#&gt; ds 2 parent 1 103.8 100.174 3.62597 7.9096 0.458428
-#&gt; ds 2 parent 1 108.6 100.174 8.42597 7.9096 1.065287
-#&gt; ds 2 parent 3 91.0 97.169 -6.16895 7.6723 -0.804055
-#&gt; ds 2 parent 3 84.9 97.169 -12.26895 7.6723 -1.599124
-#&gt; ds 2 parent 7 79.3 91.427 -12.12652 7.2189 -1.679833
-#&gt; ds 2 parent 7 100.9 91.427 9.47348 7.2189 1.312320
-#&gt; ds 2 parent 14 77.3 82.182 -4.88174 6.4889 -0.752318
-#&gt; ds 2 parent 14 83.5 82.182 1.31826 6.4889 0.203155
-#&gt; ds 2 parent 28 66.8 66.402 0.39792 5.2430 0.075895
-#&gt; ds 2 parent 28 63.3 66.402 -3.10208 5.2430 -0.591662
-#&gt; ds 2 parent 60 40.8 40.789 0.01138 3.2206 0.003532
-#&gt; ds 2 parent 60 44.8 40.789 4.01138 3.2206 1.245537
-#&gt; ds 2 parent 90 27.8 25.830 1.97002 2.0395 0.965937
-#&gt; ds 2 parent 90 27.0 25.830 1.17002 2.0395 0.573682
-#&gt; ds 2 parent 120 15.2 16.357 -1.15721 1.2915 -0.895991
-#&gt; ds 2 parent 120 15.5 16.357 -0.85721 1.2915 -0.663710
-#&gt; ds 3 parent 0 97.7 101.907 -4.20726 8.0464 -0.522873
-#&gt; ds 3 parent 0 88.2 101.907 -13.70726 8.0464 -1.703521
-#&gt; ds 3 parent 1 109.9 99.522 10.37805 7.8581 1.320685
-#&gt; ds 3 parent 1 97.8 99.522 -1.72195 7.8581 -0.219130
-#&gt; ds 3 parent 3 100.5 94.918 5.58248 7.4945 0.744875
-#&gt; ds 3 parent 3 77.4 94.918 -17.51752 7.4945 -2.337375
-#&gt; ds 3 parent 7 78.3 86.338 -8.03788 6.8171 -1.179077
-#&gt; ds 3 parent 7 90.3 86.338 3.96212 6.8171 0.581204
-#&gt; ds 3 parent 14 76.0 73.147 2.85281 5.7756 0.493944
-#&gt; ds 3 parent 14 79.1 73.147 5.95281 5.7756 1.030687
-#&gt; ds 3 parent 28 46.0 52.504 -6.50373 4.1456 -1.568826
-#&gt; ds 3 parent 28 53.4 52.504 0.89627 4.1456 0.216197
-#&gt; ds 3 parent 60 25.1 24.605 0.49461 1.9428 0.254586
-#&gt; ds 3 parent 60 21.4 24.605 -3.20539 1.9428 -1.649882
-#&gt; ds 3 parent 90 11.0 12.090 -1.09046 0.9546 -1.142271
-#&gt; ds 3 parent 90 14.2 12.090 2.10954 0.9546 2.209770
-#&gt; ds 3 parent 120 5.8 5.941 -0.14094 0.4691 -0.300464
-#&gt; ds 3 parent 120 6.1 5.941 0.15906 0.4691 0.339077
-#&gt; ds 4 parent 0 95.3 101.177 -5.87672 7.9887 -0.735625
-#&gt; ds 4 parent 0 102.0 101.177 0.82328 7.9887 0.103056
-#&gt; ds 4 parent 1 104.4 100.716 3.68438 7.9523 0.463307
-#&gt; ds 4 parent 1 105.4 100.716 4.68438 7.9523 0.589057
-#&gt; ds 4 parent 3 113.7 99.800 13.90026 7.8800 1.763989
-#&gt; ds 4 parent 3 82.3 99.800 -17.49974 7.8800 -2.220774
-#&gt; ds 4 parent 7 98.1 97.993 0.10713 7.7374 0.013846
-#&gt; ds 4 parent 7 87.8 97.993 -10.19287 7.7374 -1.317359
-#&gt; ds 4 parent 14 97.9 94.909 2.99079 7.4939 0.399098
-#&gt; ds 4 parent 14 104.8 94.909 9.89079 7.4939 1.319851
-#&gt; ds 4 parent 28 85.0 89.030 -4.02995 7.0297 -0.573279
-#&gt; ds 4 parent 28 77.2 89.030 -11.82995 7.0297 -1.682864
-#&gt; ds 4 parent 60 82.2 76.923 5.27690 6.0737 0.868808
-#&gt; ds 4 parent 60 86.1 76.923 9.17690 6.0737 1.510919
-#&gt; ds 4 parent 90 70.5 67.073 3.42743 5.2959 0.647182
-#&gt; ds 4 parent 90 61.7 67.073 -5.37257 5.2959 -1.014470
-#&gt; ds 4 parent 120 60.0 58.483 1.51654 4.6178 0.328416
-#&gt; ds 4 parent 120 56.4 58.483 -2.08346 4.6178 -0.451184
-#&gt; ds 5 parent 0 92.6 101.752 -9.15161 8.0341 -1.139091
-#&gt; ds 5 parent 0 116.5 101.752 14.74839 8.0341 1.835716
-#&gt; ds 5 parent 1 108.0 100.069 7.93112 7.9013 1.003778
-#&gt; ds 5 parent 1 104.9 100.069 4.83112 7.9013 0.611436
-#&gt; ds 5 parent 3 100.5 96.786 3.71355 7.6421 0.485934
-#&gt; ds 5 parent 3 89.5 96.786 -7.28645 7.6421 -0.953462
-#&gt; ds 5 parent 7 91.7 90.541 1.15895 7.1490 0.162114
-#&gt; ds 5 parent 7 95.1 90.541 4.55895 7.1490 0.637707
-#&gt; ds 5 parent 14 82.2 80.566 1.63437 6.3613 0.256923
-#&gt; ds 5 parent 14 84.5 80.566 3.93437 6.3613 0.618483
-#&gt; ds 5 parent 28 60.5 63.791 -3.29084 5.0368 -0.653357
-#&gt; ds 5 parent 28 72.8 63.791 9.00916 5.0368 1.788662
-#&gt; ds 5 parent 60 38.3 37.412 0.88840 2.9540 0.300748
-#&gt; ds 5 parent 60 40.7 37.412 3.28840 2.9540 1.113217
-#&gt; ds 5 parent 90 22.5 22.685 -0.18500 1.7912 -0.103287
-#&gt; ds 5 parent 90 20.8 22.685 -1.88500 1.7912 -1.052387
-#&gt; ds 5 parent 120 13.4 13.755 -0.35534 1.0861 -0.327173
-#&gt; ds 5 parent 120 13.8 13.755 0.04466 1.0861 0.041118</div><div class='input'>
+#&gt; ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451
+#&gt; ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594
+#&gt; ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313
+#&gt; ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725
+#&gt; ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796
+#&gt; ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812
+#&gt; ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081
+#&gt; ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065
+#&gt; ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987
+#&gt; ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480
+#&gt; ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857
+#&gt; ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364
+#&gt; ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008
+#&gt; ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898
+#&gt; ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252
+#&gt; ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335
+#&gt; ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423
+#&gt; ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549
+#&gt; ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943
+#&gt; ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245
+#&gt; ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361
+#&gt; ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626
+#&gt; ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297
+#&gt; ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874
+#&gt; ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251
+#&gt; ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647
+#&gt; ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366
+#&gt; ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571
+#&gt; ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748
+#&gt; ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002
+#&gt; ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679
+#&gt; ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485
+#&gt; ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198
+#&gt; ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171
+#&gt; ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595
+#&gt; ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547
+#&gt; ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009
+#&gt; ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739
+#&gt; ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858
+#&gt; ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921
+#&gt; ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603
+#&gt; ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360
+#&gt; ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813
+#&gt; ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620
+#&gt; ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848
+#&gt; ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722
+#&gt; ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842
+#&gt; ds 3 parent 28 53.4 52.394 1.00596 4.1390 0.243046
+#&gt; ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676
+#&gt; ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664
+#&gt; ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199
+#&gt; ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776
+#&gt; ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178
+#&gt; ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282
+#&gt; ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057
+#&gt; ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784
+#&gt; ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025
+#&gt; ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205
+#&gt; ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218
+#&gt; ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886
+#&gt; ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706
+#&gt; ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270
+#&gt; ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357
+#&gt; ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521
+#&gt; ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001
+#&gt; ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017
+#&gt; ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526
+#&gt; ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571
+#&gt; ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733
+#&gt; ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591
+#&gt; ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058
+#&gt; ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530
+#&gt; ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485
+#&gt; ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531
+#&gt; ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413
+#&gt; ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655
+#&gt; ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477
+#&gt; ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382
+#&gt; ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267
+#&gt; ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304
+#&gt; ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295
+#&gt; ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141
+#&gt; ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178
+#&gt; ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062
+#&gt; ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835
+#&gt; ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174
+#&gt; ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913
+#&gt; ds 5 parent 90 20.8 22.692 -1.89165 1.7926 -1.055273
+#&gt; ds 5 parent 120 13.4 13.768 -0.36790 1.0876 -0.338259
+#&gt; ds 5 parent 120 13.8 13.768 0.03210 1.0876 0.029517</div><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
index 722415fb..1166abb1 100644
--- a/docs/dev/reference/summary.saem.mmkin.html
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span>
</span>
</div>
@@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.</p>
quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span>
<span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Jan 11 12:42:40 2021"
+#&gt; [1] "Tue Mar 9 17:35:19 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Jan 11 12:42:53 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+#&gt; [1] "Tue Mar 9 17:35:30 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
-#&gt; mkin version used for pre-fitting: 0.9.50.4
-#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Jan 11 12:42:54 2021
-#&gt; Date of summary: Mon Jan 11 12:42:54 2021
+#&gt; mkin version used for pre-fitting: 1.0.4.9000
+#&gt; R version used for fitting: 4.0.4
+#&gt; Date of fit: Tue Mar 9 17:35:31 2021
+#&gt; Date of summary: Tue Mar 9 17:35:31 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 13.298 s using 300, 100 iterations
+#&gt; Fitted in 12.058 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Two-component variance function
#&gt;
@@ -291,7 +291,7 @@ saemix authors for the parts inherited from saemix.</p>
#&gt; parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2
#&gt; 101.65645 -4.05368 -0.94311 -2.35943 -4.07006
#&gt; g_qlogis
-#&gt; -0.01133
+#&gt; -0.01132
#&gt;
#&gt; Fixed degradation parameter values:
#&gt; None
@@ -299,232 +299,232 @@ saemix authors for the parts inherited from saemix.</p>
#&gt; Results:
#&gt;
#&gt; Likelihood computed by importance sampling
-#&gt; AIC BIC logLik
-#&gt; 830 824.5 -401
+#&gt; AIC BIC logLik
+#&gt; 825.9 820.4 -398.9
#&gt;
#&gt; Optimised parameters:
-#&gt; est. lower upper
-#&gt; parent_0 101.4423 97.862 105.0224
-#&gt; log_k_m1 -4.0703 -4.191 -3.9495
-#&gt; f_parent_qlogis -0.9539 -1.313 -0.5949
-#&gt; log_k1 -2.9724 -3.811 -2.1342
-#&gt; log_k2 -3.4977 -4.206 -2.7895
-#&gt; g_qlogis -0.0449 -1.116 1.0262
+#&gt; est. lower upper
+#&gt; parent_0 101.118986 97.368 104.8695
+#&gt; log_k_m1 -4.057591 -4.177 -3.9379
+#&gt; f_parent_qlogis -0.933087 -1.290 -0.5763
+#&gt; log_k1 -2.945520 -3.833 -2.0576
+#&gt; log_k2 -3.531954 -4.310 -2.7542
+#&gt; g_qlogis -0.009584 -1.688 1.6687
#&gt;
#&gt; Correlation:
#&gt; prnt_0 lg_k_1 f_prn_ log_k1 log_k2
-#&gt; log_k_m1 -0.207
-#&gt; f_parent_qlogis -0.148 0.202
-#&gt; log_k1 0.040 -0.038 -0.022
-#&gt; log_k2 0.022 -0.015 -0.009 0.001
-#&gt; g_qlogis -0.012 0.005 0.011 -0.173 -0.130
+#&gt; log_k_m1 -0.198
+#&gt; f_parent_qlogis -0.153 0.184
+#&gt; log_k1 0.080 -0.077 -0.045
+#&gt; log_k2 0.005 0.008 -0.003 -0.019
+#&gt; g_qlogis -0.059 0.048 0.041 -0.334 -0.253
#&gt;
#&gt; Random effects:
-#&gt; est. lower upper
-#&gt; SD.parent_0 2.88564 -0.5163 6.2876
-#&gt; SD.log_k_m1 0.08502 -0.0427 0.2127
-#&gt; SD.f_parent_qlogis 0.38857 0.1350 0.6421
-#&gt; SD.log_k1 0.92338 0.3296 1.5172
-#&gt; SD.log_k2 0.78644 0.2817 1.2912
-#&gt; SD.g_qlogis 0.34614 -0.8727 1.5650
+#&gt; est. lower upper
+#&gt; SD.parent_0 2.97797 -0.62927 6.5852
+#&gt; SD.log_k_m1 0.09235 -0.02448 0.2092
+#&gt; SD.f_parent_qlogis 0.38712 0.13469 0.6396
+#&gt; SD.log_k1 0.88671 0.27052 1.5029
+#&gt; SD.log_k2 0.80497 0.25587 1.3541
+#&gt; SD.g_qlogis 0.36812 -3.56188 4.2981
#&gt;
#&gt; Variance model:
#&gt; est. lower upper
-#&gt; a.1 0.65859 0.49250 0.82469
-#&gt; b.1 0.06411 0.05006 0.07817
+#&gt; a.1 0.85879 0.68143 1.03615
+#&gt; b.1 0.07787 0.06288 0.09286
#&gt;
#&gt; Backtransformed parameters:
#&gt; est. lower upper
-#&gt; parent_0 101.44231 97.86220 105.02241
-#&gt; k_m1 0.01707 0.01513 0.01926
-#&gt; f_parent_to_m1 0.27811 0.21201 0.35551
-#&gt; k1 0.05118 0.02213 0.11834
-#&gt; k2 0.03027 0.01491 0.06145
-#&gt; g 0.48878 0.24675 0.73618
+#&gt; parent_0 101.11899 97.36850 104.86947
+#&gt; k_m1 0.01729 0.01534 0.01949
+#&gt; f_parent_to_m1 0.28230 0.21587 0.35979
+#&gt; k1 0.05257 0.02163 0.12776
+#&gt; k2 0.02925 0.01344 0.06366
+#&gt; g 0.49760 0.15606 0.84140
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
-#&gt; parent_m1 0.2781
-#&gt; parent_sink 0.7219
+#&gt; parent_m1 0.2823
+#&gt; parent_sink 0.7177
#&gt;
#&gt; Estimated disappearance times:
#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
-#&gt; parent 17.53 61.64 18.55 13.54 22.9
-#&gt; m1 40.60 134.88 NA NA NA
+#&gt; parent 17.47 62.31 18.76 13.18 23.7
+#&gt; m1 40.09 133.17 NA NA NA
#&gt;
#&gt; Data:
-#&gt; ds name time observed predicted residual std standardized
-#&gt; ds 1 parent 0 89.8 9.869e+01 8.894553 6.3618 1.398124
-#&gt; ds 1 parent 0 104.1 9.869e+01 -5.405447 6.3618 -0.849676
-#&gt; ds 1 parent 1 88.7 9.413e+01 5.426448 6.0706 0.893897
-#&gt; ds 1 parent 1 95.5 9.413e+01 -1.373552 6.0706 -0.226265
-#&gt; ds 1 parent 3 81.8 8.576e+01 3.961821 5.5377 0.715422
-#&gt; ds 1 parent 3 94.5 8.576e+01 -8.738179 5.5377 -1.577932
-#&gt; ds 1 parent 7 71.5 7.168e+01 0.184828 4.6429 0.039809
-#&gt; ds 1 parent 7 70.3 7.168e+01 1.384828 4.6429 0.298270
-#&gt; ds 1 parent 14 54.2 5.351e+01 -0.688235 3.4934 -0.197008
-#&gt; ds 1 parent 14 49.6 5.351e+01 3.911765 3.4934 1.119747
-#&gt; ds 1 parent 28 31.5 3.209e+01 0.590445 2.1603 0.273322
-#&gt; ds 1 parent 28 28.8 3.209e+01 3.290445 2.1603 1.523177
-#&gt; ds 1 parent 60 12.1 1.272e+01 0.618158 1.0481 0.589761
-#&gt; ds 1 parent 60 13.6 1.272e+01 -0.881842 1.0481 -0.841332
-#&gt; ds 1 parent 90 6.2 6.085e+00 -0.115212 0.7655 -0.150512
-#&gt; ds 1 parent 90 8.3 6.085e+00 -2.215212 0.7655 -2.893953
-#&gt; ds 1 parent 120 2.2 3.009e+00 0.809439 0.6863 1.179470
-#&gt; ds 1 parent 120 2.4 3.009e+00 0.609439 0.6863 0.888041
-#&gt; ds 1 m1 1 0.3 1.129e+00 0.828817 0.6626 1.250938
-#&gt; ds 1 m1 1 0.2 1.129e+00 0.928817 0.6626 1.401869
-#&gt; ds 1 m1 3 2.2 3.141e+00 0.940880 0.6887 1.366187
-#&gt; ds 1 m1 3 3.0 3.141e+00 0.140880 0.6887 0.204562
-#&gt; ds 1 m1 7 6.5 6.326e+00 -0.174162 0.7735 -0.225175
-#&gt; ds 1 m1 7 5.0 6.326e+00 1.325838 0.7735 1.714181
-#&gt; ds 1 m1 14 10.2 9.883e+00 -0.317417 0.9139 -0.347326
-#&gt; ds 1 m1 14 9.5 9.883e+00 0.382583 0.9139 0.418631
-#&gt; ds 1 m1 28 12.2 1.251e+01 0.309856 1.0378 0.298572
-#&gt; ds 1 m1 28 13.4 1.251e+01 -0.890144 1.0378 -0.857726
-#&gt; ds 1 m1 60 11.8 1.086e+01 -0.940009 0.9584 -0.980812
-#&gt; ds 1 m1 60 13.2 1.086e+01 -2.340009 0.9584 -2.441581
-#&gt; ds 1 m1 90 6.6 7.823e+00 1.222977 0.8278 1.477332
-#&gt; ds 1 m1 90 9.3 7.823e+00 -1.477023 0.8278 -1.784214
-#&gt; ds 1 m1 120 3.5 5.315e+00 1.815201 0.7415 2.447906
-#&gt; ds 1 m1 120 5.4 5.315e+00 -0.084799 0.7415 -0.114356
-#&gt; ds 2 parent 0 118.0 1.031e+02 -14.876736 6.6443 -2.239038
-#&gt; ds 2 parent 0 99.8 1.031e+02 3.323264 6.6443 0.500171
-#&gt; ds 2 parent 1 90.2 9.757e+01 7.371379 6.2902 1.171891
-#&gt; ds 2 parent 1 94.6 9.757e+01 2.971379 6.2902 0.472386
-#&gt; ds 2 parent 3 96.1 8.788e+01 -8.222746 5.6724 -1.449599
-#&gt; ds 2 parent 3 78.4 8.788e+01 9.477254 5.6724 1.670758
-#&gt; ds 2 parent 7 77.9 7.293e+01 -4.972272 4.7218 -1.053054
-#&gt; ds 2 parent 7 77.7 7.293e+01 -4.772272 4.7218 -1.010697
-#&gt; ds 2 parent 14 56.0 5.602e+01 0.016773 3.6513 0.004594
-#&gt; ds 2 parent 14 54.7 5.602e+01 1.316773 3.6513 0.360633
-#&gt; ds 2 parent 28 36.6 3.855e+01 1.945779 2.5575 0.760803
-#&gt; ds 2 parent 28 36.8 3.855e+01 1.745779 2.5575 0.682603
-#&gt; ds 2 parent 60 22.1 2.101e+01 -1.086693 1.4996 -0.724663
-#&gt; ds 2 parent 60 24.7 2.101e+01 -3.686693 1.4996 -2.458475
-#&gt; ds 2 parent 90 12.4 1.246e+01 0.058759 1.0353 0.056757
-#&gt; ds 2 parent 90 10.8 1.246e+01 1.658759 1.0353 1.602256
-#&gt; ds 2 parent 120 6.8 7.406e+00 0.606226 0.8119 0.746659
-#&gt; ds 2 parent 120 7.9 7.406e+00 -0.493774 0.8119 -0.608157
-#&gt; ds 2 m1 1 1.3 1.438e+00 0.138236 0.6650 0.207869
-#&gt; ds 2 m1 3 3.7 3.879e+00 0.178617 0.7040 0.253726
-#&gt; ds 2 m1 3 4.7 3.879e+00 -0.821383 0.7040 -1.166780
-#&gt; ds 2 m1 7 8.1 7.389e+00 -0.710951 0.8113 -0.876337
-#&gt; ds 2 m1 7 7.9 7.389e+00 -0.510951 0.8113 -0.629812
-#&gt; ds 2 m1 14 10.1 1.069e+01 0.593533 0.9507 0.624328
-#&gt; ds 2 m1 14 10.3 1.069e+01 0.393533 0.9507 0.413951
-#&gt; ds 2 m1 28 10.7 1.240e+01 1.703647 1.0325 1.649956
-#&gt; ds 2 m1 28 12.2 1.240e+01 0.203647 1.0325 0.197229
-#&gt; ds 2 m1 60 10.7 1.055e+01 -0.147672 0.9442 -0.156405
-#&gt; ds 2 m1 60 12.5 1.055e+01 -1.947672 0.9442 -2.062848
-#&gt; ds 2 m1 90 9.1 8.010e+00 -1.090041 0.8351 -1.305210
-#&gt; ds 2 m1 90 7.4 8.010e+00 0.609959 0.8351 0.730362
-#&gt; ds 2 m1 120 6.1 5.793e+00 -0.306797 0.7561 -0.405759
-#&gt; ds 2 m1 120 4.5 5.793e+00 1.293203 0.7561 1.710347
-#&gt; ds 3 parent 0 106.2 1.035e+02 -2.712344 6.6675 -0.406801
-#&gt; ds 3 parent 0 106.9 1.035e+02 -3.412344 6.6675 -0.511788
-#&gt; ds 3 parent 1 107.4 9.548e+01 -11.924044 6.1566 -1.936801
-#&gt; ds 3 parent 1 96.1 9.548e+01 -0.624044 6.1566 -0.101362
-#&gt; ds 3 parent 3 79.4 8.246e+01 3.056105 5.3274 0.573662
-#&gt; ds 3 parent 3 82.6 8.246e+01 -0.143895 5.3274 -0.027010
-#&gt; ds 3 parent 7 63.9 6.489e+01 0.991141 4.2122 0.235304
-#&gt; ds 3 parent 7 62.4 6.489e+01 2.491141 4.2122 0.591416
-#&gt; ds 3 parent 14 51.0 4.869e+01 -2.306824 3.1906 -0.723013
-#&gt; ds 3 parent 14 47.1 4.869e+01 1.593176 3.1906 0.499338
-#&gt; ds 3 parent 28 36.1 3.480e+01 -1.304261 2.3260 -0.560722
-#&gt; ds 3 parent 28 36.6 3.480e+01 -1.804261 2.3260 -0.775679
-#&gt; ds 3 parent 60 20.1 1.988e+01 -0.221952 1.4346 -0.154719
-#&gt; ds 3 parent 60 19.8 1.988e+01 0.078048 1.4346 0.054406
-#&gt; ds 3 parent 90 11.3 1.194e+01 0.642458 1.0099 0.636132
-#&gt; ds 3 parent 90 10.7 1.194e+01 1.242458 1.0099 1.230224
-#&gt; ds 3 parent 120 8.2 7.176e+00 -1.023847 0.8034 -1.274423
-#&gt; ds 3 parent 120 7.3 7.176e+00 -0.123847 0.8034 -0.154158
-#&gt; ds 3 m1 0 0.8 8.527e-13 -0.800000 0.6586 -1.214712
-#&gt; ds 3 m1 1 1.8 1.856e+00 0.055925 0.6693 0.083562
-#&gt; ds 3 m1 1 2.3 1.856e+00 -0.444075 0.6693 -0.663537
-#&gt; ds 3 m1 3 4.2 4.780e+00 0.580164 0.7264 0.798676
-#&gt; ds 3 m1 3 4.1 4.780e+00 0.680164 0.7264 0.936340
-#&gt; ds 3 m1 7 6.8 8.410e+00 1.609920 0.8512 1.891455
-#&gt; ds 3 m1 7 10.1 8.410e+00 -1.690080 0.8512 -1.985633
-#&gt; ds 3 m1 14 11.4 1.098e+01 -0.424444 0.9638 -0.440389
-#&gt; ds 3 m1 14 12.8 1.098e+01 -1.824444 0.9638 -1.892979
-#&gt; ds 3 m1 28 11.5 1.142e+01 -0.079336 0.9848 -0.080558
-#&gt; ds 3 m1 28 10.6 1.142e+01 0.820664 0.9848 0.833311
-#&gt; ds 3 m1 60 7.5 9.110e+00 1.610231 0.8803 1.829222
-#&gt; ds 3 m1 60 8.6 9.110e+00 0.510231 0.8803 0.579622
-#&gt; ds 3 m1 90 7.3 6.799e+00 -0.501085 0.7898 -0.634463
-#&gt; ds 3 m1 90 8.1 6.799e+00 -1.301085 0.7898 -1.647404
-#&gt; ds 3 m1 120 5.3 4.868e+00 -0.431505 0.7288 -0.592064
-#&gt; ds 3 m1 120 3.8 4.868e+00 1.068495 0.7288 1.466073
-#&gt; ds 4 parent 0 104.7 9.926e+01 -5.444622 6.3975 -0.851049
-#&gt; ds 4 parent 0 88.3 9.926e+01 10.955378 6.3975 1.712436
-#&gt; ds 4 parent 1 94.2 9.618e+01 1.978413 6.2013 0.319030
-#&gt; ds 4 parent 1 94.6 9.618e+01 1.578413 6.2013 0.254527
-#&gt; ds 4 parent 3 78.1 9.037e+01 12.268550 5.8311 2.103985
-#&gt; ds 4 parent 3 96.5 9.037e+01 -6.131450 5.8311 -1.051508
-#&gt; ds 4 parent 7 76.2 7.999e+01 3.794958 5.1708 0.733918
-#&gt; ds 4 parent 7 77.8 7.999e+01 2.194958 5.1708 0.424489
-#&gt; ds 4 parent 14 70.8 6.518e+01 -5.624996 4.2301 -1.329742
-#&gt; ds 4 parent 14 67.3 6.518e+01 -2.124996 4.2301 -0.502346
-#&gt; ds 4 parent 28 43.1 4.462e+01 1.517860 2.9354 0.517085
-#&gt; ds 4 parent 28 45.1 4.462e+01 -0.482140 2.9354 -0.164249
-#&gt; ds 4 parent 60 21.3 2.130e+01 -0.003305 1.5159 -0.002180
-#&gt; ds 4 parent 60 23.5 2.130e+01 -2.203305 1.5159 -1.453435
-#&gt; ds 4 parent 90 11.8 1.180e+01 0.002834 1.0032 0.002825
-#&gt; ds 4 parent 90 12.1 1.180e+01 -0.297166 1.0032 -0.296226
-#&gt; ds 4 parent 120 7.0 6.868e+00 -0.132251 0.7922 -0.166937
-#&gt; ds 4 parent 120 6.2 6.868e+00 0.667749 0.7922 0.842879
-#&gt; ds 4 m1 0 1.6 0.000e+00 -1.600000 0.6586 -2.429424
-#&gt; ds 4 m1 1 0.9 6.826e-01 -0.217363 0.6600 -0.329315
-#&gt; ds 4 m1 3 3.7 1.935e+00 -1.765082 0.6702 -2.633768
-#&gt; ds 4 m1 3 2.0 1.935e+00 -0.065082 0.6702 -0.097112
-#&gt; ds 4 m1 7 3.6 4.035e+00 0.434805 0.7076 0.614501
-#&gt; ds 4 m1 7 3.8 4.035e+00 0.234805 0.7076 0.331845
-#&gt; ds 4 m1 14 7.1 6.652e+00 -0.448187 0.7846 -0.571220
-#&gt; ds 4 m1 14 6.6 6.652e+00 0.051813 0.7846 0.066036
-#&gt; ds 4 m1 28 9.5 9.156e+00 -0.343805 0.8822 -0.389696
-#&gt; ds 4 m1 28 9.3 9.156e+00 -0.143805 0.8822 -0.163000
-#&gt; ds 4 m1 60 8.3 8.848e+00 0.547762 0.8692 0.630185
-#&gt; ds 4 m1 60 9.0 8.848e+00 -0.152238 0.8692 -0.175146
-#&gt; ds 4 m1 90 6.6 6.674e+00 0.073979 0.7854 0.094194
-#&gt; ds 4 m1 90 7.7 6.674e+00 -1.026021 0.7854 -1.306390
-#&gt; ds 4 m1 120 3.7 4.668e+00 0.967537 0.7234 1.337503
-#&gt; ds 4 m1 120 3.5 4.668e+00 1.167537 0.7234 1.613979
-#&gt; ds 5 parent 0 110.4 1.022e+02 -8.170986 6.5872 -1.240433
-#&gt; ds 5 parent 0 112.1 1.022e+02 -9.870986 6.5872 -1.498509
-#&gt; ds 5 parent 1 93.5 9.513e+01 1.630764 6.1346 0.265832
-#&gt; ds 5 parent 1 91.0 9.513e+01 4.130764 6.1346 0.673359
-#&gt; ds 5 parent 3 71.0 8.296e+01 11.964279 5.3597 2.232268
-#&gt; ds 5 parent 3 89.7 8.296e+01 -6.735721 5.3597 -1.256735
-#&gt; ds 5 parent 7 60.4 6.495e+01 4.547441 4.2157 1.078684
-#&gt; ds 5 parent 7 59.1 6.495e+01 5.847441 4.2157 1.387053
-#&gt; ds 5 parent 14 56.5 4.626e+01 -10.241319 3.0380 -3.371047
-#&gt; ds 5 parent 14 47.0 4.626e+01 -0.741319 3.0380 -0.244014
-#&gt; ds 5 parent 28 30.2 3.026e+01 0.058478 2.0487 0.028544
-#&gt; ds 5 parent 28 23.9 3.026e+01 6.358478 2.0487 3.103661
-#&gt; ds 5 parent 60 17.0 1.792e+01 0.919046 1.3242 0.694024
-#&gt; ds 5 parent 60 18.7 1.792e+01 -0.780954 1.3242 -0.589742
-#&gt; ds 5 parent 90 11.3 1.187e+01 0.573917 1.0066 0.570144
-#&gt; ds 5 parent 90 11.9 1.187e+01 -0.026083 1.0066 -0.025912
-#&gt; ds 5 parent 120 9.0 7.898e+00 -1.102089 0.8307 -1.326622
-#&gt; ds 5 parent 120 8.1 7.898e+00 -0.202089 0.8307 -0.243261
-#&gt; ds 5 m1 0 0.7 -1.421e-14 -0.700000 0.6586 -1.062873
-#&gt; ds 5 m1 1 3.0 3.144e+00 0.143526 0.6887 0.208390
-#&gt; ds 5 m1 1 2.6 3.144e+00 0.543526 0.6887 0.789161
-#&gt; ds 5 m1 3 5.1 8.390e+00 3.290265 0.8504 3.869277
-#&gt; ds 5 m1 3 7.5 8.390e+00 0.890265 0.8504 1.046932
-#&gt; ds 5 m1 7 16.5 1.566e+01 -0.841368 1.2007 -0.700751
-#&gt; ds 5 m1 7 19.0 1.566e+01 -3.341368 1.2007 -2.782928
-#&gt; ds 5 m1 14 22.9 2.188e+01 -1.017753 1.5498 -0.656687
-#&gt; ds 5 m1 14 23.2 2.188e+01 -1.317753 1.5498 -0.850257
-#&gt; ds 5 m1 28 22.2 2.386e+01 1.655914 1.6652 0.994399
-#&gt; ds 5 m1 28 24.4 2.386e+01 -0.544086 1.6652 -0.326731
-#&gt; ds 5 m1 60 15.5 1.859e+01 3.091124 1.3618 2.269915
-#&gt; ds 5 m1 60 19.8 1.859e+01 -1.208876 1.3618 -0.887718
-#&gt; ds 5 m1 90 14.9 1.372e+01 -1.176815 1.0990 -1.070784
-#&gt; ds 5 m1 90 14.2 1.372e+01 -0.476815 1.0990 -0.433854
-#&gt; ds 5 m1 120 10.9 9.961e+00 -0.938796 0.9174 -1.023332
-#&gt; ds 5 m1 120 10.4 9.961e+00 -0.438796 0.9174 -0.478308</div><div class='input'><span class='co'># }</span>
+#&gt; ds name time observed predicted residual std standardized
+#&gt; ds 1 parent 0 89.8 9.838e+01 8.584661 7.7094 1.113536
+#&gt; ds 1 parent 0 104.1 9.838e+01 -5.715339 7.7094 -0.741350
+#&gt; ds 1 parent 1 88.7 9.388e+01 5.182489 7.3611 0.704041
+#&gt; ds 1 parent 1 95.5 9.388e+01 -1.617511 7.3611 -0.219739
+#&gt; ds 1 parent 3 81.8 8.563e+01 3.825382 6.7229 0.569010
+#&gt; ds 1 parent 3 94.5 8.563e+01 -8.874618 6.7229 -1.320062
+#&gt; ds 1 parent 7 71.5 7.169e+01 0.188290 5.6482 0.033336
+#&gt; ds 1 parent 7 70.3 7.169e+01 1.388290 5.6482 0.245795
+#&gt; ds 1 parent 14 54.2 5.361e+01 -0.586595 4.2624 -0.137621
+#&gt; ds 1 parent 14 49.6 5.361e+01 4.013405 4.2624 0.941587
+#&gt; ds 1 parent 28 31.5 3.219e+01 0.688936 2.6496 0.260011
+#&gt; ds 1 parent 28 28.8 3.219e+01 3.388936 2.6496 1.279016
+#&gt; ds 1 parent 60 12.1 1.278e+01 0.678998 1.3145 0.516562
+#&gt; ds 1 parent 60 13.6 1.278e+01 -0.821002 1.3145 -0.624595
+#&gt; ds 1 parent 90 6.2 6.157e+00 -0.043461 0.9835 -0.044188
+#&gt; ds 1 parent 90 8.3 6.157e+00 -2.143461 0.9835 -2.179316
+#&gt; ds 1 parent 120 2.2 3.076e+00 0.876218 0.8916 0.982775
+#&gt; ds 1 parent 120 2.4 3.076e+00 0.676218 0.8916 0.758453
+#&gt; ds 1 m1 1 0.3 1.134e+00 0.833749 0.8633 0.965750
+#&gt; ds 1 m1 1 0.2 1.134e+00 0.933749 0.8633 1.081583
+#&gt; ds 1 m1 3 2.2 3.157e+00 0.957400 0.8933 1.071763
+#&gt; ds 1 m1 3 3.0 3.157e+00 0.157400 0.8933 0.176202
+#&gt; ds 1 m1 7 6.5 6.369e+00 -0.130995 0.9917 -0.132090
+#&gt; ds 1 m1 7 5.0 6.369e+00 1.369005 0.9917 1.380438
+#&gt; ds 1 m1 14 10.2 9.971e+00 -0.229362 1.1577 -0.198112
+#&gt; ds 1 m1 14 9.5 9.971e+00 0.470638 1.1577 0.406513
+#&gt; ds 1 m1 28 12.2 1.265e+01 0.447735 1.3067 0.342637
+#&gt; ds 1 m1 28 13.4 1.265e+01 -0.752265 1.3067 -0.575683
+#&gt; ds 1 m1 60 11.8 1.097e+01 -0.832027 1.2112 -0.686945
+#&gt; ds 1 m1 60 13.2 1.097e+01 -2.232027 1.2112 -1.842825
+#&gt; ds 1 m1 90 6.6 7.876e+00 1.275985 1.0553 1.209109
+#&gt; ds 1 m1 90 9.3 7.876e+00 -1.424015 1.0553 -1.349381
+#&gt; ds 1 m1 120 3.5 5.336e+00 1.835829 0.9540 1.924292
+#&gt; ds 1 m1 120 5.4 5.336e+00 -0.064171 0.9540 -0.067263
+#&gt; ds 2 parent 0 118.0 1.092e+02 -8.812058 8.5459 -1.031142
+#&gt; ds 2 parent 0 99.8 1.092e+02 9.387942 8.5459 1.098529
+#&gt; ds 2 parent 1 90.2 1.023e+02 12.114268 8.0135 1.511724
+#&gt; ds 2 parent 1 94.6 1.023e+02 7.714268 8.0135 0.962654
+#&gt; ds 2 parent 3 96.1 9.066e+01 -5.436165 7.1122 -0.764344
+#&gt; ds 2 parent 3 78.4 9.066e+01 12.263835 7.1122 1.724339
+#&gt; ds 2 parent 7 77.9 7.365e+01 -4.245773 5.7995 -0.732090
+#&gt; ds 2 parent 7 77.7 7.365e+01 -4.045773 5.7995 -0.697604
+#&gt; ds 2 parent 14 56.0 5.593e+01 -0.073803 4.4389 -0.016626
+#&gt; ds 2 parent 14 54.7 5.593e+01 1.226197 4.4389 0.276236
+#&gt; ds 2 parent 28 36.6 3.892e+01 2.320837 3.1502 0.736737
+#&gt; ds 2 parent 28 36.8 3.892e+01 2.120837 3.1502 0.673248
+#&gt; ds 2 parent 60 22.1 2.136e+01 -0.741020 1.8719 -0.395868
+#&gt; ds 2 parent 60 24.7 2.136e+01 -3.341020 1.8719 -1.784841
+#&gt; ds 2 parent 90 12.4 1.251e+01 0.113999 1.2989 0.087765
+#&gt; ds 2 parent 90 10.8 1.251e+01 1.713999 1.2989 1.319575
+#&gt; ds 2 parent 120 6.8 7.338e+00 0.537708 1.0315 0.521281
+#&gt; ds 2 parent 120 7.9 7.338e+00 -0.562292 1.0315 -0.545113
+#&gt; ds 2 m1 1 1.3 1.576e+00 0.276176 0.8675 0.318352
+#&gt; ds 2 m1 3 3.7 4.177e+00 0.476741 0.9183 0.519146
+#&gt; ds 2 m1 3 4.7 4.177e+00 -0.523259 0.9183 -0.569801
+#&gt; ds 2 m1 7 8.1 7.724e+00 -0.376365 1.0485 -0.358970
+#&gt; ds 2 m1 7 7.9 7.724e+00 -0.176365 1.0485 -0.168214
+#&gt; ds 2 m1 14 10.1 1.077e+01 0.674433 1.2006 0.561738
+#&gt; ds 2 m1 14 10.3 1.077e+01 0.474433 1.2006 0.395158
+#&gt; ds 2 m1 28 10.7 1.212e+01 1.416179 1.2758 1.110010
+#&gt; ds 2 m1 28 12.2 1.212e+01 -0.083821 1.2758 -0.065699
+#&gt; ds 2 m1 60 10.7 1.041e+01 -0.294930 1.1807 -0.249793
+#&gt; ds 2 m1 60 12.5 1.041e+01 -2.094930 1.1807 -1.774316
+#&gt; ds 2 m1 90 9.1 8.079e+00 -1.020859 1.0646 -0.958929
+#&gt; ds 2 m1 90 7.4 8.079e+00 0.679141 1.0646 0.637941
+#&gt; ds 2 m1 120 6.1 5.968e+00 -0.131673 0.9765 -0.134843
+#&gt; ds 2 m1 120 4.5 5.968e+00 1.468327 0.9765 1.503683
+#&gt; ds 3 parent 0 106.2 1.036e+02 -2.638248 8.1101 -0.325303
+#&gt; ds 3 parent 0 106.9 1.036e+02 -3.338248 8.1101 -0.411614
+#&gt; ds 3 parent 1 107.4 9.580e+01 -11.600063 7.5094 -1.544743
+#&gt; ds 3 parent 1 96.1 9.580e+01 -0.300063 7.5094 -0.039958
+#&gt; ds 3 parent 3 79.4 8.297e+01 3.574516 6.5182 0.548391
+#&gt; ds 3 parent 3 82.6 8.297e+01 0.374516 6.5182 0.057457
+#&gt; ds 3 parent 7 63.9 6.517e+01 1.272397 5.1472 0.247200
+#&gt; ds 3 parent 7 62.4 6.517e+01 2.772397 5.1472 0.538618
+#&gt; ds 3 parent 14 51.0 4.821e+01 -2.790075 3.8512 -0.724475
+#&gt; ds 3 parent 14 47.1 4.821e+01 1.109925 3.8512 0.288205
+#&gt; ds 3 parent 28 36.1 3.385e+01 -2.250573 2.7723 -0.811811
+#&gt; ds 3 parent 28 36.6 3.385e+01 -2.750573 2.7723 -0.992168
+#&gt; ds 3 parent 60 20.1 1.964e+01 -0.455700 1.7543 -0.259760
+#&gt; ds 3 parent 60 19.8 1.964e+01 -0.155700 1.7543 -0.088753
+#&gt; ds 3 parent 90 11.3 1.210e+01 0.795458 1.2746 0.624068
+#&gt; ds 3 parent 90 10.7 1.210e+01 1.395458 1.2746 1.094792
+#&gt; ds 3 parent 120 8.2 7.451e+00 -0.749141 1.0364 -0.722816
+#&gt; ds 3 parent 120 7.3 7.451e+00 0.150859 1.0364 0.145558
+#&gt; ds 3 m1 0 0.8 3.695e-13 -0.800000 0.8588 -0.931542
+#&gt; ds 3 m1 1 1.8 1.740e+00 -0.059741 0.8694 -0.068714
+#&gt; ds 3 m1 1 2.3 1.740e+00 -0.559741 0.8694 -0.643812
+#&gt; ds 3 m1 3 4.2 4.531e+00 0.331379 0.9285 0.356913
+#&gt; ds 3 m1 3 4.1 4.531e+00 0.431379 0.9285 0.464618
+#&gt; ds 3 m1 7 6.8 8.113e+00 1.312762 1.0661 1.231333
+#&gt; ds 3 m1 7 10.1 8.113e+00 -1.987238 1.0661 -1.863971
+#&gt; ds 3 m1 14 11.4 1.079e+01 -0.613266 1.2013 -0.510507
+#&gt; ds 3 m1 14 12.8 1.079e+01 -2.013266 1.2013 -1.675923
+#&gt; ds 3 m1 28 11.5 1.133e+01 -0.174252 1.2310 -0.141553
+#&gt; ds 3 m1 28 10.6 1.133e+01 0.725748 1.2310 0.589558
+#&gt; ds 3 m1 60 7.5 8.948e+00 1.448281 1.1059 1.309561
+#&gt; ds 3 m1 60 8.6 8.948e+00 0.348281 1.1059 0.314922
+#&gt; ds 3 m1 90 7.3 6.665e+00 -0.634932 1.0034 -0.632752
+#&gt; ds 3 m1 90 8.1 6.665e+00 -1.434932 1.0034 -1.430004
+#&gt; ds 3 m1 120 5.3 4.795e+00 -0.504936 0.9365 -0.539199
+#&gt; ds 3 m1 120 3.8 4.795e+00 0.995064 0.9365 1.062586
+#&gt; ds 4 parent 0 104.7 9.985e+01 -4.850494 7.8227 -0.620050
+#&gt; ds 4 parent 0 88.3 9.985e+01 11.549506 7.8227 1.476402
+#&gt; ds 4 parent 1 94.2 9.676e+01 2.556304 7.5834 0.337093
+#&gt; ds 4 parent 1 94.6 9.676e+01 2.156304 7.5834 0.284346
+#&gt; ds 4 parent 3 78.1 9.092e+01 12.817485 7.1318 1.797230
+#&gt; ds 4 parent 3 96.5 9.092e+01 -5.582515 7.1318 -0.782764
+#&gt; ds 4 parent 7 76.2 8.050e+01 4.297338 6.3270 0.679204
+#&gt; ds 4 parent 7 77.8 8.050e+01 2.697338 6.3270 0.426320
+#&gt; ds 4 parent 14 70.8 6.562e+01 -5.179989 5.1816 -0.999687
+#&gt; ds 4 parent 14 67.3 6.562e+01 -1.679989 5.1816 -0.324222
+#&gt; ds 4 parent 28 43.1 4.499e+01 1.886936 3.6069 0.523140
+#&gt; ds 4 parent 28 45.1 4.499e+01 -0.113064 3.6069 -0.031346
+#&gt; ds 4 parent 60 21.3 2.151e+01 0.214840 1.8827 0.114114
+#&gt; ds 4 parent 60 23.5 2.151e+01 -1.985160 1.8827 -1.054433
+#&gt; ds 4 parent 90 11.8 1.190e+01 0.098528 1.2633 0.077990
+#&gt; ds 4 parent 90 12.1 1.190e+01 -0.201472 1.2633 -0.159475
+#&gt; ds 4 parent 120 7.0 6.886e+00 -0.113832 1.0125 -0.112431
+#&gt; ds 4 parent 120 6.2 6.886e+00 0.686168 1.0125 0.677724
+#&gt; ds 4 m1 0 1.6 4.263e-14 -1.600000 0.8588 -1.863085
+#&gt; ds 4 m1 1 0.9 7.140e-01 -0.185984 0.8606 -0.216112
+#&gt; ds 4 m1 3 3.7 2.022e+00 -1.678243 0.8731 -1.922160
+#&gt; ds 4 m1 3 2.0 2.022e+00 0.021757 0.8731 0.024919
+#&gt; ds 4 m1 7 3.6 4.207e+00 0.607229 0.9192 0.660633
+#&gt; ds 4 m1 7 3.8 4.207e+00 0.407229 0.9192 0.443044
+#&gt; ds 4 m1 14 7.1 6.912e+00 -0.188339 1.0135 -0.185828
+#&gt; ds 4 m1 14 6.6 6.912e+00 0.311661 1.0135 0.307506
+#&gt; ds 4 m1 28 9.5 9.449e+00 -0.050714 1.1309 -0.044843
+#&gt; ds 4 m1 28 9.3 9.449e+00 0.149286 1.1309 0.132004
+#&gt; ds 4 m1 60 8.3 8.997e+00 0.697403 1.1083 0.629230
+#&gt; ds 4 m1 60 9.0 8.997e+00 -0.002597 1.1083 -0.002343
+#&gt; ds 4 m1 90 6.6 6.697e+00 0.096928 1.0047 0.096472
+#&gt; ds 4 m1 90 7.7 6.697e+00 -1.003072 1.0047 -0.998348
+#&gt; ds 4 m1 120 3.7 4.622e+00 0.921607 0.9312 0.989749
+#&gt; ds 4 m1 120 3.5 4.622e+00 1.121607 0.9312 1.204537
+#&gt; ds 5 parent 0 110.4 1.045e+02 -5.942426 8.1795 -0.726502
+#&gt; ds 5 parent 0 112.1 1.045e+02 -7.642426 8.1795 -0.934338
+#&gt; ds 5 parent 1 93.5 9.739e+01 3.893915 7.6327 0.510162
+#&gt; ds 5 parent 1 91.0 9.739e+01 6.393915 7.6327 0.837700
+#&gt; ds 5 parent 3 71.0 8.519e+01 14.188275 6.6891 2.121098
+#&gt; ds 5 parent 3 89.7 8.519e+01 -4.511725 6.6891 -0.674487
+#&gt; ds 5 parent 7 60.4 6.684e+01 6.439546 5.2753 1.220701
+#&gt; ds 5 parent 7 59.1 6.684e+01 7.739546 5.2753 1.467133
+#&gt; ds 5 parent 14 56.5 4.736e+01 -9.138979 3.7868 -2.413407
+#&gt; ds 5 parent 14 47.0 4.736e+01 0.361021 3.7868 0.095338
+#&gt; ds 5 parent 28 30.2 3.033e+01 0.131178 2.5132 0.052195
+#&gt; ds 5 parent 28 23.9 3.033e+01 6.431178 2.5132 2.558936
+#&gt; ds 5 parent 60 17.0 1.771e+01 0.705246 1.6243 0.434177
+#&gt; ds 5 parent 60 18.7 1.771e+01 -0.994754 1.6243 -0.612409
+#&gt; ds 5 parent 90 11.3 1.180e+01 0.504856 1.2580 0.401315
+#&gt; ds 5 parent 90 11.9 1.180e+01 -0.095144 1.2580 -0.075631
+#&gt; ds 5 parent 120 9.0 7.917e+00 -1.083499 1.0571 -1.024928
+#&gt; ds 5 parent 120 8.1 7.917e+00 -0.183499 1.0571 -0.173579
+#&gt; ds 5 m1 0 0.7 3.553e-15 -0.700000 0.8588 -0.815100
+#&gt; ds 5 m1 1 3.0 3.204e+00 0.204414 0.8943 0.228572
+#&gt; ds 5 m1 1 2.6 3.204e+00 0.604414 0.8943 0.675845
+#&gt; ds 5 m1 3 5.1 8.586e+00 3.485889 1.0884 3.202858
+#&gt; ds 5 m1 3 7.5 8.586e+00 1.085889 1.0884 0.997722
+#&gt; ds 5 m1 7 16.5 1.612e+01 -0.376855 1.5211 -0.247743
+#&gt; ds 5 m1 7 19.0 1.612e+01 -2.876855 1.5211 -1.891237
+#&gt; ds 5 m1 14 22.9 2.267e+01 -0.228264 1.9633 -0.116267
+#&gt; ds 5 m1 14 23.2 2.267e+01 -0.528264 1.9633 -0.269072
+#&gt; ds 5 m1 28 22.2 2.468e+01 2.480178 2.1050 1.178211
+#&gt; ds 5 m1 28 24.4 2.468e+01 0.280178 2.1050 0.133099
+#&gt; ds 5 m1 60 15.5 1.860e+01 3.099615 1.6838 1.840794
+#&gt; ds 5 m1 60 19.8 1.860e+01 -1.200385 1.6838 -0.712883
+#&gt; ds 5 m1 90 14.9 1.326e+01 -1.636345 1.3433 -1.218195
+#&gt; ds 5 m1 90 14.2 1.326e+01 -0.936345 1.3433 -0.697072
+#&gt; ds 5 m1 120 10.9 9.348e+00 -1.551535 1.1258 -1.378133
+#&gt; ds 5 m1 120 10.4 9.348e+00 -1.051535 1.1258 -0.934014</div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014-1.png b/docs/dev/reference/synthetic_data_for_UBA_2014-1.png
index 351b21aa..89975db5 100644
--- a/docs/dev/reference/synthetic_data_for_UBA_2014-1.png
+++ b/docs/dev/reference/synthetic_data_for_UBA_2014-1.png
Binary files differ
diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014.html b/docs/dev/reference/synthetic_data_for_UBA_2014.html
index 1edc7c1e..33a0ace2 100644
--- a/docs/dev/reference/synthetic_data_for_UBA_2014.html
+++ b/docs/dev/reference/synthetic_data_for_UBA_2014.html
@@ -87,7 +87,7 @@ Compare also the code in the example section to see the degradation models." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -136,7 +136,7 @@ Compare also the code in the example section to see the degradation models." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -297,10 +297,10 @@ Compare also the code in the example section to see the degradation models." />
quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.4
+</div><div class='output co'>#&gt; mkin version used for fitting: 1.0.3.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Nov 30 16:01:42 2020
-#&gt; Date of summary: Mon Nov 30 16:01:42 2020
+#&gt; Date of fit: Mon Feb 15 17:13:29 2021
+#&gt; Date of summary: Mon Feb 15 17:13:29 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -309,7 +309,7 @@ Compare also the code in the example section to see the degradation models." />
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 822 model solutions performed in 0.652 s
+#&gt; Fitted using 833 model solutions performed in 0.649 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -361,15 +361,15 @@ Compare also the code in the example section to see the degradation models." />
#&gt; log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01
#&gt; f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00
#&gt; f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01
-#&gt; sigma -7.941e-08 -9.143e-09 -1.268e-08 5.947e-08 5.657e-08
+#&gt; sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08
#&gt; f_M1_qlogis sigma
-#&gt; parent_0 1.614e-01 -7.941e-08
-#&gt; log_k_parent 4.102e-01 -9.143e-09
-#&gt; log_k_M1 -8.109e-01 -1.268e-08
-#&gt; log_k_M2 5.419e-01 5.947e-08
-#&gt; f_parent_qlogis -8.605e-01 5.657e-08
-#&gt; f_M1_qlogis 1.000e+00 -2.382e-10
-#&gt; sigma -2.382e-10 1.000e+00
+#&gt; parent_0 1.614e-01 -2.900e-08
+#&gt; log_k_parent 4.102e-01 -8.030e-09
+#&gt; log_k_M1 -8.109e-01 -2.741e-08
+#&gt; log_k_M2 5.419e-01 3.938e-08
+#&gt; f_parent_qlogis -8.605e-01 -2.681e-08
+#&gt; f_M1_qlogis 1.000e+00 4.971e-08
+#&gt; sigma 4.971e-08 1.000e+00
#&gt;
#&gt; Backtransformed parameters:
#&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -416,7 +416,7 @@ Compare also the code in the example section to see the degradation models." />
#&gt; 7 parent 0.3 5.772e-01 -0.27717
#&gt; 14 parent 3.5 3.264e-03 3.49674
#&gt; 28 parent 3.2 1.045e-07 3.20000
-#&gt; 90 parent 0.6 9.532e-10 0.60000
+#&gt; 90 parent 0.6 9.530e-10 0.60000
#&gt; 120 parent 3.5 -5.940e-10 3.50000
#&gt; 1 M1 36.4 3.479e+01 1.61088
#&gt; 1 M1 37.4 3.479e+01 2.61088
@@ -427,7 +427,7 @@ Compare also the code in the example section to see the degradation models." />
#&gt; 14 M1 5.8 1.995e+00 3.80469
#&gt; 14 M1 1.2 1.995e+00 -0.79531
#&gt; 60 M1 0.5 2.111e-06 0.50000
-#&gt; 90 M1 3.2 -9.671e-10 3.20000
+#&gt; 90 M1 3.2 -9.670e-10 3.20000
#&gt; 120 M1 1.5 7.670e-10 1.50000
#&gt; 120 M1 0.6 7.670e-10 0.60000
#&gt; 1 M2 4.8 4.455e+00 0.34517
diff --git a/docs/dev/reference/test_data_from_UBA_2014-1.png b/docs/dev/reference/test_data_from_UBA_2014-1.png
index 9e0afad2..7bf0bd0f 100644
--- a/docs/dev/reference/test_data_from_UBA_2014-1.png
+++ b/docs/dev/reference/test_data_from_UBA_2014-1.png
Binary files differ
diff --git a/docs/dev/reference/test_data_from_UBA_2014-2.png b/docs/dev/reference/test_data_from_UBA_2014-2.png
index e889efde..fc1f77e0 100644
--- a/docs/dev/reference/test_data_from_UBA_2014-2.png
+++ b/docs/dev/reference/test_data_from_UBA_2014-2.png
Binary files differ
diff --git a/docs/dev/reference/test_data_from_UBA_2014.html b/docs/dev/reference/test_data_from_UBA_2014.html
index 89ec3480..539b8287 100644
--- a/docs/dev/reference/test_data_from_UBA_2014.html
+++ b/docs/dev/reference/test_data_from_UBA_2014.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -122,7 +122,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -203,25 +203,25 @@
</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='op'>(</span><span class='va'>f_soil</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span><span class='op'>)</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://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; parent_0 76.55425649 0.859186399 89.1008710 1.113861e-26 74.755959406
+#&gt; parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418
#&gt; k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575
-#&gt; k_M1 0.84258614 0.806159820 1.0451850 1.545267e-01 0.113779670
-#&gt; k_M2 0.04210880 0.017083035 2.4649483 1.170188e-02 0.018013857
-#&gt; k_M3 0.01122918 0.007245855 1.5497385 6.885052e-02 0.002909431
-#&gt; f_parent_to_M1 0.32240200 0.240783909 1.3389682 9.819073e-02 NA
-#&gt; f_parent_to_M2 0.16099855 0.033691953 4.7785463 6.531137e-05 NA
-#&gt; f_M1_to_M3 0.27921507 0.269423745 1.0363417 1.565266e-01 0.022978220
-#&gt; f_M2_to_M3 0.55641253 0.595119954 0.9349586 1.807707e-01 0.008002509
+#&gt; k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609
+#&gt; k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857
+#&gt; k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431
+#&gt; f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA
+#&gt; f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA
+#&gt; f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205
+#&gt; f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509
#&gt; sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778
#&gt; Upper
-#&gt; parent_0 78.35255357
+#&gt; parent_0 78.35255358
#&gt; k_parent 0.13084582
-#&gt; k_M1 6.23970352
+#&gt; k_M1 6.23970702
#&gt; k_M2 0.09843260
#&gt; k_M3 0.04333992
#&gt; f_parent_to_M1 NA
#&gt; f_parent_to_M2 NA
-#&gt; f_M1_to_M3 0.86450768
+#&gt; f_M1_to_M3 0.86450775
#&gt; f_M2_to_M3 0.99489895
#&gt; sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span>
</div><div class='output co'>#&gt; err.min n.optim df
diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html
index 46b66073..75d6a1f9 100644
--- a/docs/dev/reference/transform_odeparms.html
+++ b/docs/dev/reference/transform_odeparms.html
@@ -77,7 +77,7 @@ the ilr transformation is used." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -126,7 +126,7 @@ the ilr transformation is used." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -231,50 +231,64 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</
<pre class="examples"><div class='input'>
<span class='va'>SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
- m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
-<span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+ m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
+<span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
+<span class='va'>FOCUS_D</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># remove zero values to avoid warning</span>
+<span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>fit.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
<span class='co'># Transformed and backtransformed parameters</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.5985 1.5702 96.404 102.79
-#&gt; log_k_parent -2.3157 0.0409 -2.399 -2.23
-#&gt; log_k_m1 -5.2475 0.1332 -5.518 -4.98
-#&gt; f_parent_qlogis 0.0579 0.0893 -0.124 0.24
-#&gt; sigma 3.1255 0.3585 2.396 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931
-#&gt; k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073
-#&gt; k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
-#&gt; f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596
-#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'>
+</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60 1.5702 96.40 102.79
+#&gt; log_k_parent_sink -3.04 0.0763 -3.19 -2.88
+#&gt; log_k_parent_m1 -2.98 0.0403 -3.06 -2.90
+#&gt; log_k_m1_sink -5.25 0.1332 -5.52 -4.98
+#&gt; sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931
+#&gt; k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560
+#&gt; k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551
+#&gt; k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
+#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'>
<span class='co'># \dontrun{</span>
-<span class='co'># Compare to the version without transforming rate parameters</span>
-<span class='va'>fit.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='error'>Error in if (cost &lt; cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.006 0 0.005</span></div><div class='input'><span class='va'>fit.2.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'fit.2' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found</span></div><div class='input'><span class='co'># }</span>
+<span class='co'># Compare to the version without transforming rate parameters (does not work</span>
+<span class='co'># with analytical solution, we get NA values for m1 in predictions)</span>
+<span class='va'>fit.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>,
+ solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>fit.2.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.59848 1.57022 96.40384 1.03e+02
+#&gt; k_parent_sink 0.04792 0.00365 0.04049 5.54e-02
+#&gt; k_parent_m1 0.05078 0.00205 0.04661 5.49e-02
+#&gt; k_m1_sink 0.00526 0.00070 0.00384 6.69e-03
+#&gt; sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02
+#&gt; k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02
+#&gt; k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02
+#&gt; k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03
+#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'><span class='co'># }</span>
<span class='va'>initials</span> <span class='op'>&lt;-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>$</span><span class='va'>value</span>
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>initials</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>)</span>
<span class='va'>transformed</span> <span class='op'>&lt;-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>$</span><span class='va'>value</span>
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>transformed</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>)</span>
<span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; parent_0 log_k_parent log_k_m1 f_parent_qlogis
-#&gt; 100.750000 -2.302585 -2.301586 0.000000 </div><div class='input'><span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1
-#&gt; 100.7500 0.1000 0.1001 0.5000 </div><div class='input'>
+</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
+#&gt; 100.7500 0.1000 0.1001 0.1002 </div><div class='input'>
<span class='co'># \dontrun{</span>
-<span class='co'># The case of formation fractions</span>
+<span class='co'># The case of formation fractions (this is now the default)</span>
<span class='va'>SFO_SFO.ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
-<span class='va'>fit.ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span>
+<span class='va'>fit.ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>fit.ff.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
#&gt; parent_0 99.5985 1.5702 96.404 102.79
@@ -299,8 +313,8 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</
use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
-<span class='va'>fit.ff.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='va'>fit.ff.2.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span>
+<span class='va'>fit.ff.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>fit.ff.2.s</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
#&gt; parent_0 84.79 3.012 78.67 90.91
diff --git a/docs/dev/reference/update.mkinfit-1.png b/docs/dev/reference/update.mkinfit-1.png
index 7d2f1bdb..df8473c1 100644
--- a/docs/dev/reference/update.mkinfit-1.png
+++ b/docs/dev/reference/update.mkinfit-1.png
Binary files differ
diff --git a/docs/dev/reference/update.mkinfit-2.png b/docs/dev/reference/update.mkinfit-2.png
index 8dcabcdc..13c99b44 100644
--- a/docs/dev/reference/update.mkinfit-2.png
+++ b/docs/dev/reference/update.mkinfit-2.png
Binary files differ
diff --git a/docs/dev/reference/update.mkinfit.html b/docs/dev/reference/update.mkinfit.html
index 10a93373..83f45028 100644
--- a/docs/dev/reference/update.mkinfit.html
+++ b/docs/dev/reference/update.mkinfit.html
@@ -75,7 +75,7 @@ override these starting values." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -124,7 +124,7 @@ override these starting values." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>

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