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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-09 23:14:39 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-09 23:14:39 +0100
commit0b677308e3ffbf742880f05cc54da469f3ecc854 (patch)
tree26dab561d6f5a31923b28b5fdf6c1859727dfe7f /docs/reference
parent5aec8e34680e05671347f7577ae36c9ad8e37063 (diff)
Another rebuild of the static docs
Now with rbenchmark installed, to get results for the compiled_models vignette
Diffstat (limited to 'docs/reference')
-rw-r--r--docs/reference/DFOP.solution-1.pngbin17865 -> 18578 bytes
-rw-r--r--docs/reference/DFOP.solution.html5
-rw-r--r--docs/reference/Extract.mmkin.html16
-rw-r--r--docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html8
-rw-r--r--docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html8
-rw-r--r--docs/reference/FOCUS_2006_HS_ref_A_to_F.html8
-rw-r--r--docs/reference/FOCUS_2006_SFO_ref_A_to_F.html8
-rw-r--r--docs/reference/FOCUS_2006_datasets.html4
-rw-r--r--docs/reference/FOMC.solution-1.pngbin17331 -> 18068 bytes
-rw-r--r--docs/reference/FOMC.solution.html8
-rw-r--r--docs/reference/HS.solution-1.pngbin17211 -> 17999 bytes
-rw-r--r--docs/reference/HS.solution.html5
-rw-r--r--docs/reference/IORE.solution-1.pngbin16988 -> 17721 bytes
-rw-r--r--docs/reference/IORE.solution.html5
-rw-r--r--docs/reference/SFO.solution.html4
-rw-r--r--docs/reference/SFORB.solution.html8
-rw-r--r--docs/reference/add_err-1.pngbin83052 -> 85947 bytes
-rw-r--r--docs/reference/add_err-2.pngbin47153 -> 48008 bytes
-rw-r--r--docs/reference/add_err-3.pngbin48003 -> 49035 bytes
-rw-r--r--docs/reference/add_err.html6
-rw-r--r--docs/reference/endpoints.html7
-rw-r--r--docs/reference/geometric_mean.html4
-rw-r--r--docs/reference/ilr.html4
-rw-r--r--docs/reference/index.html1
-rw-r--r--docs/reference/max_twa_parent.html8
-rw-r--r--docs/reference/mccall81_245T.html10
-rw-r--r--docs/reference/mkin_long_to_wide.html6
-rw-r--r--docs/reference/mkin_wide_to_long.html5
-rw-r--r--docs/reference/mkinds.html4
-rw-r--r--docs/reference/mkinerrmin.html5
-rw-r--r--docs/reference/mkinfit.html22
-rw-r--r--docs/reference/mkinmod.html9
-rw-r--r--docs/reference/mkinparplot-1.pngbin15186 -> 15645 bytes
-rw-r--r--docs/reference/mkinparplot.html5
-rw-r--r--docs/reference/mkinplot.html4
-rw-r--r--docs/reference/mkinpredict.html8
-rw-r--r--docs/reference/mkinresplot-1.pngbin13625 -> 14009 bytes
-rw-r--r--docs/reference/mkinresplot.html7
-rw-r--r--docs/reference/mkinsub.html5
-rw-r--r--docs/reference/mmkin.html5
-rw-r--r--docs/reference/plot.mkinfit-1.pngbin42225 -> 43100 bytes
-rw-r--r--docs/reference/plot.mkinfit-2.pngbin50584 -> 51815 bytes
-rw-r--r--docs/reference/plot.mkinfit-3.pngbin41316 -> 42604 bytes
-rw-r--r--docs/reference/plot.mkinfit-4.pngbin55160 -> 57866 bytes
-rw-r--r--docs/reference/plot.mkinfit.html9
-rw-r--r--docs/reference/plot.mmkin-1.pngbin31636 -> 32597 bytes
-rw-r--r--docs/reference/plot.mmkin-2.pngbin31920 -> 32965 bytes
-rw-r--r--docs/reference/plot.mmkin-3.pngbin24031 -> 24581 bytes
-rw-r--r--docs/reference/plot.mmkin.html8
-rw-r--r--docs/reference/print.mkinds.html4
-rw-r--r--docs/reference/print.mkinmod.html4
-rw-r--r--docs/reference/schaefer07_complex_case.html6
-rw-r--r--docs/reference/sigma_rl.html6
-rw-r--r--docs/reference/summary.mkinfit.html13
-rw-r--r--docs/reference/synthetic_data_for_UBA.html16
-rw-r--r--docs/reference/test_data_from_UBA_2014.html5
-rw-r--r--docs/reference/transform_odeparms.html18
57 files changed, 19 insertions, 282 deletions
diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png
index 1549a73b..e9268f94 100644
--- a/docs/reference/DFOP.solution-1.png
+++ b/docs/reference/DFOP.solution-1.png
Binary files differ
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index ff1ad823..f89a66e2 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -27,11 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" />
-
-<meta property="og:description" content="Function describing decline from a defined starting value using the sum
- of two exponential decline functions." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 11738484..3b96f9ae 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -27,10 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" />
-
-<meta property="og:description" content="Subsetting method for mmkin objects." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -263,7 +259,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.058 0.000 0.057
+#&gt; 0.06 0.00 0.06
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -452,8 +448,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555ad80908&gt;
-#&gt; &lt;environment: 0x55555b1b4b90&gt;
+#&gt; &lt;bytecode: 0x5555599fd348&gt;
+#&gt; &lt;environment: 0x555557684190&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -475,8 +471,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555b174428&gt;
-#&gt; &lt;environment: 0x55555b1b4b90&gt;
+#&gt; &lt;bytecode: 0x555559feb960&gt;
+#&gt; &lt;environment: 0x555557684190&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -543,7 +539,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Thu Mar 1 14:26:09 2018"
+#&gt; [1] "Fri Mar 9 23:08:11 2018"
#&gt;
#&gt; $version
#&gt; [1] "0.9.47.1"
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index 5fb3ccfe..de986f3f 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -27,14 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B" />
-
-<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values
-generated with different software packages. Taken directly from FOCUS (2006).
-The results from fitting the data with the Topfit software was removed, as
-the initial concentration of the parent compound was fixed to a value of 100
-in this fit." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index c1665dee..4bc0fd4b 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -27,14 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" />
-
-<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values
-generated with different software packages. Taken directly from FOCUS (2006).
-The results from fitting the data with the Topfit software was removed, as
-the initial concentration of the parent compound was fixed to a value of 100
-in this fit." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index db3d228d..bf0331cc 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -27,14 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F" />
-
-<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values
-generated with different software packages. Taken directly from FOCUS (2006).
-The results from fitting the data with the Topfit software was removed, as
-the initial concentration of the parent compound was fixed to a value of 100
-in this fit." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index cc4fcb1d..6f05cbb9 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -27,14 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F" />
-
-<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values
-generated with different software packages. Taken directly from FOCUS (2006).
-The results from fitting the data with the Topfit software was removed, as
-the initial concentration of the parent compound was fixed to a value of 100
-in this fit." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 4548c983..9ea69f23 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -27,10 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets" />
-
-<meta property="og:description" content="Data taken from FOCUS (2006), p. 258." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png
index 58178df5..f10cff4e 100644
--- a/docs/reference/FOMC.solution-1.png
+++ b/docs/reference/FOMC.solution-1.png
Binary files differ
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 810b0eba..b5b4c87c 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -27,14 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" />
-
-<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
- a decreasing rate constant.
-The form given here differs slightly from the original reference by Gustafson
- and Holden (1990). The parameter beta corresponds to 1/beta in the
- original equation." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png
index e259134e..5e04d343 100644
--- a/docs/reference/HS.solution-1.png
+++ b/docs/reference/HS.solution-1.png
Binary files differ
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 79358efb..0dc432ef 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -27,11 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Hockey-Stick kinetics — HS.solution" />
-
-<meta property="og:description" content="Function describing two exponential decline functions with a break point
- between them." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png
index 674c25d3..e421d562 100644
--- a/docs/reference/IORE.solution-1.png
+++ b/docs/reference/IORE.solution-1.png
Binary files differ
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index f705ab2f..b055534a 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -27,11 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" />
-
-<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
- a concentration dependent rate constant." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index a7934a35..eda43e4d 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -27,10 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Single First-Order kinetics — SFO.solution" />
-
-<meta property="og:description" content="Function describing exponential decline from a defined starting value." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index aaae7cdd..2b6b2bc6 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -27,14 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Single First-Order Reversible Binding kinetics — SFORB.solution" />
-
-<meta property="og:description" content="Function describing the solution of the differential equations describing
- the kinetic model with first-order terms for a two-way transfer from a free
- to a bound fraction, and a first-order degradation term for the free
- fraction. The initial condition is a defined amount in the free fraction and
- no substance in the bound fraction." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png
index 4f9b1534..fecfc52d 100644
--- a/docs/reference/add_err-1.png
+++ b/docs/reference/add_err-1.png
Binary files differ
diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png
index 8fcf4625..907001ed 100644
--- a/docs/reference/add_err-2.png
+++ b/docs/reference/add_err-2.png
Binary files differ
diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png
index e44839a6..3786d934 100644
--- a/docs/reference/add_err-3.png
+++ b/docs/reference/add_err-3.png
Binary files differ
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 42bec993..407e1a3e 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -27,12 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" />
-
-<meta property="og:description" content="Normally distributed errors are added to data predicted for a specific
- degradation model using mkinpredict. The variance of the error
- may depend on the predicted value and is specified as a standard deviation." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index c45a0b7c..4ab395cb 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -27,13 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints" />
-
-<meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions from kinetic models
-fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites,
-the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but
-with the advantage that the SFORB model can also be used for metabolites." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 2d46b4de..7e27c1dc 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -27,10 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Calculate the geometric mean — geometric_mean" />
-
-<meta property="og:description" content="Function calculating the geometric mean of numeric vectors" />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 2c51001f..7ed15db5 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -27,10 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" />
-
-<meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio transformations." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 218194ad..84bc1dfc 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -27,7 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Function reference" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 5d6baf6a..9e1e3974 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -27,14 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent" />
-
-<meta property="og:description" content="This function calculates maximum moving window time weighted average concentrations
-(TWAs) for kinetic models fitted with mkinfit. Currently, only
-calculations for the parent are implemented for the SFO, FOMC and DFOP models,
-using the analytical formulas given in the PEC soil section of the FOCUS
-guidance." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index ec7f8ccd..30aa894e 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -27,12 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" />
-
-<meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
- 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
- extracts." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -151,8 +145,8 @@
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.1
#&gt; R version used for fitting: 3.4.3
-#&gt; Date of fit: Thu Mar 1 14:26:15 2018
-#&gt; Date of summary: Thu Mar 1 14:26:15 2018
+#&gt; Date of fit: Fri Mar 9 23:08:18 2018
+#&gt; Date of summary: Fri Mar 9 23:08:18 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index a5432dac..dc781aaf 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -27,12 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide" />
-
-<meta property="og:description" content="This function takes a dataframe in the long form as required by modCost
- and converts it into a dataframe with one independent variable and several
- dependent variables as columns." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 6798efa6..2a8d20a3 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -27,11 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long" />
-
-<meta property="og:description" content="This function simply takes a dataframe with one independent variable and several
- dependent variable and converts it into the long form as required by modCost." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index ab06e903..fd707cfd 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -27,10 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="A dataset class for mkin — mkinds" />
-
-<meta property="og:description" content="A dataset class for mkin" />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 496cce15..045e5805 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -27,11 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" />
-
-<meta property="og:description" content="This function finds the smallest relative error still resulting in passing the
-chi-squared test as defined in the FOCUS kinetics report from 2006." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 4fb5ef9a..10052053 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -27,20 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" />
-
-<meta property="og:description" content="This function uses the Flexible Modelling Environment package
- FME to create a function calculating the model cost, i.e. the
- deviation between the kinetic model and the observed data. This model cost is
- then minimised using the Port algorithm nlminb,
- using the specified initial or fixed parameters and starting values.
- Per default, parameters in the kinetic models are internally transformed in order
- to better satisfy the assumption of a normal distribution of their estimators.
- In each step of the optimsation, the kinetic model is solved using the
- function mkinpredict. The variance of the residuals for each
- observed variable can optionally be iteratively reweighted until convergence
- using the argument reweight.method = "obs"." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -414,15 +400,15 @@
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.1
#&gt; R version used for fitting: 3.4.3
-#&gt; Date of fit: Thu Mar 1 14:26:18 2018
-#&gt; Date of summary: Thu Mar 1 14:26:18 2018
+#&gt; Date of fit: Fri Mar 9 23:08:20 2018
+#&gt; Date of summary: Fri Mar 9 23:08:20 2018
#&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 with method Port using 64 model solutions performed in 0.135 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.148 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -491,7 +477,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.84 0.00 0.84 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.839 0.000 0.840 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index c1287905..032fcbb6 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -27,15 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" />
-
-<meta property="og:description" content="The function usually takes several expressions, each assigning a compound name to
- a list, specifying the kinetic model type and reaction or transfer to other
- observed compartments. Instead of specifying several expressions, a list
- of lists can be given in the speclist argument.
-For the definition of model types and their parameters, the equations given
- in the FOCUS and NAFTA guidance documents are used." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png
index 42811535..1e7603d7 100644
--- a/docs/reference/mkinparplot-1.png
+++ b/docs/reference/mkinparplot-1.png
Binary files differ
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 30954168..e416d67c 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -27,11 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" />
-
-<meta property="og:description" content="This function plots the confidence intervals for the parameters
- fitted using mkinfit." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 5df3f872..e1ee1607 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -27,10 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — mkinplot" />
-
-<meta property="og:description" content="Deprecated function. It now only calls the plot method plot.mkinfit." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index df6316e1..7354c496 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -27,12 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" />
-
-<meta property="og:description" content="This function produces a time series for all the observed variables in a
- kinetic model as specified by mkinmod, using a specific set of
- kinetic parameters and initial values for the state variables." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -311,7 +305,7 @@
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png
index 8636baf2..5b201616 100644
--- a/docs/reference/mkinresplot-1.png
+++ b/docs/reference/mkinresplot-1.png
Binary files differ
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 036917f1..b4b6b116 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -27,13 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" />
-
-<meta property="og:description" content="This function plots the residuals for the specified subset of the
- observed variables from an mkinfit object. A combined plot of the fitted
- model and the residuals can be obtained using plot.mkinfit
- using the argument show_residuals = TRUE." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 7724220f..b4915112 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -27,11 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" />
-
-<meta property="og:description" content="This is a convenience function to set up the lists used as arguments for
- mkinmod." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index e97e3f81..78033dd2 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -27,11 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" />
-
-<meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets
- specified in its first two arguments." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png
index 2bb8f5dd..0d54d2fe 100644
--- a/docs/reference/plot.mkinfit-1.png
+++ b/docs/reference/plot.mkinfit-1.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png
index 22a3f8b0..377d63b6 100644
--- a/docs/reference/plot.mkinfit-2.png
+++ b/docs/reference/plot.mkinfit-2.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png
index 93e859c7..b23ddfe7 100644
--- a/docs/reference/plot.mkinfit-3.png
+++ b/docs/reference/plot.mkinfit-3.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png
index 27edd6f3..0dd9f4d6 100644
--- a/docs/reference/plot.mkinfit-4.png
+++ b/docs/reference/plot.mkinfit-4.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 4bdad93f..b6dd1525 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -27,15 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" />
-
-<meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters
- from a previous successful call to mkinfit and plots
- the observed data together with the solution of the fitted model.
-If the current plot device is a tikz device,
- then latex is being used for the formatting of the chi2 error level,
- if show_errmin = TRUE." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png
index 2554b68b..c2c25e90 100644
--- a/docs/reference/plot.mmkin-1.png
+++ b/docs/reference/plot.mmkin-1.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
index 9a66294f..b40ae0d5 100644
--- a/docs/reference/plot.mmkin-2.png
+++ b/docs/reference/plot.mmkin-2.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png
index b0f7fa21..dfbe014f 100644
--- a/docs/reference/plot.mmkin-3.png
+++ b/docs/reference/plot.mmkin-3.png
Binary files differ
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 11da6685..8b80273c 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -27,14 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin" />
-
-<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the same model
- fitted for at least one dataset is shown. When it is a column, the fit of at least one model
- to the same dataset is shown.
-If the current plot device is a tikz device,
- then latex is being used for the formatting of the chi2 error level." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 8e0d18b2..02882776 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -27,10 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Print mkinds objects — print.mkinds" />
-
-<meta property="og:description" content="Print mkinds objects." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index db15cc60..cd6678a6 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -27,10 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Print mkinmod objects — print.mkinmod" />
-
-<meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its components." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 6c53f805..04c72edd 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -27,12 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" />
-
-<meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the
- software quality of KinGUI in the original publication (Schäfer et al., 2007).
- The results from the fitting are also included." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html
index 868c0d4f..4b287e55 100644
--- a/docs/reference/sigma_rl.html
+++ b/docs/reference/sigma_rl.html
@@ -27,12 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Two component error model of Rocke and Lorenzato — sigma_rl" />
-
-<meta property="og:description" content="Function describing the standard deviation of the measurement error
- in dependence of the measured value \(y\):
-$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 977ff8d8..f34736b3 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -27,13 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" />
-
-<meta property="og:description" content="Lists model equations, the summary as returned by summary.modFit,
- the chi2 error levels calculated according to FOCUS guidance (2006) as far
- as defined therein, and optionally the data, consisting of observed, predicted
- and residual values." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -191,15 +184,15 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.1
#&gt; R version used for fitting: 3.4.3
-#&gt; Date of fit: Thu Mar 1 14:26:27 2018
-#&gt; Date of summary: Thu Mar 1 14:26:27 2018
+#&gt; Date of fit: Fri Mar 9 23:08:29 2018
+#&gt; Date of summary: Fri Mar 9 23:08:29 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.076 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.075 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 192e8dc2..396a6e2b 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -27,22 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" />
-
-<meta property="og:description" content="The 12 datasets were generated using four different models and three different
- variance components. The four models are either the SFO or the DFOP model with either
- two sequential or two parallel metabolites.
-Variance component 'a' is based on a normal distribution with standard deviation of 3,
- Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7.
- Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the
- minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07
- for the increase of the standard deviation with y.
-Initial concentrations for metabolites and all values where adding the variance component resulted
- in a value below the assumed limit of detection of 0.1 were set to NA.
-As an example, the first dataset has the title SFO_lin_a and is based on the SFO model
- with two sequential metabolites (linear pathway), with added variance component 'a'.
-Compare also the code in the example section to see the degradation models." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index c4292d9c..13e072c6 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -27,11 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" />
-
-<meta property="og:description" content="The datasets were used for the comparative validation of several kinetic evaluation
- software packages (Ranke, 2014)." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 630a5103..266db603 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -27,18 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" />
-
-<meta property="og:description" content="The transformations are intended to map parameters that should only take
- on restricted values to the full scale of real numbers. For kinetic rate
- constants and other paramters that can only take on positive values, a
- simple log transformation is used. For compositional parameters, such as
- the formations fractions that should always sum up to 1 and can not be
- negative, the ilr transformation is used.
-The transformation of sets of formation fractions is fragile, as it supposes
- the same ordering of the components in forward and backward transformation.
- This is no problem for the internal use in mkinfit." />
-<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -185,8 +173,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.1
#&gt; R version used for fitting: 3.4.3
-#&gt; Date of fit: Thu Mar 1 14:26:28 2018
-#&gt; Date of summary: Thu Mar 1 14:26:28 2018
+#&gt; Date of fit: Fri Mar 9 23:08:30 2018
+#&gt; Date of summary: Fri Mar 9 23:08:30 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -194,7 +182,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.571 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.657 s
#&gt;
#&gt; Weighting: none
#&gt;

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