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-rw-r--r--R/nafta.R10
-rw-r--r--docs/articles/FOCUS_D.html8
-rw-r--r--docs/articles/FOCUS_L.html42
-rw-r--r--docs/articles/index.html2
-rw-r--r--docs/articles/mkin.html2
-rw-r--r--docs/articles/twa.html2
-rw-r--r--docs/articles/web_only/FOCUS_Z.html2
-rw-r--r--docs/articles/web_only/compiled_models.html14
-rw-r--r--docs/authors.html2
-rw-r--r--docs/index.html2
-rw-r--r--docs/news/index.html2
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/AIC.mmkin.html2
-rw-r--r--docs/reference/CAKE_export.html2
-rw-r--r--docs/reference/DFOP.solution.html2
-rw-r--r--docs/reference/Extract.mmkin.html14
-rw-r--r--docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html2
-rw-r--r--docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_HS_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_SFO_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_datasets.html2
-rw-r--r--docs/reference/FOMC.solution.html2
-rw-r--r--docs/reference/HS.solution.html2
-rw-r--r--docs/reference/IORE.solution.html2
-rw-r--r--docs/reference/NAFTA_2015_datasets.html9
-rw-r--r--docs/reference/SFO.solution.html2
-rw-r--r--docs/reference/SFORB.solution.html2
-rw-r--r--docs/reference/add_err.html2
-rw-r--r--docs/reference/endpoints.html2
-rw-r--r--docs/reference/geometric_mean.html2
-rw-r--r--docs/reference/ilr.html2
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/logLik.mkinfit.html2
-rw-r--r--docs/reference/logistic.solution.html2
-rw-r--r--docs/reference/max_twa_parent.html2
-rw-r--r--docs/reference/mccall81_245T.html14
-rw-r--r--docs/reference/mkin_long_to_wide.html2
-rw-r--r--docs/reference/mkin_wide_to_long.html2
-rw-r--r--docs/reference/mkinds.html2
-rw-r--r--docs/reference/mkinerrmin.html2
-rw-r--r--docs/reference/mkinfit.html48
-rw-r--r--docs/reference/mkinmod.html4
-rw-r--r--docs/reference/mkinparplot.html2
-rw-r--r--docs/reference/mkinplot.html2
-rw-r--r--docs/reference/mkinpredict.html6
-rw-r--r--docs/reference/mkinresplot.html2
-rw-r--r--docs/reference/mkinsub.html2
-rw-r--r--docs/reference/mmkin.html6
-rw-r--r--docs/reference/nafta.html9
-rw-r--r--docs/reference/plot.mkinfit.html2
-rw-r--r--docs/reference/plot.mmkin.html2
-rw-r--r--docs/reference/plot.nafta.html2
-rw-r--r--docs/reference/print.mkinds.html2
-rw-r--r--docs/reference/print.mkinmod.html2
-rw-r--r--docs/reference/print.nafta.html2
-rw-r--r--docs/reference/schaefer07_complex_case.html2
-rw-r--r--docs/reference/sigma_twocomp.html2
-rw-r--r--docs/reference/summary.mkinfit.html8
-rw-r--r--docs/reference/synthetic_data_for_UBA.html2
-rw-r--r--docs/reference/test_data_from_UBA_2014.html2
-rw-r--r--docs/reference/transform_odeparms.html26
-rw-r--r--tests/testthat/test_plots_twa.R2
62 files changed, 165 insertions, 149 deletions
diff --git a/R/nafta.R b/R/nafta.R
index 102a9ad6..2af2404f 100644
--- a/R/nafta.R
+++ b/R/nafta.R
@@ -65,7 +65,10 @@ plot.nafta <- function(x, legend = FALSE, main = "auto", ...) {
}
print.nafta <- function(x, quiet = TRUE, ...) {
- cat("Parameters:\n")
+ cat("Sums of squares:\n")
+ print(x$S)
+ print(x$S_c)
+ cat("\nParameters:\n")
print(x$parameters)
t_rep <- .evaluate_nafta_results(x$S, x$S_c, x$distimes, quiet = quiet)
cat("\nDTx values:\n")
@@ -95,8 +98,9 @@ print.nafta <- function(x, quiet = TRUE, ...) {
t_rep <- t_IORE
} else {
if (!quiet) {
- message("The representative half-life of the IORE model is longer than the one corresponding to the terminal degradation rate found with the DFOP model.")
- message("The reprentative half-life obtained from the DFOP model may be used")
+ message("The representative half-life of the IORE model is longer than the one corresponding")
+ message("to the terminal degradation rate found with the DFOP model.")
+ message("The representative half-life obtained from the DFOP model may be used")
}
t_rep <- t_DFOP2
}
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index a470cdb6..0875ce0f 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -163,8 +163,8 @@
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Feb 25 14:54:38 2019
-## Date of summary: Mon Feb 25 14:54:38 2019
+## Date of fit: Mon Feb 25 15:25:02 2019
+## Date of summary: Mon Feb 25 15:25:02 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -172,7 +172,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.712 s
+## Fitted with method Port using 153 model solutions performed in 0.689 s
##
## Weighting: none
##
@@ -292,7 +292,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index e8a81075..14827789 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -111,8 +111,8 @@
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Feb 25 14:54:40 2019
-## Date of summary: Mon Feb 25 14:54:40 2019
+## Date of fit: Mon Feb 25 15:25:04 2019
+## Date of summary: Mon Feb 25 15:25:04 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -202,15 +202,15 @@
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Feb 25 14:54:42 2019
-## Date of summary: Mon Feb 25 14:54:42 2019
+## Date of fit: Mon Feb 25 15:25:06 2019
+## Date of summary: Mon Feb 25 15:25:06 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 611 model solutions performed in 1.529 s
+## Fitted with method Port using 611 model solutions performed in 1.516 s
##
## Weighting: none
##
@@ -297,15 +297,15 @@
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Feb 25 14:54:42 2019
-## Date of summary: Mon Feb 25 14:54:42 2019
+## Date of fit: Mon Feb 25 15:25:06 2019
+## Date of summary: Mon Feb 25 15:25:06 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.199 s
+## Fitted with method Port using 81 model solutions performed in 0.198 s
##
## Weighting: none
##
@@ -368,8 +368,8 @@
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Feb 25 14:54:44 2019
-## Date of summary: Mon Feb 25 14:54:44 2019
+## Date of fit: Mon Feb 25 15:25:07 2019
+## Date of summary: Mon Feb 25 15:25:07 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.853 s
+## Fitted with method Port using 336 model solutions performed in 0.85 s
##
## Weighting: none
##
@@ -460,8 +460,8 @@
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Feb 25 14:54:45 2019
-## Date of summary: Mon Feb 25 14:54:45 2019
+## Date of fit: Mon Feb 25 15:25:08 2019
+## Date of summary: Mon Feb 25 15:25:09 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.348 s
+## Fitted with method Port using 137 model solutions performed in 0.346 s
##
## Weighting: none
##
@@ -561,15 +561,15 @@
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Feb 25 14:54:45 2019
-## Date of summary: Mon Feb 25 14:54:45 2019
+## Date of fit: Mon Feb 25 15:25:09 2019
+## Date of summary: Mon Feb 25 15:25:09 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.112 s
+## Fitted with method Port using 46 model solutions performed in 0.111 s
##
## Weighting: none
##
@@ -621,15 +621,15 @@
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Mon Feb 25 14:54:45 2019
-## Date of summary: Mon Feb 25 14:54:45 2019
+## Date of fit: Mon Feb 25 15:25:09 2019
+## Date of summary: Mon Feb 25 15:25:09 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.165 s
+## Fitted with method Port using 66 model solutions performed in 0.164 s
##
## Weighting: none
##
@@ -724,7 +724,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index b2b11a3f..a1c08835 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -140,7 +140,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index bffd19dd..24520f74 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -247,7 +247,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 83b05989..bf56eff2 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -136,7 +136,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index c3ee7415..48f08bfc 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -321,7 +321,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 4209d2bc..16f0cc7a 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -126,14 +126,14 @@
<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.394 1.000 2.388 0.004
-## 1 deSolve, not compiled 3 17.923 7.487 17.910 0.000
-## 2 Eigenvalue based 3 3.021 1.262 3.018 0.000
+## 3 deSolve, compiled 3 2.328 1.000 2.327 0
+## 1 deSolve, not compiled 3 17.641 7.578 17.633 0
+## 2 Eigenvalue based 3 2.873 1.234 2.871 0
## user.child sys.child
## 3 0 0
## 1 0 0
## 2 0 0</code></pre>
-<p>We see that using the compiled model is by a factor of around 7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p>
+<p>We see that using the compiled model is by a factor of around 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
<h2 class="hasAnchor">
@@ -157,8 +157,8 @@
<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 4.162 1.000 4.158 0
-## 1 deSolve, not compiled 3 37.536 9.019 37.517 0
+## 2 deSolve, compiled 3 4.126 1.000 4.125 0
+## 1 deSolve, not compiled 3 37.487 9.086 37.467 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
@@ -190,7 +190,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/authors.html b/docs/authors.html
index 78296059..1c3101aa 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -148,7 +148,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/index.html b/docs/index.html
index 1fe49776..75cf8c00 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -202,7 +202,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index cd82d187..a66f5bbc 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -720,7 +720,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 7b40553c..2783dff9 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
pandoc: 2.2.1
-pkgdown: 1.3.0
+pkgdown: 1.3.0.9000
pkgdown_sha: ~
articles:
FOCUS_D: FOCUS_D.html
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html
index 3d10d36e..69552d5f 100644
--- a/docs/reference/AIC.mmkin.html
+++ b/docs/reference/AIC.mmkin.html
@@ -198,7 +198,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html
index 886c1922..74e77339 100644
--- a/docs/reference/CAKE_export.html
+++ b/docs/reference/CAKE_export.html
@@ -229,7 +229,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 9bc215f0..40e2a0fa 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -196,7 +196,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 95b1558e..f86ff43a 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -280,7 +280,7 @@
#&gt;
#&gt; $time
#&gt; User System verstrichen
-#&gt; 0.196 0.000 0.196
+#&gt; 0.196 0.000 0.198
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -469,8 +469,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x555559255c78&gt;
-#&gt; &lt;environment: 0x55555add1128&gt;
+#&gt; &lt;bytecode: 0x5555592a5fc0&gt;
+#&gt; &lt;environment: 0x55555ba81950&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -492,8 +492,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555a1e9540&gt;
-#&gt; &lt;environment: 0x55555add1128&gt;
+#&gt; &lt;bytecode: 0x55555a5e0ee8&gt;
+#&gt; &lt;environment: 0x55555ba81950&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -560,7 +560,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Mon Feb 25 14:52:43 2019"
+#&gt; [1] "Mon Feb 25 15:23:07 2019"
#&gt;
#&gt; $version
#&gt; [1] "0.9.48.1"
@@ -593,7 +593,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
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 9a43e010..9babae16 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -184,7 +184,7 @@ in this fit.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
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 663600dd..6e11464e 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -183,7 +183,7 @@ in this fit.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
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 58cab325..59219e45 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -184,7 +184,7 @@ in this fit.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
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 f9cf0e11..67df3476 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -182,7 +182,7 @@ in this fit.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 56f58d03..7d38639b 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -180,7 +180,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index fe6944d3..43466474 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -210,7 +210,7 @@ The form given here differs slightly from the original reference by Gustafson
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 6997ebae..048a24c3 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -197,7 +197,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 103a1ae3..9646461c 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -211,7 +211,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/NAFTA_2015_datasets.html b/docs/reference/NAFTA_2015_datasets.html
index 9ef56fb0..be080428 100644
--- a/docs/reference/NAFTA_2015_datasets.html
+++ b/docs/reference/NAFTA_2015_datasets.html
@@ -152,7 +152,12 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>MRID_555555</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The reprentative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Parameters:
+ <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>MRID_555555</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Sums of squares:
+#&gt; SFO IORE DFOP
+#&gt; 1378.6832 615.7730 517.8836
+#&gt; [1] 717.4598
+#&gt;
+#&gt; Parameters:
#&gt; $SFO
#&gt; Estimate Pr(&gt;t) Lower Upper
#&gt; parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063
@@ -201,7 +206,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 325a4285..dd04ad1a 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -185,7 +185,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index f22b3af5..19566257 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -202,7 +202,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index c2db5b52..40f23bee 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -254,7 +254,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index e241c7b9..bd23c95a 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -191,7 +191,7 @@ with the advantage that the SFORB model can also be used for metabolites.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index e52ac866..e5a12b7d 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -171,7 +171,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 4c8af606..0ab8f0a3 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -193,7 +193,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 24f3df0c..24403ad6 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -485,7 +485,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index 1e3b5702..2f211431 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -231,7 +231,7 @@ In the case of iterative reweighting, the variances obtained by this
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 728fbaa9..a30059fe 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -237,7 +237,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 2c10b624..17be80d5 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -193,7 +193,7 @@ guidance.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index bcc871d8..d4501489 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -160,8 +160,8 @@
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:53:05 2019
-#&gt; Date of summary: Mon Feb 25 14:53:05 2019
+#&gt; Date of fit: Mon Feb 25 15:23:29 2019
+#&gt; Date of summary: Mon Feb 25 15:23:29 2019
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -171,7 +171,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 574 model solutions performed in 3.873 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.852 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -249,8 +249,8 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:53:07 2019
-#&gt; Date of summary: Mon Feb 25 14:53:07 2019
+#&gt; Date of fit: Mon Feb 25 15:23:31 2019
+#&gt; Date of summary: Mon Feb 25 15:23:31 2019
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -260,7 +260,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.623 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.604 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -362,7 +362,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index f8849a3e..f034f955 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -205,7 +205,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 04eaff8b..e874f9bf 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -183,7 +183,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 7a87c11e..a9362c2b 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -173,7 +173,7 @@ in order to be compatible with mkinfit</p></dd>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index c155a838..149006a5 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -209,7 +209,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 80278890..ffc87dfb 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -438,15 +438,15 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:53:09 2019
-#&gt; Date of summary: Mon Feb 25 14:53:09 2019
+#&gt; Date of fit: Mon Feb 25 15:23:34 2019
+#&gt; Date of summary: Mon Feb 25 15:23:34 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.168 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.163 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -515,7 +515,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.038 0.000 1.039 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 1.011 0.000 1.012 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -590,7 +590,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.827 0.000 0.827 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.826 0.000 0.827 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -628,8 +628,8 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:53:22 2019
-#&gt; Date of summary: Mon Feb 25 14:53:22 2019
+#&gt; Date of fit: Mon Feb 25 15:23:46 2019
+#&gt; Date of summary: Mon Feb 25 15:23:46 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -637,7 +637,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.898 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.849 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -745,8 +745,8 @@
#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:53:24 2019
-#&gt; Date of summary: Mon Feb 25 14:53:24 2019
+#&gt; Date of fit: Mon Feb 25 15:23:48 2019
+#&gt; Date of summary: Mon Feb 25 15:23:48 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -754,7 +754,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.572 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.529 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -867,8 +867,8 @@
#&gt; 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:53:25 2019
-#&gt; Date of summary: Mon Feb 25 14:53:25 2019
+#&gt; Date of fit: Mon Feb 25 15:23:49 2019
+#&gt; Date of summary: Mon Feb 25 15:23:49 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -876,7 +876,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.709 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.707 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -985,8 +985,8 @@
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:53:26 2019
-#&gt; Date of summary: Mon Feb 25 14:53:26 2019
+#&gt; Date of fit: Mon Feb 25 15:23:50 2019
+#&gt; Date of summary: Mon Feb 25 15:23:50 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -994,7 +994,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.81 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.803 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1105,8 +1105,8 @@
<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:53:28 2019
-#&gt; Date of summary: Mon Feb 25 14:53:28 2019
+#&gt; Date of fit: Mon Feb 25 15:23:52 2019
+#&gt; Date of summary: Mon Feb 25 15:23:52 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1114,7 +1114,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.25 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.242 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1223,8 +1223,8 @@
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:53:31 2019
-#&gt; Date of summary: Mon Feb 25 14:53:31 2019
+#&gt; Date of fit: Mon Feb 25 15:23:55 2019
+#&gt; Date of summary: Mon Feb 25 15:23:55 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1232,7 +1232,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 3.302 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.263 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1373,7 +1373,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index ba26c686..48693b0c 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -231,7 +231,7 @@ For the definition of model types and their parameters, the equations given
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file481263217c00.c 2&gt; file481263217c00.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file6703f4535ea.c 2&gt; file6703f4535ea.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
@@ -288,7 +288,7 @@ For the definition of model types and their parameters, the equations given
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 7438e0e0..f0706605 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -175,7 +175,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 2f386d45..2eed795a 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -169,7 +169,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 738eeb9d..5d786bac 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -325,7 +325,7 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.003 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
@@ -335,7 +335,7 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.047 0.000 0.047 </div><div class='input'>
+#&gt; 0.040 0.000 0.039 </div><div class='input'>
</div><div class='input'> <span class='co'># Predict from a fitted model</span>
<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 552.5739
#&gt; Model cost at call 3 : 552.5739
@@ -396,7 +396,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 702e50eb..e1ba5acb 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -222,7 +222,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 95689f48..3e0bdcbd 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -200,7 +200,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 1a60e3ea..29684bad 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -191,8 +191,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_default</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.036 0.039 7.196 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 22.818 0.000 22.834 </div><div class='input'>
+#&gt; 0.040 0.038 7.255 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 22.747 0.000 22.761 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340480 0.2659520 0.7505686 0.2494314
@@ -237,7 +237,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index c74c3939..071ea132 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -175,7 +175,12 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'>nafta</span>(<span class='no'>MRID_555555</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The reprentative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Parameters:
+ <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'>nafta</span>(<span class='no'>MRID_555555</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Sums of squares:
+#&gt; SFO IORE DFOP
+#&gt; 1378.6832 615.7730 517.8836
+#&gt; [1] 717.4598
+#&gt;
+#&gt; Parameters:
#&gt; $SFO
#&gt; Estimate Pr(&gt;t) Lower Upper
#&gt; parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063
@@ -227,7 +232,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index b46da2f1..44ac2967 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -291,7 +291,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, &#8230
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index acea2def..dd7b619d 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -215,7 +215,7 @@ If the current plot device is a tikz device,
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html
index ccc98b23..76da1ffa 100644
--- a/docs/reference/plot.nafta.html
+++ b/docs/reference/plot.nafta.html
@@ -178,7 +178,7 @@ plot(x, legend = FALSE, main = "auto", &#8230;)</pre>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index e4e142d7..1d858500 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -162,7 +162,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index d5e128a7..ace71925 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -183,7 +183,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html
index dc9373f7..ac276857 100644
--- a/docs/reference/print.nafta.html
+++ b/docs/reference/print.nafta.html
@@ -166,7 +166,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 410c95d8..b7ba3d96 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -213,7 +213,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 01b0d542..f44a1c14 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -192,7 +192,7 @@ This is the error model used for example by Werner et al. (1978). The model
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index f0d4a060..9afaf13a 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -208,15 +208,15 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:54:24 2019
-#&gt; Date of summary: Mon Feb 25 14:54:24 2019
+#&gt; Date of fit: Mon Feb 25 15:24:48 2019
+#&gt; Date of summary: Mon Feb 25 15:24:48 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.085 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.086 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -300,7 +300,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index b2b55805..6363db6f 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -301,7 +301,7 @@ summary(fit)
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 39f6d364..b3ec4699 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -226,7 +226,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 1071a932..6861f712 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,8 +202,8 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:54:32 2019
-#&gt; Date of summary: Mon Feb 25 14:54:32 2019
+#&gt; Date of fit: Mon Feb 25 15:24:56 2019
+#&gt; Date of summary: Mon Feb 25 15:24:56 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ 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 0.704 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.737 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -278,8 +278,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
</div><div class='input'><span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:54:34 2019
-#&gt; Date of summary: Mon Feb 25 14:54:34 2019
+#&gt; Date of fit: Mon Feb 25 15:24:58 2019
+#&gt; Date of summary: Mon Feb 25 15:24:58 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ 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 350 model solutions performed in 1.62 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.593 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -366,8 +366,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:54:35 2019
-#&gt; Date of summary: Mon Feb 25 14:54:35 2019
+#&gt; Date of fit: Mon Feb 25 15:24:59 2019
+#&gt; Date of summary: Mon Feb 25 15:24:59 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ 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 186 model solutions performed in 0.856 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.858 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -450,8 +450,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Feb 25 14:54:36 2019
-#&gt; Date of summary: Mon Feb 25 14:54:36 2019
+#&gt; Date of fit: Mon Feb 25 15:25:00 2019
+#&gt; Date of summary: Mon Feb 25 15:25:00 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -459,7 +459,7 @@ 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 104 model solutions performed in 0.482 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.473 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -534,7 +534,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
diff --git a/tests/testthat/test_plots_twa.R b/tests/testthat/test_plots_twa.R
index fe0ba325..0014f738 100644
--- a/tests/testthat/test_plots_twa.R
+++ b/tests/testthat/test_plots_twa.R
@@ -52,9 +52,11 @@ context("Plotting")
test_that("Plotting mmkin objects is reproducible", {
skip_on_cran()
+ plot_sep_FOCUS_C_SFO <- function() plot_sep(fits[[, "FOCUS_C"]])
mmkin_FOCUS_C <- function() plot(fits[, "FOCUS_C"])
mmkin_SFO <- function() plot(fits["SFO",])
+ vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with sep = TRUE", plot_sep_FOCUS_C_SFO)
vdiffr::expect_doppelganger("mmkin plot for FOCUS C", mmkin_FOCUS_C)
vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
})

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