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-rw-r--r--docs/articles/FOCUS_L.html42
-rw-r--r--docs/articles/compiled_models.html26
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.pngbin9973 -> 10652 bytes
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.pngbin12199 -> 11994 bytes
-rw-r--r--docs/articles/mkin_cache/html/__packages9
-rw-r--r--docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RDatabin0 -> 3274 bytes
-rw-r--r--docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdbbin0 -> 20269 bytes
-rw-r--r--docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdxbin0 -> 226 bytes
-rw-r--r--docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.pngbin112161 -> 45379 bytes
-rw-r--r--docs/reference/Extract.mmkin.html24
-rw-r--r--docs/reference/mccall81_245T.html6
-rw-r--r--docs/reference/mkinfit.html8
-rw-r--r--docs/reference/mkinpredict.html6
-rw-r--r--docs/reference/summary.mkinfit.html6
-rw-r--r--docs/reference/transform_odeparms.html6
15 files changed, 69 insertions, 64 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 2244a359..4c3e5c9b 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -63,15 +63,15 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<span class="kw">summary</span>(m.L1.SFO)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 16:56:21 2016
-## Date of summary: Fri Nov 4 16:56:21 2016
+## Date of fit: Fri Nov 4 17:13:56 2016
+## Date of summary: Fri Nov 4 17:13:56 2016
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.089 s
##
## Weighting: none
##
@@ -156,8 +156,8 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 16:56:21 2016
-## Date of summary: Fri Nov 4 16:56:21 2016
+## Date of fit: Fri Nov 4 17:13:57 2016
+## Date of summary: Fri Nov 4 17:13:57 2016
##
##
## Warning: Optimisation by method Port did not converge.
@@ -169,7 +169,7 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 188 model solutions performed in 0.46 s
+## Fitted with method Port using 188 model solutions performed in 0.444 s
##
## Weighting: none
##
@@ -253,15 +253,15 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 16:56:22 2016
-## Date of summary: Fri Nov 4 16:56:22 2016
+## Date of fit: Fri Nov 4 17:13:58 2016
+## Date of summary: Fri Nov 4 17:13:58 2016
##
## Equations:
## d_parent = - (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 0.194 s
##
## Weighting: none
##
@@ -323,8 +323,8 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 16:56:23 2016
-## Date of summary: Fri Nov 4 16:56:23 2016
+## Date of fit: Fri Nov 4 17:13:59 2016
+## Date of summary: Fri Nov 4 17:13:59 2016
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -333,7 +333,7 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.81 s
+## Fitted with method Port using 336 model solutions performed in 0.82 s
##
## Weighting: none
##
@@ -412,8 +412,8 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 16:56:24 2016
-## Date of summary: Fri Nov 4 16:56:25 2016
+## Date of fit: Fri Nov 4 17:14:00 2016
+## Date of summary: Fri Nov 4 17:14:00 2016
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -422,7 +422,7 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.335 s
+## Fitted with method Port using 137 model solutions performed in 0.336 s
##
## Weighting: none
##
@@ -512,15 +512,15 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 16:56:25 2016
-## Date of summary: Fri Nov 4 16:56:25 2016
+## Date of fit: Fri Nov 4 17:14:01 2016
+## Date of summary: Fri Nov 4 17:14:01 2016
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.109 s
+## Fitted with method Port using 46 model solutions performed in 0.114 s
##
## Weighting: none
##
@@ -572,15 +572,15 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 4 16:56:25 2016
-## Date of summary: Fri Nov 4 16:56:25 2016
+## Date of fit: Fri Nov 4 17:14:01 2016
+## Date of summary: Fri Nov 4 17:14:01 2016
##
## Equations:
## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.16 s
+## Fitted with method Port using 66 model solutions performed in 0.162 s
##
## Weighting: none
##
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index e1572b17..153841ae 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -78,21 +78,21 @@ mb<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw">micr
<span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div>
<pre><code>## Unit: milliseconds
## expr min lq mean median uq
-## deSolve, not compiled 6326.4518 6378.7429 6476.2219 6431.0341 6551.1069
-## Eigenvalue based 925.7797 935.9924 939.8725 946.2051 946.9189
-## deSolve, compiled 740.2821 750.0017 767.8440 759.7212 781.6249
+## deSolve, not compiled 6282.2220 6293.7637 6323.0479 6305.3053 6343.4608
+## Eigenvalue based 873.2553 886.5949 903.6178 899.9345 918.7990
+## deSolve, compiled 737.7899 738.8794 752.3343 739.9689 759.6065
## max neval cld
-## 6671.1797 3 b
-## 947.6327 3 a
-## 803.5287 3 a</code></pre>
+## 6381.6162 3 c
+## 937.6634 3 b
+## 779.2441 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p>
<p>We see that using the compiled model is by a factor of 8.5 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 class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) &lt;-<span class="st"> </span>smb<span class="fl">.1</span>$expr
smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
-## deSolve, not compiled 8.464993
-## Eigenvalue based 1.245464
+## deSolve, not compiled 8.521041
+## Eigenvalue based 1.216179
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -114,18 +114,18 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="
<span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div>
<pre><code>## Unit: seconds
## expr min lq mean median uq
-## deSolve, not compiled 13.619556 13.761382 13.825679 13.903207 13.928741
-## deSolve, compiled 1.316871 1.322577 1.358847 1.328283 1.379834
+## deSolve, not compiled 13.644880 13.648332 13.835874 13.651784 13.931372
+## deSolve, compiled 1.422381 1.448574 1.495091 1.474767 1.531446
## max neval cld
-## 13.954275 3 b
-## 1.431386 3 a</code></pre>
+## 14.210959 3 b
+## 1.588125 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
## 1 NA
## 2 NA</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p>
-<p>Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 9.3 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.44.9000 on</p>
<pre><code>## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
index 57730131..c52ccd5d 100644
--- a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
+++ b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
Binary files differ
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
index 50adff32..c89ef9a5 100644
--- a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
+++ b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
Binary files differ
diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index c8b1e877..03ece635 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -1,8 +1,13 @@
base
+datasets
+utils
+grDevices
+graphics
+stats
knitr
minpack.lm
rootSolve
+methods
inline
+parallel
mkin
-microbenchmark
-ggplot2
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData
new file mode 100644
index 00000000..d11ccf31
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData
Binary files differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb
new file mode 100644
index 00000000..5ac4f484
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb
Binary files differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx
new file mode 100644
index 00000000..8983f69e
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx
Binary files differ
diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index d34e3805..2e7e2244 100644
--- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
+++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
Binary files differ
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index ad4614fb..4b6545db 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -193,7 +193,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.264 0.000 0.262
+#&gt; 0.260 0.000 0.261
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -379,7 +379,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x50d32d0&gt;
+#&gt; &lt;environment: 0x5bbb4a8&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -401,7 +401,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x50d32d0&gt;
+#&gt; &lt;environment: 0x5bbb4a8&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 alpha beta
@@ -467,7 +467,7 @@
#&gt; 99.66619
#&gt;
#&gt; $date
-#&gt; [1] &quot;Fri Nov 4 17:08:52 2016&quot;
+#&gt; [1] &quot;Fri Nov 4 17:12:26 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
@@ -546,7 +546,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.068 0.000 0.067
+#&gt; 0.068 0.000 0.071
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -733,7 +733,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4f17408&gt;
+#&gt; &lt;environment: 0x5719c08&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -755,7 +755,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4f17408&gt;
+#&gt; &lt;environment: 0x5719c08&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -818,7 +818,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Fri Nov 4 17:08:51 2016&quot;
+#&gt; [1] &quot;Fri Nov 4 17:12:26 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#&gt; [[1]]
@@ -894,7 +894,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.068 0.000 0.067
+#&gt; 0.068 0.000 0.071
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -1081,7 +1081,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4f17408&gt;
+#&gt; &lt;environment: 0x5719c08&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -1103,7 +1103,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4f17408&gt;
+#&gt; &lt;environment: 0x5719c08&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -1166,7 +1166,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Fri Nov 4 17:08:51 2016&quot;
+#&gt; [1] &quot;Fri Nov 4 17:12:26 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 6eb4741b..40c21d3c 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -122,8 +122,8 @@
<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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 4 17:08:59 2016
-#&gt; Date of summary: Fri Nov 4 17:08:59 2016
+#&gt; Date of fit: Fri Nov 4 17:12:32 2016
+#&gt; Date of summary: Fri Nov 4 17:12:32 2016
#&gt;
#&gt; Equations:
#&gt; d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -133,7 +133,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.497 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.502 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 93185eff..32083843 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -359,15 +359,15 @@
<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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 4 17:09:01 2016
-#&gt; Date of summary: Fri Nov 4 17:09:01 2016
+#&gt; Date of fit: Fri Nov 4 17:12:35 2016
+#&gt; Date of summary: Fri Nov 4 17:12:35 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - (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 0.156 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.147 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -436,7 +436,7 @@
<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; 1.256 1.216 0.946 </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; 1.208 1.256 0.935 </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/mkinpredict.html b/docs/reference/mkinpredict.html
index 9f00dab7..e8302508 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -275,17 +275,17 @@
<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'>"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 elapsed
-#&gt; 0.004 0.028 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.008 0.016 0.005 </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='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; 0.000 0.020 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.000 0.016 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
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.052 0.000 0.052 </div></pre>
+#&gt; 0.036 0.000 0.035 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index f67bc1d1..60f7cdf6 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -142,15 +142,15 @@
<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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 4 17:09:10 2016
-#&gt; Date of summary: Fri Nov 4 17:09:10 2016
+#&gt; Date of fit: Fri Nov 4 17:12:43 2016
+#&gt; Date of summary: Fri Nov 4 17:12:43 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.086 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.084 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 60208ff4..f455951d 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -149,8 +149,8 @@
<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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 4 17:09:11 2016
-#&gt; Date of summary: Fri Nov 4 17:09:11 2016
+#&gt; Date of fit: Fri Nov 4 17:12:44 2016
+#&gt; Date of summary: Fri Nov 4 17:12:44 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -158,7 +158,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.638 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.656 s
#&gt;
#&gt; Weighting: none
#&gt;

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