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-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
6 files changed, 28 insertions, 28 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 1802e260..b513fac1 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -192,7 +192,7 @@
#>
#> $time
#> user system elapsed
-#> 0.256 0.000 0.256
+#> 0.252 0.000 0.253
#>
#> $mkinmod
#> <mkinmod> model generated with
@@ -378,7 +378,7 @@
#> }
#> return(mC)
#> }
-#> <environment: 0x435ac28>
+#> <environment: 0x3e9c368>
#>
#> $cost_notrans
#> function (P)
@@ -400,7 +400,7 @@
#> scaleVar = scaleVar)
#> return(mC)
#> }
-#> <environment: 0x435ac28>
+#> <environment: 0x3e9c368>
#>
#> $hessian_notrans
#> parent_0 alpha beta
@@ -466,7 +466,7 @@
#> 99.66619
#>
#> $date
-#> [1] "Thu Oct 6 09:39:06 2016"
+#> [1] "Thu Oct 6 10:47:28 2016"
#>
#> attr(,"class")
#> [1] "mkinfit" "modFit"
@@ -547,7 +547,7 @@
#>
#> $time
#> user system elapsed
-#> 0.068 0.000 0.068
+#> 0.064 0.000 0.067
#>
#> $mkinmod
#> <mkinmod> model generated with
@@ -734,7 +734,7 @@
#> }
#> return(mC)
#> }
-#> <environment: 0x4da08d0>
+#> <environment: 0x3c1a660>
#>
#> $cost_notrans
#> function (P)
@@ -756,7 +756,7 @@
#> scaleVar = scaleVar)
#> return(mC)
#> }
-#> <environment: 0x4da08d0>
+#> <environment: 0x3c1a660>
#>
#> $hessian_notrans
#> parent_0 k_parent_sink
@@ -819,7 +819,7 @@
#> 99.17407
#>
#> $date
-#> [1] "Thu Oct 6 09:39:06 2016"
+#> [1] "Thu Oct 6 10:47:28 2016"
#>
#> attr(,"class")
#> [1] "mkinfit" "modFit"
@@ -896,7 +896,7 @@
#>
#> $time
#> user system elapsed
-#> 0.068 0.000 0.068
+#> 0.064 0.000 0.067
#>
#> $mkinmod
#> <mkinmod> model generated with
@@ -1083,7 +1083,7 @@
#> }
#> return(mC)
#> }
-#> <environment: 0x4da08d0>
+#> <environment: 0x3c1a660>
#>
#> $cost_notrans
#> function (P)
@@ -1105,7 +1105,7 @@
#> scaleVar = scaleVar)
#> return(mC)
#> }
-#> <environment: 0x4da08d0>
+#> <environment: 0x3c1a660>
#>
#> $hessian_notrans
#> parent_0 k_parent_sink
@@ -1168,7 +1168,7 @@
#> 99.17407
#>
#> $date
-#> [1] "Thu Oct 6 09:39:06 2016"
+#> [1] "Thu Oct 6 10:47:28 2016"
#>
#> attr(,"class")
#> [1] "mkinfit" "modFit"
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 17e900a4..63635f9a 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: 3.3.1
-#&gt; Date of fit: Thu Oct 6 09:39:12 2016
-#&gt; Date of summary: Thu Oct 6 09:39:12 2016
+#&gt; Date of fit: Thu Oct 6 10:47:34 2016
+#&gt; Date of summary: Thu Oct 6 10:47:34 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 1.544 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.492 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 14c1b364..7acbbe5a 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -363,15 +363,15 @@
<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: 3.3.1
-#&gt; Date of fit: Thu Oct 6 09:39:14 2016
-#&gt; Date of summary: Thu Oct 6 09:39:14 2016
+#&gt; Date of fit: Thu Oct 6 10:47:36 2016
+#&gt; Date of summary: Thu Oct 6 10:47:36 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 0.16 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.152 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -441,7 +441,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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; 1.204 1.224 0.917
+#&gt; 1.240 1.280 0.973
#&gt; </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
#&gt; </div><div class='input'><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index b0899a3e..5b7cdb32 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -284,21 +284,21 @@
<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
#&gt; </div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.008 0.024 0.004
+#&gt; 0.008 0.020 0.004
#&gt; </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
#&gt; </div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.016 0.004 0.002
+#&gt; 0.016 0.004 0.003
#&gt; </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
#&gt; </div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.032 0.000 0.033
+#&gt; 0.032 0.000 0.034
#&gt; </div></pre>
</div>
<div class="col-md-3">
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 001852a5..acbf36dc 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -142,15 +142,15 @@
<h2 id="examples">Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'>mkinfit</span>(<span class='fu'>mkinmod</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: 3.3.1
-#&gt; Date of fit: Thu Oct 6 09:39:22 2016
-#&gt; Date of summary: Thu Oct 6 09:39:22 2016
+#&gt; Date of fit: Thu Oct 6 10:47:44 2016
+#&gt; Date of summary: Thu Oct 6 10:47:44 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 0.078 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.079 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 2b736098..66253bba 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -147,8 +147,8 @@
<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'>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: 3.3.1
-#&gt; Date of fit: Thu Oct 6 09:39:23 2016
-#&gt; Date of summary: Thu Oct 6 09:39:23 2016
+#&gt; Date of fit: Thu Oct 6 10:47:45 2016
+#&gt; Date of summary: Thu Oct 6 10:47:45 2016
#&gt;
#&gt; Equations:
#&gt; d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -156,7 +156,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.63 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.638 s
#&gt;
#&gt; Weighting: none
#&gt;

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