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-rw-r--r--docs/articles/FOCUS_D.html2
-rw-r--r--docs/articles/FOCUS_L.html44
-rw-r--r--docs/articles/FOCUS_Z.R93
-rw-r--r--docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RDatabin0 -> 3378 bytes
-rw-r--r--docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdbbin0 -> 858 bytes
-rw-r--r--docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdxbin0 -> 172 bytes
-rw-r--r--docs/articles/cache/__packages13
-rw-r--r--docs/articles/compiled_models.html30
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.pngbin9618 -> 9742 bytes
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.pngbin10679 -> 10742 bytes
-rw-r--r--docs/articles/mkin.html2
-rw-r--r--docs/reference/Extract.mmkin.html8
-rw-r--r--docs/reference/mccall81_245T.html12
-rw-r--r--docs/reference/mkinfit.html46
-rw-r--r--docs/reference/mkinmod.html2
-rw-r--r--docs/reference/mkinpredict.html6
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/plot.mkinfit.html4
-rw-r--r--docs/reference/plot.mmkin.html3
-rw-r--r--docs/reference/summary.mkinfit.html6
-rw-r--r--docs/reference/synthetic_data_for_UBA.html6
-rw-r--r--docs/reference/transform_odeparms.html24
22 files changed, 116 insertions, 189 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 782a789d..9640c62f 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -54,7 +54,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-11-18</h4>
+ <h4 class="date">2016-12-08</h4>
</div>
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 68054ec1..6a25282b 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -54,7 +54,7 @@
<h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-11-18</h4>
+ <h4 class="date">2016-12-08</h4>
</div>
@@ -76,15 +76,15 @@ 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 18 22:54:43 2016
-## Date of summary: Fri Nov 18 22:54:43 2016
+## Date of fit: Thu Dec 8 07:59:15 2016
+## Date of summary: Thu Dec 8 07:59:15 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.09 s
+## Fitted with method Port using 37 model solutions performed in 0.087 s
##
## Weighting: none
##
@@ -169,8 +169,8 @@ 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 18 22:54:44 2016
-## Date of summary: Fri Nov 18 22:54:44 2016
+## Date of fit: Thu Dec 8 07:59:15 2016
+## Date of summary: Thu Dec 8 07:59:15 2016
##
##
## Warning: Optimisation by method Port did not converge.
@@ -182,7 +182,7 @@ 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 0.43 s
+## Fitted with method Port using 188 model solutions performed in 0.436 s
##
## Weighting: none
##
@@ -266,15 +266,15 @@ 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 18 22:54:44 2016
-## Date of summary: Fri Nov 18 22:54:44 2016
+## Date of fit: Thu Dec 8 07:59:16 2016
+## Date of summary: Thu Dec 8 07:59:16 2016
##
## 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 0.184 s
+## Fitted with method Port using 81 model solutions performed in 0.19 s
##
## Weighting: none
##
@@ -336,8 +336,8 @@ 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 18 22:54:45 2016
-## Date of summary: Fri Nov 18 22:54:46 2016
+## Date of fit: Thu Dec 8 07:59:17 2016
+## Date of summary: Thu Dec 8 07:59:17 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -346,7 +346,7 @@ 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 0.784 s
+## Fitted with method Port using 336 model solutions performed in 0.785 s
##
## Weighting: none
##
@@ -425,8 +425,8 @@ 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 18 22:54:47 2016
-## Date of summary: Fri Nov 18 22:54:47 2016
+## Date of fit: Thu Dec 8 07:59:18 2016
+## Date of summary: Thu Dec 8 07:59:18 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -435,7 +435,7 @@ 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 0.328 s
+## Fitted with method Port using 137 model solutions performed in 0.319 s
##
## Weighting: none
##
@@ -525,15 +525,15 @@ 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 18 22:54:47 2016
-## Date of summary: Fri Nov 18 22:54:48 2016
+## Date of fit: Thu Dec 8 07:59:19 2016
+## Date of summary: Thu Dec 8 07:59:19 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.108 s
+## Fitted with method Port using 46 model solutions performed in 0.107 s
##
## Weighting: none
##
@@ -585,15 +585,15 @@ 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 18 22:54:47 2016
-## Date of summary: Fri Nov 18 22:54:48 2016
+## Date of fit: Thu Dec 8 07:59:19 2016
+## Date of summary: Thu Dec 8 07:59:19 2016
##
## 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 0.145 s
+## Fitted with method Port using 66 model solutions performed in 0.152 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R
index 5c70b57e..eacefa90 100644
--- a/docs/articles/FOCUS_Z.R
+++ b/docs/articles/FOCUS_Z.R
@@ -20,96 +20,3 @@ FOCUS_2006_Z = data.frame(
FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
-## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6-------------------
-Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
- Z1 = mkinsub("SFO"))
-m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.2a)
-summary(m.Z.2a, data = FALSE)$bpar
-
-## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6-------------------
-Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
- Z1 = mkinsub("SFO"),
- use_of_ff = "max")
-
-m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.2a.ff)
-summary(m.Z.2a.ff, data = FALSE)$bpar
-
-## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6-------------------
-Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
- Z1 = mkinsub("SFO"), use_of_ff = "max")
-m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.3)
-summary(m.Z.3, data = FALSE)$bpar
-
-## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7-------------------
-Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
- Z1 = mkinsub("SFO", "Z2", sink = FALSE),
- Z2 = mkinsub("SFO"), use_of_ff = "max")
-m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.5)
-
-## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8-------------------
-Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
- Z1 = mkinsub("SFO", "Z2", sink = FALSE),
- Z2 = mkinsub("SFO", "Z3"),
- Z3 = mkinsub("SFO"),
- use_of_ff = "max")
-m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin,
- parms.ini = m.Z.5$bparms.ode,
- quiet = TRUE)
-plot_sep(m.Z.FOCUS)
-summary(m.Z.FOCUS, data = FALSE)$bpar
-endpoints(m.Z.FOCUS)
-
-## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8-------------------
-Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
- Z1 = mkinsub("SFO", "Z2", sink = FALSE),
- Z2 = mkinsub("SFO", "Z3"),
- Z3 = mkinsub("SFORB"))
-m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.mkin.1)
-summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
-
-## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8-------------------
-Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
- Z1 = mkinsub("SFO", "Z2", sink = FALSE),
- Z2 = mkinsub("SFO"))
-m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.mkin.3)
-
-## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8------------------
-Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
- Z1 = mkinsub("SFO", "Z2", sink = FALSE),
- Z2 = mkinsub("SFO", "Z3"),
- Z3 = mkinsub("SFO"))
-m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin,
- parms.ini = m.Z.mkin.3$bparms.ode,
- quiet = TRUE)
-plot_sep(m.Z.mkin.4)
-
-## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8------------------
-Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
- Z1 = mkinsub("SFO", "Z2", sink = FALSE),
- Z2 = mkinsub("SFO", "Z3"),
- Z3 = mkinsub("SFORB"))
-m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
- parms.ini = m.Z.mkin.4$bparms.ode[1:4],
- quiet = TRUE)
-plot_sep(m.Z.mkin.5)
-
-## ----FOCUS_2006_Z_fits_11a, echo=TRUE-------------------------------
-m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
- parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
- k_Z3_bound_free = 0),
- fixed_parms = "k_Z3_bound_free",
- quiet = TRUE)
-plot_sep(m.Z.mkin.5a)
-
-## ----FOCUS_2006_Z_fits_11b, echo=TRUE-------------------------------
-mkinparplot(m.Z.mkin.5a)
-
-## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE---------------------
-endpoints(m.Z.mkin.5a)
-
diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData
new file mode 100644
index 00000000..282678c3
--- /dev/null
+++ b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData
Binary files differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb
new file mode 100644
index 00000000..9c88c526
--- /dev/null
+++ b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb
Binary files differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx
new file mode 100644
index 00000000..5f5be10e
--- /dev/null
+++ b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx
Binary files differ
diff --git a/docs/articles/cache/__packages b/docs/articles/cache/__packages
new file mode 100644
index 00000000..03ece635
--- /dev/null
+++ b/docs/articles/cache/__packages
@@ -0,0 +1,13 @@
+base
+datasets
+utils
+grDevices
+graphics
+stats
+knitr
+minpack.lm
+rootSolve
+methods
+inline
+parallel
+mkin
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 87913685..d39caf12 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -54,7 +54,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-11-18</h4>
+ <h4 class="date">2016-12-08</h4>
</div>
@@ -91,21 +91,21 @@ 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 6126.4954 6152.1764 6170.8152 6177.8573 6192.9751
-## Eigenvalue based 864.8441 891.7069 902.0212 918.5697 920.6098
-## deSolve, compiled 706.9115 711.1015 714.9195 715.2915 718.9235
+## deSolve, not compiled 6263.2932 6273.5107 6286.8574 6283.7283 6298.6394
+## Eigenvalue based 865.5257 872.4146 892.2705 879.3036 905.6429
+## deSolve, compiled 716.7534 717.9075 724.6869 719.0617 728.6537
## max neval cld
-## 6208.0929 3 c
-## 922.6498 3 b
-## 722.5556 3 a</code></pre>
+## 6313.5506 3 c
+## 931.9821 3 b
+## 738.2457 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 8.6 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 8.7 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>
<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 8.636839
-## Eigenvalue based 1.284189
+## deSolve, not compiled 8.738789
+## Eigenvalue based 1.222849
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -127,18 +127,18 @@ 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 13.163796 13.205491 13.478255 13.247187 13.635484
-## deSolve, compiled 1.267154 1.268198 1.272722 1.269242 1.275506
+## deSolve, not compiled 13.487097 13.492149 13.528060 13.497201 13.548541
+## deSolve, compiled 1.307845 1.318979 1.322967 1.330114 1.330528
## max neval cld
-## 14.023782 3 b
-## 1.281771 3 a</code></pre>
+## 13.599881 3 b
+## 1.330941 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 10.4 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 10.1 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 55aca8fa..d881a0a2 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 90ac9cbc..b3faa16f 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.html b/docs/articles/mkin.html
index 1292480b..c70f8ddf 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -54,7 +54,7 @@
<h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-11-18</h4>
+ <h4 class="date">2016-12-08</h4>
</div>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 2bba63eb..4ef3bb00 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -239,7 +239,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.08 0.00 0.08
+#&gt; 0.064 0.000 0.065
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -428,7 +428,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4807c50&gt;
+#&gt; &lt;environment: 0x5ce33e0&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -450,7 +450,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x4807c50&gt;
+#&gt; &lt;environment: 0x5ce33e0&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -513,7 +513,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Mon Nov 21 16:07:10 2016&quot;
+#&gt; [1] &quot;Thu Dec 8 07:56:34 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 1a8170ff..123af096 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -130,8 +130,8 @@
<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'>subset</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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
#&gt; <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='fu'>summary</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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:07:20 2016
-#&gt; Date of summary: Mon Nov 21 16:07:20 2016
+#&gt; Date of fit: Thu Dec 8 07:56:42 2016
+#&gt; Date of summary: Thu Dec 8 07:56:42 2016
#&gt;
#&gt;
#&gt; Warning: Optimisation by method Port did not converge.
@@ -146,7 +146,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 590 model solutions performed in 3.627 s
+#&gt; Fitted with method Port using 590 model solutions performed in 3.474 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -225,8 +225,8 @@
<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: Mon Nov 21 16:07:22 2016
-#&gt; Date of summary: Mon Nov 21 16:07:22 2016
+#&gt; Date of fit: Thu Dec 8 07:56:44 2016
+#&gt; Date of summary: Thu Dec 8 07:56:44 2016
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -236,7 +236,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.475 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.44 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index a992db8e..3dd701d3 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -374,15 +374,15 @@
<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: Mon Nov 21 16:07:24 2016
-#&gt; Date of summary: Mon Nov 21 16:07:24 2016
+#&gt; Date of fit: Thu Dec 8 07:56:46 2016
+#&gt; Date of summary: Thu Dec 8 07:56:46 2016
#&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 0.162 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.145 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -451,7 +451,7 @@
<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; 1.368 1.244 1.029 </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; 1.172 1.232 0.904 </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
@@ -528,7 +528,7 @@
#&gt; Model cost at call 152 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; user system elapsed
-#&gt; 0.784 0.032 0.773 </div><div class='input'><span class='fu'>coef</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; 0.712 0.044 0.709 </div><div class='input'><span class='fu'>coef</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
@@ -571,8 +571,8 @@
<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'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:07:35 2016
-#&gt; Date of summary: Mon Nov 21 16:07:35 2016
+#&gt; Date of fit: Thu Dec 8 07:56:57 2016
+#&gt; Date of summary: Thu Dec 8 07:56:57 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -580,7 +580,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.808 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.77 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -692,8 +692,8 @@
#&gt; 120 m1 33.31 2.879e+01 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'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:07:37 2016
-#&gt; Date of summary: Mon Nov 21 16:07:37 2016
+#&gt; Date of fit: Thu Dec 8 07:56:59 2016
+#&gt; Date of summary: Thu Dec 8 07:56:59 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -701,7 +701,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 486 model solutions performed in 2.071 s
+#&gt; Fitted with method Port using 486 model solutions performed in 2.019 s
#&gt;
#&gt; Weighting: none then iterative reweighting method obs
#&gt;
@@ -813,8 +813,8 @@
#&gt; 120 m1 33.31 2.881e+01 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'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:07:38 2016
-#&gt; Date of summary: Mon Nov 21 16:07:38 2016
+#&gt; Date of fit: Thu Dec 8 07:57:00 2016
+#&gt; Date of summary: Thu Dec 8 07:57:00 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -822,7 +822,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.645 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.65 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -935,8 +935,8 @@
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:07:39 2016
-#&gt; Date of summary: Mon Nov 21 16:07:39 2016
+#&gt; Date of fit: Thu Dec 8 07:57:01 2016
+#&gt; Date of summary: Thu Dec 8 07:57:01 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -944,7 +944,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.724 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.713 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1057,8 +1057,8 @@
<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'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:07:40 2016
-#&gt; Date of summary: Mon Nov 21 16:07:40 2016
+#&gt; Date of fit: Thu Dec 8 07:57:02 2016
+#&gt; Date of summary: Thu Dec 8 07:57:02 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1066,7 +1066,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 316 model solutions performed in 1.306 s
+#&gt; Fitted with method Port using 316 model solutions performed in 1.322 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1179,8 +1179,8 @@
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:07:43 2016
-#&gt; Date of summary: Mon Nov 21 16:07:43 2016
+#&gt; Date of fit: Thu Dec 8 07:57:05 2016
+#&gt; Date of summary: Thu Dec 8 07:57:05 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1188,7 +1188,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 648 model solutions performed in 2.758 s
+#&gt; Fitted with method Port using 648 model solutions performed in 2.818 s
#&gt;
#&gt; Weighting: manual then iterative reweighting method obs
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index dce23299..1044af6b 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -188,7 +188,7 @@
<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 file40bc52407fe7.c 2&gt; file40bc52407fe7.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file386742883b12.c 2&gt; file386742883b12.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index d4d7caff..766b6613 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -290,17 +290,17 @@
<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; 0.000 0.028 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.012 0.020 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; 0.016 0.004 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.000 0.020 0.003 </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; 0.032 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/mmkin.html b/docs/reference/mmkin.html
index 5ff63336..0127f114 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -158,8 +158,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</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 elapsed
-#&gt; 16.488 0.116 9.046 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 22.788 0.004 22.795 </div><div class='input'>
+#&gt; 16.776 0.108 9.353 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 22.696 0.000 22.701 </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; 0.7340479 0.2659521 0.7505687 0.2494313
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index f34ef5e5..9969e198 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -99,6 +99,10 @@
<p>Solves the differential equations with the optimised and fixed parameters
from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots
the observed data together with the solution of the fitted model.</p>
+
+ <p>If the current plot device is a <code><a href='http://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device,
+ then latex is being used for the formatting of the chi2 error level,
+ if <code>show_errmin = TRUE</code>.</p>
<pre># S3 method for mkinfit
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 8fd98372..1d5d0574 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -99,6 +99,9 @@
<p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), the same model
fitted for at least one dataset is shown. When it is a column, the fit of at least one model
to the same dataset is shown.</p>
+
+ <p>If the current plot device is a <code><a href='http://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device,
+ then latex is being used for the formatting of the chi2 error level.</p>
<pre><span class='co'># S3 method for mmkin</span>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 139fd061..b305410d 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -157,15 +157,15 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:08:34 2016
-#&gt; Date of summary: Mon Nov 21 16:08:34 2016
+#&gt; Date of fit: Thu Dec 8 07:57:55 2016
+#&gt; Date of summary: Thu Dec 8 07:57:55 2016
#&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 0.082 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/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index b050eb25..bc2bb02b 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -155,8 +155,8 @@
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><img src='synthetic_data_for_UBA_2014-10.png' alt='' width='540' height='400' /><div class='input'><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: Mon Nov 21 16:08:37 2016
-#&gt; Date of summary: Mon Nov 21 16:08:37 2016
+#&gt; Date of fit: Thu Dec 8 07:57:58 2016
+#&gt; Date of summary: Thu Dec 8 07:57:58 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -165,7 +165,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 351 model solutions performed in 2.261 s
+#&gt; Fitted with method Port using 351 model solutions performed in 2.152 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 2fc74a5a..e1fb0437 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -164,8 +164,8 @@
<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: Mon Nov 21 16:08:38 2016
-#&gt; Date of summary: Mon Nov 21 16:08:38 2016
+#&gt; Date of fit: Thu Dec 8 07:57:59 2016
+#&gt; Date of summary: Thu Dec 8 07:57:59 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -173,7 +173,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.637 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.621 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -241,8 +241,8 @@
<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'>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: Mon Nov 21 16:08:39 2016
-#&gt; Date of summary: Mon Nov 21 16:08:39 2016
+#&gt; Date of fit: Thu Dec 8 07:58:01 2016
+#&gt; Date of summary: Thu Dec 8 07:58:01 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -250,7 +250,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 327 model solutions performed in 1.357 s
+#&gt; Fitted with method Port using 327 model solutions performed in 1.419 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -331,8 +331,8 @@
<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'>summary</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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:08:40 2016
-#&gt; Date of summary: Mon Nov 21 16:08:40 2016
+#&gt; Date of fit: Thu Dec 8 07:58:02 2016
+#&gt; Date of summary: Thu Dec 8 07:58:02 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -340,7 +340,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.816 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.814 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -415,8 +415,8 @@
<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'>summary</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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Mon Nov 21 16:08:41 2016
-#&gt; Date of summary: Mon Nov 21 16:08:41 2016
+#&gt; Date of fit: Thu Dec 8 07:58:03 2016
+#&gt; Date of summary: Thu Dec 8 07:58:03 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -424,7 +424,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 104 model solutions performed in 0.428 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.436 s
#&gt;
#&gt; Weighting: none
#&gt;

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