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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
11 files changed, 52 insertions, 132 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>

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