diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 15:01:53 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 15:22:42 +0100 |
| commit | c6086d1dd97ad2d6420625de7b8009b1b0f85d06 (patch) | |
| tree | 1a38fd690c94a556555ec71edff443bcfe609b7b | |
| parent | 9a8dfa8bd52664929fd4197f3e9c4e65b62cad53 (diff) | |
Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)
Using branch 'jranke' on jranke/pkgdown, fixing issues
hadley/pgkdown#178 and hadley/pkgdown#213
Remove plot=TRUE from mkinfit calls also in dontrun sections of examples
to avoid a flood png files documenting the progress of the fit.
45 files changed, 6005 insertions, 289 deletions
diff --git a/GNUmakefile b/GNUmakefile index fd9e72b8..7d58995b 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -87,9 +87,9 @@ vignettes/%.html: vignettes/mkin_vignettes.css vignettes/%.Rmd vignettes: vignettes/mkin.html vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.pdf vignettes/compiled_models.html pd: - "$(RBIN)/Rscript" -e "pkgdown::build_site()" + "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE)" git add -A - git commit -m 'Static documentation rebuilt by pkgdown::build_site()' -e + git commit -m 'Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)' -e r-forge: pd rm -rf $(SDDIR)/* diff --git a/_pkgdown.yml b/_pkgdown.yml index a46bc34f..70fdcaa9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -26,7 +26,7 @@ reference: - plot.mmkin - title: Datasets and known results contents: - - FOCUS_2006_datasets + - FOCUS_2006_A - FOCUS_2006_SFO_ref_A_to_F - FOCUS_2006_FOMC_ref_A_to_F - FOCUS_2006_HS_ref_A_to_F @@ -41,7 +41,6 @@ reference: - mkin_wide_to_long - mkin_long_to_wide - mkinsub - - mkinds, print.mkinds - print.mkinmod - mkinpredict - transform_odeparms @@ -50,6 +49,7 @@ reference: - title: Analytical solutions desc: Parent only model solutions contents: + - ends_with(".solution") - SFO.solution - FOMC.solution - DFOP.solution diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 776e1093..0ce7bd07 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -41,7 +41,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-17</h4> + <h4 class="date">2016-11-18</h4> </div> diff --git a/docs/articles/FOCUS_D_cache/html/__packages b/docs/articles/FOCUS_D_cache/html/__packages index f8bbf624..c3c384b1 100644 --- a/docs/articles/FOCUS_D_cache/html/__packages +++ b/docs/articles/FOCUS_D_cache/html/__packages @@ -8,5 +8,3 @@ inline mkin rmarkdown knitr -microbenchmark -ggplot2 diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData Binary files differnew file mode 100644 index 00000000..36a4095f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx Binary files differnew file mode 100644 index 00000000..20f10d9f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData Binary files differnew file mode 100644 index 00000000..b0731d7b --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx Binary files differnew file mode 100644 index 00000000..20f10d9f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex fc237898..e44c1374 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differindex b0a7c26b..c7df3486 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index e7ec5308..c3009e4d 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -41,7 +41,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-17</h4> + <h4 class="date">2016-11-18</h4> </div> @@ -63,15 +63,15 @@ FOCUS_2006_L1_mkin <-<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: Thu Nov 17 22:58:18 2016 -## Date of summary: Thu Nov 17 22:58:18 2016 +## Date of fit: Fri Nov 18 15:22:03 2016 +## Date of summary: Fri Nov 18 15:22:03 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 0.103 s +## Fitted with method Port using 37 model solutions performed in 0.09 s ## ## Weighting: none ## @@ -156,8 +156,8 @@ FOCUS_2006_L1_mkin <-<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: Thu Nov 17 22:58:19 2016 -## Date of summary: Thu Nov 17 22:58:19 2016 +## Date of fit: Fri Nov 18 15:22:04 2016 +## Date of summary: Fri Nov 18 15:22:04 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -169,7 +169,7 @@ FOCUS_2006_L1_mkin <-<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 0.462 s +## Fitted with method Port using 188 model solutions performed in 0.445 s ## ## Weighting: none ## @@ -253,15 +253,15 @@ FOCUS_2006_L2_mkin <-<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: Thu Nov 17 22:58:20 2016 -## Date of summary: Thu Nov 17 22:58:20 2016 +## Date of fit: Fri Nov 18 15:22:05 2016 +## Date of summary: Fri Nov 18 15:22:05 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 0.195 s +## Fitted with method Port using 81 model solutions performed in 0.19 s ## ## Weighting: none ## @@ -323,8 +323,8 @@ FOCUS_2006_L2_mkin <-<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: Thu Nov 17 22:58:21 2016 -## Date of summary: Thu Nov 17 22:58:21 2016 +## Date of fit: Fri Nov 18 15:22:06 2016 +## Date of summary: Fri Nov 18 15:22:06 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -333,7 +333,7 @@ FOCUS_2006_L2_mkin <-<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 0.882 s +## Fitted with method Port using 336 model solutions performed in 0.803 s ## ## Weighting: none ## @@ -412,8 +412,8 @@ mm.L3 <-<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: Thu Nov 17 22:58:22 2016 -## Date of summary: Thu Nov 17 22:58:22 2016 +## Date of fit: Fri Nov 18 15:22:07 2016 +## Date of summary: Fri Nov 18 15:22:07 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -422,7 +422,7 @@ mm.L3 <-<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 0.338 s +## Fitted with method Port using 137 model solutions performed in 0.329 s ## ## Weighting: none ## @@ -512,15 +512,15 @@ mm.L4 <-<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: Thu Nov 17 22:58:22 2016 -## Date of summary: Thu Nov 17 22:58:23 2016 +## Date of fit: Fri Nov 18 15:22:08 2016 +## Date of summary: Fri Nov 18 15:22:08 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 0.114 s +## Fitted with method Port using 46 model solutions performed in 0.109 s ## ## Weighting: none ## @@ -572,15 +572,15 @@ mm.L4 <-<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: Thu Nov 17 22:58:23 2016 -## Date of summary: Thu Nov 17 22:58:23 2016 +## Date of fit: Fri Nov 18 15:22:08 2016 +## Date of summary: Fri Nov 18 15:22:08 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 0.151 s +## Fitted with method Port using 66 model solutions performed in 0.15 s ## ## Weighting: none ## diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 1446a357..ce149bc5 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -41,7 +41,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-17</h4> + <h4 class="date">2016-11-18</h4> </div> @@ -78,21 +78,21 @@ mb<span class="fl">.1</span> <-<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 6251.2433 6291.2435 6315.5160 6331.2438 6347.6524 -## Eigenvalue based 858.2035 903.1770 926.2132 948.1505 960.2181 -## deSolve, compiled 721.0067 739.1361 745.9964 757.2656 758.4913 +## deSolve, not compiled 6341.1795 6363.5977 6373.7748 6386.0158 6390.0724 +## Eigenvalue based 907.1699 908.8498 921.8335 910.5297 929.1653 +## deSolve, compiled 747.5311 752.3718 754.2086 757.2125 757.5474 ## max neval cld -## 6364.0611 3 c -## 972.2856 3 b -## 759.7171 3 a</code></pre> +## 6394.1290 3 c +## 947.8008 3 b +## 757.8823 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 8.4 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>) <-<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 8.360665 -## Eigenvalue based 1.252071 +## deSolve, not compiled 8.433585 +## Eigenvalue based 1.202476 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -114,11 +114,11 @@ 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 13.601046 13.602861 13.619563 13.604676 13.628821 -## deSolve, compiled 1.341581 1.346263 1.348298 1.350944 1.351657 -## max neval cld -## 13.65297 3 b -## 1.35237 3 a</code></pre> +## deSolve, not compiled 13.214250 13.248908 13.384577 13.283565 13.469740 +## deSolve, compiled 1.303868 1.307484 1.332879 1.311099 1.347384 +## max neval cld +## 13.655915 3 b +## 1.383669 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 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 Binary files differindex 3c3b9c54..53b631b1 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 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 Binary files differindex 0ec027f1..6d78194f 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 diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 4eed053a..8134287b 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -41,7 +41,7 @@ <h1>mkin - Kinetic evaluation of chemical degradation data</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-17</h4> + <h4 class="date">2016-11-18</h4> </div> diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages index ff62e6df..ae46e2d7 100644 --- a/docs/articles/mkin_cache/html/__packages +++ b/docs/articles/mkin_cache/html/__packages @@ -8,5 +8,3 @@ colorout setwidth nvimcom rmarkdown -microbenchmark -ggplot2 diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData Binary files differnew file mode 100644 index 00000000..fbc45b28 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb Binary files differnew file mode 100644 index 00000000..2b71e52b --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx Binary files differnew file mode 100644 index 00000000..bee3222a --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx 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 Binary files differindex 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 diff --git a/docs/index.html b/docs/index.html index 444b650e..93be361e 100644 --- a/docs/index.html +++ b/docs/index.html @@ -85,16 +85,16 @@ <div id="news" class="section level2"> <h2 class="hasAnchor"> <a href="#news" class="anchor"> </a>News</h2> -<p>Yes, there is a ChangeLog, for the latest <a href="http://cran.r-project.org/web/packages/mkin/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p> +<p>Yes, there is a ChangeLog, for the latest <a href="https://cran.r-project.org/package=mkin/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p> </div> <div id="credits-and-historical-remarks" class="section level2"> <h2 class="hasAnchor"> <a href="#credits-and-historical-remarks" class="anchor"> </a>Credits and historical remarks</h2> -<p><code>mkin</code> would not be possible without the underlying software stack consisting of R and the packages <a href="http://cran.r-project.org/package=deSolve">deSolve</a> and <a href="http://cran.r-project.org/package=FME">FME</a>, to say the least.</p> +<p><code>mkin</code> would not be possible without the underlying software stack consisting of R and the packages <a href="https://cran.r-project.org/package=deSolve">deSolve</a> and <a href="https://cran.r-project.org/package=FME">FME</a>, to say the least.</p> <p>It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows the work done by the <a href="http://focus.jrc.ec.europa.eu/dk">FOCUS Degradation Kinetics Workgroup</a>, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.</p> <p>Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.</p> <p>The companion package <a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> (now deprecated) was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2">started in 2008</a> and <a href="https://cran.r-project.org/src/contrib/Archive/kinfit/">first published</a> on CRAN on 01 May 2010.</p> -<p>The first <code>mkin</code> code was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8">published on 11 May 2010</a> and the <a href="http://cran.r-project.org/src/contrib/Archive/mkin">first CRAN version</a> on 18 May 2010.</p> +<p>The first <code>mkin</code> code was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8">published on 11 May 2010</a> and the <a href="https://cran.r-project.org/src/contrib/Archive/mkin">first CRAN version</a> on 18 May 2010.</p> <p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on <code>mkin</code>, but which added, amongst other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the <code>FME</code> package.</p> <p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the <a href="http://showcase.tessella.com/products/cake">CAKE website</a>, where you can also find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL license.</p> <p>Finally, there is <a href="http://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.</p> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index b437fc7d..09d7513c 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -193,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.268 0.000 0.267 +#> 0.256 0.000 0.255 #> #> $mkinmod #> <mkinmod> model generated with @@ -379,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x3a2f9e8> +#> <environment: 0x3fc5fa0> #> #> $cost_notrans #> function (P) @@ -401,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x3a2f9e8> +#> <environment: 0x3fc5fa0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -467,7 +467,7 @@ #> 99.66619 #> #> $date -#> [1] "Thu Nov 17 22:56:49 2016" +#> [1] "Fri Nov 18 15:19:25 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset @@ -546,7 +546,7 @@ #> #> $time #> user system elapsed -#> 0.116 0.000 0.115 +#> 0.064 0.000 0.066 #> #> $mkinmod #> <mkinmod> model generated with @@ -733,7 +733,7 @@ #> } #> return(mC) #> } -#> <environment: 0x42fb560> +#> <environment: 0x3b66828> #> #> $cost_notrans #> function (P) @@ -755,7 +755,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x42fb560> +#> <environment: 0x3b66828> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -818,7 +818,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Nov 17 22:56:48 2016" +#> [1] "Fri Nov 18 15:19:25 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </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'>#> [[1]] @@ -894,7 +894,7 @@ #> #> $time #> user system elapsed -#> 0.116 0.000 0.115 +#> 0.064 0.000 0.066 #> #> $mkinmod #> <mkinmod> model generated with @@ -1081,7 +1081,7 @@ #> } #> return(mC) #> } -#> <environment: 0x42fb560> +#> <environment: 0x3b66828> #> #> $cost_notrans #> function (P) @@ -1103,7 +1103,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x42fb560> +#> <environment: 0x3b66828> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1166,7 +1166,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Nov 17 22:56:48 2016" +#> [1] "Fri Nov 18 15:19:25 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/SFO.solution-2.png b/docs/reference/SFO.solution-2.png Binary files differnew file mode 100644 index 00000000..78c083c3 --- /dev/null +++ b/docs/reference/SFO.solution-2.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 2ead8f24..30d7acdf 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -110,7 +110,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)</span></div></pre> + <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><img src='SFO.solution-2.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/SFORB.solution-2.png b/docs/reference/SFORB.solution-2.png Binary files differnew file mode 100644 index 00000000..9625debf --- /dev/null +++ b/docs/reference/SFORB.solution-2.png diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index be425d83..e8ee3e04 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -119,7 +119,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)</span></div></pre> + <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><img src='SFORB.solution-2.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/index.html b/docs/reference/index.html index 32455baa..2d052a80 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -86,14 +86,14 @@ <p class="section-desc"><p>Essential functionality</p></p> - <p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</a></p> + <p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</a></p> <ul> - <li><code><a href="mkinfit.html">mkinfit</a></code></li> + <li><code><a href="mkinmod.html">mkinmod</a></code></li> </ul> - <p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</a></p> + <p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</a></p> <ul> - <li><code><a href="mkinmod.html">mkinmod</a></code></li> + <li><code><a href="mkinfit.html">mkinfit</a></code></li> </ul> <p><a href="mmkin.html">Fit one or more kinetic models with one or more state variables to one or more datasets</a></p> @@ -104,35 +104,35 @@ <p class="section-desc"><p>Functions working with mkinfit objects</p></p> - <p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p> + <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</a></p> <ul> - <li><code><a href="endpoints.html">endpoints</a></code></li> + <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li> </ul> - <p><a href="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p> + <p><a href="summary.mkinfit.html">Summary method for class "mkinfit"</a></p> <ul> - <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li> + <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li> </ul> - <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using - list(list("mkinfit"))</a></p> + <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p> <ul> - <li><code><a href="mkinparplot.html">mkinparplot</a></code></li> + <li><code><a href="mkinresplot.html">mkinresplot</a></code></li> </ul> - <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p> + <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using + list(list("mkinfit"))</a></p> <ul> - <li><code><a href="mkinresplot.html">mkinresplot</a></code></li> + <li><code><a href="mkinparplot.html">mkinparplot</a></code></li> </ul> - <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</a></p> + <p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p> <ul> - <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li> + <li><code><a href="endpoints.html">endpoints</a></code></li> </ul> - <p><a href="summary.mkinfit.html">Summary method for class "mkinfit"</a></p> + <p><a href="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p> <ul> - <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li> + <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li> </ul> <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2> <p class="section-desc"><p>Functions working with aggregated results</p></p> @@ -151,9 +151,14 @@ <p class="section-desc"></p> - <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</a></p> + <p><a href="FOCUS_2006_datasets.html">Datasets A to F from the FOCUS Kinetics report from 2006</a></p> <ul> - <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li> + <li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code></li> + </ul> + + <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</a></p> + <ul> + <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li> </ul> <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</a></p> @@ -166,9 +171,9 @@ <li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li> </ul> - <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</a></p> + <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</a></p> <ul> - <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li> + <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li> </ul> <p><a href="mccall81_245T.html">Datasets on aerobic soil metabolism of 2,4,5-T in six soils</a></p> @@ -176,47 +181,47 @@ <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li> </ul> - <p><a href="mkinds.html">A dataset class for mkin</a></p> + <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</a></p> <ul> - <li><code><a href="mkinds.html">mkinds</a></code></li> + <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li> </ul> - <p><a href="print.mkinds.html">Print mkinds objects</a></p> + <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p> <ul> - <li><code><a href="print.mkinds.html">print.mkinds</a></code></li> + <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li> </ul> - <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</a></p> + <p><a href="mkinds.html">A dataset class for mkin</a></p> <ul> - <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li> + <li><code><a href="mkinds.html">mkinds</a></code></li> </ul> - <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p> + <p><a href="print.mkinds.html">Print mkinds objects</a></p> <ul> - <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li> + <li><code><a href="print.mkinds.html">print.mkinds</a></code></li> </ul> <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2> <p class="section-desc"></p> - <p><a href="geometric_mean.html">Calculate the geometric mean</a></p> + <p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p> <ul> - <li><code><a href="geometric_mean.html">geometric_mean</a></code></li> + <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li> </ul> - <p><a href="ilr.html">Function to perform isometric log-ratio transformation</a></p> + <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p> <ul> - <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li> + <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li> </ul> - <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p> + <p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</a></p> <ul> - <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li> + <li><code><a href="mkinsub.html">mkinsub</a></code></li> </ul> - <p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p> + <p><a href="print.mkinmod.html">Print mkinmod objects</a></p> <ul> - <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li> + <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li> </ul> <p><a href="mkinpredict.html">Produce predictions from a kinetic model using specific parameters</a></p> @@ -224,19 +229,19 @@ <li><code><a href="mkinpredict.html">mkinpredict</a></code></li> </ul> - <p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</a></p> + <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</a></p> <ul> - <li><code><a href="mkinsub.html">mkinsub</a></code></li> + <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li> </ul> - <p><a href="print.mkinmod.html">Print mkinmod objects</a></p> + <p><a href="ilr.html">Function to perform isometric log-ratio transformation</a></p> <ul> - <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li> + <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li> </ul> - <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</a></p> + <p><a href="geometric_mean.html">Calculate the geometric mean</a></p> <ul> - <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li> + <li><code><a href="geometric_mean.html">geometric_mean</a></code></li> </ul> <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2> <p class="section-desc"><p>Parent only model solutions</p></p> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 4314c84e..7b294129 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -111,19 +111,253 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), <span class='kw'>phenol</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> -<span class='co'># fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span> -<span class='co'># summary(fit.1, data = FALSE)</span> -<span class='co'># </span> -<span class='co'>## ---------------------------------------------</span> + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + <span class='no'>fit.1</span> <span class='kw'><-</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>))</div><div class='output co'>#> Model cost at call 1 : 13655.2 +#> Model cost at call 2 : 13655.2 +#> Model cost at call 8 : 9191.59 +#> Model cost at call 16 : 5663.584 +#> Model cost at call 17 : 5663.582 +#> Model cost at call 18 : 5663.566 +#> Model cost at call 19 : 5663.55 +#> Model cost at call 23 : 3035.567 +#> Model cost at call 24 : 3035.566 +#> Model cost at call 26 : 3035.561 +#> Model cost at call 27 : 3035.559 +#> Model cost at call 28 : 3035.558 +#> Model cost at call 30 : 2252.97 +#> Model cost at call 31 : 2252.965 +#> Model cost at call 32 : 2252.965 +#> Model cost at call 36 : 2252.958 +#> Model cost at call 37 : 1220.201 +#> Model cost at call 38 : 1220.2 +#> Model cost at call 39 : 1220.199 +#> Model cost at call 41 : 1220.183 +#> Model cost at call 45 : 507.1358 +#> Model cost at call 48 : 507.1353 +#> Model cost at call 52 : 198.5695 +#> Model cost at call 55 : 198.5694 +#> Model cost at call 60 : 175.8239 +#> Model cost at call 63 : 175.8239 +#> Model cost at call 67 : 170.6316 +#> Model cost at call 69 : 170.6316 +#> Model cost at call 74 : 165.881 +#> Model cost at call 77 : 165.881 +#> Model cost at call 81 : 161.6423 +#> Model cost at call 84 : 161.6423 +#> Model cost at call 88 : 158.2953 +#> Model cost at call 91 : 158.2953 +#> Model cost at call 95 : 156.7311 +#> Model cost at call 97 : 156.731 +#> Model cost at call 103 : 155.998 +#> Model cost at call 106 : 155.998 +#> Model cost at call 110 : 155.6263 +#> Model cost at call 113 : 155.6262 +#> Model cost at call 116 : 155.6262 +#> Model cost at call 117 : 155.1202 +#> Model cost at call 120 : 155.1202 +#> Model cost at call 124 : 154.4133 +#> Model cost at call 125 : 153.8489 +#> Model cost at call 126 : 152.7413 +#> Model cost at call 129 : 152.7413 +#> Model cost at call 132 : 152.7413 +#> Model cost at call 133 : 150.3995 +#> Model cost at call 134 : 148.7256 +#> Model cost at call 135 : 147.2618 +#> Model cost at call 137 : 147.2618 +#> Model cost at call 139 : 147.2618 +#> Model cost at call 142 : 145.115 +#> Model cost at call 144 : 145.115 +#> Model cost at call 145 : 145.115 +#> Model cost at call 146 : 145.115 +#> Model cost at call 147 : 145.115 +#> Model cost at call 150 : 143.7878 +#> Model cost at call 157 : 142.8531 +#> Model cost at call 160 : 142.8531 +#> Model cost at call 164 : 142.7325 +#> Model cost at call 167 : 142.7325 +#> Model cost at call 169 : 142.7325 +#> Model cost at call 172 : 141.8393 +#> Model cost at call 173 : 141.8393 +#> Model cost at call 174 : 141.8393 +#> Model cost at call 179 : 141.3446 +#> Model cost at call 180 : 141.3446 +#> Model cost at call 181 : 141.3446 +#> Model cost at call 186 : 141.1111 +#> Model cost at call 193 : 140.7786 +#> Model cost at call 200 : 140.451 +#> Model cost at call 207 : 140.1395 +#> Model cost at call 214 : 139.7903 +#> Model cost at call 221 : 139.5476 +#> Model cost at call 228 : 139.4441 +#> Model cost at call 235 : 139.3204 +#> Model cost at call 242 : 139.2508 +#> Model cost at call 249 : 139.1891 +#> Model cost at call 256 : 139.1561 +#> Model cost at call 263 : 139.137 +#> Model cost at call 270 : 139.1278 +#> Model cost at call 271 : 139.1278 +#> Model cost at call 279 : 139.1211 +#> Model cost at call 280 : 139.1211 +#> Model cost at call 281 : 139.1211 +#> Model cost at call 282 : 139.1211 +#> Model cost at call 286 : 139.1179 +#> Model cost at call 287 : 139.1179 +#> Model cost at call 291 : 139.1179 +#> Model cost at call 294 : 139.1179 +#> Model cost at call 298 : 139.1158 +#> Model cost at call 299 : 139.1158 +#> Model cost at call 302 : 139.1158 +#> Model cost at call 310 : 139.1148 +#> Model cost at call 311 : 139.1148 +#> Model cost at call 315 : 139.1148 +#> Model cost at call 322 : 139.1143 +#> Model cost at call 323 : 139.1143 +#> Model cost at call 326 : 139.1143 +#> Model cost at call 334 : 139.114 +#> Model cost at call 335 : 139.114 +#> Model cost at call 338 : 139.114 +#> Model cost at call 339 : 139.114 +#> Model cost at call 346 : 139.1139 +#> Model cost at call 347 : 139.1139 +#> Model cost at call 350 : 139.1139 +#> Model cost at call 351 : 139.1139 +#> Model cost at call 358 : 139.1139 +#> Model cost at call 359 : 139.1139 +#> Model cost at call 362 : 139.1139 +#> Model cost at call 363 : 139.1139 +#> Model cost at call 370 : 139.1138 +#> Model cost at call 382 : 139.1138 +#> Model cost at call 390 : 139.1138 +#> Model cost at call 395 : 139.1138 +#> Model cost at call 403 : 139.1138 +#> Model cost at call 408 : 139.1138 +#> Model cost at call 416 : 139.1138 +#> Model cost at call 421 : 139.1138 +#> Model cost at call 429 : 139.1138 +#> Model cost at call 434 : 139.1138 +#> Model cost at call 442 : 139.1138 +#> Model cost at call 447 : 139.1138 +#> Model cost at call 455 : 139.1138 +#> Model cost at call 460 : 139.1138 +#> Model cost at call 468 : 139.1138 +#> Model cost at call 473 : 139.1138 +#> Model cost at call 481 : 139.1138 +#> Model cost at call 486 : 139.1138 +#> Model cost at call 494 : 139.1138 +#> Model cost at call 499 : 139.1138 +#> Model cost at call 507 : 139.1138 +#> Model cost at call 512 : 139.1138 +#> Model cost at call 519 : 139.1138 +#> Model cost at call 520 : 139.1138 +#> Model cost at call 525 : 139.1138 +#> Model cost at call 538 : 139.1138 +#> Model cost at call 545 : 139.1138 +#> Model cost at call 546 : 139.1138 +#> Model cost at call 551 : 139.1138 +#> Model cost at call 558 : 139.1138 +#> Model cost at call 559 : 139.1138 +#> Model cost at call 564 : 139.1138 +#> Model cost at call 571 : 139.1138 +#> Model cost at call 580 : 139.1138 +#> Model cost at call 588 : 139.1138 </div><div class='output co'>#> <span class='warning'>Warning: Optimisation by method Port did not converge.</span> +#> <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'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:19:33 2016 +#> Date of summary: Fri Nov 18 15:19:33 2016 +#> +#> +#> Warning: Optimisation by method Port did not converge. +#> Convergence code is 1 +#> +#> +#> Equations: +#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 +#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - +#> k_phenol_anisole * phenol +#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 590 model solutions performed in 3.45 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> T245_0 100.9000 state +#> k_T245_sink 0.1000 deparm +#> k_T245_phenol 0.1001 deparm +#> k_phenol_sink 0.1002 deparm +#> k_phenol_anisole 0.1003 deparm +#> k_anisole_sink 0.1004 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> T245_0 100.900000 -Inf Inf +#> log_k_T245_sink -2.302585 -Inf Inf +#> log_k_T245_phenol -2.301586 -Inf Inf +#> log_k_phenol_sink -2.300587 -Inf Inf +#> log_k_phenol_anisole -2.299590 -Inf Inf +#> log_k_anisole_sink -2.298593 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> phenol_0 0 state +#> anisole_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> T245_0 103.9000 NA NA NA +#> log_k_T245_sink -4.1130 NA NA NA +#> log_k_T245_phenol -3.6120 NA NA NA +#> log_k_phenol_sink -26.3900 NA NA NA +#> log_k_phenol_anisole -0.9037 NA NA NA +#> log_k_anisole_sink -5.0090 NA NA NA +#> +#> Parameter correlation:</div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#> Could not estimate covariance matrix; singular system: +#> +#> Residual standard error: 2.78 on 18 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA +#> k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA +#> k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA +#> k_phenol_sink 3.457e-12 1.230e-11 5.000e-01 NA NA +#> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA +#> k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 10.070 6 16 +#> T245 7.908 3 5 +#> phenol 106.445 2 5 +#> anisole 5.379 1 6 +#> +#> Resulting formation fractions: +#> ff +#> T245_sink 3.772e-01 +#> T245_phenol 6.228e-01 +#> phenol_sink 8.534e-12 +#> phenol_anisole 1.000e+00 +#> anisole_sink 1.000e+00 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> T245 15.982 53.091 +#> phenol 1.711 5.685 +#> anisole 103.784 344.763</div><div class='input'> <span class='co'># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span> <span class='no'>fit.2</span> <span class='kw'><-</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'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <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'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 17 22:56:55 2016 -#> Date of summary: Thu Nov 17 22:56:55 2016 +#> Date of fit: Fri Nov 18 15:19:35 2016 +#> Date of summary: Fri Nov 18 15:19:35 2016 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -133,7 +367,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.457 s +#> Fitted with method Port using 246 model solutions performed in 1.477 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 891bc18b..f6ffd21d 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -359,15 +359,15 @@ <span class='no'>fit</span> <span class='kw'><-</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'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 17 22:56:57 2016 -#> Date of summary: Thu Nov 17 22:56:57 2016 +#> Date of fit: Fri Nov 18 15:19:37 2016 +#> Date of summary: Fri Nov 18 15:19:37 2016 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.158 s +#> Fitted with method Port using 64 model solutions performed in 0.152 s #> #> Weighting: none #> @@ -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'>#> <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'><-</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'>#> user system elapsed -#> 1.168 1.260 0.924 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.220 1.184 0.904 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -448,63 +448,2114 @@ #> DT50 DT90 #> parent 7.022929 23.32967 #> m1 131.760712 437.69961 -#> </div><div class='input'><span class='co'>## Not run: ------------------------------------</span> -<span class='co'># # deSolve is slower when no C compiler (gcc) was available during model generation</span> -<span class='co'># print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,</span> -<span class='co'># solution_type = "deSolve")))</span> -<span class='co'># coef(fit.deSolve)</span> -<span class='co'># endpoints(fit.deSolve)</span> -<span class='co'>## ---------------------------------------------</span> +#> </div><div class='input'> +<span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span> +<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit.deSolve</span> <span class='kw'><-</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'>"deSolve"</span>)))</div><div class='output co'>#> Model cost at call 1 : 18915.53 +#> Model cost at call 2 : 18915.53 +#> Model cost at call 6 : 11424.02 +#> Model cost at call 10 : 11424 +#> Model cost at call 12 : 4094.396 +#> Model cost at call 16 : 4094.396 +#> Model cost at call 19 : 1340.595 +#> Model cost at call 20 : 1340.593 +#> Model cost at call 25 : 1072.239 +#> Model cost at call 28 : 1072.236 +#> Model cost at call 30 : 874.2614 +#> Model cost at call 33 : 874.2611 +#> Model cost at call 35 : 616.2379 +#> Model cost at call 37 : 616.2374 +#> Model cost at call 40 : 467.4388 +#> Model cost at call 42 : 467.4382 +#> Model cost at call 46 : 398.2914 +#> Model cost at call 48 : 398.2914 +#> Model cost at call 49 : 398.2913 +#> Model cost at call 51 : 395.0712 +#> Model cost at call 54 : 395.0711 +#> Model cost at call 56 : 378.3298 +#> Model cost at call 59 : 378.3298 +#> Model cost at call 62 : 376.9812 +#> Model cost at call 64 : 376.9811 +#> Model cost at call 67 : 375.2085 +#> Model cost at call 69 : 375.2085 +#> Model cost at call 70 : 375.2085 +#> Model cost at call 71 : 375.2085 +#> Model cost at call 72 : 374.5723 +#> Model cost at call 74 : 374.5723 +#> Model cost at call 77 : 374.0075 +#> Model cost at call 79 : 374.0075 +#> Model cost at call 80 : 374.0075 +#> Model cost at call 82 : 373.1711 +#> Model cost at call 84 : 373.1711 +#> Model cost at call 87 : 372.6445 +#> Model cost at call 88 : 372.1614 +#> Model cost at call 90 : 372.1614 +#> Model cost at call 91 : 372.1614 +#> Model cost at call 94 : 371.6464 +#> Model cost at call 99 : 371.4299 +#> Model cost at call 101 : 371.4299 +#> Model cost at call 104 : 371.407 +#> Model cost at call 106 : 371.407 +#> Model cost at call 107 : 371.407 +#> Model cost at call 109 : 371.2524 +#> Model cost at call 113 : 371.2524 +#> Model cost at call 114 : 371.2136 +#> Model cost at call 115 : 371.2136 +#> Model cost at call 116 : 371.2136 +#> Model cost at call 119 : 371.2134 +#> Model cost at call 120 : 371.2134 +#> Model cost at call 122 : 371.2134 +#> Model cost at call 123 : 371.2134 +#> Model cost at call 125 : 371.2134 +#> Model cost at call 126 : 371.2134 +#> Model cost at call 135 : 371.2134 +#> Model cost at call 147 : 371.2134 +#> Model cost at call 152 : 371.2134 +#> Optimisation by method Port successfully terminated. +#> user system elapsed +#> 0.712 0.040 0.707 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 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'>#> $ff +#> parent_sink parent_m1 m1_sink +#> 0.485524 0.514476 1.000000 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 7.022929 23.32967 +#> m1 131.760713 437.69961 +#> </div><div class='input'> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</span> -<span class='co'>## Not run: ------------------------------------</span> -<span class='co'># FOMC_SFO <- mkinmod(</span> -<span class='co'># parent = mkinsub("FOMC", "m1"),</span> -<span class='co'># m1 = mkinsub("SFO"))</span> -<span class='co'># # Fit the model to the FOCUS example dataset D using defaults</span> -<span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D)</span> -<span class='co'># # Use starting parameters from parent only FOMC fit</span> -<span class='co'># fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE)</span> -<span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D,</span> -<span class='co'># parms.ini = fit.FOMC$bparms.ode, plot=TRUE)</span> -<span class='co'># </span> -<span class='co'># # Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span> -<span class='co'># SFORB_SFO <- mkinmod(</span> -<span class='co'># parent = list(type = "SFORB", to = "m1", sink = TRUE),</span> -<span class='co'># m1 = list(type = "SFO"))</span> -<span class='co'># # Fit the model to the FOCUS example dataset D using defaults</span> -<span class='co'># fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D)</span> -<span class='co'># fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve")</span> -<span class='co'># # Use starting parameters from parent only SFORB fit (not really needed in this case)</span> -<span class='co'># fit.SFORB = mkinfit("SFORB", FOCUS_2006_D)</span> -<span class='co'># fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)</span> -<span class='co'>## ---------------------------------------------</span> - -<span class='co'>## Not run: ------------------------------------</span> -<span class='co'># # Weighted fits, including IRLS</span> -<span class='co'># SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),</span> -<span class='co'># m1 = mkinsub("SFO"), use_of_ff = "max")</span> -<span class='co'># f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span> -<span class='co'># summary(f.noweight)</span> -<span class='co'># f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs")</span> -<span class='co'># summary(f.irls)</span> -<span class='co'># f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean")</span> -<span class='co'># summary(f.w.mean)</span> -<span class='co'># f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value")</span> -<span class='co'># summary(f.w.value)</span> -<span class='co'>## ---------------------------------------------</span> - -<span class='co'>## Not run: ------------------------------------</span> -<span class='co'># # Manual weighting</span> -<span class='co'># dw <- FOCUS_2006_D</span> -<span class='co'># errors <- c(parent = 2, m1 = 1)</span> -<span class='co'># dw$err.man <- errors[FOCUS_2006_D$name]</span> -<span class='co'># f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man")</span> -<span class='co'># summary(f.w.man)</span> -<span class='co'># f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man",</span> -<span class='co'># reweight.method = "obs")</span> -<span class='co'># summary(f.w.man.irls)</span> -<span class='co'>## ---------------------------------------------</span></div></pre> + +<span class='no'>FOMC_SFO</span> <span class='kw'><-</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'>"FOMC"</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>))</div><div class='output co'>#> <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='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> Model cost at call 1 : 18857.28 +#> Model cost at call 4 : 18857.28 +#> Model cost at call 5 : 18857.28 +#> Model cost at call 8 : 15273.94 +#> Model cost at call 9 : 15273.93 +#> Model cost at call 12 : 15273.67 +#> Model cost at call 13 : 15273.64 +#> Model cost at call 14 : 12764.42 +#> Model cost at call 15 : 8382.7 +#> Model cost at call 20 : 8382.696 +#> Model cost at call 23 : 2729.177 +#> Model cost at call 24 : 2729.175 +#> Model cost at call 26 : 2729.164 +#> Model cost at call 30 : 2299.383 +#> Model cost at call 34 : 2299.379 +#> Model cost at call 35 : 2299.373 +#> Model cost at call 36 : 1944.782 +#> Model cost at call 40 : 1944.782 +#> Model cost at call 42 : 1328.087 +#> Model cost at call 43 : 908.661 +#> Model cost at call 44 : 908.6604 +#> Model cost at call 50 : 877.3556 +#> Model cost at call 51 : 877.3554 +#> Model cost at call 54 : 877.3546 +#> Model cost at call 56 : 769.5186 +#> Model cost at call 59 : 769.5157 +#> Model cost at call 62 : 690.3426 +#> Model cost at call 66 : 690.3425 +#> Model cost at call 68 : 608.4032 +#> Model cost at call 72 : 608.4031 +#> Model cost at call 73 : 608.4031 +#> Model cost at call 74 : 601.5178 +#> Model cost at call 78 : 601.5174 +#> Model cost at call 79 : 601.5174 +#> Model cost at call 80 : 459.9885 +#> Model cost at call 81 : 459.9883 +#> Model cost at call 83 : 459.9878 +#> Model cost at call 87 : 447.0145 +#> Model cost at call 91 : 447.0145 +#> Model cost at call 94 : 445.7322 +#> Model cost at call 97 : 445.7322 +#> Model cost at call 99 : 445.7322 +#> Model cost at call 100 : 444.6965 +#> Model cost at call 103 : 444.6965 +#> Model cost at call 106 : 442.9742 +#> Model cost at call 109 : 442.9742 +#> Model cost at call 112 : 439.9665 +#> Model cost at call 115 : 439.9665 +#> Model cost at call 116 : 439.9664 +#> Model cost at call 118 : 435.0752 +#> Model cost at call 121 : 435.0751 +#> Model cost at call 124 : 430.4718 +#> Model cost at call 127 : 430.4717 +#> Model cost at call 132 : 424.7004 +#> Model cost at call 134 : 424.7003 +#> Model cost at call 138 : 423.6102 +#> Model cost at call 141 : 423.6102 +#> Model cost at call 142 : 423.6102 +#> Model cost at call 144 : 421.1786 +#> Model cost at call 147 : 421.1786 +#> Model cost at call 148 : 421.1786 +#> Model cost at call 150 : 418.1431 +#> Model cost at call 151 : 412.8665 +#> Model cost at call 152 : 396.6067 +#> Model cost at call 154 : 396.6067 +#> Model cost at call 158 : 391.0492 +#> Model cost at call 160 : 391.0492 +#> Model cost at call 164 : 385.8205 +#> Model cost at call 165 : 385.8205 +#> Model cost at call 170 : 379.7674 +#> Model cost at call 171 : 379.7674 +#> Model cost at call 172 : 379.7674 +#> Model cost at call 176 : 374.9389 +#> Model cost at call 177 : 374.9389 +#> Model cost at call 182 : 372.727 +#> Model cost at call 185 : 372.727 +#> Model cost at call 188 : 371.5297 +#> Model cost at call 194 : 370.3738 +#> Model cost at call 195 : 370.3738 +#> Model cost at call 200 : 370.0182 +#> Model cost at call 206 : 369.8634 +#> Model cost at call 212 : 369.8188 +#> Model cost at call 213 : 369.8188 +#> Model cost at call 219 : 369.8114 +#> Model cost at call 221 : 369.8114 +#> Model cost at call 224 : 369.8114 +#> Model cost at call 226 : 369.8114 +#> Model cost at call 230 : 369.8105 +#> Model cost at call 231 : 369.8105 +#> Model cost at call 235 : 369.8105 +#> Model cost at call 236 : 369.8105 +#> Model cost at call 237 : 369.8105 +#> Model cost at call 238 : 369.8105 +#> Model cost at call 249 : 369.8105 +#> Model cost at call 260 : 369.8105 +#> Model cost at call 275 : 369.8105 +#> Model cost at call 276 : 369.8105 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='co'># Use starting parameters from parent only FOMC fit</span> +<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> Model cost at call 1 : 3237.008 +#> Model cost at call 3 : 3237.007 +#> Model cost at call 6 : 671.2571 +#> Model cost at call 7 : 671.2559 +#> Model cost at call 8 : 671.2301 +#> Model cost at call 9 : 671.2249 +#> Model cost at call 10 : 468.4899 +#> Model cost at call 12 : 468.4899 +#> Model cost at call 14 : 371.3486 +#> Model cost at call 16 : 371.3485 +#> Model cost at call 18 : 346.2972 +#> Model cost at call 19 : 346.2971 +#> Model cost at call 20 : 346.297 +#> Model cost at call 21 : 346.2969 +#> Model cost at call 22 : 269.7053 +#> Model cost at call 23 : 269.7053 +#> Model cost at call 26 : 243.9936 +#> Model cost at call 27 : 235.1625 +#> Model cost at call 28 : 235.1624 +#> Model cost at call 30 : 235.1624 +#> Model cost at call 31 : 224.2195 +#> Model cost at call 35 : 218.1922 +#> Model cost at call 36 : 218.1922 +#> Model cost at call 38 : 218.1922 +#> Model cost at call 39 : 211.5012 +#> Model cost at call 41 : 211.5012 +#> Model cost at call 43 : 207.9511 +#> Model cost at call 44 : 207.9511 +#> Model cost at call 47 : 206.5377 +#> Model cost at call 51 : 205.8736 +#> Model cost at call 55 : 205.5625 +#> Model cost at call 59 : 205.4704 +#> Model cost at call 63 : 205.4499 +#> Model cost at call 67 : 205.448 +#> Model cost at call 69 : 205.448 +#> Model cost at call 70 : 205.448 +#> Model cost at call 73 : 205.448 +#> Model cost at call 74 : 205.4478 +#> Model cost at call 75 : 205.4478 +#> Model cost at call 77 : 205.4478 +#> Model cost at call 79 : 205.4478 +#> Model cost at call 84 : 205.4478 +#> Model cost at call 95 : 205.4478 +#> Model cost at call 98 : 205.4478 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#> Model cost at call 1 : 15169.96 +#> Model cost at call 2 : 15169.96 +#> Model cost at call 7 : 8247.462 +#> Model cost at call 14 : 6734.371 +#> Model cost at call 15 : 6734.339 +#> Model cost at call 16 : 6734.136 +#> Model cost at call 20 : 4855.056 +#> Model cost at call 24 : 4855.038 +#> Model cost at call 27 : 1239.986 +#> Model cost at call 29 : 1239.985 +#> Model cost at call 34 : 1030.523 +#> Model cost at call 38 : 1030.523 +#> Model cost at call 40 : 894.2766 +#> Model cost at call 43 : 894.275 +#> Model cost at call 46 : 750.3629 +#> Model cost at call 49 : 750.3623 +#> Model cost at call 52 : 627.6819 +#> Model cost at call 55 : 627.6818 +#> Model cost at call 58 : 546.2947 +#> Model cost at call 61 : 546.2944 +#> Model cost at call 65 : 502.5529 +#> Model cost at call 69 : 502.5525 +#> Model cost at call 70 : 502.5525 +#> Model cost at call 71 : 475.2423 +#> Model cost at call 72 : 465.5298 +#> Model cost at call 75 : 465.5298 +#> Model cost at call 76 : 465.5297 +#> Model cost at call 78 : 464.9476 +#> Model cost at call 81 : 464.9476 +#> Model cost at call 82 : 464.9473 +#> Model cost at call 84 : 426.9626 +#> Model cost at call 88 : 426.9626 +#> Model cost at call 90 : 414.5235 +#> Model cost at call 93 : 414.5234 +#> Model cost at call 96 : 412.1478 +#> Model cost at call 99 : 412.1477 +#> Model cost at call 100 : 412.1477 +#> Model cost at call 101 : 412.1477 +#> Model cost at call 102 : 394.146 +#> Model cost at call 105 : 394.146 +#> Model cost at call 106 : 394.146 +#> Model cost at call 107 : 394.146 +#> Model cost at call 108 : 384.2002 +#> Model cost at call 112 : 384.2001 +#> Model cost at call 113 : 384.2001 +#> Model cost at call 115 : 380.5495 +#> Model cost at call 119 : 380.5494 +#> Model cost at call 120 : 380.5494 +#> Model cost at call 121 : 378.4803 +#> Model cost at call 123 : 378.4802 +#> Model cost at call 124 : 378.4792 +#> Model cost at call 127 : 374.8432 +#> Model cost at call 129 : 374.8431 +#> Model cost at call 133 : 372.8364 +#> Model cost at call 136 : 372.8364 +#> Model cost at call 137 : 372.8363 +#> Model cost at call 138 : 372.8363 +#> Model cost at call 141 : 372.668 +#> Model cost at call 145 : 372.6679 +#> Model cost at call 147 : 372.5882 +#> Model cost at call 150 : 372.5882 +#> Model cost at call 153 : 372.4828 +#> Model cost at call 156 : 372.4828 +#> Model cost at call 159 : 372.3639 +#> Model cost at call 162 : 372.3639 +#> Model cost at call 163 : 372.3639 +#> Model cost at call 164 : 372.3639 +#> Model cost at call 165 : 372.1959 +#> Model cost at call 168 : 372.1959 +#> Model cost at call 171 : 371.9627 +#> Model cost at call 172 : 371.7467 +#> Model cost at call 173 : 371.1161 +#> Model cost at call 174 : 370.3326 +#> Model cost at call 177 : 370.3326 +#> Model cost at call 178 : 370.3326 +#> Model cost at call 180 : 370.3267 +#> Model cost at call 186 : 370.0471 +#> Model cost at call 187 : 370.0471 +#> Model cost at call 193 : 369.9649 +#> Model cost at call 194 : 369.9649 +#> Model cost at call 196 : 369.9649 +#> Model cost at call 199 : 369.8684 +#> Model cost at call 200 : 369.8684 +#> Model cost at call 204 : 369.8684 +#> Model cost at call 206 : 369.8349 +#> Model cost at call 207 : 369.8349 +#> Model cost at call 209 : 369.8349 +#> Model cost at call 210 : 369.8349 +#> Model cost at call 211 : 369.8349 +#> Model cost at call 212 : 369.8105 +#> Model cost at call 214 : 369.8105 +#> Model cost at call 218 : 369.8105 +#> Model cost at call 220 : 369.8105 +#> Model cost at call 225 : 369.8105 +#> Model cost at call 229 : 369.8105 +#> Model cost at call 231 : 369.8105 +#> Model cost at call 232 : 369.8105 +#> Model cost at call 236 : 369.8105 +#> Model cost at call 239 : 369.8105 +#> Model cost at call 240 : 369.8105 +#> Model cost at call 255 : 369.8105 +#> Model cost at call 258 : 369.8105 +#> Optimisation by method Port successfully terminated.</div><div class='input'> +<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span> +<span class='no'>SFORB_SFO</span> <span class='kw'><-</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'>"SFORB"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <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='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> Model cost at call 1 : 19233.21 +#> Model cost at call 2 : 19233.21 +#> Model cost at call 5 : 19233.21 +#> Model cost at call 8 : 14482.65 +#> Model cost at call 11 : 14482.51 +#> Model cost at call 13 : 14482.17 +#> Model cost at call 15 : 6973.814 +#> Model cost at call 16 : 5161.041 +#> Model cost at call 17 : 5161.029 +#> Model cost at call 22 : 5161.026 +#> Model cost at call 24 : 3249.595 +#> Model cost at call 26 : 3249.595 +#> Model cost at call 27 : 3249.519 +#> Model cost at call 31 : 2615.891 +#> Model cost at call 32 : 2615.888 +#> Model cost at call 39 : 989.1788 +#> Model cost at call 44 : 989.1772 +#> Model cost at call 45 : 989.1771 +#> Model cost at call 47 : 647.4307 +#> Model cost at call 50 : 647.4302 +#> Model cost at call 51 : 647.4261 +#> Model cost at call 54 : 626.7937 +#> Model cost at call 55 : 626.7935 +#> Model cost at call 56 : 626.7931 +#> Model cost at call 61 : 527.9042 +#> Model cost at call 62 : 527.9041 +#> Model cost at call 68 : 505.8828 +#> Model cost at call 70 : 505.8828 +#> Model cost at call 73 : 505.8827 +#> Model cost at call 75 : 452.8932 +#> Model cost at call 77 : 452.893 +#> Model cost at call 82 : 414.4918 +#> Model cost at call 83 : 414.4918 +#> Model cost at call 84 : 414.4918 +#> Model cost at call 88 : 414.4917 +#> Model cost at call 89 : 408.2617 +#> Model cost at call 90 : 408.2616 +#> Model cost at call 91 : 408.2616 +#> Model cost at call 95 : 408.2615 +#> Model cost at call 96 : 384.4461 +#> Model cost at call 102 : 384.4461 +#> Model cost at call 104 : 383.4905 +#> Model cost at call 105 : 383.4905 +#> Model cost at call 106 : 383.4905 +#> Model cost at call 109 : 383.4904 +#> Model cost at call 111 : 381.8828 +#> Model cost at call 112 : 381.8827 +#> Model cost at call 118 : 380.8499 +#> Model cost at call 120 : 380.8499 +#> Model cost at call 123 : 380.8499 +#> Model cost at call 125 : 379.1403 +#> Model cost at call 127 : 379.1402 +#> Model cost at call 132 : 376.4962 +#> Model cost at call 133 : 373.0958 +#> Model cost at call 134 : 365.247 +#> Model cost at call 137 : 365.2469 +#> Model cost at call 142 : 360.8231 +#> Model cost at call 143 : 360.8231 +#> Model cost at call 146 : 360.8231 +#> Model cost at call 148 : 360.8231 +#> Model cost at call 149 : 358.3976 +#> Model cost at call 152 : 358.3976 +#> Model cost at call 154 : 358.3976 +#> Model cost at call 156 : 355.9066 +#> Model cost at call 157 : 355.9066 +#> Model cost at call 163 : 354.3386 +#> Model cost at call 164 : 353.6335 +#> Model cost at call 172 : 353.2094 +#> Model cost at call 173 : 353.2094 +#> Model cost at call 174 : 353.2093 +#> Model cost at call 177 : 353.2093 +#> Model cost at call 178 : 353.2093 +#> Model cost at call 179 : 352.6641 +#> Model cost at call 182 : 352.6641 +#> Model cost at call 183 : 352.6641 +#> Model cost at call 186 : 352.4908 +#> Model cost at call 187 : 352.4429 +#> Model cost at call 195 : 352.3246 +#> Model cost at call 203 : 352.2858 +#> Model cost at call 204 : 352.2858 +#> Model cost at call 205 : 352.2858 +#> Model cost at call 206 : 352.2858 +#> Model cost at call 207 : 352.2858 +#> Model cost at call 210 : 352.2332 +#> Model cost at call 211 : 352.2081 +#> Model cost at call 214 : 352.2081 +#> Model cost at call 216 : 352.2081 +#> Model cost at call 218 : 352.2049 +#> Model cost at call 219 : 352.2049 +#> Model cost at call 220 : 352.2049 +#> Model cost at call 226 : 352.2048 +#> Model cost at call 228 : 352.2048 +#> Model cost at call 231 : 352.2048 +#> Model cost at call 232 : 352.2048 +#> Model cost at call 238 : 352.2048 +#> Model cost at call 239 : 352.2048 +#> Model cost at call 251 : 352.2048 +#> Model cost at call 264 : 352.2048 +#> Model cost at call 283 : 352.2048 +#> Model cost at call 284 : 352.2048 +#> Model cost at call 285 : 352.2048 +#> Model cost at call 286 : 352.2048 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#> Model cost at call 1 : 19233.21 +#> Model cost at call 2 : 19233.21 +#> Model cost at call 5 : 19233.21 +#> Model cost at call 8 : 14482.65 +#> Model cost at call 11 : 14482.51 +#> Model cost at call 13 : 14482.17 +#> Model cost at call 15 : 6973.814 +#> Model cost at call 16 : 5161.041 +#> Model cost at call 17 : 5161.029 +#> Model cost at call 22 : 5161.026 +#> Model cost at call 24 : 3249.595 +#> Model cost at call 26 : 3249.595 +#> Model cost at call 27 : 3249.519 +#> Model cost at call 31 : 2615.891 +#> Model cost at call 32 : 2615.888 +#> Model cost at call 39 : 989.1788 +#> Model cost at call 44 : 989.1772 +#> Model cost at call 45 : 989.1771 +#> Model cost at call 47 : 647.4307 +#> Model cost at call 50 : 647.4302 +#> Model cost at call 51 : 647.4261 +#> Model cost at call 54 : 626.7937 +#> Model cost at call 55 : 626.7935 +#> Model cost at call 56 : 626.7931 +#> Model cost at call 61 : 527.9042 +#> Model cost at call 62 : 527.9041 +#> Model cost at call 68 : 505.8828 +#> Model cost at call 70 : 505.8828 +#> Model cost at call 73 : 505.8827 +#> Model cost at call 75 : 452.8932 +#> Model cost at call 77 : 452.893 +#> Model cost at call 82 : 414.4918 +#> Model cost at call 83 : 414.4918 +#> Model cost at call 84 : 414.4918 +#> Model cost at call 88 : 414.4917 +#> Model cost at call 89 : 408.2617 +#> Model cost at call 90 : 408.2616 +#> Model cost at call 91 : 408.2616 +#> Model cost at call 95 : 408.2615 +#> Model cost at call 96 : 384.4461 +#> Model cost at call 102 : 384.4461 +#> Model cost at call 104 : 383.4905 +#> Model cost at call 105 : 383.4905 +#> Model cost at call 106 : 383.4905 +#> Model cost at call 109 : 383.4904 +#> Model cost at call 111 : 381.8828 +#> Model cost at call 112 : 381.8827 +#> Model cost at call 118 : 380.8499 +#> Model cost at call 120 : 380.8499 +#> Model cost at call 123 : 380.8499 +#> Model cost at call 125 : 379.1403 +#> Model cost at call 127 : 379.1402 +#> Model cost at call 132 : 376.4962 +#> Model cost at call 133 : 373.0958 +#> Model cost at call 134 : 365.247 +#> Model cost at call 137 : 365.2469 +#> Model cost at call 142 : 360.8231 +#> Model cost at call 143 : 360.8231 +#> Model cost at call 146 : 360.8231 +#> Model cost at call 148 : 360.8231 +#> Model cost at call 149 : 358.3976 +#> Model cost at call 152 : 358.3976 +#> Model cost at call 154 : 358.3976 +#> Model cost at call 156 : 355.9066 +#> Model cost at call 157 : 355.9066 +#> Model cost at call 163 : 354.3386 +#> Model cost at call 164 : 353.6335 +#> Model cost at call 172 : 353.2094 +#> Model cost at call 173 : 353.2094 +#> Model cost at call 174 : 353.2093 +#> Model cost at call 177 : 353.2093 +#> Model cost at call 178 : 353.2093 +#> Model cost at call 179 : 352.6641 +#> Model cost at call 182 : 352.6641 +#> Model cost at call 183 : 352.6641 +#> Model cost at call 186 : 352.4908 +#> Model cost at call 187 : 352.4429 +#> Model cost at call 195 : 352.3246 +#> Model cost at call 203 : 352.2858 +#> Model cost at call 204 : 352.2858 +#> Model cost at call 205 : 352.2858 +#> Model cost at call 206 : 352.2858 +#> Model cost at call 207 : 352.2858 +#> Model cost at call 210 : 352.2332 +#> Model cost at call 211 : 352.2081 +#> Model cost at call 214 : 352.2081 +#> Model cost at call 216 : 352.2081 +#> Model cost at call 218 : 352.2049 +#> Model cost at call 219 : 352.2049 +#> Model cost at call 220 : 352.2049 +#> Model cost at call 226 : 352.2048 +#> Model cost at call 228 : 352.2048 +#> Model cost at call 231 : 352.2048 +#> Model cost at call 232 : 352.2048 +#> Model cost at call 238 : 352.2048 +#> Model cost at call 239 : 352.2048 +#> Model cost at call 251 : 352.2048 +#> Model cost at call 264 : 352.2048 +#> Model cost at call 283 : 352.2048 +#> Model cost at call 284 : 352.2048 +#> Model cost at call 285 : 352.2048 +#> Model cost at call 286 : 352.2048 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span> +<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> Model cost at call 1 : 10426.65 +#> Model cost at call 3 : 10426.65 +#> Model cost at call 6 : 1995.326 +#> Model cost at call 7 : 1995.322 +#> Model cost at call 8 : 1995.14 +#> Model cost at call 11 : 718.5568 +#> Model cost at call 12 : 718.5566 +#> Model cost at call 13 : 718.5563 +#> Model cost at call 16 : 408.9208 +#> Model cost at call 17 : 408.9204 +#> Model cost at call 18 : 408.9204 +#> Model cost at call 20 : 408.9203 +#> Model cost at call 21 : 402.7935 +#> Model cost at call 22 : 402.793 +#> Model cost at call 26 : 202.0443 +#> Model cost at call 28 : 202.0443 +#> Model cost at call 30 : 202.0443 +#> Model cost at call 31 : 196.438 +#> Model cost at call 36 : 196.1947 +#> Model cost at call 37 : 196.1947 +#> Model cost at call 41 : 192.9338 +#> Model cost at call 43 : 192.9338 +#> Model cost at call 45 : 192.9338 +#> Model cost at call 46 : 191.6452 +#> Model cost at call 47 : 191.6452 +#> Model cost at call 51 : 188.9328 +#> Model cost at call 54 : 188.9328 +#> Model cost at call 55 : 188.9328 +#> Model cost at call 56 : 183.6499 +#> Model cost at call 59 : 183.6499 +#> Model cost at call 62 : 181.9039 +#> Model cost at call 67 : 179.0543 +#> Model cost at call 68 : 179.0543 +#> Model cost at call 69 : 179.0543 +#> Model cost at call 70 : 179.0543 +#> Model cost at call 72 : 176.749 +#> Model cost at call 73 : 176.2321 +#> Model cost at call 74 : 176.232 +#> Model cost at call 75 : 176.232 +#> Model cost at call 76 : 176.232 +#> Model cost at call 78 : 175.3914 +#> Model cost at call 79 : 175.3914 +#> Model cost at call 81 : 175.3913 +#> Model cost at call 83 : 174.6257 +#> Model cost at call 84 : 174.6257 +#> Model cost at call 89 : 174.1476 +#> Model cost at call 92 : 174.1476 +#> Model cost at call 93 : 174.1476 +#> Model cost at call 94 : 173.8512 +#> Model cost at call 99 : 173.6987 +#> Model cost at call 104 : 173.6813 +#> Model cost at call 105 : 173.6813 +#> Model cost at call 106 : 173.6813 +#> Model cost at call 107 : 173.6813 +#> Model cost at call 108 : 173.6813 +#> Model cost at call 109 : 173.6802 +#> Model cost at call 110 : 173.6802 +#> Model cost at call 111 : 173.6802 +#> Model cost at call 112 : 173.6802 +#> Model cost at call 113 : 173.6802 +#> Model cost at call 114 : 173.6799 +#> Model cost at call 116 : 173.6799 +#> Model cost at call 118 : 173.6799 +#> Model cost at call 119 : 173.6799 +#> Model cost at call 120 : 173.6799 +#> Model cost at call 129 : 173.6799 +#> Model cost at call 141 : 173.6799 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#> Model cost at call 1 : 18365.33 +#> Model cost at call 2 : 18365.33 +#> Model cost at call 8 : 11666.4 +#> Model cost at call 9 : 10992.15 +#> Model cost at call 10 : 10992.13 +#> Model cost at call 11 : 10991.95 +#> Model cost at call 12 : 10991.17 +#> Model cost at call 14 : 10990.65 +#> Model cost at call 17 : 3940.801 +#> Model cost at call 20 : 3940.8 +#> Model cost at call 22 : 3940.798 +#> Model cost at call 24 : 3241.199 +#> Model cost at call 27 : 3241.198 +#> Model cost at call 30 : 3241.192 +#> Model cost at call 31 : 1518.749 +#> Model cost at call 37 : 1518.747 +#> Model cost at call 39 : 1091.836 +#> Model cost at call 42 : 1091.835 +#> Model cost at call 43 : 1091.835 +#> Model cost at call 44 : 1091.804 +#> Model cost at call 46 : 927.8538 +#> Model cost at call 49 : 927.8529 +#> Model cost at call 53 : 638.102 +#> Model cost at call 56 : 638.1019 +#> Model cost at call 58 : 638.1018 +#> Model cost at call 61 : 560.4352 +#> Model cost at call 62 : 560.435 +#> Model cost at call 63 : 560.4327 +#> Model cost at call 68 : 423.9629 +#> Model cost at call 69 : 423.9629 +#> Model cost at call 70 : 423.9629 +#> Model cost at call 71 : 423.9628 +#> Model cost at call 73 : 423.9628 +#> Model cost at call 75 : 395.8015 +#> Model cost at call 78 : 395.8013 +#> Model cost at call 79 : 395.8013 +#> Model cost at call 83 : 365.6975 +#> Model cost at call 84 : 365.6975 +#> Model cost at call 88 : 365.6975 +#> Model cost at call 91 : 362.9843 +#> Model cost at call 93 : 362.9843 +#> Model cost at call 98 : 361.5506 +#> Model cost at call 99 : 361.5506 +#> Model cost at call 100 : 361.5505 +#> Model cost at call 105 : 359.0492 +#> Model cost at call 106 : 359.0492 +#> Model cost at call 112 : 357.6574 +#> Model cost at call 113 : 357.6574 +#> Model cost at call 114 : 357.6574 +#> Model cost at call 115 : 357.6574 +#> Model cost at call 119 : 355.4518 +#> Model cost at call 120 : 355.4518 +#> Model cost at call 127 : 354.9045 +#> Model cost at call 129 : 354.9045 +#> Model cost at call 131 : 354.9045 +#> Model cost at call 134 : 354.4168 +#> Model cost at call 135 : 354.4168 +#> Model cost at call 137 : 354.4167 +#> Model cost at call 141 : 353.7901 +#> Model cost at call 142 : 353.7901 +#> Model cost at call 143 : 353.7899 +#> Model cost at call 149 : 353.3233 +#> Model cost at call 151 : 353.3233 +#> Model cost at call 154 : 353.3233 +#> Model cost at call 156 : 353.2939 +#> Model cost at call 158 : 353.2938 +#> Model cost at call 159 : 353.2938 +#> Model cost at call 160 : 353.2938 +#> Model cost at call 163 : 353.0571 +#> Model cost at call 165 : 353.0571 +#> Model cost at call 170 : 352.9457 +#> Model cost at call 171 : 352.7458 +#> Model cost at call 173 : 352.7457 +#> Model cost at call 178 : 352.6377 +#> Model cost at call 180 : 352.6377 +#> Model cost at call 183 : 352.6377 +#> Model cost at call 185 : 352.5377 +#> Model cost at call 187 : 352.5377 +#> Model cost at call 188 : 352.5377 +#> Model cost at call 191 : 352.5377 +#> Model cost at call 193 : 352.4479 +#> Model cost at call 195 : 352.4479 +#> Model cost at call 198 : 352.4479 +#> Model cost at call 200 : 352.4021 +#> Model cost at call 202 : 352.4021 +#> Model cost at call 205 : 352.4021 +#> Model cost at call 207 : 352.3465 +#> Model cost at call 210 : 352.3465 +#> Model cost at call 214 : 352.3031 +#> Model cost at call 216 : 352.3031 +#> Model cost at call 221 : 352.2632 +#> Model cost at call 223 : 352.2632 +#> Model cost at call 228 : 352.2367 +#> Model cost at call 230 : 352.2367 +#> Model cost at call 231 : 352.2367 +#> Model cost at call 233 : 352.2367 +#> Model cost at call 235 : 352.215 +#> Model cost at call 238 : 352.215 +#> Model cost at call 239 : 352.215 +#> Model cost at call 242 : 352.207 +#> Model cost at call 245 : 352.207 +#> Model cost at call 250 : 352.2053 +#> Model cost at call 251 : 352.2053 +#> Model cost at call 253 : 352.2053 +#> Model cost at call 256 : 352.2053 +#> Model cost at call 258 : 352.2053 +#> Model cost at call 259 : 352.2052 +#> Model cost at call 260 : 352.2052 +#> Model cost at call 263 : 352.2052 +#> Model cost at call 271 : 352.2048 +#> Model cost at call 273 : 352.2048 +#> Model cost at call 274 : 352.2048 +#> Model cost at call 281 : 352.2048 +#> Model cost at call 282 : 352.2048 +#> Model cost at call 286 : 352.2048 +#> Model cost at call 289 : 352.2048 +#> Model cost at call 294 : 352.2048 +#> Model cost at call 296 : 352.2048 +#> Model cost at call 300 : 352.2048 +#> Model cost at call 307 : 352.2048 +#> Model cost at call 325 : 352.2048 +#> Model cost at call 331 : 352.2048 +#> Model cost at call 333 : 352.2048 +#> Optimisation by method Port successfully terminated.</div><div class='input'> + + +<span class='co'># Weighted fits, including IRLS</span> +<span class='no'>SFO_SFO.ff</span> <span class='kw'><-</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='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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <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'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> Model cost at call 1 : 15156.12 +#> Model cost at call 2 : 15156.12 +#> Model cost at call 6 : 8243.644 +#> Model cost at call 12 : 6290.714 +#> Model cost at call 13 : 6290.684 +#> Model cost at call 15 : 6290.453 +#> Model cost at call 18 : 1700.75 +#> Model cost at call 20 : 1700.612 +#> Model cost at call 24 : 1190.923 +#> Model cost at call 26 : 1190.922 +#> Model cost at call 29 : 1017.417 +#> Model cost at call 31 : 1017.417 +#> Model cost at call 33 : 1017.416 +#> Model cost at call 34 : 644.0471 +#> Model cost at call 36 : 644.0469 +#> Model cost at call 38 : 644.0468 +#> Model cost at call 39 : 590.5024 +#> Model cost at call 41 : 590.5021 +#> Model cost at call 43 : 590.5015 +#> Model cost at call 44 : 543.2187 +#> Model cost at call 45 : 543.2183 +#> Model cost at call 46 : 543.2182 +#> Model cost at call 50 : 391.348 +#> Model cost at call 51 : 391.3479 +#> Model cost at call 56 : 386.4789 +#> Model cost at call 58 : 386.4789 +#> Model cost at call 60 : 386.4779 +#> Model cost at call 61 : 384.0686 +#> Model cost at call 63 : 384.0686 +#> Model cost at call 66 : 382.7812 +#> Model cost at call 68 : 382.7812 +#> Model cost at call 70 : 382.7812 +#> Model cost at call 71 : 378.9272 +#> Model cost at call 73 : 378.9272 +#> Model cost at call 75 : 378.9272 +#> Model cost at call 76 : 377.4846 +#> Model cost at call 78 : 377.4846 +#> Model cost at call 81 : 375.9738 +#> Model cost at call 83 : 375.9738 +#> Model cost at call 86 : 375.3387 +#> Model cost at call 88 : 375.3387 +#> Model cost at call 91 : 374.5774 +#> Model cost at call 93 : 374.5774 +#> Model cost at call 95 : 374.5774 +#> Model cost at call 96 : 373.5447 +#> Model cost at call 100 : 373.5446 +#> Model cost at call 102 : 373.2643 +#> Model cost at call 104 : 373.2643 +#> Model cost at call 107 : 372.6799 +#> Model cost at call 111 : 372.6798 +#> Model cost at call 114 : 372.6325 +#> Model cost at call 116 : 372.6325 +#> Model cost at call 119 : 372.6159 +#> Model cost at call 121 : 372.6159 +#> Model cost at call 123 : 372.6159 +#> Model cost at call 124 : 372.5845 +#> Model cost at call 126 : 372.5845 +#> Model cost at call 129 : 372.5375 +#> Model cost at call 130 : 372.4771 +#> Model cost at call 131 : 372.2008 +#> Model cost at call 132 : 371.4923 +#> Model cost at call 134 : 371.4923 +#> Model cost at call 137 : 371.3022 +#> Model cost at call 139 : 371.3022 +#> Model cost at call 143 : 371.2271 +#> Model cost at call 144 : 371.2271 +#> Model cost at call 148 : 371.2202 +#> Model cost at call 149 : 371.215 +#> Model cost at call 152 : 371.215 +#> Model cost at call 154 : 371.2136 +#> Model cost at call 155 : 371.2136 +#> Model cost at call 156 : 371.2136 +#> Model cost at call 160 : 371.2134 +#> Model cost at call 164 : 371.2134 +#> Model cost at call 167 : 371.2134 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:19:47 2016 +#> Date of summary: Fri Nov 18 15:19:47 2016 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 185 model solutions performed in 0.748 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.60000 1.61400 96.3300 102.9000 +#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 +#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 +#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5178 -0.1701 -0.5489 +#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 +#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 +#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent 0.098700 23.880 5.701e-24 0.090660 1.074e-01 +#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> f_parent_to_m1 0.514500 22.490 4.374e-23 0.468100 5.606e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.459 2 7 +#> m1 4.690 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5145 +#> parent_sink 0.4855 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 99.46 9.960e+01 -1.385e-01 +#> 0 parent 102.04 9.960e+01 2.442e+00 +#> 1 parent 93.50 9.024e+01 3.262e+00 +#> 1 parent 92.50 9.024e+01 2.262e+00 +#> 3 parent 63.23 7.407e+01 -1.084e+01 +#> 3 parent 68.99 7.407e+01 -5.083e+00 +#> 7 parent 52.32 4.991e+01 2.408e+00 +#> 7 parent 55.13 4.991e+01 5.218e+00 +#> 14 parent 27.27 2.501e+01 2.257e+00 +#> 14 parent 26.64 2.501e+01 1.627e+00 +#> 21 parent 11.50 1.253e+01 -1.035e+00 +#> 21 parent 11.64 1.253e+01 -8.946e-01 +#> 35 parent 2.85 3.148e+00 -2.979e-01 +#> 35 parent 2.91 3.148e+00 -2.379e-01 +#> 50 parent 0.69 7.162e-01 -2.624e-02 +#> 50 parent 0.63 7.162e-01 -8.624e-02 +#> 75 parent 0.05 6.074e-02 -1.074e-02 +#> 75 parent 0.06 6.074e-02 -7.381e-04 +#> 100 parent NA 5.151e-03 NA +#> 100 parent NA 5.151e-03 NA +#> 120 parent NA 7.155e-04 NA +#> 120 parent NA 7.155e-04 NA +#> 0 m1 0.00 0.000e+00 0.000e+00 +#> 0 m1 0.00 0.000e+00 0.000e+00 +#> 1 m1 4.84 4.803e+00 3.704e-02 +#> 1 m1 5.64 4.803e+00 8.370e-01 +#> 3 m1 12.91 1.302e+01 -1.140e-01 +#> 3 m1 12.96 1.302e+01 -6.400e-02 +#> 7 m1 22.97 2.504e+01 -2.075e+00 +#> 7 m1 24.47 2.504e+01 -5.748e-01 +#> 14 m1 41.69 3.669e+01 5.000e+00 +#> 14 m1 33.21 3.669e+01 -3.480e+00 +#> 21 m1 44.37 4.165e+01 2.717e+00 +#> 21 m1 46.44 4.165e+01 4.787e+00 +#> 35 m1 41.22 4.331e+01 -2.093e+00 +#> 35 m1 37.95 4.331e+01 -5.363e+00 +#> 50 m1 41.19 4.122e+01 -2.831e-02 +#> 50 m1 40.01 4.122e+01 -1.208e+00 +#> 75 m1 40.09 3.645e+01 3.643e+00 +#> 75 m1 33.85 3.645e+01 -2.597e+00 +#> 100 m1 31.04 3.198e+01 -9.416e-01 +#> 100 m1 33.13 3.198e+01 1.148e+00 +#> 120 m1 25.15 2.879e+01 -3.640e+00 +#> 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</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>)</div><div class='output co'>#> Model cost at call 1 : 15156.12 +#> Model cost at call 2 : 15156.12 +#> Model cost at call 6 : 8243.644 +#> Model cost at call 12 : 6290.714 +#> Model cost at call 13 : 6290.684 +#> Model cost at call 15 : 6290.453 +#> Model cost at call 18 : 1700.75 +#> Model cost at call 20 : 1700.612 +#> Model cost at call 24 : 1190.923 +#> Model cost at call 26 : 1190.922 +#> Model cost at call 29 : 1017.417 +#> Model cost at call 31 : 1017.417 +#> Model cost at call 33 : 1017.416 +#> Model cost at call 34 : 644.0471 +#> Model cost at call 36 : 644.0469 +#> Model cost at call 38 : 644.0468 +#> Model cost at call 39 : 590.5024 +#> Model cost at call 41 : 590.5021 +#> Model cost at call 43 : 590.5015 +#> Model cost at call 44 : 543.2187 +#> Model cost at call 45 : 543.2183 +#> Model cost at call 46 : 543.2182 +#> Model cost at call 50 : 391.348 +#> Model cost at call 51 : 391.3479 +#> Model cost at call 56 : 386.4789 +#> Model cost at call 58 : 386.4789 +#> Model cost at call 60 : 386.4779 +#> Model cost at call 61 : 384.0686 +#> Model cost at call 63 : 384.0686 +#> Model cost at call 66 : 382.7812 +#> Model cost at call 68 : 382.7812 +#> Model cost at call 70 : 382.7812 +#> Model cost at call 71 : 378.9272 +#> Model cost at call 73 : 378.9272 +#> Model cost at call 75 : 378.9272 +#> Model cost at call 76 : 377.4846 +#> Model cost at call 78 : 377.4846 +#> Model cost at call 81 : 375.9738 +#> Model cost at call 83 : 375.9738 +#> Model cost at call 86 : 375.3387 +#> Model cost at call 88 : 375.3387 +#> Model cost at call 91 : 374.5774 +#> Model cost at call 93 : 374.5774 +#> Model cost at call 95 : 374.5774 +#> Model cost at call 96 : 373.5447 +#> Model cost at call 100 : 373.5446 +#> Model cost at call 102 : 373.2643 +#> Model cost at call 104 : 373.2643 +#> Model cost at call 107 : 372.6799 +#> Model cost at call 111 : 372.6798 +#> Model cost at call 114 : 372.6325 +#> Model cost at call 116 : 372.6325 +#> Model cost at call 119 : 372.6159 +#> Model cost at call 121 : 372.6159 +#> Model cost at call 123 : 372.6159 +#> Model cost at call 124 : 372.5845 +#> Model cost at call 126 : 372.5845 +#> Model cost at call 129 : 372.5375 +#> Model cost at call 130 : 372.4771 +#> Model cost at call 131 : 372.2008 +#> Model cost at call 132 : 371.4923 +#> Model cost at call 134 : 371.4923 +#> Model cost at call 137 : 371.3022 +#> Model cost at call 139 : 371.3022 +#> Model cost at call 143 : 371.2271 +#> Model cost at call 144 : 371.2271 +#> Model cost at call 148 : 371.2202 +#> Model cost at call 149 : 371.215 +#> Model cost at call 152 : 371.215 +#> Model cost at call 154 : 371.2136 +#> Model cost at call 155 : 371.2136 +#> Model cost at call 156 : 371.2136 +#> Model cost at call 160 : 371.2134 +#> Model cost at call 164 : 371.2134 +#> Model cost at call 167 : 371.2134 +#> IRLS based on variance estimates for each observed variable +#> Initial variance estimates are: +#> parent m1 +#> 11.552581 7.421226 +#> Model cost at call 186 : 40 +#> Model cost at call 188 : 40 +#> Model cost at call 194 : 39.99562 +#> Model cost at call 195 : 39.99562 +#> Model cost at call 201 : 39.9956 +#> Model cost at call 203 : 39.99528 +#> Model cost at call 205 : 39.99528 +#> Model cost at call 207 : 39.99528 +#> Model cost at call 209 : 39.99515 +#> Model cost at call 211 : 39.99515 +#> Model cost at call 214 : 39.99515 +#> Model cost at call 215 : 39.99505 +#> Model cost at call 217 : 39.99505 +#> Model cost at call 219 : 39.99505 +#> Model cost at call 220 : 39.99489 +#> Model cost at call 222 : 39.99489 +#> Model cost at call 224 : 39.99489 +#> Model cost at call 225 : 39.99479 +#> Model cost at call 227 : 39.99479 +#> Model cost at call 231 : 39.99467 +#> Model cost at call 234 : 39.99467 +#> Model cost at call 235 : 39.99467 +#> Model cost at call 236 : 39.99458 +#> Model cost at call 238 : 39.99458 +#> Model cost at call 239 : 39.99458 +#> Model cost at call 241 : 39.99452 +#> Model cost at call 242 : 39.99444 +#> Model cost at call 243 : 39.99433 +#> Model cost at call 245 : 39.99433 +#> Model cost at call 248 : 39.99383 +#> Model cost at call 250 : 39.99383 +#> Model cost at call 251 : 39.99383 +#> Model cost at call 252 : 39.99383 +#> Model cost at call 253 : 39.9935 +#> Model cost at call 254 : 39.99309 +#> Model cost at call 256 : 39.99309 +#> Model cost at call 261 : 39.99295 +#> Model cost at call 264 : 39.99295 +#> Model cost at call 267 : 39.99281 +#> Model cost at call 272 : 39.99281 +#> Model cost at call 273 : 39.99278 +#> Model cost at call 276 : 39.99278 +#> Model cost at call 278 : 39.99278 +#> Model cost at call 279 : 39.99278 +#> Model cost at call 281 : 39.99278 +#> Model cost at call 283 : 39.99278 +#> Model cost at call 286 : 39.99278 +#> Model cost at call 289 : 39.99278 +#> Model cost at call 290 : 39.99278 +#> Iteration 1 yields variance estimates: +#> parent m1 +#> 11.573172 7.407968 +#> Sum of squared differences to last variance estimates: 1.5e-05 +#> Iteration 2 yields variance estimates: +#> parent m1 +#> 11.573405 7.407846 +#> Sum of squared differences to last variance estimates: 1.7e-09 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:19:50 2016 +#> Date of summary: Fri Nov 18 15:19:50 2016 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 486 model solutions performed in 2.052 s +#> +#> Weighting: none then iterative reweighting method obs +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.67000 1.79200 96.04000 103.300 +#> log_k_parent -2.31200 0.04560 -2.40400 -2.220 +#> log_k_m1 -5.25100 0.12510 -5.50500 -4.998 +#> f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5083 -0.1979 -0.6148 +#> log_k_parent 0.5083 1.0000 -0.3894 -0.6062 +#> log_k_m1 -0.1979 -0.3894 1.0000 0.7417 +#> f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000 +#> +#> Residual standard error: 1.054 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.67000 55.630 8.183e-37 96.040000 1.033e+02 +#> k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01 +#> k_m1 0.00524 7.996 8.487e-10 0.004066 6.753e-03 +#> f_parent_to_m1 0.51340 23.000 2.039e-23 0.468100 5.584e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.399 4 15 +#> parent 6.466 2 7 +#> m1 4.679 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5134 +#> parent_sink 0.4866 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.997 23.24 +#> m1 132.282 439.43 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 9.967e+01 -2.122e-01 3.402 +#> 0 parent 102.04 9.967e+01 2.368e+00 3.402 +#> 1 parent 93.50 9.027e+01 3.228e+00 3.402 +#> 1 parent 92.50 9.027e+01 2.228e+00 3.402 +#> 3 parent 63.23 7.405e+01 -1.082e+01 3.402 +#> 3 parent 68.99 7.405e+01 -5.056e+00 3.402 +#> 7 parent 52.32 4.982e+01 2.499e+00 3.402 +#> 7 parent 55.13 4.982e+01 5.309e+00 3.402 +#> 14 parent 27.27 2.490e+01 2.367e+00 3.402 +#> 14 parent 26.64 2.490e+01 1.737e+00 3.402 +#> 21 parent 11.50 1.245e+01 -9.477e-01 3.402 +#> 21 parent 11.64 1.245e+01 -8.077e-01 3.402 +#> 35 parent 2.85 3.110e+00 -2.600e-01 3.402 +#> 35 parent 2.91 3.110e+00 -2.000e-01 3.402 +#> 50 parent 0.69 7.037e-01 -1.375e-02 3.402 +#> 50 parent 0.63 7.037e-01 -7.375e-02 3.402 +#> 75 parent 0.05 5.913e-02 -9.134e-03 3.402 +#> 75 parent 0.06 5.913e-02 8.661e-04 3.402 +#> 100 parent NA 4.969e-03 NA 3.402 +#> 100 parent NA 4.969e-03 NA 3.402 +#> 120 parent NA 6.852e-04 NA 3.402 +#> 120 parent NA 6.852e-04 NA 3.402 +#> 0 m1 0.00 0.000e+00 0.000e+00 2.722 +#> 0 m1 0.00 0.000e+00 0.000e+00 2.722 +#> 1 m1 4.84 4.813e+00 2.672e-02 2.722 +#> 1 m1 5.64 4.813e+00 8.267e-01 2.722 +#> 3 m1 12.91 1.305e+01 -1.378e-01 2.722 +#> 3 m1 12.96 1.305e+01 -8.779e-02 2.722 +#> 7 m1 22.97 2.508e+01 -2.106e+00 2.722 +#> 7 m1 24.47 2.508e+01 -6.061e-01 2.722 +#> 14 m1 41.69 3.671e+01 4.983e+00 2.722 +#> 14 m1 33.21 3.671e+01 -3.497e+00 2.722 +#> 21 m1 44.37 4.165e+01 2.719e+00 2.722 +#> 21 m1 46.44 4.165e+01 4.789e+00 2.722 +#> 35 m1 41.22 4.329e+01 -2.069e+00 2.722 +#> 35 m1 37.95 4.329e+01 -5.339e+00 2.722 +#> 50 m1 41.19 4.119e+01 -3.388e-03 2.722 +#> 50 m1 40.01 4.119e+01 -1.183e+00 2.722 +#> 75 m1 40.09 3.644e+01 3.652e+00 2.722 +#> 75 m1 33.85 3.644e+01 -2.588e+00 2.722 +#> 100 m1 31.04 3.199e+01 -9.497e-01 2.722 +#> 100 m1 33.13 3.199e+01 1.140e+00 2.722 +#> 120 m1 25.15 2.881e+01 -3.659e+00 2.722 +#> 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'><-</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>)</div><div class='output co'>#> Model cost at call 1 : 19.80132 +#> Model cost at call 2 : 19.80132 +#> Model cost at call 6 : 10.68776 +#> Model cost at call 12 : 7.14353 +#> Model cost at call 13 : 7.143529 +#> Model cost at call 15 : 7.143511 +#> Model cost at call 18 : 2.189024 +#> Model cost at call 20 : 2.189019 +#> Model cost at call 23 : 1.587262 +#> Model cost at call 25 : 1.587261 +#> Model cost at call 26 : 1.58726 +#> Model cost at call 28 : 1.036794 +#> Model cost at call 29 : 1.036794 +#> Model cost at call 30 : 1.036793 +#> Model cost at call 34 : 0.4939937 +#> Model cost at call 35 : 0.4939937 +#> Model cost at call 38 : 0.4939936 +#> Model cost at call 39 : 0.4018506 +#> Model cost at call 43 : 0.4018505 +#> Model cost at call 45 : 0.3797853 +#> Model cost at call 51 : 0.3669779 +#> Model cost at call 55 : 0.3669778 +#> Model cost at call 56 : 0.3585654 +#> Model cost at call 57 : 0.3533252 +#> Model cost at call 62 : 0.3502505 +#> Model cost at call 64 : 0.3502505 +#> Model cost at call 66 : 0.3502505 +#> Model cost at call 67 : 0.3501535 +#> Model cost at call 72 : 0.3501187 +#> Model cost at call 74 : 0.3501187 +#> Model cost at call 75 : 0.3501187 +#> Model cost at call 77 : 0.3500378 +#> Model cost at call 79 : 0.3500378 +#> Model cost at call 83 : 0.349831 +#> Model cost at call 88 : 0.3494286 +#> Model cost at call 93 : 0.3488101 +#> Model cost at call 98 : 0.3481444 +#> Model cost at call 103 : 0.3478528 +#> Model cost at call 108 : 0.3478092 +#> Model cost at call 109 : 0.3478092 +#> Model cost at call 113 : 0.347807 +#> Model cost at call 116 : 0.347807 +#> Model cost at call 117 : 0.347807 +#> Model cost at call 119 : 0.347807 +#> Model cost at call 120 : 0.347807 +#> Model cost at call 125 : 0.347807 +#> Model cost at call 126 : 0.347807 +#> Model cost at call 128 : 0.347807 +#> Model cost at call 137 : 0.347807 +#> Model cost at call 148 : 0.347807 +#> Model cost at call 152 : 0.347807 +#> Model cost at call 154 : 0.347807 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:19:50 2016 +#> Date of summary: Fri Nov 18 15:19:50 2016 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 155 model solutions performed in 0.636 s +#> +#> Weighting: mean +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.7300 1.93200 95.81000 103.6000 +#> log_k_parent -2.3090 0.04837 -2.40700 -2.2110 +#> log_k_m1 -5.2550 0.12070 -5.49900 -5.0100 +#> f_parent_ilr_1 0.0354 0.06344 -0.09327 0.1641 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5004 -0.2143 -0.6514 +#> log_k_parent 0.5004 1.0000 -0.4282 -0.6383 +#> log_k_m1 -0.2143 -0.4282 1.0000 0.7390 +#> f_parent_ilr_1 -0.6514 -0.6383 0.7390 1.0000 +#> +#> Residual standard error: 0.09829 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.730000 51.630 1.166e-35 95.81000 1.036e+02 +#> k_parent 0.099360 20.670 7.304e-22 0.09007 1.096e-01 +#> k_m1 0.005224 8.287 3.649e-10 0.00409 6.672e-03 +#> f_parent_to_m1 0.512500 22.860 2.497e-23 0.46710 5.578e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.401 4 15 +#> parent 6.473 2 7 +#> m1 4.671 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5125 +#> parent_sink 0.4875 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.976 23.18 +#> m1 132.696 440.81 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 99.46 99.730570 -0.270570 +#> 0 parent 102.04 99.730570 2.309430 +#> 1 parent 93.50 90.298055 3.201945 +#> 1 parent 92.50 90.298055 2.201945 +#> 3 parent 63.23 74.025028 -10.795028 +#> 3 parent 68.99 74.025028 -5.035028 +#> 7 parent 52.32 49.748382 2.571618 +#> 7 parent 55.13 49.748382 5.381618 +#> 14 parent 27.27 24.815876 2.454124 +#> 14 parent 26.64 24.815876 1.824124 +#> 21 parent 11.50 12.378849 -0.878849 +#> 21 parent 11.64 12.378849 -0.738849 +#> 35 parent 2.85 3.080219 -0.230219 +#> 35 parent 2.91 3.080219 -0.170219 +#> 50 parent 0.69 0.693958 -0.003958 +#> 50 parent 0.63 0.693958 -0.063958 +#> 75 parent 0.05 0.057888 -0.007888 +#> 75 parent 0.06 0.057888 0.002112 +#> 100 parent NA 0.004829 NA +#> 100 parent NA 0.004829 NA +#> 120 parent NA 0.000662 NA +#> 120 parent NA 0.000662 NA +#> 0 m1 0.00 0.000000 0.000000 +#> 0 m1 0.00 0.000000 0.000000 +#> 1 m1 4.84 4.821488 0.018512 +#> 1 m1 5.64 4.821488 0.818512 +#> 3 m1 12.91 13.066692 -0.156692 +#> 3 m1 12.96 13.066692 -0.106692 +#> 7 m1 22.97 25.101058 -2.131058 +#> 7 m1 24.47 25.101058 -0.631058 +#> 14 m1 41.69 36.720923 4.969077 +#> 14 m1 33.21 36.720923 -3.510923 +#> 21 m1 44.37 41.648353 2.721647 +#> 21 m1 46.44 41.648353 4.791647 +#> 35 m1 41.22 43.269225 -2.049225 +#> 35 m1 37.95 43.269225 -5.319225 +#> 50 m1 41.19 41.173639 0.016361 +#> 50 m1 40.01 41.173639 -1.163639 +#> 75 m1 40.09 36.431224 3.658776 +#> 75 m1 33.85 36.431224 -2.581224 +#> 100 m1 31.04 31.996124 -0.956124 +#> 100 m1 33.13 31.996124 1.133876 +#> 120 m1 25.15 28.824128 -3.674128 +#> 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>)</div><div class='output co'>#> Model cost at call 1 : 11.21571 +#> Model cost at call 2 : 11.21571 +#> Model cost at call 3 : 11.21571 +#> Model cost at call 8 : 11.12803 +#> Model cost at call 10 : 11.128 +#> Model cost at call 13 : 10.88016 +#> Model cost at call 15 : 10.88016 +#> Model cost at call 18 : 10.58819 +#> Model cost at call 20 : 10.58819 +#> Model cost at call 23 : 9.71699 +#> Model cost at call 24 : 7.794026 +#> Model cost at call 26 : 7.794026 +#> Model cost at call 31 : 6.89734 +#> Model cost at call 33 : 6.897337 +#> Model cost at call 36 : 5.2239 +#> Model cost at call 37 : 3.357735 +#> Model cost at call 41 : 3.357733 +#> Model cost at call 44 : 2.982323 +#> Model cost at call 46 : 2.982322 +#> Model cost at call 49 : 2.703946 +#> Model cost at call 50 : 2.080395 +#> Model cost at call 55 : 0.5307591 +#> Model cost at call 56 : 0.5307591 +#> Model cost at call 57 : 0.5307591 +#> Model cost at call 59 : 0.5307584 +#> Model cost at call 60 : 0.3240066 +#> Model cost at call 61 : 0.3240066 +#> Model cost at call 64 : 0.3240066 +#> Model cost at call 65 : 0.2601108 +#> Model cost at call 70 : 0.2414055 +#> Model cost at call 74 : 0.2414055 +#> Model cost at call 75 : 0.2404251 +#> Model cost at call 80 : 0.2404087 +#> Model cost at call 82 : 0.2404087 +#> Model cost at call 85 : 0.2404054 +#> Model cost at call 88 : 0.2404054 +#> Model cost at call 92 : 0.2403931 +#> Model cost at call 93 : 0.2403784 +#> Model cost at call 98 : 0.2403784 +#> Model cost at call 99 : 0.2403322 +#> Model cost at call 104 : 0.2402188 +#> Model cost at call 109 : 0.2400275 +#> Model cost at call 114 : 0.239844 +#> Model cost at call 119 : 0.2397153 +#> Model cost at call 120 : 0.2397153 +#> Model cost at call 124 : 0.2396978 +#> Model cost at call 126 : 0.2396978 +#> Model cost at call 130 : 0.239697 +#> Model cost at call 131 : 0.2396963 +#> Model cost at call 133 : 0.2396963 +#> Model cost at call 138 : 0.2396962 +#> Model cost at call 139 : 0.2396962 +#> Model cost at call 141 : 0.2396962 +#> Model cost at call 144 : 0.2396962 +#> Model cost at call 147 : 0.2396962 +#> Model cost at call 156 : 0.2396962 +#> Model cost at call 167 : 0.2396962 +#> Model cost at call 169 : 0.2396962 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:19:51 2016 +#> Date of summary: Fri Nov 18 15:19:51 2016 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 174 model solutions performed in 0.789 s +#> +#> Weighting: manual +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.6600 2.712000 94.14000 105.2000 +#> log_k_parent -2.2980 0.008118 -2.31500 -2.2820 +#> log_k_m1 -5.2410 0.096690 -5.43800 -5.0450 +#> f_parent_ilr_1 0.0231 0.057990 -0.09474 0.1409 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.00000 0.6844 -0.08687 -0.7564 +#> log_k_parent 0.68435 1.0000 -0.12694 -0.5812 +#> log_k_m1 -0.08687 -0.1269 1.00000 0.5195 +#> f_parent_ilr_1 -0.75644 -0.5812 0.51951 1.0000 +#> +#> Residual standard error: 0.08396 on 34 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.660000 36.75 2.957e-29 94.14000 1.052e+02 +#> k_parent 0.100400 123.20 5.927e-47 0.09878 1.021e-01 +#> k_m1 0.005295 10.34 2.447e-12 0.00435 6.444e-03 +#> f_parent_to_m1 0.508200 24.79 1.184e-23 0.46660 5.497e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.461 4 15 +#> parent 6.520 2 7 +#> m1 4.744 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5082 +#> parent_sink 0.4918 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.902 22.93 +#> m1 130.916 434.89 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.65571 -0.195714 99.46 +#> 0 parent 102.04 99.65571 2.384286 102.04 +#> 1 parent 93.50 90.13383 3.366170 93.50 +#> 1 parent 92.50 90.13383 2.366170 92.50 +#> 3 parent 63.23 73.73252 -10.502518 63.23 +#> 3 parent 68.99 73.73252 -4.742518 68.99 +#> 7 parent 52.32 49.34027 2.979728 52.32 +#> 7 parent 55.13 49.34027 5.789728 55.13 +#> 14 parent 27.27 24.42873 2.841271 27.27 +#> 14 parent 26.64 24.42873 2.211271 26.64 +#> 21 parent 11.50 12.09484 -0.594842 11.50 +#> 21 parent 11.64 12.09484 -0.454842 11.64 +#> 35 parent 2.85 2.96482 -0.114824 2.85 +#> 35 parent 2.91 2.96482 -0.054824 2.91 +#> 50 parent 0.69 0.65733 0.032670 0.69 +#> 50 parent 0.63 0.65733 -0.027330 0.63 +#> 75 parent 0.05 0.05339 -0.003386 0.05 +#> 75 parent 0.06 0.05339 0.006614 0.06 +#> 1 m1 4.84 4.82570 0.014301 4.84 +#> 1 m1 5.64 4.82570 0.814301 5.64 +#> 3 m1 12.91 13.06402 -0.154020 12.91 +#> 3 m1 12.96 13.06402 -0.104020 12.96 +#> 7 m1 22.97 25.04656 -2.076564 22.97 +#> 7 m1 24.47 25.04656 -0.576564 24.47 +#> 14 m1 41.69 36.53601 5.153988 41.69 +#> 14 m1 33.21 36.53601 -3.326012 33.21 +#> 21 m1 44.37 41.34639 3.023609 44.37 +#> 21 m1 46.44 41.34639 5.093609 46.44 +#> 35 m1 41.22 42.82669 -1.606690 41.22 +#> 35 m1 37.95 42.82669 -4.876690 37.95 +#> 50 m1 41.19 40.67342 0.516578 41.19 +#> 50 m1 40.01 40.67342 -0.663422 40.01 +#> 75 m1 40.09 35.91105 4.178947 40.09 +#> 75 m1 33.85 35.91105 -2.061053 33.85 +#> 100 m1 31.04 31.48161 -0.441612 31.04 +#> 100 m1 33.13 31.48161 1.648388 33.13 +#> 120 m1 25.15 28.32018 -3.170181 25.15 +#> 120 m1 33.31 28.32018 4.989819 33.31</div><div class='input'> + + +<span class='co'># Manual weighting</span> +<span class='no'>dw</span> <span class='kw'><-</span> <span class='no'>FOCUS_2006_D</span> +<span class='no'>errors</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>) +<span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'><-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>] +<span class='no'>f.w.man</span> <span class='kw'><-</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>)</div><div class='output co'>#> Model cost at call 1 : 3949.676 +#> Model cost at call 2 : 3949.676 +#> Model cost at call 5 : 3949.676 +#> Model cost at call 6 : 2252.859 +#> Model cost at call 8 : 2252.858 +#> Model cost at call 9 : 2252.826 +#> Model cost at call 13 : 1567.343 +#> Model cost at call 14 : 1567.342 +#> Model cost at call 15 : 1567.333 +#> Model cost at call 18 : 1041.524 +#> Model cost at call 19 : 1041.522 +#> Model cost at call 24 : 840.4649 +#> Model cost at call 26 : 840.4646 +#> Model cost at call 29 : 782.303 +#> Model cost at call 31 : 782.3028 +#> Model cost at call 34 : 664.539 +#> Model cost at call 36 : 664.5389 +#> Model cost at call 40 : 615.7908 +#> Model cost at call 42 : 615.7907 +#> Model cost at call 45 : 569.5971 +#> Model cost at call 47 : 569.597 +#> Model cost at call 50 : 517.3175 +#> Model cost at call 52 : 517.3173 +#> Model cost at call 56 : 464.8158 +#> Model cost at call 58 : 464.8157 +#> Model cost at call 62 : 433.0031 +#> Model cost at call 64 : 433.003 +#> Model cost at call 67 : 423.7407 +#> Model cost at call 69 : 423.7406 +#> Model cost at call 70 : 423.7392 +#> Model cost at call 72 : 346.2781 +#> Model cost at call 74 : 346.278 +#> Model cost at call 75 : 346.2779 +#> Model cost at call 78 : 334.5399 +#> Model cost at call 80 : 334.5398 +#> Model cost at call 83 : 324.139 +#> Model cost at call 85 : 324.1389 +#> Model cost at call 88 : 319.7514 +#> Model cost at call 90 : 319.7514 +#> Model cost at call 94 : 300.9426 +#> Model cost at call 96 : 300.9425 +#> Model cost at call 100 : 295.8803 +#> Model cost at call 102 : 295.8803 +#> Model cost at call 105 : 290.3288 +#> Model cost at call 107 : 290.3287 +#> Model cost at call 111 : 284.3257 +#> Model cost at call 113 : 284.3257 +#> Model cost at call 116 : 282.3972 +#> Model cost at call 118 : 282.3972 +#> Model cost at call 122 : 273.7385 +#> Model cost at call 124 : 273.7385 +#> Model cost at call 128 : 271.8379 +#> Model cost at call 130 : 271.8379 +#> Model cost at call 133 : 270.064 +#> Model cost at call 135 : 270.064 +#> Model cost at call 138 : 268.0107 +#> Model cost at call 140 : 268.0107 +#> Model cost at call 144 : 265.6194 +#> Model cost at call 146 : 265.6194 +#> Model cost at call 148 : 265.6194 +#> Model cost at call 149 : 263.4825 +#> Model cost at call 151 : 263.4825 +#> Model cost at call 153 : 263.4824 +#> Model cost at call 154 : 262.0988 +#> Model cost at call 156 : 262.0988 +#> Model cost at call 160 : 260.7078 +#> Model cost at call 162 : 260.7078 +#> Model cost at call 165 : 259.9453 +#> Model cost at call 167 : 259.9453 +#> Model cost at call 170 : 258.9623 +#> Model cost at call 172 : 258.9623 +#> Model cost at call 174 : 258.962 +#> Model cost at call 176 : 258.0119 +#> Model cost at call 178 : 258.0119 +#> Model cost at call 180 : 258.0119 +#> Model cost at call 181 : 257.8698 +#> Model cost at call 183 : 257.8698 +#> Model cost at call 186 : 256.8608 +#> Model cost at call 188 : 256.8608 +#> Model cost at call 190 : 256.8608 +#> Model cost at call 191 : 256.2306 +#> Model cost at call 193 : 256.2306 +#> Model cost at call 195 : 256.2305 +#> Model cost at call 196 : 255.7119 +#> Model cost at call 198 : 255.7118 +#> Model cost at call 201 : 255.3323 +#> Model cost at call 203 : 255.3323 +#> Model cost at call 205 : 255.3323 +#> Model cost at call 206 : 254.6653 +#> Model cost at call 208 : 254.6653 +#> Model cost at call 211 : 254.3984 +#> Model cost at call 213 : 254.3984 +#> Model cost at call 216 : 253.3199 +#> Model cost at call 218 : 253.3199 +#> Model cost at call 220 : 253.3198 +#> Model cost at call 221 : 252.4845 +#> Model cost at call 223 : 252.4845 +#> Model cost at call 225 : 252.4845 +#> Model cost at call 226 : 251.6917 +#> Model cost at call 229 : 251.6917 +#> Model cost at call 230 : 251.6917 +#> Model cost at call 233 : 251.0189 +#> Model cost at call 235 : 251.0189 +#> Model cost at call 238 : 250.6912 +#> Model cost at call 240 : 250.6912 +#> Model cost at call 243 : 250.5546 +#> Model cost at call 245 : 250.5546 +#> Model cost at call 248 : 250.466 +#> Model cost at call 249 : 250.3744 +#> Model cost at call 250 : 249.9681 +#> Model cost at call 251 : 249.2215 +#> Model cost at call 260 : 248.919 +#> Model cost at call 264 : 248.919 +#> Model cost at call 265 : 248.8876 +#> Model cost at call 267 : 248.8876 +#> Model cost at call 270 : 248.8521 +#> Model cost at call 271 : 248.8178 +#> Model cost at call 272 : 248.6837 +#> Model cost at call 273 : 248.5989 +#> Model cost at call 276 : 248.5989 +#> Model cost at call 278 : 248.5935 +#> Model cost at call 280 : 248.5935 +#> Model cost at call 282 : 248.5935 +#> Model cost at call 283 : 248.5902 +#> Model cost at call 284 : 248.5902 +#> Model cost at call 289 : 248.5902 +#> Model cost at call 298 : 248.5902 +#> Model cost at call 309 : 248.5902 +#> Model cost at call 311 : 248.5902 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:19:53 2016 +#> Date of summary: Fri Nov 18 15:19:53 2016 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 316 model solutions performed in 1.337 s +#> +#> Weighting: manual +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.49000 1.33200 96.7800 102.2000 +#> log_k_parent -2.32100 0.03550 -2.3930 -2.2490 +#> log_k_m1 -5.24100 0.21280 -5.6730 -4.8100 +#> f_parent_ilr_1 0.04571 0.08966 -0.1361 0.2275 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.00000 0.5312 -0.09455 -0.3351 +#> log_k_parent 0.53123 1.0000 -0.17800 -0.3360 +#> log_k_m1 -0.09455 -0.1780 1.00000 0.7616 +#> f_parent_ilr_1 -0.33513 -0.3360 0.76156 1.0000 +#> +#> Residual standard error: 2.628 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.490000 74.69 2.222e-41 96.780000 1.022e+02 +#> k_parent 0.098140 28.17 2.012e-26 0.091320 1.055e-01 +#> k_m1 0.005292 4.70 1.873e-05 0.003437 8.148e-03 +#> f_parent_to_m1 0.516200 16.30 1.686e-18 0.452000 5.798e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.400 4 15 +#> parent 6.454 2 7 +#> m1 4.708 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5162 +#> parent_sink 0.4838 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.063 23.46 +#> m1 130.971 435.08 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.485977 -0.025977 1 +#> 0 parent 102.04 99.485977 2.554023 1 +#> 1 parent 93.50 90.186118 3.313882 1 +#> 1 parent 92.50 90.186118 2.313882 1 +#> 3 parent 63.23 74.113162 -10.883162 1 +#> 3 parent 68.99 74.113162 -5.123162 1 +#> 7 parent 52.32 50.050295 2.269705 1 +#> 7 parent 55.13 50.050295 5.079705 1 +#> 14 parent 27.27 25.179750 2.090250 1 +#> 14 parent 26.64 25.179750 1.460250 1 +#> 21 parent 11.50 12.667654 -1.167654 1 +#> 21 parent 11.64 12.667654 -1.027654 1 +#> 35 parent 2.85 3.206164 -0.356164 1 +#> 35 parent 2.91 3.206164 -0.296164 1 +#> 50 parent 0.69 0.735619 -0.045619 1 +#> 50 parent 0.63 0.735619 -0.105619 1 +#> 75 parent 0.05 0.063256 -0.013256 1 +#> 75 parent 0.06 0.063256 -0.003256 1 +#> 100 parent NA 0.005439 NA 1 +#> 100 parent NA 0.005439 NA 1 +#> 120 parent NA 0.000764 NA 1 +#> 120 parent NA 0.000764 NA 1 +#> 0 m1 0.00 0.000000 0.000000 2 +#> 0 m1 0.00 0.000000 0.000000 2 +#> 1 m1 4.84 4.787287 0.052713 2 +#> 1 m1 5.64 4.787287 0.852713 2 +#> 3 m1 12.91 12.987848 -0.077848 2 +#> 3 m1 12.96 12.987848 -0.027848 2 +#> 7 m1 22.97 24.996945 -2.026945 2 +#> 7 m1 24.47 24.996945 -0.526945 2 +#> 14 m1 41.69 36.663527 5.026473 2 +#> 14 m1 33.21 36.663527 -3.453527 2 +#> 21 m1 44.37 41.656812 2.713188 2 +#> 21 m1 46.44 41.656812 4.783188 2 +#> 35 m1 41.22 43.350311 -2.130311 2 +#> 35 m1 37.95 43.350311 -5.400311 2 +#> 50 m1 41.19 41.256364 -0.066364 2 +#> 50 m1 40.01 41.256364 -1.246364 2 +#> 75 m1 40.09 36.460566 3.629434 2 +#> 75 m1 33.85 36.460566 -2.610566 2 +#> 100 m1 31.04 31.969288 -0.929288 2 +#> 100 m1 33.13 31.969288 1.160712 2 +#> 120 m1 25.15 28.760615 -3.610615 2 +#> 120 m1 33.31 28.760615 4.549385 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'><-</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'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)</div><div class='output co'>#> Model cost at call 1 : 3949.676 +#> Model cost at call 2 : 3949.676 +#> Model cost at call 5 : 3949.676 +#> Model cost at call 6 : 2252.859 +#> Model cost at call 8 : 2252.858 +#> Model cost at call 9 : 2252.826 +#> Model cost at call 13 : 1567.343 +#> Model cost at call 14 : 1567.342 +#> Model cost at call 15 : 1567.333 +#> Model cost at call 18 : 1041.524 +#> Model cost at call 19 : 1041.522 +#> Model cost at call 24 : 840.4649 +#> Model cost at call 26 : 840.4646 +#> Model cost at call 29 : 782.303 +#> Model cost at call 31 : 782.3028 +#> Model cost at call 34 : 664.539 +#> Model cost at call 36 : 664.5389 +#> Model cost at call 40 : 615.7908 +#> Model cost at call 42 : 615.7907 +#> Model cost at call 45 : 569.5971 +#> Model cost at call 47 : 569.597 +#> Model cost at call 50 : 517.3175 +#> Model cost at call 52 : 517.3173 +#> Model cost at call 56 : 464.8158 +#> Model cost at call 58 : 464.8157 +#> Model cost at call 62 : 433.0031 +#> Model cost at call 64 : 433.003 +#> Model cost at call 67 : 423.7407 +#> Model cost at call 69 : 423.7406 +#> Model cost at call 70 : 423.7392 +#> Model cost at call 72 : 346.2781 +#> Model cost at call 74 : 346.278 +#> Model cost at call 75 : 346.2779 +#> Model cost at call 78 : 334.5399 +#> Model cost at call 80 : 334.5398 +#> Model cost at call 83 : 324.139 +#> Model cost at call 85 : 324.1389 +#> Model cost at call 88 : 319.7514 +#> Model cost at call 90 : 319.7514 +#> Model cost at call 94 : 300.9426 +#> Model cost at call 96 : 300.9425 +#> Model cost at call 100 : 295.8803 +#> Model cost at call 102 : 295.8803 +#> Model cost at call 105 : 290.3288 +#> Model cost at call 107 : 290.3287 +#> Model cost at call 111 : 284.3257 +#> Model cost at call 113 : 284.3257 +#> Model cost at call 116 : 282.3972 +#> Model cost at call 118 : 282.3972 +#> Model cost at call 122 : 273.7385 +#> Model cost at call 124 : 273.7385 +#> Model cost at call 128 : 271.8379 +#> Model cost at call 130 : 271.8379 +#> Model cost at call 133 : 270.064 +#> Model cost at call 135 : 270.064 +#> Model cost at call 138 : 268.0107 +#> Model cost at call 140 : 268.0107 +#> Model cost at call 144 : 265.6194 +#> Model cost at call 146 : 265.6194 +#> Model cost at call 148 : 265.6194 +#> Model cost at call 149 : 263.4825 +#> Model cost at call 151 : 263.4825 +#> Model cost at call 153 : 263.4824 +#> Model cost at call 154 : 262.0988 +#> Model cost at call 156 : 262.0988 +#> Model cost at call 160 : 260.7078 +#> Model cost at call 162 : 260.7078 +#> Model cost at call 165 : 259.9453 +#> Model cost at call 167 : 259.9453 +#> Model cost at call 170 : 258.9623 +#> Model cost at call 172 : 258.9623 +#> Model cost at call 174 : 258.962 +#> Model cost at call 176 : 258.0119 +#> Model cost at call 178 : 258.0119 +#> Model cost at call 180 : 258.0119 +#> Model cost at call 181 : 257.8698 +#> Model cost at call 183 : 257.8698 +#> Model cost at call 186 : 256.8608 +#> Model cost at call 188 : 256.8608 +#> Model cost at call 190 : 256.8608 +#> Model cost at call 191 : 256.2306 +#> Model cost at call 193 : 256.2306 +#> Model cost at call 195 : 256.2305 +#> Model cost at call 196 : 255.7119 +#> Model cost at call 198 : 255.7118 +#> Model cost at call 201 : 255.3323 +#> Model cost at call 203 : 255.3323 +#> Model cost at call 205 : 255.3323 +#> Model cost at call 206 : 254.6653 +#> Model cost at call 208 : 254.6653 +#> Model cost at call 211 : 254.3984 +#> Model cost at call 213 : 254.3984 +#> Model cost at call 216 : 253.3199 +#> Model cost at call 218 : 253.3199 +#> Model cost at call 220 : 253.3198 +#> Model cost at call 221 : 252.4845 +#> Model cost at call 223 : 252.4845 +#> Model cost at call 225 : 252.4845 +#> Model cost at call 226 : 251.6917 +#> Model cost at call 229 : 251.6917 +#> Model cost at call 230 : 251.6917 +#> Model cost at call 233 : 251.0189 +#> Model cost at call 235 : 251.0189 +#> Model cost at call 238 : 250.6912 +#> Model cost at call 240 : 250.6912 +#> Model cost at call 243 : 250.5546 +#> Model cost at call 245 : 250.5546 +#> Model cost at call 248 : 250.466 +#> Model cost at call 249 : 250.3744 +#> Model cost at call 250 : 249.9681 +#> Model cost at call 251 : 249.2215 +#> Model cost at call 260 : 248.919 +#> Model cost at call 264 : 248.919 +#> Model cost at call 265 : 248.8876 +#> Model cost at call 267 : 248.8876 +#> Model cost at call 270 : 248.8521 +#> Model cost at call 271 : 248.8178 +#> Model cost at call 272 : 248.6837 +#> Model cost at call 273 : 248.5989 +#> Model cost at call 276 : 248.5989 +#> Model cost at call 278 : 248.5935 +#> Model cost at call 280 : 248.5935 +#> Model cost at call 282 : 248.5935 +#> Model cost at call 283 : 248.5902 +#> Model cost at call 284 : 248.5902 +#> Model cost at call 289 : 248.5902 +#> Model cost at call 298 : 248.5902 +#> Model cost at call 309 : 248.5902 +#> Model cost at call 311 : 248.5902 +#> IRLS based on variance estimates for each observed variable +#> Initial variance estimates are: +#> parent m1 +#> 11.536305 7.443046 +#> Model cost at call 317 : 40 +#> Model cost at call 319 : 40 +#> Model cost at call 324 : 39.98891 +#> Model cost at call 325 : 39.9889 +#> Model cost at call 327 : 39.98886 +#> Model cost at call 331 : 39.98871 +#> Model cost at call 333 : 39.97254 +#> Model cost at call 336 : 39.97253 +#> Model cost at call 338 : 39.96929 +#> Model cost at call 340 : 39.96929 +#> Model cost at call 344 : 39.96849 +#> Model cost at call 346 : 39.96849 +#> Model cost at call 348 : 39.96849 +#> Model cost at call 349 : 39.96774 +#> Model cost at call 351 : 39.96774 +#> Model cost at call 353 : 39.96774 +#> Model cost at call 354 : 39.96714 +#> Model cost at call 356 : 39.96714 +#> Model cost at call 359 : 39.96617 +#> Model cost at call 361 : 39.96617 +#> Model cost at call 364 : 39.96606 +#> Model cost at call 366 : 39.96606 +#> Model cost at call 369 : 39.96551 +#> Model cost at call 371 : 39.96551 +#> Model cost at call 372 : 39.96551 +#> Model cost at call 375 : 39.96527 +#> Model cost at call 378 : 39.96527 +#> Model cost at call 379 : 39.96527 +#> Model cost at call 380 : 39.96525 +#> Model cost at call 382 : 39.96525 +#> Model cost at call 385 : 39.9651 +#> Model cost at call 387 : 39.9651 +#> Model cost at call 388 : 39.9651 +#> Model cost at call 390 : 39.96502 +#> Model cost at call 393 : 39.96502 +#> Model cost at call 396 : 39.96502 +#> Model cost at call 397 : 39.96467 +#> Model cost at call 398 : 39.96422 +#> Model cost at call 399 : 39.9624 +#> Model cost at call 400 : 39.95909 +#> Model cost at call 402 : 39.95909 +#> Model cost at call 405 : 39.9571 +#> Model cost at call 407 : 39.95709 +#> Model cost at call 413 : 39.95479 +#> Model cost at call 414 : 39.95479 +#> Model cost at call 415 : 39.95479 +#> Model cost at call 417 : 39.95479 +#> Model cost at call 419 : 39.95398 +#> Model cost at call 422 : 39.95398 +#> Model cost at call 424 : 39.95387 +#> Model cost at call 429 : 39.95384 +#> Model cost at call 432 : 39.95384 +#> Model cost at call 435 : 39.95384 +#> Model cost at call 437 : 39.95384 +#> Model cost at call 438 : 39.95384 +#> Model cost at call 446 : 39.95384 +#> Model cost at call 455 : 39.95384 +#> Model cost at call 469 : 39.95384 +#> Model cost at call 473 : 39.95384 +#> Iteration 1 yields variance estimates: +#> parent m1 +#> 11.572891 7.408116 +#> Sum of squared differences to last variance estimates: 7e-05 +#> Iteration 2 yields variance estimates: +#> parent m1 +#> 11.573402 7.407847 +#> Sum of squared differences to last variance estimates: 8.1e-09 +#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:19:55 2016 +#> Date of summary: Fri Nov 18 15:19:55 2016 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 648 model solutions performed in 2.716 s +#> +#> Weighting: manual then iterative reweighting method obs +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.67000 1.79200 96.04000 103.300 +#> log_k_parent -2.31200 0.04560 -2.40400 -2.220 +#> log_k_m1 -5.25100 0.12510 -5.50500 -4.998 +#> f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5083 -0.1979 -0.6147 +#> log_k_parent 0.5083 1.0000 -0.3894 -0.6062 +#> log_k_m1 -0.1979 -0.3894 1.0000 0.7417 +#> f_parent_ilr_1 -0.6147 -0.6062 0.7417 1.0000 +#> +#> Residual standard error: 1.054 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.67000 55.630 8.178e-37 96.040000 1.033e+02 +#> k_parent 0.09906 21.930 1.015e-22 0.090310 1.087e-01 +#> k_m1 0.00524 7.996 8.488e-10 0.004066 6.753e-03 +#> f_parent_to_m1 0.51340 23.000 2.038e-23 0.468100 5.584e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.399 4 15 +#> parent 6.466 2 7 +#> m1 4.679 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5134 +#> parent_sink 0.4866 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.997 23.24 +#> m1 132.281 439.43 +#> +#> Data: +#> time variable observed predicted residual err.ini err +#> 0 parent 99.46 9.967e+01 -2.122e-01 1 3.402 +#> 0 parent 102.04 9.967e+01 2.368e+00 1 3.402 +#> 1 parent 93.50 9.027e+01 3.228e+00 1 3.402 +#> 1 parent 92.50 9.027e+01 2.228e+00 1 3.402 +#> 3 parent 63.23 7.405e+01 -1.082e+01 1 3.402 +#> 3 parent 68.99 7.405e+01 -5.056e+00 1 3.402 +#> 7 parent 52.32 4.982e+01 2.499e+00 1 3.402 +#> 7 parent 55.13 4.982e+01 5.309e+00 1 3.402 +#> 14 parent 27.27 2.490e+01 2.367e+00 1 3.402 +#> 14 parent 26.64 2.490e+01 1.737e+00 1 3.402 +#> 21 parent 11.50 1.245e+01 -9.477e-01 1 3.402 +#> 21 parent 11.64 1.245e+01 -8.077e-01 1 3.402 +#> 35 parent 2.85 3.110e+00 -2.600e-01 1 3.402 +#> 35 parent 2.91 3.110e+00 -2.000e-01 1 3.402 +#> 50 parent 0.69 7.037e-01 -1.375e-02 1 3.402 +#> 50 parent 0.63 7.037e-01 -7.375e-02 1 3.402 +#> 75 parent 0.05 5.913e-02 -9.134e-03 1 3.402 +#> 75 parent 0.06 5.913e-02 8.659e-04 1 3.402 +#> 100 parent NA 4.969e-03 NA 1 3.402 +#> 100 parent NA 4.969e-03 NA 1 3.402 +#> 120 parent NA 6.852e-04 NA 1 3.402 +#> 120 parent NA 6.852e-04 NA 1 3.402 +#> 0 m1 0.00 0.000e+00 0.000e+00 2 2.722 +#> 0 m1 0.00 0.000e+00 0.000e+00 2 2.722 +#> 1 m1 4.84 4.813e+00 2.672e-02 2 2.722 +#> 1 m1 5.64 4.813e+00 8.267e-01 2 2.722 +#> 3 m1 12.91 1.305e+01 -1.378e-01 2 2.722 +#> 3 m1 12.96 1.305e+01 -8.778e-02 2 2.722 +#> 7 m1 22.97 2.508e+01 -2.106e+00 2 2.722 +#> 7 m1 24.47 2.508e+01 -6.061e-01 2 2.722 +#> 14 m1 41.69 3.671e+01 4.983e+00 2 2.722 +#> 14 m1 33.21 3.671e+01 -3.497e+00 2 2.722 +#> 21 m1 44.37 4.165e+01 2.719e+00 2 2.722 +#> 21 m1 46.44 4.165e+01 4.789e+00 2 2.722 +#> 35 m1 41.22 4.329e+01 -2.069e+00 2 2.722 +#> 35 m1 37.95 4.329e+01 -5.339e+00 2 2.722 +#> 50 m1 41.19 4.119e+01 -3.394e-03 2 2.722 +#> 50 m1 40.01 4.119e+01 -1.183e+00 2 2.722 +#> 75 m1 40.09 3.644e+01 3.652e+00 2 2.722 +#> 75 m1 33.85 3.644e+01 -2.588e+00 2 2.722 +#> 100 m1 31.04 3.199e+01 -9.497e-01 2 2.722 +#> 100 m1 33.13 3.199e+01 1.140e+00 2 2.722 +#> 120 m1 25.15 2.881e+01 -3.659e+00 2 2.722 +#> 120 m1 33.31 2.881e+01 4.501e+00 2 2.722</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index f328c34a..9477d648 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -164,28 +164,46 @@ <span class='no'>SFO_SFO</span> <span class='kw'><-</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>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='co'>## Not run: ------------------------------------</span> -<span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span> -<span class='co'># SFO_SFO <- mkinmod(</span> -<span class='co'># parent = list(type = "SFO", to = "m1"),</span> -<span class='co'># m1 = list(type = "SFO"))</span> -<span class='co'># </span> -<span class='co'># # Show details of creating the C function</span> -<span class='co'># SFO_SFO <- mkinmod(</span> -<span class='co'># parent = mkinsub("SFO", "m1"),</span> -<span class='co'># m1 = mkinsub("SFO"), verbose = TRUE)</span> -<span class='co'># </span> -<span class='co'># # If we have several parallel metabolites </span> -<span class='co'># # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> -<span class='co'># m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</span> -<span class='co'># M1 = mkinsub("SFO"),</span> -<span class='co'># M2 = mkinsub("SFO"),</span> -<span class='co'># use_of_ff = "max", quiet = TRUE)</span> -<span class='co'># </span> -<span class='co'># fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, </span> -<span class='co'># synthetic_data_for_UBA_2014[[12]]$data,</span> -<span class='co'># quiet = TRUE)</span> -<span class='co'>## ---------------------------------------------</span></div></pre> + +<span class='co'># The above model used to be specified like this, before the advent of mkinsub()</span> +<span class='no'>SFO_SFO</span> <span class='kw'><-</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='co'># Show details of creating the C function</span> +<span class='no'>SFO_SFO</span> <span class='kw'><-</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'>#> Compilation argument: +#> /usr/lib/R/bin/R CMD SHLIB file21efdcf882f.c 2> file21efdcf882f.c.err.txt +#> Program source: +#> 1: #include <R.h> +#> 2: +#> 3: +#> 4: static double parms [3]; +#> 5: #define k_parent_sink parms[0] +#> 6: #define k_parent_m1 parms[1] +#> 7: #define k_m1_sink parms[2] +#> 8: +#> 9: void initpar(void (* odeparms)(int *, double *)) { +#> 10: int N = 3; +#> 11: odeparms(&N, parms); +#> 12: } +#> 13: +#> 14: +#> 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { +#> 16: +#> 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0]; +#> 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1]; +#> 19: }</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='co'># If we have several parallel metabolites </span> +<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> +<span class='no'>m_synth_DFOP_par</span> <span class='kw'><-</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'>"DFOP"</span>, <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</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'>M2</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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + +<span class='no'>fit_DFOP_par_c</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, + <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 9c78d78a..546d7c88 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'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.024 0.004 0.004 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.008 0.024 0.004 </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'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.016 0.004 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.020 0.000 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'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.032 0.000 0.035 </div></pre> +#> 0.032 0.000 0.034 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mmkin-14.png b/docs/reference/mmkin-14.png Binary files differnew file mode 100644 index 00000000..9e40d451 --- /dev/null +++ b/docs/reference/mmkin-14.png diff --git a/docs/reference/mmkin-16.png b/docs/reference/mmkin-16.png Binary files differnew file mode 100644 index 00000000..72cfc5e7 --- /dev/null +++ b/docs/reference/mmkin-16.png diff --git a/docs/reference/mmkin-18.png b/docs/reference/mmkin-18.png Binary files differnew file mode 100644 index 00000000..0b315b1a --- /dev/null +++ b/docs/reference/mmkin-18.png diff --git a/docs/reference/mmkin-20.png b/docs/reference/mmkin-20.png Binary files differnew file mode 100644 index 00000000..b98940ff --- /dev/null +++ b/docs/reference/mmkin-20.png diff --git a/docs/reference/mmkin-22.png b/docs/reference/mmkin-22.png Binary files differnew file mode 100644 index 00000000..c2e9e5ae --- /dev/null +++ b/docs/reference/mmkin-22.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index f7f56164..0e39dac0 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -128,38 +128,1103 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> -<span class='co'># m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</span> -<span class='co'># M1 = mkinsub("SFO", "M2"),</span> -<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),</span> -<span class='co'># M1 = mkinsub("SFO", "M2"),</span> -<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</span> -<span class='co'># datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</span> -<span class='co'># names(datasets) <- paste("Dataset", 1:3)</span> -<span class='co'># </span> -<span class='co'># time_default <- system.time(fits.0 <- mmkin(models, datasets))</span> -<span class='co'># time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1))</span> -<span class='co'># </span> -<span class='co'># time_default</span> -<span class='co'># time_1</span> -<span class='co'># </span> -<span class='co'># endpoints(fits[["SFO_lin", 2]])</span> -<span class='co'># </span> -<span class='co'># # Plot.mkinfit handles rows or columns of mmkin result objects</span> -<span class='co'># plot(fits.0[1, ])</span> -<span class='co'># plot(fits.0[1, ], obs_var = c("M1", "M2"))</span> -<span class='co'># plot(fits.0[, 1])</span> -<span class='co'># # Use double brackets to extract a single mkinfit object, which will be plotted</span> -<span class='co'># # by plot.mkinfit</span> -<span class='co'># plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)</span> -<span class='co'># # Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> -<span class='co'># # allow to plot the observed variables separately</span> -<span class='co'># plot(fits.0[1, 1])</span> -<span class='co'>## ---------------------------------------------</span></div></pre> + <pre class="examples"><div class='input'> +<span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</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='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='st'>"M2"</span>), + <span class='kw'>M2</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'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>m_synth_FOMC_lin</span> <span class='kw'><-</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'>"FOMC"</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='st'>"M2"</span>), + <span class='kw'>M2</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'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>models</span> <span class='kw'><-</span> <span class='fu'>list</span>(<span class='kw'>SFO_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_SFO_lin</span>, <span class='kw'>FOMC_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_FOMC_lin</span>) +<span class='no'>datasets</span> <span class='kw'><-</span> <span class='fu'>lapply</span>(<span class='no'>synthetic_data_for_UBA_2014</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>) +<span class='fu'>names</span>(<span class='no'>datasets</span>) <span class='kw'><-</span> <span class='fu'>paste</span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>) + +<span class='no'>time_default</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.0</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>)) +<span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.1</span> <span class='kw'><-</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>))</div><div class='output co'>#> Model cost at call 1 : 31054.59 +#> Model cost at call 3 : 31054.59 +#> Model cost at call 8 : 15089.57 +#> Model cost at call 9 : 11464.3 +#> Model cost at call 11 : 11464.1 +#> Model cost at call 16 : 5723.32 +#> Model cost at call 17 : 5723.318 +#> Model cost at call 19 : 5723.304 +#> Model cost at call 21 : 5723.304 +#> Model cost at call 24 : 3968.126 +#> Model cost at call 25 : 3968.124 +#> Model cost at call 28 : 3968.119 +#> Model cost at call 31 : 3416.421 +#> Model cost at call 32 : 3416.42 +#> Model cost at call 36 : 3416.418 +#> Model cost at call 38 : 866.5564 +#> Model cost at call 42 : 866.5557 +#> Model cost at call 45 : 670.4833 +#> Model cost at call 47 : 670.476 +#> Model cost at call 53 : 312.9905 +#> Model cost at call 57 : 312.9904 +#> Model cost at call 58 : 312.9904 +#> Model cost at call 61 : 287.8916 +#> Model cost at call 63 : 287.8916 +#> Model cost at call 66 : 287.8916 +#> Model cost at call 69 : 284.5441 +#> Model cost at call 71 : 284.5441 +#> Model cost at call 73 : 284.5441 +#> Model cost at call 76 : 283.4533 +#> Model cost at call 78 : 283.4533 +#> Model cost at call 83 : 282.1356 +#> Model cost at call 85 : 282.1356 +#> Model cost at call 88 : 282.1356 +#> Model cost at call 90 : 280.7846 +#> Model cost at call 92 : 280.7846 +#> Model cost at call 95 : 280.7846 +#> Model cost at call 97 : 278.4856 +#> Model cost at call 98 : 274.5025 +#> Model cost at call 99 : 269.2866 +#> Model cost at call 101 : 269.2866 +#> Model cost at call 102 : 269.2866 +#> Model cost at call 103 : 269.2866 +#> Model cost at call 106 : 254.1284 +#> Model cost at call 108 : 254.1283 +#> Model cost at call 109 : 254.1283 +#> Model cost at call 112 : 254.128 +#> Model cost at call 114 : 233.1376 +#> Model cost at call 116 : 233.1376 +#> Model cost at call 118 : 233.1375 +#> Model cost at call 121 : 227.5879 +#> Model cost at call 124 : 227.5879 +#> Model cost at call 125 : 227.5878 +#> Model cost at call 129 : 217.0041 +#> Model cost at call 133 : 217.0041 +#> Model cost at call 135 : 217.0041 +#> Model cost at call 136 : 215.1367 +#> Model cost at call 138 : 215.1367 +#> Model cost at call 143 : 213.3794 +#> Model cost at call 145 : 213.3794 +#> Model cost at call 150 : 211.0201 +#> Model cost at call 152 : 211.0201 +#> Model cost at call 154 : 211.0201 +#> Model cost at call 155 : 211.0201 +#> Model cost at call 157 : 210.6426 +#> Model cost at call 159 : 210.6426 +#> Model cost at call 160 : 210.6425 +#> Model cost at call 164 : 207.6331 +#> Model cost at call 167 : 207.6331 +#> Model cost at call 171 : 206.2366 +#> Model cost at call 173 : 206.2366 +#> Model cost at call 174 : 206.2366 +#> Model cost at call 178 : 204.8117 +#> Model cost at call 180 : 204.8117 +#> Model cost at call 185 : 204.7988 +#> Model cost at call 187 : 204.7988 +#> Model cost at call 190 : 204.7988 +#> Model cost at call 192 : 203.5122 +#> Model cost at call 194 : 203.5122 +#> Model cost at call 197 : 203.5122 +#> Model cost at call 198 : 203.5122 +#> Model cost at call 199 : 203.354 +#> Model cost at call 201 : 203.354 +#> Model cost at call 204 : 203.354 +#> Model cost at call 206 : 202.6825 +#> Model cost at call 208 : 202.6825 +#> Model cost at call 209 : 202.6825 +#> Model cost at call 212 : 202.6825 +#> Model cost at call 213 : 202.4582 +#> Model cost at call 215 : 202.4582 +#> Model cost at call 220 : 202.3261 +#> Model cost at call 222 : 202.3261 +#> Model cost at call 227 : 202.2306 +#> Model cost at call 229 : 202.2306 +#> Model cost at call 231 : 202.2306 +#> Model cost at call 234 : 202.115 +#> Model cost at call 236 : 202.115 +#> Model cost at call 238 : 202.115 +#> Model cost at call 241 : 202.0397 +#> Model cost at call 243 : 202.0397 +#> Model cost at call 248 : 201.8989 +#> Model cost at call 249 : 201.8551 +#> Model cost at call 252 : 201.8551 +#> Model cost at call 257 : 201.676 +#> Model cost at call 259 : 201.676 +#> Model cost at call 264 : 201.6285 +#> Model cost at call 266 : 201.6285 +#> Model cost at call 270 : 201.6284 +#> Model cost at call 271 : 201.5876 +#> Model cost at call 272 : 201.5876 +#> Model cost at call 278 : 201.5317 +#> Model cost at call 279 : 201.5317 +#> Model cost at call 286 : 201.5207 +#> Model cost at call 287 : 201.5207 +#> Model cost at call 289 : 201.5207 +#> Model cost at call 293 : 201.5207 +#> Model cost at call 294 : 201.5207 +#> Model cost at call 296 : 201.5174 +#> Model cost at call 301 : 201.5174 +#> Model cost at call 304 : 201.5169 +#> Model cost at call 305 : 201.5169 +#> Model cost at call 306 : 201.5169 +#> Model cost at call 309 : 201.5169 +#> Model cost at call 312 : 201.5169 +#> Model cost at call 314 : 201.5169 +#> Model cost at call 322 : 201.5169 +#> Model cost at call 325 : 201.5169 +#> Model cost at call 340 : 201.5169 +#> Optimisation by method Port successfully terminated. +#> Model cost at call 1 : 35974.4 +#> Model cost at call 3 : 35974.4 +#> Model cost at call 5 : 35974.4 +#> Model cost at call 7 : 35974.4 +#> Model cost at call 9 : 13270.14 +#> Model cost at call 10 : 12432.22 +#> Model cost at call 14 : 12432.12 +#> Model cost at call 16 : 12431.88 +#> Model cost at call 18 : 5356.271 +#> Model cost at call 19 : 5356.268 +#> Model cost at call 20 : 5356.251 +#> Model cost at call 22 : 5356.245 +#> Model cost at call 27 : 1507.839 +#> Model cost at call 33 : 1507.839 +#> Model cost at call 35 : 582.0818 +#> Model cost at call 36 : 582.0813 +#> Model cost at call 38 : 582.0802 +#> Model cost at call 40 : 582.0799 +#> Model cost at call 44 : 328.9337 +#> Model cost at call 45 : 328.9335 +#> Model cost at call 51 : 328.9328 +#> Model cost at call 53 : 313.4901 +#> Model cost at call 59 : 313.49 +#> Model cost at call 60 : 313.4899 +#> Model cost at call 61 : 308.6268 +#> Model cost at call 63 : 308.6267 +#> Model cost at call 69 : 302.4454 +#> Model cost at call 73 : 302.4453 +#> Model cost at call 77 : 298.0751 +#> Model cost at call 79 : 298.075 +#> Model cost at call 85 : 293.1404 +#> Model cost at call 86 : 289.6645 +#> Model cost at call 88 : 289.6645 +#> Model cost at call 95 : 288.1617 +#> Model cost at call 101 : 288.1616 +#> Model cost at call 102 : 288.1615 +#> Model cost at call 103 : 286.7649 +#> Model cost at call 109 : 286.7649 +#> Model cost at call 111 : 284.5224 +#> Model cost at call 117 : 284.5224 +#> Model cost at call 118 : 284.5224 +#> Model cost at call 119 : 281.3466 +#> Model cost at call 125 : 281.3466 +#> Model cost at call 127 : 274.0924 +#> Model cost at call 128 : 264.929 +#> Model cost at call 133 : 264.929 +#> Model cost at call 136 : 251.3329 +#> Model cost at call 137 : 251.3329 +#> Model cost at call 140 : 251.3329 +#> Model cost at call 141 : 251.3329 +#> Model cost at call 146 : 247.7019 +#> Model cost at call 147 : 247.7019 +#> Model cost at call 149 : 247.7018 +#> Model cost at call 154 : 247.3465 +#> Model cost at call 158 : 247.3465 +#> Model cost at call 160 : 247.3464 +#> Model cost at call 162 : 244.622 +#> Model cost at call 166 : 244.622 +#> Model cost at call 170 : 242.5961 +#> Model cost at call 171 : 241.6973 +#> Model cost at call 173 : 241.6973 +#> Model cost at call 174 : 241.6973 +#> Model cost at call 175 : 241.6973 +#> Model cost at call 179 : 238.8924 +#> Model cost at call 181 : 238.8923 +#> Model cost at call 187 : 236.0921 +#> Model cost at call 190 : 236.0921 +#> Model cost at call 192 : 236.092 +#> Model cost at call 195 : 233.9082 +#> Model cost at call 197 : 233.9082 +#> Model cost at call 201 : 233.9082 +#> Model cost at call 202 : 233.9082 +#> Model cost at call 203 : 228.1486 +#> Model cost at call 205 : 228.1486 +#> Model cost at call 206 : 228.1485 +#> Model cost at call 207 : 228.1485 +#> Model cost at call 211 : 225.0879 +#> Model cost at call 214 : 225.0879 +#> Model cost at call 216 : 225.0879 +#> Model cost at call 218 : 225.0879 +#> Model cost at call 219 : 220.9928 +#> Model cost at call 221 : 220.9928 +#> Model cost at call 227 : 219.1889 +#> Model cost at call 229 : 219.1888 +#> Model cost at call 233 : 219.1888 +#> Model cost at call 235 : 218.6966 +#> Model cost at call 238 : 218.6966 +#> Model cost at call 239 : 218.6966 +#> Model cost at call 240 : 218.6966 +#> Model cost at call 241 : 218.6966 +#> Model cost at call 242 : 218.6966 +#> Model cost at call 243 : 214.4307 +#> Model cost at call 247 : 214.4307 +#> Model cost at call 251 : 213.6076 +#> Model cost at call 253 : 213.6076 +#> Model cost at call 254 : 213.6076 +#> Model cost at call 256 : 213.6076 +#> Model cost at call 259 : 211.0287 +#> Model cost at call 262 : 211.0287 +#> Model cost at call 263 : 211.0287 +#> Model cost at call 267 : 209.6141 +#> Model cost at call 270 : 209.6141 +#> Model cost at call 271 : 209.6141 +#> Model cost at call 276 : 207.896 +#> Model cost at call 278 : 207.896 +#> Model cost at call 284 : 206.4468 +#> Model cost at call 286 : 206.4468 +#> Model cost at call 289 : 206.4468 +#> Model cost at call 292 : 205.8789 +#> Model cost at call 296 : 205.8789 +#> Model cost at call 298 : 205.8789 +#> Model cost at call 299 : 205.8789 +#> Model cost at call 300 : 204.2634 +#> Model cost at call 301 : 204.2634 +#> Model cost at call 303 : 204.2634 +#> Model cost at call 305 : 204.2634 +#> Model cost at call 308 : 203.5453 +#> Model cost at call 309 : 203.338 +#> Model cost at call 310 : 203.338 +#> Model cost at call 313 : 203.338 +#> Model cost at call 314 : 203.338 +#> Model cost at call 316 : 203.338 +#> Model cost at call 318 : 202.797 +#> Model cost at call 321 : 202.797 +#> Model cost at call 326 : 202.4377 +#> Model cost at call 327 : 202.4377 +#> Model cost at call 334 : 202.0027 +#> Model cost at call 335 : 202.0027 +#> Model cost at call 342 : 201.8249 +#> Model cost at call 344 : 201.8249 +#> Model cost at call 349 : 201.8249 +#> Model cost at call 351 : 201.7123 +#> Model cost at call 352 : 201.7123 +#> Model cost at call 359 : 201.6476 +#> Model cost at call 361 : 201.6476 +#> Model cost at call 365 : 201.6476 +#> Model cost at call 368 : 201.5827 +#> Model cost at call 371 : 201.5827 +#> Model cost at call 378 : 201.5531 +#> Model cost at call 379 : 201.5531 +#> Model cost at call 386 : 201.5531 +#> Model cost at call 390 : 201.537 +#> Model cost at call 391 : 201.537 +#> Model cost at call 401 : 201.5281 +#> Model cost at call 402 : 201.5281 +#> Model cost at call 404 : 201.5281 +#> Model cost at call 407 : 201.5281 +#> Model cost at call 413 : 201.5231 +#> Model cost at call 417 : 201.5231 +#> Model cost at call 418 : 201.5231 +#> Model cost at call 420 : 201.5231 +#> Model cost at call 426 : 201.5199 +#> Model cost at call 428 : 201.5199 +#> Model cost at call 439 : 201.5184 +#> Model cost at call 443 : 201.5184 +#> Model cost at call 444 : 201.5184 +#> Model cost at call 446 : 201.5184 +#> Model cost at call 454 : 201.5177 +#> Model cost at call 457 : 201.5177 +#> Model cost at call 469 : 201.5174 +#> Model cost at call 473 : 201.5174 +#> Model cost at call 476 : 201.5174 +#> Model cost at call 480 : 201.5174 +#> Model cost at call 483 : 201.5174 +#> Model cost at call 484 : 201.5171 +#> Model cost at call 487 : 201.5171 +#> Model cost at call 499 : 201.517 +#> Model cost at call 506 : 201.517 +#> Model cost at call 510 : 201.517 +#> Model cost at call 514 : 201.517 +#> Model cost at call 522 : 201.517 +#> Model cost at call 526 : 201.517 +#> Model cost at call 527 : 201.517 +#> Model cost at call 529 : 201.5169 +#> Model cost at call 536 : 201.5169 +#> Model cost at call 540 : 201.5169 +#> Model cost at call 544 : 201.5169 +#> Model cost at call 556 : 201.5169 +#> Model cost at call 557 : 201.5169 +#> Model cost at call 559 : 201.5169 +#> Model cost at call 574 : 201.5169 +#> Model cost at call 575 : 201.5169 +#> Model cost at call 578 : 201.5169 +#> Model cost at call 582 : 201.5169 +#> Model cost at call 586 : 201.5169 +#> Model cost at call 589 : 201.5169 +#> Model cost at call 590 : 201.5169 +#> Model cost at call 601 : 201.5169 +#> Model cost at call 604 : 201.5169 +#> Model cost at call 617 : 201.5169 +#> Model cost at call 632 : 201.5169 +#> Model cost at call 647 : 201.5169 +#> Model cost at call 662 : 201.5169 +#> Model cost at call 680 : 201.5169 +#> Optimisation by method Port successfully terminated. +#> Model cost at call 1 : 30689.89 +#> Model cost at call 3 : 30689.89 +#> Model cost at call 8 : 16294.04 +#> Model cost at call 9 : 12699.33 +#> Model cost at call 11 : 12699.26 +#> Model cost at call 14 : 12699.05 +#> Model cost at call 17 : 9202.163 +#> Model cost at call 18 : 9202.16 +#> Model cost at call 20 : 9202.147 +#> Model cost at call 22 : 9202.147 +#> Model cost at call 25 : 6601.043 +#> Model cost at call 26 : 6601.041 +#> Model cost at call 30 : 6601.04 +#> Model cost at call 32 : 4223.705 +#> Model cost at call 34 : 4223.703 +#> Model cost at call 39 : 4223.703 +#> Model cost at call 40 : 1443.507 +#> Model cost at call 45 : 1443.507 +#> Model cost at call 49 : 1191.267 +#> Model cost at call 51 : 1191.267 +#> Model cost at call 56 : 1186.498 +#> Model cost at call 57 : 1186.498 +#> Model cost at call 58 : 1186.497 +#> Model cost at call 59 : 1186.497 +#> Model cost at call 61 : 1186.496 +#> Model cost at call 62 : 1186.494 +#> Model cost at call 63 : 1130.799 +#> Model cost at call 64 : 1130.799 +#> Model cost at call 71 : 1126.363 +#> Model cost at call 73 : 1126.363 +#> Model cost at call 78 : 1122.848 +#> Model cost at call 80 : 1122.848 +#> Model cost at call 82 : 1122.848 +#> Model cost at call 85 : 1120.954 +#> Model cost at call 87 : 1120.954 +#> Model cost at call 88 : 1120.954 +#> Model cost at call 89 : 1120.954 +#> Model cost at call 92 : 1117.156 +#> Model cost at call 95 : 1117.156 +#> Model cost at call 96 : 1117.156 +#> Model cost at call 99 : 1116.894 +#> Model cost at call 101 : 1116.894 +#> Model cost at call 104 : 1116.894 +#> Model cost at call 106 : 1113.955 +#> Model cost at call 108 : 1113.955 +#> Model cost at call 112 : 1113.955 +#> Model cost at call 113 : 1113.03 +#> Model cost at call 115 : 1113.03 +#> Model cost at call 120 : 1111.643 +#> Model cost at call 122 : 1111.643 +#> Model cost at call 127 : 1109.657 +#> Model cost at call 129 : 1109.657 +#> Model cost at call 131 : 1109.657 +#> Model cost at call 134 : 1106.725 +#> Model cost at call 136 : 1106.725 +#> Model cost at call 137 : 1106.725 +#> Model cost at call 142 : 1106.005 +#> Model cost at call 144 : 1106.005 +#> Model cost at call 145 : 1106.005 +#> Model cost at call 147 : 1106.005 +#> Model cost at call 149 : 1105.268 +#> Model cost at call 151 : 1105.268 +#> Model cost at call 153 : 1105.268 +#> Model cost at call 156 : 1104.247 +#> Model cost at call 158 : 1104.247 +#> Model cost at call 159 : 1104.247 +#> Model cost at call 161 : 1104.247 +#> Model cost at call 163 : 1103.813 +#> Model cost at call 165 : 1103.813 +#> Model cost at call 167 : 1103.813 +#> Model cost at call 170 : 1103.075 +#> Model cost at call 172 : 1103.075 +#> Model cost at call 173 : 1103.075 +#> Model cost at call 177 : 1102.447 +#> Model cost at call 179 : 1102.447 +#> Model cost at call 180 : 1102.447 +#> Model cost at call 183 : 1102.447 +#> Model cost at call 184 : 1102.038 +#> Model cost at call 185 : 1101.712 +#> Model cost at call 186 : 1101.337 +#> Model cost at call 188 : 1101.337 +#> Model cost at call 193 : 1100.37 +#> Model cost at call 195 : 1100.37 +#> Model cost at call 197 : 1100.37 +#> Model cost at call 200 : 1099.46 +#> Model cost at call 202 : 1099.46 +#> Model cost at call 207 : 1099.262 +#> Model cost at call 209 : 1099.262 +#> Model cost at call 211 : 1099.262 +#> Model cost at call 212 : 1099.261 +#> Model cost at call 214 : 1099.227 +#> Model cost at call 216 : 1099.227 +#> Model cost at call 217 : 1099.227 +#> Model cost at call 218 : 1099.227 +#> Model cost at call 221 : 1098.331 +#> Model cost at call 223 : 1098.331 +#> Model cost at call 224 : 1098.331 +#> Model cost at call 230 : 1098.24 +#> Model cost at call 235 : 1098.24 +#> Model cost at call 236 : 1098.24 +#> Model cost at call 238 : 1098.231 +#> Model cost at call 240 : 1098.231 +#> Model cost at call 245 : 1098.228 +#> Model cost at call 247 : 1098.228 +#> Model cost at call 252 : 1098.221 +#> Model cost at call 254 : 1098.221 +#> Model cost at call 255 : 1098.221 +#> Model cost at call 258 : 1098.221 +#> Model cost at call 261 : 1098.214 +#> Model cost at call 263 : 1098.214 +#> Model cost at call 268 : 1098.204 +#> Model cost at call 269 : 1098.196 +#> Model cost at call 270 : 1098.187 +#> Model cost at call 272 : 1098.187 +#> Model cost at call 273 : 1098.187 +#> Model cost at call 279 : 1098.181 +#> Model cost at call 281 : 1098.181 +#> Model cost at call 282 : 1098.181 +#> Model cost at call 284 : 1098.181 +#> Model cost at call 285 : 1098.181 +#> Model cost at call 287 : 1098.172 +#> Model cost at call 291 : 1098.172 +#> Model cost at call 293 : 1098.172 +#> Model cost at call 294 : 1098.169 +#> Model cost at call 295 : 1098.169 +#> Model cost at call 296 : 1098.169 +#> Model cost at call 301 : 1098.169 +#> Model cost at call 305 : 1098.169 +#> Model cost at call 306 : 1098.169 +#> Model cost at call 309 : 1098.169 +#> Model cost at call 314 : 1098.169 +#> Model cost at call 318 : 1098.169 +#> Model cost at call 319 : 1098.169 +#> Model cost at call 321 : 1098.169 +#> Model cost at call 324 : 1098.169 +#> Model cost at call 325 : 1098.169 +#> Model cost at call 331 : 1098.169 +#> Model cost at call 333 : 1098.169 +#> Model cost at call 336 : 1098.169 +#> Model cost at call 342 : 1098.169 +#> Model cost at call 344 : 1098.169 +#> Model cost at call 348 : 1098.169 +#> Model cost at call 352 : 1098.169 +#> Model cost at call 357 : 1098.169 +#> Model cost at call 370 : 1098.169 +#> Model cost at call 385 : 1098.169 +#> Model cost at call 386 : 1098.169 +#> Optimisation by method Port successfully terminated. +#> Model cost at call 1 : 34499.23 +#> Model cost at call 3 : 34499.23 +#> Model cost at call 5 : 34499.23 +#> Model cost at call 7 : 34499.23 +#> Model cost at call 9 : 14274.95 +#> Model cost at call 10 : 14162.89 +#> Model cost at call 14 : 14162.68 +#> Model cost at call 18 : 13341.49 +#> Model cost at call 19 : 13341.48 +#> Model cost at call 20 : 13341.47 +#> Model cost at call 22 : 13341.44 +#> Model cost at call 27 : 10055.95 +#> Model cost at call 28 : 10055.95 +#> Model cost at call 30 : 10055.95 +#> Model cost at call 35 : 7732.384 +#> Model cost at call 36 : 7732.381 +#> Model cost at call 39 : 7732.381 +#> Model cost at call 44 : 6325.124 +#> Model cost at call 45 : 6325.122 +#> Model cost at call 47 : 6325.117 +#> Model cost at call 52 : 3732.612 +#> Model cost at call 54 : 3732.611 +#> Model cost at call 61 : 1371.768 +#> Model cost at call 64 : 1371.768 +#> Model cost at call 67 : 1371.768 +#> Model cost at call 70 : 1302.633 +#> Model cost at call 74 : 1302.633 +#> Model cost at call 75 : 1302.633 +#> Model cost at call 78 : 1298.854 +#> Model cost at call 82 : 1298.854 +#> Model cost at call 84 : 1298.854 +#> Model cost at call 86 : 1245.775 +#> Model cost at call 91 : 1245.775 +#> Model cost at call 94 : 1230.679 +#> Model cost at call 96 : 1230.679 +#> Model cost at call 100 : 1230.679 +#> Model cost at call 103 : 1227.471 +#> Model cost at call 105 : 1227.471 +#> Model cost at call 109 : 1227.471 +#> Model cost at call 111 : 1225.318 +#> Model cost at call 113 : 1225.318 +#> Model cost at call 117 : 1225.318 +#> Model cost at call 118 : 1225.318 +#> Model cost at call 119 : 1221.478 +#> Model cost at call 121 : 1221.478 +#> Model cost at call 127 : 1214.191 +#> Model cost at call 128 : 1203.986 +#> Model cost at call 129 : 1164.433 +#> Model cost at call 135 : 1164.433 +#> Model cost at call 140 : 1158.843 +#> Model cost at call 145 : 1158.843 +#> Model cost at call 148 : 1156.585 +#> Model cost at call 154 : 1156.585 +#> Model cost at call 156 : 1155.177 +#> Model cost at call 159 : 1155.177 +#> Model cost at call 161 : 1155.176 +#> Model cost at call 164 : 1151.603 +#> Model cost at call 166 : 1151.603 +#> Model cost at call 167 : 1151.603 +#> Model cost at call 169 : 1151.603 +#> Model cost at call 173 : 1150.467 +#> Model cost at call 175 : 1150.467 +#> Model cost at call 176 : 1150.467 +#> Model cost at call 181 : 1150.117 +#> Model cost at call 184 : 1150.117 +#> Model cost at call 185 : 1150.117 +#> Model cost at call 187 : 1150.117 +#> Model cost at call 188 : 1150.117 +#> Model cost at call 189 : 1149.03 +#> Model cost at call 193 : 1149.03 +#> Model cost at call 195 : 1149.03 +#> Model cost at call 197 : 1148.468 +#> Model cost at call 199 : 1148.468 +#> Model cost at call 205 : 1147.297 +#> Model cost at call 207 : 1147.297 +#> Model cost at call 211 : 1147.297 +#> Model cost at call 213 : 1146.841 +#> Model cost at call 216 : 1146.841 +#> Model cost at call 217 : 1146.841 +#> Model cost at call 219 : 1146.841 +#> Model cost at call 221 : 1144.548 +#> Model cost at call 223 : 1144.548 +#> Model cost at call 229 : 1143.258 +#> Model cost at call 231 : 1143.258 +#> Model cost at call 237 : 1141.772 +#> Model cost at call 239 : 1141.772 +#> Model cost at call 240 : 1141.772 +#> Model cost at call 241 : 1141.772 +#> Model cost at call 243 : 1141.772 +#> Model cost at call 245 : 1140.849 +#> Model cost at call 251 : 1140.849 +#> Model cost at call 252 : 1140.849 +#> Model cost at call 253 : 1139.456 +#> Model cost at call 259 : 1139.456 +#> Model cost at call 261 : 1137.678 +#> Model cost at call 263 : 1137.678 +#> Model cost at call 269 : 1135.358 +#> Model cost at call 270 : 1134.128 +#> Model cost at call 272 : 1134.128 +#> Model cost at call 280 : 1133.342 +#> Model cost at call 283 : 1133.342 +#> Model cost at call 286 : 1133.342 +#> Model cost at call 288 : 1133.229 +#> Model cost at call 292 : 1133.229 +#> Model cost at call 294 : 1133.229 +#> Model cost at call 295 : 1133.229 +#> Model cost at call 296 : 1132.641 +#> Model cost at call 300 : 1132.641 +#> Model cost at call 304 : 1132.126 +#> Model cost at call 310 : 1132.126 +#> Model cost at call 312 : 1131.169 +#> Model cost at call 318 : 1131.169 +#> Model cost at call 320 : 1130.405 +#> Model cost at call 324 : 1130.405 +#> Model cost at call 328 : 1129.635 +#> Model cost at call 330 : 1129.635 +#> Model cost at call 332 : 1129.635 +#> Model cost at call 334 : 1129.635 +#> Model cost at call 336 : 1128.526 +#> Model cost at call 338 : 1128.526 +#> Model cost at call 343 : 1128.526 +#> Model cost at call 344 : 1127.498 +#> Model cost at call 346 : 1127.498 +#> Model cost at call 350 : 1127.498 +#> Model cost at call 352 : 1126.06 +#> Model cost at call 353 : 1124.911 +#> Model cost at call 356 : 1124.911 +#> Model cost at call 362 : 1120.309 +#> Model cost at call 366 : 1120.309 +#> Model cost at call 368 : 1120.308 +#> Model cost at call 369 : 1120.308 +#> Model cost at call 370 : 1117.687 +#> Model cost at call 374 : 1117.687 +#> Model cost at call 375 : 1117.687 +#> Model cost at call 378 : 1112.013 +#> Model cost at call 379 : 1112.013 +#> Model cost at call 381 : 1112.013 +#> Model cost at call 386 : 1108.648 +#> Model cost at call 387 : 1108.251 +#> Model cost at call 388 : 1108.251 +#> Model cost at call 391 : 1108.251 +#> Model cost at call 392 : 1108.251 +#> Model cost at call 395 : 1104.73 +#> Model cost at call 396 : 1104.73 +#> Model cost at call 397 : 1104.73 +#> Model cost at call 403 : 1103.277 +#> Model cost at call 404 : 1103.277 +#> Model cost at call 411 : 1101.351 +#> Model cost at call 414 : 1101.351 +#> Model cost at call 416 : 1101.351 +#> Model cost at call 417 : 1101.351 +#> Model cost at call 419 : 1100.36 +#> Model cost at call 420 : 1100.36 +#> Model cost at call 421 : 1100.36 +#> Model cost at call 427 : 1099.596 +#> Model cost at call 431 : 1099.596 +#> Model cost at call 432 : 1099.596 +#> Model cost at call 435 : 1099.029 +#> Model cost at call 437 : 1099.029 +#> Model cost at call 444 : 1098.722 +#> Model cost at call 447 : 1098.722 +#> Model cost at call 448 : 1098.722 +#> Model cost at call 453 : 1098.441 +#> Model cost at call 455 : 1098.441 +#> Model cost at call 458 : 1098.441 +#> Model cost at call 463 : 1098.314 +#> Model cost at call 464 : 1098.314 +#> Model cost at call 469 : 1098.314 +#> Model cost at call 471 : 1098.314 +#> Model cost at call 475 : 1098.245 +#> Model cost at call 477 : 1098.245 +#> Model cost at call 480 : 1098.245 +#> Model cost at call 486 : 1098.209 +#> Model cost at call 487 : 1098.209 +#> Model cost at call 489 : 1098.209 +#> Model cost at call 493 : 1098.209 +#> Model cost at call 505 : 1098.209 +#> Model cost at call 506 : 1098.209 +#> Model cost at call 510 : 1098.209 +#> Model cost at call 518 : 1098.209 +#> Model cost at call 519 : 1098.209 +#> Model cost at call 522 : 1098.209 +#> Model cost at call 526 : 1098.209 +#> Model cost at call 528 : 1098.209 +#> Model cost at call 530 : 1098.209 +#> Model cost at call 533 : 1098.209 +#> Model cost at call 534 : 1098.209 +#> Model cost at call 536 : 1098.209 +#> Model cost at call 542 : 1098.209 +#> Model cost at call 549 : 1098.207 +#> Model cost at call 551 : 1098.207 +#> Model cost at call 552 : 1098.207 +#> Model cost at call 555 : 1098.207 +#> Model cost at call 564 : 1098.205 +#> Model cost at call 566 : 1098.205 +#> Model cost at call 567 : 1098.205 +#> Model cost at call 570 : 1098.205 +#> Model cost at call 579 : 1098.2 +#> Model cost at call 580 : 1098.191 +#> Model cost at call 581 : 1098.191 +#> Model cost at call 583 : 1098.191 +#> Model cost at call 586 : 1098.191 +#> Model cost at call 587 : 1098.191 +#> Model cost at call 589 : 1098.191 +#> Model cost at call 595 : 1098.186 +#> Model cost at call 596 : 1098.186 +#> Model cost at call 606 : 1098.18 +#> Model cost at call 609 : 1098.18 +#> Model cost at call 610 : 1098.18 +#> Model cost at call 616 : 1098.177 +#> Model cost at call 619 : 1098.177 +#> Model cost at call 620 : 1098.177 +#> Model cost at call 627 : 1098.173 +#> Model cost at call 630 : 1098.173 +#> Model cost at call 631 : 1098.173 +#> Model cost at call 636 : 1098.173 +#> Model cost at call 641 : 1098.172 +#> Model cost at call 642 : 1098.172 +#> Model cost at call 653 : 1098.172 +#> Model cost at call 654 : 1098.172 +#> Model cost at call 664 : 1098.172 +#> Model cost at call 669 : 1098.172 +#> Model cost at call 671 : 1098.172 +#> Model cost at call 675 : 1098.172 +#> Model cost at call 678 : 1098.172 +#> Model cost at call 680 : 1098.172 +#> Model cost at call 683 : 1098.172 +#> Model cost at call 684 : 1098.172 +#> Model cost at call 686 : 1098.172 +#> Model cost at call 690 : 1098.172 +#> Model cost at call 702 : 1098.172 +#> Model cost at call 704 : 1098.172 +#> Model cost at call 708 : 1098.172 +#> Model cost at call 721 : 1098.172 +#> Model cost at call 723 : 1098.172 +#> Model cost at call 736 : 1098.172 +#> Model cost at call 738 : 1098.172 +#> Model cost at call 751 : 1098.172 +#> Model cost at call 753 : 1098.172 +#> Model cost at call 766 : 1098.172 +#> Model cost at call 767 : 1098.172 +#> Model cost at call 768 : 1098.172 +#> Model cost at call 770 : 1098.172 +#> Model cost at call 783 : 1098.172 +#> Model cost at call 784 : 1098.172 +#> Model cost at call 785 : 1098.172 +#> Model cost at call 799 : 1098.172 +#> Model cost at call 800 : 1098.172 +#> Model cost at call 814 : 1098.172 +#> Model cost at call 815 : 1098.172 +#> Model cost at call 816 : 1098.172 +#> Model cost at call 822 : 1098.172 +#> Model cost at call 830 : 1098.172 +#> Model cost at call 831 : 1098.172 +#> Model cost at call 834 : 1098.172 +#> Model cost at call 845 : 1098.172 +#> Model cost at call 846 : 1098.172 +#> Model cost at call 849 : 1098.172 +#> Model cost at call 860 : 1098.171 +#> Model cost at call 861 : 1098.171 +#> Model cost at call 864 : 1098.171 +#> Model cost at call 875 : 1098.171 +#> Model cost at call 876 : 1098.171 +#> Model cost at call 879 : 1098.171 +#> Model cost at call 890 : 1098.17 +#> Model cost at call 891 : 1098.17 +#> Model cost at call 894 : 1098.17 +#> Model cost at call 904 : 1098.169 +#> Model cost at call 905 : 1098.169 +#> Model cost at call 908 : 1098.169 +#> Model cost at call 909 : 1098.169 +#> Model cost at call 919 : 1098.169 +#> Model cost at call 921 : 1098.169 +#> Model cost at call 931 : 1098.169 +#> Model cost at call 932 : 1098.169 +#> Model cost at call 934 : 1098.169 +#> Model cost at call 936 : 1098.169 +#> Model cost at call 937 : 1098.169 +#> Model cost at call 944 : 1098.169 +#> Model cost at call 947 : 1098.169 +#> Model cost at call 949 : 1098.169 +#> Model cost at call 951 : 1098.169 +#> Model cost at call 952 : 1098.169 +#> Model cost at call 954 : 1098.169 +#> Model cost at call 964 : 1098.169 +#> Model cost at call 967 : 1098.169 +#> Model cost at call 969 : 1098.169 +#> Model cost at call 982 : 1098.169 +#> Model cost at call 1017 : 1098.169 +#> Model cost at call 1018 : 1098.169 +#> Model cost at call 1022 : 1098.169 +#> Model cost at call 1029 : 1098.169 +#> Model cost at call 1033 : 1098.169 +#> Model cost at call 1038 : 1098.169 +#> Model cost at call 1048 : 1098.169 +#> Model cost at call 1049 : 1098.169 +#> Model cost at call 1055 : 1098.169 +#> Model cost at call 1063 : 1098.169 +#> Model cost at call 1074 : 1098.169 +#> Model cost at call 1079 : 1098.169 +#> Model cost at call 1089 : 1098.169 +#> Model cost at call 1120 : 1098.169 +#> Model cost at call 1124 : 1098.169 +#> Model cost at call 1139 : 1098.169 +#> Model cost at call 1154 : 1098.169 +#> Model cost at call 1170 : 1098.169 +#> Model cost at call 1185 : 1098.169 +#> Model cost at call 1200 : 1098.169 +#> Model cost at call 1215 : 1098.169 +#> Model cost at call 1231 : 1098.169 +#> Model cost at call 1246 : 1098.169 +#> Model cost at call 1247 : 1098.169 +#> Model cost at call 1248 : 1098.169 +#> Model cost at call 1258 : 1098.169 +#> Model cost at call 1263 : 1098.169 +#> Model cost at call 1278 : 1098.169 +#> Model cost at call 1295 : 1098.169 +#> Model cost at call 1296 : 1098.169 +#> Model cost at call 1297 : 1098.169 +#> Model cost at call 1298 : 1098.169 +#> Model cost at call 1306 : 1098.169 +#> Model cost at call 1308 : 1098.169 +#> Optimisation by method Port successfully terminated. +#> Model cost at call 1 : 31389.19 +#> Model cost at call 3 : 31389.19 +#> Model cost at call 8 : 15003.41 +#> Model cost at call 9 : 11136.21 +#> Model cost at call 11 : 11135.87 +#> Model cost at call 16 : 4800.182 +#> Model cost at call 17 : 4800.181 +#> Model cost at call 19 : 4800.163 +#> Model cost at call 24 : 3036.068 +#> Model cost at call 25 : 3036.068 +#> Model cost at call 26 : 3036.052 +#> Model cost at call 31 : 1361.371 +#> Model cost at call 33 : 1361.371 +#> Model cost at call 40 : 494.6738 +#> Model cost at call 41 : 494.6736 +#> Model cost at call 45 : 494.6734 +#> Model cost at call 48 : 260.2631 +#> Model cost at call 49 : 260.2629 +#> Model cost at call 55 : 248.3035 +#> Model cost at call 56 : 248.3034 +#> Model cost at call 57 : 248.3023 +#> Model cost at call 62 : 171.6337 +#> Model cost at call 63 : 171.6337 +#> Model cost at call 70 : 167.3473 +#> Model cost at call 72 : 167.3473 +#> Model cost at call 73 : 167.3473 +#> Model cost at call 78 : 165.9868 +#> Model cost at call 80 : 165.9868 +#> Model cost at call 83 : 165.9868 +#> Model cost at call 85 : 165.2025 +#> Model cost at call 87 : 165.2024 +#> Model cost at call 92 : 163.5932 +#> Model cost at call 94 : 163.5932 +#> Model cost at call 96 : 163.5932 +#> Model cost at call 99 : 159.4289 +#> Model cost at call 100 : 147.5939 +#> Model cost at call 105 : 147.5939 +#> Model cost at call 108 : 139.3925 +#> Model cost at call 113 : 139.3925 +#> Model cost at call 115 : 139.392 +#> Model cost at call 116 : 123.9799 +#> Model cost at call 117 : 123.9798 +#> Model cost at call 118 : 123.9795 +#> Model cost at call 124 : 103.8653 +#> Model cost at call 125 : 103.8653 +#> Model cost at call 126 : 103.8652 +#> Model cost at call 131 : 96.14276 +#> Model cost at call 134 : 96.14275 +#> Model cost at call 135 : 96.14274 +#> Model cost at call 139 : 95.96056 +#> Model cost at call 141 : 95.96056 +#> Model cost at call 142 : 95.96056 +#> Model cost at call 145 : 95.96056 +#> Model cost at call 146 : 95.90851 +#> Model cost at call 148 : 95.9085 +#> Model cost at call 153 : 95.84671 +#> Model cost at call 155 : 95.8467 +#> Model cost at call 161 : 95.82479 +#> Model cost at call 163 : 95.82479 +#> Model cost at call 166 : 95.82479 +#> Model cost at call 168 : 95.81938 +#> Model cost at call 170 : 95.81938 +#> Model cost at call 174 : 95.81938 +#> Model cost at call 175 : 95.81558 +#> Model cost at call 177 : 95.81558 +#> Model cost at call 178 : 95.81558 +#> Model cost at call 180 : 95.81558 +#> Model cost at call 181 : 95.81558 +#> Model cost at call 183 : 95.81558 +#> Model cost at call 184 : 95.8118 +#> Model cost at call 186 : 95.8118 +#> Model cost at call 188 : 95.8118 +#> Model cost at call 191 : 95.80885 +#> Model cost at call 192 : 95.80353 +#> Model cost at call 193 : 95.78121 +#> Model cost at call 194 : 95.72164 +#> Model cost at call 197 : 95.72164 +#> Model cost at call 201 : 95.72163 +#> Model cost at call 206 : 95.71206 +#> Model cost at call 208 : 95.71205 +#> Model cost at call 213 : 95.70874 +#> Model cost at call 215 : 95.70874 +#> Model cost at call 219 : 95.70874 +#> Model cost at call 221 : 95.70751 +#> Model cost at call 222 : 95.70404 +#> Model cost at call 223 : 95.69259 +#> Model cost at call 224 : 95.68092 +#> Model cost at call 226 : 95.68092 +#> Model cost at call 227 : 95.68092 +#> Model cost at call 233 : 95.67595 +#> Model cost at call 235 : 95.67595 +#> Model cost at call 236 : 95.67595 +#> Model cost at call 242 : 95.67219 +#> Model cost at call 244 : 95.67219 +#> Model cost at call 245 : 95.67219 +#> Model cost at call 249 : 95.66939 +#> Model cost at call 251 : 95.66939 +#> Model cost at call 253 : 95.66939 +#> Model cost at call 254 : 95.66939 +#> Model cost at call 256 : 95.66904 +#> Model cost at call 257 : 95.66904 +#> Model cost at call 260 : 95.66904 +#> Model cost at call 265 : 95.66857 +#> Model cost at call 267 : 95.66856 +#> Model cost at call 273 : 95.66822 +#> Model cost at call 275 : 95.66822 +#> Model cost at call 276 : 95.66822 +#> Model cost at call 282 : 95.66809 +#> Model cost at call 283 : 95.66809 +#> Model cost at call 291 : 95.66805 +#> Model cost at call 293 : 95.66805 +#> Model cost at call 295 : 95.66805 +#> Model cost at call 297 : 95.66805 +#> Model cost at call 298 : 95.66805 +#> Model cost at call 302 : 95.66805 +#> Model cost at call 304 : 95.66805 +#> Model cost at call 306 : 95.66805 +#> Model cost at call 309 : 95.66805 +#> Model cost at call 314 : 95.66805 +#> Model cost at call 315 : 95.66805 +#> Model cost at call 328 : 95.66805 +#> Optimisation by method Port successfully terminated. +#> Model cost at call 1 : 36597.78 +#> Model cost at call 3 : 36597.78 +#> Model cost at call 5 : 36597.78 +#> Model cost at call 7 : 36597.78 +#> Model cost at call 9 : 13188.26 +#> Model cost at call 10 : 12648.25 +#> Model cost at call 14 : 12648.13 +#> Model cost at call 16 : 12647.92 +#> Model cost at call 18 : 6148.715 +#> Model cost at call 19 : 6148.712 +#> Model cost at call 20 : 6148.695 +#> Model cost at call 22 : 6148.683 +#> Model cost at call 27 : 1490.597 +#> Model cost at call 33 : 1490.597 +#> Model cost at call 35 : 594.2031 +#> Model cost at call 36 : 594.2023 +#> Model cost at call 38 : 594.201 +#> Model cost at call 40 : 594.2009 +#> Model cost at call 44 : 230.6504 +#> Model cost at call 45 : 230.6503 +#> Model cost at call 48 : 230.6503 +#> Model cost at call 50 : 230.6495 +#> Model cost at call 51 : 230.6494 +#> Model cost at call 53 : 186.2336 +#> Model cost at call 57 : 186.2336 +#> Model cost at call 59 : 186.2336 +#> Model cost at call 60 : 186.2336 +#> Model cost at call 62 : 181.3507 +#> Model cost at call 66 : 181.3507 +#> Model cost at call 70 : 180.733 +#> Model cost at call 74 : 180.733 +#> Model cost at call 76 : 180.7329 +#> Model cost at call 77 : 180.7329 +#> Model cost at call 78 : 175.5254 +#> Model cost at call 80 : 175.5253 +#> Model cost at call 86 : 173.1139 +#> Model cost at call 88 : 173.1139 +#> Model cost at call 94 : 168.0503 +#> Model cost at call 96 : 168.0502 +#> Model cost at call 102 : 164.9084 +#> Model cost at call 104 : 164.9084 +#> Model cost at call 105 : 164.9084 +#> Model cost at call 110 : 159.7912 +#> Model cost at call 112 : 159.7912 +#> Model cost at call 113 : 159.7912 +#> Model cost at call 116 : 159.7911 +#> Model cost at call 117 : 159.7911 +#> Model cost at call 118 : 158.6003 +#> Model cost at call 122 : 158.6002 +#> Model cost at call 124 : 158.6002 +#> Model cost at call 126 : 150.4132 +#> Model cost at call 132 : 150.4132 +#> Model cost at call 133 : 150.4132 +#> Model cost at call 134 : 146.5123 +#> Model cost at call 140 : 146.5122 +#> Model cost at call 142 : 136.6018 +#> Model cost at call 145 : 136.6018 +#> Model cost at call 149 : 136.6018 +#> Model cost at call 150 : 133.91 +#> Model cost at call 153 : 133.91 +#> Model cost at call 155 : 133.91 +#> Model cost at call 156 : 133.91 +#> Model cost at call 158 : 124.7878 +#> Model cost at call 162 : 124.7878 +#> Model cost at call 163 : 124.7878 +#> Model cost at call 167 : 124.2615 +#> Model cost at call 169 : 124.2614 +#> Model cost at call 170 : 124.2614 +#> Model cost at call 175 : 123.2425 +#> Model cost at call 179 : 123.2425 +#> Model cost at call 180 : 123.2425 +#> Model cost at call 181 : 123.2425 +#> Model cost at call 182 : 123.2425 +#> Model cost at call 183 : 120.7214 +#> Model cost at call 185 : 120.7214 +#> Model cost at call 191 : 119.2706 +#> Model cost at call 192 : 117.872 +#> Model cost at call 193 : 114.6257 +#> Model cost at call 198 : 114.6257 +#> Model cost at call 201 : 111.8985 +#> Model cost at call 203 : 111.8985 +#> Model cost at call 206 : 111.8984 +#> Model cost at call 209 : 111.6987 +#> Model cost at call 212 : 111.6987 +#> Model cost at call 213 : 111.6986 +#> Model cost at call 217 : 107.9995 +#> Model cost at call 219 : 107.9995 +#> Model cost at call 225 : 106.1322 +#> Model cost at call 226 : 104.6907 +#> Model cost at call 227 : 104.6316 +#> Model cost at call 229 : 104.6316 +#> Model cost at call 232 : 104.6315 +#> Model cost at call 239 : 103.3421 +#> Model cost at call 245 : 103.3421 +#> Model cost at call 246 : 103.3421 +#> Model cost at call 247 : 103.1772 +#> Model cost at call 248 : 103.1772 +#> Model cost at call 249 : 103.1772 +#> Model cost at call 250 : 103.1772 +#> Model cost at call 253 : 103.1772 +#> Model cost at call 255 : 102.8623 +#> Model cost at call 256 : 102.8623 +#> Model cost at call 262 : 102.8623 +#> Model cost at call 263 : 102.6013 +#> Model cost at call 266 : 102.6013 +#> Model cost at call 271 : 102.0341 +#> Model cost at call 272 : 101.25 +#> Model cost at call 273 : 99.17557 +#> Model cost at call 274 : 99.17556 +#> Model cost at call 282 : 99.06481 +#> Model cost at call 284 : 99.06479 +#> Model cost at call 290 : 98.57515 +#> Model cost at call 294 : 98.57514 +#> Model cost at call 296 : 98.57514 +#> Model cost at call 298 : 98.05781 +#> Model cost at call 304 : 98.05781 +#> Model cost at call 305 : 98.05781 +#> Model cost at call 306 : 97.81766 +#> Model cost at call 307 : 97.63972 +#> Model cost at call 308 : 97.63971 +#> Model cost at call 315 : 97.15447 +#> Model cost at call 317 : 97.15447 +#> Model cost at call 321 : 97.15446 +#> Model cost at call 323 : 96.25231 +#> Model cost at call 324 : 96.25231 +#> Model cost at call 328 : 96.25231 +#> Model cost at call 331 : 95.48051 +#> Model cost at call 334 : 95.4805 +#> Model cost at call 339 : 95.08754 +#> Model cost at call 341 : 95.08754 +#> Model cost at call 347 : 94.9916 +#> Model cost at call 348 : 94.9916 +#> Model cost at call 350 : 94.9916 +#> Model cost at call 355 : 94.93856 +#> Model cost at call 356 : 94.93856 +#> Model cost at call 357 : 94.93856 +#> Model cost at call 363 : 94.92067 +#> Model cost at call 366 : 94.92067 +#> Model cost at call 367 : 94.92067 +#> Model cost at call 369 : 94.92067 +#> Model cost at call 370 : 94.92067 +#> Model cost at call 371 : 94.91762 +#> Model cost at call 372 : 94.91762 +#> Model cost at call 373 : 94.91762 +#> Model cost at call 379 : 94.91744 +#> Model cost at call 380 : 94.91744 +#> Model cost at call 385 : 94.91744 +#> Model cost at call 387 : 94.91744 +#> Model cost at call 393 : 94.91743 +#> Model cost at call 394 : 94.91743 +#> Model cost at call 404 : 94.91743 +#> Model cost at call 407 : 94.91743 +#> Model cost at call 408 : 94.91743 +#> Model cost at call 423 : 94.91743 +#> Model cost at call 442 : 94.91743 +#> Model cost at call 446 : 94.91743 +#> Model cost at call 447 : 94.91743 +#> Optimisation by method Port successfully terminated.</div><div class='input'> +<span class='no'>time_default</span></div><div class='output co'>#> user system elapsed +#> 16.180 0.132 9.130 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed +#> 22.856 0.000 22.858 </div><div class='input'> +<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> <span class='error'>Error in endpoints(fits[["SFO_lin", 2]]): Objekt 'fits' nicht gefunden</span></div><div class='input'> +<span class='co'># Plot.mkinfit handles rows or columns of mmkin result objects</span> +<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-14.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-16.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-18.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> +<span class='co'># by plot.mkinfit</span> +<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='mmkin-20.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> +<span class='co'># allow to plot the observed variables separately</span> +<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-22.png' alt='' width='540' height='400' /><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index e2f845d9..9bb6d4ee 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -116,7 +116,1059 @@ <span class='kw'>A1</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), <span class='kw'>B1</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='kw'>C1</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='kw'>A2</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'>## Not run: mkinfit(model, data, plot=TRUE)</span></div></pre> + <span class='kw'>A2</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>)</div><div class='output co'>#> Model cost at call 1 : 2511.655 +#> Model cost at call 2 : 2511.655 +#> Model cost at call 11 : 1436.639 +#> Model cost at call 12 : 1436.638 +#> Model cost at call 13 : 1436.566 +#> Model cost at call 21 : 643.6583 +#> Model cost at call 22 : 643.6583 +#> Model cost at call 23 : 643.6582 +#> Model cost at call 29 : 643.6576 +#> Model cost at call 31 : 454.0244 +#> Model cost at call 32 : 454.0241 +#> Model cost at call 34 : 454.0229 +#> Model cost at call 43 : 378.1144 +#> Model cost at call 45 : 378.1143 +#> Model cost at call 53 : 357.245 +#> Model cost at call 55 : 357.2449 +#> Model cost at call 56 : 357.2447 +#> Model cost at call 63 : 354.3415 +#> Model cost at call 64 : 354.3415 +#> Model cost at call 65 : 354.3413 +#> Model cost at call 73 : 332.49 +#> Model cost at call 74 : 332.49 +#> Model cost at call 81 : 332.4899 +#> Model cost at call 83 : 315.2962 +#> Model cost at call 84 : 306.3085 +#> Model cost at call 86 : 306.3084 +#> Model cost at call 87 : 306.3084 +#> Model cost at call 92 : 306.3083 +#> Model cost at call 94 : 290.6377 +#> Model cost at call 96 : 290.6375 +#> Model cost at call 98 : 290.6375 +#> Model cost at call 101 : 290.6371 +#> Model cost at call 105 : 269.09 +#> Model cost at call 107 : 269.0899 +#> Model cost at call 115 : 259.7551 +#> Model cost at call 120 : 259.7549 +#> Model cost at call 123 : 259.7547 +#> Model cost at call 126 : 253.7973 +#> Model cost at call 128 : 253.7972 +#> Model cost at call 137 : 251.7358 +#> Model cost at call 139 : 251.7358 +#> Model cost at call 147 : 250.7394 +#> Model cost at call 149 : 250.7393 +#> Model cost at call 157 : 249.1148 +#> Model cost at call 159 : 249.1148 +#> Model cost at call 167 : 246.8768 +#> Model cost at call 169 : 246.8768 +#> Model cost at call 177 : 244.9758 +#> Model cost at call 179 : 244.9758 +#> Model cost at call 187 : 243.2914 +#> Model cost at call 189 : 243.2914 +#> Model cost at call 190 : 243.2914 +#> Model cost at call 194 : 243.2914 +#> Model cost at call 199 : 242.9202 +#> Model cost at call 201 : 242.9202 +#> Model cost at call 202 : 242.9202 +#> Model cost at call 209 : 242.7695 +#> Model cost at call 211 : 242.7695 +#> Model cost at call 216 : 242.7695 +#> Model cost at call 219 : 242.5771 +#> Model cost at call 221 : 242.5771 +#> Model cost at call 229 : 242.4402 +#> Model cost at call 231 : 242.4402 +#> Model cost at call 239 : 242.1878 +#> Model cost at call 241 : 242.1878 +#> Model cost at call 249 : 242.0553 +#> Model cost at call 251 : 242.0553 +#> Model cost at call 256 : 242.0553 +#> Model cost at call 259 : 241.8761 +#> Model cost at call 260 : 241.7412 +#> Model cost at call 261 : 241.6954 +#> Model cost at call 264 : 241.6954 +#> Model cost at call 275 : 241.5982 +#> Model cost at call 277 : 241.5982 +#> Model cost at call 285 : 241.5459 +#> Model cost at call 287 : 241.5459 +#> Model cost at call 295 : 241.4837 +#> Model cost at call 297 : 241.4837 +#> Model cost at call 305 : 241.3882 +#> Model cost at call 306 : 241.3161 +#> Model cost at call 307 : 241.2315 +#> Model cost at call 309 : 241.2315 +#> Model cost at call 314 : 241.2315 +#> Model cost at call 317 : 240.9738 +#> Model cost at call 322 : 240.9738 +#> Model cost at call 327 : 240.8244 +#> Model cost at call 329 : 240.8244 +#> Model cost at call 337 : 240.7005 +#> Model cost at call 339 : 240.7005 +#> Model cost at call 342 : 240.7005 +#> Model cost at call 347 : 240.629 +#> Model cost at call 350 : 240.629 +#> Model cost at call 357 : 240.6193 +#> Model cost at call 358 : 240.6193 +#> Model cost at call 364 : 240.6193 +#> Model cost at call 367 : 240.6193 +#> Model cost at call 369 : 240.5873 +#> Model cost at call 374 : 240.5873 +#> Model cost at call 380 : 240.578 +#> Model cost at call 382 : 240.578 +#> Model cost at call 390 : 240.5723 +#> Model cost at call 393 : 240.5723 +#> Model cost at call 403 : 240.569 +#> Model cost at call 404 : 240.569 +#> Model cost at call 413 : 240.569 +#> Model cost at call 415 : 240.5688 +#> Model cost at call 416 : 240.5688 +#> Model cost at call 417 : 240.5688 +#> Model cost at call 431 : 240.5686 +#> Model cost at call 432 : 240.5686 +#> Model cost at call 434 : 240.5686 +#> Model cost at call 443 : 240.5686 +#> Model cost at call 444 : 240.5686 +#> Model cost at call 447 : 240.5686 +#> Model cost at call 449 : 240.5686 +#> Model cost at call 450 : 240.5686 +#> Model cost at call 466 : 240.5686 +#> Model cost at call 470 : 240.5686 +#> Model cost at call 485 : 240.5686 +#> Model cost at call 509 : 240.5686 +#> Optimisation by method Port successfully terminated.</div><div class='output co'>#> $par +#> parent_0 log_k_parent log_k_A1 log_k_B1 log_k_C1 +#> 91.9181598 -3.0020485 -4.2735924 -3.9846764 -2.7852180 +#> log_k_A2 f_parent_ilr_1 f_parent_ilr_2 f_A1_ilr_1 +#> -3.7166415 0.4718588 -0.3589948 -0.1477244 +#> +#> $ssr +#> [1] 240.5686 +#> +#> $convergence +#> [1] 0 +#> +#> $iterations +#> [1] 43 +#> +#> $evaluations +#> function gradient +#> 62 441 +#> +#> $counts +#> [1] "relative convergence (4)" +#> +#> $hessian +#> parent_0 log_k_parent log_k_A1 log_k_B1 +#> parent_0 7.3650812 -92.141920 -1.001134e+01 -2.432415e+00 +#> log_k_parent -92.1419204 6632.673492 -4.316240e+01 -1.320833e+01 +#> log_k_A1 -10.0113364 -43.162398 6.071628e+02 0.000000e+00 +#> log_k_B1 -2.4324147 -13.208329 0.000000e+00 1.572303e+02 +#> log_k_C1 -4.7153201 -118.288037 -5.878291e-05 -3.073041e-06 +#> log_k_A2 -0.4360727 -5.304259 -1.977980e+01 0.000000e+00 +#> f_parent_ilr_1 10.5460899 271.145438 -5.299954e+02 1.874235e+02 +#> f_parent_ilr_2 11.6409409 222.570696 -4.773816e+02 -1.159875e+02 +#> f_A1_ilr_1 0.5572072 10.374810 2.850173e+01 0.000000e+00 +#> log_k_C1 log_k_A2 f_parent_ilr_1 f_parent_ilr_2 +#> parent_0 -4.715320e+00 -4.360727e-01 10.54609 11.64094 +#> log_k_parent -1.182880e+02 -5.304259e+00 271.14544 222.57070 +#> log_k_A1 -5.878291e-05 -1.977980e+01 -529.99537 -477.38164 +#> log_k_B1 -3.073041e-06 0.000000e+00 187.42348 -115.98754 +#> log_k_C1 3.372749e+02 -2.395674e-06 56.85184 305.98862 +#> log_k_A2 -2.395674e-06 2.749192e+01 -23.08549 -20.79373 +#> f_parent_ilr_1 5.685184e+01 -2.308549e+01 1256.24941 632.09769 +#> f_parent_ilr_2 3.059886e+02 -2.079373e+01 632.09769 1250.65147 +#> f_A1_ilr_1 3.158891e-06 -3.129286e+01 29.49830 26.56991 +#> f_A1_ilr_1 +#> parent_0 5.572072e-01 +#> log_k_parent 1.037481e+01 +#> log_k_A1 2.850173e+01 +#> log_k_B1 0.000000e+00 +#> log_k_C1 3.158891e-06 +#> log_k_A2 -3.129286e+01 +#> f_parent_ilr_1 2.949830e+01 +#> f_parent_ilr_2 2.656991e+01 +#> f_A1_ilr_1 3.998554e+01 +#> +#> $residuals +#> parent parent parent parent parent parent parent +#> -1.2818402 -1.9372115 -0.5105519 3.8165318 -2.3531716 4.8043342 -2.2775432 +#> parent A1 A1 A1 A1 A1 A1 +#> -5.3608524 4.1967522 2.9032987 -1.3124875 -0.6021093 2.5092324 -1.8861396 +#> B1 B1 B1 B1 B1 C1 C1 +#> 4.3801768 5.5002481 -5.7917184 1.3852658 0.5313301 1.2796458 1.7105311 +#> C1 C1 C1 C1 C1 A2 A2 +#> 3.7116712 -0.1182953 0.5228429 -0.8570298 -3.5476556 -0.5447276 -1.3652404 +#> A2 A2 A2 A2 A2 +#> -0.3330261 -0.5802059 0.1285850 0.2119280 -0.1381990 +#> +#> $ms +#> [1] 7.289956 +#> +#> $var_ms +#> parent A1 B1 C1 A2 +#> 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002 +#> +#> $var_ms_unscaled +#> parent A1 B1 C1 A2 +#> 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002 +#> +#> $var_ms_unweighted +#> parent A1 B1 C1 A2 +#> 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002 +#> +#> $rank +#> [1] 9 +#> +#> $df.residual +#> [1] 24 +#> +#> $solution_type +#> [1] "deSolve" +#> +#> $transform_rates +#> [1] TRUE +#> +#> $transform_fractions +#> [1] TRUE +#> +#> $method.modFit +#> [1] "Port" +#> +#> $maxit.modFit +#> [1] "auto" +#> +#> $calls +#> [1] 523 +#> +#> $time +#> user system elapsed +#> 5.004 0.000 5.004 +#> +#> $mkinmod +#> <mkinmod> model generated with +#> Use of formation fractions $use_of_ff: max +#> Specification $spec: +#> $parent +#> $type: SFO; $to: A1, B1, C1; $sink: FALSE +#> $A1 +#> $type: SFO; $to: A2; $sink: TRUE +#> $B1 +#> $type: SFO; $sink: TRUE +#> $C1 +#> $type: SFO; $sink: TRUE +#> $A2 +#> $type: SFO; $sink: TRUE +#> Coefficient matrix $coefmat available +#> Compiled model $cf available +#> +#> $observed +#> name time value +#> 1 parent 0 93.20 +#> 2 parent 1 89.40 +#> 3 parent 3 79.70 +#> 4 parent 7 61.10 +#> 5 parent 14 48.20 +#> 6 parent 30 15.90 +#> 7 parent 62 6.50 +#> 8 parent 100 6.00 +#> 9 A1 0 NA +#> 10 A1 1 NA +#> 11 A1 3 0.55 +#> 12 A1 7 6.87 +#> 13 A1 14 17.08 +#> 14 A1 30 21.68 +#> 15 A1 62 15.77 +#> 16 A1 100 13.63 +#> 17 B1 0 NA +#> 18 B1 1 NA +#> 19 B1 3 NA +#> 20 B1 7 0.55 +#> 21 B1 14 2.31 +#> 22 B1 30 15.76 +#> 23 B1 62 6.36 +#> 24 B1 100 3.74 +#> 25 C1 0 NA +#> 26 C1 1 0.55 +#> 27 C1 3 3.20 +#> 28 C1 7 5.46 +#> 29 C1 14 12.55 +#> 30 C1 30 10.45 +#> 31 C1 62 4.74 +#> 32 C1 100 4.33 +#> 33 A2 0 NA +#> 34 A2 1 0.55 +#> 35 A2 3 1.41 +#> 36 A2 7 0.55 +#> 37 A2 14 1.29 +#> 38 A2 30 1.95 +#> 39 A2 62 3.54 +#> 40 A2 100 3.86 +#> +#> $obs_vars +#> [1] "parent" "A1" "B1" "C1" "A2" +#> +#> $predicted +#> name time value +#> 1 parent 0.000000 91.918159794 +#> 2 parent 1.000000 87.462788491 +#> 3 parent 1.010101 87.418904506 +#> 4 parent 2.020202 83.139880984 +#> 5 parent 3.000000 79.189448055 +#> 6 parent 3.030303 79.070309209 +#> 7 parent 4.040404 75.199936833 +#> 8 parent 5.050505 71.519013349 +#> 9 parent 6.060606 68.018265517 +#> 10 parent 7.000000 64.916531757 +#> 11 parent 7.070707 64.688874011 +#> 12 parent 8.080808 61.522451197 +#> 13 parent 9.090909 58.511020005 +#> 14 parent 10.101010 55.646993828 +#> 15 parent 11.111111 52.923157412 +#> 16 parent 12.121212 50.332648680 +#> 17 parent 13.131313 47.868941444 +#> 18 parent 14.000000 45.846828365 +#> 19 parent 14.141414 45.525828960 +#> 20 parent 15.151515 43.297408299 +#> 21 parent 16.161616 41.178065468 +#> 22 parent 17.171717 39.162461272 +#> 23 parent 18.181818 37.245517861 +#> 24 parent 19.191919 35.422405939 +#> 25 parent 20.202020 33.688532595 +#> 26 parent 21.212121 32.039529737 +#> 27 parent 22.222222 30.471243081 +#> 28 parent 23.232323 28.979721692 +#> 29 parent 24.242424 27.561208025 +#> 30 parent 25.252525 26.212128463 +#> 31 parent 26.262626 24.929084310 +#> 32 parent 27.272727 23.708843233 +#> 33 parent 28.282828 22.548331117 +#> 34 parent 29.292929 21.444624318 +#> 35 parent 30.000000 20.704334210 +#> 36 parent 30.303030 20.394942302 +#> 37 parent 31.313131 19.396640638 +#> 38 parent 32.323232 18.447204335 +#> 39 parent 33.333333 17.544241506 +#> 40 parent 34.343434 16.685477346 +#> 41 parent 35.353535 15.868748397 +#> 42 parent 36.363636 15.091997098 +#> 43 parent 37.373737 14.353266603 +#> 44 parent 38.383838 13.650695852 +#> 45 parent 39.393939 12.982514879 +#> 46 parent 40.404040 12.347040357 +#> 47 parent 41.414141 11.742671354 +#> 48 parent 42.424242 11.167885303 +#> 49 parent 43.434343 10.621234162 +#> 50 parent 44.444444 10.101340770 +#> 51 parent 45.454545 9.606895375 +#> 52 parent 46.464646 9.136652336 +#> 53 parent 47.474747 8.689426985 +#> 54 parent 48.484848 8.264092640 +#> 55 parent 49.494949 7.859577770 +#> 56 parent 50.505051 7.474863293 +#> 57 parent 51.515152 7.108980009 +#> 58 parent 52.525253 6.761006160 +#> 59 parent 53.535354 6.430065106 +#> 60 parent 54.545455 6.115323117 +#> 61 parent 55.555556 5.815987274 +#> 62 parent 56.565657 5.531303470 +#> 63 parent 57.575758 5.260554508 +#> 64 parent 58.585859 5.003058299 +#> 65 parent 59.595960 4.758166141 +#> 66 parent 60.606061 4.525261085 +#> 67 parent 61.616162 4.303756381 +#> 68 parent 62.000000 4.222456793 +#> 69 parent 62.626263 4.093093997 +#> 70 parent 63.636364 3.892743220 +#> 71 parent 64.646465 3.702199310 +#> 72 parent 65.656566 3.520982238 +#> 73 parent 66.666667 3.348635468 +#> 74 parent 67.676768 3.184724813 +#> 75 parent 68.686869 3.028837337 +#> 76 parent 69.696970 2.880580317 +#> 77 parent 70.707071 2.739580256 +#> 78 parent 71.717172 2.605481934 +#> 79 parent 72.727273 2.477947523 +#> 80 parent 73.737374 2.356655730 +#> 81 parent 74.747475 2.241300986 +#> 82 parent 75.757576 2.131592683 +#> 83 parent 76.767677 2.027254437 +#> 84 parent 77.777778 1.928023390 +#> 85 parent 78.787879 1.833649553 +#> 86 parent 79.797980 1.743895173 +#> 87 parent 80.808081 1.658534134 +#> 88 parent 81.818182 1.577351390 +#> 89 parent 82.828283 1.500142419 +#> 90 parent 83.838384 1.426712710 +#> 91 parent 84.848485 1.356877275 +#> 92 parent 85.858586 1.290460179 +#> 93 parent 86.868687 1.227294099 +#> 94 parent 87.878788 1.167219904 +#> 95 parent 88.888889 1.110086250 +#> 96 parent 89.898990 1.055749203 +#> 97 parent 90.909091 1.004071872 +#> 98 parent 91.919192 0.954924068 +#> 99 parent 92.929293 0.908181975 +#> 100 parent 93.939394 0.863727837 +#> 101 parent 94.949495 0.821449662 +#> 102 parent 95.959596 0.781240940 +#> 103 parent 96.969697 0.743000375 +#> 104 parent 97.979798 0.706631627 +#> 105 parent 98.989899 0.672043075 +#> 106 parent 100.000000 0.639147580 +#> 107 A1 0.000000 0.000000000 +#> 108 A1 1.000000 1.685461006 +#> 109 A1 1.010101 1.701940789 +#> 110 A1 2.020202 3.296791533 +#> 111 A1 3.000000 4.746752202 +#> 112 A1 3.030303 4.790126465 +#> 113 A1 4.040404 6.187242320 +#> 114 A1 5.050505 7.493171988 +#> 115 A1 6.060606 8.712697491 +#> 116 A1 7.000000 9.773298725 +#> 117 A1 7.070707 9.850362326 +#> 118 A1 8.080808 10.910483202 +#> 119 A1 9.090909 11.897161206 +#> 120 A1 10.101010 12.814292412 +#> 121 A1 11.111111 13.665577981 +#> 122 A1 12.121212 14.454533757 +#> 123 A1 13.131313 15.184499397 +#> 124 A1 14.000000 15.767512526 +#> 125 A1 14.141414 15.858647054 +#> 126 A1 15.151515 16.479989628 +#> 127 A1 16.161616 17.051388624 +#> 128 A1 17.171717 17.575561608 +#> 129 A1 18.181818 18.055089316 +#> 130 A1 19.191919 18.492422399 +#> 131 A1 20.202020 18.889887843 +#> 132 A1 21.212121 19.249695079 +#> 133 A1 22.222222 19.573941783 +#> 134 A1 23.232323 19.864619397 +#> 135 A1 24.242424 20.123618383 +#> 136 A1 25.252525 20.352733211 +#> 137 A1 26.262626 20.553667106 +#> 138 A1 27.272727 20.728036563 +#> 139 A1 28.282828 20.877375640 +#> 140 A1 29.292929 21.003140039 +#> 141 A1 30.000000 21.077890710 +#> 142 A1 30.303030 21.106710984 +#> 143 A1 31.313131 21.189398917 +#> 144 A1 32.323232 21.252447002 +#> 145 A1 33.333333 21.297034466 +#> 146 A1 34.343434 21.324279770 +#> 147 A1 35.353535 21.335243623 +#> 148 A1 36.363636 21.330931858 +#> 149 A1 37.373737 21.312298151 +#> 150 A1 38.383838 21.280246621 +#> 151 A1 39.393939 21.235634295 +#> 152 A1 40.404040 21.179273450 +#> 153 A1 41.414141 21.111933845 +#> 154 A1 42.424242 21.034344838 +#> 155 A1 43.434343 20.947197407 +#> 156 A1 44.444444 20.851146060 +#> 157 A1 45.454545 20.746810660 +#> 158 A1 46.464646 20.634778158 +#> 159 A1 47.474747 20.515604239 +#> 160 A1 48.484848 20.389814887 +#> 161 A1 49.494949 20.257907875 +#> 162 A1 50.505051 20.120354180 +#> 163 A1 51.515152 19.977599327 +#> 164 A1 52.525253 19.830064674 +#> 165 A1 53.535354 19.678148618 +#> 166 A1 54.545455 19.522227762 +#> 167 A1 55.555556 19.362658007 +#> 168 A1 56.565657 19.199775600 +#> 169 A1 57.575758 19.033898126 +#> 170 A1 58.585859 18.865325451 +#> 171 A1 59.595960 18.694340625 +#> 172 A1 60.606061 18.521210729 +#> 173 A1 61.616162 18.346187688 +#> 174 A1 62.000000 18.279232408 +#> 175 A1 62.626263 18.169509043 +#> 176 A1 63.636364 17.991398686 +#> 177 A1 64.646465 17.812067549 +#> 178 A1 65.656566 17.631714275 +#> 179 A1 66.666667 17.450525840 +#> 180 A1 67.676768 17.268678156 +#> 181 A1 68.686869 17.086336636 +#> 182 A1 69.696970 16.903656738 +#> 183 A1 70.707071 16.720784474 +#> 184 A1 71.717172 16.537856901 +#> 185 A1 72.727273 16.355002582 +#> 186 A1 73.737374 16.172342031 +#> 187 A1 74.747475 15.989988127 +#> 188 A1 75.757576 15.808046514 +#> 189 A1 76.767677 15.626615980 +#> 190 A1 77.777778 15.445788814 +#> 191 A1 78.787879 15.265651148 +#> 192 A1 79.797980 15.086283284 +#> 193 A1 80.808081 14.907759996 +#> 194 A1 81.818182 14.730150830 +#> 195 A1 82.828283 14.553520376 +#> 196 A1 83.838384 14.377928535 +#> 197 A1 84.848485 14.203430771 +#> 198 A1 85.858586 14.030078345 +#> 199 A1 86.868687 13.857918547 +#> 200 A1 87.878788 13.686994907 +#> 201 A1 88.888889 13.517347398 +#> 202 A1 89.898990 13.349012635 +#> 203 A1 90.909091 13.182024056 +#> 204 A1 91.919192 13.016412097 +#> 205 A1 92.929293 12.852204356 +#> 206 A1 93.939394 12.689425755 +#> 207 A1 94.949495 12.528098688 +#> 208 A1 95.959596 12.368243159 +#> 209 A1 96.969697 12.209876925 +#> 210 A1 97.979798 12.053015616 +#> 211 A1 98.989899 11.897672861 +#> 212 A1 100.000000 11.743860400 +#> 213 B1 0.000000 0.000000000 +#> 214 B1 1.000000 0.862762059 +#> 215 B1 1.010101 0.871177048 +#> 216 B1 2.020202 1.683497848 +#> 217 B1 3.000000 2.418226457 +#> 218 B1 3.030303 2.440145075 +#> 219 B1 4.040404 3.144139999 +#> 220 B1 5.050505 3.798350490 +#> 221 B1 6.060606 4.405498633 +#> 222 B1 7.000000 4.930176837 +#> 223 B1 7.070707 4.968167964 +#> 224 B1 8.080808 5.488810347 +#> 225 B1 9.090909 5.969752521 +#> 226 B1 10.101010 6.413202316 +#> 227 B1 11.111111 6.821254568 +#> 228 B1 12.121212 7.195896744 +#> 229 B1 13.131313 7.539014282 +#> 230 B1 14.000000 7.810248132 +#> 231 B1 14.141414 7.852395679 +#> 232 B1 15.151515 8.137737320 +#> 233 B1 16.161616 8.396648072 +#> 234 B1 17.171717 8.630653651 +#> 235 B1 18.181818 8.841200774 +#> 236 B1 19.191919 9.029661109 +#> 237 B1 20.202020 9.197335022 +#> 238 B1 21.212121 9.345455150 +#> 239 B1 22.222222 9.475189788 +#> 240 B1 23.232323 9.587646116 +#> 241 B1 24.242424 9.683873262 +#> 242 B1 25.252525 9.764865214 +#> 243 B1 26.262626 9.831563593 +#> 244 B1 27.272727 9.884860284 +#> 245 B1 28.282828 9.925599936 +#> 246 B1 29.292929 9.954582344 +#> 247 B1 30.000000 9.968281596 +#> 248 B1 30.303030 9.972564708 +#> 249 B1 31.313131 9.980263783 +#> 250 B1 32.323232 9.978357919 +#> 251 B1 33.333333 9.967489009 +#> 252 B1 34.343434 9.948264327 +#> 253 B1 35.353535 9.921258285 +#> 254 B1 36.363636 9.887014102 +#> 255 B1 37.373737 9.846045383 +#> 256 B1 38.383838 9.798837632 +#> 257 B1 39.393939 9.745849674 +#> 258 B1 40.404040 9.687515023 +#> 259 B1 41.414141 9.624243169 +#> 260 B1 42.424242 9.556420809 +#> 261 B1 43.434343 9.484413012 +#> 262 B1 44.444444 9.408564328 +#> 263 B1 45.454545 9.329199843 +#> 264 B1 46.464646 9.246626179 +#> 265 B1 47.474747 9.161132446 +#> 266 B1 48.484848 9.072991146 +#> 267 B1 49.494949 8.982459028 +#> 268 B1 50.505051 8.889777910 +#> 269 B1 51.515152 8.795175451 +#> 270 B1 52.525253 8.698865886 +#> 271 B1 53.535354 8.601050726 +#> 272 B1 54.545455 8.501919425 +#> 273 B1 55.555556 8.401650008 +#> 274 B1 56.565657 8.300409672 +#> 275 B1 57.575758 8.198355355 +#> 276 B1 58.585859 8.095634277 +#> 277 B1 59.595960 7.992384454 +#> 278 B1 60.606061 7.888735183 +#> 279 B1 61.616162 7.784807509 +#> 280 B1 62.000000 7.745265792 +#> 281 B1 62.626263 7.680714664 +#> 282 B1 63.636364 7.576562482 +#> 283 B1 64.646465 7.472449799 +#> 284 B1 65.656566 7.368468826 +#> 285 B1 66.666667 7.264705509 +#> 286 B1 67.676768 7.161239868 +#> 287 B1 68.686869 7.058146319 +#> 288 B1 69.696970 6.955493978 +#> 289 B1 70.707071 6.853346953 +#> 290 B1 71.717172 6.751764620 +#> 291 B1 72.727273 6.650801882 +#> 292 B1 73.737374 6.550509419 +#> 293 B1 74.747475 6.450933922 +#> 294 B1 75.757576 6.352118318 +#> 295 B1 76.767677 6.254101979 +#> 296 B1 77.777778 6.156920928 +#> 297 B1 78.787879 6.060608023 +#> 298 B1 79.797980 5.965193142 +#> 299 B1 80.808081 5.870703355 +#> 300 B1 81.818182 5.777163083 +#> 301 B1 82.828283 5.684594257 +#> 302 B1 83.838384 5.593016458 +#> 303 B1 84.848485 5.502447062 +#> 304 B1 85.858586 5.412901366 +#> 305 B1 86.868687 5.324392718 +#> 306 B1 87.878788 5.236932630 +#> 307 B1 88.888889 5.150530889 +#> 308 B1 89.898990 5.065195670 +#> 309 B1 90.909091 4.980933628 +#> 310 B1 91.919192 4.897749999 +#> 311 B1 92.929293 4.815648688 +#> 312 B1 93.939394 4.734632351 +#> 313 B1 94.949495 4.654702481 +#> 314 B1 95.959596 4.575859481 +#> 315 B1 96.969697 4.498102737 +#> 316 B1 97.979798 4.421430686 +#> 317 B1 98.989899 4.345840882 +#> 318 B1 100.000000 4.271330056 +#> 319 C1 0.000000 0.000000000 +#> 320 C1 1.000000 1.829645786 +#> 321 C1 1.010101 1.847087763 +#> 322 C1 2.020202 3.492133303 +#> 323 C1 3.000000 4.910531064 +#> 324 C1 3.030303 4.951772742 +#> 325 C1 4.040404 6.241420142 +#> 326 C1 5.050505 7.375351980 +#> 327 C1 6.060606 8.366785999 +#> 328 C1 7.000000 9.171671206 +#> 329 C1 7.070707 9.227954769 +#> 330 C1 8.080808 9.970174354 +#> 331 C1 9.090909 10.603908370 +#> 332 C1 10.101010 11.138827767 +#> 333 C1 11.111111 11.583866567 +#> 334 C1 12.121212 11.947273869 +#> 335 C1 13.131313 12.236662337 +#> 336 C1 14.000000 12.431704739 +#> 337 C1 14.141414 12.459053419 +#> 338 C1 15.151515 12.620919488 +#> 339 C1 16.161616 12.728223141 +#> 340 C1 17.171717 12.786453805 +#> 341 C1 18.181818 12.800661859 +#> 342 C1 19.191919 12.775490422 +#> 343 C1 20.202020 12.715204956 +#> 344 C1 21.212121 12.623720845 +#> 345 C1 22.222222 12.504629065 +#> 346 C1 23.232323 12.361220091 +#> 347 C1 24.242424 12.196506142 +#> 348 C1 25.252525 12.013241882 +#> 349 C1 26.262626 11.813943686 +#> 350 C1 27.272727 11.600907551 +#> 351 C1 28.282828 11.376225763 +#> 352 C1 29.292929 11.141802382 +#> 353 C1 30.000000 10.972842888 +#> 354 C1 30.303030 10.899367648 +#> 355 C1 31.313131 10.650491354 +#> 356 C1 32.323232 10.396595286 +#> 357 C1 33.333333 10.138964763 +#> 358 C1 34.343434 9.878759358 +#> 359 C1 35.353535 9.617022857 +#> 360 C1 36.363636 9.354692485 +#> 361 C1 37.373737 9.092607481 +#> 362 C1 38.383838 8.831517041 +#> 363 C1 39.393939 8.572087685 +#> 364 C1 40.404040 8.314910084 +#> 365 C1 41.414141 8.060505385 +#> 366 C1 42.424242 7.809331068 +#> 367 C1 43.434343 7.561786371 +#> 368 C1 44.444444 7.318217302 +#> 369 C1 45.454545 7.078921287 +#> 370 C1 46.464646 6.844151456 +#> 371 C1 47.474747 6.614120611 +#> 372 C1 48.484848 6.389004885 +#> 373 C1 49.494949 6.168947129 +#> 374 C1 50.505051 5.954060026 +#> 375 C1 51.515152 5.744428970 +#> 376 C1 52.525253 5.540114721 +#> 377 C1 53.535354 5.341155842 +#> 378 C1 54.545455 5.147570951 +#> 379 C1 55.555556 4.959360784 +#> 380 C1 56.565657 4.776510102 +#> 381 C1 57.575758 4.598989433 +#> 382 C1 58.585859 4.426756673 +#> 383 C1 59.595960 4.259758556 +#> 384 C1 60.606061 4.097932000 +#> 385 C1 61.616162 3.941205338 +#> 386 C1 62.000000 3.882970158 +#> 387 C1 62.626263 3.789499444 +#> 388 C1 63.636364 3.642728760 +#> 389 C1 64.646465 3.500802233 +#> 390 C1 65.656566 3.363624171 +#> 391 C1 66.666667 3.231095021 +#> 392 C1 67.676768 3.103112069 +#> 393 C1 68.686869 2.979570086 +#> 394 C1 69.696970 2.860361903 +#> 395 C1 70.707071 2.745378939 +#> 396 C1 71.717172 2.634511667 +#> 397 C1 72.727273 2.527650041 +#> 398 C1 73.737374 2.424683880 +#> 399 C1 74.747475 2.325503203 +#> 400 C1 75.757576 2.229998536 +#> 401 C1 76.767677 2.138061182 +#> 402 C1 77.777778 2.049583458 +#> 403 C1 78.787879 1.964458908 +#> 404 C1 79.797980 1.882582485 +#> 405 C1 80.808081 1.803850715 +#> 406 C1 81.818182 1.728161832 +#> 407 C1 82.828283 1.655415900 +#> 408 C1 83.838384 1.585514911 +#> 409 C1 84.848485 1.518362874 +#> 410 C1 85.858586 1.453865880 +#> 411 C1 86.868687 1.391932162 +#> 412 C1 87.878788 1.332472134 +#> 413 C1 88.888889 1.275398429 +#> 414 C1 89.898990 1.220625918 +#> 415 C1 90.909091 1.168071723 +#> 416 C1 91.919192 1.117655227 +#> 417 C1 92.929293 1.069298066 +#> 418 C1 93.939394 1.022924125 +#> 419 C1 94.949495 0.978459525 +#> 420 C1 95.959596 0.935832597 +#> 421 C1 96.969697 0.894973866 +#> 422 C1 97.979798 0.855816021 +#> 423 C1 98.989899 0.818293881 +#> 424 C1 100.000000 0.782344364 +#> 425 A2 0.000000 0.000000000 +#> 426 A2 1.000000 0.005272357 +#> 427 A2 1.010101 0.005377817 +#> 428 A2 2.020202 0.020885524 +#> 429 A2 3.000000 0.044759575 +#> 430 A2 3.030303 0.045628064 +#> 431 A2 4.040404 0.078765936 +#> 432 A2 5.050505 0.119512155 +#> 433 A2 6.060606 0.167129381 +#> 434 A2 7.000000 0.216973934 +#> 435 A2 7.070707 0.220927189 +#> 436 A2 8.080808 0.280259484 +#> 437 A2 9.090909 0.344522046 +#> 438 A2 10.101010 0.413150206 +#> 439 A2 11.111111 0.485616641 +#> 440 A2 12.121212 0.561429288 +#> 441 A2 13.131313 0.640129357 +#> 442 A2 14.000000 0.709794102 +#> 443 A2 14.141414 0.721289460 +#> 444 A2 15.151515 0.804511827 +#> 445 A2 16.161616 0.889426625 +#> 446 A2 17.171717 0.975690359 +#> 447 A2 18.181818 1.062984358 +#> 448 A2 19.191919 1.151013342 +#> 449 A2 20.202020 1.239504068 +#> 450 A2 21.212121 1.328204041 +#> 451 A2 22.222222 1.416880297 +#> 452 A2 23.232323 1.505318253 +#> 453 A2 24.242424 1.593320615 +#> 454 A2 25.252525 1.680706344 +#> 455 A2 26.262626 1.767309680 +#> 456 A2 27.272727 1.852979219 +#> 457 A2 28.282828 1.937577034 +#> 458 A2 29.292929 2.020977853 +#> 459 A2 30.000000 2.078585030 +#> 460 A2 30.303030 2.103068270 +#> 461 A2 31.313131 2.183746011 +#> 462 A2 32.323232 2.262919231 +#> 463 A2 33.333333 2.340505852 +#> 464 A2 34.343434 2.416432940 +#> 465 A2 35.353535 2.490636111 +#> 466 A2 36.363636 2.563058979 +#> 467 A2 37.373737 2.633652622 +#> 468 A2 38.383838 2.702375089 +#> 469 A2 39.393939 2.769190926 +#> 470 A2 40.404040 2.834070737 +#> 471 A2 41.414141 2.896990764 +#> 472 A2 42.424242 2.957932489 +#> 473 A2 43.434343 3.016882265 +#> 474 A2 44.444444 3.073830964 +#> 475 A2 45.454545 3.128773647 +#> 476 A2 46.464646 3.181709250 +#> 477 A2 47.474747 3.232640290 +#> 478 A2 48.484848 3.281572591 +#> 479 A2 49.494949 3.328515022 +#> 480 A2 50.505051 3.373479253 +#> 481 A2 51.515152 3.416479521 +#> 482 A2 52.525253 3.457532417 +#> 483 A2 53.535354 3.496656681 +#> 484 A2 54.545455 3.533873012 +#> 485 A2 55.555556 3.569203883 +#> 486 A2 56.565657 3.602673379 +#> 487 A2 57.575758 3.634307034 +#> 488 A2 58.585859 3.664131686 +#> 489 A2 59.595960 3.692175334 +#> 490 A2 60.606061 3.718467012 +#> 491 A2 61.616162 3.743036663 +#> 492 A2 62.000000 3.751927986 +#> 493 A2 62.626263 3.765915028 +#> 494 A2 63.636364 3.787133539 +#> 495 A2 64.646465 3.806724217 +#> 496 A2 65.656566 3.824719582 +#> 497 A2 66.666667 3.841152565 +#> 498 A2 67.676768 3.856056426 +#> 499 A2 68.686869 3.869464684 +#> 500 A2 69.696970 3.881411040 +#> 501 A2 70.707071 3.891929316 +#> 502 A2 71.717172 3.901053396 +#> 503 A2 72.727273 3.908817168 +#> 504 A2 73.737374 3.915254472 +#> 505 A2 74.747475 3.920399054 +#> 506 A2 75.757576 3.924284521 +#> 507 A2 76.767677 3.926944303 +#> 508 A2 77.777778 3.928411610 +#> 509 A2 78.787879 3.928719404 +#> 510 A2 79.797980 3.927900364 +#> 511 A2 80.808081 3.925986861 +#> 512 A2 81.818182 3.923010926 +#> 513 A2 82.828283 3.919004234 +#> 514 A2 83.838384 3.913998077 +#> 515 A2 84.848485 3.908023347 +#> 516 A2 85.858586 3.901110518 +#> 517 A2 86.868687 3.893289633 +#> 518 A2 87.878788 3.884590288 +#> 519 A2 88.888889 3.875041619 +#> 520 A2 89.898990 3.864672297 +#> 521 A2 90.909091 3.853510511 +#> 522 A2 91.919192 3.841583970 +#> 523 A2 92.929293 3.828919886 +#> 524 A2 93.939394 3.815544978 +#> 525 A2 94.949495 3.801485462 +#> 526 A2 95.959596 3.786767051 +#> 527 A2 96.969697 3.771414951 +#> 528 A2 97.979798 3.755453860 +#> 529 A2 98.989899 3.738907968 +#> 530 A2 100.000000 3.721800959 +#> +#> $cost +#> function (P) +#> { +#> assign("calls", calls + 1, inherits = TRUE) +#> if (trace_parms) +#> cat(P, "\n") +#> if (length(state.ini.optim) > 0) { +#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) +#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) +#> } +#> else { +#> odeini <- state.ini.fixed +#> names(odeini) <- state.ini.fixed.boxnames +#> } +#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], +#> transparms.fixed) +#> parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, +#> transform_fractions = transform_fractions) +#> out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, +#> use_compiled = use_compiled, method.ode = method.ode, +#> atol = atol, rtol = rtol, ...) +#> assign("out_predicted", out, inherits = TRUE) +#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, +#> scaleVar = scaleVar) +#> if (mC$model < cost.old) { +#> if (!quiet) +#> cat("Model cost at call ", calls, ": ", mC$model, +#> "\n") +#> if (plot) { +#> outtimes_plot = seq(min(observed$time), max(observed$time), +#> length.out = 100) +#> out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, +#> solution_type = solution_type, use_compiled = use_compiled, +#> method.ode = method.ode, atol = atol, rtol = rtol, +#> ...) +#> plot(0, type = "n", xlim = range(observed$time), +#> ylim = c(0, max(observed$value, na.rm = TRUE)), +#> xlab = "Time", ylab = "Observed") +#> col_obs <- pch_obs <- 1:length(obs_vars) +#> lty_obs <- rep(1, length(obs_vars)) +#> names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars +#> for (obs_var in obs_vars) { +#> points(subset(observed, name == obs_var, c(time, +#> value)), pch = pch_obs[obs_var], col = col_obs[obs_var]) +#> } +#> matlines(out_plot$time, out_plot[-1], col = col_obs, +#> lty = lty_obs) +#> legend("topright", inset = c(0.05, 0.05), legend = obs_vars, +#> col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) +#> } +#> assign("cost.old", mC$model, inherits = TRUE) +#> } +#> return(mC) +#> } +#> <environment: 0x36a83b0> +#> +#> $cost_notrans +#> function (P) +#> { +#> if (length(state.ini.optim) > 0) { +#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) +#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) +#> } +#> else { +#> odeini <- state.ini.fixed +#> names(odeini) <- state.ini.fixed.boxnames +#> } +#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], +#> parms.fixed) +#> out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, +#> use_compiled = use_compiled, method.ode = method.ode, +#> atol = atol, rtol = rtol, ...) +#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, +#> scaleVar = scaleVar) +#> return(mC) +#> } +#> <environment: 0x36a83b0> +#> +#> $hessian_notrans +#> parent_0 k_parent k_A1 k_B1 +#> parent_0 7.365081 -1854.5113 -7.186039e+02 -1.307858e+02 +#> k_parent -1854.511330 2686790.7676 -6.235542e+04 -1.429363e+04 +#> k_A1 -718.603865 -62355.4211 3.128242e+06 0.000000e+00 +#> k_B1 -130.785796 -14293.6348 0.000000e+00 4.545506e+05 +#> k_C1 -76.404274 -38575.9391 1.190516e-02 -9.422820e-04 +#> k_A2 -17.933942 -4390.5079 -5.838973e+04 0.000000e+00 +#> f_parent_to_A1 75.150866 43257.2599 -1.733841e+05 0.000000e+00 +#> f_parent_to_B1 29.265575 17940.1132 0.000000e+00 -6.150198e+04 +#> f_parent_to_C1 20.661354 19692.5582 -6.146186e-05 -1.990817e-03 +#> f_A1_to_A2 1.593279 597.0744 5.849840e+03 0.000000e+00 +#> k_C1 k_A2 f_parent_to_A1 f_parent_to_B1 +#> parent_0 -7.640427e+01 -1.793394e+01 7.515087e+01 2.926558e+01 +#> k_parent -3.857594e+04 -4.390508e+03 4.325726e+04 1.794011e+04 +#> k_A1 1.190516e-02 -5.838973e+04 -1.733841e+05 0.000000e+00 +#> k_B1 -9.422820e-04 0.000000e+00 0.000000e+00 -6.150198e+04 +#> k_C1 8.855106e+04 4.105787e-04 -1.354551e-03 5.852620e-04 +#> k_A2 4.105787e-04 4.649850e+04 -4.327086e+03 0.000000e+00 +#> f_parent_to_A1 -1.354551e-03 -4.327086e+03 1.813234e+04 0.000000e+00 +#> f_parent_to_B1 5.852620e-04 0.000000e+00 0.000000e+00 1.376213e+04 +#> f_parent_to_C1 -1.658031e+04 2.903794e-04 1.946385e-03 1.325258e-03 +#> f_A1_to_A2 -4.367402e-05 -3.679910e+03 3.844249e+02 0.000000e+00 +#> f_parent_to_C1 f_A1_to_A2 +#> parent_0 2.066135e+01 1.593279e+00 +#> k_parent 1.969256e+04 5.970744e+02 +#> k_A1 -6.146186e-05 5.849840e+03 +#> k_B1 -1.990817e-03 0.000000e+00 +#> k_C1 -1.658031e+04 -4.367402e-05 +#> k_A2 2.903794e-04 -3.679910e+03 +#> f_parent_to_A1 1.946385e-03 3.844249e+02 +#> f_parent_to_B1 1.325258e-03 0.000000e+00 +#> f_parent_to_C1 4.483759e+03 -3.796730e-05 +#> f_A1_to_A2 -3.796730e-05 3.269288e+02 +#> +#> $start +#> value type +#> parent_0 93.2000000 state +#> k_parent 0.1000000 deparm +#> k_A1 0.1001000 deparm +#> k_B1 0.1002000 deparm +#> k_C1 0.1003000 deparm +#> k_A2 0.1004000 deparm +#> f_parent_to_A1 0.3333333 deparm +#> f_parent_to_B1 0.3333333 deparm +#> f_parent_to_C1 0.3333333 deparm +#> f_A1_to_A2 0.5000000 deparm +#> +#> $start_transformed +#> value lower upper +#> parent_0 93.200000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_A1 -2.301586 -Inf Inf +#> log_k_B1 -2.300587 -Inf Inf +#> log_k_C1 -2.299590 -Inf Inf +#> log_k_A2 -2.298593 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> f_parent_ilr_2 0.000000 -Inf Inf +#> f_A1_ilr_1 0.000000 -Inf Inf +#> +#> $fixed +#> value type +#> A1_0 0 state +#> B1_0 0 state +#> C1_0 0 state +#> A2_0 0 state +#> +#> $data +#> time variable observed predicted residual +#> 1 0 parent 93.20 91.918159794 1.2818402 +#> 2 1 parent 89.40 87.462788491 1.9372115 +#> 3 3 parent 79.70 79.189448055 0.5105519 +#> 4 7 parent 61.10 64.916531757 -3.8165318 +#> 5 14 parent 48.20 45.846828365 2.3531716 +#> 6 30 parent 15.90 20.704334210 -4.8043342 +#> 7 62 parent 6.50 4.222456793 2.2775432 +#> 8 100 parent 6.00 0.639147580 5.3608524 +#> 9 0 A1 NA 0.000000000 NA +#> 10 1 A1 NA 1.685461006 NA +#> 11 3 A1 0.55 4.746752202 -4.1967522 +#> 12 7 A1 6.87 9.773298725 -2.9032987 +#> 13 14 A1 17.08 15.767512526 1.3124875 +#> 14 30 A1 21.68 21.077890710 0.6021093 +#> 15 62 A1 15.77 18.279232408 -2.5092324 +#> 16 100 A1 13.63 11.743860400 1.8861396 +#> 17 0 B1 NA 0.000000000 NA +#> 18 1 B1 NA 0.862762059 NA +#> 19 3 B1 NA 2.418226457 NA +#> 20 7 B1 0.55 4.930176837 -4.3801768 +#> 21 14 B1 2.31 7.810248132 -5.5002481 +#> 22 30 B1 15.76 9.968281596 5.7917184 +#> 23 62 B1 6.36 7.745265792 -1.3852658 +#> 24 100 B1 3.74 4.271330056 -0.5313301 +#> 25 0 C1 NA 0.000000000 NA +#> 26 1 C1 0.55 1.829645786 -1.2796458 +#> 27 3 C1 3.20 4.910531064 -1.7105311 +#> 28 7 C1 5.46 9.171671206 -3.7116712 +#> 29 14 C1 12.55 12.431704739 0.1182953 +#> 30 30 C1 10.45 10.972842888 -0.5228429 +#> 31 62 C1 4.74 3.882970158 0.8570298 +#> 32 100 C1 4.33 0.782344364 3.5476556 +#> 33 0 A2 NA 0.000000000 NA +#> 34 1 A2 0.55 0.005272357 0.5447276 +#> 35 3 A2 1.41 0.044759575 1.3652404 +#> 36 7 A2 0.55 0.216973934 0.3330261 +#> 37 14 A2 1.29 0.709794102 0.5802059 +#> 38 30 A2 1.95 2.078585030 -0.1285850 +#> 39 62 A2 3.54 3.751927986 -0.2119280 +#> 40 100 A2 3.86 3.721800959 0.1381990 +#> +#> $atol +#> [1] 1e-08 +#> +#> $rtol +#> [1] 1e-10 +#> +#> $weight.ini +#> [1] "none" +#> +#> $reweight.tol +#> [1] 1e-08 +#> +#> $reweight.max.iter +#> [1] 10 +#> +#> $bparms.optim +#> parent_0 k_parent k_A1 k_B1 k_C1 +#> 91.91815979 0.04968519 0.01393165 0.01859846 0.06171564 +#> k_A2 f_parent_to_A1 f_parent_to_B1 f_parent_to_C1 f_A1_to_A2 +#> 0.02431549 0.38096192 0.19546676 0.42357132 0.44796066 +#> +#> $bparms.fixed +#> A1_0 B1_0 C1_0 A2_0 +#> 0 0 0 0 +#> +#> $bparms.ode +#> k_parent f_parent_to_A1 f_parent_to_B1 f_parent_to_C1 k_A1 +#> 0.04968519 0.38096192 0.19546676 0.42357132 0.01393165 +#> f_A1_to_A2 k_B1 k_C1 k_A2 +#> 0.44796066 0.01859846 0.06171564 0.02431549 +#> +#> $bparms.state +#> parent A1 B1 C1 A2 +#> 91.91816 0.00000 0.00000 0.00000 0.00000 +#> +#> $date +#> [1] "Fri Nov 18 15:20:45 2016" +#> +#> attr(,"class") +#> [1] "mkinfit" "modFit" </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 8dc57fb7..b334b3aa 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'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 17 22:57:05 2016 -#> Date of summary: Thu Nov 17 22:57:05 2016 +#> Date of fit: Fri Nov 18 15:20:45 2016 +#> Date of summary: Fri Nov 18 15:20:45 2016 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.085 s +#> Fitted with method Port using 35 model solutions performed in 0.081 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index c6f29582..97407402 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -121,28 +121,856 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> -<span class='co'># m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),</span> -<span class='co'># M1 = list(type = "SFO", to = "M2"),</span> -<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># </span> -<span class='co'># m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),</span> -<span class='co'># sink = FALSE),</span> -<span class='co'># M1 = list(type = "SFO"),</span> -<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"),</span> -<span class='co'># M1 = list(type = "SFO", to = "M2"),</span> -<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),</span> -<span class='co'># sink = FALSE),</span> -<span class='co'># M1 = list(type = "SFO"),</span> -<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)</span> -<span class='co'>## ---------------------------------------------</span></div></pre> + <pre class="examples"><div class='input'> +<span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), + <span class='kw'>M1</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>), + <span class='kw'>M2</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + +<span class='no'>m_synth_SFO_par</span> <span class='kw'><-</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='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), + <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), + <span class='kw'>M1</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='kw'>M2</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>m_synth_DFOP_lin</span> <span class='kw'><-</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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), + <span class='kw'>M1</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>), + <span class='kw'>M2</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>m_synth_DFOP_par</span> <span class='kw'><-</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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), + <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), + <span class='kw'>M1</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='kw'>M2</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<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>)</div><div class='output co'>#> Model cost at call 1 : 31054.59 +#> Model cost at call 3 : 31054.59 +#> Model cost at call 8 : 15089.57 +#> Model cost at call 9 : 11464.3 +#> Model cost at call 11 : 11464.1 +#> Model cost at call 16 : 5723.32 +#> Model cost at call 17 : 5723.318 +#> Model cost at call 19 : 5723.304 +#> Model cost at call 21 : 5723.304 +#> Model cost at call 24 : 3968.126 +#> Model cost at call 25 : 3968.124 +#> Model cost at call 28 : 3968.119 +#> Model cost at call 31 : 3416.421 +#> Model cost at call 32 : 3416.42 +#> Model cost at call 36 : 3416.418 +#> Model cost at call 38 : 866.5564 +#> Model cost at call 42 : 866.5557 +#> Model cost at call 45 : 670.4833 +#> Model cost at call 47 : 670.476 +#> Model cost at call 53 : 312.9905 +#> Model cost at call 57 : 312.9904 +#> Model cost at call 58 : 312.9904 +#> Model cost at call 61 : 287.8916 +#> Model cost at call 63 : 287.8916 +#> Model cost at call 66 : 287.8916 +#> Model cost at call 69 : 284.5441 +#> Model cost at call 71 : 284.5441 +#> Model cost at call 73 : 284.5441 +#> Model cost at call 76 : 283.4533 +#> Model cost at call 78 : 283.4533 +#> Model cost at call 83 : 282.1356 +#> Model cost at call 85 : 282.1356 +#> Model cost at call 88 : 282.1356 +#> Model cost at call 90 : 280.7846 +#> Model cost at call 92 : 280.7846 +#> Model cost at call 95 : 280.7846 +#> Model cost at call 97 : 278.4856 +#> Model cost at call 98 : 274.5025 +#> Model cost at call 99 : 269.2866 +#> Model cost at call 101 : 269.2866 +#> Model cost at call 102 : 269.2866 +#> Model cost at call 103 : 269.2866 +#> Model cost at call 106 : 254.1284 +#> Model cost at call 108 : 254.1283 +#> Model cost at call 109 : 254.1283 +#> Model cost at call 112 : 254.128 +#> Model cost at call 114 : 233.1376 +#> Model cost at call 116 : 233.1376 +#> Model cost at call 118 : 233.1375 +#> Model cost at call 121 : 227.5879 +#> Model cost at call 124 : 227.5879 +#> Model cost at call 125 : 227.5878 +#> Model cost at call 129 : 217.0041 +#> Model cost at call 133 : 217.0041 +#> Model cost at call 135 : 217.0041 +#> Model cost at call 136 : 215.1367 +#> Model cost at call 138 : 215.1367 +#> Model cost at call 143 : 213.3794 +#> Model cost at call 145 : 213.3794 +#> Model cost at call 150 : 211.0201 +#> Model cost at call 152 : 211.0201 +#> Model cost at call 154 : 211.0201 +#> Model cost at call 155 : 211.0201 +#> Model cost at call 157 : 210.6426 +#> Model cost at call 159 : 210.6426 +#> Model cost at call 160 : 210.6425 +#> Model cost at call 164 : 207.6331 +#> Model cost at call 167 : 207.6331 +#> Model cost at call 171 : 206.2366 +#> Model cost at call 173 : 206.2366 +#> Model cost at call 174 : 206.2366 +#> Model cost at call 178 : 204.8117 +#> Model cost at call 180 : 204.8117 +#> Model cost at call 185 : 204.7988 +#> Model cost at call 187 : 204.7988 +#> Model cost at call 190 : 204.7988 +#> Model cost at call 192 : 203.5122 +#> Model cost at call 194 : 203.5122 +#> Model cost at call 197 : 203.5122 +#> Model cost at call 198 : 203.5122 +#> Model cost at call 199 : 203.354 +#> Model cost at call 201 : 203.354 +#> Model cost at call 204 : 203.354 +#> Model cost at call 206 : 202.6825 +#> Model cost at call 208 : 202.6825 +#> Model cost at call 209 : 202.6825 +#> Model cost at call 212 : 202.6825 +#> Model cost at call 213 : 202.4582 +#> Model cost at call 215 : 202.4582 +#> Model cost at call 220 : 202.3261 +#> Model cost at call 222 : 202.3261 +#> Model cost at call 227 : 202.2306 +#> Model cost at call 229 : 202.2306 +#> Model cost at call 231 : 202.2306 +#> Model cost at call 234 : 202.115 +#> Model cost at call 236 : 202.115 +#> Model cost at call 238 : 202.115 +#> Model cost at call 241 : 202.0397 +#> Model cost at call 243 : 202.0397 +#> Model cost at call 248 : 201.8989 +#> Model cost at call 249 : 201.8551 +#> Model cost at call 252 : 201.8551 +#> Model cost at call 257 : 201.676 +#> Model cost at call 259 : 201.676 +#> Model cost at call 264 : 201.6285 +#> Model cost at call 266 : 201.6285 +#> Model cost at call 270 : 201.6284 +#> Model cost at call 271 : 201.5876 +#> Model cost at call 272 : 201.5876 +#> Model cost at call 278 : 201.5317 +#> Model cost at call 279 : 201.5317 +#> Model cost at call 286 : 201.5207 +#> Model cost at call 287 : 201.5207 +#> Model cost at call 289 : 201.5207 +#> Model cost at call 293 : 201.5207 +#> Model cost at call 294 : 201.5207 +#> Model cost at call 296 : 201.5174 +#> Model cost at call 301 : 201.5174 +#> Model cost at call 304 : 201.5169 +#> Model cost at call 305 : 201.5169 +#> Model cost at call 306 : 201.5169 +#> Model cost at call 309 : 201.5169 +#> Model cost at call 312 : 201.5169 +#> Model cost at call 314 : 201.5169 +#> Model cost at call 322 : 201.5169 +#> Model cost at call 325 : 201.5169 +#> Model cost at call 340 : 201.5169 +#> Optimisation by method Port successfully terminated.</div><div class='output co'>#> $par +#> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1 +#> 102.0624835 -0.3020316 -1.2067882 -3.9007519 0.8491684 +#> f_M1_ilr_1 +#> 0.6780411 +#> +#> $ssr +#> [1] 201.5169 +#> +#> $convergence +#> [1] 0 +#> +#> $iterations +#> [1] 43 +#> +#> $evaluations +#> function gradient +#> 56 281 +#> +#> $counts +#> [1] "relative convergence (4)" +#> +#> $hessian +#> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1 +#> parent_0 8.433594 -29.66715 -18.40708 -68.90161 115.9976 +#> log_k_parent -29.667146 10561.33531 675.33998 55.94284 1666.8940 +#> log_k_M1 -18.407082 675.33998 6274.11801 44.01714 -614.5674 +#> log_k_M2 -68.901614 55.94284 44.01714 5021.66991 -2300.4467 +#> f_parent_ilr_1 115.997604 1666.89403 -614.56735 -2300.44667 3872.8569 +#> f_M1_ilr_1 92.819176 604.06870 1483.45826 -2755.79082 3098.9947 +#> f_M1_ilr_1 +#> parent_0 92.81918 +#> log_k_parent 604.06870 +#> log_k_M1 1483.45826 +#> log_k_M2 -2755.79082 +#> f_parent_ilr_1 3098.99466 +#> f_M1_ilr_1 3712.39824 +#> +#> $residuals +#> parent parent parent parent parent parent +#> 0.56248353 0.86248353 -5.17118695 1.22881305 0.70772795 3.50772795 +#> parent parent parent parent parent parent +#> -0.52282962 0.27717038 -3.49673606 -3.19999990 -0.60000000 -3.50000000 +#> M1 M1 M1 M1 M1 M1 +#> -1.61088639 -2.61088639 5.07026619 -0.42973381 0.38714436 -2.31285564 +#> M1 M1 M1 M1 M1 M1 +#> -3.80468869 0.79531131 -0.49999789 -3.20000000 -1.50000000 -0.60000000 +#> M2 M2 M2 M2 M2 M2 +#> -0.34517017 0.62526794 2.22526794 -0.07941701 -1.17941701 -3.83353798 +#> M2 M2 M2 M2 M2 M2 +#> 1.26646202 0.87274743 2.47274743 -0.21837410 0.98162590 -0.47130583 +#> M2 M2 M2 +#> -0.67130583 -4.27893112 2.22106888 +#> +#> $ms +#> [1] 5.1671 +#> +#> $var_ms +#> parent M1 M2 +#> 6.461983 5.750942 3.664121 +#> +#> $var_ms_unscaled +#> parent M1 M2 +#> 6.461983 5.750942 3.664121 +#> +#> $var_ms_unweighted +#> parent M1 M2 +#> 6.461983 5.750942 3.664121 +#> +#> $rank +#> [1] 6 +#> +#> $df.residual +#> [1] 33 +#> +#> $solution_type +#> [1] "deSolve" +#> +#> $transform_rates +#> [1] TRUE +#> +#> $transform_fractions +#> [1] TRUE +#> +#> $method.modFit +#> [1] "Port" +#> +#> $maxit.modFit +#> [1] "auto" +#> +#> $calls +#> [1] 351 +#> +#> $time +#> user system elapsed +#> 2.116 0.000 2.113 +#> +#> $mkinmod +#> <mkinmod> model generated with +#> Use of formation fractions $use_of_ff: max +#> Specification $spec: +#> $parent +#> $type: SFO; $to: M1; $sink: TRUE +#> $M1 +#> $type: SFO; $to: M2; $sink: TRUE +#> $M2 +#> $type: SFO; $sink: TRUE +#> Coefficient matrix $coefmat available +#> Compiled model $cf available +#> +#> $observed +#> name time value override err +#> 1 parent 0 101.5 NA 1 +#> 2 parent 0 101.2 NA 1 +#> 3 parent 1 53.9 NA 1 +#> 4 parent 1 47.5 NA 1 +#> 5 parent 3 10.4 NA 1 +#> 6 parent 3 7.6 NA 1 +#> 7 parent 7 1.1 NA 1 +#> 8 parent 7 0.3 NA 1 +#> 9 parent 14 NA NA 1 +#> 10 parent 14 3.5 NA 1 +#> 11 parent 28 NA NA 1 +#> 12 parent 28 3.2 NA 1 +#> 13 parent 60 NA NA 1 +#> 14 parent 60 NA NA 1 +#> 15 parent 90 0.6 NA 1 +#> 16 parent 90 NA NA 1 +#> 17 parent 120 NA NA 1 +#> 18 parent 120 3.5 NA 1 +#> 19 M1 0 NA NA 1 +#> 20 M1 0 NA NA 1 +#> 21 M1 1 36.4 NA 1 +#> 22 M1 1 37.4 NA 1 +#> 23 M1 3 34.3 NA 1 +#> 24 M1 3 39.8 NA 1 +#> 25 M1 7 15.1 NA 1 +#> 26 M1 7 17.8 NA 1 +#> 27 M1 14 5.8 NA 1 +#> 28 M1 14 1.2 NA 1 +#> 29 M1 28 NA NA 1 +#> 30 M1 28 NA NA 1 +#> 31 M1 60 0.5 NA 1 +#> 32 M1 60 NA NA 1 +#> 33 M1 90 NA NA 1 +#> 34 M1 90 3.2 NA 1 +#> 35 M1 120 1.5 NA 1 +#> 36 M1 120 0.6 NA 1 +#> 37 M2 0 NA NA 1 +#> 38 M2 0 NA NA 1 +#> 39 M2 1 NA NA 1 +#> 40 M2 1 4.8 NA 1 +#> 41 M2 3 20.9 NA 1 +#> 42 M2 3 19.3 NA 1 +#> 43 M2 7 42.0 NA 1 +#> 44 M2 7 43.1 NA 1 +#> 45 M2 14 49.4 NA 1 +#> 46 M2 14 44.3 NA 1 +#> 47 M2 28 34.6 NA 1 +#> 48 M2 28 33.0 NA 1 +#> 49 M2 60 18.8 NA 1 +#> 50 M2 60 17.6 NA 1 +#> 51 M2 90 10.6 NA 1 +#> 52 M2 90 10.8 NA 1 +#> 53 M2 120 9.8 NA 1 +#> 54 M2 120 3.3 NA 1 +#> +#> $obs_vars +#> [1] "parent" "M1" "M2" +#> +#> $predicted +#> name time value +#> 1 parent 0.000000 1.020625e+02 +#> 2 parent 1.000000 4.872881e+01 +#> 3 parent 1.212121 4.165603e+01 +#> 4 parent 2.424242 1.700159e+01 +#> 5 parent 3.000000 1.110773e+01 +#> 6 parent 3.636364 6.939072e+00 +#> 7 parent 4.848485 2.832130e+00 +#> 8 parent 6.060606 1.155912e+00 +#> 9 parent 7.000000 5.771704e-01 +#> 10 parent 7.272727 4.717769e-01 +#> 11 parent 8.484848 1.925522e-01 +#> 12 parent 9.696970 7.858872e-02 +#> 13 parent 10.909091 3.207539e-02 +#> 14 parent 12.121212 1.309133e-02 +#> 15 parent 13.333333 5.343128e-03 +#> 16 parent 14.000000 3.263939e-03 +#> 17 parent 14.545455 2.180757e-03 +#> 18 parent 15.757576 8.900590e-04 +#> 19 parent 16.969697 3.632705e-04 +#> 20 parent 18.181818 1.482660e-04 +#> 21 parent 19.393939 6.051327e-05 +#> 22 parent 20.606061 2.469808e-05 +#> 23 parent 21.818182 1.008035e-05 +#> 24 parent 23.030303 4.114467e-06 +#> 25 parent 24.242424 1.679140e-06 +#> 26 parent 25.454545 6.853728e-07 +#> 27 parent 26.666667 2.797450e-07 +#> 28 parent 27.878788 1.142138e-07 +#> 29 parent 28.000000 1.044512e-07 +#> 30 parent 29.090909 4.657425e-08 +#> 31 parent 30.303030 1.900245e-08 +#> 32 parent 31.515152 7.760238e-09 +#> 33 parent 32.727273 3.164577e-09 +#> 34 parent 33.939394 1.291779e-09 +#> 35 parent 35.151515 5.261577e-10 +#> 36 parent 36.363636 2.132915e-10 +#> 37 parent 37.575758 8.767818e-11 +#> 38 parent 38.787879 3.442792e-11 +#> 39 parent 40.000000 1.827291e-11 +#> 40 parent 41.212121 3.771071e-12 +#> 41 parent 42.424242 6.084856e-12 +#> 42 parent 43.636364 -3.377858e-12 +#> 43 parent 44.848485 5.870338e-12 +#> 44 parent 46.060606 -6.263257e-12 +#> 45 parent 47.272727 8.743492e-12 +#> 46 parent 48.484848 -9.381771e-12 +#> 47 parent 49.696970 1.403389e-11 +#> 48 parent 50.909091 -3.592528e-11 +#> 49 parent 52.121212 -8.487459e-11 +#> 50 parent 53.333333 -3.309153e-12 +#> 51 parent 54.545455 -2.966799e-11 +#> 52 parent 55.757576 -4.723329e-11 +#> 53 parent 56.969697 7.635833e-11 +#> 54 parent 58.181818 -1.887064e-11 +#> 55 parent 59.393939 -1.548352e-10 +#> 56 parent 60.000000 -1.053819e-10 +#> 57 parent 60.606061 5.780435e-12 +#> 58 parent 61.818182 9.056244e-11 +#> 59 parent 63.030303 -8.889581e-11 +#> 60 parent 64.242424 -6.653389e-11 +#> 61 parent 65.454545 1.181114e-10 +#> 62 parent 66.666667 -9.226329e-12 +#> 63 parent 67.878788 -8.897326e-11 +#> 64 parent 69.090909 1.984998e-10 +#> 65 parent 70.303030 3.255550e-11 +#> 66 parent 71.515152 -2.991002e-10 +#> 67 parent 72.727273 2.254268e-10 +#> 68 parent 73.939394 2.696039e-10 +#> 69 parent 75.151515 1.226806e-10 +#> 70 parent 76.363636 3.447399e-11 +#> 71 parent 77.575758 2.048902e-11 +#> 72 parent 78.787879 6.830755e-12 +#> 73 parent 80.000000 8.242171e-13 +#> 74 parent 81.212121 -5.357740e-12 +#> 75 parent 82.424242 2.198907e-11 +#> 76 parent 83.636364 3.739511e-11 +#> 77 parent 84.848485 -6.616091e-12 +#> 78 parent 86.060606 -2.562689e-12 +#> 79 parent 87.272727 4.089395e-11 +#> 80 parent 88.484848 -2.042159e-11 +#> 81 parent 89.696970 -4.088127e-11 +#> 82 parent 90.000000 -1.874889e-11 +#> 83 parent 90.909091 4.225747e-11 +#> 84 parent 92.121212 8.054402e-12 +#> 85 parent 93.333333 3.917595e-12 +#> 86 parent 94.545455 6.591454e-12 +#> 87 parent 95.757576 2.790958e-11 +#> 88 parent 96.969697 2.720721e-12 +#> 89 parent 98.181818 -1.304470e-12 +#> 90 parent 99.393939 1.345055e-11 +#> 91 parent 100.606061 -9.662077e-12 +#> 92 parent 101.818182 -2.086798e-11 +#> 93 parent 103.030303 9.332507e-12 +#> 94 parent 104.242424 -6.752606e-12 +#> 95 parent 105.454545 -3.326620e-11 +#> 96 parent 106.666667 2.500680e-11 +#> 97 parent 107.878788 2.184148e-11 +#> 98 parent 109.090909 -5.985657e-11 +#> 99 parent 110.303030 -8.750836e-14 +#> 100 parent 111.515152 1.820588e-12 +#> 101 parent 112.727273 -1.261472e-11 +#> 102 parent 113.939394 1.455439e-11 +#> 103 parent 115.151515 1.945812e-12 +#> 104 parent 116.363636 9.598249e-13 +#> 105 parent 117.575758 1.724679e-12 +#> 106 parent 118.787879 -1.334504e-12 +#> 107 parent 120.000000 -2.804801e-11 +#> 108 M1 0.000000 0.000000e+00 +#> 109 M1 1.000000 3.478911e+01 +#> 110 M1 1.212121 3.791354e+01 +#> 111 M1 2.424242 4.185645e+01 +#> 112 M1 3.000000 3.937027e+01 +#> 113 M1 3.636364 3.544167e+01 +#> 114 M1 4.848485 2.723995e+01 +#> 115 M1 6.060606 2.000711e+01 +#> 116 M1 7.000000 1.548714e+01 +#> 117 M1 7.272727 1.435144e+01 +#> 118 M1 8.484848 1.016177e+01 +#> 119 M1 9.696970 7.142649e+00 +#> 120 M1 10.909091 4.999441e+00 +#> 121 M1 12.121212 3.490801e+00 +#> 122 M1 13.333333 2.433954e+00 +#> 123 M1 14.000000 1.995311e+00 +#> 124 M1 14.545455 1.695664e+00 +#> 125 M1 15.757576 1.180746e+00 +#> 126 M1 16.969697 8.219589e-01 +#> 127 M1 18.181818 5.720991e-01 +#> 128 M1 19.393939 3.981531e-01 +#> 129 M1 20.606061 2.770793e-01 +#> 130 M1 21.818182 1.928162e-01 +#> 131 M1 23.030303 1.341758e-01 +#> 132 M1 24.242424 9.336844e-02 +#> 133 M1 25.454545 6.497152e-02 +#> 134 M1 26.666667 4.521101e-02 +#> 135 M1 27.878788 3.146041e-02 +#> 136 M1 28.000000 3.034005e-02 +#> 137 M1 29.090909 2.189192e-02 +#> 138 M1 30.303030 1.523362e-02 +#> 139 M1 31.515152 1.060040e-02 +#> 140 M1 32.727273 7.376345e-03 +#> 141 M1 33.939394 5.132870e-03 +#> 142 M1 35.151515 3.571730e-03 +#> 143 M1 36.363636 2.485406e-03 +#> 144 M1 37.575758 1.729482e-03 +#> 145 M1 38.787879 1.203467e-03 +#> 146 M1 40.000000 8.374380e-04 +#> 147 M1 41.212121 5.827347e-04 +#> 148 M1 42.424242 4.054989e-04 +#> 149 M1 43.636364 2.821681e-04 +#> 150 M1 44.848485 1.963481e-04 +#> 151 M1 46.060606 1.366297e-04 +#> 152 M1 47.272727 9.507439e-05 +#> 153 M1 48.484848 6.615797e-05 +#> 154 M1 49.696970 4.603629e-05 +#> 155 M1 50.909091 3.203434e-05 +#> 156 M1 52.121212 2.229196e-05 +#> 157 M1 53.333333 1.551223e-05 +#> 158 M1 54.545455 1.079420e-05 +#> 159 M1 55.757576 7.511255e-06 +#> 160 M1 56.969697 5.226640e-06 +#> 161 M1 58.181818 3.636450e-06 +#> 162 M1 59.393939 2.530191e-06 +#> 163 M1 60.000000 2.110651e-06 +#> 164 M1 60.606061 1.760625e-06 +#> 165 M1 61.818182 1.225095e-06 +#> 166 M1 63.030303 8.527010e-07 +#> 167 M1 64.242424 5.934161e-07 +#> 168 M1 65.454545 4.127474e-07 +#> 169 M1 66.666667 2.874114e-07 +#> 170 M1 67.878788 2.001921e-07 +#> 171 M1 69.090909 1.389331e-07 +#> 172 M1 70.303030 9.678549e-08 +#> 173 M1 71.515152 6.777214e-08 +#> 174 M1 72.727273 4.658761e-08 +#> 175 M1 73.939394 3.226837e-08 +#> 176 M1 75.151515 2.253752e-08 +#> 177 M1 76.363636 1.574843e-08 +#> 178 M1 77.575758 1.096303e-08 +#> 179 M1 78.787879 7.638209e-09 +#> 180 M1 80.000000 5.319996e-09 +#> 181 M1 81.212121 3.709993e-09 +#> 182 M1 82.424242 2.548810e-09 +#> 183 M1 83.636364 1.744629e-09 +#> 184 M1 84.848485 1.256081e-09 +#> 185 M1 86.060606 8.714672e-10 +#> 186 M1 87.272727 5.511830e-10 +#> 187 M1 88.484848 4.466725e-10 +#> 188 M1 89.696970 3.452654e-10 +#> 189 M1 90.000000 2.913252e-10 +#> 190 M1 90.909091 1.489262e-10 +#> 191 M1 92.121212 1.311985e-10 +#> 192 M1 93.333333 9.347248e-11 +#> 193 M1 94.545455 6.004640e-11 +#> 194 M1 95.757576 1.166926e-11 +#> 195 M1 96.969697 2.968203e-11 +#> 196 M1 98.181818 2.478228e-11 +#> 197 M1 99.393939 -1.291838e-12 +#> 198 M1 100.606061 2.366481e-11 +#> 199 M1 101.818182 3.472871e-11 +#> 200 M1 103.030303 -6.633877e-12 +#> 201 M1 104.242424 1.248743e-11 +#> 202 M1 105.454545 4.557313e-11 +#> 203 M1 106.666667 -3.046261e-11 +#> 204 M1 107.878788 -2.693037e-11 +#> 205 M1 109.090909 7.816593e-11 +#> 206 M1 110.303030 7.276098e-13 +#> 207 M1 111.515152 -1.922924e-12 +#> 208 M1 112.727273 1.658481e-11 +#> 209 M1 113.939394 -1.858452e-11 +#> 210 M1 115.151515 -2.368198e-12 +#> 211 M1 116.363636 -1.138989e-12 +#> 212 M1 117.575758 -2.157011e-12 +#> 213 M1 118.787879 1.771568e-12 +#> 214 M1 120.000000 3.624738e-11 +#> 215 M2 0.000000 0.000000e+00 +#> 216 M2 1.000000 4.454830e+00 +#> 217 M2 1.212121 6.103803e+00 +#> 218 M2 2.424242 1.667567e+01 +#> 219 M2 3.000000 2.152527e+01 +#> 220 M2 3.636364 2.637280e+01 +#> 221 M2 4.848485 3.384106e+01 +#> 222 M2 6.060606 3.910279e+01 +#> 223 M2 7.000000 4.192058e+01 +#> 224 M2 7.272727 4.256708e+01 +#> 225 M2 8.484848 4.467909e+01 +#> 226 M2 9.696970 4.581396e+01 +#> 227 M2 10.909091 4.625927e+01 +#> 228 M2 12.121212 4.622588e+01 +#> 229 M2 13.333333 4.586473e+01 +#> 230 M2 14.000000 4.556646e+01 +#> 231 M2 14.545455 4.528249e+01 +#> 232 M2 15.757576 4.455394e+01 +#> 233 M2 16.969697 4.373119e+01 +#> 234 M2 18.181818 4.285048e+01 +#> 235 M2 19.393939 4.193685e+01 +#> 236 M2 20.606061 4.100759e+01 +#> 237 M2 21.818182 4.007456e+01 +#> 238 M2 23.030303 3.914584e+01 +#> 239 M2 24.242424 3.822688e+01 +#> 240 M2 25.454545 3.732133e+01 +#> 241 M2 26.666667 3.643154e+01 +#> 242 M2 27.878788 3.555901e+01 +#> 243 M2 28.000000 3.547275e+01 +#> 244 M2 29.090909 3.470463e+01 +#> 245 M2 30.303030 3.386887e+01 +#> 246 M2 31.515152 3.305190e+01 +#> 247 M2 32.727273 3.225371e+01 +#> 248 M2 33.939394 3.147416e+01 +#> 249 M2 35.151515 3.071300e+01 +#> 250 M2 36.363636 2.996993e+01 +#> 251 M2 37.575758 2.924463e+01 +#> 252 M2 38.787879 2.853672e+01 +#> 253 M2 40.000000 2.784585e+01 +#> 254 M2 41.212121 2.717163e+01 +#> 255 M2 42.424242 2.651368e+01 +#> 256 M2 43.636364 2.587163e+01 +#> 257 M2 44.848485 2.524511e+01 +#> 258 M2 46.060606 2.463374e+01 +#> 259 M2 47.272727 2.403716e+01 +#> 260 M2 48.484848 2.345502e+01 +#> 261 M2 49.696970 2.288698e+01 +#> 262 M2 50.909091 2.233268e+01 +#> 263 M2 52.121212 2.179181e+01 +#> 264 M2 53.333333 2.126404e+01 +#> 265 M2 54.545455 2.074905e+01 +#> 266 M2 55.757576 2.024653e+01 +#> 267 M2 56.969697 1.975618e+01 +#> 268 M2 58.181818 1.927770e+01 +#> 269 M2 59.393939 1.881081e+01 +#> 270 M2 60.000000 1.858163e+01 +#> 271 M2 60.606061 1.835523e+01 +#> 272 M2 61.818182 1.791068e+01 +#> 273 M2 63.030303 1.747690e+01 +#> 274 M2 64.242424 1.705363e+01 +#> 275 M2 65.454545 1.664061e+01 +#> 276 M2 66.666667 1.623759e+01 +#> 277 M2 67.878788 1.584433e+01 +#> 278 M2 69.090909 1.546059e+01 +#> 279 M2 70.303030 1.508615e+01 +#> 280 M2 71.515152 1.472078e+01 +#> 281 M2 72.727273 1.436425e+01 +#> 282 M2 73.939394 1.401636e+01 +#> 283 M2 75.151515 1.367690e+01 +#> 284 M2 76.363636 1.334566e+01 +#> 285 M2 77.575758 1.302244e+01 +#> 286 M2 78.787879 1.270705e+01 +#> 287 M2 80.000000 1.239929e+01 +#> 288 M2 81.212121 1.209899e+01 +#> 289 M2 82.424242 1.180597e+01 +#> 290 M2 83.636364 1.152004e+01 +#> 291 M2 84.848485 1.124103e+01 +#> 292 M2 86.060606 1.096878e+01 +#> 293 M2 87.272727 1.070313e+01 +#> 294 M2 88.484848 1.044391e+01 +#> 295 M2 89.696970 1.019097e+01 +#> 296 M2 90.000000 1.012869e+01 +#> 297 M2 90.909091 9.944151e+00 +#> 298 M2 92.121212 9.703312e+00 +#> 299 M2 93.333333 9.468307e+00 +#> 300 M2 94.545455 9.238993e+00 +#> 301 M2 95.757576 9.015233e+00 +#> 302 M2 96.969697 8.796892e+00 +#> 303 M2 98.181818 8.583839e+00 +#> 304 M2 99.393939 8.375946e+00 +#> 305 M2 100.606061 8.173088e+00 +#> 306 M2 101.818182 7.975143e+00 +#> 307 M2 103.030303 7.781992e+00 +#> 308 M2 104.242424 7.593520e+00 +#> 309 M2 105.454545 7.409611e+00 +#> 310 M2 106.666667 7.230157e+00 +#> 311 M2 107.878788 7.055049e+00 +#> 312 M2 109.090909 6.884182e+00 +#> 313 M2 110.303030 6.717454e+00 +#> 314 M2 111.515152 6.554763e+00 +#> 315 M2 112.727273 6.396012e+00 +#> 316 M2 113.939394 6.241107e+00 +#> 317 M2 115.151515 6.089953e+00 +#> 318 M2 116.363636 5.942460e+00 +#> 319 M2 117.575758 5.798538e+00 +#> 320 M2 118.787879 5.658103e+00 +#> 321 M2 120.000000 5.521069e+00 +#> +#> $cost +#> function (P) +#> { +#> assign("calls", calls + 1, inherits = TRUE) +#> if (trace_parms) +#> cat(P, "\n") +#> if (length(state.ini.optim) > 0) { +#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) +#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) +#> } +#> else { +#> odeini <- state.ini.fixed +#> names(odeini) <- state.ini.fixed.boxnames +#> } +#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], +#> transparms.fixed) +#> parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, +#> transform_fractions = transform_fractions) +#> out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, +#> use_compiled = use_compiled, method.ode = method.ode, +#> atol = atol, rtol = rtol, ...) +#> assign("out_predicted", out, inherits = TRUE) +#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, +#> scaleVar = scaleVar) +#> if (mC$model < cost.old) { +#> if (!quiet) +#> cat("Model cost at call ", calls, ": ", mC$model, +#> "\n") +#> if (plot) { +#> outtimes_plot = seq(min(observed$time), max(observed$time), +#> length.out = 100) +#> out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, +#> solution_type = solution_type, use_compiled = use_compiled, +#> method.ode = method.ode, atol = atol, rtol = rtol, +#> ...) +#> plot(0, type = "n", xlim = range(observed$time), +#> ylim = c(0, max(observed$value, na.rm = TRUE)), +#> xlab = "Time", ylab = "Observed") +#> col_obs <- pch_obs <- 1:length(obs_vars) +#> lty_obs <- rep(1, length(obs_vars)) +#> names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars +#> for (obs_var in obs_vars) { +#> points(subset(observed, name == obs_var, c(time, +#> value)), pch = pch_obs[obs_var], col = col_obs[obs_var]) +#> } +#> matlines(out_plot$time, out_plot[-1], col = col_obs, +#> lty = lty_obs) +#> legend("topright", inset = c(0.05, 0.05), legend = obs_vars, +#> col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) +#> } +#> assign("cost.old", mC$model, inherits = TRUE) +#> } +#> return(mC) +#> } +#> <environment: 0x3ff8420> +#> +#> $cost_notrans +#> function (P) +#> { +#> if (length(state.ini.optim) > 0) { +#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) +#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) +#> } +#> else { +#> odeini <- state.ini.fixed +#> names(odeini) <- state.ini.fixed.boxnames +#> } +#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], +#> parms.fixed) +#> out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, +#> use_compiled = use_compiled, method.ode = method.ode, +#> atol = atol, rtol = rtol, ...) +#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, +#> scaleVar = scaleVar) +#> return(mC) +#> } +#> <environment: 0x3ff8420> +#> +#> $hessian_notrans +#> parent_0 k_parent k_M1 k_M2 f_parent_to_M1 +#> parent_0 8.433594 -40.12785 -61.53042 -3406.469 461.2995 +#> k_parent -40.127847 19322.43697 3053.54654 3740.691 8966.4055 +#> k_M1 -61.530424 3053.54654 70106.05907 7274.316 -8169.6841 +#> k_M2 -3406.468786 3740.69112 7274.31610 12274341.595 -452294.7998 +#> f_parent_to_M1 461.299501 8966.40549 -8169.68407 -452294.800 61249.1755 +#> f_M1_to_M2 327.648696 2884.22668 17504.38651 -480941.198 43503.6440 +#> f_M1_to_M2 +#> parent_0 327.6487 +#> k_parent 2884.2267 +#> k_M1 17504.3865 +#> k_M2 -480941.1983 +#> f_parent_to_M1 43503.6440 +#> f_M1_to_M2 46258.9775 +#> +#> $start +#> value type +#> parent_0 101.3500 state +#> k_parent 0.1000 deparm +#> k_M1 0.1001 deparm +#> k_M2 0.1002 deparm +#> f_parent_to_M1 0.5000 deparm +#> f_M1_to_M2 0.5000 deparm +#> +#> $start_transformed +#> value lower upper +#> parent_0 101.350000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_M1 -2.301586 -Inf Inf +#> log_k_M2 -2.300587 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> f_M1_ilr_1 0.000000 -Inf Inf +#> +#> $fixed +#> value type +#> M1_0 0 state +#> M2_0 0 state +#> +#> $data +#> time variable observed predicted residual +#> 1 0 parent 101.5 1.020625e+02 -0.56248353 +#> 2 0 parent 101.2 1.020625e+02 -0.86248353 +#> 3 1 parent 53.9 4.872881e+01 5.17118695 +#> 4 1 parent 47.5 4.872881e+01 -1.22881305 +#> 5 3 parent 10.4 1.110773e+01 -0.70772795 +#> 6 3 parent 7.6 1.110773e+01 -3.50772795 +#> 7 7 parent 1.1 5.771704e-01 0.52282962 +#> 8 7 parent 0.3 5.771704e-01 -0.27717038 +#> 9 14 parent NA 3.263939e-03 NA +#> 10 14 parent 3.5 3.263939e-03 3.49673606 +#> 11 28 parent NA 1.044512e-07 NA +#> 12 28 parent 3.2 1.044512e-07 3.19999990 +#> 13 60 parent NA -1.053819e-10 NA +#> 14 60 parent NA -1.053819e-10 NA +#> 15 90 parent 0.6 -1.874889e-11 0.60000000 +#> 16 90 parent NA -1.874889e-11 NA +#> 17 120 parent NA -2.804801e-11 NA +#> 18 120 parent 3.5 -2.804801e-11 3.50000000 +#> 19 0 M1 NA 0.000000e+00 NA +#> 20 0 M1 NA 0.000000e+00 NA +#> 21 1 M1 36.4 3.478911e+01 1.61088639 +#> 22 1 M1 37.4 3.478911e+01 2.61088639 +#> 23 3 M1 34.3 3.937027e+01 -5.07026619 +#> 24 3 M1 39.8 3.937027e+01 0.42973381 +#> 25 7 M1 15.1 1.548714e+01 -0.38714436 +#> 26 7 M1 17.8 1.548714e+01 2.31285564 +#> 27 14 M1 5.8 1.995311e+00 3.80468869 +#> 28 14 M1 1.2 1.995311e+00 -0.79531131 +#> 29 28 M1 NA 3.034005e-02 NA +#> 30 28 M1 NA 3.034005e-02 NA +#> 31 60 M1 0.5 2.110651e-06 0.49999789 +#> 32 60 M1 NA 2.110651e-06 NA +#> 33 90 M1 NA 2.913252e-10 NA +#> 34 90 M1 3.2 2.913252e-10 3.20000000 +#> 35 120 M1 1.5 3.624738e-11 1.50000000 +#> 36 120 M1 0.6 3.624738e-11 0.60000000 +#> 37 0 M2 NA 0.000000e+00 NA +#> 38 0 M2 NA 0.000000e+00 NA +#> 39 1 M2 NA 4.454830e+00 NA +#> 40 1 M2 4.8 4.454830e+00 0.34517017 +#> 41 3 M2 20.9 2.152527e+01 -0.62526794 +#> 42 3 M2 19.3 2.152527e+01 -2.22526794 +#> 43 7 M2 42.0 4.192058e+01 0.07941701 +#> 44 7 M2 43.1 4.192058e+01 1.17941701 +#> 45 14 M2 49.4 4.556646e+01 3.83353798 +#> 46 14 M2 44.3 4.556646e+01 -1.26646202 +#> 47 28 M2 34.6 3.547275e+01 -0.87274743 +#> 48 28 M2 33.0 3.547275e+01 -2.47274743 +#> 49 60 M2 18.8 1.858163e+01 0.21837410 +#> 50 60 M2 17.6 1.858163e+01 -0.98162590 +#> 51 90 M2 10.6 1.012869e+01 0.47130583 +#> 52 90 M2 10.8 1.012869e+01 0.67130583 +#> 53 120 M2 9.8 5.521069e+00 4.27893112 +#> 54 120 M2 3.3 5.521069e+00 -2.22106888 +#> +#> $atol +#> [1] 1e-08 +#> +#> $rtol +#> [1] 1e-10 +#> +#> $weight.ini +#> [1] "none" +#> +#> $reweight.tol +#> [1] 1e-08 +#> +#> $reweight.max.iter +#> [1] 10 +#> +#> $bparms.optim +#> parent_0 k_parent k_M1 k_M2 f_parent_to_M1 +#> 102.0624835 0.7393147 0.2991566 0.0202267 0.7686858 +#> f_M1_to_M2 +#> 0.7229005 +#> +#> $bparms.fixed +#> M1_0 M2_0 +#> 0 0 +#> +#> $bparms.ode +#> k_parent f_parent_to_M1 k_M1 f_M1_to_M2 k_M2 +#> 0.7393147 0.7686858 0.2991566 0.7229005 0.0202267 +#> +#> $bparms.state +#> parent M1 M2 +#> 102.0625 0.0000 0.0000 +#> +#> $date +#> [1] "Fri Nov 18 15:20:48 2016" +#> +#> attr(,"class") +#> [1] "mkinfit" "modFit" </div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 00af0267..08fbf368 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'><-</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'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 17 22:57:06 2016 -#> Date of summary: Thu Nov 17 22:57:06 2016 +#> Date of fit: Fri Nov 18 15:20:49 2016 +#> Date of summary: Fri Nov 18 15:20:49 2016 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -158,7 +158,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.684 s +#> Fitted with method Port using 153 model solutions performed in 0.681 s #> #> Weighting: none #> @@ -222,10 +222,220 @@ #> DT50 DT90 #> parent 7.023 23.33 #> m1 131.761 437.70</div><div class='input'> -<span class='co'>## Not run: ------------------------------------</span> -<span class='co'># fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span> -<span class='co'># summary(fit.2, data=FALSE)</span> -<span class='co'>## ---------------------------------------------</span> + +<span class='no'>fit.2</span> <span class='kw'><-</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>)</div><div class='output co'>#> Model cost at call 1 : 18915.53 +#> Model cost at call 2 : 18915.53 +#> Model cost at call 7 : 10205.88 +#> Model cost at call 10 : 10205.05 +#> Model cost at call 13 : 8136.609 +#> Model cost at call 18 : 2504.352 +#> Model cost at call 20 : 2504.35 +#> Model cost at call 22 : 2504.285 +#> Model cost at call 25 : 1747.542 +#> Model cost at call 27 : 1745.941 +#> Model cost at call 29 : 1745.431 +#> Model cost at call 30 : 1341.034 +#> Model cost at call 34 : 1341.034 +#> Model cost at call 35 : 1032.65 +#> Model cost at call 39 : 1032.649 +#> Model cost at call 40 : 919.9522 +#> Model cost at call 42 : 919.952 +#> Model cost at call 44 : 919.9518 +#> Model cost at call 45 : 903.8272 +#> Model cost at call 47 : 903.827 +#> Model cost at call 49 : 903.8268 +#> Model cost at call 50 : 780.8699 +#> Model cost at call 52 : 780.8698 +#> Model cost at call 54 : 780.8697 +#> Model cost at call 55 : 734.3043 +#> Model cost at call 57 : 734.3036 +#> Model cost at call 60 : 717.8438 +#> Model cost at call 67 : 676.3908 +#> Model cost at call 68 : 676.3907 +#> Model cost at call 69 : 676.3906 +#> Model cost at call 71 : 676.3885 +#> Model cost at call 72 : 642.2738 +#> Model cost at call 73 : 642.2738 +#> Model cost at call 76 : 642.2738 +#> Model cost at call 77 : 604.7128 +#> Model cost at call 78 : 604.7126 +#> Model cost at call 82 : 560.1285 +#> Model cost at call 83 : 560.1285 +#> Model cost at call 86 : 560.1285 +#> Model cost at call 87 : 521.6932 +#> Model cost at call 88 : 521.6932 +#> Model cost at call 91 : 521.6931 +#> Model cost at call 92 : 453.6483 +#> Model cost at call 93 : 453.6483 +#> Model cost at call 96 : 453.6483 +#> Model cost at call 98 : 422.5498 +#> Model cost at call 102 : 422.5497 +#> Model cost at call 106 : 413.6426 +#> Model cost at call 108 : 413.6416 +#> Model cost at call 111 : 407.4639 +#> Model cost at call 113 : 407.4639 +#> Model cost at call 115 : 407.4639 +#> Model cost at call 116 : 403.6974 +#> Model cost at call 118 : 403.6973 +#> Model cost at call 120 : 403.6973 +#> Model cost at call 121 : 396.004 +#> Model cost at call 123 : 396.004 +#> Model cost at call 126 : 391.2533 +#> Model cost at call 128 : 391.2533 +#> Model cost at call 130 : 391.2533 +#> Model cost at call 131 : 388.4056 +#> Model cost at call 133 : 388.4056 +#> Model cost at call 135 : 388.4055 +#> Model cost at call 137 : 384.0739 +#> Model cost at call 139 : 384.0734 +#> Model cost at call 143 : 383.6352 +#> Model cost at call 145 : 383.635 +#> Model cost at call 148 : 381.1342 +#> Model cost at call 152 : 381.1342 +#> Model cost at call 153 : 380.1443 +#> Model cost at call 157 : 380.1443 +#> Model cost at call 158 : 378.5615 +#> Model cost at call 162 : 378.5614 +#> Model cost at call 164 : 378.4583 +#> Model cost at call 168 : 378.4583 +#> Model cost at call 169 : 377.7047 +#> Model cost at call 173 : 377.7047 +#> Model cost at call 175 : 377.7042 +#> Model cost at call 178 : 377.7042 +#> Model cost at call 179 : 377.7042 +#> Model cost at call 180 : 377.1553 +#> Model cost at call 182 : 377.1553 +#> Model cost at call 183 : 377.1553 +#> Model cost at call 185 : 377.0866 +#> Model cost at call 187 : 377.0866 +#> Model cost at call 190 : 377.0288 +#> Model cost at call 194 : 377.0288 +#> Model cost at call 196 : 376.9814 +#> Model cost at call 200 : 376.9814 +#> Model cost at call 201 : 376.9488 +#> Model cost at call 203 : 376.9488 +#> Model cost at call 205 : 376.9488 +#> Model cost at call 206 : 376.9184 +#> Model cost at call 208 : 376.9184 +#> Model cost at call 211 : 376.9095 +#> Model cost at call 213 : 376.9095 +#> Model cost at call 215 : 376.9095 +#> Model cost at call 216 : 376.901 +#> Model cost at call 218 : 376.901 +#> Model cost at call 221 : 376.8936 +#> Model cost at call 225 : 376.8936 +#> Model cost at call 226 : 376.8848 +#> Model cost at call 227 : 376.8608 +#> Model cost at call 228 : 376.7665 +#> Model cost at call 229 : 376.4162 +#> Model cost at call 230 : 375.4439 +#> Model cost at call 235 : 375.4439 +#> Model cost at call 237 : 375.2281 +#> Model cost at call 241 : 375.2281 +#> Model cost at call 242 : 374.3381 +#> Model cost at call 244 : 374.3381 +#> Model cost at call 251 : 374.2632 +#> Model cost at call 253 : 374.2632 +#> Model cost at call 256 : 374.2391 +#> Model cost at call 257 : 374.2247 +#> Model cost at call 259 : 374.2247 +#> Model cost at call 261 : 374.2247 +#> Model cost at call 263 : 374.2024 +#> Model cost at call 266 : 374.2024 +#> Model cost at call 270 : 374.1952 +#> Model cost at call 274 : 374.1952 +#> Model cost at call 275 : 374.186 +#> Model cost at call 279 : 374.186 +#> Model cost at call 280 : 374.1724 +#> Model cost at call 281 : 374.156 +#> Model cost at call 282 : 374.0763 +#> Model cost at call 283 : 373.7692 +#> Model cost at call 284 : 372.729 +#> Model cost at call 285 : 371.4251 +#> Model cost at call 287 : 371.4251 +#> Model cost at call 290 : 371.2142 +#> Model cost at call 291 : 371.2142 +#> Model cost at call 292 : 371.2142 +#> Model cost at call 295 : 371.2134 +#> Model cost at call 298 : 371.2134 +#> Model cost at call 300 : 371.2134 +#> Model cost at call 309 : 371.2134 +#> Model cost at call 320 : 371.2134 +#> Optimisation by method Port successfully terminated.</div><div class='input'><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'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:20:51 2016 +#> Date of summary: Fri Nov 18 15:20:51 2016 +#> +#> Equations: +#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent +#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 327 model solutions performed in 1.34 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent_sink 0.1000 deparm +#> k_parent_m1 0.1001 deparm +#> k_m1_sink 0.1002 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.7500 -Inf Inf +#> k_parent_sink 0.1000 0 Inf +#> k_parent_m1 0.1001 0 Inf +#> k_m1_sink 0.1002 0 Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.600000 1.6140000 96.330000 1.029e+02 +#> k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02 +#> k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02 +#> k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03 +#> +#> Parameter correlation: +#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> parent_0 1.00000 0.6075 -0.06625 -0.1701 +#> k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 +#> k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 +#> k_m1_sink -0.17006 -0.6253 0.47164 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02 +#> k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02 +#> k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.827 3 6 +#> m1 4.490 1 9 +#> +#> Resulting formation fractions: +#> ff +#> parent_sink 0.4855 +#> parent_m1 0.5145 +#> m1_sink 1.0000 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70</div><div class='input'> <span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> <span class='fu'>names</span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start</span>) @@ -234,29 +444,286 @@ <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink #> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> -<span class='co'>## Not run: ------------------------------------</span> -<span class='co'># # The case of formation fractions</span> -<span class='co'># SFO_SFO.ff <- mkinmod(</span> -<span class='co'># parent = list(type = "SFO", to = "m1", sink = TRUE),</span> -<span class='co'># m1 = list(type = "SFO"),</span> -<span class='co'># use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span> -<span class='co'># summary(fit.ff, data = FALSE)</span> -<span class='co'># initials <- c("f_parent_to_m1" = 0.5)</span> -<span class='co'># transformed <- transform_odeparms(initials, SFO_SFO.ff)</span> -<span class='co'># backtransform_odeparms(transformed, SFO_SFO.ff)</span> -<span class='co'># </span> -<span class='co'># # And without sink</span> -<span class='co'># SFO_SFO.ff.2 <- mkinmod(</span> -<span class='co'># parent = list(type = "SFO", to = "m1", sink = FALSE),</span> -<span class='co'># m1 = list(type = "SFO"),</span> -<span class='co'># use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># </span> -<span class='co'># fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)</span> -<span class='co'># summary(fit.ff.2, data = FALSE)</span> -<span class='co'>## ---------------------------------------------</span></div></pre> + +<span class='co'># The case of formation fractions</span> +<span class='no'>SFO_SFO.ff</span> <span class='kw'><-</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), + <span class='kw'>m1</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>fit.ff</span> <span class='kw'><-</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>)</div><div class='output co'>#> Model cost at call 1 : 15156.12 +#> Model cost at call 2 : 15156.12 +#> Model cost at call 6 : 8243.644 +#> Model cost at call 12 : 6290.714 +#> Model cost at call 13 : 6290.684 +#> Model cost at call 15 : 6290.453 +#> Model cost at call 18 : 1700.75 +#> Model cost at call 20 : 1700.612 +#> Model cost at call 24 : 1190.923 +#> Model cost at call 26 : 1190.922 +#> Model cost at call 29 : 1017.417 +#> Model cost at call 31 : 1017.417 +#> Model cost at call 33 : 1017.416 +#> Model cost at call 34 : 644.0471 +#> Model cost at call 36 : 644.0469 +#> Model cost at call 38 : 644.0468 +#> Model cost at call 39 : 590.5024 +#> Model cost at call 41 : 590.5021 +#> Model cost at call 43 : 590.5015 +#> Model cost at call 44 : 543.2187 +#> Model cost at call 45 : 543.2183 +#> Model cost at call 46 : 543.2182 +#> Model cost at call 50 : 391.348 +#> Model cost at call 51 : 391.3479 +#> Model cost at call 56 : 386.4789 +#> Model cost at call 58 : 386.4789 +#> Model cost at call 60 : 386.4779 +#> Model cost at call 61 : 384.0686 +#> Model cost at call 63 : 384.0686 +#> Model cost at call 66 : 382.7812 +#> Model cost at call 68 : 382.7812 +#> Model cost at call 70 : 382.7812 +#> Model cost at call 71 : 378.9272 +#> Model cost at call 73 : 378.9272 +#> Model cost at call 75 : 378.9272 +#> Model cost at call 76 : 377.4846 +#> Model cost at call 78 : 377.4846 +#> Model cost at call 81 : 375.9738 +#> Model cost at call 83 : 375.9738 +#> Model cost at call 86 : 375.3387 +#> Model cost at call 88 : 375.3387 +#> Model cost at call 91 : 374.5774 +#> Model cost at call 93 : 374.5774 +#> Model cost at call 95 : 374.5774 +#> Model cost at call 96 : 373.5447 +#> Model cost at call 100 : 373.5446 +#> Model cost at call 102 : 373.2643 +#> Model cost at call 104 : 373.2643 +#> Model cost at call 107 : 372.6799 +#> Model cost at call 111 : 372.6798 +#> Model cost at call 114 : 372.6325 +#> Model cost at call 116 : 372.6325 +#> Model cost at call 119 : 372.6159 +#> Model cost at call 121 : 372.6159 +#> Model cost at call 123 : 372.6159 +#> Model cost at call 124 : 372.5845 +#> Model cost at call 126 : 372.5845 +#> Model cost at call 129 : 372.5375 +#> Model cost at call 130 : 372.4771 +#> Model cost at call 131 : 372.2008 +#> Model cost at call 132 : 371.4923 +#> Model cost at call 134 : 371.4923 +#> Model cost at call 137 : 371.3022 +#> Model cost at call 139 : 371.3022 +#> Model cost at call 143 : 371.2271 +#> Model cost at call 144 : 371.2271 +#> Model cost at call 148 : 371.2202 +#> Model cost at call 149 : 371.215 +#> Model cost at call 152 : 371.215 +#> Model cost at call 154 : 371.2136 +#> Model cost at call 155 : 371.2136 +#> Model cost at call 156 : 371.2136 +#> Model cost at call 160 : 371.2134 +#> Model cost at call 164 : 371.2134 +#> Model cost at call 167 : 371.2134 +#> Optimisation by method Port successfully terminated.</div><div class='input'><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'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:20:52 2016 +#> Date of summary: Fri Nov 18 15:20:52 2016 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 185 model solutions performed in 0.764 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.60000 1.61400 96.3300 102.9000 +#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 +#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 +#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5178 -0.1701 -0.5489 +#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 +#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 +#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent 0.098700 23.880 5.701e-24 0.090660 1.074e-01 +#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> f_parent_to_m1 0.514500 22.490 4.374e-23 0.468100 5.606e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.459 2 7 +#> m1 4.690 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5145 +#> parent_sink 0.4855 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) +<span class='no'>transformed</span> <span class='kw'><-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>) +<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#> f_parent_to_m1 +#> 0.5 </div><div class='input'> +<span class='co'># And without sink</span> +<span class='no'>SFO_SFO.ff.2</span> <span class='kw'><-</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), + <span class='kw'>m1</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + +<span class='no'>fit.ff.2</span> <span class='kw'><-</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>)</div><div class='output co'>#> Model cost at call 1 : 12435.14 +#> Model cost at call 2 : 12435.14 +#> Model cost at call 5 : 8276.306 +#> Model cost at call 6 : 8276.294 +#> Model cost at call 7 : 8275.676 +#> Model cost at call 9 : 5256.953 +#> Model cost at call 11 : 5256.951 +#> Model cost at call 12 : 5256.943 +#> Model cost at call 14 : 4469.745 +#> Model cost at call 18 : 4462.927 +#> Model cost at call 21 : 4462.925 +#> Model cost at call 22 : 4376.059 +#> Model cost at call 24 : 4376.058 +#> Model cost at call 27 : 4366.956 +#> Model cost at call 29 : 4366.956 +#> Model cost at call 31 : 4365.275 +#> Model cost at call 33 : 4365.275 +#> Model cost at call 35 : 4351.877 +#> Model cost at call 37 : 4351.877 +#> Model cost at call 39 : 4338.109 +#> Model cost at call 41 : 4338.109 +#> Model cost at call 43 : 4297.053 +#> Model cost at call 44 : 4218.591 +#> Model cost at call 45 : 3940.397 +#> Model cost at call 46 : 3690.395 +#> Model cost at call 48 : 3690.395 +#> Model cost at call 49 : 3690.385 +#> Model cost at call 50 : 3038.366 +#> Model cost at call 53 : 3038.365 +#> Model cost at call 54 : 2637.866 +#> Model cost at call 57 : 2637.865 +#> Model cost at call 59 : 2588.01 +#> Model cost at call 60 : 2588.009 +#> Model cost at call 63 : 2576.742 +#> Model cost at call 66 : 2576.742 +#> Model cost at call 67 : 2574 +#> Model cost at call 68 : 2574 +#> Model cost at call 69 : 2574 +#> Model cost at call 71 : 2569.76 +#> Model cost at call 73 : 2569.76 +#> Model cost at call 74 : 2569.76 +#> Model cost at call 75 : 2569.403 +#> Model cost at call 76 : 2569.403 +#> Model cost at call 79 : 2569.4 +#> Model cost at call 80 : 2569.4 +#> Model cost at call 81 : 2569.4 +#> Model cost at call 83 : 2569.4 +#> Model cost at call 86 : 2569.4 +#> Model cost at call 90 : 2569.4 +#> Model cost at call 99 : 2569.4 +#> Model cost at call 100 : 2569.4 +#> Optimisation by method Port successfully terminated.</div><div class='input'><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'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 15:20:52 2016 +#> Date of summary: Fri Nov 18 15:20:52 2016 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 104 model solutions performed in 0.44 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 84.790 2.96500 78.78 90.800 +#> log_k_parent -2.756 0.08088 -2.92 -2.593 +#> log_k_m1 -4.214 0.11150 -4.44 -3.988 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 +#> parent_0 1.0000 0.11059 0.46156 +#> log_k_parent 0.1106 1.00000 0.06274 +#> log_k_m1 0.4616 0.06274 1.00000 +#> +#> Residual standard error: 8.333 on 37 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000 +#> k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483 +#> k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 19.66 3 16 +#> parent 17.56 2 7 +#> m1 18.71 1 9 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 10.91 36.25 +#> m1 46.89 155.75</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index f2df212f..aa38b462 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -277,9 +277,9 @@ FOMC_SFO <- mkinmod( # Fit the model to the FOCUS example dataset D using defaults fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D) # Use starting parameters from parent only FOMC fit -fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE) +fit.FOMC = mkinfit("FOMC", FOCUS_2006_D) fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, - parms.ini = fit.FOMC$bparms.ode, plot=TRUE) + parms.ini = fit.FOMC$bparms.ode) # Use stepwise fitting, using optimised parameters from parent only fit, SFORB SFORB_SFO <- mkinmod( diff --git a/man/schaefer07_complex_case.Rd b/man/schaefer07_complex_case.Rd index 01b27e3a..c666d08b 100644 --- a/man/schaefer07_complex_case.Rd +++ b/man/schaefer07_complex_case.Rd @@ -36,6 +36,6 @@ model <- mkinmod( B1 = list(type = "SFO"),
C1 = list(type = "SFO"),
A2 = list(type = "SFO"), use_of_ff = "max")
-\dontrun{mkinfit(model, data, plot=TRUE)}
+\dontrun{mkinfit(model, data)}
}
\keyword{datasets}
|
