diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 11:38:43 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 11:38:43 +0200 |
| commit | c4a35c0e141a4bb05ba508914bebdc2884109e76 (patch) | |
| tree | 81464f3e17e683dfc7614dadf0899850517954f7 /docs | |
| parent | dd65f3503e9d091c82aedcf91635fcf40f778bf9 (diff) | |
Exclude more example code from CRAN checks
to avoid NOTES about long execution times.
Static documentation rebuilt by pkgdown with run_dont_run = TRUE
Diffstat (limited to 'docs')
61 files changed, 1335 insertions, 227 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 195570b1..3ed8004e 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index f7bbf961..cc069d1a 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -110,15 +110,15 @@ <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 06:39:28 2018 -## Date of summary: Fri Sep 14 06:39:28 2018 +## Date of fit: Fri Sep 14 11:36:13 2018 +## Date of summary: Fri Sep 14 11:36:13 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.091 s +## Fitted with method Port using 37 model solutions performed in 0.085 s ## ## Weighting: none ## @@ -201,15 +201,15 @@ <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 06:39:30 2018 -## Date of summary: Fri Sep 14 06:39:30 2018 +## Date of fit: Fri Sep 14 11:36:14 2018 +## Date of summary: Fri Sep 14 11:36:14 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.333 s +## Fitted with method Port using 611 model solutions performed in 1.405 s ## ## Weighting: none ## @@ -296,15 +296,15 @@ <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 06:39:30 2018 -## Date of summary: Fri Sep 14 06:39:30 2018 +## Date of fit: Fri Sep 14 11:36:15 2018 +## Date of summary: Fri Sep 14 11:36:15 2018 ## ## 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 0.172 s +## Fitted with method Port using 81 model solutions performed in 0.188 s ## ## Weighting: none ## @@ -367,8 +367,8 @@ <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 06:39:31 2018 -## Date of summary: Fri Sep 14 06:39:31 2018 +## Date of fit: Fri Sep 14 11:36:16 2018 +## Date of summary: Fri Sep 14 11:36:16 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -377,7 +377,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.742 s +## Fitted with method Port using 336 model solutions performed in 0.833 s ## ## Weighting: none ## @@ -459,8 +459,8 @@ <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 06:39:32 2018 -## Date of summary: Fri Sep 14 06:39:32 2018 +## Date of fit: Fri Sep 14 11:36:17 2018 +## Date of summary: Fri Sep 14 11:36:17 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -469,7 +469,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.312 s +## Fitted with method Port using 137 model solutions performed in 0.335 s ## ## Weighting: none ## @@ -560,15 +560,15 @@ <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><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>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 06:39:33 2018 -## Date of summary: Fri Sep 14 06:39:33 2018 +## Date of fit: Fri Sep 14 11:36:18 2018 +## Date of summary: Fri Sep 14 11:36:18 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.097 s +## Fitted with method Port using 46 model solutions performed in 0.099 s ## ## Weighting: none ## @@ -620,15 +620,15 @@ <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><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>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.3 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 06:39:33 2018 -## Date of summary: Fri Sep 14 06:39:33 2018 +## Date of fit: Fri Sep 14 11:36:18 2018 +## Date of summary: Fri Sep 14 11:36:18 2018 ## ## 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 0.143 s +## Fitted with method Port using 66 model solutions performed in 0.152 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html index 9753abd6..ff0bd537 100644 --- a/docs/articles/FOCUS_Z.html +++ b/docs/articles/FOCUS_Z.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index d93fe9e1..a6598fd4 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -125,9 +125,9 @@ <a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.110 1.000 2.108 0 -## 1 deSolve, not compiled 3 16.442 7.792 16.433 0 -## 2 Eigenvalue based 3 2.593 1.229 2.592 0 +## 3 deSolve, compiled 3 2.205 1.000 2.203 0 +## 1 deSolve, not compiled 3 17.206 7.803 17.196 0 +## 2 Eigenvalue based 3 2.829 1.283 2.828 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -156,8 +156,8 @@ <a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 3.781 1.000 3.778 0 -## 1 deSolve, not compiled 3 34.742 9.189 34.725 0 +## 2 deSolve, compiled 3 3.874 1.000 3.866 0.004 +## 1 deSolve, not compiled 3 35.712 9.218 35.692 0.000 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> diff --git a/docs/articles/index.html b/docs/articles/index.html index dcaf33b8..e20ad2d4 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 4d62b50d..bc76c2cf 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 2952e887..a2f7f72a 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/authors.html b/docs/authors.html index 20849b4a..61cf4fbc 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/index.html b/docs/index.html index ba838a39..5a3864bf 100644 --- a/docs/index.html +++ b/docs/index.html @@ -36,7 +36,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/news/index.html b/docs/news/index.html index b76ca884..6cc7351d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -117,12 +117,20 @@ </div> - <div id="mkin-0-9-47-3-2018-09-13" class="section level1"> + <div id="mkin-0-9-47-4-2018-09-14" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-47-3-2018-09-13" class="anchor"></a>mkin 0.9.47.3 (2018-09-13)<small> Unreleased </small> +<a href="#mkin-0-9-47-4-2018-09-14" class="anchor"></a>mkin 0.9.47.4 (2018-09-14)<small> Unreleased </small> </h1> <ul> -<li><p>‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’</p></li> +<li>Exclude more example code from testing on CRAN to avoid NOTES from long execution times</li> +</ul> +</div> + <div id="mkin-0-9-47-3-not-released-to-cran" class="section level1"> +<h1 class="page-header"> +<a href="#mkin-0-9-47-3-not-released-to-cran" class="anchor"></a>mkin 0.9.47.3 (not released to CRAN)<small> Unreleased </small> +</h1> +<ul> +<li><p>‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’</p></li> <li><p>Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’</p></li> </ul> </div> @@ -648,7 +656,8 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0-9-47-3-2018-09-13">0.9.47.3</a></li> + <li><a href="#mkin-0-9-47-4-2018-09-14">0.9.47.4</a></li> + <li><a href="#mkin-0-9-47-3-not-released-to-cran">0.9.47.3</a></li> <li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li> <li><a href="#mkin-0-9-47-1-2018-02-06">0.9.47.1</a></li> <li><a href="#mkin-0-9-46-3-2017-11-16">0.9.46.3</a></li> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 22709123..2f714f2c 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 94c4d336..922479a1 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.165 0.000 0.165 +#> 0.164 0.000 0.164 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bd36378> -#> <environment: 0x55555bd42bc8> +#> <bytecode: 0x55555bd535f0> +#> <environment: 0x55555bd1c770> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555c995188> -#> <environment: 0x55555bd42bc8> +#> <bytecode: 0x55555c9c70f8> +#> <environment: 0x55555bd1c770> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,10 +558,10 @@ #> 99.17407 #> #> $date -#> [1] "Fri Sep 14 06:38:57 2018" +#> [1] "Fri Sep 14 11:34:38 2018" #> #> $version -#> [1] "0.9.47.3" +#> [1] "0.9.47.4" #> #> $Rversion #> [1] "3.5.1" diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 2b6886ff..bea35e09 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 73b2450b..9122a546 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index e5621863..3d5677e8 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 872d68a9..524fbd79 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 232be6f3..a0bcc65d 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index c4f3158d..10f33260 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -65,7 +65,7 @@ The form given here differs slightly from the original reference by Gustafson </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 8f1ff8de..cb9eb353 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index ae09fcf7..23f82d13 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/SFO.solution-1.png b/docs/reference/SFO.solution-1.png Binary files differnew file mode 100644 index 00000000..9e6bd786 --- /dev/null +++ b/docs/reference/SFO.solution-1.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index f4e8eb42..087ff46f 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -160,9 +160,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> -<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>) -<span class='co'># }</span></pre> + <pre class="examples"><div class='input'> </div><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><div class='img'><img src='SFO.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/SFORB.solution-1.png b/docs/reference/SFORB.solution-1.png Binary files differnew file mode 100644 index 00000000..6739fe6b --- /dev/null +++ b/docs/reference/SFORB.solution-1.png diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index e568bd5a..61989c40 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -177,9 +177,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> -<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>) -<span class='co'># }</span></pre> + <pre class="examples"><div class='input'> </div><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><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 99871884..b3324064 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index e39d1c15..fdf465a5 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -64,7 +64,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index a5c63aeb..bddbab1a 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index ec49468a..e780d26b 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index af7642e6..185991d6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 8d31b0d2..ef7209bf 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -65,7 +65,7 @@ guidance." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index cea92155..ac2adf1e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -155,19 +155,11 @@ <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'> </div><span class='co'># NOT RUN {</span> - <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>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <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>) - -<span class='co'># }</span><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span> - <span class='co'># 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 used for fitting: 0.9.47.3 + <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'> </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>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <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 used for fitting: 0.9.47.4 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 06:39:07 2018 -#> Date of summary: Fri Sep 14 06:39:07 2018 +#> Date of fit: Fri Sep 14 11:34:50 2018 +#> Date of summary: Fri Sep 14 11:34:50 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -177,7 +169,96 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.423 s +#> Fitted with method Port using 574 model solutions performed in 3.33 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 -25.0800 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 1.286e-11 4.575e-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 3.175e-11 +#> 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 convergence, no covariance matrix ...</span> + <span class='co'># 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 used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:34:51 2018 +#> Date of summary: Fri Sep 14 11:34:51 2018 +#> +#> 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 246 model solutions performed in 1.417 s #> #> Weighting: none #> @@ -257,7 +338,7 @@ #> DT50 DT90 #> T245 15.982 53.091 #> phenol 1.711 5.685 -#> anisole 103.784 344.763</div></pre> +#> anisole 103.784 344.763</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/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 8d53bc1b..b83287ff 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index e7342cee..e2b4ef61 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 16086f3e..c77945b9 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index c8fd8272..a18b226e 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -62,7 +62,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -178,8 +178,8 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p> <span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.0640 4 15 #> parent 0.0646 2 7 -#> m1 0.0469 2 8</div><div class='input'><span class='no'>fit_FOCUS_E</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_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df +#> m1 0.0469 2 8</div><div class='input'> <span class='no'>fit_FOCUS_E</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_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.1544 4 13 #> parent 0.1659 2 7 #> m1 0.1095 2 6</div></pre> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index b1c42168..13029e91 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -432,17 +432,17 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <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 used for fitting: 0.9.47.3 +<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 06:39:09 2018 -#> Date of summary: Fri Sep 14 06:39:09 2018 +#> Date of fit: Fri Sep 14 11:34:54 2018 +#> Date of summary: Fri Sep 14 11:34:54 2018 #> #> 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 0.157 s +#> Fitted with method Port using 64 model solutions performed in 0.141 s #> #> Weighting: none #> @@ -511,7 +511,7 @@ <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 verstrichen -#> 0.892 0.000 0.892 </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 +#> 0.906 0.000 0.907 </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 @@ -523,19 +523,86 @@ #> DT50 DT90 #> parent 7.022929 23.32967 #> m1 131.760712 437.69961 -#> </div><span class='co'># NOT RUN {</span> -<span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</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>))) -<span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>) -<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>) -<span class='co'># }</span><div class='input'> + <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 : 874.2615 +#> Model cost at call 33 : 874.2611 +#> Model cost at call 35 : 616.2377 +#> Model cost at call 37 : 616.2372 +#> Model cost at call 40 : 467.4386 +#> Model cost at call 42 : 467.4381 +#> 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 : 371.4071 +#> Model cost at call 106 : 371.4071 +#> Model cost at call 107 : 371.4071 +#> 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 146 : 371.2134 +#> Optimisation by method Port successfully terminated. +#> User System verstrichen +#> 0.714 0.000 0.715 </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 131.760711 437.69961 +#> </div><div class='input'> # Use stepwise fitting, using optimised parameters from parent only fit, FOMC -</div><span class='co'># NOT RUN {</span> -<span class='no'>FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( +</div><div class='input'><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>)) -<span class='co'># Fit the model to the FOCUS example dataset D using defaults</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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -545,40 +612,733 @@ <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>)) -<span class='co'># Fit the model to the FOCUS example dataset D using defaults</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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='co'># }</span><div class='input'> -</div><span class='co'># NOT RUN {</span> -<span class='co'># Weighted fits, including IRLS</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>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='input'> +</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>) -<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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.noweight</span>) -<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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.irls</span>) -<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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>) -<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>, + <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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:05 2018 +#> Date of summary: Fri Sep 14 11:35:05 2018 +#> +#> 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 186 model solutions performed in 0.763 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 5.700e-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 4.375e-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 99.59848 -1.385e-01 +#> 0 parent 102.04 99.59848 2.442e+00 +#> 1 parent 93.50 90.23787 3.262e+00 +#> 1 parent 92.50 90.23787 2.262e+00 +#> 3 parent 63.23 74.07319 -1.084e+01 +#> 3 parent 68.99 74.07319 -5.083e+00 +#> 7 parent 52.32 49.91206 2.408e+00 +#> 7 parent 55.13 49.91206 5.218e+00 +#> 14 parent 27.27 25.01257 2.257e+00 +#> 14 parent 26.64 25.01257 1.627e+00 +#> 21 parent 11.50 12.53462 -1.035e+00 +#> 21 parent 11.64 12.53462 -8.946e-01 +#> 35 parent 2.85 3.14787 -2.979e-01 +#> 35 parent 2.91 3.14787 -2.379e-01 +#> 50 parent 0.69 0.71624 -2.624e-02 +#> 50 parent 0.63 0.71624 -8.624e-02 +#> 75 parent 0.05 0.06074 -1.074e-02 +#> 75 parent 0.06 0.06074 -7.381e-04 +#> 0 m1 0.00 0.00000 0.000e+00 +#> 0 m1 0.00 0.00000 0.000e+00 +#> 1 m1 4.84 4.80296 3.704e-02 +#> 1 m1 5.64 4.80296 8.370e-01 +#> 3 m1 12.91 13.02400 -1.140e-01 +#> 3 m1 12.96 13.02400 -6.400e-02 +#> 7 m1 22.97 25.04476 -2.075e+00 +#> 7 m1 24.47 25.04476 -5.748e-01 +#> 14 m1 41.69 36.69002 5.000e+00 +#> 14 m1 33.21 36.69002 -3.480e+00 +#> 21 m1 44.37 41.65310 2.717e+00 +#> 21 m1 46.44 41.65310 4.787e+00 +#> 35 m1 41.22 43.31312 -2.093e+00 +#> 35 m1 37.95 43.31312 -5.363e+00 +#> 50 m1 41.19 41.21831 -2.831e-02 +#> 50 m1 40.01 41.21831 -1.208e+00 +#> 75 m1 40.09 36.44703 3.643e+00 +#> 75 m1 33.85 36.44703 -2.597e+00 +#> 100 m1 31.04 31.98163 -9.416e-01 +#> 100 m1 33.13 31.98163 1.148e+00 +#> 120 m1 25.15 28.78984 -3.640e+00 +#> 120 m1 33.31 28.78984 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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:07 2018 +#> Date of summary: Fri Sep 14 11:35:07 2018 +#> +#> 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 551 model solutions performed in 2.297 s +#> +#> Weighting: none +#> +#> Iterative reweighting with method obs +#> Final mean squared residuals of observed variables: +#> parent m1 +#> 11.573407 7.407845 +#> +#> 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 -2.219 +#> 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 8.185e-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 8.486e-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 132.282 439.43 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.67218 -2.122e-01 3.402 +#> 0 parent 102.04 99.67218 2.368e+00 3.402 +#> 1 parent 93.50 90.27153 3.228e+00 3.402 +#> 1 parent 92.50 90.27153 2.228e+00 3.402 +#> 3 parent 63.23 74.04648 -1.082e+01 3.402 +#> 3 parent 68.99 74.04648 -5.056e+00 3.402 +#> 7 parent 52.32 49.82092 2.499e+00 3.402 +#> 7 parent 55.13 49.82092 5.309e+00 3.402 +#> 14 parent 27.27 24.90288 2.367e+00 3.402 +#> 14 parent 26.64 24.90288 1.737e+00 3.402 +#> 21 parent 11.50 12.44765 -9.476e-01 3.402 +#> 21 parent 11.64 12.44765 -8.076e-01 3.402 +#> 35 parent 2.85 3.11002 -2.600e-01 3.402 +#> 35 parent 2.91 3.11002 -2.000e-01 3.402 +#> 50 parent 0.69 0.70374 -1.374e-02 3.402 +#> 50 parent 0.63 0.70374 -7.374e-02 3.402 +#> 75 parent 0.05 0.05913 -9.134e-03 3.402 +#> 75 parent 0.06 0.05913 8.662e-04 3.402 +#> 0 m1 0.00 0.00000 0.000e+00 2.722 +#> 0 m1 0.00 0.00000 0.000e+00 2.722 +#> 1 m1 4.84 4.81328 2.672e-02 2.722 +#> 1 m1 5.64 4.81328 8.267e-01 2.722 +#> 3 m1 12.91 13.04779 -1.378e-01 2.722 +#> 3 m1 12.96 13.04779 -8.779e-02 2.722 +#> 7 m1 22.97 25.07615 -2.106e+00 2.722 +#> 7 m1 24.47 25.07615 -6.062e-01 2.722 +#> 14 m1 41.69 36.70729 4.983e+00 2.722 +#> 14 m1 33.21 36.70729 -3.497e+00 2.722 +#> 21 m1 44.37 41.65050 2.720e+00 2.722 +#> 21 m1 46.44 41.65050 4.790e+00 2.722 +#> 35 m1 41.22 43.28866 -2.069e+00 2.722 +#> 35 m1 37.95 43.28866 -5.339e+00 2.722 +#> 50 m1 41.19 41.19339 -3.386e-03 2.722 +#> 50 m1 40.01 41.19339 -1.183e+00 2.722 +#> 75 m1 40.09 36.43820 3.652e+00 2.722 +#> 75 m1 33.85 36.43820 -2.588e+00 2.722 +#> 100 m1 31.04 31.98971 -9.497e-01 2.722 +#> 100 m1 33.13 31.98971 1.140e+00 2.722 +#> 120 m1 25.15 28.80898 -3.659e+00 2.722 +#> 120 m1 33.31 28.80898 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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:08 2018 +#> Date of summary: Fri Sep 14 11:35:08 2018 +#> +#> 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 0.618 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 99.73057 -0.270570 +#> 0 parent 102.04 99.73057 2.309430 +#> 1 parent 93.50 90.29805 3.201945 +#> 1 parent 92.50 90.29805 2.201945 +#> 3 parent 63.23 74.02503 -10.795028 +#> 3 parent 68.99 74.02503 -5.035028 +#> 7 parent 52.32 49.74838 2.571618 +#> 7 parent 55.13 49.74838 5.381618 +#> 14 parent 27.27 24.81588 2.454124 +#> 14 parent 26.64 24.81588 1.824124 +#> 21 parent 11.50 12.37885 -0.878849 +#> 21 parent 11.64 12.37885 -0.738849 +#> 35 parent 2.85 3.08022 -0.230219 +#> 35 parent 2.91 3.08022 -0.170219 +#> 50 parent 0.69 0.69396 -0.003958 +#> 50 parent 0.63 0.69396 -0.063958 +#> 75 parent 0.05 0.05789 -0.007888 +#> 75 parent 0.06 0.05789 0.002112 +#> 0 m1 0.00 0.00000 0.000000 +#> 0 m1 0.00 0.00000 0.000000 +#> 1 m1 4.84 4.82149 0.018512 +#> 1 m1 5.64 4.82149 0.818512 +#> 3 m1 12.91 13.06669 -0.156692 +#> 3 m1 12.96 13.06669 -0.106692 +#> 7 m1 22.97 25.10106 -2.131058 +#> 7 m1 24.47 25.10106 -0.631058 +#> 14 m1 41.69 36.72092 4.969077 +#> 14 m1 33.21 36.72092 -3.510923 +#> 21 m1 44.37 41.64835 2.721647 +#> 21 m1 46.44 41.64835 4.791647 +#> 35 m1 41.22 43.26923 -2.049225 +#> 35 m1 37.95 43.26923 -5.319225 +#> 50 m1 41.19 41.17364 0.016361 +#> 50 m1 40.01 41.17364 -1.163639 +#> 75 m1 40.09 36.43122 3.658776 +#> 75 m1 33.85 36.43122 -2.581224 +#> 100 m1 31.04 31.99612 -0.956124 +#> 100 m1 33.13 31.99612 1.133876 +#> 120 m1 25.15 28.82413 -3.674128 +#> 120 m1 33.31 28.82413 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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.value</span>) -<span class='co'># }</span><div class='input'> -</div><span class='co'># NOT RUN {</span> -<span class='co'># Manual weighting</span> +<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:09 2018 +#> Date of summary: Fri Sep 14 11:35:09 2018 +#> +#> 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 0.704 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 0.6843 -0.08687 -0.7564 +#> log_k_parent 0.68435 1.0000 -0.12695 -0.5812 +#> log_k_m1 -0.08687 -0.1269 1.00000 0.5195 +#> f_parent_ilr_1 -0.75644 -0.5812 0.51952 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 -0.195715 99.46 +#> 0 parent 102.04 99.65571 2.384285 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'> +</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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man</span>) -<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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, +<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:10 2018 +#> Date of summary: Fri Sep 14 11:35:10 2018 +#> +#> 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 270 model solutions performed in 1.109 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 -0.09456 -0.3351 +#> log_k_parent 0.53123 1.0000 -0.17800 -0.3360 +#> log_k_m1 -0.09456 -0.1780 1.00000 0.7616 +#> f_parent_ilr_1 -0.33514 -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 2.221e-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 99.48598 -0.025979 1 +#> 0 parent 102.04 99.48598 2.554021 1 +#> 1 parent 93.50 90.18612 3.313880 1 +#> 1 parent 92.50 90.18612 2.313880 1 +#> 3 parent 63.23 74.11316 -10.883163 1 +#> 3 parent 68.99 74.11316 -5.123163 1 +#> 7 parent 52.32 50.05030 2.269705 1 +#> 7 parent 55.13 50.05030 5.079705 1 +#> 14 parent 27.27 25.17975 2.090250 1 +#> 14 parent 26.64 25.17975 1.460250 1 +#> 21 parent 11.50 12.66765 -1.167654 1 +#> 21 parent 11.64 12.66765 -1.027654 1 +#> 35 parent 2.85 3.20616 -0.356164 1 +#> 35 parent 2.91 3.20616 -0.296164 1 +#> 50 parent 0.69 0.73562 -0.045619 1 +#> 50 parent 0.63 0.73562 -0.105619 1 +#> 75 parent 0.05 0.06326 -0.013256 1 +#> 75 parent 0.06 0.06326 -0.003256 1 +#> 0 m1 0.00 0.00000 0.000000 2 +#> 0 m1 0.00 0.00000 0.000000 2 +#> 1 m1 4.84 4.78729 0.052713 2 +#> 1 m1 5.64 4.78729 0.852713 2 +#> 3 m1 12.91 12.98785 -0.077848 2 +#> 3 m1 12.96 12.98785 -0.027848 2 +#> 7 m1 22.97 24.99695 -2.026946 2 +#> 7 m1 24.47 24.99695 -0.526946 2 +#> 14 m1 41.69 36.66353 5.026472 2 +#> 14 m1 33.21 36.66353 -3.453528 2 +#> 21 m1 44.37 41.65681 2.713186 2 +#> 21 m1 46.44 41.65681 4.783186 2 +#> 35 m1 41.22 43.35031 -2.130314 2 +#> 35 m1 37.95 43.35031 -5.400314 2 +#> 50 m1 41.19 41.25637 -0.066368 2 +#> 50 m1 40.01 41.25637 -1.246368 2 +#> 75 m1 40.09 36.46057 3.629429 2 +#> 75 m1 33.85 36.46057 -2.610571 2 +#> 100 m1 31.04 31.96929 -0.929293 2 +#> 100 m1 33.13 31.96929 1.160707 2 +#> 120 m1 25.15 28.76062 -3.610621 2 +#> 120 m1 33.31 28.76062 4.549379 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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>) -<span class='co'># }</span></pre> +<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:13 2018 +#> Date of summary: Fri Sep 14 11:35:13 2018 +#> +#> 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 692 model solutions performed in 2.903 s +#> +#> Weighting: manual +#> +#> Iterative reweighting with method obs +#> Final mean squared residuals of observed variables: +#> parent m1 +#> 11.573406 7.407846 +#> +#> 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 8.185e-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 8.486e-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.ini err +#> 0 parent 99.46 99.67217 -2.122e-01 1 3.402 +#> 0 parent 102.04 99.67217 2.368e+00 1 3.402 +#> 1 parent 93.50 90.27152 3.228e+00 1 3.402 +#> 1 parent 92.50 90.27152 2.228e+00 1 3.402 +#> 3 parent 63.23 74.04648 -1.082e+01 1 3.402 +#> 3 parent 68.99 74.04648 -5.056e+00 1 3.402 +#> 7 parent 52.32 49.82092 2.499e+00 1 3.402 +#> 7 parent 55.13 49.82092 5.309e+00 1 3.402 +#> 14 parent 27.27 24.90288 2.367e+00 1 3.402 +#> 14 parent 26.64 24.90288 1.737e+00 1 3.402 +#> 21 parent 11.50 12.44765 -9.477e-01 1 3.402 +#> 21 parent 11.64 12.44765 -8.077e-01 1 3.402 +#> 35 parent 2.85 3.11002 -2.600e-01 1 3.402 +#> 35 parent 2.91 3.11002 -2.000e-01 1 3.402 +#> 50 parent 0.69 0.70375 -1.375e-02 1 3.402 +#> 50 parent 0.63 0.70375 -7.375e-02 1 3.402 +#> 75 parent 0.05 0.05913 -9.134e-03 1 3.402 +#> 75 parent 0.06 0.05913 8.661e-04 1 3.402 +#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 +#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 +#> 1 m1 4.84 4.81328 2.672e-02 2 2.722 +#> 1 m1 5.64 4.81328 8.267e-01 2 2.722 +#> 3 m1 12.91 13.04779 -1.378e-01 2 2.722 +#> 3 m1 12.96 13.04779 -8.779e-02 2 2.722 +#> 7 m1 22.97 25.07615 -2.106e+00 2 2.722 +#> 7 m1 24.47 25.07615 -6.062e-01 2 2.722 +#> 14 m1 41.69 36.70729 4.983e+00 2 2.722 +#> 14 m1 33.21 36.70729 -3.497e+00 2 2.722 +#> 21 m1 44.37 41.65050 2.719e+00 2 2.722 +#> 21 m1 46.44 41.65050 4.789e+00 2 2.722 +#> 35 m1 41.22 43.28866 -2.069e+00 2 2.722 +#> 35 m1 37.95 43.28866 -5.339e+00 2 2.722 +#> 50 m1 41.19 41.19339 -3.387e-03 2 2.722 +#> 50 m1 40.01 41.19339 -1.183e+00 2 2.722 +#> 75 m1 40.09 36.43820 3.652e+00 2 2.722 +#> 75 m1 33.85 36.43820 -2.588e+00 2 2.722 +#> 100 m1 31.04 31.98971 -9.497e-01 2 2.722 +#> 100 m1 33.13 31.98971 1.140e+00 2 2.722 +#> 120 m1 25.15 28.80897 -3.659e+00 2 2.722 +#> 120 m1 33.31 28.80897 4.501e+00 2 2.722</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 a0eade3b..857e0c74 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -66,7 +66,7 @@ For the definition of model types and their parameters, the equations given </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -221,17 +221,35 @@ For the definition of model types and their parameters, the equations given <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'> -</div><span class='co'># NOT RUN {</span> -<span class='co'># The above model used to be specified like this, before the advent of mkinsub()</span> +</div><div class='input'><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>)) - + <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>) - + <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 file3c104e6e45e4.c 2> file3c104e6e45e4.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>)), @@ -241,8 +259,7 @@ For the definition of model types and their parameters, the equations given <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>) -<span class='co'># }</span></pre> + <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/mkinparplot.html b/docs/reference/mkinparplot.html index 75d22288..adcd2a3b 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 6aa67e5b..2d878175 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 6c2ba992..ffd6e89f 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -321,17 +321,17 @@ <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 verstrichen -#> 0.004 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.001 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.001 </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 verstrichen -#> 0.035 0.000 0.036 </div></pre> +#> 0.035 0.000 0.035 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 4ba540b2..b4e1e747 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 65de0664..a34f1dae 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differnew file mode 100644 index 00000000..6f24b369 --- /dev/null +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differnew file mode 100644 index 00000000..1ed2b216 --- /dev/null +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differnew file mode 100644 index 00000000..952e6af3 --- /dev/null +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differnew file mode 100644 index 00000000..cad6ee11 --- /dev/null +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differnew file mode 100644 index 00000000..7ab171d1 --- /dev/null +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 557da0d7..621571c1 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -175,15 +175,12 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><span class='co'># NOT RUN {</span> -<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>), + <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>) - + <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>) - + <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>) @@ -191,23 +188,29 @@ <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='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) -<span class='no'>time_default</span> -<span class='no'>time_1</span> - -<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]]) - +<span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen +#> 0.046 0.033 6.654 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 20.150 0.000 20.163 </div><div class='input'> +<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff +#> parent_M1 parent_sink M1_M2 M1_sink +#> 0.7340480 0.2659520 0.7505686 0.2494314 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 0.8777689 2.915885 +#> M1 2.3257453 7.725959 +#> M2 33.7200874 112.015706 +#> </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>, ]) -<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>)) -<span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>]) -<span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> +<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><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><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><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 and can be plotted using plot_sep</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>) -<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</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><div class='img'><img src='mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</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='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>]) -<span class='co'># }</span></pre> +<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 765f1628..4fec74c9 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -66,7 +66,7 @@ If the current plot device is a tikz device, </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 0599907d..478a5682 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -65,7 +65,7 @@ If the current plot device is a tikz device, </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 86bb58e5..f59325f9 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index bc4c644a..299fdfbb 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png Binary files differnew file mode 100644 index 00000000..6a621369 --- /dev/null +++ b/docs/reference/schaefer07_complex_case-1.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index b212aa53..9fd60805 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -159,12 +159,22 @@ <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'> </div><span class='co'># NOT RUN {</span> - <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>plot</span>(<span class='no'>fit</span>) - <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>) - -<span class='co'># }</span><div class='input'> <span class='co'># Compare with the results obtained in the original publication</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'> </div><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'>plot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></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_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink +#> 0.3809621 0.1954665 0.4235714 0.0000000 0.4479674 0.5520326 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 13.95078 46.34350 +#> A1 49.75342 165.27728 +#> B1 37.26913 123.80536 +#> C1 11.23133 37.30968 +#> A2 28.50591 94.69457 +#> </div><div class='input'> </div><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span> <span class='fu'>print</span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#> compound parameter KinGUI ModelMaker deviation #> 1 parent degradation rate 0.0496 0.0506 2.0 #> 2 parent DT50 13.9900 13.6900 2.2 diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index c8000ae5..6db7d74c 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -66,7 +66,7 @@ This is the error model used for example by Werner et al. (1978). The model </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 28447e64..1d0a7c52 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -204,17 +204,17 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.47.3 + <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 06:39:24 2018 -#> Date of summary: Fri Sep 14 06:39:24 2018 +#> Date of fit: Fri Sep 14 11:35:59 2018 +#> Date of summary: Fri Sep 14 11:35:59 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.081 s +#> Fitted with method Port using 35 model solutions performed in 0.076 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index dd44a450..25cfc012 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -76,7 +76,7 @@ Compare also the code in the example section to see the degradation models." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -176,8 +176,7 @@ Compare also the code in the example section to see the degradation models." /> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"># NOT RUN { -# The data have been generated using the following kinetic models + <pre class="examples"><div class='input'># The data have been generated using the following kinetic models m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), M1 = list(type = "SFO", to = "M2"), M2 = list(type = "SFO"), use_of_ff = "max") @@ -275,8 +274,10 @@ fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data, quiet = TRUE) plot_sep(fit) summary(fit) -# } -</pre> +</div><div class='output co'>#> <span class='error'>Error: <text>:67:43: Unerwartete(s) SPECIAL</span> +#> <span class='error'>66: </span> +#> <span class='error'>67: d_rep[d_rep$time == 0 & d_rep$name <!-- %in%</span> +#> <span class='error'> ^</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differnew file mode 100644 index 00000000..47670389 --- /dev/null +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differnew file mode 100644 index 00000000..8d282842 --- /dev/null +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index f9032c84..a30161a2 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -146,35 +146,63 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> - <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span> + <pre class="examples"><div class='input'> </div><div class='input'> <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span> <span class='co'># guidance. Due to the strong correlation of the parameter estimates, the</span> <span class='co'># covariance matrix is not returned. Note that level P-II evaluations are</span> <span class='co'># generally considered deprecated due to the frequent occurrence of such</span> <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span> <span class='co'># model).</span> <span class='no'>m_ws</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>), - <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>)) - <span class='no'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>) - - <span class='fu'>summary</span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span> - <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>) - + <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</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_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'>summary</span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> parent_w_0 9.598567e+01 2.33959800 4.102657e+01 9.568967e-19 NA +#> k_parent_w_sink 3.603743e-01 0.03497750 1.030303e+01 4.989002e-09 NA +#> k_parent_w_parent_s 6.031371e-02 0.01746024 3.454346e+00 1.514723e-03 NA +#> k_parent_s_sink 5.108539e-11 0.10382001 4.920572e-10 5.000000e-01 NA +#> k_parent_s_parent_w 7.419672e-02 0.11338240 6.543936e-01 2.608069e-01 NA +#> Upper +#> parent_w_0 NA +#> k_parent_w_sink NA +#> k_parent_w_parent_s NA +#> k_parent_s_sink NA +#> k_parent_s_parent_w NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.09246946 5 6 +#> parent_w 0.06377096 3 3 +#> parent_s 0.20882324 2 3</div><div class='input'> <span class='co'># This is the evaluation used for the validation of software packages</span> <span class='co'># in the expertise from 2014</span> <span class='no'>m_soil</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='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='st'>"M3"</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='st'>"M3"</span>), <span class='kw'>M3</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'>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_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>)) - <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span> - <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>) - -<span class='co'># }</span></pre> + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> parent_0 76.55425584 0.943443794 81.1434198 4.422336e-30 74.602593773 +#> k_parent 0.12081956 0.004815515 25.0896457 1.639665e-18 0.111257517 +#> k_M1 0.84258651 0.930121548 0.9058886 1.871938e-01 0.085876516 +#> k_M2 0.04210878 0.013729902 3.0669396 2.729137e-03 0.021450630 +#> k_M3 0.01122919 0.008044865 1.3958206 8.804912e-02 0.002550984 +#> f_parent_to_M1 0.32240199 0.278620579 1.1571363 1.295467e-01 NA +#> f_parent_to_M2 0.16099854 0.030548888 5.2701931 1.196190e-05 NA +#> f_M1_to_M3 0.27921500 0.314732842 0.8871492 1.920908e-01 0.015016983 +#> f_M2_to_M3 0.55641333 0.650246995 0.8556954 2.004966e-01 0.005360555 +#> Upper +#> parent_0 78.50591790 +#> k_parent 0.13120341 +#> k_M1 8.26712661 +#> k_M2 0.08266188 +#> k_M3 0.04942981 +#> f_parent_to_M1 NA +#> f_parent_to_M2 NA +#> f_M1_to_M3 0.90777163 +#> f_M2_to_M3 0.99658633</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.09649963 9 20 +#> parent 0.04721283 2 6 +#> M1 0.26551209 2 5 +#> M2 0.20327575 2 5 +#> M3 0.05196549 3 4</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 a31b075e..c0ca534c 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes <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>))</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</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 used for fitting: 0.9.47.3 +<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 used for fitting: 0.9.47.4 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 06:39:25 2018 -#> Date of summary: Fri Sep 14 06:39:25 2018 +#> Date of fit: Fri Sep 14 11:36:07 2018 +#> Date of summary: Fri Sep 14 11:36:07 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.642 s +#> Fitted with method Port using 153 model solutions performed in 0.627 s #> #> Weighting: none #> @@ -273,10 +273,82 @@ The transformation of sets of formation fractions is fragile, as it supposes #> DT50 DT90 #> parent 7.023 23.33 #> m1 131.761 437.70</div><div class='input'> -</div><span class='co'># NOT RUN {</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>, <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>) -<span class='co'># }</span><div class='input'> +</div><div class='input'><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>, <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 used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:36:08 2018 +#> Date of summary: Fri Sep 14 11:36:08 2018 +#> +#> 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 350 model solutions performed in 1.437 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>) <span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span> @@ -284,29 +356,160 @@ The transformation of sets of formation fractions is fragile, as it supposes <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'> -</div><span class='co'># NOT RUN {</span> -<span class='co'># The case of formation fractions</span> +</div><div class='input'><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>) - + <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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) -<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='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 used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:36:09 2018 +#> Date of summary: Fri Sep 14 11:36:09 2018 +#> +#> 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 186 model solutions performed in 0.773 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 5.700e-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 4.375e-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>) - +<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>) - + <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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) -<span class='co'># }</span></pre> +<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 used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:36:10 2018 +#> Date of summary: Fri Sep 14 11:36:10 2018 +#> +#> 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 0.424 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 0.11058 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></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |
