diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-07-04 08:10:33 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-07-04 08:10:33 +0200 |
| commit | 7e8d788d298b8e1492fd8f62d88456e99e0f5992 (patch) | |
| tree | 0ec78730e5d6cd5367420b2f04effbd1cc1b0f3f /docs | |
| parent | d004cfb133b2b38808a736916152b85c5df6568f (diff) | |
Address failures of CRAN checks, improve NEWSv0.9.49.5
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs')
| -rw-r--r-- | docs/articles/FOCUS_D.html | 8 | ||||
| -rw-r--r-- | docs/articles/FOCUS_L.html | 40 | ||||
| -rw-r--r-- | docs/articles/mkin.html | 2 | ||||
| -rw-r--r-- | docs/articles/twa.html | 2 | ||||
| -rw-r--r-- | docs/articles/web_only/FOCUS_Z.html | 2 | ||||
| -rw-r--r-- | docs/articles/web_only/NAFTA_examples.html | 2 | ||||
| -rw-r--r-- | docs/articles/web_only/benchmarks.html | 24 | ||||
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 12 | ||||
| -rw-r--r-- | docs/news/index.html | 9 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 28 | ||||
| -rw-r--r-- | docs/reference/mkinmod.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 4 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 4 |
14 files changed, 72 insertions, 71 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 88a3fa6a..ed41e555 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-07-03</h4> + <h4 class="date">2019-07-04</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -168,8 +168,8 @@ <div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed Jul 3 16:39:00 2019 -## Date of summary: Wed Jul 3 16:39:00 2019 +## Date of fit: Thu Jul 4 08:04:23 2019 +## Date of summary: Thu Jul 4 08:04:24 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -177,7 +177,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted using 389 model solutions performed in 0.977 s +## Fitted using 389 model solutions performed in 0.982 s ## ## Error model: Constant variance ## diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 1b54252f..0060bd69 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-07-03</h4> + <h4 class="date">2019-07-04</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -114,15 +114,15 @@ <a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed Jul 3 16:39:02 2019 -## Date of summary: Wed Jul 3 16:39:02 2019 +## Date of fit: Thu Jul 4 08:04:26 2019 +## Date of summary: Thu Jul 4 08:04:26 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 133 model solutions performed in 0.279 s +## Fitted using 133 model solutions performed in 0.278 s ## ## Error model: Constant variance ## @@ -216,8 +216,8 @@ ## finite result is doubtful</code></pre> <pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed Jul 3 16:39:04 2019 -## Date of summary: Wed Jul 3 16:39:04 2019 +## Date of fit: Thu Jul 4 08:04:28 2019 +## Date of summary: Thu Jul 4 08:04:28 2019 ## ## ## Warning: Optimisation did not converge: @@ -229,7 +229,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 899 model solutions performed in 1.874 s +## Fitted using 899 model solutions performed in 1.876 s ## ## Error model: Constant variance ## @@ -321,15 +321,15 @@ <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed Jul 3 16:39:05 2019 -## Date of summary: Wed Jul 3 16:39:05 2019 +## Date of fit: Thu Jul 4 08:04:29 2019 +## Date of summary: Thu Jul 4 08:04:29 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 239 model solutions performed in 0.485 s +## Fitted using 239 model solutions performed in 0.486 s ## ## Error model: Constant variance ## @@ -397,8 +397,8 @@ <div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed Jul 3 16:39:07 2019 -## Date of summary: Wed Jul 3 16:39:07 2019 +## Date of fit: Thu Jul 4 08:04:30 2019 +## Date of summary: Thu Jul 4 08:04:30 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -497,8 +497,8 @@ <div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed Jul 3 16:39:08 2019 -## Date of summary: Wed Jul 3 16:39:09 2019 +## Date of fit: Thu Jul 4 08:04:32 2019 +## Date of summary: Thu Jul 4 08:04:32 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -507,7 +507,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 373 model solutions performed in 0.772 s +## Fitted using 373 model solutions performed in 0.773 s ## ## Error model: Constant variance ## @@ -603,8 +603,8 @@ <div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed Jul 3 16:39:09 2019 -## Date of summary: Wed Jul 3 16:39:10 2019 +## Date of fit: Thu Jul 4 08:04:33 2019 +## Date of summary: Thu Jul 4 08:04:33 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -668,15 +668,15 @@ <div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed Jul 3 16:39:10 2019 -## Date of summary: Wed Jul 3 16:39:10 2019 +## Date of fit: Thu Jul 4 08:04:33 2019 +## Date of summary: Thu Jul 4 08:04:33 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 224 model solutions performed in 0.452 s +## Fitted using 224 model solutions performed in 0.453 s ## ## Error model: Constant variance ## diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index df694259..8ad4a8e9 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -88,7 +88,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-07-03</h4> + <h4 class="date">2019-07-04</h4> <div class="hidden name"><code>mkin.Rmd</code></div> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 34b85796..98e5efdf 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -88,7 +88,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-07-03</h4> + <h4 class="date">2019-07-04</h4> <div class="hidden name"><code>twa.Rmd</code></div> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index b82e1e01..4a856b71 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-07-03</h4> + <h4 class="date">2019-07-04</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index c1922b64..3f6ff8b9 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -88,7 +88,7 @@ <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-07-03</h4> + <h4 class="date">2019-07-04</h4> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index c68db93b..005834cc 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -88,7 +88,7 @@ <h1>Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-07-03</h4> + <h4 class="date">2019-07-04</h4> <div class="hidden name"><code>benchmarks.Rmd</code></div> @@ -202,77 +202,77 @@ ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.820 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.843 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.917 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.863 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.415 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.417 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.588 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.484 ## t5 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.317 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.307 ## t6 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.556 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.538 ## t7 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.213 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.196 ## t8 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.851 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.853 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.645 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.643 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.734 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.733 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.489</code></pre> +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.511</code></pre> <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div> </div> </div> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index b30488a0..3fc54cfa 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -88,7 +88,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-07-03</h4> + <h4 class="date">2019-07-04</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -163,9 +163,9 @@ ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 3.043 1.000 3.042 0 -## 1 deSolve, not compiled 3 28.630 9.408 28.616 0 -## 2 Eigenvalue based 3 4.291 1.410 4.289 0 +## 3 deSolve, compiled 3 3.061 1.000 3.059 0 +## 1 deSolve, not compiled 3 28.502 9.311 28.487 0 +## 2 Eigenvalue based 3 4.321 1.412 4.318 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -214,8 +214,8 @@ ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 4.800 1.000 4.795 0.002 -## 1 deSolve, not compiled 3 53.371 11.119 53.346 0.000 +## 2 deSolve, compiled 3 4.818 1.000 4.814 0 +## 1 deSolve, not compiled 3 53.275 11.057 53.249 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> diff --git a/docs/news/index.html b/docs/news/index.html index f8504768..0b82cbcc 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -122,9 +122,9 @@ </div> - <div id="mkin-0-9-49-5-2019-07-03" class="section level1"> + <div id="mkin-0-9-49-5-2019-07-04" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-49-5-2019-07-03" class="anchor"></a>mkin 0.9.49.5 (2019-07-03)<small> Unreleased </small> +<a href="#mkin-0-9-49-5-2019-07-04" class="anchor"></a>mkin 0.9.49.5 (2019-07-04)<small> Unreleased </small> </h1> <ul> <li><p>Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm ‘d_3’ tries direct minimization and a three-step procedure, and returns the model with the highest likelihood.</p></li> @@ -134,10 +134,11 @@ <li><p>Remove dependency on FME, only use nlminb for optimisation (‘Port’ algorithm). I cannot remember cases where one of the other optimisation algorithms was preferable, except that I sometime used Levenberg-Marquardt for speed in cases where I did not expect to get trapped in a local minimum.</p></li> <li><p>Use the numDeriv package to calculate hessians. This results in slightly different confidence intervals, takes a bit longer, but is apparently more robust</p></li> <li><p>Add a simple benchmark vignette to document the impact on performance.</p></li> -<li><p>The code for manual weighting was removed. This functionality might get added again at a later time.</p></li> +<li><p>The code for manual weighting was removed. This functionality might get added again at a later time. For the time being, please use an earlier version, e.g. 0.9.48.1 if you want to do manual weighting.</p></li> <li><p>The fitting time reported in the summary now includes the time used for calculation of the hessians</p></li> <li><p>Adapt tests</p></li> <li><p>Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting in parallel via mmkin this could go unnoticed.</p></li> +<li><p>Add example datasets obtained from risk assessment reports published by the European Food Safety Agency.</p></li> </ul> </div> <div id="mkin-0-9-48-1-2019-03-04" class="section level1"> @@ -698,7 +699,7 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0-9-49-5-2019-07-03">0.9.49.5</a></li> + <li><a href="#mkin-0-9-49-5-2019-07-04">0.9.49.5</a></li> <li><a href="#mkin-0-9-48-1-2019-03-04">0.9.48.1</a></li> <li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li> <li><a href="#mkin-0-9-47-3">0.9.47.3</a></li> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3e20fc5d..0983007e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -399,15 +399,15 @@ Per default, parameters in the kinetic models are internally transformed in <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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed Jul 3 16:36:58 2019 -#> Date of summary: Wed Jul 3 16:36:58 2019 +#> Date of fit: Thu Jul 4 08:02:21 2019 +#> Date of summary: Thu Jul 4 08:02:21 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.46 s +#> Fitted using 222 model solutions performed in 0.464 s #> #> Error model: Constant variance #> @@ -481,7 +481,7 @@ Per default, parameters in the kinetic models are internally transformed in <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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 1.497 0.000 1.499 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</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 +#> 1.507 0.004 1.511 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</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 #> @@ -553,7 +553,7 @@ Per default, parameters in the kinetic models are internally transformed in #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 1.079 0.000 1.079 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</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 +#> 1.078 0.000 1.078 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</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 #> @@ -585,8 +585,8 @@ Per default, parameters in the kinetic models are internally transformed in <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed Jul 3 16:37:14 2019 -#> Date of summary: Wed Jul 3 16:37:14 2019 +#> Date of fit: Thu Jul 4 08:02:37 2019 +#> Date of summary: Thu Jul 4 08:02:37 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -594,7 +594,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.107 s +#> Fitted using 421 model solutions performed in 1.096 s #> #> Error model: Constant variance #> @@ -704,8 +704,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 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.obs</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed Jul 3 16:37:17 2019 -#> Date of summary: Wed Jul 3 16:37:17 2019 +#> Date of fit: Thu Jul 4 08:02:40 2019 +#> Date of summary: Thu Jul 4 08:02:40 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -713,7 +713,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 979 model solutions performed in 2.612 s +#> Fitted using 979 model solutions performed in 2.574 s #> #> Error model: Variance unique to each observed variable #> @@ -836,8 +836,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.80429 -3.654e+00 #> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed Jul 3 16:37:26 2019 -#> Date of summary: Wed Jul 3 16:37:26 2019 +#> Date of fit: Thu Jul 4 08:02:49 2019 +#> Date of summary: Thu Jul 4 08:02:49 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -845,7 +845,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.522 s +#> Fitted using 2289 model solutions performed in 9.379 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index f1793541..39fe631b 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -234,7 +234,7 @@ 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>), <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 file24f24fd75f75.c 2> file24f24fd75f75.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file6e9c38dae9ed.c 2> file6e9c38dae9ed.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 9c4263b6..ef847245 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -328,7 +328,7 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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 -#> 0.003 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( +#> 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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 @@ -338,7 +338,7 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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 -#> 0.022 0.000 0.022 </div><div class='input'> +#> 0.022 0.000 0.021 </div><div class='input'> </div><div class='input'> <span class='co'># Predict from a fitted model</span> <span class='no'>f</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_C</span>)</div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 552.5739 #> Sum of squared residuals at call 3: 552.5739 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 7a34ac7d..38c46b6e 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -194,8 +194,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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></div><div class='output co'>#> User System verstrichen -#> 0.036 0.048 5.130 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 19.222 0.000 19.233 </div><div class='input'> +#> 0.055 0.032 5.069 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 19.260 0.000 19.271 </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 #> 0.7340481 0.2659519 0.7505684 0.2494316 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 4f2c9ecb..c4d2653d 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -211,8 +211,8 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed Jul 3 16:38:45 2019 -#> Date of summary: Wed Jul 3 16:38:45 2019 +#> Date of fit: Thu Jul 4 08:04:08 2019 +#> Date of summary: Thu Jul 4 08:04:08 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent |