diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-07-29 15:15:41 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-07-29 15:15:41 +0200 |
| commit | 20d7834a633d32b663c6bcc1a7f7b0300aa65d5b (patch) | |
| tree | 77338f14ecaf26a4059ada9933ffde1fb5c19072 /docs | |
| parent | 5447af959b2a9b0dc52695bf6a309f346ced085a (diff) | |
Bump version, update NEWS and rebuild pkdown docsv0.9.46
Diffstat (limited to 'docs')
48 files changed, 123 insertions, 104 deletions
diff --git a/docs/index.html b/docs/index.html index 7ac6f226..9898d6f5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -134,7 +134,7 @@ <h2 class="hasAnchor"> <a href="#credits-and-historical-remarks" class="anchor"></a>Credits and historical remarks</h2> <p><code>mkin</code> would not be possible without the underlying software stack consisting of R and the packages <a href="https://cran.r-project.org/package=deSolve">deSolve</a> and <a href="https://cran.r-project.org/package=FME">FME</a>, to say the least.</p> -<p>It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows the work done by the <a href="http://focus.jrc.ec.europa.eu/dk">FOCUS Degradation Kinetics Workgroup</a>, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.</p> +<p>It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows the work done by the <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">FOCUS Degradation Kinetics Workgroup</a>, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.</p> <p>Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.</p> <p>The companion package <a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> (now deprecated) was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2">started in 2008</a> and <a href="https://cran.r-project.org/src/contrib/Archive/kinfit/">first published</a> on CRAN on 01 May 2010.</p> <p>The first <code>mkin</code> code was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8">published on 11 May 2010</a> and the <a href="https://cran.r-project.org/src/contrib/Archive/mkin">first CRAN version</a> on 18 May 2010.</p> diff --git a/docs/news/index.html b/docs/news/index.html index 667c5c1f..b4f97681 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -105,6 +105,23 @@ </div> <div class="contents"> + <div id="mkin-0-9-46-2017-07-24" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-46-2017-07-24" class="anchor"></a>mkin 0.9.46 (2017-07-24)</h1> +<ul> +<li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li> +</ul> +</div> + <div id="mkin-0-9-45-2-2017-07-24" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-45-2-2017-07-24" class="anchor"></a>mkin 0.9.45.2 (2017-07-24)</h1> +<ul> +<li><p>Rename <code>twa</code> to <code>max_twa_parent</code> to avoid conflict with <code>twa</code> from my <code>pfm</code> package</p></li> +<li><p>Update URLs in documentation</p></li> +<li><p>Limit test code to one core to pass on windows</p></li> +<li><p>Switch from <code>microbenchmark</code> to <code>rbenchmark</code> as the former is not supported on all platforms</p></li> +</ul> +</div> <div id="mkin-0-9-45-1-2016-12-20" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-45-1-2016-12-20" class="anchor"></a>mkin 0.9.45.1 (2016-12-20)</h1> @@ -538,6 +555,8 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> + <li><a href="#mkin-0-9-46-2017-07-24">0.9.46</a></li> + <li><a href="#mkin-0-9-45-2-2017-07-24">0.9.45.2</a></li> <li><a href="#mkin-0-9-45-1-2016-12-20">0.9.45.1</a></li> <li><a href="#mkin-0-9-45-2016-12-08">0.9.45</a></li> <li><a href="#mkin-0-9-44-2016-06-29">0.9.44</a></li> diff --git a/docs/reference/DFOP.solution-2.png b/docs/reference/DFOP.solution-2.png Binary files differindex 91efcebb..0902b9df 100644 --- a/docs/reference/DFOP.solution-2.png +++ b/docs/reference/DFOP.solution-2.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 3dbacdc1..30b9d057 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -146,7 +146,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 135297cd..5d4eca29 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -398,7 +398,7 @@ #> { #> assign("calls", calls + 1, inherits = TRUE) #> if (trace_parms) -#> cat(P, "\n") +#> cat(P, "\\n") #> if (length(state.ini.optim) > 0) { #> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) #> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) @@ -420,7 +420,7 @@ #> if (mC$model < cost.old) { #> if (!quiet) #> cat("Model cost at call ", calls, ": ", mC$model, -#> "\n") +#> "\\n") #> if (plot) { #> outtimes_plot = seq(min(observed$time), max(observed$time), #> length.out = 100) @@ -447,8 +447,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x5554250> -#> <environment: 0x4eb4b18> +#> <bytecode: 0x560110508c60> +#> <environment: 0x56010f8d8c30> #> #> $cost_notrans #> function (P) @@ -470,8 +470,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x5073868> -#> <environment: 0x4eb4b18> +#> <bytecode: 0x56010fede550> +#> <environment: 0x56010f8d8c30> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -534,7 +534,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri May 5 12:44:53 2017" +#> [1] "Sat Jul 29 15:14:04 2017" #> #> attr(,"class") #> [1] "mkinfit" "modFit" 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 703dc472..d79aaff6 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -132,7 +132,7 @@ in this fit.</p> Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> 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 eec595f0..e0da5a8d 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -131,7 +131,7 @@ in this fit.</p> Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> 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 c2a90311..720073f2 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -132,7 +132,7 @@ in this fit.</p> Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> 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 24070b9c..b12abf8c 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -130,7 +130,7 @@ in this fit.</p> Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 93901bfa..65bc572a 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -123,7 +123,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> diff --git a/docs/reference/FOMC.solution-2.png b/docs/reference/FOMC.solution-2.png Binary files differindex 0efe8f07..a673bc0e 100644 --- a/docs/reference/FOMC.solution-2.png +++ b/docs/reference/FOMC.solution-2.png diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 67a37b4f..9af30b7a 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -152,7 +152,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A new model based on spatial variability. <em>Environmental Science and Technology</em> <b>24</b>, 1032-1038</p> diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png Binary files differindex 0bdb37a9..2e516447 100644 --- a/docs/reference/HS.solution-2.png +++ b/docs/reference/HS.solution-2.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 3d608a2f..8f6bbbe2 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -147,7 +147,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> diff --git a/docs/reference/IORE.solution-2.png b/docs/reference/IORE.solution-2.png Binary files differindex df268b64..a83d49c7 100644 --- a/docs/reference/IORE.solution-2.png +++ b/docs/reference/IORE.solution-2.png diff --git a/docs/reference/SFO.solution-2.png b/docs/reference/SFO.solution-2.png Binary files differindex 78c083c3..9626091f 100644 --- a/docs/reference/SFO.solution-2.png +++ b/docs/reference/SFO.solution-2.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 08928135..ef9b8eb7 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -136,7 +136,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> diff --git a/docs/reference/SFORB.solution-2.png b/docs/reference/SFORB.solution-2.png Binary files differindex 9625debf..63a50bf9 100644 --- a/docs/reference/SFORB.solution-2.png +++ b/docs/reference/SFORB.solution-2.png diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 112e157d..ebe67733 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -149,7 +149,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> diff --git a/docs/reference/add_err-4.png b/docs/reference/add_err-4.png Binary files differindex f3d04134..8bbd1758 100644 --- a/docs/reference/add_err-4.png +++ b/docs/reference/add_err-4.png diff --git a/docs/reference/add_err-6.png b/docs/reference/add_err-6.png Binary files differindex 05b27247..2a4fe33f 100644 --- a/docs/reference/add_err-6.png +++ b/docs/reference/add_err-6.png diff --git a/docs/reference/add_err-8.png b/docs/reference/add_err-8.png Binary files differindex b0182d2a..49c4a5f0 100644 --- a/docs/reference/add_err-8.png +++ b/docs/reference/add_err-8.png diff --git a/docs/reference/index.html b/docs/reference/index.html index 2d58eeeb..bf7cd233 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -102,7 +102,7 @@ <div class="page-header"> <h1> Reference - <small>version 0.9.45.2</small> + <small>version 0.9.46</small> </h1> </div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 9a681191..0111deb3 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -135,10 +135,10 @@ <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='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: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:02 2017 -#> Date of summary: Fri May 5 12:45:02 2017 + <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:14 2017 +#> Date of summary: Sat Jul 29 15:14:14 2017 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -148,7 +148,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 612 model solutions performed in 3.576 s +#> Fitted with method Port using 612 model solutions performed in 3.558 s #> #> Weighting: none #> @@ -225,10 +225,10 @@ <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:04 2017 -#> Date of summary: Fri May 5 12:45:04 2017 + <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:15 2017 +#> Date of summary: Sat Jul 29 15:14:15 2017 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -238,7 +238,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.461 s +#> Fitted with method Port using 246 model solutions performed in 1.431 s #> #> Weighting: none #> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 678750cd..67b7a35e 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -146,7 +146,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p> Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 875bd1dd..cdf7c7ef 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -377,17 +377,17 @@ <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: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:06 2017 -#> Date of summary: Fri May 5 12:45:06 2017 +<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:18 2017 +#> Date of summary: Sat Jul 29 15:14:18 2017 #> #> 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 0.206 s +#> Fitted with method Port using 64 model solutions performed in 0.141 s #> #> Weighting: none #> @@ -456,7 +456,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 0.912 0.000 0.915 </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 +#> 0.888 0.000 0.890 </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 @@ -535,7 +535,7 @@ #> Model cost at call 153 : 371.2134 #> Optimisation by method Port successfully terminated. #> user system elapsed -#> 0.792 0.000 0.793 </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 +#> 0.728 0.000 0.729 </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 @@ -576,10 +576,10 @@ <span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <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: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:17 2017 -#> Date of summary: Fri May 5 12:45:17 2017 +<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:28 2017 +#> Date of summary: Sat Jul 29 15:14:28 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -697,10 +697,10 @@ #> 100 m1 33.13 3.198e+01 1.148e+00 #> 120 m1 25.15 2.879e+01 -3.640e+00 #> 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <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: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:19 2017 -#> Date of summary: Fri May 5 12:45:19 2017 +<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:30 2017 +#> Date of summary: Sat Jul 29 15:14:30 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -708,7 +708,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 468 model solutions performed in 1.925 s +#> Fitted with method Port using 468 model solutions performed in 1.914 s #> #> Weighting: none then iterative reweighting method obs #> @@ -818,10 +818,10 @@ #> 100 m1 33.13 3.199e+01 1.140e+00 2.722 #> 120 m1 25.15 2.881e+01 -3.659e+00 2.722 #> 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <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: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:20 2017 -#> Date of summary: Fri May 5 12:45:20 2017 +<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:31 2017 +#> Date of summary: Sat Jul 29 15:14:31 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -829,7 +829,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.699 s +#> Fitted with method Port using 155 model solutions performed in 0.692 s #> #> Weighting: mean #> @@ -940,10 +940,10 @@ #> 120 m1 25.15 28.824128 -3.674128 #> 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:21 2017 -#> Date of summary: Fri May 5 12:45:21 2017 +<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:32 2017 +#> Date of summary: Sat Jul 29 15:14:32 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -951,7 +951,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.767 s +#> Fitted with method Port using 174 model solutions performed in 0.701 s #> #> Weighting: manual #> @@ -1062,10 +1062,10 @@ <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>)</div><div class='output co'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:22 2017 -#> Date of summary: Fri May 5 12:45:22 2017 +<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:33 2017 +#> Date of summary: Sat Jul 29 15:14:33 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1073,7 +1073,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 297 model solutions performed in 1.276 s +#> Fitted with method Port using 297 model solutions performed in 1.223 s #> #> Weighting: manual #> @@ -1184,10 +1184,10 @@ #> 120 m1 25.15 28.760616 -3.610616 2 #> 120 m1 33.31 28.760616 4.549384 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>)</div><div class='output co'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:25 2017 -#> Date of summary: Fri May 5 12:45:25 2017 +<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:36 2017 +#> Date of summary: Sat Jul 29 15:14:36 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1195,7 +1195,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 628 model solutions performed in 2.626 s +#> Fitted with method Port using 628 model solutions performed in 2.578 s #> #> Weighting: manual then iterative reweighting method obs #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index de9815d4..5703b188 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -182,7 +182,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> @@ -205,7 +205,7 @@ <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 file70ea30edf42a.c 2> file70ea30edf42a.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file519167a14b3a.c 2> file519167a14b3a.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png Binary files differindex 8b32f554..c9f4aadb 100644 --- a/docs/reference/mkinparplot-4.png +++ b/docs/reference/mkinparplot-4.png diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 327a7d8d..b3453e6c 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -299,17 +299,17 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.004 0.000 0.004 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.004 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 elapsed -#> 0.004 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.000 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 elapsed -#> 0.032 0.000 0.033 </div></pre> +#> 0.032 0.000 0.032 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinresplot-4.png b/docs/reference/mkinresplot-4.png Binary files differindex 7dbd7522..5f3a65e3 100644 --- a/docs/reference/mkinresplot-4.png +++ b/docs/reference/mkinresplot-4.png diff --git a/docs/reference/mmkin-15.png b/docs/reference/mmkin-15.png Binary files differindex f50a6185..e8a23a55 100644 --- a/docs/reference/mmkin-15.png +++ b/docs/reference/mmkin-15.png diff --git a/docs/reference/mmkin-17.png b/docs/reference/mmkin-17.png Binary files differindex 72cfc5e7..01bb3ae3 100644 --- a/docs/reference/mmkin-17.png +++ b/docs/reference/mmkin-17.png diff --git a/docs/reference/mmkin-19.png b/docs/reference/mmkin-19.png Binary files differindex 0b315b1a..b5ac70f7 100644 --- a/docs/reference/mmkin-19.png +++ b/docs/reference/mmkin-19.png diff --git a/docs/reference/mmkin-21.png b/docs/reference/mmkin-21.png Binary files differindex b98940ff..7e15e1b3 100644 --- a/docs/reference/mmkin-21.png +++ b/docs/reference/mmkin-21.png diff --git a/docs/reference/mmkin-23.png b/docs/reference/mmkin-23.png Binary files differindex 5ca52efb..45e8efc1 100644 --- a/docs/reference/mmkin-23.png +++ b/docs/reference/mmkin-23.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index fe10c88f..d649563f 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -168,8 +168,8 @@ #> <span class='warning'>Convergence code is 1</span></div><div class='output co'>#> <span class='warning'>Warning: Optimisation by method Port did not converge.</span> #> <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='no'>time_default</span></div><div class='output co'>#> user system elapsed -#> 16.092 0.132 11.761 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed -#> 25.004 0.000 25.000 </div><div class='input'> +#> 15.992 0.188 11.440 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed +#> 24.576 0.000 24.578 </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 #> 0.7340479 0.2659521 0.7505687 0.2494313 diff --git a/docs/reference/plot.mkinfit-10.png b/docs/reference/plot.mkinfit-10.png Binary files differindex 09bb687c..87d3351d 100644 --- a/docs/reference/plot.mkinfit-10.png +++ b/docs/reference/plot.mkinfit-10.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex 1e90d789..cb52d4ac 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differindex 1dfbbe4c..8e0faa21 100644 --- a/docs/reference/plot.mkinfit-6.png +++ b/docs/reference/plot.mkinfit-6.png diff --git a/docs/reference/plot.mkinfit-8.png b/docs/reference/plot.mkinfit-8.png Binary files differindex e4ab674a..129f1445 100644 --- a/docs/reference/plot.mkinfit-8.png +++ b/docs/reference/plot.mkinfit-8.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex a26e413f..7739e3b0 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex f23ed172..e2eb3aae 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png Binary files differindex dc24d92f..3bbd390a 100644 --- a/docs/reference/plot.mmkin-6.png +++ b/docs/reference/plot.mmkin-6.png diff --git a/docs/reference/schaefer07_complex_case-4.png b/docs/reference/schaefer07_complex_case-4.png Binary files differindex b87ccb82..b90185a1 100644 --- a/docs/reference/schaefer07_complex_case-4.png +++ b/docs/reference/schaefer07_complex_case-4.png diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index dbed926d..f20e3948 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -177,21 +177,21 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> + <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <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: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:20 2017 -#> Date of summary: Fri May 5 12:46:20 2017 + <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: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:30 2017 +#> Date of summary: Sat Jul 29 15:15:30 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.082 s +#> Fitted with method Port using 35 model solutions performed in 0.084 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index d8ff3a1e..173af92e 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -156,10 +156,10 @@ <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><img src='synthetic_data_for_UBA_2014-10.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:23 2017 -#> Date of summary: Fri May 5 12:46:23 2017 +<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><img src='synthetic_data_for_UBA_2014-10.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:33 2017 +#> Date of summary: Sat Jul 29 15:15:34 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -168,7 +168,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 381 model solutions performed in 2.203 s +#> Fitted with method Port using 381 model solutions performed in 2.241 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA_2014-10.png b/docs/reference/synthetic_data_for_UBA_2014-10.png Binary files differindex b98940ff..7e15e1b3 100644 --- a/docs/reference/synthetic_data_for_UBA_2014-10.png +++ b/docs/reference/synthetic_data_for_UBA_2014-10.png diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index c14740c2..bbf15a41 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -170,10 +170,10 @@ <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: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:24 2017 -#> Date of summary: Fri May 5 12:46:24 2017 +<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:35 2017 +#> Date of summary: Sat Jul 29 15:15:35 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -181,7 +181,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.61 s +#> Fitted with method Port using 153 model solutions performed in 0.608 s #> #> Weighting: none #> @@ -247,10 +247,10 @@ #> m1 131.761 437.70</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: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:26 2017 -#> Date of summary: Fri May 5 12:46:26 2017 +<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:36 2017 +#> Date of summary: Sat Jul 29 15:15:36 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -258,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 352 model solutions performed in 1.437 s +#> Fitted with method Port using 352 model solutions performed in 1.401 s #> #> Weighting: none #> @@ -337,10 +337,10 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:27 2017 -#> Date of summary: Fri May 5 12:46:27 2017 +<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:37 2017 +#> Date of summary: Sat Jul 29 15:15:37 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -348,7 +348,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.776 s +#> Fitted with method Port using 185 model solutions performed in 0.772 s #> #> Weighting: none #> @@ -421,10 +421,10 @@ <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>)</div><div class='output co'>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:28 2017 -#> Date of summary: Fri May 5 12:46:28 2017 +<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:38 2017 +#> Date of summary: Sat Jul 29 15:15:38 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -432,7 +432,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.433 s +#> Fitted with method Port using 104 model solutions performed in 0.416 s #> #> Weighting: none #> |
