diff options
Diffstat (limited to 'docs')
177 files changed, 815 insertions, 567 deletions
diff --git a/docs/404.html b/docs/404.html index f038fb95..48cba3d7 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 786b2c47..f3a56065 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -94,13 +94,13 @@ - </header><div class="row"> + </header><script src="FOCUS_D_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2021-02-03</h4> + <h4 class="date">Last change 31 January 2019 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.rmd</code></div> @@ -185,10 +185,10 @@ <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 1.0.0 +<pre><code>## mkin version used for fitting: 1.0.3 ## R version used for fitting: 4.0.3 -## Date of fit: Wed Feb 3 17:32:13 2021 -## Date of summary: Wed Feb 3 17:32:14 2021 +## Date of fit: Mon Feb 15 13:46:23 2021 +## Date of summary: Mon Feb 15 13:46:23 2021 ## ## Equations: ## d_parent/dt = - k_parent * parent @@ -196,7 +196,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 401 model solutions performed in 0.161 s +## Fitted using 401 model solutions performed in 0.162 s ## ## Error model: Constant variance ## @@ -239,11 +239,11 @@ ## ## Parameter correlation: ## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma -## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.171e-06 -## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.481e-07 -## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.209e-07 +## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06 +## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07 +## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07 ## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06 -## sigma -1.171e-06 -8.481e-07 8.209e-07 1.305e-06 1.000e+00 +## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. diff --git a/docs/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex 5278038a..abf26715 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js b/docs/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 4c3bed4c..53e4e1d3 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -94,13 +94,13 @@ - </header><div class="row"> + </header><script src="FOCUS_L_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2021-02-03</h4> + <h4 class="date">Last change 17 November 2016 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small> <div class="hidden name"><code>FOCUS_L.rmd</code></div> @@ -126,17 +126,17 @@ <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">m.L1.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 1.0.0 +<pre><code>## mkin version used for fitting: 1.0.3 ## R version used for fitting: 4.0.3 -## Date of fit: Wed Feb 3 17:32:16 2021 -## Date of summary: Wed Feb 3 17:32:16 2021 +## Date of fit: Mon Feb 15 13:46:25 2021 +## Date of summary: Mon Feb 15 13:46:25 2021 ## ## Equations: ## d_parent/dt = - k_parent * parent ## ## Model predictions using solution type analytical ## -## Fitted using 133 model solutions performed in 0.031 s +## Fitted using 133 model solutions performed in 0.032 s ## ## Error model: Constant variance ## @@ -232,17 +232,17 @@ <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> -<pre><code>## mkin version used for fitting: 1.0.0 +<pre><code>## mkin version used for fitting: 1.0.3 ## R version used for fitting: 4.0.3 -## Date of fit: Wed Feb 3 17:32:16 2021 -## Date of summary: Wed Feb 3 17:32:16 2021 +## Date of fit: Mon Feb 15 13:46:26 2021 +## Date of summary: Mon Feb 15 13:46:26 2021 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 380 model solutions performed in 0.085 s +## Fitted using 369 model solutions performed in 0.083 s ## ## Error model: Constant variance ## @@ -270,22 +270,22 @@ ## ## Results: ## -## AIC BIC logLik -## 95.88778 99.44927 -43.94389 +## AIC BIC logLik +## 95.88781 99.44929 -43.9439 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 92.47 1.2820 89.720 95.220 -## log_alpha 16.92 NaN NaN NaN -## log_beta 19.26 NaN NaN NaN -## sigma 2.78 0.4501 1.814 3.745 +## log_alpha 13.78 NaN NaN NaN +## log_beta 16.13 NaN NaN NaN +## sigma 2.78 0.4598 1.794 3.766 ## ## Parameter correlation: -## parent_0 log_alpha log_beta sigma -## parent_0 1.000000 NaN NaN 0.002218 -## log_alpha NaN 1 NaN NaN -## log_beta NaN NaN 1 NaN -## sigma 0.002218 NaN NaN 1.000000 +## parent_0 log_alpha log_beta sigma +## parent_0 1.0000000 NaN NaN 0.0001671 +## log_alpha NaN 1 NaN NaN +## log_beta NaN NaN 1 NaN +## sigma 0.0001671 NaN NaN 1.0000000 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -293,9 +293,9 @@ ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 9.247e+01 NA NA 89.720 95.220 -## alpha 2.223e+07 NA NA NA NA -## beta 2.325e+08 NA NA NA NA -## sigma 2.780e+00 NA NA 1.814 3.745 +## alpha 9.658e+05 NA NA NA NA +## beta 1.010e+07 NA NA NA NA +## sigma 2.780e+00 NA NA 1.794 3.766 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df @@ -344,10 +344,10 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 1.0.0 +<pre><code>## mkin version used for fitting: 1.0.3 ## R version used for fitting: 4.0.3 -## Date of fit: Wed Feb 3 17:32:17 2021 -## Date of summary: Wed Feb 3 17:32:17 2021 +## Date of fit: Mon Feb 15 13:46:26 2021 +## Date of summary: Mon Feb 15 13:46:26 2021 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -389,10 +389,10 @@ ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09 -## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.617e-07 -## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.386e-07 -## sigma -7.436e-09 -1.617e-07 -1.386e-07 1.000e+00 +## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.828e-09 +## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.602e-07 +## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.372e-07 +## sigma -7.828e-09 -1.602e-07 -1.372e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -425,10 +425,10 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 1.0.0 +<pre><code>## mkin version used for fitting: 1.0.3 ## R version used for fitting: 4.0.3 -## Date of fit: Wed Feb 3 17:32:17 2021 -## Date of summary: Wed Feb 3 17:32:17 2021 +## Date of fit: Mon Feb 15 13:46:27 2021 +## Date of summary: Mon Feb 15 13:46:27 2021 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -437,7 +437,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 581 model solutions performed in 0.133 s +## Fitted using 581 model solutions performed in 0.134 s ## ## Error model: Constant variance ## @@ -468,18 +468,18 @@ ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 93.950 9.998e-01 91.5900 96.3100 -## log_k1 3.117 1.929e+03 -4558.0000 4564.0000 +## log_k1 3.112 1.842e+03 -4353.0000 4359.0000 ## log_k2 -1.088 6.285e-02 -1.2370 -0.9394 ## g_qlogis -0.399 9.946e-02 -0.6342 -0.1638 ## sigma 1.414 2.886e-01 0.7314 2.0960 ## ## Parameter correlation: -## parent_0 log_k1 log_k2 g_qlogis sigma -## parent_0 1.000e+00 6.459e-07 9.147e-11 2.665e-01 8.413e-11 -## log_k1 6.459e-07 1.000e+00 1.061e-04 -2.087e-04 -9.802e-06 -## log_k2 9.147e-11 1.061e-04 1.000e+00 -7.903e-01 -2.429e-09 -## g_qlogis 2.665e-01 -2.087e-04 -7.903e-01 1.000e+00 4.049e-09 -## sigma 8.413e-11 -9.802e-06 -2.429e-09 4.049e-09 1.000e+00 +## parent_0 log_k1 log_k2 g_qlogis sigma +## parent_0 1.000e+00 6.783e-07 -3.390e-10 2.665e-01 -2.967e-10 +## log_k1 6.783e-07 1.000e+00 1.116e-04 -2.196e-04 -1.031e-05 +## log_k2 -3.390e-10 1.116e-04 1.000e+00 -7.903e-01 2.917e-09 +## g_qlogis 2.665e-01 -2.196e-04 -7.903e-01 1.000e+00 -4.408e-09 +## sigma -2.967e-10 -1.031e-05 2.917e-09 -4.408e-09 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -487,7 +487,7 @@ ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100 -## k1 22.5800 5.303e-04 4.998e-01 0.0000 Inf +## k1 22.4800 5.553e-04 4.998e-01 0.0000 Inf ## k2 0.3369 1.591e+01 4.697e-07 0.2904 0.3909 ## g 0.4016 1.680e+01 3.238e-07 0.3466 0.4591 ## sigma 1.4140 4.899e+00 8.776e-04 0.7314 2.0960 @@ -499,7 +499,7 @@ ## ## Estimated disappearance times: ## DT50 DT90 DT50back DT50_k1 DT50_k2 -## parent 0.5335 5.311 1.599 0.0307 2.058</code></pre> +## parent 0.5335 5.311 1.599 0.03084 2.058</code></pre> <p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.</p> </div> </div> @@ -531,10 +531,10 @@ <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 1.0.0 +<pre><code>## mkin version used for fitting: 1.0.3 ## R version used for fitting: 4.0.3 -## Date of fit: Wed Feb 3 17:32:18 2021 -## Date of summary: Wed Feb 3 17:32:18 2021 +## Date of fit: Mon Feb 15 13:46:27 2021 +## Date of summary: Mon Feb 15 13:46:28 2021 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -581,11 +581,11 @@ ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_qlogis sigma -## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.671e-08 -## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.148e-07 +## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.664e-08 +## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.147e-07 ## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.022e-06 -## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.929e-07 -## sigma -9.671e-08 7.148e-07 1.022e-06 -7.929e-07 1.000e+00 +## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.926e-07 +## sigma -9.664e-08 7.147e-07 1.022e-06 -7.926e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -644,17 +644,17 @@ <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 1.0.0 +<pre><code>## mkin version used for fitting: 1.0.3 ## R version used for fitting: 4.0.3 -## Date of fit: Wed Feb 3 17:32:19 2021 -## Date of summary: Wed Feb 3 17:32:19 2021 +## Date of fit: Mon Feb 15 13:46:28 2021 +## Date of summary: Mon Feb 15 13:46:28 2021 ## ## Equations: ## d_parent/dt = - k_parent * parent ## ## Model predictions using solution type analytical ## -## Fitted using 142 model solutions performed in 0.03 s +## Fitted using 142 model solutions performed in 0.031 s ## ## Error model: Constant variance ## @@ -709,17 +709,17 @@ ## parent 106 352</code></pre> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 1.0.0 +<pre><code>## mkin version used for fitting: 1.0.3 ## R version used for fitting: 4.0.3 -## Date of fit: Wed Feb 3 17:32:19 2021 -## Date of summary: Wed Feb 3 17:32:19 2021 +## Date of fit: Mon Feb 15 13:46:28 2021 +## Date of summary: Mon Feb 15 13:46:28 2021 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 224 model solutions performed in 0.046 s +## Fitted using 224 model solutions performed in 0.047 s ## ## Error model: Constant variance ## @@ -754,10 +754,10 @@ ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.456e-07 -## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.169e-08 -## log_beta -5.543e-01 9.889e-01 1.000e+00 4.910e-08 -## sigma -2.456e-07 2.169e-08 4.910e-08 1.000e+00 +## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.468e-07 +## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.478e-08 +## log_beta -5.543e-01 9.889e-01 1.000e+00 5.211e-08 +## sigma -2.468e-07 2.478e-08 5.211e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -781,7 +781,7 @@ <div id="references" class="section level1 unnumbered"> <h1 class="hasAnchor"> <a href="#references" class="anchor"></a>References</h1> -<div id="refs" class="references"> +<div id="refs" class="references hanging-indent"> <div id="ref-ranke2014"> <p>Ranke, Johannes. 2014. “Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0.” Umweltbundesamt Projektnummer 27452.</p> </div> diff --git a/docs/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png Binary files differindex 80ca888e..e9c0b0a0 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png Binary files differindex 12e380da..3e03954d 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png Binary files differindex 8b2954c7..8c9e8fd4 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png Binary files differindex 922d1f0e..b3aa8334 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png Binary files differindex be3cbcd0..477829a5 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png Binary files differindex 55080b33..c0e08884 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png Binary files differindex d7b0793a..310b4f3b 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png diff --git a/docs/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js b/docs/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/index.html b/docs/articles/index.html index 52770090..22753e8d 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index e240323f..6dbb093d 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -94,13 +94,13 @@ - </header><div class="row"> + </header><script src="mkin_files/header-attrs-2.6/header-attrs.js"></script><script src="mkin_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2021-02-03</h4> + <h4 class="date">Last change 15 February 2021 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/mkin.rmd"><code>vignettes/mkin.rmd</code></a></small> <div class="hidden name"><code>mkin.rmd</code></div> @@ -148,28 +148,34 @@ <div id="background" class="section level1"> <h1 class="hasAnchor"> <a href="#background" class="anchor"></a>Background</h1> -<p>Many approaches are possible regarding the evaluation of chemical degradation data.</p> -<p>The <code>mkin</code> package <span class="citation">(Ranke 2019)</span> implements the approach recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe <span class="citation">(FOCUS Work Group on Degradation Kinetics 2006, 2014)</span> for simple decline data series, data series with transformation products, commonly termed metabolites, and for data series for more than one compartment. It is also possible to include back reactions, so equilibrium reactions and equilibrium partitioning can be specified, although this oftentimes leads to an overparameterisation of the model.</p> +<p>The <code>mkin</code> package <span class="citation">(Ranke 2021)</span> implements the approach to degradation kinetics recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe <span class="citation">(FOCUS Work Group on Degradation Kinetics 2006, 2014)</span>. It covers data series describing the decline of one compound, data series with transformation products (commonly termed metabolites) and data series for more than one compartment. It is possible to include back reactions. Therefore, equilibrium reactions and equilibrium partitioning can be specified, although this often leads to an overparameterisation of the model.</p> <p>When the first <code>mkin</code> code was published in 2010, the most commonly used tools for fitting more complex kinetic degradation models to experimental data were KinGUI <span class="citation">(Schäfer et al. 2007)</span>, a MATLAB based tool with a graphical user interface that was specifically tailored to the task and included some output as proposed by the FOCUS Kinetics Workgroup, and ModelMaker, a general purpose compartment based tool providing infrastructure for fitting dynamic simulation models based on differential equations to data.</p> -<p>The code was first uploaded to the BerliOS platform. When this was taken down, the version control history was imported into the R-Forge site (see <em>e.g.</em> <a href="https://cgit.jrwb.de/mkin/commit/?id=30cbb4092f6d2d3beff5800603374a0d009ad770">the initial commit on 11 May 2010</a>), where the code is still occasionally updated.</p> -<p>At that time, the R package <code>FME</code> (Flexible Modelling Environment) <span class="citation">(Soetaert and Petzoldt 2010)</span> was already available, and provided a good basis for developing a package specifically tailored to the task. The remaining challenge was to make it as easy as possible for the users (including the author of this vignette) to specify the system of differential equations and to include the output requested by the FOCUS guidance, such as the relative standard deviation that has to be assumed for the residuals, such that the <span class="math inline">\(\chi^2\)</span> goodness-of-fit test as defined by the FOCUS kinetics workgroup would pass using an significance level <span class="math inline">\(\alpha\)</span> of 0.05. This relative error, expressed as a percentage, is often termed <span class="math inline">\(\chi^2\)</span> error level or similar.</p> -<p>Also, <code>mkin</code> introduced using analytical solutions for parent only kinetics for improved optimization speed. Later, Eigenvalue based solutions were introduced to <code>mkin</code> for the case of linear differential equations (<em>i.e.</em> where the FOMC or DFOP models were not used for the parent compound), greatly improving the optimization speed for these cases. This, however, has become somehow obsolete, as the use of compiled code described below gives even smaller execution times.</p> +<p>The ‘mkin’ code was first uploaded to the BerliOS development platform. When this was taken down, the version control history was imported into the R-Forge site (see <em>e.g.</em> <a href="https://cgit.jrwb.de/mkin/commit/?id=30cbb4092f6d2d3beff5800603374a0d009ad770">the initial commit on 11 May 2010</a>), where the code is still being updated.</p> +<p>At that time, the R package <code>FME</code> (Flexible Modelling Environment) <span class="citation">(Soetaert and Petzoldt 2010)</span> was already available, and provided a good basis for developing a package specifically tailored to the task. The remaining challenge was to make it as easy as possible for the users (including the author of this vignette) to specify the system of differential equations and to include the output requested by the FOCUS guidance, such as the <span class="math inline">\(\chi^2\)</span> error level as defined in this guidance.</p> +<p>Also, <code>mkin</code> introduced using analytical solutions for parent only kinetics for improved optimization speed. Later, Eigenvalue based solutions were introduced to <code>mkin</code> for the case of linear differential equations (<em>i.e.</em> where the FOMC or DFOP models were not used for the parent compound), greatly improving the optimization speed for these cases. This, has become somehow obsolete, as the use of compiled code described below gives even faster execution times.</p> <p>The possibility to specify back-reactions and a biphasic model (SFORB) for metabolites were present in <code>mkin</code> from the very beginning.</p> <div id="derived-software-tools" class="section level2"> <h2 class="hasAnchor"> <a href="#derived-software-tools" class="anchor"></a>Derived software tools</h2> -<p>Soon after the publication of <code>mkin</code>, two derived tools were published, namely KinGUII (available from Bayer Crop Science) and CAKE (commissioned to Tessella by Syngenta), which added a graphical user interface (GUI), and added fitting by iteratively reweighted least squares (IRLS) and characterisation of likely parameter distributions by Markov Chain Monte Carlo (MCMC) sampling.</p> -<p>CAKE focuses on a smooth use experience, sacrificing some flexibility in the model definition, originally allowing only two primary metabolites in parallel. The current version 3.3 of CAKE release in March 2016 uses a basic scheme for up to six metabolites in a flexible arrangement, but does not support back-reactions (non-instantaneous equilibria) or biphasic kinetics for metabolites.</p> +<p>Soon after the publication of <code>mkin</code>, two derived tools were published, namely KinGUII (developed at Bayer Crop Science) and CAKE (commissioned to Tessella by Syngenta), which added a graphical user interface (GUI), and added fitting by iteratively reweighted least squares (IRLS) and characterisation of likely parameter distributions by Markov Chain Monte Carlo (MCMC) sampling.</p> +<p>CAKE focuses on a smooth use experience, sacrificing some flexibility in the model definition, originally allowing only two primary metabolites in parallel. The current version 3.4 of CAKE released in May 2020 uses a scheme for up to six metabolites in a flexible arrangement and supports biphasic modelling of metabolites, but does not support back-reactions (non-instantaneous equilibria).</p> <p>KinGUI offers an even more flexible widget for specifying complex kinetic models. Back-reactions (non-instantaneous equilibria) were supported early on, but until 2014, only simple first-order models could be specified for transformation products. Starting with KinGUII version 2.1, biphasic modelling of metabolites was also available in KinGUII.</p> <p>A further graphical user interface (GUI) that has recently been brought to a decent degree of maturity is the browser based GUI named <code>gmkin</code>. Please see its <a href="https://pkgdown.jrwb.de/gmkin/">documentation page</a> and <a href="https://pkgdown.jrwb.de/gmkin/articles/gmkin_manual.html">manual</a> for further information.</p> <p>A comparison of scope, usability and numerical results obtained with these tools has been recently been published by <span class="citation">Ranke, Wöltjen, and Meinecke (2018)</span>.</p> </div> -<div id="recent-developments" class="section level2"> -<h2 class="hasAnchor"> -<a href="#recent-developments" class="anchor"></a>Recent developments</h2> -<p>Currently (July 2019), the main features available in <code>mkin</code> which are not present in KinGUII or CAKE, are the speed increase by using compiled code when a compiler is present, parallel model fitting on multicore machines using the <code>mmkin</code> function, and the estimation of parameter confidence intervals based on transformed parameters.</p> -<p>In addition, the possibility to use two alternative error models to constant variance have been integrated. The variance by variable error model introduced by <span class="citation">Gao et al. (2011)</span> has been available via an iteratively reweighted least squares (IRLS) procedure since mkin <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-22-2013-10-26">version 0.9-22</a>. With <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-49-5-2019-07-04">release 0.9.49.5</a>, the IRLS algorithm has been replaced by direct or step-wise maximisation of the likelihood function, which makes it possible not only to fit the variance by variable error model but also a <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component error model</a> inspired by error models developed in analytical chemistry.</p> </div> +<div id="unique-features" class="section level1"> +<h1 class="hasAnchor"> +<a href="#unique-features" class="anchor"></a>Unique features</h1> +<p>Currently, the main unique features available in <code>mkin</code> are</p> +<ul> +<li>the <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">speed increase</a> by using compiled code when a compiler is present,</li> +<li>parallel model fitting on multicore machines using the <a href="https://pkgdown.jrwb.de/mkin/reference/mmkin.html"><code>mmkin</code> function</a>,</li> +<li>the estimation of parameter confidence intervals based on transformed parameters (see below) and</li> +<li>the possibility to use the <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component error model</a> +</li> +</ul> +<p>The iteratively reweighted least squares fitting of different variances for each variable as introduced by <span class="citation">Gao et al. (2011)</span> has been available in mkin since <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-22-2013-10-26">version 0.9-22</a>. With <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-49-5-2019-07-04">release 0.9.49.5</a>, the IRLS algorithm has been complemented by direct or step-wise maximisation of the likelihood function, which makes it possible not only to fit the variance by variable error model but also a <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component error model</a> inspired by error models developed in analytical chemistry <span class="citation">(Ranke and Meinecke 2019)</span>.</p> </div> <div id="internal-parameter-transformations" class="section level1"> <h1 class="hasAnchor"> @@ -177,13 +183,13 @@ <p>For rate constants, the log transformation is used, as proposed by Bates and Watts <span class="citation">(1988, 77, 149)</span>. Approximate intervals are constructed for the transformed rate constants <span class="citation">(compare Bates and Watts 1988, 135)</span>, <em>i.e.</em> for their logarithms. Confidence intervals for the rate constants are then obtained using the appropriate backtransformation using the exponential function.</p> <p>In the first version of <code>mkin</code> allowing for specifying models using formation fractions, a home-made reparameterisation was used in order to ensure that the sum of formation fractions would not exceed unity.</p> <p>This method is still used in the current version of KinGUII (v2.1 from April 2014), with a modification that allows for fixing the pathway to sink to zero. CAKE uses penalties in the objective function in order to enforce this constraint.</p> -<p>In 2012, an alternative reparameterisation of the formation fractions was proposed together with René Lehmann <span class="citation">(Ranke and Lehmann 2012)</span>, based on isometric logratio transformation (ILR). The aim was to improve the validity of the linear approximation of the objective function during the parameter estimation procedure as well as in the subsequent calculation of parameter confidence intervals.</p> +<p>In 2012, an alternative reparameterisation of the formation fractions was proposed together with René Lehmann <span class="citation">(Ranke and Lehmann 2012)</span>, based on isometric logratio transformation (ILR). The aim was to improve the validity of the linear approximation of the objective function during the parameter estimation procedure as well as in the subsequent calculation of parameter confidence intervals. In the current version of mkin, a logit transformation is used for parameters that are bound between 0 and 1, such as the g parameter of the DFOP model.</p> <div id="confidence-intervals-based-on-transformed-parameters" class="section level2"> <h2 class="hasAnchor"> <a href="#confidence-intervals-based-on-transformed-parameters" class="anchor"></a>Confidence intervals based on transformed parameters</h2> <p>In the first attempt at providing improved parameter confidence intervals introduced to <code>mkin</code> in 2013, confidence intervals obtained from FME on the transformed parameters were simply all backtransformed one by one to yield asymmetric confidence intervals for the backtransformed parameters.</p> <p>However, while there is a 1:1 relation between the rate constants in the model and the transformed parameters fitted in the model, the parameters obtained by the isometric logratio transformation are calculated from the set of formation fractions that quantify the paths to each of the compounds formed from a specific parent compound, and no such 1:1 relation exists.</p> -<p>Therefore, parameter confidence intervals for formation fractions obtained with this method only appear valid for the case of a single transformation product, where only one formation fraction is to be estimated, directly corresponding to one component of the ilr transformed parameter.</p> +<p>Therefore, parameter confidence intervals for formation fractions obtained with this method only appear valid for the case of a single transformation product, where currently the logit transformation is used for the formation fraction.</p> <p>The confidence intervals obtained by backtransformation for the cases where a 1:1 relation between transformed and original parameter exist are considered by the author of this vignette to be more accurate than those obtained using a re-estimation of the Hessian matrix after backtransformation, as implemented in the FME package.</p> </div> <div id="parameter-t-test-based-on-untransformed-parameters" class="section level2"> @@ -198,36 +204,39 @@ <h1 class="hasAnchor"> <a href="#references" class="anchor"></a>References</h1> <!-- vim: set foldmethod=syntax: --> -<div id="refs" class="references"> +<div id="refs" class="references hanging-indent"> <div id="ref-bates1988"> <p>Bates, D., and D. Watts. 1988. <em>Nonlinear Regression and Its Applications</em>. Wiley-Interscience.</p> </div> <div id="ref-FOCUS2006"> -<p>FOCUS Work Group on Degradation Kinetics. 2006. <em>Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. Report of the Focus Work Group on Degradation Kinetics</em>. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> +<p>FOCUS Work Group on Degradation Kinetics. 2006. <em>Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. Report of the Focus Work Group on Degradation Kinetics</em>. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> </div> <div id="ref-FOCUSkinetics2014"> -<p>———. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> +<p>———. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> </div> <div id="ref-gao11"> -<p>Gao, Z., J.W. Green, J. Vanderborght, and W. Schmitt. 2011. “Improving Uncertainty Analysis in Kinetic Evaluations Using Iteratively Reweighted Least Squares.” Journal. <em>Environmental Science and Technology</em> 45: 4429–37.</p> +<p>Gao, Z., J. W. Green, J. Vanderborght, and W. Schmitt. 2011. “Improving Uncertainty Analysis in Kinetic Evaluations Using Iteratively Reweighted Least Squares.” Journal. <em>Environmental Science and Technology</em> 45: 4429–37.</p> </div> <div id="ref-pkg:mkin"> -<p>Ranke, J. 2019. <em>‘mkin‘: Kinetic Evaluation of Chemical Degradation Data</em>. <a href="https://CRAN.R-project.org/package=mkin" class="uri">https://CRAN.R-project.org/package=mkin</a>.</p> +<p>Ranke, J. 2021. <em>‘mkin‘: Kinetic Evaluation of Chemical Degradation Data</em>. <a href="https://CRAN.R-project.org/package=mkin">https://CRAN.R-project.org/package=mkin</a>.</p> </div> <div id="ref-ranke2012"> <p>Ranke, J., and R. Lehmann. 2012. “Parameter Reliability in Kinetic Evaluation of Environmental Metabolism Data - Assessment and the Influence of Model Specification.” In <em>SETAC World 20-24 May</em>. Berlin.</p> </div> <div id="ref-ranke2015"> -<p>———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In <em>XV Symposium on Pesticide Chemistry 2-4 September 2015</em>. Piacenza. <a href="http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf" class="uri">http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</a>.</p> +<p>———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In <em>XV Symposium on Pesticide Chemistry 2-4 September 2015</em>. Piacenza. <a href="http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf">http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</a>.</p> +</div> +<div id="ref-ranke2019"> +<p>Ranke, Johannes, and Stefan Meinecke. 2019. “Error Models for the Kinetic Evaluation of Chemical Degradation Data.” <em>Environments</em> 6 (12). <a href="https://doi.org/10.3390/environments6120124">https://doi.org/10.3390/environments6120124</a>.</p> </div> <div id="ref-ranke2018"> -<p>Ranke, Johannes, Janina Wöltjen, and Stefan Meinecke. 2018. “Comparison of Software Tools for Kinetic Evaluation of Chemical Degradation Data.” <em>Environmental Sciences Europe</em> 30 (1): 17. <a href="https://doi.org/10.1186/s12302-018-0145-1" class="uri">https://doi.org/10.1186/s12302-018-0145-1</a>.</p> +<p>Ranke, Johannes, Janina Wöltjen, and Stefan Meinecke. 2018. “Comparison of Software Tools for Kinetic Evaluation of Chemical Degradation Data.” <em>Environmental Sciences Europe</em> 30 (1): 17. <a href="https://doi.org/10.1186/s12302-018-0145-1">https://doi.org/10.1186/s12302-018-0145-1</a>.</p> </div> <div id="ref-schaefer2007"> <p>Schäfer, D., B. Mikolasch, P. Rainbird, and B. Harvey. 2007. “KinGUI: A New Kinetic Software Tool for Evaluations According to FOCUS Degradation Kinetics.” In <em>Proceedings of the Xiii Symposium Pesticide Chemistry</em>, edited by Del Re A. A. M., Capri E., Fragoulis G., and Trevisan M., 916–23. Piacenza.</p> </div> <div id="ref-soetaert2010"> -<p>Soetaert, Karline, and Thomas Petzoldt. 2010. “Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME.” <em>Journal of Statistical Software</em> 33 (3): 1–28. <a href="https://www.jstatsoft.org/v33/i03/" class="uri">https://www.jstatsoft.org/v33/i03/</a>.</p> +<p>Soetaert, Karline, and Thomas Petzoldt. 2010. “Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME.” <em>Journal of Statistical Software</em> 33 (3): 1–28. <a href="https://www.jstatsoft.org/v33/i03/">https://www.jstatsoft.org/v33/i03/</a>.</p> </div> </div> </div> diff --git a/docs/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex 8acd92af..bf38fdd7 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/articles/mkin_files/header-attrs-2.6/header-attrs.js b/docs/articles/mkin_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/mkin_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/twa.html b/docs/articles/twa.html index c270659b..2e3d2f96 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -94,13 +94,13 @@ - </header><div class="row"> + </header><script src="twa_files/header-attrs-2.6/header-attrs.js"></script><script src="twa_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2021-02-03</h4> + <h4 class="date">Last change 18 September 2019 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/twa.rmd"><code>vignettes/twa.rmd</code></a></small> <div class="hidden name"><code>twa.rmd</code></div> @@ -141,9 +141,9 @@ \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) + \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \]</span></p> <p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the <code><a href="../reference/max_twa_parent.html">max_twa_parent()</a></code> function. If the same is needed for metabolites, the function <code><a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html">pfm::max_twa()</a></code> from the ‘pfm’ package can be used.</p> -<div id="refs" class="references"> +<div id="refs" class="references hanging-indent"> <div id="ref-FOCUSkinetics2014"> -<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> +<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> </div> </div> </div> diff --git a/docs/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/twa_files/header-attrs-2.6/header-attrs.js b/docs/articles/twa_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/twa_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 8bdcbe30..57fc3545 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -94,13 +94,13 @@ - </header><div class="row"> + </header><script src="FOCUS_Z_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2021-02-03</h4> + <h4 class="date">Last change 16 January 2018 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="hidden name"><code>FOCUS_Z.rmd</code></div> @@ -237,12 +237,12 @@ <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 96.839001 1.994273 48.5585 4.0276e-42 92.827060 100.850943 -## k_Z0 2.215367 0.118456 18.7021 1.0410e-23 1.989432 2.466960 -## k_Z1 0.478310 0.028258 16.9265 6.2430e-22 0.424712 0.538673 -## k_Z2 0.451628 0.042139 10.7176 1.6313e-14 0.374337 0.544877 -## k_Z3 0.058692 0.015245 3.8498 1.7806e-04 0.034806 0.098972 -## f_Z2_to_Z3 0.471498 0.058350 8.0805 9.6614e-11 0.357741 0.588294 +## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664 +## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989 +## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666 +## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872 +## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965 +## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274 ## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</code></pre> <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> @@ -253,9 +253,9 @@ ## $distimes ## DT50 DT90 ## Z0 0.31288 1.0394 -## Z1 1.44916 4.8140 +## Z1 1.44917 4.8141 ## Z2 1.53478 5.0984 -## Z3 11.80983 39.2314</code></pre> +## Z3 11.80986 39.2315</code></pre> <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> </div> <div id="using-the-sforb-model" class="section level1"> @@ -351,13 +351,13 @@ ## ## $SFORB ## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471371 0.0075126 0.0800070 0.0000000 +## 2.4471322 0.0075125 0.0800069 0.0000000 ## ## $distimes ## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.35666 0.28325 92.265 NA NA +## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA ## Z1 1.5148 5.0320 NA NA NA NA NA -## Z2 1.6414 5.4525 NA NA NA NA NA +## Z2 1.6414 5.4526 NA NA NA NA NA ## Z3 NA NA NA NA NA 8.6636 Inf</code></pre> <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> </div> @@ -365,9 +365,9 @@ <h1 class="hasAnchor"> <a href="#references" class="anchor"></a>References</h1> <!-- vim: set foldmethod=syntax: --> -<div id="refs" class="references"> +<div id="refs" class="references hanging-indent"> <div id="ref-FOCUSkinetics2014"> -<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> +<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> </div> </div> </div> diff --git a/docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differindex 3da22dad..2213c446 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png Binary files differindex 8c152f77..61b04d3a 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png Binary files differindex 732e6c65..409f1203 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png Binary files differindex cf6d45ca..4d6820cd 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png Binary files differindex 5c29341c..2e504961 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png Binary files differindex 3da22dad..2213c446 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png Binary files differindex 02a97a1e..7ab743af 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png Binary files differindex d070e7ed..2e0dce77 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png Binary files differindex 65309e3b..458299c1 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png Binary files differindex 22610e84..eb833066 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png Binary files differindex 47d46a9f..e7501cbb 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index d3e23253..e79375b3 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -94,13 +94,13 @@ - </header><div class="row"> + </header><script src="NAFTA_examples_files/header-attrs-2.6/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>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">2021-02-03</h4> + <h4 class="date">26 February 2019 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> @@ -156,7 +156,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 ## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.42e-12 5.00e-01 0.0000 Inf +## k2 2.26e-12 5.00e-01 0.0000 Inf ## g 6.47e-01 3.67e-06 0.6248 0.6677 ## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## @@ -165,7 +165,7 @@ ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.22e+11 2.86e+11 +## DFOP 55.5 5.59e+11 3.07e+11 ## ## Representative half-life: ## [1] 321.51</code></pre> @@ -207,7 +207,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 1.10e-11 5.00e-01 0.0000 Inf +## k2 8.63e-12 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## @@ -216,7 +216,7 @@ ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.03e+11 6.29e+10 +## DFOP 83.6 1.32e+11 8.04e+10 ## ## Representative half-life: ## [1] 215.87</code></pre> @@ -258,7 +258,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 ## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.60e-11 5.00e-01 0.0000 Inf +## k2 3.22e-11 5.00e-01 0.0000 Inf ## g 8.61e-01 7.55e-06 0.8314 0.8867 ## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## @@ -267,7 +267,7 @@ ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 9.07e+09 1.93e+10 +## DFOP 34.1 1.01e+10 2.15e+10 ## ## Representative half-life: ## [1] 53.17</code></pre> @@ -309,7 +309,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 ## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 2.89e-10 5.00e-01 0.0000 Inf +## k2 3.63e-10 5.00e-01 0.0000 Inf ## g 6.06e-01 2.19e-01 0.4826 0.7178 ## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## @@ -318,7 +318,7 @@ ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 4.75e+09 2.40e+09 +## DFOP 96.4 3.77e+09 1.91e+09 ## ## Representative half-life: ## [1] 454.55</code></pre> @@ -420,7 +420,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 9.03e-13 5.00e-01 0.000 Inf +## k2 9.02e-13 5.00e-01 0.000 Inf ## g 6.52e-01 8.13e-06 0.642 0.661 ## sigma 7.88e-01 6.13e-02 0.481 1.095 ## @@ -429,7 +429,7 @@ ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.38e+12 7.67e+11 +## DFOP 10.5 1.38e+12 7.69e+11 ## ## Representative half-life: ## [1] 101.43</code></pre> @@ -441,15 +441,16 @@ <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -473,12 +474,12 @@ ## sigma 1.288 1.76e-04 0.7456 1.830 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 NA 93.1355 96.2891 -## k1 0.0389 NA 0.0266 0.0569 -## k2 0.0389 NA 0.0255 0.0592 -## g 0.5256 NA NA NA -## sigma 1.5957 NA 0.9135 2.2779 +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 1.61e-16 93.1355 96.2891 +## k1 0.0389 1.08e-04 0.0266 0.0569 +## k2 0.0389 2.23e-04 0.0255 0.0592 +## g 0.5256 NaN NA NA +## sigma 1.5957 2.50e-04 0.9135 2.2779 ## ## ## DTx values: @@ -494,15 +495,18 @@ <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is +## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -528,9 +532,9 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 101.7315 1.41e-09 91.6534 111.8097 -## k1 0.0495 5.63e-03 0.0240 0.1020 -## k2 0.0495 1.93e-03 0.0272 0.0903 -## g 0.4487 NaN 0.0000 1.0000 +## k1 0.0495 6.58e-03 0.0303 0.0809 +## k2 0.0495 2.60e-03 0.0410 0.0598 +## g 0.4487 5.00e-01 NA NA ## sigma 8.0152 2.50e-04 4.5886 11.4418 ## ## @@ -551,14 +555,14 @@ <div id="example-on-page-11" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> -<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb57"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -594,10 +598,10 @@ ## DT50 DT90 DT50_rep ## SFO 2.16e+02 7.18e+02 2.16e+02 ## IORE 9.73e+02 1.37e+08 4.11e+07 -## DFOP 3.07e+11 1.93e+12 6.97e+11 +## DFOP 3.07e+11 1.93e+12 6.98e+11 ## ## Representative half-life: -## [1] 41148171</code></pre> +## [1] 41148170</code></pre> <p>In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.</p> </div> </div> @@ -608,19 +612,21 @@ <div id="example-on-page-12-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> -<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance -## matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance ## matrix</code></pre> +<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is +## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -644,12 +650,12 @@ ## sigma 3.965 NA NA NA ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 2.74e-10 NA NA -## k1 0.124 2.53e-05 NA NA -## k2 0.124 2.52e-02 NA NA -## g 0.793 5.00e-01 NA NA -## sigma 7.048 2.50e-04 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 2.74e-10 92.2366 108.805 +## k1 0.124 2.53e-05 0.0908 0.170 +## k2 0.124 2.52e-02 0.0456 0.339 +## g 0.793 NaN NA NA +## sigma 7.048 2.50e-04 4.0349 10.061 ## ## ## DTx values: @@ -664,20 +670,18 @@ <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb66"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre> <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> +<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb75"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -702,11 +706,11 @@ ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 NA NaN NaN -## k1 0.0589 NA NA NA -## k2 0.0589 NA NA NA -## g 0.6473 NA NA NA -## sigma 3.4323 NA NaN NaN +## parent_0 97.6840 NaN NaN NaN +## k1 0.0589 NaN NA NA +## k2 0.0589 NaN NA NA +## g 0.6473 NaN NA NA +## sigma 3.4323 NaN NaN NaN ## ## ## DTx values: @@ -721,18 +725,14 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb77"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb84"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -758,9 +758,9 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 92.73500 NA 8.95e+01 95.92118 -## k1 0.00258 NA 4.25e-04 0.01569 -## k2 0.00258 NA 1.76e-03 0.00379 -## g 0.16452 NA NA NA +## k1 0.00258 NA 4.14e-04 0.01611 +## k2 0.00258 NA 1.74e-03 0.00383 +## g 0.16452 NA 0.00e+00 1.00000 ## sigma 3.41172 NA 2.02e+00 4.79960 ## ## @@ -777,7 +777,7 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> @@ -785,10 +785,10 @@ ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb92"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb93"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -815,7 +815,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 ## k1 9.53e-03 1.20e-01 0.00638 0.0143 -## k2 5.33e-12 5.00e-01 0.00000 Inf +## k2 6.08e-12 5.00e-01 0.00000 Inf ## g 3.98e-01 2.19e-01 0.30481 0.4998 ## sigma 1.17e+00 7.68e-06 0.77406 1.5610 ## @@ -824,7 +824,7 @@ ## DT50 DT90 DT50_rep ## SFO 2.48e+02 8.25e+02 2.48e+02 ## IORE 4.34e+02 2.22e+04 6.70e+03 -## DFOP 3.48e+10 3.37e+11 1.30e+11 +## DFOP 3.05e+10 2.95e+11 1.14e+11 ## ## Representative half-life: ## [1] 6697.44</code></pre> @@ -833,14 +833,14 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb99"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -864,12 +864,12 @@ ## sigma 3.105 1.78e-04 1.795 4.416 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 NA 94.21913 101.7159 -## k1 0.00952 NA 0.00221 0.0411 -## k2 0.00952 NA 0.00626 0.0145 -## g 0.21241 NA 0.00000 1.0000 -## sigma 4.18778 NA 2.39747 5.9781 +## Estimate Pr(>t) Lower Upper +## parent_0 97.96751 2.85e-13 94.21913 101.7159 +## k1 0.00952 6.28e-02 0.00250 0.0363 +## k2 0.00952 1.27e-04 0.00646 0.0140 +## g 0.21241 5.00e-01 0.00000 1.0000 +## sigma 4.18778 2.50e-04 2.39747 5.9781 ## ## ## DTx values: @@ -880,7 +880,7 @@ ## ## Representative half-life: ## [1] 41.33</code></pre> -<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> @@ -888,10 +888,10 @@ ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb107"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb108"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -909,7 +909,7 @@ ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 99.83 1.81e-16 97.51348 102.14 +## parent_0 99.83 1.81e-16 97.51349 102.14 ## k__iore_parent 0.38 3.22e-01 0.00352 41.05 ## N_parent 0.00 5.00e-01 -1.07696 1.08 ## sigma 2.21 2.57e-04 1.23245 3.19 @@ -936,16 +936,16 @@ <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb115"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb116"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb119"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -996,7 +996,7 @@ <div id="references" class="section level1 unnumbered"> <h1 class="hasAnchor"> <a href="#references" class="anchor"></a>References</h1> -<div id="refs" class="references"> +<div id="refs" class="references hanging-indent"> <div id="ref-usepa2015"> <p>US EPA. 2015. “Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-Life Values and Characterizing Pesticide Degradation.”</p> </div> diff --git a/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png Binary files differindex bfe9b278..f5420ce8 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png Binary files differindex bc8eb665..0ae4bd9f 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png Binary files differindex 54ff98b8..57a48119 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12a-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png Binary files differindex 99fb589d..c42d45f0 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p12b-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png Binary files differindex f3332d5d..52dea51e 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png Binary files differindex 7e24c2ff..ca1f29be 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png Binary files differindex 52b849d7..f69e6d3b 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png Binary files differindex 42f39959..71fcd257 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png Binary files differindex e5358265..820501a3 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png Binary files differindex 7b23f706..e264d2ea 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png Binary files differindex d99f0d2d..e5b656a4 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png Binary files differindex ca68c20b..c9664c77 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png Binary files differindex 74cb76af..a81f814c 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png Binary files differindex 87dc1fab..75d72e7c 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png Binary files differindex 0d111357..3ce13a97 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png Binary files differindex 73b85767..e2cf2f83 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index e15358a0..d7b81f20 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -94,13 +94,13 @@ - </header><div class="row"> + </header><script src="benchmarks_files/header-attrs-2.6/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2021-02-03</h4> + <h4 class="date">Last change 13 May 2020 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.rmd"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -135,17 +135,11 @@ m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span> <span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> <span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>, - error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></code></pre></div> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: -## iteration limit reached without convergence (10) - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: -## iteration limit reached without convergence (10)</code></pre> -<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>, + error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> +<span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></code></pre></div> <p>Two metabolites, synthetic data:</p> -<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>, M1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>, M2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, @@ -172,7 +166,7 @@ error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> <span class="va">t11</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">DFOP_par_c</span><span class="op">)</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></code></pre></div> -<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">mkin_benchmarks</span><span class="op">[</span><span class="va">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"t"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">11</span><span class="op">)</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">t1</span>, <span class="va">t2</span>, <span class="va">t3</span>, <span class="va">t4</span>, <span class="va">t5</span>, <span class="va">t6</span>, <span class="va">t7</span>, <span class="va">t8</span>, <span class="va">t9</span>, <span class="va">t10</span>, <span class="va">t11</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span><span class="op">(</span><span class="va">mkin_benchmarks</span>, file <span class="op">=</span> <span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span><span class="op">)</span></code></pre></div> @@ -234,9 +228,9 @@ <td align="right">3.729</td> </tr> <tr class="odd"> -<td align="left">1.0.0</td> -<td align="right">1.770</td> -<td align="right">3.703</td> +<td align="left">1.0.3</td> +<td align="right">1.722</td> +<td align="right">3.419</td> </tr> </tbody> </table> @@ -302,10 +296,10 @@ <td align="right">2.810</td> </tr> <tr class="odd"> -<td align="left">1.0.0</td> -<td align="right">1.373</td> -<td align="right">7.127</td> -<td align="right">2.762</td> +<td align="left">1.0.3</td> +<td align="right">1.402</td> +<td align="right">6.343</td> +<td align="right">2.802</td> </tr> </tbody> </table> @@ -313,7 +307,7 @@ <div id="two-metabolites" class="section level3"> <h3 class="hasAnchor"> <a href="#two-metabolites" class="anchor"></a>Two metabolites</h3> -<p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p> +<p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p> <table class="table"> <thead><tr class="header"> <th align="left">mkin version</th> @@ -398,13 +392,13 @@ <td align="right">3.105</td> </tr> <tr class="odd"> -<td align="left">1.0.0</td> -<td align="right">0.775</td> -<td align="right">1.269</td> -<td align="right">1.467</td> -<td align="right">3.767</td> -<td align="right">1.919</td> -<td align="right">2.942</td> +<td align="left">1.0.3</td> +<td align="right">0.771</td> +<td align="right">1.251</td> +<td align="right">1.464</td> +<td align="right">3.074</td> +<td align="right">1.940</td> +<td align="right">2.831</td> </tr> </tbody> </table> diff --git a/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index e45655b6..ce8d8481 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -94,13 +94,13 @@ - </header><div class="row"> + </header><script src="compiled_models_files/header-attrs-2.6/header-attrs.js"></script><script src="compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2021-02-03</h4> + <h4 class="date">2021-02-15</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.rmd"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> @@ -159,9 +159,9 @@ <span class="op">}</span></code></pre></div> <pre><code>## test replications relative elapsed ## 4 analytical 1 1.000 0.181 -## 3 deSolve, compiled 1 1.818 0.329 -## 2 Eigenvalue based 1 2.061 0.373 -## 1 deSolve, not compiled 1 43.923 7.950</code></pre> +## 3 deSolve, compiled 1 1.812 0.328 +## 2 Eigenvalue based 1 2.088 0.378 +## 1 deSolve, not compiled 1 45.923 8.312</code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> <div id="model-without-analytical-solution" class="section level2"> @@ -188,13 +188,13 @@ <span class="op">}</span></code></pre></div> <pre><code>## Temporary DLL for differentials generated and loaded</code></pre> <pre><code>## test replications relative elapsed -## 2 deSolve, compiled 1 1.000 0.474 -## 1 deSolve, not compiled 1 30.179 14.305</code></pre> -<p>Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 1.0.0 on</p> +## 2 deSolve, compiled 1 1.000 0.486 +## 1 deSolve, not compiled 1 31.597 15.356</code></pre> +<p>Here we get a performance benefit of a factor of 32 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 1.0.3 on</p> <pre><code>## R version 4.0.3 (2020-10-10) ## Platform: x86_64-pc-linux-gnu (64-bit) -## Running under: Debian GNU/Linux 10 (buster)</code></pre> +## Running under: Debian GNU/Linux bullseye/sid</code></pre> <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> </div> </div> diff --git a/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/authors.html b/docs/authors.html index e80c3930..61d29bf0 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/index.html b/docs/index.html index 51571c81..88f118ea 100644 --- a/docs/index.html +++ b/docs/index.html @@ -37,7 +37,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -132,23 +132,40 @@ <div id="features" class="section level2"> <h2 class="hasAnchor"> <a href="#features" class="anchor"></a>Features</h2> +<div id="general" class="section level3"> +<h3 class="hasAnchor"> +<a href="#general" class="anchor"></a>General</h3> <ul> <li>Highly flexible model specification using <a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li> -<li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li> <li>Model solution (forward modelling) in the function <a href="https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li> -<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li> -<li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric log-ratio transformation that is now used for the formation fractions.</li> -<li>A side effect of this is that when parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which can not occur in a single experiment with a single defined radiolabel position.</li> <li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li> <li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li> <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li> -<li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.</li> -<li>Three different error models can be selected using the argument <code>error_model</code> to the <a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html"><code>mkinfit</code></a> function.</li> <li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) should now be specified as <code>error_model = "obs"</code>.</li> -<li>A two-component error model similar to the one proposed by <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">Rocke and Lorenzato</a> can be selected using the argument <code>error_model = "tc"</code>.</li> +</ul> +</div> +<div id="unique-in-mkin" class="section level3"> +<h3 class="hasAnchor"> +<a href="#unique-in-mkin" class="anchor"></a>Unique in mkin</h3> +<ul> +<li>Three different error models can be selected using the argument <code>error_model</code> to the <a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html"><code>mkinfit</code></a> function. A two-component error model similar to the one proposed by <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">Rocke and Lorenzato</a> can be selected using the argument <code>error_model = "tc"</code>.</li> +<li>Model comparisons using the Akaike Information Criterion (AIC) are supported which can also be used for non-constant variance. In such cases the FOCUS chi-squared error level is not meaningful.</li> +<li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution.</li> +<li>When parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which cannot occur in a single experiment with a single defined radiolabel position.</li> +<li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite. Mathematically, the SFORB model is equivalent to the DFOP model used by other tools for biphasic metabolite curves. However, the SFORB model has the advantage that there is a mechanistic interpretation of the model parameters.</li> <li>Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> method. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils).</li> </ul> </div> +<div id="performance" class="section level3"> +<h3 class="hasAnchor"> +<a href="#performance" class="anchor"></a>Performance</h3> +<ul> +<li>Parallel fitting of several models to several datasets is supported, see for example <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li> +<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li> +<li>Even if no compiler is installed, many degradation models still give <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html">very good performance</a>, as current versions of mkin also have <a href="https://jrwb.de/performance-improvements-mkin/">analytical solutions for some models with one metabolite</a>, and if SFO or SFORB are used for the parent compound, Eigenvalue based solutions of the degradation model are available.</li> +</ul> +</div> +</div> <div id="gui" class="section level2"> <h2 class="hasAnchor"> <a href="#gui" class="anchor"></a>GUI</h2> @@ -157,7 +174,7 @@ <div id="news" class="section level2"> <h2 class="hasAnchor"> <a href="#news" class="anchor"></a>News</h2> -<p>There is a ChangeLog, for the latest <a href="https://cran.r-project.org/package=mkin/news/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p> +<p>There is a list of changes for the latest <a href="https://cran.r-project.org/package=mkin/news/news.html">CRAN release</a> and one for each github branch, e.g. <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">the main branch</a>.</p> </div> <div id="credits-and-historical-remarks" class="section level2"> <h2 class="hasAnchor"> @@ -170,6 +187,16 @@ <p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on <code>mkin</code>, but which added, among other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the <code>FME</code> package.</p> <p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the <a href="https://www.tessella.com/showcase/computer-assisted-kinetic-evaluation">CAKE website</a>, where you can also find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL license.</p> <p>Finally, there is <a href="https://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.</p> +<p>Thanks to René Lehmann, formerly working at the Umweltbundesamt, for the nice cooperation cooperation on parameter transformations, especially the isometric log-ratio transformation that is now used for formation fractions in case there are more than two transformation targets.</p> +<p>Many inspirations for improvements of mkin resulted from doing kinetic evaluations of degradation data for my clients while working at Harlan Laboratories and at Eurofins Regulatory AG, and now as an independent consultant.</p> +<p>Funding was received from the Umweltbundesamt in the course of the projects</p> +<ul> +<li>Grant Number 112407 (Testing and validation of modelling software as an alternative to ModelMaker 4.0, 2014-2015)</li> +<li>Project Number 56703 (Optimization of gmkin for routine use in the Umweltbundesamt, 2015)</li> +<li>Project Number 112407 (Testing the feasibility of using an error model according to Rocke and Lorenzato for more realistic parameter estimates in the kinetic evaluation of degradation data, 2018-2019)</li> +<li>Project Number 120667 (Development of objective criteria for the evaluation of the visual fit in the kinetic evaluation of degradation data, 2019-2020)</li> +<li>Project 146839 (Checking the feasibility of using mixed-effects models for the derivation of kinetic modelling parameters from degradation studies, 2020-2021)</li> +</ul> </div> <div id="references" class="section level2"> <h2 class="hasAnchor"> diff --git a/docs/news/index.html b/docs/news/index.html index 766e6549..82fb92bd 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -141,6 +141,14 @@ <small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small> </div> + <div id="mkin-103" class="section level1"> +<h1 class="page-header" data-toc-text="1.0.3"> +<a href="#mkin-103" class="anchor"></a>mkin 1.0.3<small> Unreleased </small> +</h1> +<ul> +<li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li> +</ul> +</div> <div id="mkin-102" class="section level1"> <h1 class="page-header" data-toc-text="1.0.2"> <a href="#mkin-102" class="anchor"></a>mkin 1.0.2<small> Unreleased </small> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index f1fe0ec9..847dd4c5 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-02-13T05:53Z +last_built: 2021-02-15T13:07Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index f54fd70f..fbc90802 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -73,7 +73,7 @@ same dataset." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -187,8 +187,7 @@ dataframe if there are several fits in the column).</p> <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS A"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>false convergence (8)</span></div><div class='input'> <span class='co'># We get a warning because the FOMC model does not converge for the</span> + <span class='co'># We get a warning because the FOMC model does not converge for the</span> <span class='co'># FOCUS A dataset, as it is well described by SFO</span> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># We get a single number for a single fit</span> @@ -199,15 +198,15 @@ dataframe if there are several fits in the column).</p> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> df AIC #> SFO 3 55.28197 -#> FOMC 4 57.28211 +#> FOMC 4 57.28222 #> DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span>, k <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># If we do not penalize additional parameters, we get nearly the same</span> </div><div class='output co'>#> df AIC #> SFO 3 49.28197 -#> FOMC 4 49.28211 +#> FOMC 4 49.28222 #> DFOP 5 49.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Comparing the BIC gives a very similar picture</span> </div><div class='output co'>#> df BIC #> SFO 3 55.52030 -#> FOMC 4 57.59987 +#> FOMC 4 57.59999 #> DFOP 5 59.67918</div><div class='input'> <span class='co'># For FOCUS C, the more complex models fit better</span> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index dcccca1b..05cd04a7 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -73,7 +73,7 @@ specified as well." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index b78e73ef..e2d47f1b 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index cff29301..d04f98cc 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -73,7 +73,7 @@ two exponential decline functions." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 4e3cbe64..5a99cf1b 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -220,7 +220,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></td> <span class='op'>)</span> </div><div class='output co'>#> $par #> parent_0 log_alpha log_beta sigma -#> 99.666193 2.549849 5.050586 1.890202 +#> 99.666192 2.549850 5.050586 1.890202 #> #> $objective #> [1] 28.58291 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 d37fa5a5..ba1cb19a 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -76,7 +76,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index d3f7894c..cfb60536 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index a18abad5..c90bcdbb 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index e0fbc498..7b2747dc 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 543e24ad..7a39dcd0 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index c376227c..9136b882 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -73,7 +73,7 @@ a decreasing rate constant." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 8a90fec3..e3009bcc 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -73,7 +73,7 @@ between them." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 8e6a2792..f1a40d44 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -73,7 +73,7 @@ a concentration dependent rate constant." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png Binary files differindex 76d724f0..4f0d7833 100644 --- a/docs/reference/NAFTA_SOP_2015-1.png +++ b/docs/reference/NAFTA_SOP_2015-1.png diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 301bf684..de9db9eb 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png Binary files differindex eec3dd9b..9417685e 100644 --- a/docs/reference/NAFTA_SOP_Attachment-1.png +++ b/docs/reference/NAFTA_SOP_Attachment-1.png diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 03a45bc3..0b063e2c 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -193,7 +193,7 @@ #> Estimate Pr(>t) Lower Upper #> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 #> k1 2.67e-02 5.05e-06 0.0243 0.0295 -#> k2 2.42e-12 5.00e-01 0.0000 Inf +#> k2 2.26e-12 5.00e-01 0.0000 Inf #> g 6.47e-01 3.67e-06 0.6248 0.6677 #> sigma 1.27e+00 8.91e-06 0.8395 1.6929 #> @@ -202,7 +202,7 @@ #> DT50 DT90 DT50_rep #> SFO 67.7 2.25e+02 6.77e+01 #> IORE 58.2 1.07e+03 3.22e+02 -#> DFOP 55.5 5.22e+11 2.86e+11 +#> DFOP 55.5 5.59e+11 3.07e+11 #> #> Representative half-life: #> [1] 321.51</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span> diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex 762a3dd4..7f498242 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex d24e35b4..54c31a3f 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex e96adeb3..19198739 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 91058d4b..1028a9c4 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png Binary files differindex 91058d4b..aa844051 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png Binary files differindex 74f43dfa..81525882 100644 --- a/docs/reference/Rplot006.png +++ b/docs/reference/Rplot006.png diff --git a/docs/reference/Rplot007.png b/docs/reference/Rplot007.png Binary files differindex fce3b6ee..10b7455a 100644 --- a/docs/reference/Rplot007.png +++ b/docs/reference/Rplot007.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 7e4fb237..826a0472 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 7254c451..b2062e30 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -76,7 +76,7 @@ and no substance in the bound fraction." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 9d333cbb..9ba106db 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 07cf0032..493a761a 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 2009aaf4..6fbecd14 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -74,7 +74,7 @@ may depend on the predicted value and is specified as a standard deviation." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 77ee9cef..6399b839 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -74,7 +74,7 @@ by Burnham and Anderson (2004)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index b71e039a..06e78459 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -285,13 +285,13 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class='va'>f_d_1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> user system elapsed -#> 4.324 0.980 3.960 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> +#> 4.255 1.029 3.937 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> <span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span> <span class='co'># minor interest), we get a nice performance improvement if we use at least 4 cores</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> user system elapsed -#> 1.480 0.109 0.905 </div><div class='input'><span class='va'>ci_profile</span> +#> 1.469 0.092 0.911 </div><div class='input'><span class='va'>ci_profile</span> </div><div class='output co'>#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent_sink 0.040762501 5.549764e-02 @@ -349,14 +349,14 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> <span class='va'>ci_quadratic_transformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833585 102.79311650 +#> parent_0 96.403833578 102.79311649 #> k_parent 0.090823771 0.10725430 #> k_m1 0.004012219 0.00689755 #> f_parent_to_m1 0.469118824 0.55959615 #> sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> <span class='va'>ci_quadratic_untransformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833589 1.027931e+02 +#> parent_0 96.403833583 1.027931e+02 #> k_parent 0.090491913 1.069035e-01 #> k_m1 0.003835485 6.685823e-03 #> f_parent_to_m1 0.469113477 5.598387e-01 @@ -374,15 +374,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> f_parent_to_m1 TRUE FALSE #> sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217234 +#> parent_0 0.0005408690 0.0002217233 #> k_parent 0.0009598532 0.0009001864 -#> k_m1 0.0307283044 0.0290588365 -#> f_parent_to_m1 0.0046881768 0.0027780063 +#> k_m1 0.0307283041 0.0290588361 +#> f_parent_to_m1 0.0046881769 0.0027780063 #> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217233 -#> k_parent 0.0046102155 0.0023732281 -#> k_m1 0.0146740688 0.0025291817 +#> parent_0 0.0005408689 0.0002217232 +#> k_parent 0.0046102156 0.0023732281 +#> k_m1 0.0146740690 0.0025291820 #> f_parent_to_m1 0.0046995211 0.0023457712 #> sigma 0.0550252516 0.0327066836</div><div class='input'> <span class='co'># The profiling for the following fit does not finish in a reasonable time,</span> @@ -396,18 +396,18 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, error_model_algorithm <span class='op'>=</span> <span class='st'>"direct"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.596126334 106.19944007 -#> k_M1 0.037605408 0.04490759 -#> k_M2 0.008568739 0.01087675 -#> f_parent_to_M1 0.021463787 0.62023881 -#> f_parent_to_M2 0.015166531 0.37975349 -#> k1 0.273897467 0.33388084 -#> k2 0.018614555 0.02250379 -#> g 0.671943606 0.73583278 -#> sigma_low 0.251283766 0.83992113 -#> rsd_high 0.040411014 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> +#> parent_0 94.596039609 106.19954892 +#> k_M1 0.037605368 0.04490762 +#> k_M2 0.008568731 0.01087676 +#> f_parent_to_M1 0.021462489 0.62023882 +#> f_parent_to_M2 0.015165617 0.37975348 +#> k1 0.273897348 0.33388101 +#> k2 0.018614554 0.02250378 +#> g 0.671943411 0.73583305 +#> sigma_low 0.251283495 0.83992077 +#> rsd_high 0.040411024 0.07662008</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> </div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59613 106.1994</div><div class='input'><span class='co'># }</span> +#> parent_0 94.59604 106.1995</div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index ed49e37e..82583f1a 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -182,7 +182,7 @@ replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child #> 1 analytical 2 0.389 1.000 0.389 0 0 -#> 2 deSolve 2 0.689 1.771 0.688 0 0 +#> 2 deSolve 2 0.690 1.774 0.690 0 0 #> sys.child #> 1 0 #> 2 0</div><div class='input'> <span class='va'>DFOP_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> @@ -193,8 +193,8 @@ deSolve <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>DFOP_SFO</span>, <span class='va'>FOCUS_D</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, replications <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> </div><div class='output co'>#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.825 1.000 0.825 0 0 -#> 2 deSolve 2 1.574 1.908 1.573 0 0 +#> 1 analytical 2 0.817 1.000 0.818 0 0 +#> 2 deSolve 2 1.591 1.947 1.591 0 0 #> sys.child #> 1 0 #> 2 0</div><div class='input'><span class='co'># }</span> diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 435848c2..6845f74f 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -77,7 +77,7 @@ constrained by data protection regulations." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index e42ca9fe..584079d2 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png Binary files differindex 22f38cc2..33946ded 100644 --- a/docs/reference/experimental_data_for_UBA-1.png +++ b/docs/reference/experimental_data_for_UBA-1.png diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 9333a34f..77f75678 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -100,7 +100,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index 6917b4b3..aa494b27 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -73,7 +73,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index f0c766da..61f235db 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -73,7 +73,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index a0e341c9..44703806 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index b91ef055..671faf5d 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -73,7 +73,7 @@ transformations." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 7b1bc4f1..e21304b9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex 43e6a00f..6afd084b 100644 --- a/docs/reference/loftest-3.png +++ b/docs/reference/loftest-3.png diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png Binary files differindex cf7e5862..43460a65 100644 --- a/docs/reference/loftest-5.png +++ b/docs/reference/loftest-5.png diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index 614b8eea..6e72774e 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -75,7 +75,7 @@ lrtest.default from the lmtest package." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 8d984e55..9e5b4069 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -76,7 +76,7 @@ the error model." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png Binary files differindex 79bf3453..73e6436d 100644 --- a/docs/reference/logistic.solution-2.png +++ b/docs/reference/logistic.solution-2.png diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 404344a3..d11e1b3c 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -73,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -240,10 +240,10 @@ Version 1.1, 18 December 2014 <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span> </div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02 -#> kmax 6.398190e-02 0.0143201031 4.467978 3.841829e-04 3.929235e-02 +#> parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-16 1.016451e+02 +#> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02 #> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08 -#> r 2.263946e-01 0.1718110715 1.317695 1.061044e-01 4.335843e-02 +#> r 2.263946e-01 0.1718110662 1.317695 1.061043e-01 4.335843e-02 #> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00 #> Upper #> parent_0 109.9341588 diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index e39314d9..d670fb0c 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -76,7 +76,7 @@ and can be expressed by fixing the parameters of the other." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 2aa5d5f1..4d473893 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -78,7 +78,7 @@ soil section of the FOCUS guidance." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png Binary files differindex 58ae716a..91fe060e 100644 --- a/docs/reference/mccall81_245T-1.png +++ b/docs/reference/mccall81_245T-1.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index b99138a0..b7dca4a7 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -74,7 +74,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -181,30 +181,30 @@ <span class='va'>fit.1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</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://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) -#> T245_0 1.038550e+02 2.1847074888 47.537272 4.472189e-18 +#> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18 #> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13 -#> k_phenol 4.050581e-01 0.2986993400 1.356073 9.756988e-02 -#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07 -#> f_T245_to_phenol 6.227599e-01 0.3985340295 1.562627 6.949412e-02 -#> f_phenol_to_anisole 1.000000e+00 0.6718439378 1.488441 7.867787e-02 -#> sigma 2.514628e+00 0.4907558750 5.123989 6.233156e-05 +#> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02 +#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07 +#> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02 +#> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02 +#> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05 #> Lower Upper -#> T245_0 99.246061370 1.084640e+02 +#> T245_0 99.246061385 1.084640e+02 #> k_T245 0.039631621 4.746194e-02 -#> k_phenol 0.218013878 7.525762e-01 +#> k_phenol 0.218013879 7.525762e-01 #> k_anisole 0.005370739 8.305299e-03 -#> f_T245_to_phenol 0.547559083 6.924813e-01 +#> f_T245_to_phenol 0.547559081 6.924813e-01 #> f_phenol_to_anisole 0.000000000 1.000000e+00 #> sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784092 344.76329 +#> anisole 103.784093 344.76329 #> </div><div class='input'> <span class='co'># formation fraction from phenol to anisol is practically 1. As we cannot</span> <span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span> <span class='co'># the sink in the model generation</span> @@ -215,28 +215,28 @@ quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1623653027 48.028439 4.993108e-19 99.271020526 -#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573555e-14 0.039650977 -#> k_phenol 4.050582e-01 0.1177237248 3.440752 1.679252e-03 0.218746585 -#> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 -#> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198825 2.039410e-12 0.547975628 +#> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284 +#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976 +#> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587 +#> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 +#> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637 #> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 #> Upper -#> T245_0 108.43904097 +#> T245_0 108.43904074 #> k_T245 0.04743877 -#> k_phenol 0.75005577 +#> k_phenol 0.75005585 #> k_anisole 0.00829550 -#> f_T245_to_phenol 0.69212306 +#> f_T245_to_phenol 0.69212308 #> sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 +#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 -#> anisole 103.784092 344.76329 +#> anisole 103.784093 344.76329 #> </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> </div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span> </div></pre> diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png Binary files differindex 05beffc9..28a376f4 100644 --- a/docs/reference/mixed-1.png +++ b/docs/reference/mixed-1.png diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index f5429f8b..23d955e3 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -235,18 +235,16 @@ #> Status of individual fits: #> #> dataset -#> model 1 2 3 4 5 6 7 8 -#> DFOP-SFO OK OK OK OK OK C OK OK +#> model 1 2 3 4 5 6 7 8 +#> DFOP-SFO OK OK OK OK OK OK OK OK #> #> OK: No warnings -#> C: Optimisation did not converge: -#> iteration limit reached without convergence (10) #> #> Mean fitted parameters: #> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 -#> 100.606304 -8.759216 -0.002001 -3.350539 -3.989549 +#> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 #> g_qlogis -#> -0.090353 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_mixed</span><span class='op'>)</span> +#> -0.087392 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_mixed</span><span class='op'>)</span> </div><div class='img'><img src='mixed-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 7eca35de..c82da5dd 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -74,7 +74,7 @@ variable and several dependent variables as columns." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 5df8972f..15619fba 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -74,7 +74,7 @@ mkinfit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 543ea68d..5111a9e0 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -75,7 +75,7 @@ provided by this package come as mkinds objects nevertheless." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 74d3a26c..003e5e8f 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -75,7 +75,7 @@ dataset if no data are supplied." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 161eadca..f22b4350 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -73,7 +73,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 2509e4c1..361ce79a 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -76,7 +76,7 @@ using the argument show_errplot = TRUE." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png Binary files differindex bbc0ccb6..de2a90a9 100644 --- a/docs/reference/mkinfit-1.png +++ b/docs/reference/mkinfit-1.png diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 4d8aeb40..180f2ee7 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -80,7 +80,7 @@ likelihood function." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -431,10 +431,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 <span class='co'># Use shorthand notation for parent only degradation</span> <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> mkin version used for fitting: 1.0.0 +</div><div class='output co'>#> mkin version used for fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:28:58 2021 -#> Date of summary: Wed Feb 3 17:28:58 2021 +#> Date of fit: Mon Feb 15 13:43:26 2021 +#> Date of summary: Mon Feb 15 13:43:26 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -476,10 +476,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.758e-08 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.007e-07 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.568e-08 -#> sigma 4.758e-08 1.007e-07 8.568e-08 1.000e+00 +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08 +#> sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -548,7 +548,7 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span> </div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma_low -#> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049884e-03 +#> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049883e-03 #> rsd_high #> 7.928118e-02 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span> </div><div class='output co'>#> $ff @@ -575,9 +575,9 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>}</span> </div><div class='output co'>#> test relative elapsed -#> 3 analytical 1.000 0.542 -#> 1 deSolve_compiled 1.812 0.982 -#> 2 eigen 2.234 1.211</div><div class='input'><span class='co'># }</span> +#> 3 analytical 1.000 0.550 +#> 1 deSolve_compiled 1.731 0.952 +#> 2 eigen 2.662 1.464</div><div class='input'><span class='co'># }</span> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span> <span class='co'># \dontrun{</span> @@ -587,22 +587,21 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit.FOMC_SFO</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># Again, we get a warning and try a more sophisticated error model</span> <span class='va'>fit.FOMC_SFO.tc</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='co'># This model has a higher likelihood, but not significantly so</span> +<span class='co'># This model has a higher likelihood, but not significantly so</span> <span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.tc</span>, <span class='va'>fit.FOMC_SFO.tc</span><span class='op'>)</span> </div><div class='output co'>#> Likelihood ratio test #> #> Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0 #> Model 2: SFO_SFO with error model tc and fixed parameter(s) m1_0 #> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 7 -64.870 -#> 2 6 -64.983 -1 0.2259 0.6346</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span> +#> 1 7 -64.829 +#> 2 6 -64.983 -1 0.3075 0.5792</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span> <span class='co'># and beta indicate overparameterisation</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.FOMC_SFO.tc</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 1.0.0 +</div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:29:09 2021 -#> Date of summary: Wed Feb 3 17:29:09 2021 +#> Date of fit: Mon Feb 15 13:43:38 2021 +#> Date of summary: Mon Feb 15 13:43:38 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -611,12 +610,12 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 #> #> Model predictions using solution type deSolve #> -#> Fitted using 4273 model solutions performed in 3.195 s +#> Fitted using 3729 model solutions performed in 2.802 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Three-step fitting yielded a higher likelihood than direct fitting +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type @@ -642,72 +641,67 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6 #> value type #> m1_0 0 state #> -#> -#> Warning(s): -#> Optimisation did not converge: -#> iteration limit reached without convergence (10) -#> #> Results: #> -#> AIC BIC logLik -#> 143.7396 155.2027 -64.86982 +#> AIC BIC logLik +#> 143.658 155.1211 -64.82902 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 1.016e+02 1.90600 97.7400 105.5000 -#> log_k_m1 -5.285e+00 0.09286 -5.4740 -5.0950 -#> f_parent_qlogis 6.482e-04 0.06164 -0.1251 0.1264 -#> log_alpha 5.467e+00 NaN NaN NaN -#> log_beta 7.750e+00 NaN NaN NaN -#> sigma_low 0.000e+00 NaN NaN NaN -#> rsd_high 7.989e-02 NaN NaN NaN +#> Estimate Std. Error Lower Upper +#> parent_0 101.600000 2.6400000 96.240000 107.000000 +#> log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000 +#> f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800 +#> log_alpha 5.522000 0.0077320 5.506000 5.538000 +#> log_beta 7.806000 NaN NaN NaN +#> sigma_low 0.002488 0.0002431 0.001992 0.002984 +#> rsd_high 0.079210 0.0093280 0.060180 0.098230 #> #> Parameter correlation: -#> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta -#> parent_0 1.0000000 -0.0002167 -0.6060 NaN NaN -#> log_k_m1 -0.0002167 1.0000000 0.5474 NaN NaN -#> f_parent_qlogis -0.6060320 0.5474423 1.0000 NaN NaN -#> log_alpha NaN NaN NaN 1 NaN -#> log_beta NaN NaN NaN NaN 1 -#> sigma_low NaN NaN NaN NaN NaN -#> rsd_high NaN NaN NaN NaN NaN -#> sigma_low rsd_high -#> parent_0 NaN NaN -#> log_k_m1 NaN NaN -#> f_parent_qlogis NaN NaN -#> log_alpha NaN NaN -#> log_beta NaN NaN -#> sigma_low 1 NaN -#> rsd_high NaN 1 +#> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta +#> parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN +#> log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN +#> f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN +#> log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN +#> log_beta NaN NaN NaN NaN 1 +#> sigma_low 0.016073 0.001586 0.01548 5.87007 NaN +#> rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN +#> sigma_low rsd_high +#> parent_0 0.016073 0.006626 +#> log_k_m1 0.001586 -0.011700 +#> f_parent_qlogis 0.015476 -0.053566 +#> log_alpha 5.870075 0.048487 +#> log_beta NaN NaN +#> sigma_low 1.000000 -0.652558 +#> rsd_high -0.652558 1.000000 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper -#> parent_0 1.016e+02 32.5400 7.812e-26 97.740000 1.055e+02 -#> k_m1 5.069e-03 10.0400 1.448e-11 0.004194 6.126e-03 -#> f_parent_to_m1 5.002e-01 20.7300 5.001e-20 0.468800 5.315e-01 -#> alpha 2.367e+02 0.6205 2.697e-01 NA NA -#> beta 2.322e+03 0.6114 2.727e-01 NA NA -#> sigma_low 0.000e+00 NaN NaN NaN NaN -#> rsd_high 7.989e-02 8.6630 4.393e-10 NaN NaN +#> parent_0 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02 +#> k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03 +#> f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01 +#> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02 +#> beta 2.455e+03 0.5549 2.915e-01 NA NA +#> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03 +#> rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df -#> All data 6.782 5 14 -#> parent 7.142 3 6 -#> m1 4.639 2 8 +#> All data 6.781 5 14 +#> parent 7.141 3 6 +#> m1 4.640 2 8 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.5002 -#> parent_sink 0.4998 +#> parent_m1 0.5004 +#> parent_sink 0.4996 #> #> Estimated disappearance times: -#> DT50 DT90 DT50back -#> parent 6.81 22.7 6.833 -#> m1 136.74 454.2 NA</div><div class='input'> +#> DT50 DT90 DT50back +#> parent 6.812 22.7 6.834 +#> m1 136.661 454.0 NA</div><div class='input'> <span class='co'># We can easily use starting parameters from the parent only fit (only for illustration)</span> <span class='va'>fit.FOMC</span> <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>fit.FOMC_SFO</span> <span class='op'><-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 43e5cc23..4ce9468a 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -78,7 +78,7 @@ mkinmod." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -348,7 +348,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span>, name <span class='op'>=</span> <span class='st'>"SFO_SFO"</span>, dll_dir <span class='op'>=</span> <span class='va'>DLL_dir</span>, unload <span class='op'>=</span> <span class='cn'>TRUE</span>, overwrite <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Copied DLL from /tmp/Rtmp1BYo7R/file5c60502538f0.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span> +</div><div class='output co'>#> <span class='message'>Copied DLL from /tmp/RtmpiJ2M4Z/filee097a4a94a921.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span> <span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS</a></span><span class='op'>(</span><span class='va'>SFO_SFO.2</span>, file <span class='op'>=</span> <span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span> <span class='co'># Terminate the R session here if you would like to check, and then do</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://pkgdown.jrwb.de/mkin/'>mkin</a></span><span class='op'>)</span> @@ -397,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> #> }) #> return(predicted) #> } -#> <environment: 0x55555caa9ee0></div><div class='input'> +#> <environment: 0x55555b0c2760></div><div class='input'> <span class='co'># If we have several parallel metabolites</span> <span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> <span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'>mkinmod</span><span class='op'>(</span> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex dcf3e4b5..c9ed49eb 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index b4d11dcb..c298f5d2 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -73,7 +73,7 @@ mkinfit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -176,7 +176,8 @@ effect, namely to produce a plot.</p> phenol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"anisole"</span><span class='op'>)</span><span class='op'>)</span>, anisole <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</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'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</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'>#> <span class='warning'>Warning: Optimisation did not converge:</span> +#> <span class='warning'>false convergence (8)</span></div><div class='input'><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> </div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 1f0be544..b20a8c96 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -73,7 +73,7 @@ plot.mkinfit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 035a21f9..25e26419 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -410,8 +410,8 @@ as these always return mapped output.</p></td> </div><div class='output co'>#> test relative elapsed #> 2 deSolve_compiled 1.0 0.005 #> 4 analytical 1.0 0.005 -#> 1 eigen 4.0 0.020 -#> 3 deSolve 44.6 0.223</div><div class='input'> +#> 1 eigen 4.4 0.022 +#> 3 deSolve 47.0 0.235</div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Predict from a fitted model</span> <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 69517f36..04ff15b8 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -75,7 +75,7 @@ argument show_residuals = TRUE." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex cce02aed..0db3379f 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex 4f2529fa..024a9892 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex fb5d4470..a23d7cb9 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 4f11753e..89975db5 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex 5d653de9..a2f34983 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 77f815da..c9800fe7 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -75,7 +75,7 @@ datasets specified in its first two arguments." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -234,19 +234,19 @@ plotting.</p></div> <span class='va'>time_default</span> </div><div class='output co'>#> user system elapsed -#> 4.634 0.317 1.280 </div><div class='input'><span class='va'>time_1</span> +#> 4.630 0.415 1.717 </div><div class='input'><span class='va'>time_1</span> </div><div class='output co'>#> user system elapsed -#> 5.249 0.016 5.267 </div><div class='input'> +#> 5.694 0.000 5.694 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340478 0.2659522 0.7505687 0.2494313 +#> 0.7340481 0.2659519 0.7505683 0.2494317 #> #> $distimes #> DT50 DT90 #> parent 0.877769 2.915885 -#> M1 2.325746 7.725960 -#> M2 33.720083 112.015691 +#> M1 2.325744 7.725956 +#> M2 33.720100 112.015749 #> </div><div class='input'> <span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span><span class='op'>)</span> @@ -273,12 +273,10 @@ plotting.</p></div> #> dataset #> model A B C D #> SFO OK OK OK OK -#> FOMC C OK OK OK +#> FOMC OK OK OK OK #> DFOP OK OK OK OK #> -#> OK: No warnings -#> C: Optimisation did not converge: -#> false convergence (8)</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> +#> OK: No warnings</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> <span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span> <span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span> <span class='co'># }</span> diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png Binary files differindex 76d724f0..4f0d7833 100644 --- a/docs/reference/nafta-1.png +++ b/docs/reference/nafta-1.png diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index c6c1b173..29e03251 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -76,7 +76,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex 82b952f7..728cc557 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex 6bc121d1..e8167455 100644 --- a/docs/reference/nlme-2.png +++ b/docs/reference/nlme-2.png diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index f9e68b7f..7b0c6a97 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png Binary files differindex 546a3731..9186c135 100644 --- a/docs/reference/nlme.mmkin-1.png +++ b/docs/reference/nlme.mmkin-1.png diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png Binary files differindex 7b5b4ab0..d395fe02 100644 --- a/docs/reference/nlme.mmkin-2.png +++ b/docs/reference/nlme.mmkin-2.png diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex 7c04df4b..40518a59 100644 --- a/docs/reference/nlme.mmkin-3.png +++ b/docs/reference/nlme.mmkin-3.png diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 2e4f6337..189e34ef 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -157,7 +157,7 @@ have been obtained by fitting the same model to a list of datasets.</p> data <span class='op'>=</span> <span class='st'>"auto"</span>, fixed <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>as.list</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>el</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/eval.html'>eval</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/parse.html'>parse</a></span><span class='op'>(</span>text <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='va'>el</span>, <span class='fl'>1</span>, sep <span class='op'>=</span> <span class='st'>"~"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>, - random <span class='op'>=</span> <span class='fu'>pdDiag</span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>, + random <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span><span class='op'>(</span><span class='va'>fixed</span><span class='op'>)</span>, <span class='va'>groups</span>, start <span class='op'>=</span> <span class='fu'><a href='nlme_function.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>model</span>, random <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, correlation <span class='op'>=</span> <span class='cn'>NULL</span>, @@ -290,7 +290,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value #> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 -#> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> +#> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: @@ -318,7 +318,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as </div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 10.79857 100.7937 30.34192 4.193937 43.85442 +#> parent 10.79857 100.7937 30.34193 4.193938 43.85443 #> </div><div class='input'> <span class='va'>ds_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span> @@ -350,8 +350,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as </div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 -#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</div><div class='input'> +#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 +#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3273 <.0001</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_sink parent_A1 A1_sink @@ -364,12 +364,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_A1 parent_sink -#> 0.2768574 0.7231426 +#> 0.2768575 0.7231425 #> #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 11.07091 104.6320 31.49738 4.462384 46.20825 -#> A1 162.30523 539.1663 NA NA NA +#> parent 11.07091 104.6320 31.49737 4.462384 46.20825 +#> A1 162.30492 539.1653 NA NA NA #> </div><div class='input'> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span> <span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span> @@ -396,7 +396,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Fixed effects: #> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> parent_0 log_k1 log_k2 g_qlogis -#> 94.04775 -1.82340 -4.16715 0.05685 +#> 94.04774 -1.82340 -4.16716 0.05686 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) @@ -410,7 +410,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 2.23224114 0.01262341 </div><div class='input'> +#> 2.23223147 0.01262395 </div><div class='input'> <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> <span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span> @@ -442,7 +442,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Formula: ~1 | name #> Parameter estimates: #> parent A1 -#> 1.0000000 0.2050003 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, +#> 1.0000000 0.2049995 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span><span class='op'>)</span> <span class='va'>f_2_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_2</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> @@ -452,8 +452,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_dfop_sfo_obs</span><span class='op'>)</span> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 -#> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32089 +#> f_nlme_dfop_sfo 1 13 843.8548 884.6201 -408.9274 +#> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093 #> p-value #> f_nlme_dfop_sfo #> f_nlme_dfop_sfo_obs <.0001</div><div class='input'> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index dff8a285..6b9948c3 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index ab5888fa..e45d6a5c 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -74,7 +74,7 @@ considering the error structure that was assumed for the fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -219,10 +219,10 @@ such matrices is returned.</p> #> #> $DFOP #> Dataset 7 -#> parent_0 91.058971597 +#> parent_0 91.058971589 #> k1 0.044946770 #> k2 0.002868336 -#> g 0.526942414 +#> g 0.526942415 #> sigma 2.221302196 #> </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>)</span> </div><div class='output co'>#> $SFO @@ -233,17 +233,17 @@ such matrices is returned.</p> #> #> $FOMC #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458 +#> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459 #> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272 #> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224 #> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778 #> #> $DFOP #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 96.55213663 91.058971597 90.34509493 98.14858820 94.311323733 +#> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734 #> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857 #> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417 -#> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880 +#> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880 #> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831 #> </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> $SFO diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 46303c44..4b72a308 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 376c812f..a11d1680 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex bc44de88..6631aa68 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differindex eb8cbd92..946b20c5 100644 --- a/docs/reference/plot.mkinfit-6.png +++ b/docs/reference/plot.mkinfit-6.png diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png Binary files differindex 92a664f4..10807ea8 100644 --- a/docs/reference/plot.mkinfit-7.png +++ b/docs/reference/plot.mkinfit-7.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 1be0f9af..b80c672d 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex f12b7907..647dfb8a 100644 --- a/docs/reference/plot.mmkin-1.png +++ b/docs/reference/plot.mmkin-1.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex e3127554..1bc1c9db 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 5448976e..50d6ffac 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 9a25fc50..e049fa16 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png Binary files differindex 82b422b5..2421995b 100644 --- a/docs/reference/plot.mmkin-5.png +++ b/docs/reference/plot.mmkin-5.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 4e9836ec..20f9033d 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -76,7 +76,7 @@ the fit of at least one model to the same dataset is shown." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 29cc984a..544ee5eb 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -73,7 +73,7 @@ function (SFO, then IORE, then DFOP)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 2bfeb582..864c4ff9 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -79,7 +79,7 @@ below to see their documentation. </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index db7c1a40..c5c2dcaf 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -175,7 +175,7 @@ standard deviation obtained from the fitted error model?</p></td> </div><div class='output co'>#> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702 #> [7] -0.03269080 1.45347823 -0.88423697</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>f</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208 -#> [7] -0.04695354 2.08761977 -1.27002287</div></pre> +#> [7] -0.04695355 2.08761977 -1.27002287</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"> diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png Binary files differindex be903641..96aab2dc 100644 --- a/docs/reference/schaefer07_complex_case-1.png +++ b/docs/reference/schaefer07_complex_case-1.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 74f71f46..979e4c29 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -74,7 +74,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -186,15 +186,15 @@ </div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809620 0.1954665 0.4235715 0.0000000 0.4479662 0.5520338 +#> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 #> #> $distimes #> DT50 DT90 #> parent 13.95078 46.34350 -#> A1 49.75343 165.27731 -#> B1 37.26912 123.80533 -#> C1 11.23131 37.30959 -#> A2 28.50569 94.69386 +#> A1 49.75342 165.27728 +#> B1 37.26908 123.80520 +#> C1 11.23131 37.30961 +#> A2 28.50624 94.69567 #> </div><div class='input'> <span class='co'># }</span> <span class='co'># Compare with the results obtained in the original publication</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_results</span><span class='op'>)</span> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 46ca562a..397582f0 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -73,7 +73,7 @@ dependence of the measured value \(y\):" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -188,6 +188,10 @@ Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry 24(11), 1895-1898.</p> <p>Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> +<p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical +Degradation Data. <em>Environments</em> 6(12) 124 +doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6120124</a> +.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='va'>times</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 7be427bf..67a50216 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -76,7 +76,7 @@ values." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -236,17 +236,17 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <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://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>FOCUS_2006_A</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> mkin version used for fitting: 1.0.0 +</div><div class='output co'>#> mkin version used for fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:32:02 2021 -#> Date of summary: Wed Feb 3 17:32:02 2021 +#> Date of fit: Mon Feb 15 13:46:11 2021 +#> Date of summary: Mon Feb 15 13:46:11 2021 #> #> Equations: #> d_parent/dt = - k_parent * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.028 s +#> Fitted using 131 model solutions performed in 0.029 s #> #> Error model: Constant variance #> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index bc60b53e..d6840425 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -264,11 +264,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> </div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> #> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> </div><div class='output co'>#> <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> nlme version used for fitting: 3.1.151 -#> mkin version used for pre-fitting: 1.0.0 +</div><div class='output co'>#> nlme version used for fitting: 3.1.152 +#> mkin version used for pre-fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:32:05 2021 -#> Date of summary: Wed Feb 3 17:32:05 2021 +#> Date of fit: Mon Feb 15 13:46:13 2021 +#> Date of summary: Mon Feb 15 13:46:13 2021 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -278,7 +278,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 0.526 s using 4 iterations +#> Fitted in 0.553 s using 4 iterations #> #> Variance model: Two-component variance function #> @@ -307,19 +307,19 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> Formula: list(parent_0 ~ 1, log_k_parent ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k_parent Residual -#> StdDev: 6.91e-05 0.5863 1 +#> parent_0 log_k_parent Residual +#> StdDev: 6.924e-05 0.5863 1 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 0.0001206605 0.0789967776 +#> 0.0001208853 0.0789968036 #> #> Backtransformed parameters with asymmetric confidence intervals: #> lower est. upper -#> parent_0 99.370883 101.59243 103.81398 +#> parent_0 99.370882 101.59243 103.81398 #> k_parent 0.006923 0.01168 0.01972 #> #> Estimated disappearance times: @@ -330,68 +330,68 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> ds name time observed predicted residual std standardized #> ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451 #> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594 -#> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288314 +#> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313 #> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725 #> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796 -#> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788813 +#> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812 #> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081 #> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065 -#> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401988 +#> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987 #> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480 #> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857 -#> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523365 +#> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364 #> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008 #> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898 -#> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561253 +#> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252 #> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335 #> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423 #> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549 -#> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785944 +#> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943 #> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245 -#> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473362 -#> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080627 +#> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361 +#> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626 #> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297 #> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874 -#> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667252 -#> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326648 +#> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251 +#> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647 #> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366 #> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571 #> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748 #> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002 #> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679 -#> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249486 +#> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485 #> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198 #> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171 -#> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901596 +#> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595 #> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547 #> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009 -#> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668740 -#> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362859 +#> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739 +#> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858 #> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921 #> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603 #> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360 -#> ds 3 parent 7 78.3 86.093 -7.79273 6.8010 -1.145813 -#> ds 3 parent 7 90.3 86.093 4.20727 6.8010 0.618621 -#> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527849 -#> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065723 +#> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813 +#> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620 +#> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848 +#> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722 #> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842 #> ds 3 parent 28 53.4 52.394 1.00596 4.1390 0.243046 #> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676 -#> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638665 -#> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143200 -#> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206777 +#> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664 +#> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199 +#> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776 #> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178 #> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282 #> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057 -#> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050785 +#> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784 #> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025 #> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205 #> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218 -#> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260887 +#> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886 #> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706 #> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270 #> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357 -#> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271522 +#> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521 #> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001 #> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017 #> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526 @@ -400,18 +400,18 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> #> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591 #> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058 #> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530 -#> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120486 +#> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485 #> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531 #> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413 -#> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631656 +#> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655 #> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477 -#> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935383 +#> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382 #> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267 -#> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656305 -#> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273296 +#> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304 +#> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295 #> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141 #> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178 -#> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802063 +#> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062 #> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835 #> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174 #> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913 diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 4f11753e..89975db5 100644 --- a/docs/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index af8bdcb2..c37b986e 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -87,7 +87,7 @@ Compare also the code in the example section to see the degradation models." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -297,10 +297,10 @@ Compare also the code in the example section to see the degradation models." /> quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> </div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> mkin version used for fitting: 1.0.0 +</div><div class='output co'>#> mkin version used for fitting: 1.0.3 #> R version used for fitting: 4.0.3 -#> Date of fit: Wed Feb 3 17:32:06 2021 -#> Date of summary: Wed Feb 3 17:32:06 2021 +#> Date of fit: Mon Feb 15 13:46:15 2021 +#> Date of summary: Mon Feb 15 13:46:15 2021 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -309,7 +309,7 @@ Compare also the code in the example section to see the degradation models." /> #> #> Model predictions using solution type deSolve #> -#> Fitted using 822 model solutions performed in 0.645 s +#> Fitted using 833 model solutions performed in 0.665 s #> #> Error model: Constant variance #> @@ -361,15 +361,15 @@ Compare also the code in the example section to see the degradation models." /> #> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01 #> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00 #> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01 -#> sigma -7.941e-08 -9.143e-09 -1.268e-08 5.947e-08 5.657e-08 +#> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08 #> f_M1_qlogis sigma -#> parent_0 1.614e-01 -7.941e-08 -#> log_k_parent 4.102e-01 -9.143e-09 -#> log_k_M1 -8.109e-01 -1.268e-08 -#> log_k_M2 5.419e-01 5.947e-08 -#> f_parent_qlogis -8.605e-01 5.657e-08 -#> f_M1_qlogis 1.000e+00 -2.382e-10 -#> sigma -2.382e-10 1.000e+00 +#> parent_0 1.614e-01 -2.900e-08 +#> log_k_parent 4.102e-01 -8.030e-09 +#> log_k_M1 -8.109e-01 -2.741e-08 +#> log_k_M2 5.419e-01 3.938e-08 +#> f_parent_qlogis -8.605e-01 -2.681e-08 +#> f_M1_qlogis 1.000e+00 4.971e-08 +#> sigma 4.971e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -416,7 +416,7 @@ Compare also the code in the example section to see the degradation models." /> #> 7 parent 0.3 5.772e-01 -0.27717 #> 14 parent 3.5 3.264e-03 3.49674 #> 28 parent 3.2 1.045e-07 3.20000 -#> 90 parent 0.6 9.532e-10 0.60000 +#> 90 parent 0.6 9.530e-10 0.60000 #> 120 parent 3.5 -5.940e-10 3.50000 #> 1 M1 36.4 3.479e+01 1.61088 #> 1 M1 37.4 3.479e+01 2.61088 @@ -427,7 +427,7 @@ Compare also the code in the example section to see the degradation models." /> #> 14 M1 5.8 1.995e+00 3.80469 #> 14 M1 1.2 1.995e+00 -0.79531 #> 60 M1 0.5 2.111e-06 0.50000 -#> 90 M1 3.2 -9.671e-10 3.20000 +#> 90 M1 3.2 -9.670e-10 3.20000 #> 120 M1 1.5 7.670e-10 1.50000 #> 120 M1 0.6 7.670e-10 0.60000 #> 1 M2 4.8 4.455e+00 0.34517 diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differindex 168103ee..7bf0bd0f 100644 --- a/docs/reference/test_data_from_UBA_2014-1.png +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differindex 68288aed..fc1f77e0 100644 --- a/docs/reference/test_data_from_UBA_2014-2.png +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index eeaef9e0..c0056d45 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -73,7 +73,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -203,25 +203,25 @@ </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='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_soil</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span><span class='op'>)</span> </div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 76.55425649 0.859186399 89.1008710 1.113861e-26 74.755959406 +#> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418 #> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575 -#> k_M1 0.84258614 0.806159820 1.0451850 1.545267e-01 0.113779670 -#> k_M2 0.04210880 0.017083035 2.4649483 1.170188e-02 0.018013857 -#> k_M3 0.01122918 0.007245855 1.5497385 6.885052e-02 0.002909431 -#> f_parent_to_M1 0.32240200 0.240783909 1.3389682 9.819073e-02 NA -#> f_parent_to_M2 0.16099855 0.033691953 4.7785463 6.531137e-05 NA -#> f_M1_to_M3 0.27921507 0.269423745 1.0363417 1.565266e-01 0.022978220 -#> f_M2_to_M3 0.55641253 0.595119954 0.9349586 1.807707e-01 0.008002509 +#> k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609 +#> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857 +#> k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431 +#> f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA +#> f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA +#> f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205 +#> f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509 #> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 #> Upper -#> parent_0 78.35255357 +#> parent_0 78.35255358 #> k_parent 0.13084582 -#> k_M1 6.23970352 +#> k_M1 6.23970702 #> k_M2 0.09843260 #> k_M3 0.04333992 #> f_parent_to_M1 NA #> f_parent_to_M2 NA -#> f_M1_to_M3 0.86450768 +#> f_M1_to_M3 0.86450775 #> f_M2_to_M3 0.99489895 #> sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span> </div><div class='output co'>#> err.min n.optim df diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index e2cb876b..c3c756f6 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -77,7 +77,7 @@ the ilr transformation is used." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> @@ -259,13 +259,13 @@ This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</ <span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.59849 1.57022 96.40385 1.03e+02 +#> parent_0 99.59848 1.57022 96.40384 1.03e+02 #> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 #> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 #> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 #> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> </div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59849 1.57022 63.43 2.30e-36 96.40385 1.03e+02 +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 #> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 #> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 #> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index f7149d84..09050e53 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -75,7 +75,7 @@ override these starting values." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span> </span> </div> |
