diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-05-19 17:08:43 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-05-19 17:10:16 +0200 |
| commit | cf54ccca37d27480dbf8d59eb027300518f7ad75 (patch) | |
| tree | 81a9d5955f716a74822ecb65dc83daeeb7efbba6 /docs | |
| parent | c931057ce8f05d3a0dfefea72b73903efb82e900 (diff) | |
Prepare release of v1.2.4v1.2.4
- Update DESCRIPTION
- Update Makefile to document how to use R-patched
- Remove markup from two URLs to avoid CRAN NOTE
- Switch two vignettes from html_document to html_vignette to save space
in the docs directory, also avoiding a CRAN NOTE
- Complete rebuild of pkgdown docs for release
Diffstat (limited to 'docs')
168 files changed, 2530 insertions, 2745 deletions
diff --git a/docs/404.html b/docs/404.html index 4d888396..b9ab1f25 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ </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">1.2.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 0d2f56f5..19367c68 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -135,7 +135,7 @@ D</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change 31 January 2019 -(rebuilt 2023-04-20)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_D.rmd" class="external-link"><code>vignettes/FOCUS_D.rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.rmd</code></div> @@ -237,10 +237,10 @@ the <code>mkinparplot</code> function.</p> <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><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Thu Apr 20 07:37:14 2023 </span></span> -<span><span class="co">## Date of summary: Thu Apr 20 07:37:14 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.4 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 09:20:23 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 09:20:23 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> @@ -248,7 +248,7 @@ the <code>mkinparplot</code> function.</p> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 401 model solutions performed in 0.047 s</span></span> +<span><span class="co">## Fitted using 401 model solutions performed in 0.048 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -292,10 +292,10 @@ the <code>mkinparplot</code> function.</p> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma</span></span> <span><span class="co">## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06</span></span> -<span><span class="co">## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07</span></span> -<span><span class="co">## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07</span></span> +<span><span class="co">## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.479e-07</span></span> +<span><span class="co">## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.211e-07</span></span> <span><span class="co">## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06</span></span> -<span><span class="co">## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00</span></span> +<span><span class="co">## sigma -1.172e-06 -8.479e-07 8.211e-07 1.305e-06 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index e47ed9d7..dabb16f2 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -134,8 +134,8 @@ to L3</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 18 May 2022 -(rebuilt 2023-04-20)</h4> + <h4 data-toc-skip class="date">Last change 18 May 2023 +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small> <div class="hidden name"><code>FOCUS_L.rmd</code></div> @@ -169,10 +169,10 @@ report.</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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> <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Thu Apr 20 07:37:15 2023 </span></span> -<span><span class="co">## Date of summary: Thu Apr 20 07:37:15 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.4 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 09:20:25 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 09:20:25 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> @@ -276,17 +276,17 @@ objects.</p> <pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> <span><span class="co">## is doubtful</span></span></code></pre> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Thu Apr 20 07:37:16 2023 </span></span> -<span><span class="co">## Date of summary: Thu Apr 20 07:37:16 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.4 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 09:20:25 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 09:20:25 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 369 model solutions performed in 0.025 s</span></span> +<span><span class="co">## Fitted using 342 model solutions performed in 0.021 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -314,22 +314,22 @@ objects.</p> <span><span class="co">## </span></span> <span><span class="co">## Results:</span></span> <span><span class="co">## </span></span> -<span><span class="co">## AIC BIC logLik</span></span> -<span><span class="co">## 95.88781 99.44929 -43.9439</span></span> +<span><span class="co">## AIC BIC logLik</span></span> +<span><span class="co">## 95.88782 99.44931 -43.94391</span></span> <span><span class="co">## </span></span> <span><span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span></span> <span><span class="co">## Estimate Std. Error Lower Upper</span></span> <span><span class="co">## parent_0 92.47 1.2820 89.720 95.220</span></span> -<span><span class="co">## log_alpha 13.78 NaN NaN NaN</span></span> -<span><span class="co">## log_beta 16.13 NaN NaN NaN</span></span> -<span><span class="co">## sigma 2.78 0.4598 1.794 3.766</span></span> +<span><span class="co">## log_alpha 13.20 NaN NaN NaN</span></span> +<span><span class="co">## log_beta 15.54 NaN NaN NaN</span></span> +<span><span class="co">## sigma 2.78 0.4607 1.792 3.768</span></span> <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> -<span><span class="co">## parent_0 log_alpha log_beta sigma</span></span> -<span><span class="co">## parent_0 1.0000000 NaN NaN 0.0001671</span></span> -<span><span class="co">## log_alpha NaN 1 NaN NaN</span></span> -<span><span class="co">## log_beta NaN NaN 1 NaN</span></span> -<span><span class="co">## sigma 0.0001671 NaN NaN 1.0000000</span></span> +<span><span class="co">## parent_0 log_alpha log_beta sigma</span></span> +<span><span class="co">## parent_0 1.000000 NaN NaN 0.000603</span></span> +<span><span class="co">## log_alpha NaN 1 NaN NaN</span></span> +<span><span class="co">## log_beta NaN NaN 1 NaN</span></span> +<span><span class="co">## sigma 0.000603 NaN NaN 1.000000</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -337,9 +337,9 @@ objects.</p> <span><span class="co">## for estimators of untransformed parameters.</span></span> <span><span class="co">## Estimate t value Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 9.247e+01 NA NA 89.720 95.220</span></span> -<span><span class="co">## alpha 9.658e+05 NA NA NA NA</span></span> -<span><span class="co">## beta 1.010e+07 NA NA NA NA</span></span> -<span><span class="co">## sigma 2.780e+00 NA NA 1.794 3.766</span></span> +<span><span class="co">## alpha 5.386e+05 NA NA NA NA</span></span> +<span><span class="co">## beta 5.633e+06 NA NA NA NA</span></span> +<span><span class="co">## sigma 2.780e+00 NA NA 1.792 3.768</span></span> <span><span class="co">## </span></span> <span><span class="co">## FOCUS Chi2 error levels in percent:</span></span> <span><span class="co">## err.min n.optim df</span></span> @@ -347,8 +347,8 @@ objects.</p> <span><span class="co">## parent 3.619 3 6</span></span> <span><span class="co">## </span></span> <span><span class="co">## Estimated disappearance times:</span></span> -<span><span class="co">## DT50 DT90 DT50back</span></span> -<span><span class="co">## parent 7.25 24.08 7.25</span></span></code></pre> +<span><span class="co">## DT50 DT90 DT50back</span></span> +<span><span class="co">## parent 7.249 24.08 7.249</span></span></code></pre> <p>We get a warning that the default optimisation algorithm <code>Port</code> did not converge, which is an indication that the model is overparameterised, <em>i.e.</em> contains too many parameters @@ -427,17 +427,17 @@ kinetics.</p> <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><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Thu Apr 20 07:37:16 2023 </span></span> -<span><span class="co">## Date of summary: Thu Apr 20 07:37:16 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.4 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 09:20:25 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 09:20:25 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 239 model solutions performed in 0.015 s</span></span> +<span><span class="co">## Fitted using 239 model solutions performed in 0.013 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -472,10 +472,10 @@ kinetics.</p> <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_alpha log_beta sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.828e-09</span></span> -<span><span class="co">## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.602e-07</span></span> -<span><span class="co">## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.372e-07</span></span> -<span><span class="co">## sigma -7.828e-09 -1.602e-07 -1.372e-07 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09</span></span> +<span><span class="co">## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.617e-07</span></span> +<span><span class="co">## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.386e-07</span></span> +<span><span class="co">## sigma -7.436e-09 -1.617e-07 -1.386e-07 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -511,10 +511,10 @@ the data.</p> <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><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Thu Apr 20 07:37:16 2023 </span></span> -<span><span class="co">## Date of summary: Thu Apr 20 07:37:16 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.4 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 09:20:25 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 09:20:25 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -523,7 +523,7 @@ the data.</p> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 581 model solutions performed in 0.04 s</span></span> +<span><span class="co">## Fitted using 581 model solutions performed in 0.038 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -554,18 +554,18 @@ the data.</p> <span><span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span></span> <span><span class="co">## Estimate Std. Error Lower Upper</span></span> <span><span class="co">## parent_0 93.950 9.998e-01 91.5900 96.3100</span></span> -<span><span class="co">## log_k1 3.112 1.842e+03 -4353.0000 4359.0000</span></span> +<span><span class="co">## log_k1 3.113 1.849e+03 -4369.0000 4375.0000</span></span> <span><span class="co">## log_k2 -1.088 6.285e-02 -1.2370 -0.9394</span></span> <span><span class="co">## g_qlogis -0.399 9.946e-02 -0.6342 -0.1638</span></span> <span><span class="co">## sigma 1.414 2.886e-01 0.7314 2.0960</span></span> <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_k1 log_k2 g_qlogis sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 6.783e-07 -3.390e-10 2.665e-01 -2.967e-10</span></span> -<span><span class="co">## log_k1 6.783e-07 1.000e+00 1.116e-04 -2.196e-04 -1.031e-05</span></span> -<span><span class="co">## log_k2 -3.390e-10 1.116e-04 1.000e+00 -7.903e-01 2.917e-09</span></span> -<span><span class="co">## g_qlogis 2.665e-01 -2.196e-04 -7.903e-01 1.000e+00 -4.408e-09</span></span> -<span><span class="co">## sigma -2.967e-10 -1.031e-05 2.917e-09 -4.408e-09 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 6.763e-07 -8.944e-10 2.665e-01 -1.083e-09</span></span> +<span><span class="co">## log_k1 6.763e-07 1.000e+00 1.112e-04 -2.187e-04 -1.027e-05</span></span> +<span><span class="co">## log_k2 -8.944e-10 1.112e-04 1.000e+00 -7.903e-01 9.464e-09</span></span> +<span><span class="co">## g_qlogis 2.665e-01 -2.187e-04 -7.903e-01 1.000e+00 -1.532e-08</span></span> +<span><span class="co">## sigma -1.083e-09 -1.027e-05 9.464e-09 -1.532e-08 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -573,7 +573,7 @@ the data.</p> <span><span class="co">## for estimators of untransformed parameters.</span></span> <span><span class="co">## Estimate t value Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100</span></span> -<span><span class="co">## k1 22.4800 5.553e-04 4.998e-01 0.0000 Inf</span></span> +<span><span class="co">## k1 22.4900 5.533e-04 4.998e-01 0.0000 Inf</span></span> <span><span class="co">## k2 0.3369 1.591e+01 4.697e-07 0.2904 0.3909</span></span> <span><span class="co">## g 0.4016 1.680e+01 3.238e-07 0.3466 0.4591</span></span> <span><span class="co">## sigma 1.4140 4.899e+00 8.776e-04 0.7314 2.0960</span></span> @@ -585,7 +585,7 @@ the data.</p> <span><span class="co">## </span></span> <span><span class="co">## Estimated disappearance times:</span></span> <span><span class="co">## DT50 DT90 DT50back DT50_k1 DT50_k2</span></span> -<span><span class="co">## parent 0.5335 5.311 1.599 0.03084 2.058</span></span></code></pre> +<span><span class="co">## parent 0.5335 5.311 1.599 0.03083 2.058</span></span></code></pre> <p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion.</p> </div> @@ -628,10 +628,10 @@ 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><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Thu Apr 20 07:37:17 2023 </span></span> -<span><span class="co">## Date of summary: Thu Apr 20 07:37:17 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.4 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 09:20:26 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 09:20:26 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -640,7 +640,7 @@ summary and plot functions working on mkinfit objects.</p> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 376 model solutions performed in 0.024 s</span></span> +<span><span class="co">## Fitted using 376 model solutions performed in 0.021 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -678,11 +678,11 @@ summary and plot functions working on mkinfit objects.</p> <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_k1 log_k2 g_qlogis sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.664e-08</span></span> -<span><span class="co">## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.147e-07</span></span> +<span><span class="co">## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.696e-08</span></span> +<span><span class="co">## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.148e-07</span></span> <span><span class="co">## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.022e-06</span></span> -<span><span class="co">## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.926e-07</span></span> -<span><span class="co">## sigma -9.664e-08 7.147e-07 1.022e-06 -7.926e-07 1.000e+00</span></span> +<span><span class="co">## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.930e-07</span></span> +<span><span class="co">## sigma -9.696e-08 7.148e-07 1.022e-06 -7.930e-07 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -755,17 +755,17 @@ 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><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Thu Apr 20 07:37:17 2023 </span></span> -<span><span class="co">## Date of summary: Thu Apr 20 07:37:17 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.4 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 09:20:26 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 09:20:26 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 142 model solutions performed in 0.009 s</span></span> +<span><span class="co">## Fitted using 142 model solutions performed in 0.008 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -797,9 +797,9 @@ appears negligible.</p> <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_k_parent sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 5.938e-01 3.387e-07</span></span> -<span><span class="co">## log_k_parent 5.938e-01 1.000e+00 5.830e-07</span></span> -<span><span class="co">## sigma 3.387e-07 5.830e-07 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 5.938e-01 3.430e-07</span></span> +<span><span class="co">## log_k_parent 5.938e-01 1.000e+00 5.885e-07</span></span> +<span><span class="co">## sigma 3.430e-07 5.885e-07 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> @@ -820,17 +820,17 @@ appears negligible.</p> <span><span class="co">## parent 106 352</span></span></code></pre> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Thu Apr 20 07:37:17 2023 </span></span> -<span><span class="co">## Date of summary: Thu Apr 20 07:37:17 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.4 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 09:20:26 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 09:20:26 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 224 model solutions performed in 0.014 s</span></span> +<span><span class="co">## Fitted using 224 model solutions performed in 0.012 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -865,10 +865,10 @@ appears negligible.</p> <span><span class="co">## </span></span> <span><span class="co">## Parameter correlation:</span></span> <span><span class="co">## parent_0 log_alpha log_beta sigma</span></span> -<span><span class="co">## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.468e-07</span></span> -<span><span class="co">## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.478e-08</span></span> -<span><span class="co">## log_beta -5.543e-01 9.889e-01 1.000e+00 5.211e-08</span></span> -<span><span class="co">## sigma -2.468e-07 2.478e-08 5.211e-08 1.000e+00</span></span> +<span><span class="co">## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.447e-07</span></span> +<span><span class="co">## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.198e-08</span></span> +<span><span class="co">## log_beta -5.543e-01 9.889e-01 1.000e+00 4.923e-08</span></span> +<span><span class="co">## sigma -2.447e-07 2.198e-08 4.923e-08 1.000e+00</span></span> <span><span class="co">## </span></span> <span><span class="co">## Backtransformed parameters:</span></span> <span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> 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 11706305..c732be75 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-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png Binary files differindex c3f55dd6..dfeb7907 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/index.html b/docs/articles/index.html index 991f8994..7060b377 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ </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">1.2.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -111,7 +111,7 @@ <dd> </dd><dt><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></dt> <dd> - </dd><dt><a href="mkin.html">Introduction to mkin</a></dt> + </dd><dt><a href="mkin.html">Short introduction to mkin</a></dt> <dd> </dd><dt><a href="prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></dt> <dd> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 88c63bef..6213916b 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -5,13 +5,13 @@ <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Introduction to mkin • mkin</title> +<title>Short introduction to mkin • mkin</title> <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"> <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to mkin"> +<script src="../pkgdown.js"></script><meta property="og:title" content="Short introduction to mkin"> <meta property="og:description" content="mkin"> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -129,12 +129,12 @@ </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> - <h1 data-toc-skip>Introduction to mkin</h1> + <h1 data-toc-skip>Short introduction to mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 15 February 2021 -(rebuilt 2023-04-20)</h4> + <h4 data-toc-skip class="date">Last change 18 May 2023 +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small> <div class="hidden name"><code>mkin.rmd</code></div> 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 7ba861ea..65c1a613 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/prebuilt/2022_cyan_pathway.html b/docs/articles/prebuilt/2022_cyan_pathway.html index cd63fa3c..c22c6735 100644 --- a/docs/articles/prebuilt/2022_cyan_pathway.html +++ b/docs/articles/prebuilt/2022_cyan_pathway.html @@ -33,7 +33,7 @@ </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">1.2.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -135,7 +135,7 @@ residue data on cyantraniliprole</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 20 April 2023</h4> +last compiled on 19 Mai 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_cyan_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_cyan_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_cyan_pathway.rmd</code></div> @@ -155,7 +155,7 @@ be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.3 which is currently under +<p>The mkin package is used in version 1.2.4 which is currently under development. The newly introduced functionality that is used here is a simplification of excluding random effects for a set of fits based on a related set of fits with a reduced model, and the documentation of the @@ -1356,9 +1356,9 @@ when the two-component error model is used.</p> <tr class="odd"> <td align="left">SFORB tc</td> <td align="right">10</td> -<td align="right">700.1</td> -<td align="right">696.2</td> -<td align="right">-340.1</td> +<td align="right">700.0</td> +<td align="right">696.1</td> +<td align="right">-340.0</td> </tr> <tr class="even"> <td align="left">HS tc</td> @@ -1447,7 +1447,7 @@ pathway fits are performed for all datasets.</p> <td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> -<td align="left">OK</td> +<td align="left">C</td> <td align="left">OK</td> </tr> <tr class="even"> @@ -1511,7 +1511,7 @@ pathway fits are performed for all datasets.</p> <td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> -<td align="left">C</td> +<td align="left">OK</td> </tr> <tr class="odd"> <td align="left">dfop_path_1</td> @@ -1524,7 +1524,7 @@ pathway fits are performed for all datasets.</p> <tr class="even"> <td align="left">sforb_path_1</td> <td align="left">OK</td> -<td align="left">C</td> +<td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> @@ -1535,7 +1535,7 @@ pathway fits are performed for all datasets.</p> <td align="left">OK</td> <td align="left">C</td> <td align="left">OK</td> -<td align="left">OK</td> +<td align="left">C</td> </tr> </tbody> </table> @@ -1564,7 +1564,7 @@ which is currently under development.</p> <tbody> <tr class="odd"> <td align="left">sfo_path_1</td> -<td align="left">Fth, FO</td> +<td align="left">FO</td> <td align="left">Fth, FO</td> </tr> <tr class="even"> @@ -1584,8 +1584,8 @@ which is currently under development.</p> </tr> <tr class="odd"> <td align="left">hs_path_1</td> -<td align="left">Fth, FO</td> -<td align="left">Fth, FO</td> +<td align="left">FO</td> +<td align="left">E</td> </tr> </tbody> </table> @@ -1634,7 +1634,7 @@ sd(f_JCZ38_qlogis)</td> <tr class="odd"> <td align="left">hs_path_1</td> <td align="left">NA</td> -<td align="left">NA</td> +<td align="left">E</td> </tr> </tbody> </table> @@ -1654,30 +1654,30 @@ or SFORB for the parent compound provide the best fit.</p> <tr class="odd"> <td align="left">sfo_path_1 const</td> <td align="right">16</td> -<td align="right">2692.8</td> -<td align="right">2686.6</td> -<td align="right">-1330.4</td> +<td align="right">2693.0</td> +<td align="right">2686.8</td> +<td align="right">-1330.5</td> </tr> <tr class="even"> <td align="left">sfo_path_1 tc</td> <td align="right">17</td> -<td align="right">2657.7</td> -<td align="right">2651.1</td> -<td align="right">-1311.9</td> +<td align="right">2657.6</td> +<td align="right">2651.0</td> +<td align="right">-1311.8</td> </tr> <tr class="odd"> <td align="left">fomc_path_1 const</td> <td align="right">18</td> -<td align="right">2427.8</td> -<td align="right">2420.8</td> -<td align="right">-1195.9</td> +<td align="right">2427.9</td> +<td align="right">2420.9</td> +<td align="right">-1196.0</td> </tr> <tr class="even"> <td align="left">fomc_path_1 tc</td> <td align="right">19</td> -<td align="right">2423.4</td> -<td align="right">2416.0</td> -<td align="right">-1192.7</td> +<td align="right">2423.6</td> +<td align="right">2416.2</td> +<td align="right">-1192.8</td> </tr> <tr class="odd"> <td align="left">dfop_path_1 const</td> @@ -1696,30 +1696,23 @@ or SFORB for the parent compound provide the best fit.</p> <tr class="odd"> <td align="left">hs_path_1 const</td> <td align="right">20</td> -<td align="right">2427.3</td> -<td align="right">2419.5</td> -<td align="right">-1193.7</td> +<td align="right">2427.2</td> +<td align="right">2419.4</td> +<td align="right">-1193.6</td> </tr> <tr class="even"> <td align="left">dfop_path_1 tc</td> <td align="right">20</td> <td align="right">2398.0</td> -<td align="right">2390.2</td> +<td align="right">2390.1</td> <td align="right">-1179.0</td> </tr> <tr class="odd"> <td align="left">sforb_path_1 tc</td> <td align="right">20</td> -<td align="right">2399.8</td> -<td align="right">2392.0</td> -<td align="right">-1179.9</td> -</tr> -<tr class="even"> -<td align="left">hs_path_1 tc</td> -<td align="right">21</td> -<td align="right">2422.3</td> -<td align="right">2414.1</td> -<td align="right">-1190.2</td> +<td align="right">2399.9</td> +<td align="right">2392.1</td> +<td align="right">-1180.0</td> </tr> </tbody> </table> @@ -1827,7 +1820,7 @@ alternative pathway fits.</p> <td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> -<td align="left">C</td> +<td align="left">OK</td> <td align="left">OK</td> </tr> </tbody> @@ -1850,7 +1843,7 @@ the fits to the Sassafras soil data.</p> <tr class="odd"> <td align="left">fomc_path_2</td> <td align="left">OK</td> -<td align="left">C</td> +<td align="left">OK</td> <td align="left">OK</td> <td align="left">C</td> <td align="left">OK</td> @@ -1858,7 +1851,7 @@ the fits to the Sassafras soil data.</p> <tr class="even"> <td align="left">dfop_path_2</td> <td align="left">OK</td> -<td align="left">OK</td> +<td align="left">C</td> <td align="left">OK</td> <td align="left">C</td> <td align="left">OK</td> @@ -1868,7 +1861,7 @@ the fits to the Sassafras soil data.</p> <td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> -<td align="left">OK</td> +<td align="left">C</td> <td align="left">OK</td> </tr> </tbody> @@ -1891,8 +1884,8 @@ parent and the Sassafras dataset.</p> <tbody> <tr class="odd"> <td align="left">fomc_path_2</td> +<td align="left">E</td> <td align="left">OK</td> -<td align="left">FO</td> </tr> <tr class="even"> <td align="left">dfop_path_2</td> @@ -1924,8 +1917,8 @@ successfully.</p> <tbody> <tr class="odd"> <td align="left">fomc_path_2</td> -<td align="left">sd(f_JCZ38_qlogis), sd(f_JSE76_qlogis)</td> -<td align="left">NA</td> +<td align="left">E</td> +<td align="left">sd(f_JSE76_qlogis)</td> </tr> <tr class="even"> <td align="left">dfop_path_2</td> @@ -1954,46 +1947,39 @@ JCZ38 are ill-defined.</p> </tr></thead> <tbody> <tr class="odd"> -<td align="left">fomc_path_2 const</td> -<td align="right">20</td> -<td align="right">2308.3</td> -<td align="right">2300.5</td> -<td align="right">-1134.2</td> -</tr> -<tr class="even"> <td align="left">fomc_path_2 tc</td> <td align="right">21</td> -<td align="right">2248.3</td> -<td align="right">2240.1</td> -<td align="right">-1103.2</td> +<td align="right">2249.0</td> +<td align="right">2240.8</td> +<td align="right">-1103.5</td> </tr> -<tr class="odd"> +<tr class="even"> <td align="left">dfop_path_2 const</td> <td align="right">22</td> -<td align="right">2289.6</td> -<td align="right">2281.0</td> -<td align="right">-1122.8</td> +<td align="right">2288.4</td> +<td align="right">2279.8</td> +<td align="right">-1122.2</td> </tr> -<tr class="even"> +<tr class="odd"> <td align="left">sforb_path_2 const</td> <td align="right">22</td> -<td align="right">2284.1</td> -<td align="right">2275.5</td> -<td align="right">-1120.0</td> +<td align="right">2283.3</td> +<td align="right">2274.7</td> +<td align="right">-1119.7</td> </tr> -<tr class="odd"> +<tr class="even"> <td align="left">dfop_path_2 tc</td> <td align="right">22</td> <td align="right">2234.4</td> <td align="right">2225.8</td> <td align="right">-1095.2</td> </tr> -<tr class="even"> +<tr class="odd"> <td align="left">sforb_path_2 tc</td> <td align="right">22</td> -<td align="right">2240.4</td> -<td align="right">2231.8</td> -<td align="right">-1098.2</td> +<td align="right">2239.7</td> +<td align="right">2231.1</td> +<td align="right">-1097.9</td> </tr> </tbody> </table> @@ -2120,37 +2106,37 @@ confidence intervals for the optimised parameters are available.</p> <tr class="odd"> <td align="left">fomc_path_2 tc</td> <td align="right">19</td> -<td align="right">2250.9</td> -<td align="right">2243.5</td> -<td align="right">-1106.5</td> +<td align="right">2249.1</td> +<td align="right">2241.6</td> +<td align="right">-1105.5</td> </tr> <tr class="even"> <td align="left">dfop_path_2 const</td> <td align="right">20</td> -<td align="right">2281.7</td> -<td align="right">2273.9</td> -<td align="right">-1120.8</td> +<td align="right">2282.2</td> +<td align="right">2274.4</td> +<td align="right">-1121.1</td> </tr> <tr class="odd"> <td align="left">sforb_path_2 const</td> <td align="right">20</td> -<td align="right">2279.5</td> -<td align="right">2271.7</td> -<td align="right">-1119.7</td> +<td align="right">2279.7</td> +<td align="right">2271.9</td> +<td align="right">-1119.9</td> </tr> <tr class="even"> <td align="left">dfop_path_2 tc</td> <td align="right">20</td> -<td align="right">2231.5</td> -<td align="right">2223.7</td> -<td align="right">-1095.8</td> +<td align="right">2237.3</td> +<td align="right">2229.5</td> +<td align="right">-1098.6</td> </tr> <tr class="odd"> <td align="left">sforb_path_2 tc</td> <td align="right">20</td> -<td align="right">2235.7</td> -<td align="right">2227.9</td> -<td align="right">-1097.9</td> +<td align="right">2241.3</td> +<td align="right">2233.5</td> +<td align="right">-1100.7</td> </tr> </tbody> </table> @@ -2219,10 +2205,10 @@ Hierarchical SFO path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:44:55 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:27:54 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2235,7 +2221,7 @@ Data: Model predictions using solution type deSolve -Fitted in 431.793 s +Fitted in 422.743 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2244,7 +2230,7 @@ Starting values for degradation parameters: cyan_0 log_k_cyan log_k_JCZ38 log_k_J9Z38 log_k_JSE76 95.3304 -3.8459 -3.1305 -5.0678 -5.3196 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis - 0.8158 22.5404 10.4289 + 0.8158 23.5335 11.8774 Fixed degradation parameter values: None @@ -2266,8 +2252,8 @@ log_k_JCZ38 0.0000 0.000 0.00 log_k_J9Z38 0.0000 0.000 0.00 log_k_JSE76 0.0000 0.000 0.00 f_cyan_ilr_1 0.7714 0.000 0.00 -f_cyan_ilr_2 0.0000 8.684 0.00 -f_JCZ38_qlogis 0.0000 0.000 13.48 +f_cyan_ilr_2 0.0000 9.247 0.00 +f_JCZ38_qlogis 0.0000 0.000 16.61 Starting values for error model parameters: a.1 @@ -2277,68 +2263,68 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2693 2687 -1330 + 2693 2687 -1331 Optimised parameters: - est. lower upper -cyan_0 95.0946 NA NA -log_k_cyan -3.8544 NA NA -log_k_JCZ38 -3.0402 NA NA -log_k_J9Z38 -5.0109 NA NA -log_k_JSE76 -5.2857 NA NA -f_cyan_ilr_1 0.8069 NA NA -f_cyan_ilr_2 16.6623 NA NA -f_JCZ38_qlogis 1.3602 NA NA -a.1 4.8326 NA NA -SD.log_k_cyan 0.5842 NA NA -SD.log_k_JCZ38 1.2680 NA NA -SD.log_k_J9Z38 0.3626 NA NA -SD.log_k_JSE76 0.5244 NA NA -SD.f_cyan_ilr_1 0.2752 NA NA -SD.f_cyan_ilr_2 2.3556 NA NA -SD.f_JCZ38_qlogis 0.2400 NA NA + est. lower upper +cyan_0 95.1279 9.354e+01 9.671e+01 +log_k_cyan -3.8527 -4.367e+00 -3.338e+00 +log_k_JCZ38 -3.0381 -4.187e+00 -1.889e+00 +log_k_J9Z38 -5.0095 -5.623e+00 -4.396e+00 +log_k_JSE76 -5.3357 -6.025e+00 -4.646e+00 +f_cyan_ilr_1 0.8050 5.174e-01 1.093e+00 +f_cyan_ilr_2 12.4820 -1.050e+06 1.051e+06 +f_JCZ38_qlogis 1.2912 3.561e-01 2.226e+00 +a.1 4.8393 NA NA +SD.log_k_cyan 0.5840 NA NA +SD.log_k_JCZ38 1.2740 NA NA +SD.log_k_J9Z38 0.3172 NA NA +SD.log_k_JSE76 0.5677 NA NA +SD.f_cyan_ilr_1 0.2623 NA NA +SD.f_cyan_ilr_2 1.3724 NA NA +SD.f_JCZ38_qlogis 0.1464 NA NA Correlation is not available Random effects: est. lower upper -SD.log_k_cyan 0.5842 NA NA -SD.log_k_JCZ38 1.2680 NA NA -SD.log_k_J9Z38 0.3626 NA NA -SD.log_k_JSE76 0.5244 NA NA -SD.f_cyan_ilr_1 0.2752 NA NA -SD.f_cyan_ilr_2 2.3556 NA NA -SD.f_JCZ38_qlogis 0.2400 NA NA +SD.log_k_cyan 0.5840 NA NA +SD.log_k_JCZ38 1.2740 NA NA +SD.log_k_J9Z38 0.3172 NA NA +SD.log_k_JSE76 0.5677 NA NA +SD.f_cyan_ilr_1 0.2623 NA NA +SD.f_cyan_ilr_2 1.3724 NA NA +SD.f_JCZ38_qlogis 0.1464 NA NA Variance model: est. lower upper -a.1 4.833 NA NA +a.1 4.839 NA NA Backtransformed parameters: - est. lower upper -cyan_0 95.094581 NA NA -k_cyan 0.021186 NA NA -k_JCZ38 0.047825 NA NA -k_J9Z38 0.006665 NA NA -k_JSE76 0.005063 NA NA -f_cyan_to_JCZ38 0.757885 NA NA -f_cyan_to_J9Z38 0.242115 NA NA -f_JCZ38_to_JSE76 0.795792 NA NA + est. lower upper +cyan_0 95.127935 93.542456 96.713413 +k_cyan 0.021221 0.012687 0.035497 +k_JCZ38 0.047924 0.015189 0.151213 +k_J9Z38 0.006674 0.003612 0.012332 +k_JSE76 0.004817 0.002417 0.009601 +f_cyan_to_JCZ38 0.757402 NA NA +f_cyan_to_J9Z38 0.242597 NA NA +f_JCZ38_to_JSE76 0.784347 0.588098 0.902582 Resulting formation fractions: ff -cyan_JCZ38 7.579e-01 -cyan_J9Z38 2.421e-01 -cyan_sink 5.877e-10 -JCZ38_JSE76 7.958e-01 -JCZ38_sink 2.042e-01 +cyan_JCZ38 7.574e-01 +cyan_J9Z38 2.426e-01 +cyan_sink 9.839e-08 +JCZ38_JSE76 7.843e-01 +JCZ38_sink 2.157e-01 Estimated disappearance times: DT50 DT90 -cyan 32.72 108.68 -JCZ38 14.49 48.15 -J9Z38 103.99 345.46 -JSE76 136.90 454.76 +cyan 32.66 108.50 +JCZ38 14.46 48.05 +J9Z38 103.86 345.00 +JSE76 143.91 478.04 </code></pre> <p></p> @@ -2347,10 +2333,10 @@ Hierarchical SFO path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:44:53 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:27:49 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2363,7 +2349,7 @@ Data: Model predictions using solution type deSolve -Fitted in 429.526 s +Fitted in 417.436 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2372,7 +2358,7 @@ Starting values for degradation parameters: cyan_0 log_k_cyan log_k_JCZ38 log_k_J9Z38 log_k_JSE76 96.0039 -3.8907 -3.1276 -5.0069 -4.9367 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis - 0.7937 20.0030 15.1336 + 0.7937 22.3422 17.8932 Fixed degradation parameter values: None @@ -2394,8 +2380,8 @@ log_k_JCZ38 0.0000 0.000 0.00 log_k_J9Z38 0.0000 0.000 0.00 log_k_JSE76 0.0000 0.000 0.00 f_cyan_ilr_1 0.7598 0.000 0.00 -f_cyan_ilr_2 0.0000 7.334 0.00 -f_JCZ38_qlogis 0.0000 0.000 11.78 +f_cyan_ilr_2 0.0000 8.939 0.00 +f_JCZ38_qlogis 0.0000 0.000 14.49 Starting values for error model parameters: a.1 b.1 @@ -2409,66 +2395,66 @@ Likelihood computed by importance sampling Optimised parameters: est. lower upper -cyan_0 94.72923 NA NA -log_k_cyan -3.91670 NA NA -log_k_JCZ38 -3.12917 NA NA -log_k_J9Z38 -5.06070 NA NA -log_k_JSE76 -5.09254 NA NA -f_cyan_ilr_1 0.81116 NA NA -f_cyan_ilr_2 39.97850 NA NA -f_JCZ38_qlogis 3.09728 NA NA -a.1 3.95044 NA NA -b.1 0.07998 NA NA -SD.log_k_cyan 0.58855 NA NA -SD.log_k_JCZ38 1.29753 NA NA -SD.log_k_J9Z38 0.62851 NA NA -SD.log_k_JSE76 0.37235 NA NA -SD.f_cyan_ilr_1 0.37346 NA NA -SD.f_cyan_ilr_2 1.41667 NA NA -SD.f_JCZ38_qlogis 1.81467 NA NA +cyan_0 94.81681 NA NA +log_k_cyan -3.91558 NA NA +log_k_JCZ38 -3.12715 NA NA +log_k_J9Z38 -5.04840 NA NA +log_k_JSE76 -5.10443 NA NA +f_cyan_ilr_1 0.80760 NA NA +f_cyan_ilr_2 48.66960 NA NA +f_JCZ38_qlogis 3.03397 NA NA +a.1 3.93879 NA NA +b.1 0.08057 NA NA +SD.log_k_cyan 0.58921 NA NA +SD.log_k_JCZ38 1.29813 NA NA +SD.log_k_J9Z38 0.68372 NA NA +SD.log_k_JSE76 0.35128 NA NA +SD.f_cyan_ilr_1 0.38352 NA NA +SD.f_cyan_ilr_2 4.98884 NA NA +SD.f_JCZ38_qlogis 1.75636 NA NA Correlation is not available Random effects: est. lower upper -SD.log_k_cyan 0.5886 NA NA -SD.log_k_JCZ38 1.2975 NA NA -SD.log_k_J9Z38 0.6285 NA NA -SD.log_k_JSE76 0.3724 NA NA -SD.f_cyan_ilr_1 0.3735 NA NA -SD.f_cyan_ilr_2 1.4167 NA NA -SD.f_JCZ38_qlogis 1.8147 NA NA +SD.log_k_cyan 0.5892 NA NA +SD.log_k_JCZ38 1.2981 NA NA +SD.log_k_J9Z38 0.6837 NA NA +SD.log_k_JSE76 0.3513 NA NA +SD.f_cyan_ilr_1 0.3835 NA NA +SD.f_cyan_ilr_2 4.9888 NA NA +SD.f_JCZ38_qlogis 1.7564 NA NA Variance model: est. lower upper -a.1 3.95044 NA NA -b.1 0.07998 NA NA +a.1 3.93879 NA NA +b.1 0.08057 NA NA Backtransformed parameters: - est. lower upper -cyan_0 94.729229 NA NA -k_cyan 0.019907 NA NA -k_JCZ38 0.043754 NA NA -k_J9Z38 0.006341 NA NA -k_JSE76 0.006142 NA NA -f_cyan_to_JCZ38 0.758991 NA NA -f_cyan_to_J9Z38 0.241009 NA NA -f_JCZ38_to_JSE76 0.956781 NA NA + est. lower upper +cyan_0 94.81681 NA NA +k_cyan 0.01993 NA NA +k_JCZ38 0.04384 NA NA +k_J9Z38 0.00642 NA NA +k_JSE76 0.00607 NA NA +f_cyan_to_JCZ38 0.75807 NA NA +f_cyan_to_J9Z38 0.24193 NA NA +f_JCZ38_to_JSE76 0.95409 NA NA Resulting formation fractions: ff -cyan_JCZ38 0.75899 -cyan_J9Z38 0.24101 +cyan_JCZ38 0.75807 +cyan_J9Z38 0.24193 cyan_sink 0.00000 -JCZ38_JSE76 0.95678 -JCZ38_sink 0.04322 +JCZ38_JSE76 0.95409 +JCZ38_sink 0.04591 Estimated disappearance times: DT50 DT90 -cyan 34.82 115.67 -JCZ38 15.84 52.63 -J9Z38 109.31 363.12 -JSE76 112.85 374.87 +cyan 34.78 115.54 +JCZ38 15.81 52.52 +J9Z38 107.97 358.68 +JSE76 114.20 379.35 </code></pre> <p></p> @@ -2477,10 +2463,10 @@ Hierarchical FOMC path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:45:50 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:28:29 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2495,7 +2481,7 @@ Data: Model predictions using solution type deSolve -Fitted in 477.996 s +Fitted in 457.122 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2504,7 +2490,7 @@ Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 101.2314 -3.3680 -5.1108 -5.9416 0.7144 f_cyan_ilr_2 f_JCZ38_qlogis log_alpha log_beta - 7.3870 15.7604 -0.1791 2.9811 + 7.0229 14.9234 -0.1791 2.9811 Fixed degradation parameter values: None @@ -2526,8 +2512,8 @@ log_k_JCZ38 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_2 12.33 0.00 0.0000 0.0000 -f_JCZ38_qlogis 0.00 20.42 0.0000 0.0000 +f_cyan_ilr_2 11.57 0.00 0.0000 0.0000 +f_JCZ38_qlogis 0.00 18.81 0.0000 0.0000 log_alpha 0.00 0.00 0.4144 0.0000 log_beta 0.00 0.00 0.0000 0.5077 @@ -2542,78 +2528,78 @@ Likelihood computed by importance sampling 2428 2421 -1196 Optimised parameters: - est. lower upper -cyan_0 101.0225 98.306270 103.7387 -log_k_JCZ38 -3.3786 -4.770657 -1.9866 -log_k_J9Z38 -5.2603 -5.902085 -4.6186 -log_k_JSE76 -6.1427 -7.318336 -4.9671 -f_cyan_ilr_1 0.7437 0.421215 1.0663 -f_cyan_ilr_2 0.9108 0.267977 1.5537 -f_JCZ38_qlogis 2.0487 0.524897 3.5724 -log_alpha -0.2268 -0.618049 0.1644 -log_beta 2.8986 2.700701 3.0964 -a.1 3.4058 3.169913 3.6416 -SD.cyan_0 2.5279 0.454190 4.6016 -SD.log_k_JCZ38 1.5636 0.572824 2.5543 -SD.log_k_J9Z38 0.5316 -0.004405 1.0677 -SD.log_k_JSE76 0.9903 0.106325 1.8742 -SD.f_cyan_ilr_1 0.3464 0.112066 0.5807 -SD.f_cyan_ilr_2 0.2804 -0.393900 0.9546 -SD.f_JCZ38_qlogis 0.9416 -0.152986 2.0362 -SD.log_alpha 0.4273 0.161044 0.6936 + est. lower upper +cyan_0 101.1664 98.51265 103.8202 +log_k_JCZ38 -3.3883 -4.78250 -1.9941 +log_k_J9Z38 -5.3087 -5.91564 -4.7017 +log_k_JSE76 -6.1313 -7.30061 -4.9619 +f_cyan_ilr_1 0.7456 0.43782 1.0534 +f_cyan_ilr_2 0.8181 0.24956 1.3866 +f_JCZ38_qlogis 2.0467 0.61165 3.4817 +log_alpha -0.2391 -0.62806 0.1499 +log_beta 2.8739 2.67664 3.0711 +a.1 3.4160 3.17960 3.6525 +SD.cyan_0 2.4355 0.40399 4.4671 +SD.log_k_JCZ38 1.5654 0.57311 2.5576 +SD.log_k_J9Z38 0.4645 -0.06533 0.9943 +SD.log_k_JSE76 0.9841 0.10738 1.8609 +SD.f_cyan_ilr_1 0.3285 0.10546 0.5515 +SD.f_cyan_ilr_2 0.2276 -0.38711 0.8424 +SD.f_JCZ38_qlogis 0.8340 -0.20970 1.8777 +SD.log_alpha 0.4250 0.16017 0.6898 Correlation: cyan_0 l__JCZ3 l__J9Z3 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 log_lph -log_k_JCZ38 -0.0156 -log_k_J9Z38 -0.0493 0.0073 -log_k_JSE76 -0.0329 0.0018 0.0069 -f_cyan_ilr_1 -0.0086 0.0180 -0.1406 0.0012 -f_cyan_ilr_2 -0.2629 0.0779 0.2826 0.0274 0.0099 -f_JCZ38_qlogis 0.0713 -0.0747 -0.0505 0.1169 -0.1022 -0.4893 -log_alpha -0.0556 0.0120 0.0336 0.0193 0.0036 0.0840 -0.0489 -log_beta -0.2898 0.0460 0.1305 0.0768 0.0190 0.4071 -0.1981 0.2772 +log_k_JCZ38 -0.0159 +log_k_J9Z38 -0.0546 0.0080 +log_k_JSE76 -0.0337 0.0016 0.0074 +f_cyan_ilr_1 -0.0095 0.0194 -0.1573 0.0003 +f_cyan_ilr_2 -0.2733 0.0799 0.3059 0.0263 0.0125 +f_JCZ38_qlogis 0.0755 -0.0783 -0.0516 0.1222 -0.1155 -0.5231 +log_alpha -0.0567 0.0120 0.0351 0.0189 0.0040 0.0829 -0.0502 +log_beta -0.2980 0.0461 0.1382 0.0758 0.0209 0.4079 -0.2053 0.2759 Random effects: - est. lower upper -SD.cyan_0 2.5279 0.454190 4.6016 -SD.log_k_JCZ38 1.5636 0.572824 2.5543 -SD.log_k_J9Z38 0.5316 -0.004405 1.0677 -SD.log_k_JSE76 0.9903 0.106325 1.8742 -SD.f_cyan_ilr_1 0.3464 0.112066 0.5807 -SD.f_cyan_ilr_2 0.2804 -0.393900 0.9546 -SD.f_JCZ38_qlogis 0.9416 -0.152986 2.0362 -SD.log_alpha 0.4273 0.161044 0.6936 + est. lower upper +SD.cyan_0 2.4355 0.40399 4.4671 +SD.log_k_JCZ38 1.5654 0.57311 2.5576 +SD.log_k_J9Z38 0.4645 -0.06533 0.9943 +SD.log_k_JSE76 0.9841 0.10738 1.8609 +SD.f_cyan_ilr_1 0.3285 0.10546 0.5515 +SD.f_cyan_ilr_2 0.2276 -0.38711 0.8424 +SD.f_JCZ38_qlogis 0.8340 -0.20970 1.8777 +SD.log_alpha 0.4250 0.16017 0.6898 Variance model: est. lower upper -a.1 3.406 3.17 3.642 +a.1 3.416 3.18 3.652 Backtransformed parameters: est. lower upper -cyan_0 1.010e+02 9.831e+01 1.037e+02 -k_JCZ38 3.409e-02 8.475e-03 1.372e-01 -k_J9Z38 5.194e-03 2.734e-03 9.867e-03 -k_JSE76 2.149e-03 6.633e-04 6.963e-03 -f_cyan_to_JCZ38 6.481e-01 NA NA -f_cyan_to_J9Z38 2.264e-01 NA NA -f_JCZ38_to_JSE76 8.858e-01 6.283e-01 9.727e-01 -alpha 7.971e-01 5.390e-01 1.179e+00 -beta 1.815e+01 1.489e+01 2.212e+01 +cyan_0 1.012e+02 9.851e+01 103.82023 +k_JCZ38 3.377e-02 8.375e-03 0.13614 +k_J9Z38 4.948e-03 2.697e-03 0.00908 +k_JSE76 2.174e-03 6.751e-04 0.00700 +f_cyan_to_JCZ38 6.389e-01 NA NA +f_cyan_to_J9Z38 2.226e-01 NA NA +f_JCZ38_to_JSE76 8.856e-01 6.483e-01 0.97016 +alpha 7.873e-01 5.336e-01 1.16166 +beta 1.771e+01 1.454e+01 21.56509 Resulting formation fractions: ff -cyan_JCZ38 0.6481 -cyan_J9Z38 0.2264 -cyan_sink 0.1255 -JCZ38_JSE76 0.8858 -JCZ38_sink 0.1142 +cyan_JCZ38 0.6389 +cyan_J9Z38 0.2226 +cyan_sink 0.1385 +JCZ38_JSE76 0.8856 +JCZ38_sink 0.1144 Estimated disappearance times: DT50 DT90 DT50back -cyan 25.15 308.01 92.72 -JCZ38 20.33 67.54 NA -J9Z38 133.46 443.35 NA -JSE76 322.53 1071.42 NA +cyan 25.00 312.06 93.94 +JCZ38 20.53 68.19 NA +J9Z38 140.07 465.32 NA +JSE76 318.86 1059.22 NA </code></pre> <p></p> @@ -2622,10 +2608,10 @@ Hierarchical FOMC path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:45:45 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:28:21 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2640,41 +2626,41 @@ Data: Model predictions using solution type deSolve -Fitted in 480.648 s +Fitted in 449.531 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 101.13827 -3.32493 -5.08921 -5.93478 0.71330 + 101.13294 -3.32499 -5.09097 -5.93566 0.71359 f_cyan_ilr_2 f_JCZ38_qlogis log_alpha log_beta - 10.05989 12.79248 -0.09621 3.10646 + 10.30315 14.62272 -0.09633 3.10634 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 5.643 0.000 0.000 0.00 0.0000 -log_k_JCZ38 0.000 2.319 0.000 0.00 0.0000 -log_k_J9Z38 0.000 0.000 1.731 0.00 0.0000 -log_k_JSE76 0.000 0.000 0.000 1.86 0.0000 -f_cyan_ilr_1 0.000 0.000 0.000 0.00 0.7186 -f_cyan_ilr_2 0.000 0.000 0.000 0.00 0.0000 -f_JCZ38_qlogis 0.000 0.000 0.000 0.00 0.0000 -log_alpha 0.000 0.000 0.000 0.00 0.0000 -log_beta 0.000 0.000 0.000 0.00 0.0000 +cyan_0 5.649 0.000 0.00 0.00 0.0000 +log_k_JCZ38 0.000 2.319 0.00 0.00 0.0000 +log_k_J9Z38 0.000 0.000 1.73 0.00 0.0000 +log_k_JSE76 0.000 0.000 0.00 1.86 0.0000 +f_cyan_ilr_1 0.000 0.000 0.00 0.00 0.7183 +f_cyan_ilr_2 0.000 0.000 0.00 0.00 0.0000 +f_JCZ38_qlogis 0.000 0.000 0.00 0.00 0.0000 +log_alpha 0.000 0.000 0.00 0.00 0.0000 +log_beta 0.000 0.000 0.00 0.00 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis log_alpha log_beta cyan_0 0.00 0.00 0.0000 0.0000 log_k_JCZ38 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_2 12.49 0.00 0.0000 0.0000 -f_JCZ38_qlogis 0.00 20.19 0.0000 0.0000 +f_cyan_ilr_2 12.85 0.00 0.0000 0.0000 +f_JCZ38_qlogis 0.00 18.54 0.0000 0.0000 log_alpha 0.00 0.00 0.3142 0.0000 -log_beta 0.00 0.00 0.0000 0.7331 +log_beta 0.00 0.00 0.0000 0.7333 Starting values for error model parameters: a.1 b.1 @@ -2684,74 +2670,74 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2423 2416 -1193 + 2424 2416 -1193 Optimised parameters: est. lower upper -cyan_0 100.57649 NA NA -log_k_JCZ38 -3.46250 NA NA -log_k_J9Z38 -5.24442 NA NA -log_k_JSE76 -5.75229 NA NA -f_cyan_ilr_1 0.68480 NA NA -f_cyan_ilr_2 0.61670 NA NA -f_JCZ38_qlogis 87.97407 NA NA -log_alpha -0.15699 NA NA -log_beta 3.01540 NA NA -a.1 3.11518 NA NA -b.1 0.04445 NA NA -SD.log_k_JCZ38 1.40732 NA NA -SD.log_k_J9Z38 0.56510 NA NA -SD.log_k_JSE76 0.72067 NA NA -SD.f_cyan_ilr_1 0.31199 NA NA -SD.f_cyan_ilr_2 0.36894 NA NA -SD.f_JCZ38_qlogis 6.92892 NA NA -SD.log_alpha 0.25662 NA NA -SD.log_beta 0.35845 NA NA +cyan_0 100.65667 NA NA +log_k_JCZ38 -3.45782 NA NA +log_k_J9Z38 -5.23476 NA NA +log_k_JSE76 -5.71827 NA NA +f_cyan_ilr_1 0.68389 NA NA +f_cyan_ilr_2 0.61027 NA NA +f_JCZ38_qlogis 116.27482 NA NA +log_alpha -0.14484 NA NA +log_beta 3.03220 NA NA +a.1 3.11051 NA NA +b.1 0.04508 NA NA +SD.log_k_JCZ38 1.39961 NA NA +SD.log_k_J9Z38 0.57920 NA NA +SD.log_k_JSE76 0.68364 NA NA +SD.f_cyan_ilr_1 0.31477 NA NA +SD.f_cyan_ilr_2 0.37716 NA NA +SD.f_JCZ38_qlogis 5.52695 NA NA +SD.log_alpha 0.22823 NA NA +SD.log_beta 0.39161 NA NA Correlation is not available Random effects: est. lower upper -SD.log_k_JCZ38 1.4073 NA NA -SD.log_k_J9Z38 0.5651 NA NA -SD.log_k_JSE76 0.7207 NA NA -SD.f_cyan_ilr_1 0.3120 NA NA -SD.f_cyan_ilr_2 0.3689 NA NA -SD.f_JCZ38_qlogis 6.9289 NA NA -SD.log_alpha 0.2566 NA NA -SD.log_beta 0.3585 NA NA +SD.log_k_JCZ38 1.3996 NA NA +SD.log_k_J9Z38 0.5792 NA NA +SD.log_k_JSE76 0.6836 NA NA +SD.f_cyan_ilr_1 0.3148 NA NA +SD.f_cyan_ilr_2 0.3772 NA NA +SD.f_JCZ38_qlogis 5.5270 NA NA +SD.log_alpha 0.2282 NA NA +SD.log_beta 0.3916 NA NA Variance model: est. lower upper -a.1 3.11518 NA NA -b.1 0.04445 NA NA +a.1 3.11051 NA NA +b.1 0.04508 NA NA Backtransformed parameters: est. lower upper -cyan_0 1.006e+02 NA NA -k_JCZ38 3.135e-02 NA NA -k_J9Z38 5.277e-03 NA NA -k_JSE76 3.175e-03 NA NA -f_cyan_to_JCZ38 5.991e-01 NA NA -f_cyan_to_J9Z38 2.275e-01 NA NA +cyan_0 1.007e+02 NA NA +k_JCZ38 3.150e-02 NA NA +k_J9Z38 5.328e-03 NA NA +k_JSE76 3.285e-03 NA NA +f_cyan_to_JCZ38 5.980e-01 NA NA +f_cyan_to_J9Z38 2.273e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA -alpha 8.547e-01 NA NA -beta 2.040e+01 NA NA +alpha 8.652e-01 NA NA +beta 2.074e+01 NA NA Resulting formation fractions: ff -cyan_JCZ38 0.5991 -cyan_J9Z38 0.2275 -cyan_sink 0.1734 +cyan_JCZ38 0.5980 +cyan_J9Z38 0.2273 +cyan_sink 0.1746 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 Estimated disappearance times: - DT50 DT90 DT50back -cyan 25.50 281.29 84.68 -JCZ38 22.11 73.44 NA -J9Z38 131.36 436.35 NA -JSE76 218.28 725.11 NA + DT50 DT90 DT50back +cyan 25.48 276.2 83.15 +JCZ38 22.01 73.1 NA +J9Z38 130.09 432.2 NA +JSE76 210.98 700.9 NA </code></pre> <p></p> @@ -2760,10 +2746,10 @@ Hierarchical DFOP path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:46:41 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:29:15 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2782,16 +2768,16 @@ Data: Model predictions using solution type deSolve -Fitted in 528.713 s +Fitted in 503.737 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 102.0644 -3.4008 -5.0024 -5.8613 0.6855 + 102.0643 -3.4008 -5.0024 -5.8612 0.6855 f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 g_qlogis - 1.2365 13.7245 -1.8641 -4.5063 -0.6468 + 1.2366 13.6901 -1.8641 -4.5063 -0.6468 Fixed degradation parameter values: None @@ -2815,7 +2801,7 @@ log_k_J9Z38 0.00 0.00 0.0000 0.0000 0.000 log_k_JSE76 0.00 0.00 0.0000 0.0000 0.000 f_cyan_ilr_1 0.00 0.00 0.0000 0.0000 0.000 f_cyan_ilr_2 1.28 0.00 0.0000 0.0000 0.000 -f_JCZ38_qlogis 0.00 16.11 0.0000 0.0000 0.000 +f_JCZ38_qlogis 0.00 16.08 0.0000 0.0000 0.000 log_k1 0.00 0.00 0.9866 0.0000 0.000 log_k2 0.00 0.00 0.0000 0.5953 0.000 g_qlogis 0.00 0.00 0.0000 0.0000 1.583 @@ -2832,72 +2818,72 @@ Likelihood computed by importance sampling Optimised parameters: est. lower upper -cyan_0 102.6079 NA NA -log_k_JCZ38 -3.4855 NA NA -log_k_J9Z38 -5.1686 NA NA -log_k_JSE76 -5.6697 NA NA -f_cyan_ilr_1 0.6714 NA NA -f_cyan_ilr_2 0.4986 NA NA -f_JCZ38_qlogis 55.4760 NA NA -log_k1 -1.8409 NA NA -log_k2 -4.4915 NA NA -g_qlogis -0.6403 NA NA -a.1 3.2387 NA NA -SD.log_k_JCZ38 1.4524 NA NA -SD.log_k_J9Z38 0.5151 NA NA -SD.log_k_JSE76 0.6514 NA NA -SD.f_cyan_ilr_1 0.3023 NA NA -SD.f_cyan_ilr_2 0.2959 NA NA -SD.f_JCZ38_qlogis 1.9984 NA NA -SD.log_k1 0.5188 NA NA -SD.log_k2 0.3894 NA NA -SD.g_qlogis 0.8579 NA NA +cyan_0 102.5565 NA NA +log_k_JCZ38 -3.4729 NA NA +log_k_J9Z38 -5.1533 NA NA +log_k_JSE76 -5.6669 NA NA +f_cyan_ilr_1 0.6665 NA NA +f_cyan_ilr_2 0.5191 NA NA +f_JCZ38_qlogis 37.0113 NA NA +log_k1 -1.8497 NA NA +log_k2 -4.4931 NA NA +g_qlogis -0.6383 NA NA +a.1 3.2397 NA NA +SD.log_k_JCZ38 1.4286 NA NA +SD.log_k_J9Z38 0.5312 NA NA +SD.log_k_JSE76 0.6627 NA NA +SD.f_cyan_ilr_1 0.3013 NA NA +SD.f_cyan_ilr_2 0.2980 NA NA +SD.f_JCZ38_qlogis 0.1637 NA NA +SD.log_k1 0.5069 NA NA +SD.log_k2 0.3828 NA NA +SD.g_qlogis 0.8641 NA NA Correlation is not available Random effects: est. lower upper -SD.log_k_JCZ38 1.4524 NA NA -SD.log_k_J9Z38 0.5151 NA NA -SD.log_k_JSE76 0.6514 NA NA -SD.f_cyan_ilr_1 0.3023 NA NA -SD.f_cyan_ilr_2 0.2959 NA NA -SD.f_JCZ38_qlogis 1.9984 NA NA -SD.log_k1 0.5188 NA NA -SD.log_k2 0.3894 NA NA -SD.g_qlogis 0.8579 NA NA +SD.log_k_JCZ38 1.4286 NA NA +SD.log_k_J9Z38 0.5312 NA NA +SD.log_k_JSE76 0.6627 NA NA +SD.f_cyan_ilr_1 0.3013 NA NA +SD.f_cyan_ilr_2 0.2980 NA NA +SD.f_JCZ38_qlogis 0.1637 NA NA +SD.log_k1 0.5069 NA NA +SD.log_k2 0.3828 NA NA +SD.g_qlogis 0.8641 NA NA Variance model: - est. lower upper -a.1 3.239 NA NA + est. lower upper +a.1 3.24 NA NA Backtransformed parameters: est. lower upper cyan_0 1.026e+02 NA NA -k_JCZ38 3.064e-02 NA NA -k_J9Z38 5.692e-03 NA NA -k_JSE76 3.449e-03 NA NA -f_cyan_to_JCZ38 5.798e-01 NA NA -f_cyan_to_J9Z38 2.243e-01 NA NA +k_JCZ38 3.103e-02 NA NA +k_J9Z38 5.780e-03 NA NA +k_JSE76 3.459e-03 NA NA +f_cyan_to_JCZ38 5.813e-01 NA NA +f_cyan_to_J9Z38 2.265e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA -k1 1.587e-01 NA NA -k2 1.120e-02 NA NA -g 3.452e-01 NA NA +k1 1.573e-01 NA NA +k2 1.119e-02 NA NA +g 3.456e-01 NA NA Resulting formation fractions: ff -cyan_JCZ38 0.5798 -cyan_J9Z38 0.2243 -cyan_sink 0.1958 +cyan_JCZ38 0.5813 +cyan_J9Z38 0.2265 +cyan_sink 0.1922 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -cyan 25.21 167.73 50.49 4.368 61.87 -JCZ38 22.62 75.15 NA NA NA -J9Z38 121.77 404.50 NA NA NA -JSE76 200.98 667.64 NA NA NA +cyan 25.23 167.94 50.55 4.407 61.97 +JCZ38 22.34 74.22 NA NA NA +J9Z38 119.92 398.36 NA NA NA +JSE76 200.41 665.76 NA NA NA </code></pre> <p></p> @@ -2906,10 +2892,10 @@ Hierarchical DFOP path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:49:05 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:31:24 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2928,7 +2914,7 @@ Data: Model predictions using solution type deSolve -Fitted in 673.139 s +Fitted in 632.55 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2937,7 +2923,7 @@ Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 101.3964 -3.3626 -4.9792 -5.8727 0.6814 f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 g_qlogis - 6.7799 13.7245 -1.9222 -4.5035 -0.7172 + 6.8713 13.6901 -1.9222 -4.5035 -0.7172 Fixed degradation parameter values: None @@ -2948,7 +2934,7 @@ cyan_0 5.317 0.000 0.000 0.000 0.0000 log_k_JCZ38 0.000 2.272 0.000 0.000 0.0000 log_k_J9Z38 0.000 0.000 1.633 0.000 0.0000 log_k_JSE76 0.000 0.000 0.000 1.271 0.0000 -f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6838 +f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6839 f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 log_k1 0.000 0.000 0.000 0.000 0.0000 @@ -2960,8 +2946,8 @@ log_k_JCZ38 0.00 0.00 0.0000 0.0000 0.000 log_k_J9Z38 0.00 0.00 0.0000 0.0000 0.000 log_k_JSE76 0.00 0.00 0.0000 0.0000 0.000 f_cyan_ilr_1 0.00 0.00 0.0000 0.0000 0.000 -f_cyan_ilr_2 11.77 0.00 0.0000 0.0000 0.000 -f_JCZ38_qlogis 0.00 16.11 0.0000 0.0000 0.000 +f_cyan_ilr_2 11.95 0.00 0.0000 0.0000 0.000 +f_JCZ38_qlogis 0.00 16.08 0.0000 0.0000 0.000 log_k1 0.00 0.00 0.9496 0.0000 0.000 log_k2 0.00 0.00 0.0000 0.5846 0.000 g_qlogis 0.00 0.00 0.0000 0.0000 1.719 @@ -2977,73 +2963,73 @@ Likelihood computed by importance sampling 2398 2390 -1179 Optimised parameters: - est. lower upper -cyan_0 100.8076 NA NA -log_k_JCZ38 -3.4684 NA NA -log_k_J9Z38 -5.0844 NA NA -log_k_JSE76 -5.5743 NA NA -f_cyan_ilr_1 0.6669 NA NA -f_cyan_ilr_2 0.7912 NA NA -f_JCZ38_qlogis 84.1825 NA NA -log_k1 -2.1671 NA NA -log_k2 -4.5447 NA NA -g_qlogis -0.5631 NA NA -a.1 2.9627 NA NA -b.1 0.0444 NA NA -SD.log_k_JCZ38 1.4044 NA NA -SD.log_k_J9Z38 0.6410 NA NA -SD.log_k_JSE76 0.5391 NA NA -SD.f_cyan_ilr_1 0.3203 NA NA -SD.f_cyan_ilr_2 0.5038 NA NA -SD.f_JCZ38_qlogis 3.5865 NA NA -SD.log_k2 0.3119 NA NA -SD.g_qlogis 0.8276 NA NA + est. lower upper +cyan_0 100.69709 NA NA +log_k_JCZ38 -3.46669 NA NA +log_k_J9Z38 -5.05076 NA NA +log_k_JSE76 -5.55558 NA NA +f_cyan_ilr_1 0.66045 NA NA +f_cyan_ilr_2 0.84275 NA NA +f_JCZ38_qlogis 64.22404 NA NA +log_k1 -2.17715 NA NA +log_k2 -4.55002 NA NA +g_qlogis -0.55920 NA NA +a.1 2.95785 NA NA +b.1 0.04456 NA NA +SD.log_k_JCZ38 1.39881 NA NA +SD.log_k_J9Z38 0.67788 NA NA +SD.log_k_JSE76 0.52603 NA NA +SD.f_cyan_ilr_1 0.32490 NA NA +SD.f_cyan_ilr_2 0.53923 NA NA +SD.f_JCZ38_qlogis 2.75576 NA NA +SD.log_k2 0.30694 NA NA +SD.g_qlogis 0.83619 NA NA Correlation is not available Random effects: est. lower upper -SD.log_k_JCZ38 1.4044 NA NA -SD.log_k_J9Z38 0.6410 NA NA -SD.log_k_JSE76 0.5391 NA NA -SD.f_cyan_ilr_1 0.3203 NA NA -SD.f_cyan_ilr_2 0.5038 NA NA -SD.f_JCZ38_qlogis 3.5865 NA NA -SD.log_k2 0.3119 NA NA -SD.g_qlogis 0.8276 NA NA +SD.log_k_JCZ38 1.3988 NA NA +SD.log_k_J9Z38 0.6779 NA NA +SD.log_k_JSE76 0.5260 NA NA +SD.f_cyan_ilr_1 0.3249 NA NA +SD.f_cyan_ilr_2 0.5392 NA NA +SD.f_JCZ38_qlogis 2.7558 NA NA +SD.log_k2 0.3069 NA NA +SD.g_qlogis 0.8362 NA NA Variance model: - est. lower upper -a.1 2.9627 NA NA -b.1 0.0444 NA NA + est. lower upper +a.1 2.95785 NA NA +b.1 0.04456 NA NA Backtransformed parameters: est. lower upper -cyan_0 1.008e+02 NA NA -k_JCZ38 3.117e-02 NA NA -k_J9Z38 6.193e-03 NA NA -k_JSE76 3.794e-03 NA NA -f_cyan_to_JCZ38 6.149e-01 NA NA -f_cyan_to_J9Z38 2.395e-01 NA NA +cyan_0 1.007e+02 NA NA +k_JCZ38 3.122e-02 NA NA +k_J9Z38 6.404e-03 NA NA +k_JSE76 3.866e-03 NA NA +f_cyan_to_JCZ38 6.187e-01 NA NA +f_cyan_to_J9Z38 2.431e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA -k1 1.145e-01 NA NA -k2 1.062e-02 NA NA -g 3.628e-01 NA NA +k1 1.134e-01 NA NA +k2 1.057e-02 NA NA +g 3.637e-01 NA NA Resulting formation fractions: ff -cyan_JCZ38 0.6149 -cyan_J9Z38 0.2395 -cyan_sink 0.1456 +cyan_JCZ38 0.6187 +cyan_J9Z38 0.2431 +cyan_sink 0.1382 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -cyan 26.26 174.32 52.47 6.053 65.25 -JCZ38 22.24 73.88 NA NA NA -J9Z38 111.93 371.82 NA NA NA -JSE76 182.69 606.88 NA NA NA +cyan 26.35 175.12 52.72 6.114 65.6 +JCZ38 22.20 73.75 NA NA NA +J9Z38 108.23 359.53 NA NA NA +JSE76 179.30 595.62 NA NA NA </code></pre> <p></p> @@ -3052,10 +3038,10 @@ Hierarchical SFORB path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:46:35 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:29:23 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3073,7 +3059,7 @@ Data: Model predictions using solution type deSolve -Fitted in 531.17 s +Fitted in 511.715 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3086,7 +3072,7 @@ log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 -5.8613 0.6855 1.2366 f_JCZ38_qlogis - 13.7418 + 13.7395 Fixed degradation parameter values: None @@ -3124,7 +3110,7 @@ log_k_J9Z38 0.0000 0.00 0.00 log_k_JSE76 0.0000 0.00 0.00 f_cyan_ilr_1 0.6852 0.00 0.00 f_cyan_ilr_2 0.0000 1.28 0.00 -f_JCZ38_qlogis 0.0000 0.00 16.14 +f_JCZ38_qlogis 0.0000 0.00 16.13 Starting values for error model parameters: a.1 @@ -3138,77 +3124,77 @@ Likelihood computed by importance sampling Optimised parameters: est. lower upper -cyan_free_0 102.7803 NA NA -log_k_cyan_free -2.8068 NA NA -log_k_cyan_free_bound -2.5714 NA NA -log_k_cyan_bound_free -3.4426 NA NA -log_k_JCZ38 -3.4994 NA NA -log_k_J9Z38 -5.1148 NA NA -log_k_JSE76 -5.6335 NA NA -f_cyan_ilr_1 0.6597 NA NA -f_cyan_ilr_2 0.5132 NA NA -f_JCZ38_qlogis 37.2090 NA NA -a.1 3.2367 NA NA -SD.log_k_cyan_free 0.3161 NA NA -SD.log_k_cyan_free_bound 0.8103 NA NA -SD.log_k_cyan_bound_free 0.5554 NA NA -SD.log_k_JCZ38 1.4858 NA NA -SD.log_k_J9Z38 0.5859 NA NA -SD.log_k_JSE76 0.6195 NA NA -SD.f_cyan_ilr_1 0.3118 NA NA -SD.f_cyan_ilr_2 0.3344 NA NA -SD.f_JCZ38_qlogis 0.5518 NA NA +cyan_free_0 102.8136 NA NA +log_k_cyan_free -2.7935 NA NA +log_k_cyan_free_bound -2.5440 NA NA +log_k_cyan_bound_free -3.4303 NA NA +log_k_JCZ38 -3.5010 NA NA +log_k_J9Z38 -5.1226 NA NA +log_k_JSE76 -5.6314 NA NA +f_cyan_ilr_1 0.6609 NA NA +f_cyan_ilr_2 0.5085 NA NA +f_JCZ38_qlogis 44.0153 NA NA +a.1 3.2318 NA NA +SD.log_k_cyan_free 0.3211 NA NA +SD.log_k_cyan_free_bound 0.8408 NA NA +SD.log_k_cyan_bound_free 0.5724 NA NA +SD.log_k_JCZ38 1.4925 NA NA +SD.log_k_J9Z38 0.5816 NA NA +SD.log_k_JSE76 0.6037 NA NA +SD.f_cyan_ilr_1 0.3115 NA NA +SD.f_cyan_ilr_2 0.3436 NA NA +SD.f_JCZ38_qlogis 4.8937 NA NA Correlation is not available Random effects: est. lower upper -SD.log_k_cyan_free 0.3161 NA NA -SD.log_k_cyan_free_bound 0.8103 NA NA -SD.log_k_cyan_bound_free 0.5554 NA NA -SD.log_k_JCZ38 1.4858 NA NA -SD.log_k_J9Z38 0.5859 NA NA -SD.log_k_JSE76 0.6195 NA NA -SD.f_cyan_ilr_1 0.3118 NA NA -SD.f_cyan_ilr_2 0.3344 NA NA -SD.f_JCZ38_qlogis 0.5518 NA NA +SD.log_k_cyan_free 0.3211 NA NA +SD.log_k_cyan_free_bound 0.8408 NA NA +SD.log_k_cyan_bound_free 0.5724 NA NA +SD.log_k_JCZ38 1.4925 NA NA +SD.log_k_J9Z38 0.5816 NA NA +SD.log_k_JSE76 0.6037 NA NA +SD.f_cyan_ilr_1 0.3115 NA NA +SD.f_cyan_ilr_2 0.3436 NA NA +SD.f_JCZ38_qlogis 4.8937 NA NA Variance model: est. lower upper -a.1 3.237 NA NA +a.1 3.232 NA NA Backtransformed parameters: est. lower upper cyan_free_0 1.028e+02 NA NA -k_cyan_free 6.040e-02 NA NA -k_cyan_free_bound 7.643e-02 NA NA -k_cyan_bound_free 3.198e-02 NA NA -k_JCZ38 3.022e-02 NA NA -k_J9Z38 6.007e-03 NA NA -k_JSE76 3.576e-03 NA NA -f_cyan_free_to_JCZ38 5.787e-01 NA NA -f_cyan_free_to_J9Z38 2.277e-01 NA NA +k_cyan_free 6.120e-02 NA NA +k_cyan_free_bound 7.855e-02 NA NA +k_cyan_bound_free 3.238e-02 NA NA +k_JCZ38 3.017e-02 NA NA +k_J9Z38 5.961e-03 NA NA +k_JSE76 3.584e-03 NA NA +f_cyan_free_to_JCZ38 5.784e-01 NA NA +f_cyan_free_to_J9Z38 2.271e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g -0.15646 0.01235 0.33341 +0.15973 0.01241 0.33124 Resulting formation fractions: ff -cyan_free_JCZ38 0.5787 -cyan_free_J9Z38 0.2277 -cyan_free_sink 0.1936 +cyan_free_JCZ38 0.5784 +cyan_free_J9Z38 0.2271 +cyan_free_sink 0.1945 cyan_free 1.0000 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 Estimated disappearance times: - DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 -cyan 24.48 153.7 46.26 4.43 56.15 -JCZ38 22.94 76.2 NA NA NA -J9Z38 115.39 383.3 NA NA NA -JSE76 193.84 643.9 NA NA NA + DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 +cyan 24.51 153.18 46.11 4.34 55.87 +JCZ38 22.98 76.33 NA NA NA +J9Z38 116.28 386.29 NA NA NA +JSE76 193.42 642.53 NA NA NA </code></pre> <p></p> @@ -3217,10 +3203,10 @@ Hierarchical SFORB path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:49:08 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:31:23 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3238,7 +3224,7 @@ Data: Model predictions using solution type deSolve -Fitted in 675.659 s +Fitted in 630.627 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3249,9 +3235,9 @@ Starting values for degradation parameters: log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 -3.4376 -3.3626 -4.9792 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 - -5.8727 0.6814 6.8139 + -5.8727 0.6814 6.7399 f_JCZ38_qlogis - 13.7419 + 13.7395 Fixed degradation parameter values: None @@ -3288,8 +3274,8 @@ log_k_JCZ38 0.0000 0.00 0.00 log_k_J9Z38 0.0000 0.00 0.00 log_k_JSE76 0.0000 0.00 0.00 f_cyan_ilr_1 0.6838 0.00 0.00 -f_cyan_ilr_2 0.0000 11.84 0.00 -f_JCZ38_qlogis 0.0000 0.00 16.14 +f_cyan_ilr_2 0.0000 11.69 0.00 +f_JCZ38_qlogis 0.0000 0.00 16.13 Starting values for error model parameters: a.1 b.1 @@ -3303,77 +3289,77 @@ Likelihood computed by importance sampling Optimised parameters: est. lower upper -cyan_free_0 100.69983 NA NA -log_k_cyan_free -3.11584 NA NA -log_k_cyan_free_bound -3.15216 NA NA -log_k_cyan_bound_free -3.65986 NA NA -log_k_JCZ38 -3.47811 NA NA -log_k_J9Z38 -5.08835 NA NA -log_k_JSE76 -5.55514 NA NA -f_cyan_ilr_1 0.66764 NA NA -f_cyan_ilr_2 0.78329 NA NA -f_JCZ38_qlogis 25.35245 NA NA -a.1 2.99088 NA NA -b.1 0.04346 NA NA -SD.log_k_cyan_free 0.48797 NA NA -SD.log_k_cyan_bound_free 0.27243 NA NA -SD.log_k_JCZ38 1.42450 NA NA -SD.log_k_J9Z38 0.63496 NA NA -SD.log_k_JSE76 0.55951 NA NA -SD.f_cyan_ilr_1 0.32687 NA NA -SD.f_cyan_ilr_2 0.48056 NA NA -SD.f_JCZ38_qlogis 0.43818 NA NA +cyan_free_0 100.56004 NA NA +log_k_cyan_free -3.12657 NA NA +log_k_cyan_free_bound -3.16825 NA NA +log_k_cyan_bound_free -3.66003 NA NA +log_k_JCZ38 -3.47278 NA NA +log_k_J9Z38 -5.06823 NA NA +log_k_JSE76 -5.54327 NA NA +f_cyan_ilr_1 0.66631 NA NA +f_cyan_ilr_2 0.82898 NA NA +f_JCZ38_qlogis 38.31115 NA NA +a.1 2.98352 NA NA +b.1 0.04388 NA NA +SD.log_k_cyan_free 0.49145 NA NA +SD.log_k_cyan_bound_free 0.27347 NA NA +SD.log_k_JCZ38 1.41193 NA NA +SD.log_k_J9Z38 0.66073 NA NA +SD.log_k_JSE76 0.55885 NA NA +SD.f_cyan_ilr_1 0.33020 NA NA +SD.f_cyan_ilr_2 0.51367 NA NA +SD.f_JCZ38_qlogis 5.52122 NA NA Correlation is not available Random effects: est. lower upper -SD.log_k_cyan_free 0.4880 NA NA -SD.log_k_cyan_bound_free 0.2724 NA NA -SD.log_k_JCZ38 1.4245 NA NA -SD.log_k_J9Z38 0.6350 NA NA -SD.log_k_JSE76 0.5595 NA NA -SD.f_cyan_ilr_1 0.3269 NA NA -SD.f_cyan_ilr_2 0.4806 NA NA -SD.f_JCZ38_qlogis 0.4382 NA NA +SD.log_k_cyan_free 0.4914 NA NA +SD.log_k_cyan_bound_free 0.2735 NA NA +SD.log_k_JCZ38 1.4119 NA NA +SD.log_k_J9Z38 0.6607 NA NA +SD.log_k_JSE76 0.5589 NA NA +SD.f_cyan_ilr_1 0.3302 NA NA +SD.f_cyan_ilr_2 0.5137 NA NA +SD.f_JCZ38_qlogis 5.5212 NA NA Variance model: est. lower upper -a.1 2.99088 NA NA -b.1 0.04346 NA NA +a.1 2.98352 NA NA +b.1 0.04388 NA NA Backtransformed parameters: est. lower upper -cyan_free_0 1.007e+02 NA NA -k_cyan_free 4.434e-02 NA NA -k_cyan_free_bound 4.276e-02 NA NA -k_cyan_bound_free 2.574e-02 NA NA -k_JCZ38 3.087e-02 NA NA -k_J9Z38 6.168e-03 NA NA -k_JSE76 3.868e-03 NA NA -f_cyan_free_to_JCZ38 6.143e-01 NA NA -f_cyan_free_to_J9Z38 2.389e-01 NA NA +cyan_free_0 1.006e+02 NA NA +k_cyan_free 4.387e-02 NA NA +k_cyan_free_bound 4.208e-02 NA NA +k_cyan_bound_free 2.573e-02 NA NA +k_JCZ38 3.103e-02 NA NA +k_J9Z38 6.294e-03 NA NA +k_JSE76 3.914e-03 NA NA +f_cyan_free_to_JCZ38 6.188e-01 NA NA +f_cyan_free_to_J9Z38 2.412e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g -0.10161 0.01123 0.36636 +0.10044 0.01124 0.36580 Resulting formation fractions: - ff -cyan_free_JCZ38 6.143e-01 -cyan_free_J9Z38 2.389e-01 -cyan_free_sink 1.468e-01 -cyan_free 1.000e+00 -JCZ38_JSE76 1.000e+00 -JCZ38_sink 9.763e-12 + ff +cyan_free_JCZ38 0.6188 +cyan_free_J9Z38 0.2412 +cyan_free_sink 0.1400 +cyan_free 1.0000 +JCZ38_JSE76 1.0000 +JCZ38_sink 0.0000 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 -cyan 25.91 164.4 49.49 6.822 61.72 -JCZ38 22.46 74.6 NA NA NA -J9Z38 112.37 373.3 NA NA NA -JSE76 179.22 595.4 NA NA NA +cyan 26.05 164.4 49.48 6.901 61.67 +JCZ38 22.34 74.2 NA NA NA +J9Z38 110.14 365.9 NA NA NA +JSE76 177.11 588.3 NA NA NA </code></pre> <p></p> @@ -3382,10 +3368,10 @@ Hierarchical HS path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:46:30 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:28:57 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3400,27 +3386,27 @@ Data: Model predictions using solution type deSolve -Fitted in 525.846 s +Fitted in 485.304 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 102.8738 -3.4490 -4.9348 -5.5989 0.6469 + 102.8845 -3.4495 -4.9355 -5.6040 0.6468 f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb - 1.2854 9.7193 -2.9084 -4.1810 1.7813 + 1.2396 9.7220 -2.9079 -4.1810 1.7813 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 5.409 0.00 0.00 0.000 0.0000 +cyan_0 5.406 0.00 0.00 0.000 0.0000 log_k_JCZ38 0.000 2.33 0.00 0.000 0.0000 log_k_J9Z38 0.000 0.00 1.59 0.000 0.0000 -log_k_JSE76 0.000 0.00 0.00 1.006 0.0000 -f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.6371 +log_k_JSE76 0.000 0.00 0.00 1.013 0.0000 +f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.6367 f_cyan_ilr_2 0.000 0.00 0.00 0.000 0.0000 f_JCZ38_qlogis 0.000 0.00 0.00 0.000 0.0000 log_k1 0.000 0.00 0.00 0.000 0.0000 @@ -3432,11 +3418,11 @@ log_k_JCZ38 0.000 0.00 0.0000 0.0000 0.0000 log_k_J9Z38 0.000 0.00 0.0000 0.0000 0.0000 log_k_JSE76 0.000 0.00 0.0000 0.0000 0.0000 f_cyan_ilr_1 0.000 0.00 0.0000 0.0000 0.0000 -f_cyan_ilr_2 2.167 0.00 0.0000 0.0000 0.0000 -f_JCZ38_qlogis 0.000 10.22 0.0000 0.0000 0.0000 -log_k1 0.000 0.00 0.7003 0.0000 0.0000 +f_cyan_ilr_2 2.038 0.00 0.0000 0.0000 0.0000 +f_JCZ38_qlogis 0.000 10.33 0.0000 0.0000 0.0000 +log_k1 0.000 0.00 0.7006 0.0000 0.0000 log_k2 0.000 0.00 0.0000 0.8928 0.0000 -log_tb 0.000 0.00 0.0000 0.0000 0.6774 +log_tb 0.000 0.00 0.0000 0.0000 0.6773 Starting values for error model parameters: a.1 @@ -3446,220 +3432,76 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2427 2420 -1194 - -Optimised parameters: - est. lower upper -cyan_0 101.84849 NA NA -log_k_JCZ38 -3.47365 NA NA -log_k_J9Z38 -5.10562 NA NA -log_k_JSE76 -5.60318 NA NA -f_cyan_ilr_1 0.66127 NA NA -f_cyan_ilr_2 0.60283 NA NA -f_JCZ38_qlogis 45.06408 NA NA -log_k1 -3.10124 NA NA -log_k2 -4.39028 NA NA -log_tb 2.32256 NA NA -a.1 3.32683 NA NA -SD.log_k_JCZ38 1.41427 NA NA -SD.log_k_J9Z38 0.54767 NA NA -SD.log_k_JSE76 0.62147 NA NA -SD.f_cyan_ilr_1 0.30189 NA NA -SD.f_cyan_ilr_2 0.34960 NA NA -SD.f_JCZ38_qlogis 0.04644 NA NA -SD.log_k1 0.39534 NA NA -SD.log_k2 0.43468 NA NA -SD.log_tb 0.60781 NA NA - -Correlation is not available - -Random effects: - est. lower upper -SD.log_k_JCZ38 1.41427 NA NA -SD.log_k_J9Z38 0.54767 NA NA -SD.log_k_JSE76 0.62147 NA NA -SD.f_cyan_ilr_1 0.30189 NA NA -SD.f_cyan_ilr_2 0.34960 NA NA -SD.f_JCZ38_qlogis 0.04644 NA NA -SD.log_k1 0.39534 NA NA -SD.log_k2 0.43468 NA NA -SD.log_tb 0.60781 NA NA - -Variance model: - est. lower upper -a.1 3.327 NA NA - -Backtransformed parameters: - est. lower upper -cyan_0 1.018e+02 NA NA -k_JCZ38 3.100e-02 NA NA -k_J9Z38 6.063e-03 NA NA -k_JSE76 3.686e-03 NA NA -f_cyan_to_JCZ38 5.910e-01 NA NA -f_cyan_to_J9Z38 2.320e-01 NA NA -f_JCZ38_to_JSE76 1.000e+00 NA NA -k1 4.499e-02 NA NA -k2 1.240e-02 NA NA -tb 1.020e+01 NA NA - -Resulting formation fractions: - ff -cyan_JCZ38 0.591 -cyan_J9Z38 0.232 -cyan_sink 0.177 -JCZ38_JSE76 1.000 -JCZ38_sink 0.000 - -Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -cyan 29.09 158.91 47.84 15.41 55.91 -JCZ38 22.36 74.27 NA NA NA -J9Z38 114.33 379.80 NA NA NA -JSE76 188.04 624.66 NA NA NA - -</code></pre> -<p></p> -<caption> -Hierarchical HS path 1 fit with two-component error -</caption> -<pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:46:19 2023 -Date of summary: Thu Apr 20 20:01:30 2023 - -Equations: -d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan -d_JCZ38/dt = + f_cyan_to_JCZ38 * ifelse(time <= tb, k1, k2) * cyan - - k_JCZ38 * JCZ38 -d_J9Z38/dt = + f_cyan_to_J9Z38 * ifelse(time <= tb, k1, k2) * cyan - - k_J9Z38 * J9Z38 -d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 - -Data: -433 observations of 4 variable(s) grouped in 5 datasets - -Model predictions using solution type deSolve - -Fitted in 514.968 s -Using 300, 100 iterations and 10 chains - -Variance model: Two-component variance function - -Starting values for degradation parameters: - cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 101.168 -3.358 -4.941 -5.794 0.676 - f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb - 5.740 13.863 -3.147 -4.262 2.173 - -Fixed degradation parameter values: -None - -Starting values for random effects (square root of initial entries in omega): - cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 5.79 0.000 0.000 0.000 0.0000 -log_k_JCZ38 0.00 2.271 0.000 0.000 0.0000 -log_k_J9Z38 0.00 0.000 1.614 0.000 0.0000 -log_k_JSE76 0.00 0.000 0.000 1.264 0.0000 -f_cyan_ilr_1 0.00 0.000 0.000 0.000 0.6761 -f_cyan_ilr_2 0.00 0.000 0.000 0.000 0.0000 -f_JCZ38_qlogis 0.00 0.000 0.000 0.000 0.0000 -log_k1 0.00 0.000 0.000 0.000 0.0000 -log_k2 0.00 0.000 0.000 0.000 0.0000 -log_tb 0.00 0.000 0.000 0.000 0.0000 - f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb -cyan_0 0.000 0.00 0.0000 0.0000 0.000 -log_k_JCZ38 0.000 0.00 0.0000 0.0000 0.000 -log_k_J9Z38 0.000 0.00 0.0000 0.0000 0.000 -log_k_JSE76 0.000 0.00 0.0000 0.0000 0.000 -f_cyan_ilr_1 0.000 0.00 0.0000 0.0000 0.000 -f_cyan_ilr_2 9.572 0.00 0.0000 0.0000 0.000 -f_JCZ38_qlogis 0.000 19.19 0.0000 0.0000 0.000 -log_k1 0.000 0.00 0.8705 0.0000 0.000 -log_k2 0.000 0.00 0.0000 0.9288 0.000 -log_tb 0.000 0.00 0.0000 0.0000 1.065 - -Starting values for error model parameters: -a.1 b.1 - 1 1 - -Results: - -Likelihood computed by importance sampling - AIC BIC logLik - 2422 2414 -1190 + 2427 2419 -1194 Optimised parameters: - est. lower upper -cyan_0 100.9521 NA NA -log_k_JCZ38 -3.4629 NA NA -log_k_J9Z38 -5.0346 NA NA -log_k_JSE76 -5.5722 NA NA -f_cyan_ilr_1 0.6560 NA NA -f_cyan_ilr_2 0.7983 NA NA -f_JCZ38_qlogis 42.7949 NA NA -log_k1 -3.1721 NA NA -log_k2 -4.4039 NA NA -log_tb 2.3994 NA NA -a.1 3.0586 NA NA -b.1 0.0380 NA NA -SD.log_k_JCZ38 1.3754 NA NA -SD.log_k_J9Z38 0.6703 NA NA -SD.log_k_JSE76 0.5876 NA NA -SD.f_cyan_ilr_1 0.3272 NA NA -SD.f_cyan_ilr_2 0.5300 NA NA -SD.f_JCZ38_qlogis 6.4465 NA NA -SD.log_k1 0.4135 NA NA -SD.log_k2 0.4182 NA NA -SD.log_tb 0.6035 NA NA + est. lower upper +cyan_0 101.9660 1.005e+02 1.035e+02 +log_k_JCZ38 -3.4698 -4.716e+00 -2.224e+00 +log_k_J9Z38 -5.0947 -5.740e+00 -4.450e+00 +log_k_JSE76 -5.5977 -6.321e+00 -4.875e+00 +f_cyan_ilr_1 0.6595 3.734e-01 9.456e-01 +f_cyan_ilr_2 0.5905 1.664e-01 1.015e+00 +f_JCZ38_qlogis 25.8627 -4.224e+05 4.225e+05 +log_k1 -3.0884 -3.453e+00 -2.723e+00 +log_k2 -4.3877 -4.778e+00 -3.998e+00 +log_tb 2.3057 1.715e+00 2.896e+00 +a.1 3.3228 NA NA +SD.log_k_JCZ38 1.4071 NA NA +SD.log_k_J9Z38 0.5774 NA NA +SD.log_k_JSE76 0.6214 NA NA +SD.f_cyan_ilr_1 0.3058 NA NA +SD.f_cyan_ilr_2 0.3470 NA NA +SD.f_JCZ38_qlogis 0.0644 NA NA +SD.log_k1 0.3994 NA NA +SD.log_k2 0.4373 NA NA +SD.log_tb 0.6419 NA NA Correlation is not available Random effects: est. lower upper -SD.log_k_JCZ38 1.3754 NA NA -SD.log_k_J9Z38 0.6703 NA NA -SD.log_k_JSE76 0.5876 NA NA -SD.f_cyan_ilr_1 0.3272 NA NA -SD.f_cyan_ilr_2 0.5300 NA NA -SD.f_JCZ38_qlogis 6.4465 NA NA -SD.log_k1 0.4135 NA NA -SD.log_k2 0.4182 NA NA -SD.log_tb 0.6035 NA NA +SD.log_k_JCZ38 1.4071 NA NA +SD.log_k_J9Z38 0.5774 NA NA +SD.log_k_JSE76 0.6214 NA NA +SD.f_cyan_ilr_1 0.3058 NA NA +SD.f_cyan_ilr_2 0.3470 NA NA +SD.f_JCZ38_qlogis 0.0644 NA NA +SD.log_k1 0.3994 NA NA +SD.log_k2 0.4373 NA NA +SD.log_tb 0.6419 NA NA Variance model: est. lower upper -a.1 3.059 NA NA -b.1 0.038 NA NA +a.1 3.323 NA NA Backtransformed parameters: - est. lower upper -cyan_0 1.010e+02 NA NA -k_JCZ38 3.134e-02 NA NA -k_J9Z38 6.509e-03 NA NA -k_JSE76 3.802e-03 NA NA -f_cyan_to_JCZ38 6.127e-01 NA NA -f_cyan_to_J9Z38 2.423e-01 NA NA -f_JCZ38_to_JSE76 1.000e+00 NA NA -k1 4.191e-02 NA NA -k2 1.223e-02 NA NA -tb 1.102e+01 NA NA + est. lower upper +cyan_0 1.020e+02 1.005e+02 1.035e+02 +k_JCZ38 3.112e-02 8.951e-03 1.082e-01 +k_J9Z38 6.129e-03 3.216e-03 1.168e-02 +k_JSE76 3.706e-03 1.798e-03 7.639e-03 +f_cyan_to_JCZ38 5.890e-01 NA NA +f_cyan_to_J9Z38 2.318e-01 NA NA +f_JCZ38_to_JSE76 1.000e+00 0.000e+00 1.000e+00 +k1 4.558e-02 3.164e-02 6.565e-02 +k2 1.243e-02 8.417e-03 1.835e-02 +tb 1.003e+01 5.557e+00 1.811e+01 Resulting formation fractions: - ff -cyan_JCZ38 0.6127 -cyan_J9Z38 0.2423 -cyan_sink 0.1449 -JCZ38_JSE76 1.0000 -JCZ38_sink 0.0000 + ff +cyan_JCZ38 5.890e-01 +cyan_J9Z38 2.318e-01 +cyan_sink 1.793e-01 +JCZ38_JSE76 1.000e+00 +JCZ38_sink 5.861e-12 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -cyan 29.94 161.54 48.63 16.54 56.68 -JCZ38 22.12 73.47 NA NA NA -J9Z38 106.50 353.77 NA NA NA -JSE76 182.30 605.60 NA NA NA +cyan 29.02 158.51 47.72 15.21 55.77 +JCZ38 22.27 73.98 NA NA NA +J9Z38 113.09 375.69 NA NA NA +JSE76 187.01 621.23 NA NA NA </code></pre> <p></p> @@ -3668,14 +3510,14 @@ JSE76 182.30 605.60 NA NA NA <h4 id="pathway-2">Pathway 2<a class="anchor" aria-label="anchor" href="#pathway-2"></a> </h4> <caption> -Hierarchical FOMC path 2 fit with constant variance +Hierarchical FOMC path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:58:00 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:39:30 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3690,88 +3532,89 @@ Data: Model predictions using solution type deSolve -Fitted in 522.351 s +Fitted in 474.942 s Using 300, 100 iterations and 10 chains -Variance model: Constant variance +Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 101.8173 -1.8998 -5.1449 -2.5415 0.6705 + 102.4477 -1.8631 -5.1087 -2.5114 0.6826 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta - 4.4669 16.1281 13.3327 -0.2314 2.8738 + 4.7944 15.9616 13.1566 -0.1564 2.9781 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 5.742 0.000 0.000 0.00 0.0000 -log_k_JCZ38 0.000 1.402 0.000 0.00 0.0000 -log_k_J9Z38 0.000 0.000 1.718 0.00 0.0000 -log_k_JSE76 0.000 0.000 0.000 3.57 0.0000 -f_cyan_ilr_1 0.000 0.000 0.000 0.00 0.5926 -f_cyan_ilr_2 0.000 0.000 0.000 0.00 0.0000 -f_JCZ38_qlogis 0.000 0.000 0.000 0.00 0.0000 -f_JSE76_qlogis 0.000 0.000 0.000 0.00 0.0000 -log_alpha 0.000 0.000 0.000 0.00 0.0000 -log_beta 0.000 0.000 0.000 0.00 0.0000 +cyan_0 7.701 0.000 0.000 0.000 0.0000 +log_k_JCZ38 0.000 1.448 0.000 0.000 0.0000 +log_k_J9Z38 0.000 0.000 1.724 0.000 0.0000 +log_k_JSE76 0.000 0.000 0.000 3.659 0.0000 +f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6356 +f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 +f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 +f_JSE76_qlogis 0.000 0.000 0.000 0.000 0.0000 +log_alpha 0.000 0.000 0.000 0.000 0.0000 +log_beta 0.000 0.000 0.000 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta cyan_0 0.00 0.00 0.00 0.0000 0.0000 log_k_JCZ38 0.00 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_2 10.56 0.00 0.00 0.0000 0.0000 -f_JCZ38_qlogis 0.00 12.04 0.00 0.0000 0.0000 -f_JSE76_qlogis 0.00 0.00 15.26 0.0000 0.0000 -log_alpha 0.00 0.00 0.00 0.4708 0.0000 -log_beta 0.00 0.00 0.00 0.0000 0.4432 +f_cyan_ilr_2 10.32 0.00 0.00 0.0000 0.0000 +f_JCZ38_qlogis 0.00 12.23 0.00 0.0000 0.0000 +f_JSE76_qlogis 0.00 0.00 14.99 0.0000 0.0000 +log_alpha 0.00 0.00 0.00 0.3924 0.0000 +log_beta 0.00 0.00 0.00 0.0000 0.5639 Starting values for error model parameters: -a.1 - 1 +a.1 b.1 + 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik - 2308 2301 -1134 + 2249 2241 -1104 Optimised parameters: - est. lower upper -cyan_0 101.9586 99.22024 104.69700 -log_k_JCZ38 -2.4861 -3.17661 -1.79560 -log_k_J9Z38 -5.3926 -6.08842 -4.69684 -log_k_JSE76 -3.1193 -4.12904 -2.10962 -f_cyan_ilr_1 0.7368 0.42085 1.05276 -f_cyan_ilr_2 0.6196 0.06052 1.17861 -f_JCZ38_qlogis 4.8970 -4.68003 14.47398 -f_JSE76_qlogis 4.4066 -1.02087 9.83398 -log_alpha -0.3021 -0.68264 0.07838 -log_beta 2.7438 2.57970 2.90786 -a.1 2.9008 2.69920 3.10245 -SD.cyan_0 2.7081 0.64216 4.77401 -SD.log_k_JCZ38 0.7043 0.19951 1.20907 -SD.log_k_J9Z38 0.6248 0.05790 1.19180 -SD.log_k_JSE76 1.0750 0.33157 1.81839 -SD.f_cyan_ilr_1 0.3429 0.11688 0.56892 -SD.f_cyan_ilr_2 0.4774 0.09381 0.86097 -SD.f_JCZ38_qlogis 1.5565 -7.83970 10.95279 -SD.f_JSE76_qlogis 1.6871 -1.25577 4.63000 -SD.log_alpha 0.4216 0.15913 0.68405 + est. lower upper +cyan_0 101.55265 9.920e+01 103.90593 +log_k_JCZ38 -2.32302 -2.832e+00 -1.81416 +log_k_J9Z38 -5.13082 -5.942e+00 -4.31990 +log_k_JSE76 -3.01756 -4.262e+00 -1.77360 +f_cyan_ilr_1 0.70850 3.657e-01 1.05135 +f_cyan_ilr_2 0.95775 2.612e-01 1.65432 +f_JCZ38_qlogis 3.86105 9.248e-01 6.79733 +f_JSE76_qlogis 7.51583 -1.120e+02 127.03921 +log_alpha -0.15308 -4.508e-01 0.14462 +log_beta 2.99165 2.711e+00 3.27202 +a.1 2.04034 1.811e+00 2.26968 +b.1 0.06924 5.745e-02 0.08104 +SD.log_k_JCZ38 0.50818 1.390e-01 0.87736 +SD.log_k_J9Z38 0.86597 2.652e-01 1.46671 +SD.log_k_JSE76 1.38092 4.864e-01 2.27541 +SD.f_cyan_ilr_1 0.38204 1.354e-01 0.62864 +SD.f_cyan_ilr_2 0.55129 7.198e-02 1.03060 +SD.f_JCZ38_qlogis 1.88457 1.710e-02 3.75205 +SD.f_JSE76_qlogis 2.64018 -2.450e+03 2455.27887 +SD.log_alpha 0.31860 1.047e-01 0.53249 +SD.log_beta 0.24195 1.273e-02 0.47117 Correlation: cyan_0 l__JCZ3 l__J9Z3 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 f_JSE76 -log_k_JCZ38 -0.0167 -log_k_J9Z38 -0.0307 0.0057 -log_k_JSE76 -0.0032 0.1358 0.0009 -f_cyan_ilr_1 -0.0087 0.0206 -0.1158 -0.0009 -f_cyan_ilr_2 -0.1598 0.0690 0.1770 0.0002 -0.0007 -f_JCZ38_qlogis 0.0966 -0.1132 -0.0440 0.0182 -0.1385 -0.4583 -f_JSE76_qlogis -0.0647 0.1157 0.0333 -0.0026 0.1110 0.3620 -0.8586 -log_alpha -0.0389 0.0113 0.0209 0.0021 0.0041 0.0451 -0.0605 0.0412 -log_beta -0.2508 0.0533 0.0977 0.0098 0.0220 0.2741 -0.2934 0.1999 +log_k_JCZ38 -0.0235 +log_k_J9Z38 -0.0442 0.0047 +log_k_JSE76 -0.0023 0.0966 0.0006 +f_cyan_ilr_1 -0.0032 0.0070 -0.0536 -0.0001 +f_cyan_ilr_2 -0.5189 0.0452 0.1152 0.0013 -0.0304 +f_JCZ38_qlogis 0.1088 -0.0848 -0.0240 0.0040 -0.0384 -0.2303 +f_JSE76_qlogis -0.0545 0.1315 0.0195 0.0020 0.0252 0.1737 -0.5939 +log_alpha -0.0445 0.0056 0.0261 0.0019 -0.0055 0.0586 -0.0239 -0.0284 +log_beta -0.2388 0.0163 0.0566 0.0040 -0.0078 0.2183 -0.0714 -0.0332 log_lph log_k_JCZ38 log_k_J9Z38 @@ -3781,199 +3624,54 @@ f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha -log_beta 0.2281 +log_beta 0.2135 Random effects: - est. lower upper -SD.cyan_0 2.7081 0.64216 4.7740 -SD.log_k_JCZ38 0.7043 0.19951 1.2091 -SD.log_k_J9Z38 0.6248 0.05790 1.1918 -SD.log_k_JSE76 1.0750 0.33157 1.8184 -SD.f_cyan_ilr_1 0.3429 0.11688 0.5689 -SD.f_cyan_ilr_2 0.4774 0.09381 0.8610 -SD.f_JCZ38_qlogis 1.5565 -7.83970 10.9528 -SD.f_JSE76_qlogis 1.6871 -1.25577 4.6300 -SD.log_alpha 0.4216 0.15913 0.6840 - -Variance model: - est. lower upper -a.1 2.901 2.699 3.102 - -Backtransformed parameters: - est. lower upper -cyan_0 101.95862 99.220240 1.047e+02 -k_JCZ38 0.08323 0.041727 1.660e-01 -k_J9Z38 0.00455 0.002269 9.124e-03 -k_JSE76 0.04419 0.016098 1.213e-01 -f_cyan_to_JCZ38 0.61318 NA NA -f_cyan_to_J9Z38 0.21630 NA NA -f_JCZ38_to_JSE76 0.99259 0.009193 1.000e+00 -f_JSE76_to_JCZ38 0.98795 0.264857 9.999e-01 -alpha 0.73924 0.505281 1.082e+00 -beta 15.54568 13.193194 1.832e+01 - -Resulting formation fractions: - ff -cyan_JCZ38 0.613182 -cyan_J9Z38 0.216298 -cyan_sink 0.170519 -JCZ38_JSE76 0.992586 -JCZ38_sink 0.007414 -JSE76_JCZ38 0.987950 -JSE76_sink 0.012050 - -Estimated disappearance times: - DT50 DT90 DT50back -cyan 24.157 334.68 100.7 -JCZ38 8.328 27.66 NA -J9Z38 152.341 506.06 NA -JSE76 15.687 52.11 NA - -</code></pre> -<p></p> -<caption> -Hierarchical FOMC path 2 fit with two-component error -</caption> -<pre><code> -saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:57:52 2023 -Date of summary: Thu Apr 20 20:01:30 2023 - -Equations: -d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan -d_JCZ38/dt = + f_cyan_to_JCZ38 * (alpha/beta) * 1/((time/beta) + 1) * - cyan - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 -d_J9Z38/dt = + f_cyan_to_J9Z38 * (alpha/beta) * 1/((time/beta) + 1) * - cyan - k_J9Z38 * J9Z38 -d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 - -Data: -433 observations of 4 variable(s) grouped in 5 datasets - -Model predictions using solution type deSolve - -Fitted in 514.301 s -Using 300, 100 iterations and 10 chains - -Variance model: Two-component variance function - -Starting values for degradation parameters: - cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 101.9028 -1.9055 -5.0249 -2.5646 0.6807 - f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta - 4.8883 16.0676 9.3923 -0.1346 3.0364 - -Fixed degradation parameter values: -None - -Starting values for random effects (square root of initial entries in omega): - cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 6.321 0.000 0.000 0.000 0.0000 -log_k_JCZ38 0.000 1.392 0.000 0.000 0.0000 -log_k_J9Z38 0.000 0.000 1.561 0.000 0.0000 -log_k_JSE76 0.000 0.000 0.000 3.614 0.0000 -f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6339 -f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 -f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 -f_JSE76_qlogis 0.000 0.000 0.000 0.000 0.0000 -log_alpha 0.000 0.000 0.000 0.000 0.0000 -log_beta 0.000 0.000 0.000 0.000 0.0000 - f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta -cyan_0 0.00 0.00 0.00 0.0000 0.0000 -log_k_JCZ38 0.00 0.00 0.00 0.0000 0.0000 -log_k_J9Z38 0.00 0.00 0.00 0.0000 0.0000 -log_k_JSE76 0.00 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_1 0.00 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_2 10.41 0.00 0.00 0.0000 0.0000 -f_JCZ38_qlogis 0.00 12.24 0.00 0.0000 0.0000 -f_JSE76_qlogis 0.00 0.00 15.13 0.0000 0.0000 -log_alpha 0.00 0.00 0.00 0.3701 0.0000 -log_beta 0.00 0.00 0.00 0.0000 0.5662 - -Starting values for error model parameters: -a.1 b.1 - 1 1 - -Results: - -Likelihood computed by importance sampling - AIC BIC logLik - 2248 2240 -1103 - -Optimised parameters: - est. lower upper -cyan_0 101.55545 9.920e+01 1.039e+02 -log_k_JCZ38 -2.37354 -2.928e+00 -1.819e+00 -log_k_J9Z38 -5.14736 -5.960e+00 -4.335e+00 -log_k_JSE76 -3.07802 -4.243e+00 -1.913e+00 -f_cyan_ilr_1 0.71263 3.655e-01 1.060e+00 -f_cyan_ilr_2 0.95202 2.701e-01 1.634e+00 -f_JCZ38_qlogis 3.58473 1.251e+00 5.919e+00 -f_JSE76_qlogis 19.03623 -1.037e+07 1.037e+07 -log_alpha -0.15297 -4.490e-01 1.431e-01 -log_beta 2.99230 2.706e+00 3.278e+00 -a.1 2.04816 NA NA -b.1 0.06886 NA NA -SD.log_k_JCZ38 0.56174 NA NA -SD.log_k_J9Z38 0.86509 NA NA -SD.log_k_JSE76 1.28450 NA NA -SD.f_cyan_ilr_1 0.38705 NA NA -SD.f_cyan_ilr_2 0.54153 NA NA -SD.f_JCZ38_qlogis 1.65311 NA NA -SD.f_JSE76_qlogis 7.51468 NA NA -SD.log_alpha 0.31586 NA NA -SD.log_beta 0.24696 NA NA - -Correlation is not available - -Random effects: - est. lower upper -SD.log_k_JCZ38 0.5617 NA NA -SD.log_k_J9Z38 0.8651 NA NA -SD.log_k_JSE76 1.2845 NA NA -SD.f_cyan_ilr_1 0.3870 NA NA -SD.f_cyan_ilr_2 0.5415 NA NA -SD.f_JCZ38_qlogis 1.6531 NA NA -SD.f_JSE76_qlogis 7.5147 NA NA -SD.log_alpha 0.3159 NA NA -SD.log_beta 0.2470 NA NA + est. lower upper +SD.log_k_JCZ38 0.5082 1.390e-01 0.8774 +SD.log_k_J9Z38 0.8660 2.652e-01 1.4667 +SD.log_k_JSE76 1.3809 4.864e-01 2.2754 +SD.f_cyan_ilr_1 0.3820 1.354e-01 0.6286 +SD.f_cyan_ilr_2 0.5513 7.198e-02 1.0306 +SD.f_JCZ38_qlogis 1.8846 1.710e-02 3.7520 +SD.f_JSE76_qlogis 2.6402 -2.450e+03 2455.2789 +SD.log_alpha 0.3186 1.047e-01 0.5325 +SD.log_beta 0.2420 1.273e-02 0.4712 Variance model: - est. lower upper -a.1 2.04816 NA NA -b.1 0.06886 NA NA + est. lower upper +a.1 2.04034 1.81101 2.26968 +b.1 0.06924 0.05745 0.08104 Backtransformed parameters: - est. lower upper -cyan_0 1.016e+02 99.20301 103.9079 -k_JCZ38 9.315e-02 0.05349 0.1622 -k_J9Z38 5.815e-03 0.00258 0.0131 -k_JSE76 4.605e-02 0.01436 0.1477 -f_cyan_to_JCZ38 6.438e-01 NA NA -f_cyan_to_J9Z38 2.350e-01 NA NA -f_JCZ38_to_JSE76 9.730e-01 0.77745 0.9973 -f_JSE76_to_JCZ38 1.000e+00 0.00000 1.0000 -alpha 8.582e-01 0.63824 1.1538 -beta 1.993e+01 14.97621 26.5262 + est. lower upper +cyan_0 1.016e+02 9.920e+01 103.9059 +k_JCZ38 9.798e-02 5.890e-02 0.1630 +k_J9Z38 5.912e-03 2.627e-03 0.0133 +k_JSE76 4.892e-02 1.410e-02 0.1697 +f_cyan_to_JCZ38 6.432e-01 NA NA +f_cyan_to_J9Z38 2.362e-01 NA NA +f_JCZ38_to_JSE76 9.794e-01 7.160e-01 0.9989 +f_JSE76_to_JCZ38 9.995e-01 2.268e-49 1.0000 +alpha 8.581e-01 6.371e-01 1.1556 +beta 1.992e+01 1.505e+01 26.3646 Resulting formation fractions: ff -cyan_JCZ38 6.438e-01 -cyan_J9Z38 2.350e-01 -cyan_sink 1.212e-01 -JCZ38_JSE76 9.730e-01 -JCZ38_sink 2.700e-02 -JSE76_JCZ38 1.000e+00 -JSE76_sink 5.403e-09 +cyan_JCZ38 0.6432301 +cyan_J9Z38 0.2361657 +cyan_sink 0.1206042 +JCZ38_JSE76 0.9793879 +JCZ38_sink 0.0206121 +JSE76_JCZ38 0.9994559 +JSE76_sink 0.0005441 Estimated disappearance times: DT50 DT90 DT50back -cyan 24.771 271.70 81.79 -JCZ38 7.441 24.72 NA -J9Z38 119.205 395.99 NA -JSE76 15.052 50.00 NA +cyan 24.759 271.61 81.76 +JCZ38 7.075 23.50 NA +J9Z38 117.249 389.49 NA +JSE76 14.169 47.07 NA </code></pre> <p></p> @@ -3982,10 +3680,10 @@ Hierarchical DFOP path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:58:43 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:40:29 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4005,25 +3703,25 @@ Data: Model predictions using solution type deSolve -Fitted in 565.562 s +Fitted in 533.901 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 102.4358 -2.3107 -5.3123 -3.7120 0.6753 + 102.4380 -2.3107 -5.3123 -3.7120 0.6757 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 - 1.1462 12.4095 12.3630 -1.9317 -4.4557 + 1.1439 13.1194 12.3492 -1.9317 -4.4557 g_qlogis - -0.5648 + -0.5644 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 4.594 0.0000 0.000 0.0 0.0000 +cyan_0 4.591 0.0000 0.000 0.0 0.0000 log_k_JCZ38 0.000 0.7966 0.000 0.0 0.0000 log_k_J9Z38 0.000 0.0000 1.561 0.0 0.0000 log_k_JSE76 0.000 0.0000 0.000 0.8 0.0000 @@ -4035,17 +3733,17 @@ log_k1 0.000 0.0000 0.000 0.0 0.0000 log_k2 0.000 0.0000 0.000 0.0 0.0000 g_qlogis 0.000 0.0000 0.000 0.0 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 -cyan_0 0.000 0.00 0.0 0.000 0.0000 -log_k_JCZ38 0.000 0.00 0.0 0.000 0.0000 -log_k_J9Z38 0.000 0.00 0.0 0.000 0.0000 -log_k_JSE76 0.000 0.00 0.0 0.000 0.0000 -f_cyan_ilr_1 0.000 0.00 0.0 0.000 0.0000 -f_cyan_ilr_2 1.797 0.00 0.0 0.000 0.0000 -f_JCZ38_qlogis 0.000 13.85 0.0 0.000 0.0000 -f_JSE76_qlogis 0.000 0.00 14.1 0.000 0.0000 -log_k1 0.000 0.00 0.0 1.106 0.0000 -log_k2 0.000 0.00 0.0 0.000 0.6141 -g_qlogis 0.000 0.00 0.0 0.000 0.0000 +cyan_0 0.000 0.00 0.00 0.000 0.0000 +log_k_JCZ38 0.000 0.00 0.00 0.000 0.0000 +log_k_J9Z38 0.000 0.00 0.00 0.000 0.0000 +log_k_JSE76 0.000 0.00 0.00 0.000 0.0000 +f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.0000 +f_cyan_ilr_2 1.797 0.00 0.00 0.000 0.0000 +f_JCZ38_qlogis 0.000 13.86 0.00 0.000 0.0000 +f_JSE76_qlogis 0.000 0.00 13.91 0.000 0.0000 +log_k1 0.000 0.00 0.00 1.106 0.0000 +log_k2 0.000 0.00 0.00 0.000 0.6141 +g_qlogis 0.000 0.00 0.00 0.000 0.0000 g_qlogis cyan_0 0.000 log_k_JCZ38 0.000 @@ -4067,45 +3765,45 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2290 2281 -1123 + 2288 2280 -1122 Optimised parameters: - est. lower upper -cyan_0 102.6903 101.44420 103.9365 -log_k_JCZ38 -2.4018 -2.98058 -1.8230 -log_k_J9Z38 -5.1865 -5.92931 -4.4437 -log_k_JSE76 -3.0784 -4.25226 -1.9045 -f_cyan_ilr_1 0.7157 0.37625 1.0551 -f_cyan_ilr_2 0.7073 0.20136 1.2132 -f_JCZ38_qlogis 4.6797 0.43240 8.9269 -f_JSE76_qlogis 5.0080 -1.01380 11.0299 -log_k1 -1.9620 -2.62909 -1.2949 -log_k2 -4.4894 -4.94958 -4.0292 -g_qlogis -0.4658 -1.34443 0.4129 -a.1 2.7158 2.52576 2.9059 -SD.log_k_JCZ38 0.5818 0.15679 1.0067 -SD.log_k_J9Z38 0.7421 0.16751 1.3167 -SD.log_k_JSE76 1.2841 0.43247 2.1356 -SD.f_cyan_ilr_1 0.3748 0.13040 0.6192 -SD.f_cyan_ilr_2 0.4550 0.08396 0.8261 -SD.f_JCZ38_qlogis 2.0862 -0.73390 4.9062 -SD.f_JSE76_qlogis 1.9585 -3.14773 7.0647 -SD.log_k1 0.7389 0.25761 1.2201 -SD.log_k2 0.5132 0.18143 0.8450 -SD.g_qlogis 0.9870 0.35773 1.6164 + est. lower upper +cyan_0 102.7204 1.014e+02 1.040e+02 +log_k_JCZ38 -2.8925 -4.044e+00 -1.741e+00 +log_k_J9Z38 -5.1430 -5.828e+00 -4.457e+00 +log_k_JSE76 -3.5577 -4.174e+00 -2.941e+00 +f_cyan_ilr_1 0.6929 3.788e-01 1.007e+00 +f_cyan_ilr_2 0.6066 5.342e-02 1.160e+00 +f_JCZ38_qlogis 9.8071 -2.819e+03 2.838e+03 +f_JSE76_qlogis 2.2229 5.684e-01 3.877e+00 +log_k1 -1.9339 -2.609e+00 -1.258e+00 +log_k2 -4.4709 -4.935e+00 -4.007e+00 +g_qlogis -0.4987 -1.373e+00 3.757e-01 +a.1 2.7368 2.545e+00 2.928e+00 +SD.log_k_JCZ38 1.2747 4.577e-01 2.092e+00 +SD.log_k_J9Z38 0.6758 1.418e-01 1.210e+00 +SD.log_k_JSE76 0.5869 1.169e-01 1.057e+00 +SD.f_cyan_ilr_1 0.3392 1.161e-01 5.622e-01 +SD.f_cyan_ilr_2 0.4200 8.501e-02 7.550e-01 +SD.f_JCZ38_qlogis 0.8511 -1.137e+06 1.137e+06 +SD.f_JSE76_qlogis 0.3767 -5.238e-01 1.277e+00 +SD.log_k1 0.7475 2.601e-01 1.235e+00 +SD.log_k2 0.5179 1.837e-01 8.521e-01 +SD.g_qlogis 0.9817 3.553e-01 1.608e+00 Correlation: cyan_0 l__JCZ3 l__J9Z3 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 f_JSE76 -log_k_JCZ38 -0.0170 -log_k_J9Z38 -0.0457 0.0016 -log_k_JSE76 -0.0046 0.1183 0.0005 -f_cyan_ilr_1 0.0079 0.0072 -0.0909 0.0003 -f_cyan_ilr_2 -0.3114 0.0343 0.1542 0.0023 -0.0519 -f_JCZ38_qlogis 0.0777 -0.0601 -0.0152 0.0080 -0.0520 -0.2524 -f_JSE76_qlogis -0.0356 0.0817 0.0073 0.0051 0.0388 0.1959 -0.6236 -log_k1 0.0848 -0.0028 0.0010 -0.0010 -0.0014 -0.0245 0.0121 -0.0177 -log_k2 0.0274 -0.0001 0.0075 0.0000 -0.0023 -0.0060 0.0000 -0.0130 -g_qlogis 0.0159 0.0002 -0.0095 0.0002 0.0029 -0.0140 -0.0001 0.0149 +log_k_JCZ38 -0.0351 +log_k_J9Z38 -0.0541 0.0043 +log_k_JSE76 -0.0078 0.0900 -0.0014 +f_cyan_ilr_1 -0.0249 0.0268 -0.0962 0.0000 +f_cyan_ilr_2 -0.3560 0.0848 0.1545 -0.0022 0.0463 +f_JCZ38_qlogis 0.2005 -0.1226 -0.0347 0.0514 -0.1840 -0.5906 +f_JSE76_qlogis -0.1638 0.1307 0.0266 0.0001 0.1645 0.5181 -0.9297 +log_k1 0.0881 -0.0071 0.0005 -0.0070 -0.0064 -0.0346 0.0316 -0.0341 +log_k2 0.0238 -0.0003 0.0082 -0.0022 -0.0017 -0.0017 -0.0002 -0.0076 +g_qlogis 0.0198 -0.0002 -0.0109 0.0034 0.0017 -0.0176 0.0044 0.0051 log_k1 log_k2 log_k_JCZ38 log_k_J9Z38 @@ -4115,56 +3813,56 @@ f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 -log_k2 0.0280 -g_qlogis -0.0278 -0.0310 +log_k2 0.0276 +g_qlogis -0.0283 -0.0309 Random effects: - est. lower upper -SD.log_k_JCZ38 0.5818 0.15679 1.0067 -SD.log_k_J9Z38 0.7421 0.16751 1.3167 -SD.log_k_JSE76 1.2841 0.43247 2.1356 -SD.f_cyan_ilr_1 0.3748 0.13040 0.6192 -SD.f_cyan_ilr_2 0.4550 0.08396 0.8261 -SD.f_JCZ38_qlogis 2.0862 -0.73390 4.9062 -SD.f_JSE76_qlogis 1.9585 -3.14773 7.0647 -SD.log_k1 0.7389 0.25761 1.2201 -SD.log_k2 0.5132 0.18143 0.8450 -SD.g_qlogis 0.9870 0.35773 1.6164 + est. lower upper +SD.log_k_JCZ38 1.2747 4.577e-01 2.092e+00 +SD.log_k_J9Z38 0.6758 1.418e-01 1.210e+00 +SD.log_k_JSE76 0.5869 1.169e-01 1.057e+00 +SD.f_cyan_ilr_1 0.3392 1.161e-01 5.622e-01 +SD.f_cyan_ilr_2 0.4200 8.501e-02 7.550e-01 +SD.f_JCZ38_qlogis 0.8511 -1.137e+06 1.137e+06 +SD.f_JSE76_qlogis 0.3767 -5.238e-01 1.277e+00 +SD.log_k1 0.7475 2.601e-01 1.235e+00 +SD.log_k2 0.5179 1.837e-01 8.521e-01 +SD.g_qlogis 0.9817 3.553e-01 1.608e+00 Variance model: est. lower upper -a.1 2.716 2.526 2.906 +a.1 2.737 2.545 2.928 Backtransformed parameters: est. lower upper -cyan_0 1.027e+02 1.014e+02 103.93649 -k_JCZ38 9.056e-02 5.076e-02 0.16154 -k_J9Z38 5.591e-03 2.660e-03 0.01175 -k_JSE76 4.603e-02 1.423e-02 0.14890 -f_cyan_to_JCZ38 6.184e-01 NA NA -f_cyan_to_J9Z38 2.248e-01 NA NA -f_JCZ38_to_JSE76 9.908e-01 6.064e-01 0.99987 -f_JSE76_to_JCZ38 9.934e-01 2.662e-01 0.99998 -k1 1.406e-01 7.214e-02 0.27393 -k2 1.123e-02 7.086e-03 0.01779 -g 3.856e-01 2.068e-01 0.60177 +cyan_0 102.72037 1.014e+02 104.00464 +k_JCZ38 0.05544 1.752e-02 0.17539 +k_J9Z38 0.00584 2.942e-03 0.01159 +k_JSE76 0.02850 1.539e-02 0.05279 +f_cyan_to_JCZ38 0.59995 NA NA +f_cyan_to_J9Z38 0.22519 NA NA +f_JCZ38_to_JSE76 0.99994 0.000e+00 1.00000 +f_JSE76_to_JCZ38 0.90229 6.384e-01 0.97971 +k1 0.14459 7.357e-02 0.28414 +k2 0.01144 7.192e-03 0.01819 +g 0.37784 2.021e-01 0.59284 Resulting formation fractions: - ff -cyan_JCZ38 0.618443 -cyan_J9Z38 0.224770 -cyan_sink 0.156787 -JCZ38_JSE76 0.990803 -JCZ38_sink 0.009197 -JSE76_JCZ38 0.993360 -JSE76_sink 0.006640 + ff +cyan_JCZ38 5.999e-01 +cyan_J9Z38 2.252e-01 +cyan_sink 1.749e-01 +JCZ38_JSE76 9.999e-01 +JCZ38_sink 5.506e-05 +JSE76_JCZ38 9.023e-01 +JSE76_sink 9.771e-02 Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -cyan 21.674 161.70 48.68 4.931 61.74 -JCZ38 7.654 25.43 NA NA NA -J9Z38 123.966 411.81 NA NA NA -JSE76 15.057 50.02 NA NA NA + DT50 DT90 DT50back DT50_k1 DT50_k2 +cyan 21.93 159.83 48.11 4.794 60.6 +JCZ38 12.50 41.53 NA NA NA +J9Z38 118.69 394.27 NA NA NA +JSE76 24.32 80.78 NA NA NA </code></pre> <p></p> @@ -4173,10 +3871,10 @@ Hierarchical DFOP path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 08:01:24 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:43:04 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4196,59 +3894,59 @@ Data: Model predictions using solution type deSolve -Fitted in 726.501 s +Fitted in 688.913 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 101.7523 -1.5948 -5.0119 -2.2723 0.6719 + 101.7393 -1.4493 -5.0118 -2.1269 0.6720 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 - 5.1681 12.8238 12.4130 -2.0057 -4.5526 + 7.3362 13.4423 13.2659 -2.0061 -4.5527 g_qlogis - -0.5805 + -0.5806 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 5.627 0.000 0.000 0.000 0.0000 -log_k_JCZ38 0.000 2.327 0.000 0.000 0.0000 -log_k_J9Z38 0.000 0.000 1.664 0.000 0.0000 -log_k_JSE76 0.000 0.000 0.000 4.566 0.0000 -f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6519 -f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 -f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 -f_JSE76_qlogis 0.000 0.000 0.000 0.000 0.0000 -log_k1 0.000 0.000 0.000 0.000 0.0000 -log_k2 0.000 0.000 0.000 0.000 0.0000 -g_qlogis 0.000 0.000 0.000 0.000 0.0000 +cyan_0 5.604 0.00 0.000 0.000 0.0000 +log_k_JCZ38 0.000 2.77 0.000 0.000 0.0000 +log_k_J9Z38 0.000 0.00 1.662 0.000 0.0000 +log_k_JSE76 0.000 0.00 0.000 5.021 0.0000 +f_cyan_ilr_1 0.000 0.00 0.000 0.000 0.6519 +f_cyan_ilr_2 0.000 0.00 0.000 0.000 0.0000 +f_JCZ38_qlogis 0.000 0.00 0.000 0.000 0.0000 +f_JSE76_qlogis 0.000 0.00 0.000 0.000 0.0000 +log_k1 0.000 0.00 0.000 0.000 0.0000 +log_k2 0.000 0.00 0.000 0.000 0.0000 +g_qlogis 0.000 0.00 0.000 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 -cyan_0 0.0 0.00 0.00 0.0000 0.0000 -log_k_JCZ38 0.0 0.00 0.00 0.0000 0.0000 -log_k_J9Z38 0.0 0.00 0.00 0.0000 0.0000 -log_k_JSE76 0.0 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_1 0.0 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_2 10.1 0.00 0.00 0.0000 0.0000 -f_JCZ38_qlogis 0.0 13.99 0.00 0.0000 0.0000 -f_JSE76_qlogis 0.0 0.00 14.15 0.0000 0.0000 -log_k1 0.0 0.00 0.00 0.8452 0.0000 -log_k2 0.0 0.00 0.00 0.0000 0.5968 -g_qlogis 0.0 0.00 0.00 0.0000 0.0000 +cyan_0 0.00 0.00 0.00 0.0000 0.0000 +log_k_JCZ38 0.00 0.00 0.00 0.0000 0.0000 +log_k_J9Z38 0.00 0.00 0.00 0.0000 0.0000 +log_k_JSE76 0.00 0.00 0.00 0.0000 0.0000 +f_cyan_ilr_1 0.00 0.00 0.00 0.0000 0.0000 +f_cyan_ilr_2 13.37 0.00 0.00 0.0000 0.0000 +f_JCZ38_qlogis 0.00 14.21 0.00 0.0000 0.0000 +f_JSE76_qlogis 0.00 0.00 14.58 0.0000 0.0000 +log_k1 0.00 0.00 0.00 0.8453 0.0000 +log_k2 0.00 0.00 0.00 0.0000 0.5969 +g_qlogis 0.00 0.00 0.00 0.0000 0.0000 g_qlogis -cyan_0 0.000 -log_k_JCZ38 0.000 -log_k_J9Z38 0.000 -log_k_JSE76 0.000 -f_cyan_ilr_1 0.000 -f_cyan_ilr_2 0.000 -f_JCZ38_qlogis 0.000 -f_JSE76_qlogis 0.000 -log_k1 0.000 -log_k2 0.000 -g_qlogis 1.691 +cyan_0 0.00 +log_k_JCZ38 0.00 +log_k_J9Z38 0.00 +log_k_JSE76 0.00 +f_cyan_ilr_1 0.00 +f_cyan_ilr_2 0.00 +f_JCZ38_qlogis 0.00 +f_JSE76_qlogis 0.00 +log_k1 0.00 +log_k2 0.00 +g_qlogis 1.69 Starting values for error model parameters: a.1 b.1 @@ -4261,42 +3959,42 @@ Likelihood computed by importance sampling 2234 2226 -1095 Optimised parameters: - est. lower upper -cyan_0 101.10667 9.903e+01 103.18265 -log_k_JCZ38 -2.49437 -3.297e+00 -1.69221 -log_k_J9Z38 -5.08171 -5.875e+00 -4.28846 -log_k_JSE76 -3.20072 -4.180e+00 -2.22163 -f_cyan_ilr_1 0.71059 3.639e-01 1.05727 -f_cyan_ilr_2 1.15398 2.981e-01 2.00984 -f_JCZ38_qlogis 3.18027 1.056e+00 5.30452 -f_JSE76_qlogis 5.61578 -2.505e+01 36.28077 -log_k1 -2.38875 -2.517e+00 -2.26045 -log_k2 -4.67246 -4.928e+00 -4.41715 -g_qlogis -0.28231 -1.135e+00 0.57058 -a.1 2.08190 1.856e+00 2.30785 -b.1 0.06114 5.015e-02 0.07214 -SD.log_k_JCZ38 0.84622 2.637e-01 1.42873 -SD.log_k_J9Z38 0.84564 2.566e-01 1.43464 -SD.log_k_JSE76 1.04385 3.242e-01 1.76351 -SD.f_cyan_ilr_1 0.38568 1.362e-01 0.63514 -SD.f_cyan_ilr_2 0.68046 7.166e-02 1.28925 -SD.f_JCZ38_qlogis 1.25244 -4.213e-02 2.54700 -SD.f_JSE76_qlogis 0.28202 -1.515e+03 1515.87968 -SD.log_k2 0.25749 7.655e-02 0.43843 -SD.g_qlogis 0.94535 3.490e-01 1.54174 + est. lower upper +cyan_0 101.25496 99.14662 103.36331 +log_k_JCZ38 -2.55593 -3.32972 -1.78215 +log_k_J9Z38 -5.07103 -5.85423 -4.28783 +log_k_JSE76 -3.25468 -4.17577 -2.33360 +f_cyan_ilr_1 0.70139 0.35924 1.04355 +f_cyan_ilr_2 1.07712 0.17789 1.97636 +f_JCZ38_qlogis 3.57483 0.05990 7.08976 +f_JSE76_qlogis 4.54884 -7.25628 16.35395 +log_k1 -2.38201 -2.51639 -2.24763 +log_k2 -4.66741 -4.91865 -4.41617 +g_qlogis -0.28446 -1.14192 0.57300 +a.1 2.05925 1.83267 2.28582 +b.1 0.06172 0.05076 0.07268 +SD.log_k_JCZ38 0.81137 0.25296 1.36977 +SD.log_k_J9Z38 0.83542 0.25396 1.41689 +SD.log_k_JSE76 0.97903 0.30100 1.65707 +SD.f_cyan_ilr_1 0.37878 0.13374 0.62382 +SD.f_cyan_ilr_2 0.67274 0.10102 1.24446 +SD.f_JCZ38_qlogis 1.35327 -0.42361 3.13015 +SD.f_JSE76_qlogis 1.43956 -19.15140 22.03052 +SD.log_k2 0.25329 0.07521 0.43138 +SD.g_qlogis 0.95167 0.35149 1.55184 Correlation: cyan_0 l__JCZ3 l__J9Z3 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 f_JSE76 -log_k_JCZ38 -0.0086 -log_k_J9Z38 -0.0363 -0.0007 -log_k_JSE76 0.0015 0.1210 -0.0017 -f_cyan_ilr_1 -0.0048 0.0095 -0.0572 0.0030 -f_cyan_ilr_2 -0.4788 0.0328 0.1143 0.0027 -0.0316 -f_JCZ38_qlogis 0.0736 -0.0664 -0.0137 0.0145 -0.0444 -0.2175 -f_JSE76_qlogis -0.0137 0.0971 0.0035 0.0009 0.0293 0.1333 -0.6767 -log_k1 0.2345 -0.0350 -0.0099 -0.0113 -0.0126 -0.1652 0.1756 -0.2161 -log_k2 0.0440 -0.0133 0.0199 -0.0040 -0.0097 -0.0119 0.0604 -0.1306 -g_qlogis 0.0438 0.0078 -0.0123 0.0029 0.0046 -0.0363 -0.0318 0.0736 +log_k_JCZ38 -0.0265 +log_k_J9Z38 -0.0392 0.0024 +log_k_JSE76 0.0011 0.1220 -0.0016 +f_cyan_ilr_1 -0.0161 0.0217 -0.0552 0.0034 +f_cyan_ilr_2 -0.4718 0.0829 0.1102 0.0042 0.0095 +f_JCZ38_qlogis 0.1609 -0.1318 -0.0277 0.0081 -0.1040 -0.4559 +f_JSE76_qlogis -0.1289 0.1494 0.0219 0.0012 0.1004 0.4309 -0.8543 +log_k1 0.2618 -0.0739 -0.0167 -0.0148 -0.0444 -0.2768 0.3518 -0.3818 +log_k2 0.0603 -0.0217 0.0174 -0.0058 -0.0197 -0.0533 0.0923 -0.1281 +g_qlogis 0.0362 0.0115 -0.0111 0.0040 0.0095 -0.0116 -0.0439 0.0651 log_k1 log_k2 log_k_JCZ38 log_k_J9Z38 @@ -4306,56 +4004,56 @@ f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 -log_k2 0.3198 -g_qlogis -0.1666 -0.0954 +log_k2 0.3269 +g_qlogis -0.1656 -0.0928 Random effects: - est. lower upper -SD.log_k_JCZ38 0.8462 2.637e-01 1.4287 -SD.log_k_J9Z38 0.8456 2.566e-01 1.4346 -SD.log_k_JSE76 1.0439 3.242e-01 1.7635 -SD.f_cyan_ilr_1 0.3857 1.362e-01 0.6351 -SD.f_cyan_ilr_2 0.6805 7.166e-02 1.2893 -SD.f_JCZ38_qlogis 1.2524 -4.213e-02 2.5470 -SD.f_JSE76_qlogis 0.2820 -1.515e+03 1515.8797 -SD.log_k2 0.2575 7.655e-02 0.4384 -SD.g_qlogis 0.9453 3.490e-01 1.5417 + est. lower upper +SD.log_k_JCZ38 0.8114 0.25296 1.3698 +SD.log_k_J9Z38 0.8354 0.25396 1.4169 +SD.log_k_JSE76 0.9790 0.30100 1.6571 +SD.f_cyan_ilr_1 0.3788 0.13374 0.6238 +SD.f_cyan_ilr_2 0.6727 0.10102 1.2445 +SD.f_JCZ38_qlogis 1.3533 -0.42361 3.1301 +SD.f_JSE76_qlogis 1.4396 -19.15140 22.0305 +SD.log_k2 0.2533 0.07521 0.4314 +SD.g_qlogis 0.9517 0.35149 1.5518 Variance model: est. lower upper -a.1 2.08190 1.85595 2.30785 -b.1 0.06114 0.05015 0.07214 +a.1 2.05925 1.83267 2.28582 +b.1 0.06172 0.05076 0.07268 Backtransformed parameters: est. lower upper -cyan_0 1.011e+02 9.903e+01 103.18265 -k_JCZ38 8.255e-02 3.701e-02 0.18411 -k_J9Z38 6.209e-03 2.809e-03 0.01373 -k_JSE76 4.073e-02 1.530e-02 0.10843 -f_cyan_to_JCZ38 6.608e-01 NA NA -f_cyan_to_J9Z38 2.419e-01 NA NA -f_JCZ38_to_JSE76 9.601e-01 7.419e-01 0.99506 -f_JSE76_to_JCZ38 9.964e-01 1.322e-11 1.00000 -k1 9.174e-02 8.070e-02 0.10430 -k2 9.349e-03 7.243e-03 0.01207 -g 4.299e-01 2.432e-01 0.63890 +cyan_0 1.013e+02 9.915e+01 103.36331 +k_JCZ38 7.762e-02 3.580e-02 0.16828 +k_J9Z38 6.276e-03 2.868e-03 0.01373 +k_JSE76 3.859e-02 1.536e-02 0.09695 +f_cyan_to_JCZ38 6.520e-01 NA NA +f_cyan_to_J9Z38 2.418e-01 NA NA +f_JCZ38_to_JSE76 9.727e-01 5.150e-01 0.99917 +f_JSE76_to_JCZ38 9.895e-01 7.052e-04 1.00000 +k1 9.236e-02 8.075e-02 0.10565 +k2 9.397e-03 7.309e-03 0.01208 +g 4.294e-01 2.420e-01 0.63945 Resulting formation fractions: - ff -cyan_JCZ38 0.660808 -cyan_J9Z38 0.241904 -cyan_sink 0.097288 -JCZ38_JSE76 0.960085 -JCZ38_sink 0.039915 -JSE76_JCZ38 0.996373 -JSE76_sink 0.003627 + ff +cyan_JCZ38 0.65203 +cyan_J9Z38 0.24181 +cyan_sink 0.10616 +JCZ38_JSE76 0.97274 +JCZ38_sink 0.02726 +JSE76_JCZ38 0.98953 +JSE76_sink 0.01047 Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -cyan 24.359 186.18 56.05 7.555 74.14 -JCZ38 8.397 27.89 NA NA NA -J9Z38 111.631 370.83 NA NA NA -JSE76 17.017 56.53 NA NA NA + DT50 DT90 DT50back DT50_k1 DT50_k2 +cyan 24.26 185.34 55.79 7.504 73.77 +JCZ38 8.93 29.66 NA NA NA +J9Z38 110.45 366.89 NA NA NA +JSE76 17.96 59.66 NA NA NA </code></pre> <p></p> @@ -4364,10 +4062,10 @@ Hierarchical SFORB path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 07:58:46 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:40:32 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4385,20 +4083,20 @@ Data: Model predictions using solution type deSolve -Fitted in 568.562 s +Fitted in 536.94 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound - 102.4394 -2.7673 -2.8942 + 102.4395 -2.7673 -2.8942 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 -3.6201 -2.3107 -5.3123 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 -3.7120 0.6754 1.1448 f_JCZ38_qlogis f_JSE76_qlogis - 13.2672 13.3538 + 14.8408 15.4734 Fixed degradation parameter values: None @@ -4429,17 +4127,17 @@ f_cyan_ilr_2 0.000 0.0000 0.000 0.0 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0 f_JSE76_qlogis 0.000 0.0000 0.000 0.0 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis -cyan_free_0 0.0000 0.000 0.00 0.00 -log_k_cyan_free 0.0000 0.000 0.00 0.00 -log_k_cyan_free_bound 0.0000 0.000 0.00 0.00 -log_k_cyan_bound_free 0.0000 0.000 0.00 0.00 -log_k_JCZ38 0.0000 0.000 0.00 0.00 -log_k_J9Z38 0.0000 0.000 0.00 0.00 -log_k_JSE76 0.0000 0.000 0.00 0.00 -f_cyan_ilr_1 0.6349 0.000 0.00 0.00 -f_cyan_ilr_2 0.0000 1.797 0.00 0.00 -f_JCZ38_qlogis 0.0000 0.000 13.84 0.00 -f_JSE76_qlogis 0.0000 0.000 0.00 14.66 +cyan_free_0 0.0000 0.000 0.0 0.00 +log_k_cyan_free 0.0000 0.000 0.0 0.00 +log_k_cyan_free_bound 0.0000 0.000 0.0 0.00 +log_k_cyan_bound_free 0.0000 0.000 0.0 0.00 +log_k_JCZ38 0.0000 0.000 0.0 0.00 +log_k_J9Z38 0.0000 0.000 0.0 0.00 +log_k_JSE76 0.0000 0.000 0.0 0.00 +f_cyan_ilr_1 0.6349 0.000 0.0 0.00 +f_cyan_ilr_2 0.0000 1.797 0.0 0.00 +f_JCZ38_qlogis 0.0000 0.000 15.6 0.00 +f_JSE76_qlogis 0.0000 0.000 0.0 17.52 Starting values for error model parameters: a.1 @@ -4449,45 +4147,45 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2284 2275 -1120 + 2283 2275 -1120 Optimised parameters: - est. lower upper -cyan_free_0 102.7730 1.015e+02 1.041e+02 -log_k_cyan_free -2.8530 -3.167e+00 -2.539e+00 -log_k_cyan_free_bound -2.7326 -3.543e+00 -1.922e+00 -log_k_cyan_bound_free -3.5582 -4.126e+00 -2.990e+00 -log_k_JCZ38 -2.3810 -2.921e+00 -1.841e+00 -log_k_J9Z38 -5.2301 -5.963e+00 -4.497e+00 -log_k_JSE76 -3.0286 -4.286e+00 -1.771e+00 -f_cyan_ilr_1 0.7081 3.733e-01 1.043e+00 -f_cyan_ilr_2 0.5847 7.846e-03 1.162e+00 -f_JCZ38_qlogis 9.5676 -1.323e+03 1.342e+03 -f_JSE76_qlogis 3.7042 7.254e-02 7.336e+00 -a.1 2.7222 2.532e+00 2.913e+00 -SD.log_k_cyan_free 0.3338 1.086e-01 5.589e-01 -SD.log_k_cyan_free_bound 0.8888 3.023e-01 1.475e+00 -SD.log_k_cyan_bound_free 0.6220 2.063e-01 1.038e+00 -SD.log_k_JCZ38 0.5221 1.334e-01 9.108e-01 -SD.log_k_J9Z38 0.7104 1.371e-01 1.284e+00 -SD.log_k_JSE76 1.3837 4.753e-01 2.292e+00 -SD.f_cyan_ilr_1 0.3620 1.248e-01 5.992e-01 -SD.f_cyan_ilr_2 0.4259 8.145e-02 7.704e-01 -SD.f_JCZ38_qlogis 3.5332 -1.037e+05 1.037e+05 -SD.f_JSE76_qlogis 1.6990 -2.771e-01 3.675e+00 + est. lower upper +cyan_free_0 102.6517 101.40815 103.8952 +log_k_cyan_free -2.8729 -3.18649 -2.5593 +log_k_cyan_free_bound -2.7803 -3.60525 -1.9552 +log_k_cyan_bound_free -3.5845 -4.16644 -3.0026 +log_k_JCZ38 -2.3411 -2.89698 -1.7852 +log_k_J9Z38 -5.2487 -6.01271 -4.4847 +log_k_JSE76 -3.0259 -4.28274 -1.7690 +f_cyan_ilr_1 0.7289 0.38214 1.0756 +f_cyan_ilr_2 0.6891 0.18277 1.1954 +f_JCZ38_qlogis 4.2162 0.47015 7.9622 +f_JSE76_qlogis 5.8911 -20.19088 31.9730 +a.1 2.7159 2.52587 2.9060 +SD.log_k_cyan_free 0.3354 0.10979 0.5610 +SD.log_k_cyan_free_bound 0.9061 0.30969 1.5025 +SD.log_k_cyan_bound_free 0.6376 0.21229 1.0628 +SD.log_k_JCZ38 0.5499 0.14533 0.9545 +SD.log_k_J9Z38 0.7457 0.15106 1.3404 +SD.log_k_JSE76 1.3822 0.47329 2.2912 +SD.f_cyan_ilr_1 0.3820 0.13280 0.6313 +SD.f_cyan_ilr_2 0.4317 0.06803 0.7953 +SD.f_JCZ38_qlogis 1.8258 -0.25423 3.9059 +SD.f_JSE76_qlogis 2.2348 -83.33679 87.8065 Correlation: cyn_f_0 lg_k_c_ lg_k_cyn_f_ lg_k_cyn_b_ l__JCZ3 l__J9Z3 -log_k_cyan_free 0.2126 -log_k_cyan_free_bound 0.0894 0.0871 -log_k_cyan_bound_free 0.0033 0.0410 0.0583 -log_k_JCZ38 -0.0708 -0.0280 -0.0147 0.0019 -log_k_J9Z38 -0.0535 -0.0138 0.0012 0.0148 0.0085 -log_k_JSE76 -0.0066 -0.0030 -0.0021 -0.0005 0.1090 0.0010 -f_cyan_ilr_1 -0.0364 -0.0157 -0.0095 -0.0015 0.0458 -0.0960 -f_cyan_ilr_2 -0.3814 -0.1104 -0.0423 0.0146 0.1540 0.1526 -f_JCZ38_qlogis 0.2507 0.0969 0.0482 -0.0097 -0.2282 -0.0363 -f_JSE76_qlogis -0.1648 -0.0710 -0.0443 -0.0087 0.2002 0.0226 +log_k_cyan_free 0.1944 +log_k_cyan_free_bound 0.0815 0.0814 +log_k_cyan_bound_free 0.0106 0.0426 0.0585 +log_k_JCZ38 -0.0231 -0.0106 -0.0089 -0.0051 +log_k_J9Z38 -0.0457 -0.0108 0.0019 0.0129 0.0032 +log_k_JSE76 -0.0054 -0.0024 -0.0017 -0.0005 0.1108 0.0009 +f_cyan_ilr_1 0.0051 -0.0005 -0.0035 -0.0056 0.0131 -0.0967 +f_cyan_ilr_2 -0.3182 -0.0771 -0.0309 -0.0038 0.0680 0.1643 +f_JCZ38_qlogis 0.0834 0.0369 0.0302 0.0172 -0.1145 -0.0204 +f_JSE76_qlogis -0.0553 -0.0365 -0.0441 -0.0414 0.1579 0.0175 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 log_k_cyan_free log_k_cyan_free_bound @@ -4495,63 +4193,63 @@ log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 -f_cyan_ilr_1 0.0001 -f_cyan_ilr_2 0.0031 0.0586 -f_JCZ38_qlogis 0.0023 -0.1867 -0.6255 -f_JSE76_qlogis 0.0082 0.1356 0.4519 -0.7951 +f_cyan_ilr_1 -0.0002 +f_cyan_ilr_2 0.0020 -0.0415 +f_JCZ38_qlogis 0.0052 -0.0665 -0.3437 +f_JSE76_qlogis 0.0066 0.0635 0.3491 -0.7487 Random effects: - est. lower upper -SD.log_k_cyan_free 0.3338 1.086e-01 5.589e-01 -SD.log_k_cyan_free_bound 0.8888 3.023e-01 1.475e+00 -SD.log_k_cyan_bound_free 0.6220 2.063e-01 1.038e+00 -SD.log_k_JCZ38 0.5221 1.334e-01 9.108e-01 -SD.log_k_J9Z38 0.7104 1.371e-01 1.284e+00 -SD.log_k_JSE76 1.3837 4.753e-01 2.292e+00 -SD.f_cyan_ilr_1 0.3620 1.248e-01 5.992e-01 -SD.f_cyan_ilr_2 0.4259 8.145e-02 7.704e-01 -SD.f_JCZ38_qlogis 3.5332 -1.037e+05 1.037e+05 -SD.f_JSE76_qlogis 1.6990 -2.771e-01 3.675e+00 + est. lower upper +SD.log_k_cyan_free 0.3354 0.10979 0.5610 +SD.log_k_cyan_free_bound 0.9061 0.30969 1.5025 +SD.log_k_cyan_bound_free 0.6376 0.21229 1.0628 +SD.log_k_JCZ38 0.5499 0.14533 0.9545 +SD.log_k_J9Z38 0.7457 0.15106 1.3404 +SD.log_k_JSE76 1.3822 0.47329 2.2912 +SD.f_cyan_ilr_1 0.3820 0.13280 0.6313 +SD.f_cyan_ilr_2 0.4317 0.06803 0.7953 +SD.f_JCZ38_qlogis 1.8258 -0.25423 3.9059 +SD.f_JSE76_qlogis 2.2348 -83.33679 87.8065 Variance model: est. lower upper -a.1 2.722 2.532 2.913 +a.1 2.716 2.526 2.906 Backtransformed parameters: est. lower upper -cyan_free_0 1.028e+02 1.015e+02 104.06475 -k_cyan_free 5.767e-02 4.213e-02 0.07894 -k_cyan_free_bound 6.505e-02 2.892e-02 0.14633 -k_cyan_bound_free 2.849e-02 1.614e-02 0.05028 -k_JCZ38 9.246e-02 5.390e-02 0.15859 -k_J9Z38 5.353e-03 2.572e-03 0.01114 -k_JSE76 4.838e-02 1.376e-02 0.17009 -f_cyan_free_to_JCZ38 6.011e-01 5.028e-01 0.83792 -f_cyan_free_to_J9Z38 2.208e-01 5.028e-01 0.83792 -f_JCZ38_to_JSE76 9.999e-01 0.000e+00 1.00000 -f_JSE76_to_JCZ38 9.760e-01 5.181e-01 0.99935 +cyan_free_0 1.027e+02 1.014e+02 103.89517 +k_cyan_free 5.654e-02 4.132e-02 0.07736 +k_cyan_free_bound 6.202e-02 2.718e-02 0.14153 +k_cyan_bound_free 2.775e-02 1.551e-02 0.04966 +k_JCZ38 9.622e-02 5.519e-02 0.16777 +k_J9Z38 5.254e-03 2.447e-03 0.01128 +k_JSE76 4.852e-02 1.380e-02 0.17051 +f_cyan_free_to_JCZ38 6.197e-01 5.643e-01 0.84429 +f_cyan_free_to_J9Z38 2.211e-01 5.643e-01 0.84429 +f_JCZ38_to_JSE76 9.855e-01 6.154e-01 0.99965 +f_JSE76_to_JCZ38 9.972e-01 1.703e-09 1.00000 Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g -0.13942 0.01178 0.35948 +0.13466 0.01165 0.36490 Resulting formation fractions: - ff -cyan_free_JCZ38 6.011e-01 -cyan_free_J9Z38 2.208e-01 -cyan_free_sink 1.780e-01 -cyan_free 1.000e+00 -JCZ38_JSE76 9.999e-01 -JCZ38_sink 6.996e-05 -JSE76_JCZ38 9.760e-01 -JSE76_sink 2.403e-02 + ff +cyan_free_JCZ38 0.619745 +cyan_free_J9Z38 0.221083 +cyan_free_sink 0.159172 +cyan_free 1.000000 +JCZ38_JSE76 0.985460 +JCZ38_sink 0.014540 +JSE76_JCZ38 0.997244 +JSE76_sink 0.002756 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 -cyan 23.390 157.60 47.44 4.971 58.82 -JCZ38 7.497 24.90 NA NA NA -J9Z38 129.482 430.13 NA NA NA -JSE76 14.326 47.59 NA NA NA +cyan 23.293 158.67 47.77 5.147 59.5 +JCZ38 7.203 23.93 NA NA NA +J9Z38 131.918 438.22 NA NA NA +JSE76 14.287 47.46 NA NA NA </code></pre> <p></p> @@ -4560,10 +4258,10 @@ Hierarchical SFORB path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 08:01:30 2023 -Date of summary: Thu Apr 20 20:01:30 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:42:47 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4581,20 +4279,20 @@ Data: Model predictions using solution type deSolve -Fitted in 732.212 s +Fitted in 671.849 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound - 101.751 -2.837 -3.016 + 101.7511 -2.8370 -3.0162 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 - -3.660 -2.299 -5.313 + -3.6600 -2.2988 -5.3129 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 - -3.699 0.672 5.873 + -3.6991 0.6722 4.8596 f_JCZ38_qlogis f_JSE76_qlogis - 13.216 13.338 + 13.4678 14.2149 Fixed degradation parameter values: None @@ -4625,17 +4323,17 @@ f_cyan_ilr_2 0.000 0.0000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0000 f_JSE76_qlogis 0.000 0.0000 0.000 0.0000 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis -cyan_free_0 0.0000 0.00 0.00 0.00 -log_k_cyan_free 0.0000 0.00 0.00 0.00 -log_k_cyan_free_bound 0.0000 0.00 0.00 0.00 -log_k_cyan_bound_free 0.0000 0.00 0.00 0.00 -log_k_JCZ38 0.0000 0.00 0.00 0.00 -log_k_J9Z38 0.0000 0.00 0.00 0.00 -log_k_JSE76 0.0000 0.00 0.00 0.00 -f_cyan_ilr_1 0.6519 0.00 0.00 0.00 -f_cyan_ilr_2 0.0000 10.78 0.00 0.00 -f_JCZ38_qlogis 0.0000 0.00 13.96 0.00 -f_JSE76_qlogis 0.0000 0.00 0.00 14.69 +cyan_free_0 0.0000 0.000 0.00 0.00 +log_k_cyan_free 0.0000 0.000 0.00 0.00 +log_k_cyan_free_bound 0.0000 0.000 0.00 0.00 +log_k_cyan_bound_free 0.0000 0.000 0.00 0.00 +log_k_JCZ38 0.0000 0.000 0.00 0.00 +log_k_J9Z38 0.0000 0.000 0.00 0.00 +log_k_JSE76 0.0000 0.000 0.00 0.00 +f_cyan_ilr_1 0.6518 0.000 0.00 0.00 +f_cyan_ilr_2 0.0000 9.981 0.00 0.00 +f_JCZ38_qlogis 0.0000 0.000 14.26 0.00 +f_JSE76_qlogis 0.0000 0.000 0.00 16.17 Starting values for error model parameters: a.1 b.1 @@ -4645,45 +4343,45 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2240 2232 -1098 + 2240 2231 -1098 Optimised parameters: - est. lower upper -cyan_free_0 101.10205 98.99221 103.2119 -log_k_cyan_free -3.16929 -3.61395 -2.7246 -log_k_cyan_free_bound -3.38259 -3.63022 -3.1350 -log_k_cyan_bound_free -3.81075 -4.13888 -3.4826 -log_k_JCZ38 -2.42057 -3.00756 -1.8336 -log_k_J9Z38 -5.07501 -5.85138 -4.2986 -log_k_JSE76 -3.12442 -4.21277 -2.0361 -f_cyan_ilr_1 0.70577 0.35788 1.0537 -f_cyan_ilr_2 1.14824 0.15810 2.1384 -f_JCZ38_qlogis 3.52245 0.43257 6.6123 -f_JSE76_qlogis 5.65140 -21.22295 32.5257 -a.1 2.07062 1.84329 2.2980 -b.1 0.06227 0.05124 0.0733 -SD.log_k_cyan_free 0.49468 0.18566 0.8037 -SD.log_k_cyan_bound_free 0.28972 0.07188 0.5076 -SD.log_k_JCZ38 0.58852 0.16800 1.0090 -SD.log_k_J9Z38 0.82500 0.24730 1.4027 -SD.log_k_JSE76 1.19201 0.40313 1.9809 -SD.f_cyan_ilr_1 0.38534 0.13640 0.6343 -SD.f_cyan_ilr_2 0.72463 0.10076 1.3485 -SD.f_JCZ38_qlogis 1.38223 -0.20997 2.9744 -SD.f_JSE76_qlogis 2.07989 -72.53027 76.6901 + est. lower upper +cyan_free_0 100.73014 9.873e+01 1.027e+02 +log_k_cyan_free -3.19634 -3.641e+00 -2.752e+00 +log_k_cyan_free_bound -3.43533 -3.674e+00 -3.197e+00 +log_k_cyan_bound_free -3.83282 -4.163e+00 -3.503e+00 +log_k_JCZ38 -2.51065 -3.225e+00 -1.796e+00 +log_k_J9Z38 -5.02539 -5.825e+00 -4.226e+00 +log_k_JSE76 -3.24777 -4.163e+00 -2.333e+00 +f_cyan_ilr_1 0.70640 3.562e-01 1.057e+00 +f_cyan_ilr_2 1.42704 3.170e-01 2.537e+00 +f_JCZ38_qlogis 2.84779 1.042e+00 4.654e+00 +f_JSE76_qlogis 8.63674 -6.407e+02 6.580e+02 +a.1 2.07082 1.846e+00 2.296e+00 +b.1 0.06227 5.120e-02 7.334e-02 +SD.log_k_cyan_free 0.49674 1.865e-01 8.069e-01 +SD.log_k_cyan_bound_free 0.28537 6.808e-02 5.027e-01 +SD.log_k_JCZ38 0.74846 2.305e-01 1.266e+00 +SD.log_k_J9Z38 0.86077 2.713e-01 1.450e+00 +SD.log_k_JSE76 0.97613 3.030e-01 1.649e+00 +SD.f_cyan_ilr_1 0.38994 1.382e-01 6.417e-01 +SD.f_cyan_ilr_2 0.82869 3.917e-02 1.618e+00 +SD.f_JCZ38_qlogis 1.05000 -2.809e-02 2.128e+00 +SD.f_JSE76_qlogis 0.44681 -3.986e+05 3.986e+05 Correlation: cyn_f_0 lg_k_c_ lg_k_cyn_f_ lg_k_cyn_b_ l__JCZ3 l__J9Z3 -log_k_cyan_free 0.1117 -log_k_cyan_free_bound 0.1763 0.1828 -log_k_cyan_bound_free 0.0120 0.0593 0.5030 -log_k_JCZ38 -0.0459 -0.0230 -0.0931 -0.0337 -log_k_J9Z38 -0.0381 -0.0123 -0.0139 0.0237 0.0063 -log_k_JSE76 -0.0044 -0.0038 -0.0175 -0.0072 0.1120 0.0003 -f_cyan_ilr_1 -0.0199 -0.0087 -0.0407 -0.0233 0.0268 -0.0552 -f_cyan_ilr_2 -0.4806 -0.1015 -0.2291 -0.0269 0.1156 0.1113 -f_JCZ38_qlogis 0.1805 0.0825 0.3085 0.0963 -0.1674 -0.0314 -f_JSE76_qlogis -0.1586 -0.0810 -0.3560 -0.1563 0.2025 0.0278 +log_k_cyan_free 0.0936 +log_k_cyan_free_bound 0.1302 0.1627 +log_k_cyan_bound_free 0.0029 0.0525 0.5181 +log_k_JCZ38 -0.0116 -0.0077 -0.0430 -0.0236 +log_k_J9Z38 -0.0192 -0.0077 -0.0048 0.0229 -0.0005 +log_k_JSE76 0.0007 -0.0020 -0.0134 -0.0072 0.1225 -0.0016 +f_cyan_ilr_1 -0.0118 -0.0027 -0.0132 -0.0118 0.0127 -0.0505 +f_cyan_ilr_2 -0.4643 -0.0762 -0.1245 0.0137 0.0497 0.1003 +f_JCZ38_qlogis 0.0710 0.0371 0.1826 0.0925 -0.0869 -0.0130 +f_JSE76_qlogis -0.0367 -0.0270 -0.2274 -0.1865 0.1244 0.0098 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 log_k_cyan_free log_k_cyan_free_bound @@ -4691,63 +4389,63 @@ log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 -f_cyan_ilr_1 0.0024 -f_cyan_ilr_2 0.0087 0.0172 -f_JCZ38_qlogis -0.0016 -0.1047 -0.4656 -f_JSE76_qlogis 0.0119 0.1034 0.4584 -0.8137 +f_cyan_ilr_1 0.0036 +f_cyan_ilr_2 0.0050 -0.0201 +f_JCZ38_qlogis 0.0142 -0.0529 -0.2698 +f_JSE76_qlogis 0.0064 0.0345 0.2015 -0.7058 Random effects: - est. lower upper -SD.log_k_cyan_free 0.4947 0.18566 0.8037 -SD.log_k_cyan_bound_free 0.2897 0.07188 0.5076 -SD.log_k_JCZ38 0.5885 0.16800 1.0090 -SD.log_k_J9Z38 0.8250 0.24730 1.4027 -SD.log_k_JSE76 1.1920 0.40313 1.9809 -SD.f_cyan_ilr_1 0.3853 0.13640 0.6343 -SD.f_cyan_ilr_2 0.7246 0.10076 1.3485 -SD.f_JCZ38_qlogis 1.3822 -0.20997 2.9744 -SD.f_JSE76_qlogis 2.0799 -72.53027 76.6901 + est. lower upper +SD.log_k_cyan_free 0.4967 1.865e-01 8.069e-01 +SD.log_k_cyan_bound_free 0.2854 6.808e-02 5.027e-01 +SD.log_k_JCZ38 0.7485 2.305e-01 1.266e+00 +SD.log_k_J9Z38 0.8608 2.713e-01 1.450e+00 +SD.log_k_JSE76 0.9761 3.030e-01 1.649e+00 +SD.f_cyan_ilr_1 0.3899 1.382e-01 6.417e-01 +SD.f_cyan_ilr_2 0.8287 3.917e-02 1.618e+00 +SD.f_JCZ38_qlogis 1.0500 -2.809e-02 2.128e+00 +SD.f_JSE76_qlogis 0.4468 -3.986e+05 3.986e+05 Variance model: - est. lower upper -a.1 2.07062 1.84329 2.2980 -b.1 0.06227 0.05124 0.0733 + est. lower upper +a.1 2.07082 1.8458 2.29588 +b.1 0.06227 0.0512 0.07334 Backtransformed parameters: - est. lower upper -cyan_free_0 1.011e+02 9.899e+01 103.21190 -k_cyan_free 4.203e-02 2.695e-02 0.06557 -k_cyan_free_bound 3.396e-02 2.651e-02 0.04350 -k_cyan_bound_free 2.213e-02 1.594e-02 0.03073 -k_JCZ38 8.887e-02 4.941e-02 0.15984 -k_J9Z38 6.251e-03 2.876e-03 0.01359 -k_JSE76 4.396e-02 1.481e-02 0.13054 -f_cyan_free_to_JCZ38 6.590e-01 5.557e-01 0.95365 -f_cyan_free_to_J9Z38 2.429e-01 5.557e-01 0.95365 -f_JCZ38_to_JSE76 9.713e-01 6.065e-01 0.99866 -f_JSE76_to_JCZ38 9.965e-01 6.067e-10 1.00000 + est. lower upper +cyan_free_0 1.007e+02 9.873e+01 102.72898 +k_cyan_free 4.091e-02 2.623e-02 0.06382 +k_cyan_free_bound 3.221e-02 2.537e-02 0.04090 +k_cyan_bound_free 2.165e-02 1.557e-02 0.03011 +k_JCZ38 8.122e-02 3.975e-02 0.16594 +k_J9Z38 6.569e-03 2.954e-03 0.01461 +k_JSE76 3.886e-02 1.556e-02 0.09703 +f_cyan_free_to_JCZ38 6.785e-01 6.102e-01 0.97309 +f_cyan_free_to_J9Z38 2.498e-01 6.102e-01 0.97309 +f_JCZ38_to_JSE76 9.452e-01 7.392e-01 0.99056 +f_JSE76_to_JCZ38 9.998e-01 5.580e-279 1.00000 Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g -0.08749 0.01063 0.40855 +0.08426 0.01051 0.41220 Resulting formation fractions: - ff -cyan_free_JCZ38 0.65905 -cyan_free_J9Z38 0.24291 -cyan_free_sink 0.09805 -cyan_free 1.00000 -JCZ38_JSE76 0.97132 -JCZ38_sink 0.02868 -JSE76_JCZ38 0.99650 -JSE76_sink 0.00350 + ff +cyan_free_JCZ38 0.6784541 +cyan_free_J9Z38 0.2498405 +cyan_free_sink 0.0717054 +cyan_free 1.0000000 +JCZ38_JSE76 0.9452043 +JCZ38_sink 0.0547957 +JSE76_JCZ38 0.9998226 +JSE76_sink 0.0001774 Estimated disappearance times: - DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 -cyan 24.91 167.16 50.32 7.922 65.19 -JCZ38 7.80 25.91 NA NA NA -J9Z38 110.89 368.36 NA NA NA -JSE76 15.77 52.38 NA NA NA + DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 +cyan 25.237 168.51 50.73 8.226 65.95 +JCZ38 8.535 28.35 NA NA NA +J9Z38 105.517 350.52 NA NA NA +JSE76 17.837 59.25 NA NA NA </code></pre> <p></p> @@ -4761,10 +4459,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 08:15:01 2023 -Date of summary: Thu Apr 20 20:01:31 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:55:35 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -4779,27 +4477,27 @@ Data: Model predictions using solution type deSolve -Fitted in 808.728 s +Fitted in 748.54 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 101.9028 -1.9055 -5.0249 -2.5646 0.6807 + 102.4477 -1.8631 -5.1087 -2.5114 0.6826 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta - 4.8883 16.0676 9.3923 -0.1346 3.0364 + 4.7944 15.9616 13.1566 -0.1564 2.9781 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 6.321 0.000 0.000 0.000 0.0000 -log_k_JCZ38 0.000 1.392 0.000 0.000 0.0000 -log_k_J9Z38 0.000 0.000 1.561 0.000 0.0000 -log_k_JSE76 0.000 0.000 0.000 3.614 0.0000 -f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6339 +cyan_0 7.701 0.000 0.000 0.000 0.0000 +log_k_JCZ38 0.000 1.448 0.000 0.000 0.0000 +log_k_J9Z38 0.000 0.000 1.724 0.000 0.0000 +log_k_JSE76 0.000 0.000 0.000 3.659 0.0000 +f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6356 f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 f_JSE76_qlogis 0.000 0.000 0.000 0.000 0.0000 @@ -4811,11 +4509,11 @@ log_k_JCZ38 0.00 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_2 10.41 0.00 0.00 0.0000 0.0000 -f_JCZ38_qlogis 0.00 12.24 0.00 0.0000 0.0000 -f_JSE76_qlogis 0.00 0.00 15.13 0.0000 0.0000 -log_alpha 0.00 0.00 0.00 0.3701 0.0000 -log_beta 0.00 0.00 0.00 0.0000 0.5662 +f_cyan_ilr_2 10.32 0.00 0.00 0.0000 0.0000 +f_JCZ38_qlogis 0.00 12.23 0.00 0.0000 0.0000 +f_JSE76_qlogis 0.00 0.00 14.99 0.0000 0.0000 +log_alpha 0.00 0.00 0.00 0.3924 0.0000 +log_beta 0.00 0.00 0.00 0.0000 0.5639 Starting values for error model parameters: a.1 b.1 @@ -4825,76 +4523,76 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2251 2244 -1106 + 2249 2242 -1106 Optimised parameters: - est. lower upper -cyan_0 101.05768 NA NA -log_k_JCZ38 -2.73252 NA NA -log_k_J9Z38 -5.07399 NA NA -log_k_JSE76 -3.52863 NA NA -f_cyan_ilr_1 0.72176 NA NA -f_cyan_ilr_2 1.34610 NA NA -f_JCZ38_qlogis 2.08337 NA NA -f_JSE76_qlogis 1590.31880 NA NA -log_alpha -0.09336 NA NA -log_beta 3.10191 NA NA -a.1 2.08557 1.85439 2.31675 -b.1 0.06998 0.05800 0.08197 -SD.log_k_JCZ38 1.20053 0.43329 1.96777 -SD.log_k_J9Z38 0.85854 0.26708 1.45000 -SD.log_k_JSE76 0.62528 0.16061 1.08995 -SD.f_cyan_ilr_1 0.35190 0.12340 0.58039 -SD.f_cyan_ilr_2 0.85385 0.15391 1.55378 -SD.log_alpha 0.28971 0.08718 0.49225 -SD.log_beta 0.31614 0.05938 0.57290 + est. lower upper +cyan_0 101.24524 NA NA +log_k_JCZ38 -2.85375 NA NA +log_k_J9Z38 -5.07729 NA NA +log_k_JSE76 -3.53511 NA NA +f_cyan_ilr_1 0.67478 NA NA +f_cyan_ilr_2 0.97152 NA NA +f_JCZ38_qlogis 213.48001 NA NA +f_JSE76_qlogis 2.02040 NA NA +log_alpha -0.11041 NA NA +log_beta 3.06575 NA NA +a.1 2.05279 1.82393 2.28166 +b.1 0.07116 0.05910 0.08322 +SD.log_k_JCZ38 1.21713 0.44160 1.99266 +SD.log_k_J9Z38 0.88268 0.27541 1.48995 +SD.log_k_JSE76 0.59452 0.15005 1.03898 +SD.f_cyan_ilr_1 0.35370 0.12409 0.58331 +SD.f_cyan_ilr_2 0.78186 0.18547 1.37824 +SD.log_alpha 0.27781 0.08168 0.47394 +SD.log_beta 0.32608 0.06490 0.58726 Correlation is not available Random effects: est. lower upper -SD.log_k_JCZ38 1.2005 0.43329 1.9678 -SD.log_k_J9Z38 0.8585 0.26708 1.4500 -SD.log_k_JSE76 0.6253 0.16061 1.0900 -SD.f_cyan_ilr_1 0.3519 0.12340 0.5804 -SD.f_cyan_ilr_2 0.8538 0.15391 1.5538 -SD.log_alpha 0.2897 0.08718 0.4923 -SD.log_beta 0.3161 0.05938 0.5729 +SD.log_k_JCZ38 1.2171 0.44160 1.9927 +SD.log_k_J9Z38 0.8827 0.27541 1.4900 +SD.log_k_JSE76 0.5945 0.15005 1.0390 +SD.f_cyan_ilr_1 0.3537 0.12409 0.5833 +SD.f_cyan_ilr_2 0.7819 0.18547 1.3782 +SD.log_alpha 0.2778 0.08168 0.4739 +SD.log_beta 0.3261 0.06490 0.5873 Variance model: - est. lower upper -a.1 2.08557 1.854 2.31675 -b.1 0.06998 0.058 0.08197 + est. lower upper +a.1 2.05279 1.8239 2.28166 +b.1 0.07116 0.0591 0.08322 Backtransformed parameters: est. lower upper -cyan_0 1.011e+02 NA NA -k_JCZ38 6.506e-02 NA NA -k_J9Z38 6.257e-03 NA NA -k_JSE76 2.935e-02 NA NA -f_cyan_to_JCZ38 6.776e-01 NA NA -f_cyan_to_J9Z38 2.442e-01 NA NA -f_JCZ38_to_JSE76 8.893e-01 NA NA -f_JSE76_to_JCZ38 1.000e+00 NA NA -alpha 9.109e-01 NA NA -beta 2.224e+01 NA NA +cyan_0 1.012e+02 NA NA +k_JCZ38 5.763e-02 NA NA +k_J9Z38 6.237e-03 NA NA +k_JSE76 2.916e-02 NA NA +f_cyan_to_JCZ38 6.354e-01 NA NA +f_cyan_to_J9Z38 2.447e-01 NA NA +f_JCZ38_to_JSE76 1.000e+00 NA NA +f_JSE76_to_JCZ38 8.829e-01 NA NA +alpha 8.955e-01 NA NA +beta 2.145e+01 NA NA Resulting formation fractions: - ff -cyan_JCZ38 0.67761 -cyan_J9Z38 0.24417 -cyan_sink 0.07822 -JCZ38_JSE76 0.88928 -JCZ38_sink 0.11072 -JSE76_JCZ38 1.00000 -JSE76_sink 0.00000 + ff +cyan_JCZ38 0.6354 +cyan_J9Z38 0.2447 +cyan_sink 0.1200 +JCZ38_JSE76 1.0000 +JCZ38_sink 0.0000 +JSE76_JCZ38 0.8829 +JSE76_sink 0.1171 Estimated disappearance times: DT50 DT90 DT50back -cyan 25.36 256.37 77.18 -JCZ38 10.65 35.39 NA -J9Z38 110.77 367.98 NA -JSE76 23.62 78.47 NA +cyan 25.07 259.21 78.03 +JCZ38 12.03 39.96 NA +J9Z38 111.14 369.19 NA +JSE76 23.77 78.98 NA </code></pre> <p></p> @@ -4904,10 +4602,10 @@ variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 08:16:32 2023 -Date of summary: Thu Apr 20 20:01:31 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:57:10 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4927,25 +4625,25 @@ Data: Model predictions using solution type deSolve -Fitted in 900.061 s +Fitted in 843.793 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 102.4358 -2.3107 -5.3123 -3.7120 0.6753 + 102.4380 -2.3107 -5.3123 -3.7120 0.6757 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 - 1.1462 12.4095 12.3630 -1.9317 -4.4557 + 1.1439 13.1194 12.3492 -1.9317 -4.4557 g_qlogis - -0.5648 + -0.5644 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 4.594 0.0000 0.000 0.0 0.0000 +cyan_0 4.591 0.0000 0.000 0.0 0.0000 log_k_JCZ38 0.000 0.7966 0.000 0.0 0.0000 log_k_J9Z38 0.000 0.0000 1.561 0.0 0.0000 log_k_JSE76 0.000 0.0000 0.000 0.8 0.0000 @@ -4957,17 +4655,17 @@ log_k1 0.000 0.0000 0.000 0.0 0.0000 log_k2 0.000 0.0000 0.000 0.0 0.0000 g_qlogis 0.000 0.0000 0.000 0.0 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 -cyan_0 0.000 0.00 0.0 0.000 0.0000 -log_k_JCZ38 0.000 0.00 0.0 0.000 0.0000 -log_k_J9Z38 0.000 0.00 0.0 0.000 0.0000 -log_k_JSE76 0.000 0.00 0.0 0.000 0.0000 -f_cyan_ilr_1 0.000 0.00 0.0 0.000 0.0000 -f_cyan_ilr_2 1.797 0.00 0.0 0.000 0.0000 -f_JCZ38_qlogis 0.000 13.85 0.0 0.000 0.0000 -f_JSE76_qlogis 0.000 0.00 14.1 0.000 0.0000 -log_k1 0.000 0.00 0.0 1.106 0.0000 -log_k2 0.000 0.00 0.0 0.000 0.6141 -g_qlogis 0.000 0.00 0.0 0.000 0.0000 +cyan_0 0.000 0.00 0.00 0.000 0.0000 +log_k_JCZ38 0.000 0.00 0.00 0.000 0.0000 +log_k_J9Z38 0.000 0.00 0.00 0.000 0.0000 +log_k_JSE76 0.000 0.00 0.00 0.000 0.0000 +f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.0000 +f_cyan_ilr_2 1.797 0.00 0.00 0.000 0.0000 +f_JCZ38_qlogis 0.000 13.86 0.00 0.000 0.0000 +f_JSE76_qlogis 0.000 0.00 13.91 0.000 0.0000 +log_k1 0.000 0.00 0.00 1.106 0.0000 +log_k2 0.000 0.00 0.00 0.000 0.6141 +g_qlogis 0.000 0.00 0.00 0.000 0.0000 g_qlogis cyan_0 0.000 log_k_JCZ38 0.000 @@ -4993,74 +4691,74 @@ Likelihood computed by importance sampling Optimised parameters: est. lower upper -cyan_0 102.5254 NA NA -log_k_JCZ38 -2.9358 NA NA -log_k_J9Z38 -5.1424 NA NA -log_k_JSE76 -3.6458 NA NA -f_cyan_ilr_1 0.6957 NA NA -f_cyan_ilr_2 0.6635 NA NA -f_JCZ38_qlogis 4984.8163 NA NA -f_JSE76_qlogis 1.9415 NA NA -log_k1 -1.9456 NA NA -log_k2 -4.4705 NA NA -g_qlogis -0.5117 NA NA -a.1 2.7455 2.55392 2.9370 -SD.log_k_JCZ38 1.3163 0.47635 2.1563 -SD.log_k_J9Z38 0.7162 0.16133 1.2711 -SD.log_k_JSE76 0.6457 0.15249 1.1390 -SD.f_cyan_ilr_1 0.3424 0.11714 0.5677 -SD.f_cyan_ilr_2 0.4524 0.09709 0.8077 -SD.log_k1 0.7353 0.25445 1.2161 -SD.log_k2 0.5137 0.18206 0.8453 -SD.g_qlogis 0.9857 0.35651 1.6148 +cyan_0 102.6036 NA NA +log_k_JCZ38 -2.9348 NA NA +log_k_J9Z38 -5.1617 NA NA +log_k_JSE76 -3.6396 NA NA +f_cyan_ilr_1 0.6991 NA NA +f_cyan_ilr_2 0.6341 NA NA +f_JCZ38_qlogis 4232.3011 NA NA +f_JSE76_qlogis 1.9658 NA NA +log_k1 -1.9503 NA NA +log_k2 -4.4745 NA NA +g_qlogis -0.4967 NA NA +a.1 2.7461 2.59274 2.8994 +SD.log_k_JCZ38 1.3178 0.47602 2.1596 +SD.log_k_J9Z38 0.7022 0.15061 1.2538 +SD.log_k_JSE76 0.6566 0.15613 1.1570 +SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 +SD.f_cyan_ilr_2 0.4385 0.09482 0.7821 +SD.log_k1 0.7381 0.25599 1.2202 +SD.log_k2 0.5133 0.18152 0.8450 +SD.g_qlogis 0.9866 0.35681 1.6164 Correlation is not available Random effects: est. lower upper -SD.log_k_JCZ38 1.3163 0.47635 2.1563 -SD.log_k_J9Z38 0.7162 0.16133 1.2711 -SD.log_k_JSE76 0.6457 0.15249 1.1390 -SD.f_cyan_ilr_1 0.3424 0.11714 0.5677 -SD.f_cyan_ilr_2 0.4524 0.09709 0.8077 -SD.log_k1 0.7353 0.25445 1.2161 -SD.log_k2 0.5137 0.18206 0.8453 -SD.g_qlogis 0.9857 0.35651 1.6148 +SD.log_k_JCZ38 1.3178 0.47602 2.1596 +SD.log_k_J9Z38 0.7022 0.15061 1.2538 +SD.log_k_JSE76 0.6566 0.15613 1.1570 +SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 +SD.f_cyan_ilr_2 0.4385 0.09482 0.7821 +SD.log_k1 0.7381 0.25599 1.2202 +SD.log_k2 0.5133 0.18152 0.8450 +SD.g_qlogis 0.9866 0.35681 1.6164 Variance model: est. lower upper -a.1 2.745 2.554 2.937 +a.1 2.746 2.593 2.899 Backtransformed parameters: est. lower upper -cyan_0 1.025e+02 NA NA -k_JCZ38 5.309e-02 NA NA -k_J9Z38 5.844e-03 NA NA -k_JSE76 2.610e-02 NA NA -f_cyan_to_JCZ38 6.079e-01 NA NA -f_cyan_to_J9Z38 2.272e-01 NA NA +cyan_0 1.026e+02 NA NA +k_JCZ38 5.314e-02 NA NA +k_J9Z38 5.732e-03 NA NA +k_JSE76 2.626e-02 NA NA +f_cyan_to_JCZ38 6.051e-01 NA NA +f_cyan_to_J9Z38 2.251e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA -f_JSE76_to_JCZ38 8.745e-01 NA NA -k1 1.429e-01 NA NA -k2 1.144e-02 NA NA -g 3.748e-01 NA NA +f_JSE76_to_JCZ38 8.772e-01 NA NA +k1 1.422e-01 NA NA +k2 1.140e-02 NA NA +g 3.783e-01 NA NA Resulting formation fractions: ff -cyan_JCZ38 0.6079 -cyan_J9Z38 0.2272 -cyan_sink 0.1649 +cyan_JCZ38 0.6051 +cyan_J9Z38 0.2251 +cyan_sink 0.1698 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 -JSE76_JCZ38 0.8745 -JSE76_sink 0.1255 +JSE76_JCZ38 0.8772 +JSE76_sink 0.1228 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -cyan 22.29 160.20 48.22 4.85 60.58 -JCZ38 13.06 43.37 NA NA NA -J9Z38 118.61 394.02 NA NA NA -JSE76 26.56 88.22 NA NA NA +cyan 22.05 160.35 48.27 4.873 60.83 +JCZ38 13.04 43.33 NA NA NA +J9Z38 120.93 401.73 NA NA NA +JSE76 26.39 87.68 NA NA NA </code></pre> <p></p> @@ -5070,10 +4768,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 08:16:47 2023 -Date of summary: Thu Apr 20 20:01:31 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:57:32 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -5093,59 +4791,59 @@ Data: Model predictions using solution type deSolve -Fitted in 914.763 s +Fitted in 865.636 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 101.7523 -1.5948 -5.0119 -2.2723 0.6719 + 101.7393 -1.4493 -5.0118 -2.1269 0.6720 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 - 5.1681 12.8238 12.4130 -2.0057 -4.5526 + 7.3362 13.4423 13.2659 -2.0061 -4.5527 g_qlogis - -0.5805 + -0.5806 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 5.627 0.000 0.000 0.000 0.0000 -log_k_JCZ38 0.000 2.327 0.000 0.000 0.0000 -log_k_J9Z38 0.000 0.000 1.664 0.000 0.0000 -log_k_JSE76 0.000 0.000 0.000 4.566 0.0000 -f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6519 -f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 -f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 -f_JSE76_qlogis 0.000 0.000 0.000 0.000 0.0000 -log_k1 0.000 0.000 0.000 0.000 0.0000 -log_k2 0.000 0.000 0.000 0.000 0.0000 -g_qlogis 0.000 0.000 0.000 0.000 0.0000 +cyan_0 5.604 0.00 0.000 0.000 0.0000 +log_k_JCZ38 0.000 2.77 0.000 0.000 0.0000 +log_k_J9Z38 0.000 0.00 1.662 0.000 0.0000 +log_k_JSE76 0.000 0.00 0.000 5.021 0.0000 +f_cyan_ilr_1 0.000 0.00 0.000 0.000 0.6519 +f_cyan_ilr_2 0.000 0.00 0.000 0.000 0.0000 +f_JCZ38_qlogis 0.000 0.00 0.000 0.000 0.0000 +f_JSE76_qlogis 0.000 0.00 0.000 0.000 0.0000 +log_k1 0.000 0.00 0.000 0.000 0.0000 +log_k2 0.000 0.00 0.000 0.000 0.0000 +g_qlogis 0.000 0.00 0.000 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 -cyan_0 0.0 0.00 0.00 0.0000 0.0000 -log_k_JCZ38 0.0 0.00 0.00 0.0000 0.0000 -log_k_J9Z38 0.0 0.00 0.00 0.0000 0.0000 -log_k_JSE76 0.0 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_1 0.0 0.00 0.00 0.0000 0.0000 -f_cyan_ilr_2 10.1 0.00 0.00 0.0000 0.0000 -f_JCZ38_qlogis 0.0 13.99 0.00 0.0000 0.0000 -f_JSE76_qlogis 0.0 0.00 14.15 0.0000 0.0000 -log_k1 0.0 0.00 0.00 0.8452 0.0000 -log_k2 0.0 0.00 0.00 0.0000 0.5968 -g_qlogis 0.0 0.00 0.00 0.0000 0.0000 +cyan_0 0.00 0.00 0.00 0.0000 0.0000 +log_k_JCZ38 0.00 0.00 0.00 0.0000 0.0000 +log_k_J9Z38 0.00 0.00 0.00 0.0000 0.0000 +log_k_JSE76 0.00 0.00 0.00 0.0000 0.0000 +f_cyan_ilr_1 0.00 0.00 0.00 0.0000 0.0000 +f_cyan_ilr_2 13.37 0.00 0.00 0.0000 0.0000 +f_JCZ38_qlogis 0.00 14.21 0.00 0.0000 0.0000 +f_JSE76_qlogis 0.00 0.00 14.58 0.0000 0.0000 +log_k1 0.00 0.00 0.00 0.8453 0.0000 +log_k2 0.00 0.00 0.00 0.0000 0.5969 +g_qlogis 0.00 0.00 0.00 0.0000 0.0000 g_qlogis -cyan_0 0.000 -log_k_JCZ38 0.000 -log_k_J9Z38 0.000 -log_k_JSE76 0.000 -f_cyan_ilr_1 0.000 -f_cyan_ilr_2 0.000 -f_JCZ38_qlogis 0.000 -f_JSE76_qlogis 0.000 -log_k1 0.000 -log_k2 0.000 -g_qlogis 1.691 +cyan_0 0.00 +log_k_JCZ38 0.00 +log_k_J9Z38 0.00 +log_k_JSE76 0.00 +f_cyan_ilr_1 0.00 +f_cyan_ilr_2 0.00 +f_JCZ38_qlogis 0.00 +f_JSE76_qlogis 0.00 +log_k1 0.00 +log_k2 0.00 +g_qlogis 1.69 Starting values for error model parameters: a.1 b.1 @@ -5155,78 +4853,78 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2232 2224 -1096 + 2237 2229 -1099 Optimised parameters: est. lower upper -cyan_0 101.20051 NA NA -log_k_JCZ38 -2.93542 NA NA -log_k_J9Z38 -5.03151 NA NA -log_k_JSE76 -3.67679 NA NA -f_cyan_ilr_1 0.67290 NA NA -f_cyan_ilr_2 0.99787 NA NA -f_JCZ38_qlogis 348.32484 NA NA -f_JSE76_qlogis 1.87846 NA NA -log_k1 -2.32738 NA NA -log_k2 -4.61295 NA NA -g_qlogis -0.38342 NA NA -a.1 2.06184 1.83746 2.28622 -b.1 0.06329 0.05211 0.07447 -SD.log_k_JCZ38 1.29042 0.47468 2.10617 -SD.log_k_J9Z38 0.84235 0.25903 1.42566 -SD.log_k_JSE76 0.56930 0.13934 0.99926 -SD.f_cyan_ilr_1 0.35183 0.12298 0.58068 -SD.f_cyan_ilr_2 0.77269 0.17908 1.36631 -SD.log_k2 0.28549 0.09210 0.47888 -SD.g_qlogis 0.93830 0.34568 1.53093 +cyan_0 101.00243 NA NA +log_k_JCZ38 -2.80828 NA NA +log_k_J9Z38 -5.04449 NA NA +log_k_JSE76 -3.66981 NA NA +f_cyan_ilr_1 0.72564 NA NA +f_cyan_ilr_2 1.37978 NA NA +f_JCZ38_qlogis 1.98726 NA NA +f_JSE76_qlogis 414.80884 NA NA +log_k1 -2.38601 NA NA +log_k2 -4.63632 NA NA +g_qlogis -0.33920 NA NA +a.1 2.10837 1.88051 2.33623 +b.1 0.06223 0.05108 0.07338 +SD.log_k_JCZ38 1.30902 0.48128 2.13675 +SD.log_k_J9Z38 0.83882 0.25790 1.41974 +SD.log_k_JSE76 0.58104 0.14201 1.02008 +SD.f_cyan_ilr_1 0.35421 0.12398 0.58443 +SD.f_cyan_ilr_2 0.79373 0.12007 1.46740 +SD.log_k2 0.27476 0.08557 0.46394 +SD.g_qlogis 0.96170 0.35463 1.56878 Correlation is not available Random effects: - est. lower upper -SD.log_k_JCZ38 1.2904 0.4747 2.1062 -SD.log_k_J9Z38 0.8423 0.2590 1.4257 -SD.log_k_JSE76 0.5693 0.1393 0.9993 -SD.f_cyan_ilr_1 0.3518 0.1230 0.5807 -SD.f_cyan_ilr_2 0.7727 0.1791 1.3663 -SD.log_k2 0.2855 0.0921 0.4789 -SD.g_qlogis 0.9383 0.3457 1.5309 + est. lower upper +SD.log_k_JCZ38 1.3090 0.48128 2.1367 +SD.log_k_J9Z38 0.8388 0.25790 1.4197 +SD.log_k_JSE76 0.5810 0.14201 1.0201 +SD.f_cyan_ilr_1 0.3542 0.12398 0.5844 +SD.f_cyan_ilr_2 0.7937 0.12007 1.4674 +SD.log_k2 0.2748 0.08557 0.4639 +SD.g_qlogis 0.9617 0.35463 1.5688 Variance model: est. lower upper -a.1 2.06184 1.83746 2.28622 -b.1 0.06329 0.05211 0.07447 +a.1 2.10837 1.88051 2.33623 +b.1 0.06223 0.05108 0.07338 Backtransformed parameters: est. lower upper -cyan_0 1.012e+02 NA NA -k_JCZ38 5.311e-02 NA NA -k_J9Z38 6.529e-03 NA NA -k_JSE76 2.530e-02 NA NA -f_cyan_to_JCZ38 6.373e-01 NA NA -f_cyan_to_J9Z38 2.461e-01 NA NA -f_JCZ38_to_JSE76 1.000e+00 NA NA -f_JSE76_to_JCZ38 8.674e-01 NA NA -k1 9.755e-02 NA NA -k2 9.922e-03 NA NA -g 4.053e-01 NA NA +cyan_0 1.010e+02 NA NA +k_JCZ38 6.031e-02 NA NA +k_J9Z38 6.445e-03 NA NA +k_JSE76 2.548e-02 NA NA +f_cyan_to_JCZ38 6.808e-01 NA NA +f_cyan_to_J9Z38 2.440e-01 NA NA +f_JCZ38_to_JSE76 8.795e-01 NA NA +f_JSE76_to_JCZ38 1.000e+00 NA NA +k1 9.200e-02 NA NA +k2 9.693e-03 NA NA +g 4.160e-01 NA NA Resulting formation fractions: - ff -cyan_JCZ38 0.6373 -cyan_J9Z38 0.2461 -cyan_sink 0.1167 -JCZ38_JSE76 1.0000 -JCZ38_sink 0.0000 -JSE76_JCZ38 0.8674 -JSE76_sink 0.1326 + ff +cyan_JCZ38 0.68081 +cyan_J9Z38 0.24398 +cyan_sink 0.07521 +JCZ38_JSE76 0.87945 +JCZ38_sink 0.12055 +JSE76_JCZ38 1.00000 +JSE76_sink 0.00000 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -cyan 24.93 179.68 54.09 7.105 69.86 -JCZ38 13.05 43.36 NA NA NA -J9Z38 106.16 352.67 NA NA NA -JSE76 27.39 91.00 NA NA NA +cyan 25.00 182.05 54.8 7.535 71.51 +JCZ38 11.49 38.18 NA NA NA +J9Z38 107.55 357.28 NA NA NA +JSE76 27.20 90.36 NA NA NA </code></pre> <p></p> @@ -5236,10 +4934,10 @@ variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 08:16:33 2023 -Date of summary: Thu Apr 20 20:01:31 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:57:01 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5257,20 +4955,20 @@ Data: Model predictions using solution type deSolve -Fitted in 901.179 s +Fitted in 834.906 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound - 102.4394 -2.7673 -2.8942 + 102.4395 -2.7673 -2.8942 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 -3.6201 -2.3107 -5.3123 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 -3.7120 0.6754 1.1448 f_JCZ38_qlogis f_JSE76_qlogis - 13.2672 13.3538 + 14.8408 15.4734 Fixed degradation parameter values: None @@ -5301,17 +4999,17 @@ f_cyan_ilr_2 0.000 0.0000 0.000 0.0 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0 f_JSE76_qlogis 0.000 0.0000 0.000 0.0 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis -cyan_free_0 0.0000 0.000 0.00 0.00 -log_k_cyan_free 0.0000 0.000 0.00 0.00 -log_k_cyan_free_bound 0.0000 0.000 0.00 0.00 -log_k_cyan_bound_free 0.0000 0.000 0.00 0.00 -log_k_JCZ38 0.0000 0.000 0.00 0.00 -log_k_J9Z38 0.0000 0.000 0.00 0.00 -log_k_JSE76 0.0000 0.000 0.00 0.00 -f_cyan_ilr_1 0.6349 0.000 0.00 0.00 -f_cyan_ilr_2 0.0000 1.797 0.00 0.00 -f_JCZ38_qlogis 0.0000 0.000 13.84 0.00 -f_JSE76_qlogis 0.0000 0.000 0.00 14.66 +cyan_free_0 0.0000 0.000 0.0 0.00 +log_k_cyan_free 0.0000 0.000 0.0 0.00 +log_k_cyan_free_bound 0.0000 0.000 0.0 0.00 +log_k_cyan_bound_free 0.0000 0.000 0.0 0.00 +log_k_JCZ38 0.0000 0.000 0.0 0.00 +log_k_J9Z38 0.0000 0.000 0.0 0.00 +log_k_JSE76 0.0000 0.000 0.0 0.00 +f_cyan_ilr_1 0.6349 0.000 0.0 0.00 +f_cyan_ilr_2 0.0000 1.797 0.0 0.00 +f_JCZ38_qlogis 0.0000 0.000 15.6 0.00 +f_JSE76_qlogis 0.0000 0.000 0.0 17.52 Starting values for error model parameters: a.1 @@ -5321,83 +5019,83 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2279 2272 -1120 + 2280 2272 -1120 Optimised parameters: est. lower upper -cyan_free_0 102.5621 NA NA -log_k_cyan_free -2.8531 NA NA -log_k_cyan_free_bound -2.6916 NA NA -log_k_cyan_bound_free -3.5032 NA NA -log_k_JCZ38 -2.9436 NA NA -log_k_J9Z38 -5.1140 NA NA -log_k_JSE76 -3.6472 NA NA -f_cyan_ilr_1 0.6887 NA NA -f_cyan_ilr_2 0.6874 NA NA -f_JCZ38_qlogis 4063.6389 NA NA -f_JSE76_qlogis 1.9556 NA NA -a.1 2.7460 2.55451 2.9376 -SD.log_k_cyan_free 0.3131 0.09841 0.5277 -SD.log_k_cyan_free_bound 0.8850 0.29909 1.4710 -SD.log_k_cyan_bound_free 0.6167 0.20391 1.0295 -SD.log_k_JCZ38 1.3555 0.49101 2.2200 -SD.log_k_J9Z38 0.7200 0.16166 1.2783 -SD.log_k_JSE76 0.6252 0.14619 1.1042 -SD.f_cyan_ilr_1 0.3386 0.11447 0.5627 -SD.f_cyan_ilr_2 0.4699 0.09810 0.8417 +cyan_free_0 102.6532 NA NA +log_k_cyan_free -2.8547 NA NA +log_k_cyan_free_bound -2.7004 NA NA +log_k_cyan_bound_free -3.5078 NA NA +log_k_JCZ38 -2.9255 NA NA +log_k_J9Z38 -5.1089 NA NA +log_k_JSE76 -3.6263 NA NA +f_cyan_ilr_1 0.6873 NA NA +f_cyan_ilr_2 0.6498 NA NA +f_JCZ38_qlogis 3624.2149 NA NA +f_JSE76_qlogis 1.9991 NA NA +a.1 2.7472 2.55559 2.9388 +SD.log_k_cyan_free 0.3227 0.10296 0.5423 +SD.log_k_cyan_free_bound 0.8757 0.29525 1.4562 +SD.log_k_cyan_bound_free 0.6128 0.20220 1.0233 +SD.log_k_JCZ38 1.3431 0.48474 2.2014 +SD.log_k_J9Z38 0.6881 0.14714 1.2291 +SD.log_k_JSE76 0.6461 0.15321 1.1390 +SD.f_cyan_ilr_1 0.3361 0.11376 0.5585 +SD.f_cyan_ilr_2 0.4286 0.08419 0.7730 Correlation is not available Random effects: est. lower upper -SD.log_k_cyan_free 0.3131 0.09841 0.5277 -SD.log_k_cyan_free_bound 0.8850 0.29909 1.4710 -SD.log_k_cyan_bound_free 0.6167 0.20391 1.0295 -SD.log_k_JCZ38 1.3555 0.49101 2.2200 -SD.log_k_J9Z38 0.7200 0.16166 1.2783 -SD.log_k_JSE76 0.6252 0.14619 1.1042 -SD.f_cyan_ilr_1 0.3386 0.11447 0.5627 -SD.f_cyan_ilr_2 0.4699 0.09810 0.8417 +SD.log_k_cyan_free 0.3227 0.10296 0.5423 +SD.log_k_cyan_free_bound 0.8757 0.29525 1.4562 +SD.log_k_cyan_bound_free 0.6128 0.20220 1.0233 +SD.log_k_JCZ38 1.3431 0.48474 2.2014 +SD.log_k_J9Z38 0.6881 0.14714 1.2291 +SD.log_k_JSE76 0.6461 0.15321 1.1390 +SD.f_cyan_ilr_1 0.3361 0.11376 0.5585 +SD.f_cyan_ilr_2 0.4286 0.08419 0.7730 Variance model: est. lower upper -a.1 2.746 2.555 2.938 +a.1 2.747 2.556 2.939 Backtransformed parameters: est. lower upper -cyan_free_0 1.026e+02 NA NA -k_cyan_free 5.767e-02 NA NA -k_cyan_free_bound 6.777e-02 NA NA -k_cyan_bound_free 3.010e-02 NA NA -k_JCZ38 5.267e-02 NA NA -k_J9Z38 6.012e-03 NA NA -k_JSE76 2.606e-02 NA NA -f_cyan_free_to_JCZ38 6.089e-01 NA NA -f_cyan_free_to_J9Z38 2.299e-01 NA NA +cyan_free_0 1.027e+02 NA NA +k_cyan_free 5.758e-02 NA NA +k_cyan_free_bound 6.718e-02 NA NA +k_cyan_bound_free 2.996e-02 NA NA +k_JCZ38 5.364e-02 NA NA +k_J9Z38 6.042e-03 NA NA +k_JSE76 2.662e-02 NA NA +f_cyan_free_to_JCZ38 6.039e-01 NA NA +f_cyan_free_to_J9Z38 2.285e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA -f_JSE76_to_JCZ38 8.761e-01 NA NA +f_JSE76_to_JCZ38 8.807e-01 NA NA Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g - 0.1434 0.0121 0.3469 + 0.1426 0.0121 0.3484 Resulting formation fractions: ff -cyan_free_JCZ38 0.6089 -cyan_free_J9Z38 0.2299 -cyan_free_sink 0.1612 +cyan_free_JCZ38 0.6039 +cyan_free_J9Z38 0.2285 +cyan_free_sink 0.1676 cyan_free 1.0000 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 -JSE76_JCZ38 0.8761 -JSE76_sink 0.1239 +JSE76_JCZ38 0.8807 +JSE76_sink 0.1193 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 -cyan 23.94 155.06 46.68 4.832 57.28 -JCZ38 13.16 43.71 NA NA NA -J9Z38 115.30 383.02 NA NA NA -JSE76 26.59 88.35 NA NA NA +cyan 23.84 154.95 46.65 4.86 57.31 +JCZ38 12.92 42.93 NA NA NA +J9Z38 114.71 381.07 NA NA NA +JSE76 26.04 86.51 NA NA NA </code></pre> <p></p> @@ -5407,10 +5105,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 08:16:19 2023 -Date of summary: Thu Apr 20 20:01:31 2023 +mkin version used for pre-fitting: 1.2.4 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 09:57:17 2023 +Date of summary: Fri May 19 09:57:33 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5428,20 +5126,20 @@ Data: Model predictions using solution type deSolve -Fitted in 887.343 s +Fitted in 850.751 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound - 101.751 -2.837 -3.016 + 101.7511 -2.8370 -3.0162 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 - -3.660 -2.299 -5.313 + -3.6600 -2.2988 -5.3129 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 - -3.699 0.672 5.873 + -3.6991 0.6722 4.8596 f_JCZ38_qlogis f_JSE76_qlogis - 13.216 13.338 + 13.4678 14.2149 Fixed degradation parameter values: None @@ -5472,17 +5170,17 @@ f_cyan_ilr_2 0.000 0.0000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0000 f_JSE76_qlogis 0.000 0.0000 0.000 0.0000 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis -cyan_free_0 0.0000 0.00 0.00 0.00 -log_k_cyan_free 0.0000 0.00 0.00 0.00 -log_k_cyan_free_bound 0.0000 0.00 0.00 0.00 -log_k_cyan_bound_free 0.0000 0.00 0.00 0.00 -log_k_JCZ38 0.0000 0.00 0.00 0.00 -log_k_J9Z38 0.0000 0.00 0.00 0.00 -log_k_JSE76 0.0000 0.00 0.00 0.00 -f_cyan_ilr_1 0.6519 0.00 0.00 0.00 -f_cyan_ilr_2 0.0000 10.78 0.00 0.00 -f_JCZ38_qlogis 0.0000 0.00 13.96 0.00 -f_JSE76_qlogis 0.0000 0.00 0.00 14.69 +cyan_free_0 0.0000 0.000 0.00 0.00 +log_k_cyan_free 0.0000 0.000 0.00 0.00 +log_k_cyan_free_bound 0.0000 0.000 0.00 0.00 +log_k_cyan_bound_free 0.0000 0.000 0.00 0.00 +log_k_JCZ38 0.0000 0.000 0.00 0.00 +log_k_J9Z38 0.0000 0.000 0.00 0.00 +log_k_JSE76 0.0000 0.000 0.00 0.00 +f_cyan_ilr_1 0.6518 0.000 0.00 0.00 +f_cyan_ilr_2 0.0000 9.981 0.00 0.00 +f_JCZ38_qlogis 0.0000 0.000 14.26 0.00 +f_JSE76_qlogis 0.0000 0.000 0.00 16.17 Starting values for error model parameters: a.1 b.1 @@ -5492,83 +5190,83 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2236 2228 -1098 + 2241 2233 -1101 Optimised parameters: est. lower upper -cyan_free_0 100.72760 NA NA -log_k_cyan_free -3.18281 NA NA -log_k_cyan_free_bound -3.37924 NA NA -log_k_cyan_bound_free -3.77107 NA NA -log_k_JCZ38 -2.92811 NA NA -log_k_J9Z38 -5.02759 NA NA -log_k_JSE76 -3.65835 NA NA -f_cyan_ilr_1 0.67390 NA NA -f_cyan_ilr_2 1.15106 NA NA -f_JCZ38_qlogis 827.82299 NA NA -f_JSE76_qlogis 1.83064 NA NA -a.1 2.06921 1.84443 2.29399 -b.1 0.06391 0.05267 0.07515 -SD.log_k_cyan_free 0.50518 0.18962 0.82075 -SD.log_k_cyan_bound_free 0.30991 0.08170 0.53813 -SD.log_k_JCZ38 1.26661 0.46578 2.06744 -SD.log_k_J9Z38 0.88272 0.27813 1.48730 -SD.log_k_JSE76 0.53050 0.12561 0.93538 -SD.f_cyan_ilr_1 0.35547 0.12461 0.58633 -SD.f_cyan_ilr_2 0.91446 0.20131 1.62761 +cyan_free_0 100.95469 NA NA +log_k_cyan_free -3.18706 NA NA +log_k_cyan_free_bound -3.38455 NA NA +log_k_cyan_bound_free -3.75788 NA NA +log_k_JCZ38 -2.77024 NA NA +log_k_J9Z38 -5.03665 NA NA +log_k_JSE76 -3.60289 NA NA +f_cyan_ilr_1 0.72263 NA NA +f_cyan_ilr_2 1.45352 NA NA +f_JCZ38_qlogis 2.00778 NA NA +f_JSE76_qlogis 941.58570 NA NA +a.1 2.11130 1.88299 2.33960 +b.1 0.06299 0.05176 0.07421 +SD.log_k_cyan_free 0.50098 0.18805 0.81390 +SD.log_k_cyan_bound_free 0.31671 0.08467 0.54875 +SD.log_k_JCZ38 1.25865 0.45932 2.05798 +SD.log_k_J9Z38 0.86833 0.27222 1.46444 +SD.log_k_JSE76 0.59325 0.14711 1.03940 +SD.f_cyan_ilr_1 0.35705 0.12521 0.58890 +SD.f_cyan_ilr_2 0.88541 0.13797 1.63286 Correlation is not available Random effects: - est. lower upper -SD.log_k_cyan_free 0.5052 0.1896 0.8207 -SD.log_k_cyan_bound_free 0.3099 0.0817 0.5381 -SD.log_k_JCZ38 1.2666 0.4658 2.0674 -SD.log_k_J9Z38 0.8827 0.2781 1.4873 -SD.log_k_JSE76 0.5305 0.1256 0.9354 -SD.f_cyan_ilr_1 0.3555 0.1246 0.5863 -SD.f_cyan_ilr_2 0.9145 0.2013 1.6276 + est. lower upper +SD.log_k_cyan_free 0.5010 0.18805 0.8139 +SD.log_k_cyan_bound_free 0.3167 0.08467 0.5488 +SD.log_k_JCZ38 1.2587 0.45932 2.0580 +SD.log_k_J9Z38 0.8683 0.27222 1.4644 +SD.log_k_JSE76 0.5933 0.14711 1.0394 +SD.f_cyan_ilr_1 0.3571 0.12521 0.5889 +SD.f_cyan_ilr_2 0.8854 0.13797 1.6329 Variance model: est. lower upper -a.1 2.06921 1.84443 2.29399 -b.1 0.06391 0.05267 0.07515 +a.1 2.11130 1.88299 2.33960 +b.1 0.06299 0.05176 0.07421 Backtransformed parameters: est. lower upper -cyan_free_0 1.007e+02 NA NA -k_cyan_free 4.147e-02 NA NA -k_cyan_free_bound 3.407e-02 NA NA -k_cyan_bound_free 2.303e-02 NA NA -k_JCZ38 5.350e-02 NA NA -k_J9Z38 6.555e-03 NA NA -k_JSE76 2.578e-02 NA NA -f_cyan_free_to_JCZ38 6.505e-01 NA NA -f_cyan_free_to_J9Z38 2.508e-01 NA NA -f_JCZ38_to_JSE76 1.000e+00 NA NA -f_JSE76_to_JCZ38 8.618e-01 NA NA +cyan_free_0 1.010e+02 NA NA +k_cyan_free 4.129e-02 NA NA +k_cyan_free_bound 3.389e-02 NA NA +k_cyan_bound_free 2.333e-02 NA NA +k_JCZ38 6.265e-02 NA NA +k_J9Z38 6.495e-03 NA NA +k_JSE76 2.724e-02 NA NA +f_cyan_free_to_JCZ38 6.844e-01 NA NA +f_cyan_free_to_J9Z38 2.463e-01 NA NA +f_JCZ38_to_JSE76 8.816e-01 NA NA +f_JSE76_to_JCZ38 1.000e+00 NA NA Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g -0.08768 0.01089 0.39821 +0.08751 0.01101 0.39586 Resulting formation fractions: ff -cyan_free_JCZ38 0.65053 -cyan_free_J9Z38 0.25082 -cyan_free_sink 0.09864 +cyan_free_JCZ38 0.68444 +cyan_free_J9Z38 0.24633 +cyan_free_sink 0.06923 cyan_free 1.00000 -JCZ38_JSE76 1.00000 -JCZ38_sink 0.00000 -JSE76_JCZ38 0.86184 -JSE76_sink 0.13816 +JCZ38_JSE76 0.88161 +JCZ38_sink 0.11839 +JSE76_JCZ38 1.00000 +JSE76_sink 0.00000 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 -cyan 25.32 164.79 49.61 7.906 63.64 -JCZ38 12.96 43.04 NA NA NA -J9Z38 105.75 351.29 NA NA NA -JSE76 26.89 89.33 NA NA NA +cyan 25.36 163.36 49.18 7.921 62.95 +JCZ38 11.06 36.75 NA NA NA +J9Z38 106.71 354.49 NA NA NA +JSE76 25.44 84.51 NA NA NA </code></pre> <p></p> @@ -5577,13 +5275,13 @@ JSE76 26.89 89.33 NA NA NA <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.0 Patched (2023-05-18 r84448) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /home/jranke/svn/R/r-patched/build/lib/libRblas.so +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -5593,34 +5291,40 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.3 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4 loaded via a namespace (and not attached): - [1] pillar_1.9.0 bslib_0.4.2 compiler_4.2.3 jquerylib_0.1.4 - [5] tools_4.2.3 mclust_6.0.0 digest_0.6.31 tibble_3.2.1 - [9] jsonlite_1.8.4 evaluate_0.20 memoise_2.0.1 lifecycle_1.0.3 -[13] nlme_3.1-162 gtable_0.3.3 lattice_0.21-8 pkgconfig_2.0.3 -[17] rlang_1.1.0 DBI_1.1.3 cli_3.6.1 yaml_2.3.7 -[21] pkgdown_2.0.7 xfun_0.38 fastmap_1.1.1 gridExtra_2.3 -[25] dplyr_1.1.1 stringr_1.5.0 generics_0.1.3 desc_1.4.2 -[29] fs_1.6.1 vctrs_0.6.1 sass_0.4.5 systemfonts_1.0.4 -[33] tidyselect_1.2.0 rprojroot_2.0.3 lmtest_0.9-40 grid_4.2.3 -[37] inline_0.3.19 glue_1.6.2 R6_2.5.1 textshaping_0.3.6 -[41] fansi_1.0.4 rmarkdown_2.21 purrr_1.0.1 ggplot2_3.4.2 -[45] magrittr_2.0.3 scales_1.2.1 htmltools_0.5.5 colorspace_2.1-0 -[49] ragg_1.2.5 utf8_1.2.3 stringi_1.7.12 munsell_0.5.0 -[53] cachem_1.0.7 zoo_1.8-12 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.0 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3 +[13] jsonlite_1.8.4 processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 +[17] DBI_1.1.3 mclust_6.0.0 ps_1.7.5 gridExtra_2.3 +[21] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 codetools_0.2-19 +[25] textshaping_0.3.6 jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 +[29] rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 +[33] inline_0.3.19 tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 +[37] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 +[41] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 +[45] ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 +[49] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 +[53] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39 +[57] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 +[61] nlme_3.1-162 rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1 +[65] readxl_1.4.2 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64936316 kB</code></pre> +<pre><code>MemTotal: 64925476 kB</code></pre> </div> </div> </div> diff --git a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png Binary files differindex b969f2ff..b3d6066b 100644 --- a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png +++ b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png diff --git a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-14-1.png b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-14-1.png Binary files differindex 60393da3..341d48b9 100644 --- a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-14-1.png +++ b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-14-1.png 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b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-7-1.png diff --git a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-8-1.png Binary files differindex e30011bc..cc7d0126 100644 --- a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-8-1.png +++ b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-8-1.png diff --git a/docs/articles/prebuilt/2022_dmta_parent.html b/docs/articles/prebuilt/2022_dmta_parent.html index 378a7e8e..2da41981 100644 --- a/docs/articles/prebuilt/2022_dmta_parent.html +++ b/docs/articles/prebuilt/2022_dmta_parent.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -135,7 +135,7 @@ with residue data on dimethenamid and dimethenamid-P</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 5 January -2023, last compiled on 20 April 2023</h4> +2023, last compiled on 19 Mai 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_parent.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_parent.rmd</code></a></small> <div class="hidden name"><code>2022_dmta_parent.rmd</code></div> @@ -154,7 +154,7 @@ FOMC, DFOP and HS can be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.3. It contains the test data +<p>The mkin package is used in version 1.2.4. It contains the test data and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot function available.</p> diff --git a/docs/articles/prebuilt/2022_dmta_pathway.html b/docs/articles/prebuilt/2022_dmta_pathway.html index c8323add..ea4bd087 100644 --- a/docs/articles/prebuilt/2022_dmta_pathway.html +++ b/docs/articles/prebuilt/2022_dmta_pathway.html @@ -33,7 +33,7 @@ </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">1.2.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -135,7 +135,7 @@ residue data on dimethenamid and dimethenamid-P</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 20 April 2023</h4> +last compiled on 19 Mai 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_dmta_pathway.rmd</code></div> @@ -155,7 +155,7 @@ can be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.3, which is currently under +<p>The mkin package is used in version 1.2.4, which is currently under development. It contains the test data, and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot @@ -1496,7 +1496,7 @@ of parent models tested here.</p> <td align="left">dfop_path_1</td> <td align="left">OK</td> <td align="left">OK</td> -<td align="left">C</td> +<td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> @@ -1514,7 +1514,7 @@ of parent models tested here.</p> <td align="left">hs_path_1</td> <td align="left">C</td> <td align="left">C</td> -<td align="left">C</td> +<td align="left">OK</td> <td align="left">C</td> <td align="left">C</td> <td align="left">C</td> @@ -1552,24 +1552,24 @@ not converge with default settings.</p> <td align="left">fomc_path_1</td> <td align="left">OK</td> <td align="left">OK</td> -<td align="left">C</td> <td align="left">OK</td> <td align="left">OK</td> -<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> </tr> <tr class="odd"> <td align="left">dfop_path_1</td> <td align="left">OK</td> <td align="left">C</td> <td align="left">OK</td> -<td align="left">OK</td> +<td align="left">C</td> <td align="left">OK</td> <td align="left">OK</td> </tr> <tr class="even"> <td align="left">sforb_path_1</td> <td align="left">OK</td> -<td align="left">C</td> +<td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> @@ -1582,7 +1582,7 @@ not converge with default settings.</p> <td align="left">C</td> <td align="left">C</td> <td align="left">C</td> -<td align="left">OK</td> +<td align="left">C</td> </tr> </tbody> </table> @@ -1643,8 +1643,6 @@ than twenty minutes.</p> successfully.</p> <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> -<pre><code>Warning in FUN(X[[i]], ...): Could not obtain log likelihood with 'is' method -for sforb_path_1 const</code></pre> <table class="table"> <thead><tr class="header"> <th align="left"></th> @@ -1664,58 +1662,65 @@ for sforb_path_1 const</code></pre> <tr class="even"> <td align="left">sfo_path_1 tc</td> <td align="right">18</td> -<td align="right">2276.3</td> -<td align="right">2272.5</td> -<td align="right">-1120.1</td> +<td align="right">2276.4</td> +<td align="right">2272.7</td> +<td align="right">-1120.2</td> </tr> <tr class="odd"> <td align="left">fomc_path_1 const</td> <td align="right">19</td> -<td align="right">2099.0</td> -<td align="right">2095.0</td> -<td align="right">-1030.5</td> +<td align="right">2095.9</td> +<td align="right">2091.9</td> +<td align="right">-1028.9</td> </tr> <tr class="even"> <td align="left">fomc_path_1 tc</td> <td align="right">20</td> -<td align="right">1939.6</td> -<td align="right">1935.5</td> -<td align="right">-949.8</td> +<td align="right">1939.0</td> +<td align="right">1934.8</td> +<td align="right">-949.5</td> </tr> <tr class="odd"> <td align="left">dfop_path_1 const</td> <td align="right">21</td> -<td align="right">2038.8</td> -<td align="right">2034.4</td> -<td align="right">-998.4</td> +<td align="right">2039.7</td> +<td align="right">2035.3</td> +<td align="right">-998.8</td> </tr> <tr class="even"> -<td align="left">hs_path_1 const</td> +<td align="left">sforb_path_1 const</td> <td align="right">21</td> -<td align="right">2024.2</td> -<td align="right">2019.8</td> -<td align="right">-991.1</td> +<td align="right">2017.7</td> +<td align="right">2013.4</td> +<td align="right">-987.9</td> </tr> <tr class="odd"> +<td align="left">hs_path_1 const</td> +<td align="right">21</td> +<td align="right">2023.7</td> +<td align="right">2019.3</td> +<td align="right">-990.9</td> +</tr> +<tr class="even"> <td align="left">dfop_path_1 tc</td> <td align="right">22</td> -<td align="right">1879.8</td> -<td align="right">1875.2</td> -<td align="right">-917.9</td> +<td align="right">1881.7</td> +<td align="right">1877.1</td> +<td align="right">-918.9</td> </tr> -<tr class="even"> +<tr class="odd"> <td align="left">sforb_path_1 tc</td> <td align="right">22</td> -<td align="right">1832.9</td> -<td align="right">1828.3</td> -<td align="right">-894.4</td> +<td align="right">1832.7</td> +<td align="right">1828.1</td> +<td align="right">-894.3</td> </tr> -<tr class="odd"> +<tr class="even"> <td align="left">hs_path_1 tc</td> <td align="right">22</td> -<td align="right">1831.4</td> -<td align="right">1826.8</td> -<td align="right">-893.7</td> +<td align="right">1831.6</td> +<td align="right">1827.0</td> +<td align="right">-893.8</td> </tr> </tbody> </table> @@ -1740,7 +1745,7 @@ Matrix<a class="anchor" aria-label="anchor" href="#parameter-identifiability-bas model parameters such as standard deviations of the degradation parameters in the population and error model parameters can be found.</p> -<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> @@ -1766,7 +1771,7 @@ found.</p> </tr> <tr class="even"> <td align="left">sforb_path_1</td> -<td align="left"></td> +<td align="left">sd(log_k_DMTA_bound_free)</td> <td align="left">sd(log_k_DMTA_bound_free)</td> </tr> <tr class="odd"> @@ -1786,13 +1791,13 @@ two-component error, the random effect for the rate constant from reversibly bound DMTA to the free DMTA (<code>k_DMTA_bound_free</code>) is not well-defined. Therefore, the fit is updated without assuming a random effect for this parameter.</p> -<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">saem_sforb_path_1_tc_reduced</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span>,</span> <span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span></span> <span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">saem_sforb_path_1_tc_reduced</span><span class="op">)</span></span></code></pre></div> <p>As expected, no ill-defined parameters remain. The model comparison below shows that the reduced model is preferable.</p> -<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span>, <span class="va">saem_sforb_path_1_tc_reduced</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> @@ -1806,21 +1811,21 @@ below shows that the reduced model is preferable.</p> <tr class="odd"> <td align="left">saem_sforb_path_1_tc_reduced</td> <td align="right">21</td> -<td align="right">1830.3</td> -<td align="right">1825.9</td> +<td align="right">1830.4</td> +<td align="right">1826.0</td> <td align="right">-894.2</td> </tr> <tr class="even"> <td align="left">saem_1[[“sforb_path_1”, “tc”]]</td> <td align="right">22</td> -<td align="right">1832.9</td> -<td align="right">1828.3</td> -<td align="right">-894.4</td> +<td align="right">1832.7</td> +<td align="right">1828.1</td> +<td align="right">-894.3</td> </tr> </tbody> </table> <p>The convergence plot of the refined fit is shown below.</p> -<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_sforb_path_1_tc_reduced</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="2022_dmta_pathway_files/figure-html/saem-sforb-path-1-tc-reduced-convergence-1.png" width="700" style="display: block; margin: auto;"></p> <p>For some parameters, for example for <code>f_DMTA_ilr_1</code> and @@ -1839,14 +1844,14 @@ saemix.</p> </h3> <p>As an alternative check of parameter identifiability <span class="citation">(Duchesne et al. 2021)</span>, multistart runs were performed on the basis of the refined fit shown above.</p> -<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">saem_sforb_path_1_tc_reduced_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">saem_sforb_path_1_tc_reduced</span>,</span> <span> n <span class="op">=</span> <span class="fl">32</span>, cores <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></code></pre></div> -<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">saem_sforb_path_1_tc_reduced_multi</span><span class="op">)</span></span></code></pre></div> <pre><code><multistart> object with 32 fits: E OK -15 17 + 7 25 OK: Fit terminated successfully E: Error</code></pre> <p>Out of the 32 fits that were initiated, only 17 terminated without an @@ -1856,7 +1861,7 @@ the SAEM algorithm leads to parameter combinations for the degradation model that the numerical integration routine cannot cope with. Because of this variation of initial parameters, some of the model fits take up to two times more time than the original fit.</p> -<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/par.html" class="external-link">par</a></span><span class="op">(</span>mar <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">12.1</span>, <span class="fl">4.1</span>, <span class="fl">2.1</span>, <span class="fl">2.1</span><span class="op">)</span><span class="op">)</span></span> <span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">saem_sforb_path_1_tc_reduced_multi</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span>, las <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> @@ -1875,14 +1880,14 @@ ill-defined parameters.</p> </h2> <p>The SFORB pathway fits with full and reduced parameter distribution model are shown below.</p> -<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-3-1.png" alt="SFORB pathway fit with two-component error" width="700"><p class="caption"> SFORB pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_sforb_path_1_tc_reduced</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-4-1.png" alt="SFORB pathway fit with two-component error, reduced parameter model" width="700"><p class="caption"> @@ -1891,7 +1896,7 @@ SFORB pathway fit with two-component error, reduced parameter model </div> <p>Plots of the remaining fits and listings for all successful fits are shown in the Appendix.</p> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></code></pre></div> </div> <div class="section level2"> @@ -1931,21 +1936,21 @@ Level with Nonlinear Mixed-Effects Models.”</span> <em>Environments</em> <div class="section level3"> <h3 id="plots-of-hierarchical-fits-not-selected-for-refinement">Plots of hierarchical fits not selected for refinement<a class="anchor" aria-label="anchor" href="#plots-of-hierarchical-fits-not-selected-for-refinement"></a> </h3> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sfo_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-6-1.png" alt="SFO pathway fit with two-component error" width="700"><p class="caption"> SFO pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"fomc_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png" alt="FOMC pathway fit with two-component error" width="700"><p class="caption"> FOMC pathway fit with two-component error </p> </div> -<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <div class="figure" style="text-align: center"> <img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png" alt="HS pathway fit with two-component error" width="700"><p class="caption"> @@ -1971,13 +1976,13 @@ error<a class="anchor" aria-label="anchor" href="#improved-fit-of-the-sforb-path <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.0 Patched (2023-05-18 r84448) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /home/jranke/svn/R/r-patched/build/lib/libRblas.so +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -1987,36 +1992,39 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.3 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4 loaded via a namespace (and not attached): - [1] deSolve_1.35 zoo_1.8-12 tidyselect_1.2.0 xfun_0.38 - [5] bslib_0.4.2 purrr_1.0.1 lattice_0.21-8 colorspace_2.1-0 - [9] vctrs_0.6.1 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7 -[13] utf8_1.2.3 rlang_1.1.0 pkgbuild_1.4.0 pkgdown_2.0.7 -[17] jquerylib_0.1.4 pillar_1.9.0 glue_1.6.2 DBI_1.1.3 -[21] lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 gtable_0.3.3 -[25] ragg_1.2.5 codetools_0.2-19 memoise_2.0.1 evaluate_0.20 -[29] inline_0.3.19 callr_3.7.3 fastmap_1.1.1 ps_1.7.4 -[33] lmtest_0.9-40 fansi_1.0.4 highr_0.10 scales_1.2.1 -[37] cachem_1.0.7 desc_1.4.2 jsonlite_1.8.4 systemfonts_1.0.4 -[41] fs_1.6.1 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.4.2 -[45] digest_0.6.31 stringi_1.7.12 processx_3.8.0 dplyr_1.1.1 -[49] grid_4.2.3 rprojroot_2.0.3 cli_3.6.1 tools_4.2.3 -[53] magrittr_2.0.3 sass_0.4.5 tibble_3.2.1 crayon_1.5.2 -[57] pkgconfig_2.0.3 prettyunits_1.1.1 rmarkdown_2.21 R6_2.5.1 -[61] mclust_6.0.0 nlme_3.1-162 compiler_4.2.3 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 +[13] processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 DBI_1.1.3 +[17] mclust_6.0.0 ps_1.7.5 gridExtra_2.3 purrr_1.0.1 +[21] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 +[25] jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 rlang_1.1.1 +[29] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 inline_0.3.19 +[33] tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 +[37] ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 +[41] lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 ragg_1.2.5 +[45] callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7 +[49] bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 glue_1.6.2 +[53] systemfonts_1.0.4 highr_0.10 xfun_0.39 tibble_3.2.1 +[57] lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-162 +[61] rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1</code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64936316 kB</code></pre> +<pre><code>MemTotal: 64925476 kB</code></pre> </div> </div> </div> diff --git a/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/saem-sforb-path-1-tc-reduced-convergence-1.png b/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/saem-sforb-path-1-tc-reduced-convergence-1.png Binary files differindex 206c424d..a7187abc 100644 --- a/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/saem-sforb-path-1-tc-reduced-convergence-1.png +++ 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ac5271ec..067b144d 100644 --- a/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png +++ b/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png diff --git a/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png Binary files differindex 1c81601e..80376942 100644 --- a/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png +++ b/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png diff --git a/docs/articles/twa.html b/docs/articles/twa.html index c8c91bcb..4b48437e 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -135,7 +135,7 @@ concentrations with mkin</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change 18 September 2019 -(rebuilt 2023-04-20)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/twa.rmd" class="external-link"><code>vignettes/twa.rmd</code></a></small> <div class="hidden name"><code>twa.rmd</code></div> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 9602adb5..4cda45e3 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -134,7 +134,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 16 January 2018 -(rebuilt 2023-04-20)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="hidden name"><code>FOCUS_Z.rmd</code></div> @@ -189,7 +189,7 @@ pathway from parent directly to sink included (default in mkin).</p> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> <pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> <span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> <span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> @@ -217,7 +217,7 @@ the model formulation:</p> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> <pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> <span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> <span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> @@ -247,7 +247,7 @@ previous fit when adding a further metabolite.</p> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> <div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> <pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> <span><span class="co">## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538</span></span> <span><span class="co">## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593</span></span> @@ -299,27 +299,27 @@ accelerate the optimization.</p> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">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">$</span><span class="va">bpar</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> <pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> -<span><span class="co">## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664</span></span> -<span><span class="co">## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989</span></span> -<span><span class="co">## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666</span></span> -<span><span class="co">## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872</span></span> -<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965</span></span> -<span><span class="co">## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274</span></span> -<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></span></code></pre> +<span><span class="co">## Z0_0 96.842440 1.994291 48.5598 4.0226e-42 92.830421 100.854459</span></span> +<span><span class="co">## k_Z0 2.215425 0.118457 18.7023 1.0404e-23 1.989490 2.467019</span></span> +<span><span class="co">## k_Z1 0.478307 0.028257 16.9272 6.2332e-22 0.424709 0.538669</span></span> +<span><span class="co">## k_Z2 0.451642 0.042139 10.7178 1.6304e-14 0.374348 0.544894</span></span> +<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034804 0.098975</span></span> +<span><span class="co">## f_Z2_to_Z3 0.471483 0.058348 8.0806 9.6585e-11 0.357720 0.588287</span></span> +<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5576e-14 3.213126 4.755737</span></span></code></pre> <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> <pre><code><span><span class="co">## $ff</span></span> <span><span class="co">## Z2_Z3 Z2_sink </span></span> -<span><span class="co">## 0.4715 0.5285 </span></span> +<span><span class="co">## 0.47148 0.52852 </span></span> <span><span class="co">## </span></span> <span><span class="co">## $distimes</span></span> <span><span class="co">## DT50 DT90</span></span> -<span><span class="co">## Z0 0.31288 1.0394</span></span> -<span><span class="co">## Z1 1.44917 4.8141</span></span> -<span><span class="co">## Z2 1.53478 5.0984</span></span> -<span><span class="co">## Z3 11.80986 39.2315</span></span></code></pre> +<span><span class="co">## Z0 0.31287 1.0393</span></span> +<span><span class="co">## Z1 1.44917 4.8140</span></span> +<span><span class="co">## Z2 1.53473 5.0983</span></span> +<span><span class="co">## Z3 11.80991 39.2317</span></span></code></pre> <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> @@ -350,7 +350,7 @@ improved. However, the covariance matrix is not returned.</p> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> <div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></span></code></pre></div> <pre><code><span><span class="co">## NULL</span></span></code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the @@ -442,11 +442,11 @@ obtained.</p> <span><span class="co">## </span></span> <span><span class="co">## $SFORB</span></span> <span><span class="co">## Z0_b1 Z0_b2 Z0_g Z3_b1 Z3_b2 Z3_g </span></span> -<span><span class="co">## 2.4471322 0.0075125 0.9519862 0.0800069 0.0000000 0.9347820 </span></span> +<span><span class="co">## 2.4471342 0.0075124 0.9519866 0.0800071 0.0000000 0.9347816 </span></span> <span><span class="co">## </span></span> <span><span class="co">## $distimes</span></span> <span><span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span></span> -<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA</span></span> +<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.267 NA NA</span></span> <span><span class="co">## Z1 1.5148 5.0320 NA NA NA NA NA</span></span> <span><span class="co">## Z2 1.6414 5.4526 NA NA NA NA NA</span></span> <span><span class="co">## Z3 NA NA NA NA NA 8.6636 Inf</span></span></code></pre> 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 33269a34..c1011a35 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 6e1877f4..dfd2dd50 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 113c1b0b..74173f36 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 6b0dbc34..1c5793cc 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_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png Binary files differindex d080a57a..8c594ec9 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 3119be2d..84d473d6 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_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png Binary files differindex 1938b499..492cdcc8 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/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 49d1db33..87cef18a 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -135,7 +135,7 @@ to the US EPA SOP for the NAFTA guidance</h1> Ranke</h4> <h4 data-toc-skip class="date">26 February 2019 (rebuilt -2023-04-20)</h4> +2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> @@ -171,7 +171,7 @@ same.</p> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div> @@ -200,7 +200,7 @@ same.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span></span> <span><span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span></span> -<span><span class="co">## k2 2.26e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 3.41e-12 5.00e-01 0.0000 Inf</span></span> <span><span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span></span> <span><span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span></span> <span><span class="co">## </span></span> @@ -209,7 +209,7 @@ same.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 67.7 2.25e+02 6.77e+01</span></span> <span><span class="co">## IORE 58.2 1.07e+03 3.22e+02</span></span> -<span><span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span></span> +<span><span class="co">## DFOP 55.5 3.70e+11 2.03e+11</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 321.51</span></span></code></pre> @@ -222,7 +222,7 @@ same.</p> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div> @@ -251,7 +251,7 @@ same.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span></span> <span><span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span></span> -<span><span class="co">## k2 8.63e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 9.07e-12 5.00e-01 0.0000 Inf</span></span> <span><span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span></span> <span><span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span></span> <span><span class="co">## </span></span> @@ -260,7 +260,7 @@ same.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 86.6 2.88e+02 8.66e+01</span></span> <span><span class="co">## IORE 85.5 7.17e+02 2.16e+02</span></span> -<span><span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span></span> +<span><span class="co">## DFOP 83.6 1.25e+11 7.64e+10</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 215.87</span></span></code></pre> @@ -273,7 +273,7 @@ same.</p> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div> @@ -302,7 +302,7 @@ same.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span></span> <span><span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span></span> -<span><span class="co">## k2 3.22e-11 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 3.84e-11 5.00e-01 0.0000 Inf</span></span> <span><span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span></span> <span><span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span></span> <span><span class="co">## </span></span> @@ -311,7 +311,7 @@ same.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 38.6 1.28e+02 3.86e+01</span></span> <span><span class="co">## IORE 34.0 1.77e+02 5.32e+01</span></span> -<span><span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span></span> +<span><span class="co">## DFOP 34.1 8.50e+09 1.80e+10</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 53.17</span></span></code></pre> @@ -324,7 +324,7 @@ same.</p> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div> @@ -353,7 +353,7 @@ same.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span></span> <span><span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span></span> -<span><span class="co">## k2 3.63e-10 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 3.62e-10 5.00e-01 0.0000 Inf</span></span> <span><span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span></span> <span><span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span></span> <span><span class="co">## </span></span> @@ -362,7 +362,7 @@ same.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 94.3 3.13e+02 9.43e+01</span></span> <span><span class="co">## IORE 96.7 1.51e+03 4.55e+02</span></span> -<span><span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span></span> +<span><span class="co">## DFOP 96.4 3.79e+09 1.92e+09</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 454.55</span></span></code></pre> @@ -383,7 +383,7 @@ lower value for the rate constant is used here.</p> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div> @@ -438,7 +438,7 @@ lower value for the rate constant is used here.</p> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> <div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div> @@ -476,7 +476,7 @@ lower value for the rate constant is used here.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 16.9 5.63e+01 1.69e+01</span></span> <span><span class="co">## IORE 11.6 3.37e+02 1.01e+02</span></span> -<span><span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span></span> +<span><span class="co">## DFOP 10.5 1.38e+12 7.68e+11</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 101.43</span></span></code></pre> @@ -489,17 +489,12 @@ suggest a simple exponential decline.</p> </h3> <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -526,8 +521,8 @@ suggest a simple exponential decline.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span></span> <span><span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span></span> -<span><span class="co">## k2 0.0389 2.23e-04 0.0255 0.0592</span></span> -<span><span class="co">## g 0.5256 NaN NA NA</span></span> +<span><span class="co">## k2 0.0389 2.24e-04 0.0255 0.0592</span></span> +<span><span class="co">## g 0.5256 5.00e-01 0.0000 1.0000</span></span> <span><span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> @@ -549,18 +544,15 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from <div class="section level3"> <h3 id="example-on-page-10">Example on page 10<a class="anchor" aria-label="anchor" href="#example-on-page-10"></a> </h3> -<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -584,12 +576,12 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from <span><span class="co">## sigma 4.90 1.77e-04 2.837 6.968</span></span> <span><span class="co">## </span></span> <span><span class="co">## $DFOP</span></span> -<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> -<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span></span> -<span><span class="co">## k1 0.0495 6.58e-03 0.0303 0.0809</span></span> -<span><span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</span></span> -<span><span class="co">## g 0.4487 5.00e-01 NA NA</span></span> -<span><span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.810</span></span> +<span><span class="co">## k1 0.0495 3.04e-03 0.0188 0.131</span></span> +<span><span class="co">## k2 0.0495 4.92e-04 0.0197 0.124</span></span> +<span><span class="co">## g 0.4487 NaN 0.0000 1.000</span></span> +<span><span class="co">## sigma 8.0152 2.50e-04 4.5886 11.442</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> <span><span class="co">## DTx values:</span></span> @@ -613,14 +605,14 @@ difference in IORE model parameters between PestDF and mkin.</p> <div class="section level3"> <h3 id="example-on-page-11">Example on page 11<a class="anchor" aria-label="anchor" href="#example-on-page-11"></a> </h3> -<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -659,7 +651,7 @@ difference in IORE model parameters between PestDF and mkin.</p> <span><span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> -<span><span class="co">## [1] 41148170</span></span></code></pre> +<span><span class="co">## [1] 41148169</span></span></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> @@ -676,21 +668,17 @@ overparameterisation.</p> <div class="section level3"> <h3 id="example-on-page-12-upper-panel">Example on page 12, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-upper-panel"></a> </h3> -<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> <pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span> <span><span class="co">## matrix</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb61"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -718,7 +706,7 @@ overparameterisation.</p> <span><span class="co">## parent_0 100.521 2.74e-10 92.2366 108.805</span></span> <span><span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span></span> <span><span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span></span> -<span><span class="co">## g 0.793 NaN NA NA</span></span> +<span><span class="co">## g 0.793 NaN 0.0000 1.000</span></span> <span><span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> @@ -734,18 +722,21 @@ overparameterisation.</p> <div class="section level3"> <h3 id="example-on-page-12-lower-panel">Example on page 12, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-lower-panel"></a> </h3> -<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> +<span><span class="co">## is doubtful</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -789,14 +780,14 @@ overparameterisation.</p> <div class="section level3"> <h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a> </h3> -<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb76"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb79"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -822,8 +813,8 @@ overparameterisation.</p> <span><span class="co">## $DFOP</span></span> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span></span> -<span><span class="co">## k1 0.00258 NA 4.14e-04 0.01611</span></span> -<span><span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span></span> +<span><span class="co">## k1 0.00258 NA 4.18e-04 0.01592</span></span> +<span><span class="co">## k2 0.00258 NA 1.75e-03 0.00381</span></span> <span><span class="co">## g 0.16452 NA 0.00e+00 1.00000</span></span> <span><span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span></span> <span><span class="co">## </span></span> @@ -841,7 +832,7 @@ overparameterisation.</p> <div class="section level2"> <h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a> </h2> -<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb82"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> <pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> @@ -849,10 +840,10 @@ overparameterisation.</p> <span><span class="co">## is doubtful</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb88"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -879,7 +870,7 @@ overparameterisation.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span></span> <span><span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span></span> -<span><span class="co">## k2 6.08e-12 5.00e-01 0.00000 Inf</span></span> +<span><span class="co">## k2 5.21e-12 5.00e-01 0.00000 Inf</span></span> <span><span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span></span> <span><span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span></span> <span><span class="co">## </span></span> @@ -888,7 +879,7 @@ overparameterisation.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span></span> <span><span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span></span> -<span><span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span></span> +<span><span class="co">## DFOP 3.55e+10 3.44e+11 1.33e+11</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 6697.44</span></span></code></pre> @@ -899,14 +890,18 @@ same results in mkin and PestDF.</p> <div class="section level2"> <h2 id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero">N is less than 1 and DFOP fraction parameter is below zero<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero"></a> </h2> -<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb91"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> +<span><span class="co">## is doubtful</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb97"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -932,9 +927,9 @@ same results in mkin and PestDF.</p> <span><span class="co">## $DFOP</span></span> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span></span> -<span><span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span></span> -<span><span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span></span> -<span><span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span></span> +<span><span class="co">## k1 0.00952 6.28e-02 0.00260 0.0349</span></span> +<span><span class="co">## k2 0.00952 1.27e-04 0.00652 0.0139</span></span> +<span><span class="co">## g 0.21241 5.00e-01 NA NA</span></span> <span><span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> @@ -946,18 +941,16 @@ same results in mkin and PestDF.</p> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 41.33</span></span></code></pre> -<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb100"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> +<pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span> +<span><span class="co">## matrix</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb105"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -975,18 +968,18 @@ same results in mkin and PestDF.</p> <span><span class="co">## </span></span> <span><span class="co">## $IORE</span></span> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> -<span><span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span></span> +<span><span class="co">## parent_0 99.83 1.81e-16 97.51348 102.14</span></span> <span><span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span></span> <span><span class="co">## N_parent 0.00 5.00e-01 -1.07696 1.08</span></span> <span><span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span></span> <span><span class="co">## </span></span> <span><span class="co">## $DFOP</span></span> -<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> -<span><span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span></span> -<span><span class="co">## k1 4.86e-03 NA 8.63e-04 2.73e-02</span></span> -<span><span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span></span> -<span><span class="co">## g 1.88e-01 NA NA NA</span></span> -<span><span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA NA NA</span></span> +<span><span class="co">## k1 4.86e-03 NA NA NA</span></span> +<span><span class="co">## k2 4.86e-03 NA NA NA</span></span> +<span><span class="co">## g 1.88e-01 NA NA NA</span></span> +<span><span class="co">## sigma 2.76e+00 NA NA NA</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> <span><span class="co">## DTx values:</span></span> @@ -1005,16 +998,16 @@ mkin and PestDF.</p> <div class="section level2"> <h2 id="the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1<a class="anchor" aria-label="anchor" href="#the-dfop-fraction-parameter-is-greater-than-1"></a> </h2> -<div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb107"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></span></code></pre> <pre><code><span><span class="co">## to the terminal degradation rate found with the DFOP model.</span></span></code></pre> <pre><code><span><span class="co">## The representative half-life obtained from the DFOP model may be used</span></span></code></pre> -<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb112"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb119"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> 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 566625ea..1d4a25e0 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/p15a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png Binary files differindex b5fd7d91..aa55169e 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 dfbc996f..d17c7aae 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/p5b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png Binary files differindex 6fd175cb..9e38e696 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 856c6778..e6e3abbe 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 b078fb88..7c5d4bab 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/benchmarks.html b/docs/articles/web_only/benchmarks.html index 3e73bd12..315ad54e 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -134,7 +134,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2023-04-20)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -425,6 +425,14 @@ models fitted to two datasets, i.e. eight fits for each test.</p> <td align="right">1.406</td> <td align="right">1.948</td> </tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.4</td> +<td align="right">1.386</td> +<td align="right">1.960</td> +</tr> </tbody> </table> </div> @@ -652,6 +660,15 @@ for each test.</p> <td align="right">2.109</td> <td align="right">1.178</td> </tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.4</td> +<td align="right">0.779</td> +<td align="right">2.080</td> +<td align="right">1.106</td> +</tr> </tbody> </table> </div> @@ -963,6 +980,18 @@ dataset, i.e. one fit for each test.</p> <td align="right">0.743</td> <td align="right">0.989</td> </tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.4</td> +<td align="right">0.410</td> +<td align="right">0.526</td> +<td align="right">0.553</td> +<td align="right">1.249</td> +<td align="right">0.712</td> +<td align="right">0.948</td> +</tr> </tbody> </table> </div> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index a411dad1..3c53b40a 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -134,7 +134,7 @@ definitions in mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2023-04-20</h4> + <h4 data-toc-skip class="date">2023-05-19</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> @@ -213,10 +213,10 @@ solution is also implemented, which is included in the tests below.</p> <span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 4 analytical 1 1.000 0.103</span></span> -<span><span class="co">## 3 deSolve, compiled 1 1.291 0.133</span></span> -<span><span class="co">## 2 Eigenvalue based 1 1.718 0.177</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 22.136 2.280</span></span></code></pre> +<span><span class="co">## 4 analytical 1 1.000 0.099</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.303 0.129</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.697 0.168</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 21.475 2.126</span></span></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> @@ -247,12 +247,12 @@ compiled code is available.</p> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 2 deSolve, compiled 1 1.000 0.171</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 24.199 4.138</span></span></code></pre> -<p>Here we get a performance benefit of a factor of 24 using the version +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.165</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 22.673 3.741</span></span></code></pre> +<p>Here we get a performance benefit of a factor of 23 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 1.2.3 on</p> -<pre><code><span><span class="co">## R version 4.2.3 (2023-03-15)</span></span> +<p>This vignette was built with mkin 1.2.4 on</p> +<pre><code><span><span class="co">## R version 4.3.0 Patched (2023-05-18 r84448)</span></span> <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span> <span><span class="co">## Running under: Debian GNU/Linux 12 (bookworm)</span></span></code></pre> <pre><code><span><span class="co">## CPU model: AMD Ryzen 9 7950X 16-Core Processor</span></span></code></pre> diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index 4575067b..a89631a2 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -135,7 +135,7 @@ from 2018</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change 1 July 2022, -built on 20 Apr 2023</h4> +built on 19 May 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small> <div class="hidden name"><code>dimethenamid_2018.rmd</code></div> @@ -222,12 +222,12 @@ least in some datasets the degradation slows down towards later time points, and that the scatter of the residuals error is smaller for smaller values (panel to the right):</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_sfo_const-1.png" width="700"></p> <p>Using biexponential decline (DFOP) results in a slightly more random scatter of the residuals:</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const-1.png" width="700"></p> <p>The population curve (bold line) in the above plot results from taking the mean of the individual transformed parameters, i.e. of log k1 @@ -239,7 +239,7 @@ dominates the average. This is alleviated if only rate constants that pass the t-test for significant difference from zero (on the untransformed scale) are considered in the averaging:</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const_test-1.png" width="700"></p> <p>While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual @@ -251,7 +251,7 @@ degradation model and the error model (see below).</p> predicted residues is reduced by using the two-component error model:</p> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_tc_test-1.png" width="700"></p> <p>However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by @@ -341,7 +341,7 @@ effects does not improve the fits.</p> <p>The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.</p> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p> </div> <div class="section level4"> @@ -549,7 +549,7 @@ iterations second phase, 15 chains).</p> <span> saemix_is <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span>, <span class="va">AIC</span>, method <span class="op">=</span> <span class="st">"is"</span><span class="op">)</span></span> <span><span class="op">)</span></span> -<span><span class="fu">kable</span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> <th align="left">Degradation model</th> @@ -614,13 +614,13 @@ satisfactory precision.</p> </h2> <div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.0 Patched (2023-05-18 r84448) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /home/jranke/svn/R/r-patched/build/lib/libRblas.so +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -630,27 +630,30 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] saemix_3.2 npde_3.3 nlme_3.1-162 mkin_1.2.3 knitr_1.42 +[1] nlme_3.1-162 mkin_1.2.4 knitr_1.42 loaded via a namespace (and not attached): - [1] highr_0.10 pillar_1.9.0 bslib_0.4.2 compiler_4.2.3 - [5] jquerylib_0.1.4 tools_4.2.3 mclust_6.0.0 digest_0.6.31 - [9] tibble_3.2.1 jsonlite_1.8.4 evaluate_0.20 memoise_2.0.1 -[13] lifecycle_1.0.3 gtable_0.3.3 lattice_0.21-8 pkgconfig_2.0.3 -[17] rlang_1.1.0 DBI_1.1.3 cli_3.6.1 yaml_2.3.7 -[21] parallel_4.2.3 pkgdown_2.0.7 xfun_0.38 fastmap_1.1.1 -[25] gridExtra_2.3 dplyr_1.1.1 stringr_1.5.0 generics_0.1.3 -[29] desc_1.4.2 fs_1.6.1 vctrs_0.6.1 sass_0.4.5 -[33] systemfonts_1.0.4 tidyselect_1.2.0 rprojroot_2.0.3 lmtest_0.9-40 -[37] grid_4.2.3 glue_1.6.2 R6_2.5.1 textshaping_0.3.6 -[41] fansi_1.0.4 rmarkdown_2.21 purrr_1.0.1 ggplot2_3.4.2 -[45] magrittr_2.0.3 codetools_0.2-19 scales_1.2.1 htmltools_0.5.5 -[49] colorspace_2.1-0 ragg_1.2.5 utf8_1.2.3 stringi_1.7.12 -[53] munsell_0.5.0 cachem_1.0.7 zoo_1.8-12 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 saemix_3.2 + [5] stringi_1.7.12 lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 + [9] evaluate_0.21 grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 +[13] jsonlite_1.8.4 DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 +[17] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 textshaping_0.3.6 +[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 +[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 parallel_4.3.0 +[29] memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 +[33] vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 +[37] stringr_1.5.0 fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 +[41] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 +[45] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 xfun_0.39 +[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 npde_3.3 +[53] htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.0 </code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html index 04093e82..b9224bb0 100644 --- a/docs/articles/web_only/multistart.html +++ b/docs/articles/web_only/multistart.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -134,7 +134,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 20 April 2023 -(rebuilt 2023-04-20)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> <div class="hidden name"><code>multistart.rmd</code></div> @@ -175,7 +175,7 @@ assessment using multiple runs with different starting values.</p> parameter, so we reduce the parameter distribution model by removing the intersoil variability for k2.</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span> +<code class="sourceCode R"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu">stats</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span> <span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span> <span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span> <span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> @@ -190,18 +190,20 @@ runs:</p> <p>We can use the <code>anova</code> method to compare the models.</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_full</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span><span class="op">)</span>,</span> -<span> <span class="va">f_saem_reduced</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<span> <span class="va">f_saem_reduced</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Data: 155 observations of 1 variable(s) grouped in 6 datasets</span></span> <span><span class="co">## </span></span> -<span><span class="co">## npar AIC BIC Lik</span></span> -<span><span class="co">## f_saem_reduced 9 663.73 661.86 -322.86</span></span> -<span><span class="co">## best(f_saem_reduced_multi) 9 663.69 661.82 -322.85</span></span> -<span><span class="co">## f_saem_full 10 669.77 667.69 -324.89</span></span> -<span><span class="co">## best(f_saem_full_multi) 10 665.56 663.48 -322.78</span></span></code></pre> -<p>The reduced model gives the lowest information criteria and similar -likelihoods as the best variant of the full model. The multistart method -leads to a much lower improvement of the likelihood for the reduced -model, indicating that it converges faster.</p> +<span><span class="co">## npar AIC BIC Lik Chisq Df Pr(>Chisq)</span></span> +<span><span class="co">## f_saem_reduced 9 663.67 661.80 -322.84 </span></span> +<span><span class="co">## best(f_saem_reduced_multi) 9 663.65 661.78 -322.82 0.0219 0 </span></span> +<span><span class="co">## f_saem_full 10 670.09 668.01 -325.05 0.0000 1 1</span></span> +<span><span class="co">## best(f_saem_full_multi) 10 665.61 663.52 -322.80 4.4870 0</span></span></code></pre> +<p>The reduced model results in lower AIC and BIC values, so it is +clearly preferable. Using multiple starting values gives a large +improvement in case of the full model, because it is less well-defined, +which impedes convergence. For the reduced model, using multiple +starting values only results in a small improvement of the model +fit.</p> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png Binary files differindex 1ef2ba24..f41dc889 100644 --- a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png +++ b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png Binary files differindex b1582557..9e206791 100644 --- a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png +++ b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png Binary files differindex f0270537..c8e918cd 100644 --- a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png +++ b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png diff --git a/docs/articles/web_only/saem_benchmarks.html b/docs/articles/web_only/saem_benchmarks.html index 587ee4a2..a9637876 100644 --- a/docs/articles/web_only/saem_benchmarks.html +++ b/docs/articles/web_only/saem_benchmarks.html @@ -33,7 +33,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -134,7 +134,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2023-04-20)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> <div class="hidden name"><code>saem_benchmarks.rmd</code></div> @@ -238,22 +238,22 @@ explanation of the following preprocessing.</p> <tr class="even"> <td align="left">dfop_tc</td> <td align="right">10</td> -<td align="right">669.8</td> -<td align="right">667.7</td> -<td align="right">-324.9</td> +<td align="right">670.1</td> +<td align="right">668.0</td> +<td align="right">-325.0</td> </tr> <tr class="odd"> <td align="left">sforb_tc</td> <td align="right">10</td> -<td align="right">662.8</td> -<td align="right">660.7</td> +<td align="right">662.9</td> +<td align="right">660.8</td> <td align="right">-321.4</td> </tr> <tr class="even"> <td align="left">hs_tc</td> <td align="right">10</td> -<td align="right">667.3</td> -<td align="right">665.2</td> +<td align="right">667.2</td> +<td align="right">665.1</td> <td align="right">-323.6</td> </tr> </tbody> @@ -402,6 +402,16 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">1.926</td> <td align="right">2.398</td> </tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">0.972</td> +<td align="right">2.550</td> +<td align="right">1.987</td> +<td align="right">2.055</td> +</tr> </tbody> </table> <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> @@ -477,6 +487,16 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">3.253</td> <td align="right">3.530</td> </tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">2.127</td> +<td align="right">3.587</td> +<td align="right">3.433</td> +<td align="right">3.595</td> +</tr> </tbody> </table> </div> @@ -542,6 +562,14 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">12.841</td> <td align="right">292.688</td> </tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">12.160</td> +<td align="right">265.934</td> +</tr> </tbody> </table> </div> @@ -600,6 +628,13 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">3.2</td> <td align="right">483.027</td> </tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">456.252</td> +</tr> </tbody> </table> </div> diff --git a/docs/authors.html b/docs/authors.html index 775f84d8..313c86e9 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ </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">1.2.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -132,13 +132,13 @@ <p>Ranke J (2023). <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>. -R package version 1.2.3.1, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. +R package version 1.2.4, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. </p> <pre>@Manual{, title = {mkin: Kinetic Evaluation of Chemical Degradation Data}, author = {Johannes Ranke}, year = {2023}, - note = {R package version 1.2.3.1}, + note = {R package version 1.2.4}, url = {https://pkgdown.jrwb.de/mkin/}, }</pre> diff --git a/docs/index.html b/docs/index.html index 01300749..06cdfdfb 100644 --- a/docs/index.html +++ b/docs/index.html @@ -44,7 +44,7 @@ </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">1.2.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/news/index.html b/docs/news/index.html index 7dcccffb..16fce355 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ </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">1.2.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -105,11 +105,15 @@ </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.3.1" id="mkin-1231">mkin 1.2.3.1<a class="anchor" aria-label="anchor" href="#mkin-1231"></a></h2> -<ul><li>Small fixes to get the online docs right, rebuild online docs</li> +<h2 class="page-header" data-toc-text="1.2.4" id="mkin-124">mkin 1.2.4<a class="anchor" aria-label="anchor" href="#mkin-124"></a></h2> +<ul><li>R/endpoints.R: Fix the calculation of endpoints for user specified covariate values</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.3" id="mkin-123">mkin 1.2.3<a class="anchor" aria-label="anchor" href="#mkin-123"></a></h2> +<h2 class="page-header" data-toc-text="1.2.3.1" id="mkin-1231-unreleased">mkin 1.2.3.1 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-1231-unreleased"></a></h2> +<ul><li>Small fixes to get the online docs right (example code in R/hierarchical_kinetics, cluster setup in cyantraniliprole and dmta pathway vignettes, graphics and model comparison in multistart vignette), rebuild online docs</li> +</ul></div> + <div class="section level2"> +<h2 class="page-header" data-toc-text="1.2.3" id="mkin-123-2023-04-17">mkin 1.2.3 (2023-04-17)<a class="anchor" aria-label="anchor" href="#mkin-123-2023-04-17"></a></h2> <ul><li><p>‘R/{endpoints,parms,plot.mixed.mmkin,summary.saem.mmkin}.R’: Calculate parameters and endpoints and plot population curves for specific covariate values, or specific percentiles of covariate values used in saem fits.</p></li> <li><p>Depend on current deSolve version with the possibility to avoid resolving symbols in a shared library (compiled models) over and over, thanks to Thomas Petzoldt.</p></li> <li><p>‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Start a new cluster after creating a model stored in the user specified location, because otherwise symbols are not found by the worker processes.</p></li> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 655e436a..fdcd875b 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -16,7 +16,7 @@ articles: dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html saem_benchmarks: web_only/saem_benchmarks.html -last_built: 2023-04-20T17:56Z +last_built: 2023-05-19T09:04Z 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 a53a2735..15df31b6 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -18,7 +18,7 @@ same dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -153,6 +153,8 @@ dataframe if there are several fits in the column).</p> <span class="r-in"><span> <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" class="external-link">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></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">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></span> <span class="r-in"><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></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><span> <span class="co"># We get a warning because the FOMC model does not converge for the</span></span></span> <span class="r-in"><span> <span class="co"># FOCUS A dataset, as it is well described by SFO</span></span></span> <span class="r-in"><span></span></span> @@ -166,17 +168,17 @@ dataframe if there are several fits in the column).</p> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 55.28197</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28222</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28198</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.28197</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 49.28197</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28222</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28198</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 49.28197</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> df BIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 55.52030</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59999</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59974</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.67918</span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="co"># For FOCUS C, the more complex models fit better</span></span></span> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index b6b26286..50f4599f 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -18,7 +18,7 @@ specified as well."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/aj </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index 128d3e73..fcc3cec3 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><!-- mathjax --><script src="https: </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -132,7 +132,7 @@ constrained by data protection regulations.</p> <p>Hellenic Ministry of Rural Development and Agriculture (2014) Final addendum to the Renewal Assessment Report - public version - 2,4-D Volume 3 Annex B.8 Fate and behaviour in the environment -<a href="https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811" class="external-link">https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811</a></p> +https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811</p> </div> <div id="details"> <h2>Details</h2> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 261db8e8..ee7f7888 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -18,7 +18,7 @@ two exponential decline functions."><!-- mathjax --><script src="https://cdnjs.c </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index cfee02f5..81995a34 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -189,7 +189,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-in"><span> <span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $par</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma </span> -<span class="r-out co"><span class="r-pr">#></span> 99.666192 2.549850 5.050586 1.890202 </span> +<span class="r-out co"><span class="r-pr">#></span> 99.666192 2.549850 5.050587 1.890202 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $objective</span> <span class="r-out co"><span class="r-pr">#></span> [1] 28.58291</span> 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 55f7dafe..b9d4e4cf 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index d3f727d0..0f62dc27 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index bd03647d..4339fd5d 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index a489ecc8..eb7162a1 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 3a0cd6bd..51e699a1 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 076b5860..4ae477f8 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -18,7 +18,7 @@ a decreasing rate constant."><!-- mathjax --><script src="https://cdnjs.cloudfla </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 41e722d6..61fbc41c 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -18,7 +18,7 @@ between them."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 5d416409..942c86ca 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -18,7 +18,7 @@ a concentration dependent rate constant."><!-- mathjax --><script src="https://c </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 41629ed8..86610f6e 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 0ab49cb7..7f72e172 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -161,7 +161,7 @@ <span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span> <span class="r-out co"><span class="r-pr">#></span> k1 2.67e-02 5.05e-06 0.0243 0.0295</span> -<span class="r-out co"><span class="r-pr">#></span> k2 2.26e-12 5.00e-01 0.0000 Inf</span> +<span class="r-out co"><span class="r-pr">#></span> k2 3.41e-12 5.00e-01 0.0000 Inf</span> <span class="r-out co"><span class="r-pr">#></span> g 6.47e-01 3.67e-06 0.6248 0.6677</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.27e+00 8.91e-06 0.8395 1.6929</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -170,7 +170,7 @@ <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span> <span class="r-out co"><span class="r-pr">#></span> SFO 67.7 2.25e+02 6.77e+01</span> <span class="r-out co"><span class="r-pr">#></span> IORE 58.2 1.07e+03 3.22e+02</span> -<span class="r-out co"><span class="r-pr">#></span> DFOP 55.5 5.59e+11 3.07e+11</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 55.5 3.70e+11 2.03e+11</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> <span class="r-out co"><span class="r-pr">#></span> [1] 321.51</span> diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 377229db..d5fef0f0 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 c1324477..7274c79d 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 17555d63..b5aff531 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 0ae76e25..490fbbb5 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -21,7 +21,7 @@ and no substance in the bound fraction."><!-- mathjax --><script src="https://cd </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 225f62d9..09a92fba 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -19,7 +19,7 @@ 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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/anova.saem.mmkin.html b/docs/reference/anova.saem.mmkin.html index 273122e1..df85fc6f 100644 --- a/docs/reference/anova.saem.mmkin.html +++ b/docs/reference/anova.saem.mmkin.html @@ -20,7 +20,7 @@ the model on the previous line."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 7d4b28ef..ffb9dd82 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004)."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index dd6409b6..33c4a939 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -24,7 +24,7 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -254,7 +254,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><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" class="external-link">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></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">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" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.26 0.00 1.26 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.086 0.000 1.086 </span> <span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> <span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> <span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> @@ -262,7 +262,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 0.417 0.103 0.291 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.396 0.065 0.263 </span> <span class="r-in"><span><span class="va">ci_profile</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> @@ -329,7 +329,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">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></span> <span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833578 102.79311649</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833581 102.79311649</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090823771 0.10725430</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.004012219 0.00689755</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469118824 0.55959615</span> @@ -337,7 +337,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">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></span> <span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833583 1.027931e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833586 1.027931e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090491913 1.069035e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.003835485 6.685823e-03</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469113477 5.598387e-01</span> @@ -359,15 +359,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408690 0.0002217233</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598532 0.0009001864</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283041 0.0290588361</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881769 0.0027780063</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283045 0.0290588367</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881768 0.0027780062</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> <span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408689 0.0002217232</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102156 0.0023732281</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740690 0.0025291820</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995211 0.0023457712</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408689 0.0002217233</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102155 0.0023732280</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740687 0.0025291815</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995210 0.0023457712</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span></span> @@ -381,19 +381,19 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span> 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></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596039609 106.19954892</span> -<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605368 0.04490762</span> -<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568731 0.01087676</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021462489 0.62023882</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015165617 0.37975348</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.273897348 0.33388101</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.018614554 0.02250378</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.671943411 0.73583305</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283495 0.83992077</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411024 0.07662008</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596181875 106.19936592</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605432 0.04490757</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568745 0.01087675</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021464676 0.62023880</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015167158 0.37975350</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.273897535 0.33388072</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.018614555 0.02250379</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.671943738 0.73583261</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283679 0.83992102</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411022 0.07662008</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59604 106.1995</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59618 106.1994</span> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 6e31b269..4735f334 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -148,8 +148,8 @@ <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.238 1.000 0.239 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.293 1.231 0.294 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.218 1.000 0.217 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.273 1.252 0.274 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> @@ -162,8 +162,8 @@ <span class="r-in"><span> 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>,</span></span> <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.369 1.000 0.37 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.541 1.466 0.54 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.352 1.000 0.352 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.486 1.381 0.485 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> diff --git a/docs/reference/dimethenamid_2018-1.png b/docs/reference/dimethenamid_2018-1.png Binary files differindex 27ed5329..e570a766 100644 --- a/docs/reference/dimethenamid_2018-1.png +++ b/docs/reference/dimethenamid_2018-1.png diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 0581830c..a1c800e8 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><!-- mathjax --><script src="https: </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -132,7 +132,7 @@ constrained by data protection regulations.</p> <p>Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018) Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour Rev. 2 - November 2017 -<a href="https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716" class="external-link">https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</a></p> +https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</p> </div> <div id="details"> <h2>Details</h2> @@ -222,10 +222,10 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:32:09 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:32:09 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:15:21 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:15:21 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -238,7 +238,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 301.026 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 282.941 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -284,75 +284,75 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.3192 83.8656 92.7729</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0530 -3.5686 -2.5373</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0620 -4.9202 -3.2038</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8633 -4.2668 -3.4598</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9731 -4.4763 -3.4699</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1346 -0.2150 0.4841</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1449 -0.2593 0.5491</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3882 -1.7011 -1.0753</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8217 1.0095</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1216 0.1550</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6949 8.1508</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.4862 84.1127 92.8598</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0512 -3.5674 -2.5351</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0576 -4.9013 -3.2139</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8584 -4.2572 -3.4595</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9779 -4.4844 -3.4714</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1264 -0.2186 0.4714</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1509 -0.2547 0.5565</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3891 -1.6962 -1.0819</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9196 0.8231 1.0161</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1203 0.1551</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8154 8.0066</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6437 0.2784 1.0091</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 0.9929 0.3719 1.6139</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4530 0.1522 0.7537</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5773 0.1952 0.9595</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4063 0.1505 0.6621</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4800 0.1817 0.7783</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3582 0.1350 0.5814</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0303 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0229 -0.0032 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0372 -0.0049 0.0041 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0245 -0.0032 0.0022 0.0815 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0415 -0.0433 0.0324 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0267 -0.0893 -0.0361 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1755 -0.0135 0.0423 0.0775 0.0377 -0.0066 0.0060 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0306 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0234 -0.0032 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0380 -0.0049 0.0041 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0247 -0.0031 0.0022 0.0817 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0425 -0.0438 0.0319 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0216 -0.0267 -0.0890 -0.0349 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1805 -0.0136 0.0434 0.0791 0.0390 -0.0061 0.0053 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6949 8.1508</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8154 8.0066</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6437 0.2784 1.0091</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 0.9929 0.3719 1.6139</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4530 0.1522 0.7537</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5773 0.1952 0.9595</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4063 0.1505 0.6621</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4800 0.1817 0.7783</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3582 0.1350 0.5814</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8217 1.009</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1216 0.155</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9196 0.8231 1.0161</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1203 0.1551</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.31924 83.865625 92.77286</span> -<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04722 0.028196 0.07908</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01721 0.007298 0.04061</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02100 0.014027 0.03144</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01882 0.011375 0.03112</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14608 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12077 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11123 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.48621 84.112654 92.85977</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04730 0.028230 0.07926</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01729 0.007437 0.04020</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02110 0.014162 0.03144</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01872 0.011283 0.03107</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14551 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12169 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11062 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1461</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1208</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1112</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6219</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1455</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1217</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1106</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6222</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA 14.68 48.76</span> -<span class="r-out co"><span class="r-pr">#></span> M23 40.27 133.76</span> -<span class="r-out co"><span class="r-pr">#></span> M27 33.01 109.65</span> -<span class="r-out co"><span class="r-pr">#></span> M31 36.84 122.38</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA 14.65 48.68</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.09 133.17</span> +<span class="r-out co"><span class="r-pr">#></span> M27 32.85 109.11</span> +<span class="r-out co"><span class="r-pr">#></span> M31 37.02 122.97</span> <span class="r-in"><span><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span></span> <span class="r-in"><span><span class="co"># includes zero, we could try an alternative model without</span></span></span> <span class="r-in"><span><span class="co"># such random effects</span></span></span> diff --git a/docs/reference/ds_mixed-1.png b/docs/reference/ds_mixed-1.png Binary files differindex d8505ffd..7b73613a 100644 --- a/docs/reference/ds_mixed-1.png +++ b/docs/reference/ds_mixed-1.png diff --git a/docs/reference/ds_mixed.html b/docs/reference/ds_mixed.html index b32d5d4b..9618edae 100644 --- a/docs/reference/ds_mixed.html +++ b/docs/reference/ds_mixed.html @@ -18,7 +18,7 @@ the 'dataset_generation' directory."><!-- mathjax --><script src="https://cdnjs. </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 6029a656..b8ccdb2e 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -23,7 +23,7 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax - </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</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 49e1c6c9..f0dfab85 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 2c6b7c8d..bad2ad49 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -45,7 +45,7 @@ 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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index 8d0446d5..17a63ce2 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -18,7 +18,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- mathjax </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 2204c64f..0d460160 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -18,7 +18,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><!-- mathjax --><script </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 1d4ae683..4963ad94 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html index 98764bf0..35edf6b3 100644 --- a/docs/reference/hierarchical_kinetics.html +++ b/docs/reference/hierarchical_kinetics.html @@ -24,7 +24,7 @@ includes them.'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/l </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html index f0829482..2dc8f503 100644 --- a/docs/reference/illparms.html +++ b/docs/reference/illparms.html @@ -21,7 +21,7 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -211,6 +211,8 @@ does not output anything in the case no ill-defined parameters are found.</p> <div id="ref-examples"> <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><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="st">"FOMC"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><span><span class="fu">illparms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] "parent_0" "alpha" "beta" "sigma" </span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 48f80fdd..68041671 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -18,7 +18,7 @@ transformations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index ebfb3673..4d59b3ab 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ </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">1.2.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index 2a714fdb..d148140e 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/llhist.html b/docs/reference/llhist.html index 7b106009..c54796fc 100644 --- a/docs/reference/llhist.html +++ b/docs/reference/llhist.html @@ -18,7 +18,7 @@ original fit is shown as a red vertical line."><!-- mathjax --><script src="http </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex 9f45c74d..1b2fd838 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 1a3aaeea..f60f5ff7 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 cbb7e766..a5c5e198 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -20,7 +20,7 @@ lrtest.default from the lmtest package."><!-- mathjax --><script src="https://cd </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 2c1c9df6..1dd40d48 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -21,7 +21,7 @@ the error model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/logLik.saem.mmkin.html b/docs/reference/logLik.saem.mmkin.html index 9624e67c..2dd52ebd 100644 --- a/docs/reference/logLik.saem.mmkin.html +++ b/docs/reference/logLik.saem.mmkin.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index f4d4c952..c936637b 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -18,7 +18,7 @@ an increasing rate constant, supposedly caused by microbial growth"><!-- mathjax </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -210,10 +210,10 @@ Version 1.1, 18 December 2014 <span class="r-plt img"><img src="logistic.solution-2.png" alt="" width="700" height="433"></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-16 1.016451e+02</span> -<span class="r-out co"><span class="r-pr">#></span> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.057896e+02 1.9023449604 55.610120 3.768360e-16 1.016451e+02</span> +<span class="r-out co"><span class="r-pr">#></span> kmax 6.398190e-02 0.0143201030 4.467978 3.841828e-04 3.929235e-02</span> <span class="r-out co"><span class="r-pr">#></span> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08</span> -<span class="r-out co"><span class="r-pr">#></span> r 2.263946e-01 0.1718110662 1.317695 1.061043e-01 4.335843e-02</span> +<span class="r-out co"><span class="r-pr">#></span> r 2.263946e-01 0.1718110664 1.317695 1.061043e-01 4.335843e-02</span> <span class="r-out co"><span class="r-pr">#></span> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00</span> <span class="r-out co"><span class="r-pr">#></span> Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 109.9341588</span> diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 66237be1..aac564fa 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -21,7 +21,7 @@ and can be expressed by fixing the parameters of the other."><!-- mathjax --><sc </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 85428bf7..40995e83 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -23,7 +23,7 @@ soil section of the FOCUS guidance."><!-- mathjax --><script src="https://cdnjs. </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 7470008d..0c5cb21a 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -19,7 +19,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -154,25 +154,25 @@ <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t)</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074943 47.537272 4.472189e-18</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993738 1.356073 9.756990e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02</span> -<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340721 1.562626 6.949414e-02</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718440131 1.488441 7.867790e-02</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558973 5.123989 6.233159e-05</span> <span class="r-out co"><span class="r-pr">#></span> Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061385 1.084640e+02</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061490 1.084640e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 0.039631621 4.746194e-02</span> <span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013879 7.525762e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_anisole 0.005370739 8.305299e-03</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.547559081 6.924813e-01</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.547559080 6.924813e-01</span> <span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 0.000000000 1.000000e+00</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.706607296 3.322649e+00</span> <span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.072478e-10 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> @@ -192,23 +192,23 @@ <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653059 48.028439 4.993108e-19 99.271020328</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050582e-01 0.1177237651 3.440752 1.679255e-03 0.218746589</span> <span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197873 18.198824 2.039411e-12 0.547975634</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655</span> <span class="r-out co"><span class="r-pr">#></span> Upper</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 108.43904074</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 108.43904079</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 0.04743877</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.75005585</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.75005593</span> <span class="r-out co"><span class="r-pr">#></span> k_anisole 0.00829550</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.69212308</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.69212307</span> <span class="r-out co"><span class="r-pr">#></span> sigma 3.31827222</span> <span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.072478e-10 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index 964e8fd4..20f539cf 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mhmkin-2.png b/docs/reference/mhmkin-2.png Binary files differindex ea04ebfd..3051bddc 100644 --- a/docs/reference/mhmkin-2.png +++ b/docs/reference/mhmkin-2.png diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html index 0ca948c8..08726dfc 100644 --- a/docs/reference/mhmkin.html +++ b/docs/reference/mhmkin.html @@ -22,7 +22,7 @@ mixed-effects model fitting functions."><!-- mathjax --><script src="https://cdn </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png Binary files differindex b053d9c9..846ca6a1 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 b35794d9..91bb26ce 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -204,16 +204,18 @@ single dataframe which is convenient for plotting</p> <span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> -<span class="r-out co"><span class="r-pr">#></span> model 1 2 3 4 5 6 7 8 </span> -<span class="r-out co"><span class="r-pr">#></span> DFOP-SFO OK OK OK OK OK OK OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> model 1 2 3 4 5 6 7 8 </span> +<span class="r-out co"><span class="r-pr">#></span> DFOP-SFO OK OK OK OK OK C OK OK</span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> C: Optimisation did not converge:</span> +<span class="r-out co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> <span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Mean fitted parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 </span> +<span class="r-out co"><span class="r-pr">#></span> 100.605312 -8.758664 -0.001917 -3.350887 -3.990017 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> -0.087392 </span> +<span class="r-out co"><span class="r-pr">#></span> -0.091167 </span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mixed-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># }</span></span></span> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index cef18893..ab80a18e 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -19,7 +19,7 @@ variable and several dependent variables as columns."><!-- mathjax --><script sr </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 02524d3a..0fb06a94 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -19,7 +19,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 453bf7f2..b3c0e5d5 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -20,7 +20,7 @@ provided by this package come as mkinds objects nevertheless."><!-- mathjax -->< </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index dfd3cbb4..118f7650 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -20,7 +20,7 @@ dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.clo </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 5270f6c4..517af738 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -18,7 +18,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."><!-- ma </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 9fcef920..136cddcc 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -21,7 +21,7 @@ using the argument show_errplot = TRUE."><!-- mathjax --><script src="https://cd </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index cb5039d1..88848768 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -401,10 +401,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><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></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:32:45 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:32:45 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:15:57 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:15:57 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -446,10 +446,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.013e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_beta -3.142e-01 9.564e-01 1.000e+00 8.637e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.681e-08 1.013e-07 8.637e-08 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -534,7 +534,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> parent 6.89313 22.89848</span> -<span class="r-out co"><span class="r-pr">#></span> m1 134.15634 445.65772</span> +<span class="r-out co"><span class="r-pr">#></span> m1 134.15634 445.65771</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># We can show a quick (only one replication) benchmark for this case, as we</span></span></span> @@ -552,9 +552,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.264</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.197 0.316</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.227 0.588</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.226</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 1.845 0.417</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 2.354 0.532</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -581,10 +581,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:32:49 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:32:49 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:16:01 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:16:01 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -593,7 +593,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 0.694 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 0.718 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -633,7 +633,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 101.600000 2.6400000 96.240000 107.000000</span> <span class="r-out co"><span class="r-pr">#></span> log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.001426 0.0766900 -0.155000 0.157800</span> <span class="r-out co"><span class="r-pr">#></span> log_alpha 5.522000 0.0077320 5.506000 5.538000</span> <span class="r-out co"><span class="r-pr">#></span> log_beta 7.806000 NaN NaN NaN</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low 0.002488 0.0002431 0.001992 0.002984</span> @@ -641,30 +641,30 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000000 -0.095161 -0.76675 0.70542 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.095161 1.000000 0.51429 -0.14382 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.766750 0.514286 1.00000 -0.61393 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.705417 -0.143821 -0.61393 1.00000 NaN</span> <span class="r-out co"><span class="r-pr">#></span> log_beta NaN NaN NaN NaN 1</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.016073 0.001586 0.01548 5.87007 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.016086 0.001583 0.01547 5.87036 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.006618 -0.011695 -0.05356 0.04848 NaN</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low rsd_high</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.016073 0.006626</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.001586 -0.011700</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.015476 -0.053566</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha 5.870075 0.048487</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.016086 0.006618</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.001583 -0.011695</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.015466 -0.053560</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha 5.870361 0.048483</span> <span class="r-out co"><span class="r-pr">#></span> log_beta NaN NaN</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 1.000000 -0.652558</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high -0.652558 1.000000</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 1.000000 -0.652545</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high -0.652545 1.000000</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> <span class="r-out co"><span class="r-pr">#></span> t-test (unrealistically) based on the assumption of normal distribution</span> <span class="r-out co"><span class="r-pr">#></span> for estimators of untransformed parameters.</span> <span class="r-out co"><span class="r-pr">#></span> Estimate t value Pr(>t) Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.016e+02 32.7800 6.310e-26 9.624e+01 1.070e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 5.004e-01 20.8300 4.316e-20 4.613e-01 5.394e-01</span> <span class="r-out co"><span class="r-pr">#></span> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02</span> <span class="r-out co"><span class="r-pr">#></span> beta 2.455e+03 0.5549 2.915e-01 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03</span> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 15be073c..e4761e73 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -21,7 +21,7 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -330,7 +330,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><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>,</span></span> <span class="r-in"><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></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmp887oxB/file67a5068775fd4.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpUEfrXw/file723a02cdd855b.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">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></span> <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> @@ -383,7 +383,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55558a8511d0></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f4ce060></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 6e7bf34f..8d34b451 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 79e20139..0e7985d8 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -18,7 +18,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -144,8 +144,6 @@ effect, namely to produce a plot.</p> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span><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" class="external-link">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></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> -<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mkinparplot-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># }</span></span></span> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 6b88c87c..8a35bae9 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -18,7 +18,7 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 20ace74a..5e016527 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -19,7 +19,7 @@ kinetic parameters and initial values for the state variables."><!-- mathjax --> </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -395,10 +395,10 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1 0.002</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1 0.002</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4 0.008</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 30 0.060</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 3.5 0.007</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 29.0 0.058</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index cf21b7a1..8cdb55d0 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -20,7 +20,7 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex dae64316..9642db70 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 b281cd7e..d9aa755d 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 23b0725c..ed8e87e6 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 6c09f0de..e09dc469 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -20,7 +20,7 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -206,21 +206,21 @@ plotting.</p></div> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">time_default</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.596 0.611 0.715 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.502 0.665 0.624 </span> <span class="r-in"><span><span class="va">time_1</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 2.060 0.016 2.076 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.824 0.028 1.852 </span> <span class="r-in"><span></span></span> <span class="r-in"><span><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></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_M1 parent_sink M1_M2 M1_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 0.7340481 0.2659519 0.7505683 0.2494317 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.7340481 0.2659519 0.7505690 0.2494310 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> -<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> parent 0.877769 2.915885</span> -<span class="r-out co"><span class="r-pr">#></span> M1 2.325744 7.725956</span> -<span class="r-out co"><span class="r-pr">#></span> M2 33.720100 112.015749</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.8777689 2.915885</span> +<span class="r-out co"><span class="r-pr">#></span> M1 2.3257403 7.725942</span> +<span class="r-out co"><span class="r-pr">#></span> M2 33.7201060 112.015767</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</span></span></span> @@ -252,9 +252,11 @@ plotting.</p></div> <span class="r-out co"><span class="r-pr">#></span> dataset</span> <span class="r-out co"><span class="r-pr">#></span> model A B C D </span> <span class="r-out co"><span class="r-pr">#></span> SFO OK OK OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC C OK OK OK</span> <span class="r-out co"><span class="r-pr">#></span> DFOP OK OK OK OK</span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> C: Optimisation did not converge:</span> +<span class="r-out co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> <span class="r-in"><span><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span></span> <span class="r-in"><span><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span></span> diff --git a/docs/reference/multistart-1.png b/docs/reference/multistart-1.png Binary files differindex c7937d67..8133170b 100644 --- a/docs/reference/multistart-1.png +++ b/docs/reference/multistart-1.png diff --git a/docs/reference/multistart-2.png b/docs/reference/multistart-2.png Binary files differindex e1983f12..5cfdbd63 100644 --- a/docs/reference/multistart-2.png +++ b/docs/reference/multistart-2.png diff --git a/docs/reference/multistart.html b/docs/reference/multistart.html index a18a79b5..4da88d48 100644 --- a/docs/reference/multistart.html +++ b/docs/reference/multistart.html @@ -22,7 +22,7 @@ mixed-effects models by Duchesne et al (2021)."><!-- mathjax --><script src="htt </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -222,15 +222,13 @@ doi: 10.1186/s12859-021-04373-4.</p> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="co"># On Windows, we need to create a cluster first. When working with</span></span></span> -<span class="r-in"><span><span class="co"># such a cluster, we need to export the mmkin object to the cluster</span></span></span> -<span class="r-in"><span><span class="co"># nodes, as it is referred to when updating the saem object on the nodes.</span></span></span> +<span class="r-in"><span><span class="co"># On Windows, we need to create a PSOCK cluster first and refer to it</span></span></span> +<span class="r-in"><span><span class="co"># in the call to multistart()</span></span></span> <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">parallel</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in checkForRemoteErrors(val):</span> 16 nodes produced errors; first error: unused argument (mc.preschedule = FALSE)</span> -<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in parplot(f_saem_reduced_multi, lpos = "topright"):</span> object 'f_saem_reduced_multi' not found</span> +<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="multistart-2.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 35b67aa5..5e733f99 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -21,7 +21,7 @@ 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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex e941687c..02aa0573 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 f09fe66f..60095af6 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -20,7 +20,7 @@ datasets. They are used internally by the nlme.mmkin() method."><!-- mathjax --> </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -191,11 +191,11 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 0.0004253489 0.7058039 3.065183</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 0.0003775775 0.7058039 3.065183</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects: parent_0 + log_k_parent_sink ~ 1 </span> <span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 101.18323 0.7900461 43 128.07256 0</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.18323 0.7900461 43 128.07257 0</span> <span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.08708 0.4171755 43 -7.39995 0</span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> prnt_0</span> @@ -203,7 +203,7 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Standardized Within-Group Residuals:</span> <span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> -<span class="r-out co"><span class="r-pr">#></span> -2.38427071 -0.52059848 0.03593021 0.39987268 2.73188969 </span> +<span class="r-out co"><span class="r-pr">#></span> -2.38427070 -0.52059848 0.03593021 0.39987268 2.73188969 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Number of Observations: 47</span> <span class="r-out co"><span class="r-pr">#></span> Number of Groups: 3 </span> diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png Binary files differindex 818c23a2..762d5412 100644 --- a/docs/reference/nlme.mmkin-1.png +++ b/docs/reference/nlme.mmkin-1.png diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex b3785a78..046d0238 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 d446a2a2..d41f9abd 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -19,7 +19,7 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -256,7 +256,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -287,7 +287,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span> <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></span></span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34192 4.193936 43.85441</span> +<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34192 4.193937 43.85442</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="va">ds_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">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></span> @@ -321,9 +321,9 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-plt img"><img src="nlme.mmkin-3.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">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></span></span> -<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</span> +<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.620 -408.9273 </span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo_sfo 2 9 1085.1821 1113.404 -533.5910 1 vs 2 249.3274 <.0001</span> <span class="r-in"><span></span></span> <span class="r-in"><span> <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></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> @@ -338,12 +338,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span> <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></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 0.2768575 0.7231425 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.2768574 0.7231426 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 11.07091 104.6320 31.49737 4.462384 46.20825</span> -<span class="r-out co"><span class="r-pr">#></span> A1 162.30507 539.1658 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> parent 11.07091 104.6320 31.49737 4.462383 46.20825</span> +<span class="r-out co"><span class="r-pr">#></span> A1 162.30550 539.1672 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">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></span> @@ -371,7 +371,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> 94.04773 -1.82340 -4.16716 0.05686 </span> +<span class="r-out co"><span class="r-pr">#></span> 94.04774 -1.82340 -4.16716 0.05685 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span> @@ -385,7 +385,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 2.23223593 0.01262367 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.23222933 0.01262399 </span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="va">f_2_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">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></span> <span class="r-in"><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" class="external-link">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></span> @@ -418,7 +418,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~1 | name </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> parent A1 </span> -<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049994 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2050005 </span> <span class="r-in"><span> <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" class="external-link">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>,</span></span> <span class="r-in"><span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">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></span> <span class="r-in"><span></span></span> @@ -428,12 +428,9 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span> <span class="co"># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">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></span></span> -<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093</span> -<span class="r-out co"><span class="r-pr">#></span> p-value</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs <.0001</span> +<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.620 -408.9273 </span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.435 -394.7669 1 vs 2 28.32084 <.0001</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index 186cda01..5781c4dc 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 50034ac4..345bb1bc 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -19,7 +19,7 @@ without considering the error structure that was assumed for the fit."><!-- math </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -217,10 +217,10 @@ mmkin objects with more than one row).</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 7</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971589</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971584</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.044946770</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.002868336</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.526942415</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.526942414</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.221302196</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> @@ -232,29 +232,29 @@ mmkin objects with more than one row).</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $FOMC</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458</span> <span class="r-out co"><span class="r-pr">#></span> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272</span> <span class="r-out co"><span class="r-pr">#></span> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971584 90.34509493 98.14858820 94.311323735</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span><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></span></span> <span class="r-out co"><span class="r-pr">#></span> $SFO</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 88.522754 82.666782 86.854731 91.777931 82.148094</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 88.522754 82.666782 86.854731 91.777931 82.148095</span> <span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090</span> <span class="r-out co"><span class="r-pr">#></span> sigma 5.152745 7.040169 3.676964 6.466923 6.504577</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $FOMC</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 95.5585751 92.6837649 90.7197870 98.38393897 94.848146</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 95.5585751 92.6837649 90.7197870 98.38393898 94.848146</span> <span class="r-out co"><span class="r-pr">#></span> log_alpha 0.2916741 -0.6996015 0.4941466 0.07181816 -1.271085</span> <span class="r-out co"><span class="r-pr">#></span> log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278</span> diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html index b4d6c077..edefb059 100644 --- a/docs/reference/parplot.html +++ b/docs/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png Binary files differindex b22c1dbb..65f5593b 100644 --- a/docs/reference/plot.mixed.mmkin-2.png +++ b/docs/reference/plot.mixed.mmkin-2.png diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png Binary files differindex cd424bf2..ef4fa3a7 100644 --- a/docs/reference/plot.mixed.mmkin-3.png +++ b/docs/reference/plot.mixed.mmkin-3.png diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png Binary files differindex f6ffe4d5..d7030dea 100644 --- a/docs/reference/plot.mixed.mmkin-4.png +++ b/docs/reference/plot.mixed.mmkin-4.png diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index eb0e60b3..507684a1 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -304,7 +304,7 @@ corresponding model prediction lines for the different datasets.</p></dd> <span class="r-in"><span><span class="va">f_nlmix</span> <span class="op"><-</span> <span class="fu">nlmix</span><span class="op">(</span><span class="va">f_obs</span><span class="op">)</span></span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmix(f_obs):</span> could not find function "nlmix"</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlmix</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in plot(f_nlmix):</span> object 'f_nlmix' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'f_nlmix' not found</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># We can overlay the two variants if we generate predictions</span></span></span> <span class="r-in"><span><span class="va">pred_nlme</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span></span> diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 4bc1815c..43184bcb 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 a8525aaa..50c13686 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png Binary files differindex c2537ea7..e81d2737 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 21bc9513..3cd677be 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -19,7 +19,7 @@ observed data together with the solution of the fitted model."><!-- mathjax -->< </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex c91410fa..09caa509 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 f0a03694..c35f7c80 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 18f25bd4..455a67f3 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -21,7 +21,7 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 600a828e..0d5a0940 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -18,7 +18,7 @@ function (SFO, then IORE, then DFOP)."><!-- mathjax --><script src="https://cdnj </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/read_spreadsheet.html b/docs/reference/read_spreadsheet.html index 84e839a6..4d1aa706 100644 --- a/docs/reference/read_spreadsheet.html +++ b/docs/reference/read_spreadsheet.html @@ -22,7 +22,7 @@ factors can be given in columns named 'Temperature' and 'Moisture'."><!-- mathja </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 55315e1c..a50ee30f 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -28,7 +28,7 @@ intervals, nlme </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index acefa606..f4516026 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png Binary files differindex a74e21f8..36deeada 100644 --- a/docs/reference/saem-4.png +++ b/docs/reference/saem-4.png diff --git a/docs/reference/saem.html b/docs/reference/saem.html index e308af61..9c367984 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -380,7 +380,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq)</span> <span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.85 465.11 -226.92 </span> -<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc_tc 8 469.83 466.71 -226.92 0.015 1 0.9027</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc_tc 8 469.90 466.77 -226.95 0 1 1</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">sfo_sfo</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="st">"A1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> A1 <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></span> @@ -439,10 +439,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:34:38 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:34:38 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:17:55 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:17:55 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -457,7 +457,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 3.757 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 4.02 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> @@ -726,13 +726,13 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 70</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> T not in interval TCUR - HU (= R1) to TCUR (=R2) </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1122, R2 = 56.6407</span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1042, R2 = 56.6326</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> DINTDY- T (=R1) illegal </span> <span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 91</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> T not in interval TCUR - HU (= R1) to TCUR (=R2) </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1122, R2 = 56.6407</span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1042, R2 = 56.6326</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> DLSODA- Trouble in DINTDY. ITASK = I1, TOUT = R1</span> <span class="r-out co"><span class="r-pr">#></span> In above message, I1 = 1</span> diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png Binary files differindex 7622ae7f..41665b13 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 1f3d7860..075f22c0 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -19,7 +19,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -165,15 +165,15 @@ <span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.3809618 0.1954668 0.4235714 0.0000000 0.4479540 0.5520460 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> parent 13.95078 46.34350</span> -<span class="r-out co"><span class="r-pr">#></span> A1 49.75342 165.27728</span> -<span class="r-out co"><span class="r-pr">#></span> B1 37.26908 123.80520</span> -<span class="r-out co"><span class="r-pr">#></span> C1 11.23131 37.30961</span> -<span class="r-out co"><span class="r-pr">#></span> A2 28.50624 94.69567</span> +<span class="r-out co"><span class="r-pr">#></span> parent 13.95078 46.34349</span> +<span class="r-out co"><span class="r-pr">#></span> A1 49.75347 165.27745</span> +<span class="r-out co"><span class="r-pr">#></span> B1 37.26905 123.80511</span> +<span class="r-out co"><span class="r-pr">#></span> C1 11.23129 37.30955</span> +<span class="r-out co"><span class="r-pr">#></span> A2 28.50690 94.69789</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span> <span class="co"># }</span></span></span> <span class="r-in"><span> <span class="co"># Compare with the results obtained in the original publication</span></span></span> diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html index 5a487649..662779ca 100644 --- a/docs/reference/set_nd_nq.html +++ b/docs/reference/set_nd_nq.html @@ -21,7 +21,7 @@ it automates the proposal of Boesten et al (2015)."><!-- mathjax --><script src= </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 3018fb28..24593d2c 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -18,7 +18,7 @@ dependence of the measured value \(y\):"><!-- mathjax --><script src="https://cd </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/status.html b/docs/reference/status.html index 6b9c8f3b..1acb7c2e 100644 --- a/docs/reference/status.html +++ b/docs/reference/status.html @@ -17,7 +17,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -159,8 +159,10 @@ suitable printing method.</p> <span class="r-out co"><span class="r-pr">#></span> dataset</span> <span class="r-out co"><span class="r-pr">#></span> model FOCUS A FOCUS B</span> <span class="r-out co"><span class="r-pr">#></span> SFO OK OK </span> -<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK </span> +<span class="r-out co"><span class="r-pr">#></span> FOMC C OK </span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> C: Optimisation did not converge:</span> +<span class="r-out co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 9a419ed5..5bd1db76 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -231,17 +231,17 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</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></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:36:41 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:36:41 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:19:51 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:19:51 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.009 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.008 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/reference/summary.mmkin.html b/docs/reference/summary.mmkin.html index 32ee9940..b5f17839 100644 --- a/docs/reference/summary.mmkin.html +++ b/docs/reference/summary.mmkin.html @@ -18,7 +18,7 @@ and gives an overview of ill-defined parameters calculated by illparms."><!-- ma </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -150,16 +150,20 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">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></span> <span class="r-in"><span> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span> <span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.503 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.433 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> <span class="r-out co"><span class="r-pr">#></span> model FOCUS A FOCUS C</span> <span class="r-out co"><span class="r-pr">#></span> SFO OK OK </span> -<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK </span> +<span class="r-out co"><span class="r-pr">#></span> FOMC C OK </span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> C: Optimisation did not converge:</span> +<span class="r-out co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Ill-defined parameters:</span> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 64ae46c4..33d8c01d 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -21,7 +21,7 @@ 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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -252,10 +252,10 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.162 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:36:43 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:36:43 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:19:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:19:53 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -265,7 +265,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.187 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.175 s using 4 iterations</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -294,15 +294,15 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k_parent ~ 1)</span> <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.92e-05 0.5863 1</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.921e-05 0.5863 1</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance function:</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Constant plus proportion of variance covariate</span> <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 0.0001208154 0.0789968021 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.0001208313 0.0789967985 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters with asymmetric confidence intervals:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> @@ -352,7 +352,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668740</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603</span> @@ -366,7 +366,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206777</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057</span> @@ -381,8 +381,8 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18660 6.0838 0.852526</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08660 6.0838 1.493571</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058</span> diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index 6f7b1ac3..d9049ce5 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -21,7 +21,7 @@ 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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -285,21 +285,21 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> 810.8 805.4 -391.4</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fitted parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.86947 97.81542 103.92353</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06947 -4.16944 -3.96950</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.93256 -1.34200 -0.52312</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.37017 -2.72660 -2.01375</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.06264 -4.21344 -3.91184</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02174 -0.45898 0.41549</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.87598 0.67275 1.07922</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.07949 0.06389 0.09509</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.19170 -30.36286 30.74626</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.01883 -0.28736 0.32502</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44300 0.16391 0.72209</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.35320 0.09661 0.60978</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.13707 0.02359 0.25056</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.37478 0.04490 0.70467</span> +<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.966822 97.90584 104.0278</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.076164 -4.17485 -3.9775</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.940902 -1.35358 -0.5282</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.363988 -2.71690 -2.0111</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.060016 -4.21743 -3.9026</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.029999 -0.44766 0.3877</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.876272 0.67308 1.0795</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.079594 0.06399 0.0952</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.076322 -76.47330 76.6259</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.005052 -1.09071 1.1008</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.446968 0.16577 0.7282</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.348786 0.09502 0.6025</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.147456 0.03111 0.2638</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.348244 0.02794 0.6686</span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] "sd(parent_0)" "sd(log_k_m1)"</span> <span class="r-in"><span><span class="va">f_saem_dfop_sfo_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>,</span></span> @@ -310,30 +310,30 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 98.36731429 101.42508066 104.48284703</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01513234 0.01670094 0.01843214</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20221431 0.27608850 0.36461630</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.06915073 0.09759718 0.13774560</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01487068 0.01740389 0.02036863</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.37365671 0.48384821 0.59563299</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 98.04247057 101.09950884 104.15654711</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01528983 0.01687734 0.01862969</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20447650 0.27932896 0.36887691</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.06779844 0.09638524 0.13702550</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01495629 0.01741775 0.02028431</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.37669311 0.48368409 0.59219202</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.16439770 0.4427585 0.7211193</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.08304243 0.3345213 0.5860002</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.03146410 0.1490210 0.2665779</span> -<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.06216385 0.4023430 0.7425221</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.16515100 0.4448330 0.7245149</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.08982372 0.3447403 0.5996568</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.02806589 0.1419560 0.2558462</span> +<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.04908160 0.3801993 0.7113170</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.67696663 0.87777355 1.07858048</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.06363957 0.07878001 0.09392044</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.67539922 0.87630147 1.07720371</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.06401324 0.07920531 0.09439739</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:36:59 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:36:59 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:20:09 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:20:09 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -348,7 +348,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.185 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.513 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -357,7 +357,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 </span> <span class="r-out co"><span class="r-pr">#></span> 101.65645 -4.05368 -0.94311 -2.35943 -4.07006 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> -0.01132 </span> +<span class="r-out co"><span class="r-pr">#></span> -0.01133 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> @@ -378,236 +378,236 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> Results:</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 807 802.3 -391.5</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 806.9 802.2 -391.5</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 101.42508 98.36731 104.48285</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.09229 -4.19092 -3.99366</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.96395 -1.37251 -0.55538</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.32691 -2.67147 -1.98235</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.05106 -4.20836 -3.89376</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.06463 -0.51656 0.38730</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.87777 0.67697 1.07858</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.07878 0.06364 0.09392</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44276 0.16440 0.72112</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.33452 0.08304 0.58600</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.14902 0.03146 0.26658</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.40234 0.06216 0.74252</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.09951 98.04247 104.1565</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.08178 -4.18057 -3.9830</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.94779 -1.35855 -0.5370</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.33940 -2.69122 -1.9876</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.05027 -4.20262 -3.8979</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.06529 -0.50361 0.3730</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87630 0.67540 1.0772</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07921 0.06401 0.0944</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44483 0.16515 0.7245</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.34474 0.08982 0.5997</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.14196 0.02807 0.2558</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.38020 0.04908 0.7113</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4693 </span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2378 0.2595 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1720 -0.1593 -0.0669 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0179 0.0594 0.0035 0.1995 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.1073 -0.1060 -0.0322 -0.2299 -0.3168</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4716 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2394 0.2617 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1677 -0.1566 -0.0659 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0165 0.0638 0.0045 0.2013 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.1118 -0.1118 -0.0340 -0.2324 -0.3419</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4428 0.16440 0.7211</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.3345 0.08304 0.5860</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.1490 0.03146 0.2666</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4023 0.06216 0.7425</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4448 0.16515 0.7245</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.3447 0.08982 0.5997</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.1420 0.02807 0.2558</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.3802 0.04908 0.7113</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.87777 0.67697 1.07858</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.07878 0.06364 0.09392</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87630 0.67540 1.0772</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07921 0.06401 0.0944</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 101.4251 98.36731 104.48285</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0167 0.01513 0.01843</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.2761 0.20221 0.36462</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.0976 0.06915 0.13775</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.0174 0.01487 0.02037</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.4838 0.37366 0.59563</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.09951 98.04247 104.15655</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01688 0.01529 0.01863</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.27933 0.20448 0.36888</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.09639 0.06780 0.13703</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01742 0.01496 0.02028</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.48368 0.37669 0.59219</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2761</span> -<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7239</span> +<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2793</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7207</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 15.54 94.33 28.4 7.102 39.83</span> -<span class="r-out co"><span class="r-pr">#></span> m1 41.50 137.87 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> parent 15.66 94.28 28.38 7.191 39.8</span> +<span class="r-out co"><span class="r-pr">#></span> m1 41.07 136.43 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 89.8 1.014e+02 -11.62508 8.0383 -1.44620</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.014e+02 2.67492 8.0383 0.33277</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.650e+01 -7.80311 7.6530 -1.01961</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.650e+01 -1.00311 7.6530 -0.13107</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.753e+01 -5.72638 6.9510 -0.82382</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.753e+01 6.97362 6.9510 1.00326</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.254e+01 -1.04133 5.7818 -0.18010</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.254e+01 -2.24133 5.7818 -0.38765</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.349e+01 0.71029 4.3044 0.16502</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.349e+01 -3.88971 4.3044 -0.90366</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.167e+01 -0.16616 2.6446 -0.06283</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.167e+01 -2.86616 2.6446 -1.08379</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.279e+01 -0.69287 1.3365 -0.51843</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.279e+01 0.80713 1.3365 0.60392</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.397e+00 -0.19718 1.0122 -0.19481</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.397e+00 1.90282 1.0122 1.87996</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.323e+00 -1.12320 0.9160 -1.22623</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.323e+00 -0.92320 0.9160 -1.00788</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.179e+00 -0.87919 0.8827 -0.99605</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.179e+00 -0.97919 0.8827 -1.10935</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.273e+00 -1.07272 0.9149 -1.17256</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.273e+00 -0.27272 0.9149 -0.29811</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.559e+00 -0.05872 1.0186 -0.05765</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.559e+00 -1.55872 1.0186 -1.53032</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.016e+01 0.03787 1.1880 0.03188</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.016e+01 -0.66213 1.1880 -0.55734</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.268e+01 -0.47913 1.3297 -0.36032</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.268e+01 0.72087 1.3297 0.54211</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.078e+01 1.02493 1.2211 0.83936</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.078e+01 2.42493 1.2211 1.98588</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.705e+00 -1.10464 1.0672 -1.03509</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.705e+00 1.59536 1.0672 1.49491</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.236e+00 -1.73617 0.9699 -1.79010</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.236e+00 0.16383 0.9699 0.16892</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.014e+02 16.57492 8.0383 2.06198</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.014e+02 -1.62508 8.0383 -0.20217</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.599e+01 -5.79045 7.6129 -0.76061</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.599e+01 -1.39045 7.6129 -0.18264</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.652e+01 9.57931 6.8724 1.39388</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.652e+01 -8.12069 6.8724 -1.18164</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.197e+01 5.93429 5.7370 1.03439</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.197e+01 5.73429 5.7370 0.99953</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.555e+01 0.44657 4.4637 0.10005</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.555e+01 -0.85343 4.4637 -0.19120</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.853e+01 -1.93170 3.1599 -0.61132</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.853e+01 -1.73170 3.1599 -0.54803</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.110e+01 1.00360 1.8795 0.53396</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.110e+01 3.60360 1.8795 1.91728</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.250e+01 -0.09712 1.3190 -0.07363</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.250e+01 -1.69712 1.3190 -1.28667</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.419e+00 -0.61913 1.0546 -0.58709</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.419e+00 0.48087 1.0546 0.45599</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.422e+00 -0.12194 0.8849 -0.13781</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.831e+00 -0.13149 0.9282 -0.14166</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.831e+00 0.86851 0.9282 0.93567</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.292e+00 0.80812 1.0490 0.77034</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.292e+00 0.60812 1.0490 0.57969</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.055e+01 -0.45332 1.2090 -0.37495</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.055e+01 -0.25332 1.2090 -0.20953</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.230e+01 -1.59960 1.3074 -1.22347</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.230e+01 -0.09960 1.3074 -0.07618</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.065e+01 0.05342 1.2141 0.04400</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.065e+01 1.85342 1.2141 1.52661</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.196e+00 0.90368 1.0897 0.82930</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.196e+00 -0.79632 1.0897 -0.73078</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.997e+00 0.10252 0.9969 0.10284</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.997e+00 -1.49748 0.9969 -1.50220</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.014e+02 4.77492 8.0383 0.59402</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.014e+02 5.47492 8.0383 0.68110</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.390e+01 13.49935 7.4494 1.81214</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.390e+01 2.19935 7.4494 0.29524</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.152e+01 -2.12307 6.4821 -0.32753</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.152e+01 1.07693 6.4821 0.16614</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.446e+01 -0.55834 5.1533 -0.10834</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.446e+01 -2.05834 5.1533 -0.39942</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.826e+01 2.74073 3.9019 0.70241</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.826e+01 -1.15927 3.9019 -0.29711</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.424e+01 1.86399 2.8364 0.65718</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.424e+01 2.36399 2.8364 0.83346</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.968e+01 0.42172 1.7815 0.23672</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 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-1.00511 5.8093 -0.173019</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.251e+01 -2.20511 5.8093 -0.379585</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.356e+01 0.63921 4.3319 0.147560</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.356e+01 -3.96079 4.3319 -0.914340</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.175e+01 -0.25429 2.6634 -0.095475</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.175e+01 -2.95429 2.6634 -1.109218</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.281e+01 -0.71388 1.3409 -0.532390</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.281e+01 0.78612 1.3409 0.586271</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.405e+00 -0.20462 1.0125 -0.202083</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.405e+00 1.89538 1.0125 1.871910</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.329e+00 -1.12941 0.9151 -1.234165</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.329e+00 -0.92941 0.9151 -1.015615</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.177e+00 -0.87699 0.8812 -0.995168</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.177e+00 -0.97699 0.8812 -1.108644</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.268e+00 -1.06821 0.9137 -1.169063</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.268e+00 -0.26821 0.9137 -0.293536</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.555e+00 -0.05539 1.0186 -0.054377</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.555e+00 -1.55539 1.0186 -1.527022</span> +<span class="r-out 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co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.205e+00 0.19533 0.9684 0.201701</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.011e+02 16.90049 8.0554 2.098026</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.011e+02 -1.29951 8.0554 -0.161321</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.574e+01 -5.53784 7.6334 -0.725473</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.574e+01 -1.13784 7.6334 -0.149060</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.638e+01 9.72233 6.8975 1.409551</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.638e+01 -7.97767 6.8975 -1.156610</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.194e+01 5.95854 5.7651 1.033547</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.194e+01 5.75854 5.7651 0.998856</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.558e+01 0.42141 4.4885 0.093888</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.558e+01 -0.87859 4.4885 -0.195742</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.852e+01 -1.92382 3.1746 -0.605999</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.852e+01 -1.72382 3.1746 -0.543000</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.108e+01 1.02043 1.8856 0.541168</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.108e+01 3.62043 1.8856 1.920034</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.250e+01 -0.09675 1.3220 -0.073184</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.250e+01 -1.69675 1.3220 -1.283492</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.426e+00 -0.62587 1.0554 -0.593027</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.426e+00 0.47413 1.0554 0.449242</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.417e+00 -0.11735 0.8835 -0.132825</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.823e+00 -0.12301 0.9271 -0.132673</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.823e+00 0.87699 0.9271 0.945909</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.288e+00 0.81180 1.0494 0.773619</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.288e+00 0.61180 1.0494 0.583025</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.057e+01 -0.46957 1.2119 -0.387459</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.057e+01 -0.26957 1.2119 -0.222432</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.234e+01 -1.63555 1.3124 -1.246185</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.234e+01 -0.13555 1.3124 -0.103281</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.065e+01 0.04641 1.2165 0.038151</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.065e+01 1.84641 1.2165 1.517773</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.177e+00 0.92337 1.0896 0.847403</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.177e+00 -0.77663 1.0896 -0.712734</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.966e+00 0.13404 0.9956 0.134631</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.966e+00 -1.46596 0.9956 -1.472460</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.011e+02 5.10049 8.0554 0.633175</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.011e+02 5.80049 8.0554 0.720073</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.365e+01 13.74627 7.4695 1.840332</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.365e+01 2.44627 7.4695 0.327504</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.139e+01 -1.99118 6.5059 -0.306058</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.139e+01 1.20882 6.5059 0.185803</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.445e+01 -0.54666 5.1792 -0.105549</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.445e+01 -2.04666 5.1792 -0.395170</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.830e+01 2.69944 3.9247 0.687800</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.830e+01 -1.20056 3.9247 -0.305896</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.426e+01 1.83885 2.8516 0.644839</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.426e+01 2.33885 2.8516 0.820177</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.968e+01 0.42208 1.7881 0.236053</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.968e+01 0.12208 1.7881 0.068273</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.194e+01 -0.64013 1.2893 -0.496496</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.194e+01 -1.24013 1.2893 -0.961865</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.247e+00 0.95264 1.0476 0.909381</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.247e+00 0.05264 1.0476 0.050254</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 -2.956e-12 0.80000 0.8763 0.912928</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.757e+00 0.04318 0.8873 0.048666</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.757e+00 0.54318 0.8873 0.612186</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.566e+00 -0.36607 0.9480 -0.386149</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.566e+00 -0.46607 0.9480 -0.491634</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.157e+00 -1.35680 1.0887 -1.246241</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.157e+00 1.94320 1.0887 1.784855</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.085e+01 0.55367 1.2272 0.451182</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.085e+01 1.95367 1.2272 1.592023</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.149e+01 0.01098 1.2633 0.008689</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.149e+01 -0.88902 1.2633 -0.703717</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.295e+00 -1.79500 1.1445 -1.568351</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.295e+00 -0.69500 1.1445 -0.607245</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 7.017e+00 0.28305 1.0377 0.272775</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 7.017e+00 1.08305 1.0377 1.043720</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 5.087e+00 0.21272 0.9645 0.220547</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 5.087e+00 -1.28728 0.9645 -1.334660</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.011e+02 3.60049 8.0554 0.446965</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.011e+02 -12.79951 8.0554 -1.588930</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.755e+01 -3.35176 7.7762 -0.431030</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.755e+01 -2.95176 7.7762 -0.379591</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.095e+01 -12.85198 7.2570 -1.770981</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 96.5 9.095e+01 5.54802 7.2570 0.764508</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 76.2 7.949e+01 -3.29267 6.3569 -0.517966</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 77.8 7.949e+01 -1.69267 6.3569 -0.266272</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 70.8 6.384e+01 6.95621 5.1321 1.355423</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 67.3 6.384e+01 3.45621 5.1321 0.673445</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 43.1 4.345e+01 -0.35291 3.5515 -0.099370</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 45.1 4.345e+01 1.64709 3.5515 0.463771</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 21.3 2.137e+01 -0.07478 1.9063 -0.039229</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 23.5 2.137e+01 2.12522 1.9063 1.114813</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.205e+01 -0.24925 1.2957 -0.192375</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.205e+01 0.05075 1.2957 0.039168</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 6.967e+00 0.03315 1.0356 0.032013</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 6.967e+00 -0.76685 1.0356 -0.740510</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 1.421e-13 1.60000 0.8763 1.825856</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 7.250e-01 0.17503 0.8782 0.199310</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 2.038e+00 1.66201 0.8910 1.865236</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 2.038e+00 -0.03799 0.8910 -0.042637</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.186e+00 -0.58623 0.9369 -0.625692</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.186e+00 -0.38623 0.9369 -0.412230</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.752e+00 0.34768 1.0266 0.338666</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.752e+00 -0.15232 1.0266 -0.148372</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.034e+00 0.46628 1.1313 0.412159</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.034e+00 0.26628 1.1313 0.235373</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.634e+00 -0.33359 1.1115 -0.300112</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.634e+00 0.36641 1.1115 0.329645</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.671e+00 -0.07091 1.0233 -0.069295</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.671e+00 1.02909 1.0233 1.005691</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.823e+00 -1.12301 0.9559 -1.174763</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.823e+00 -1.32301 0.9559 -1.383979</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.011e+02 9.30049 8.0554 1.154563</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.011e+02 11.00049 8.0554 1.365601</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.440e+01 -0.90098 7.5282 -0.119681</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.440e+01 -3.40098 7.5282 -0.451764</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.287e+01 -11.86698 6.6217 -1.792122</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.287e+01 6.83302 6.6217 1.031907</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 60.4 6.562e+01 -5.22329 5.2711 -0.990936</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 59.1 6.562e+01 -6.52329 5.2711 -1.237566</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 56.5 4.739e+01 9.10588 3.8548 2.362225</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 47.0 4.739e+01 -0.39412 3.8548 -0.102240</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 30.2 3.118e+01 -0.98128 2.6206 -0.374451</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 23.9 3.118e+01 -7.28128 2.6206 -2.778500</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.804e+01 -1.03959 1.6761 -0.620224</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.804e+01 0.66041 1.6761 0.394008</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.165e+01 -0.35248 1.2727 -0.276958</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.165e+01 0.24752 1.2727 0.194488</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.556e+00 1.44368 1.0612 1.360449</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.556e+00 0.54368 1.0612 0.512338</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 -1.421e-14 0.70000 0.8763 0.798812</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.160e+00 -0.15979 0.9113 -0.175340</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.160e+00 -0.55979 0.9113 -0.614254</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.448e+00 -3.34789 1.1026 -3.036487</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.448e+00 -0.94789 1.1026 -0.859720</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.581e+01 0.68760 1.5286 0.449839</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.581e+01 3.18760 1.5286 2.085373</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.218e+01 0.71983 1.9632 0.366658</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.218e+01 1.01983 1.9632 0.519469</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.425e+01 -2.05105 2.1113 -0.971479</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.425e+01 0.14895 2.1113 0.070552</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.876e+01 -3.25968 1.7250 -1.889646</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.876e+01 1.04032 1.7250 0.603074</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.365e+01 1.25477 1.3914 0.901806</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.365e+01 0.55477 1.3914 0.398714</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.726e+00 1.17443 1.1667 1.006587</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.726e+00 0.67443 1.1667 0.578044</span> <span class="r-in"><span><span class="co"># Add a correlation between random effects of g and k2</span></span></span> <span class="r-in"><span><span class="va">cov_model_3</span> <span class="op"><-</span> <span class="va">f_saem_dfop_sfo_2</span><span class="op">$</span><span class="va">so</span><span class="op">@</span><span class="va">model</span><span class="op">@</span><span class="va">covariance.model</span></span></span> <span class="r-in"><span><span class="va">cov_model_3</span><span class="op">[</span><span class="st">"log_k2"</span>, <span class="st">"g_qlogis"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">1</span></span></span> @@ -619,34 +619,34 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 98.39888363 101.48951337 104.58014311</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01508704 0.01665986 0.01839665</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20141557 0.27540583 0.36418131</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.07708759 0.10430866 0.14114200</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01476621 0.01786384 0.02161129</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.33679867 0.45083525 0.57028162</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 98.32277831 101.40841461 104.49405092</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01510464 0.01667815 0.01841557</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20195605 0.27597108 0.36471512</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.07321367 0.10121120 0.13991523</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01466928 0.01766483 0.02127208</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.35098400 0.46314412 0.57916193</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.38085375 0.4441841 0.5075145</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.04774819 0.2660384 0.4843286</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) -0.63842736 0.1977024 1.0338321</span> -<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.22711289 0.4502227 0.6733326</span> -<span class="r-out co"><span class="r-pr">#></span> corr(log_k2,g_qlogis) -0.83271473 -0.6176939 -0.4026730</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.3832326 0.4435601 0.5038876</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.1181772 0.2996192 0.4810613</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) -0.6281964 0.1898692 1.0079349</span> +<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.1885523 0.4250717 0.6615911</span> +<span class="r-out co"><span class="r-pr">#></span> corr(log_k2,g_qlogis) -0.8453380 -0.5695240 -0.2937099</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.67347568 0.87437392 1.07527216</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.06393032 0.07912417 0.09431802</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.67302582 0.87410123 1.07517663</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.06403679 0.07925211 0.09446744</span> <span class="r-in"><span><span class="co"># The correlation does not improve the fit judged by AIC and BIC, although</span></span></span> <span class="r-in"><span><span class="co"># the likelihood is higher with the additional parameter</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, <span class="va">f_saem_dfop_sfo_2</span>, <span class="va">f_saem_dfop_sfo_3</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Data: 171 observations of 2 variable(s) grouped in 5 datasets</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> -<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_2 12 806.96 802.27 -391.48</span> -<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_3 13 807.99 802.91 -391.00</span> -<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo 14 810.83 805.36 -391.42</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_2 12 806.91 802.23 -391.46</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_3 13 807.91 802.83 -390.95</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo 14 810.83 805.36 -391.41</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> </code></pre></div> diff --git a/docs/reference/summary_listing.html b/docs/reference/summary_listing.html index 0dcc5456..9869e2e6 100644 --- a/docs/reference/summary_listing.html +++ b/docs/reference/summary_listing.html @@ -18,7 +18,7 @@ option results = "asis".'><!-- mathjax --><script src="https://cdnjs.cloudflare. </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index cd2338eb..91d7f6a6 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -32,7 +32,7 @@ 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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -269,10 +269,10 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-in"><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></span></span> <span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:37:10 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:37:10 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:20:19 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:20:19 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -281,7 +281,7 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 833 model solutions performed in 0.161 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 848 model solutions performed in 0.154 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -333,15 +333,15 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01</span> -<span class="r-out co"><span class="r-pr">#></span> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma -1.377e-08 7.536e-10 1.089e-08 -4.422e-08 7.124e-09</span> <span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 -2.900e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 -8.030e-09</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 -2.741e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 3.938e-08</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 -2.681e-08</span> -<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 4.971e-08</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 4.971e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 -1.377e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 7.536e-10</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 1.089e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 -4.422e-08</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 7.124e-09</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 -2.685e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma -2.685e-08 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -388,7 +388,7 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> 7 parent 0.3 5.772e-01 -0.27717</span> <span class="r-out co"><span class="r-pr">#></span> 14 parent 3.5 3.264e-03 3.49674</span> <span class="r-out co"><span class="r-pr">#></span> 28 parent 3.2 1.045e-07 3.20000</span> -<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.530e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.532e-10 0.60000</span> <span class="r-out co"><span class="r-pr">#></span> 120 parent 3.5 -5.940e-10 3.50000</span> <span class="r-out co"><span class="r-pr">#></span> 1 M1 36.4 3.479e+01 1.61088</span> <span class="r-out co"><span class="r-pr">#></span> 1 M1 37.4 3.479e+01 2.61088</span> @@ -399,7 +399,7 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> 14 M1 5.8 1.995e+00 3.80469</span> <span class="r-out co"><span class="r-pr">#></span> 14 M1 1.2 1.995e+00 -0.79531</span> <span class="r-out co"><span class="r-pr">#></span> 60 M1 0.5 2.111e-06 0.50000</span> -<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.670e-10 3.20000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.672e-10 3.20000</span> <span class="r-out co"><span class="r-pr">#></span> 120 M1 1.5 7.670e-10 1.50000</span> <span class="r-out co"><span class="r-pr">#></span> 120 M1 0.6 7.670e-10 0.60000</span> <span class="r-out co"><span class="r-pr">#></span> 1 M2 4.8 4.455e+00 0.34517</span> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index e57141ec..b53b5de2 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -18,7 +18,7 @@ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -179,25 +179,25 @@ <span class="r-plt img"><img src="test_data_from_UBA_2014-2.png" alt="" width="700" height="433"></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 76.55425650 0.859186398 89.1008711 1.113861e-26 74.755959420</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575</span> -<span class="r-out co"><span class="r-pr">#></span> k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.84258615 0.806159719 1.0451851 1.545266e-01 0.113779564</span> <span class="r-out co"><span class="r-pr">#></span> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857</span> -<span class="r-out co"><span class="r-pr">#></span> k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205</span> -<span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509</span> +<span class="r-out co"><span class="r-pr">#></span> k_M3 0.01122918 0.007245855 1.5497385 6.885051e-02 0.002909431</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.32240200 0.240783878 1.3389684 9.819070e-02 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.16099855 0.033691952 4.7785463 6.531136e-05 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.27921507 0.269423709 1.0363419 1.565266e-01 0.022978202</span> +<span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.55641252 0.595119937 0.9349586 1.807707e-01 0.008002509</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778</span> <span class="r-out co"><span class="r-pr">#></span> Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 78.35255358</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.13084582</span> -<span class="r-out co"><span class="r-pr">#></span> k_M1 6.23970702</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 6.23970946</span> <span class="r-out co"><span class="r-pr">#></span> k_M2 0.09843260</span> <span class="r-out co"><span class="r-pr">#></span> k_M3 0.04333992</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 NA</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.86450775</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.86450778</span> <span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.99489895</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.45337221</span> <span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span></span> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 2845c6c1..2cfe6df7 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -22,7 +22,7 @@ the ilr transformation is used."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index f941af5f..c1e5edfc 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -20,7 +20,7 @@ override these starting values."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> |
