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/reference | |
| 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/reference')
114 files changed, 605 insertions, 598 deletions
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 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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 co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.017e+01 0.03108 1.1902 0.026117</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.017e+01 -0.66892 1.1902 -0.562010</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.270e+01 -0.50262 1.3342 -0.376708</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.270e+01 0.69738 1.3342 0.522686</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.078e+01 1.01734 1.2236 0.831403</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.078e+01 2.41734 1.2236 1.975530</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.686e+00 -1.08586 1.0670 -1.017675</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.686e+00 1.61414 1.0670 1.512779</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.205e+00 -1.70467 0.9684 -1.760250</span> +<span class="r-out 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> |
