diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-07 12:03:40 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-07 14:55:21 +0100 |
| commit | 7035cde3a53781721fe15a8893fdf328c789bdd2 (patch) | |
| tree | a1e4929faf9d645caedc0ed4dcc5036252497c63 /docs/reference | |
| parent | 77c248ca40b82ec00a756cd82f12968131f78959 (diff) | |
Remove nlmixr interface for release of mkin 1.1.0
I am postponing my attempts to get the nlmixr interface to CRAN, given
some problems with nlmixr using R-devel under Windows, see
https://github.com/nlmixrdevelopment/nlmixr/issues/596
and
https://github.com/r-hub/rhub/issues/512,
which is fixed by the removal of nlmixr from the testsuite.
For the tests to be more platform independent, the biphasic mixed
effects models test dataset was defined in a way that fitting
should be more robust (less ill-defined).
Diffstat (limited to 'docs/reference')
82 files changed, 692 insertions, 670 deletions
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 35becede..a049850d 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -27,7 +27,7 @@ same dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index d36f5ed9..44297d1b 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -27,7 +27,7 @@ specified as well."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/aj <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index 85f068ee..1c47c7f7 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -31,7 +31,7 @@ constrained by data protection regulations."><!-- mathjax --><script src="https: <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 335590f7..86df2efc 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -27,7 +27,7 @@ two exponential decline functions."><!-- mathjax --><script src="https://cdnjs.c <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 49578dc7..7193e0f9 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></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 c8bfb9dd..93602958 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -30,7 +30,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> 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 c332446f..31c14505 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -30,7 +30,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> 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 151925d9..83ab4e56 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -30,7 +30,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> 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 f8e368cf..f47cba8d 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -30,7 +30,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index a1004d39..1e0e270e 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 9e3851fd..d507b9c8 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -27,7 +27,7 @@ a decreasing rate constant."><!-- mathjax --><script src="https://cdnjs.cloudfla <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 7f0ab8ea..d30c4e8a 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -27,7 +27,7 @@ between them."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index bfb69a40..fec06e0a 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -27,7 +27,7 @@ a concentration dependent rate constant."><!-- mathjax --><script src="https://c <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 1862580b..ab3ae7b8 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index e602a2b0..a9f4e36f 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex 17a35806..ca982688 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex 86d1775b..de2d61aa 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex b1cdfcc9..f8bf10bb 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex b91e73fb..69fdb09d 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 8caa8958..dfae0f69 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 45933071..40ed1338 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -30,7 +30,7 @@ and no substance in the bound fraction."><!-- mathjax --><script src="https://cd <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 50b55748..de773982 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -28,7 +28,7 @@ may depend on the predicted value and is specified as a standard deviation."><!- <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 534cdf80..1182ab8c 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -28,7 +28,7 @@ by Burnham and Anderson (2004)."><!-- mathjax --><script src="https://cdnjs.clou <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index a57164cc..806e94ca 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -33,7 +33,7 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -206,7 +206,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><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 class="r-in"><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 class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 3.933 0.000 3.934 </span> +<span class="r-out co"><span class="r-pr">#></span> 4.361 0.964 3.998 </span> <span class="r-in"><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span> <span class="r-in"><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span> <span class="r-in"><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span> @@ -214,7 +214,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"> <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 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> 1.496 0.172 0.968 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.473 0.118 0.917 </span> <span class="r-in"><span class="va">ci_profile</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> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index ca57addf..57516fba 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -120,8 +120,8 @@ <span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</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 0.446 1.000 0.446 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.756 1.695 0.756 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.406 1.000 0.407 0.000 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.698 1.719 0.695 0.003 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> @@ -134,8 +134,8 @@ <span class="r-in"> 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 class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</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 0.896 1.000 0.896 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.685 1.881 1.685 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.855 1.000 0.856 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.588 1.857 1.587 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.html b/docs/reference/dimethenamid_2018.html index 374d2287..f0bc23ee 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -31,7 +31,7 @@ constrained by data protection regulations."><!-- mathjax --><script src="https: <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -166,321 +166,19 @@ specific pieces of information in the comments.</p> <span class="r-in"><span class="va">f_dmta_mkin_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span> <span class="r-in"> <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">"DFOP-SFO3+"</span> <span class="op">=</span> <span class="va">dfop_sfo3_plus</span><span class="op">)</span>,</span> <span class="r-in"> <span class="va">dmta_ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="nlmixr.mmkin.html">nlmixr_model</a></span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> With est = 'saem', a different error model is required for each observed variableChanging the error model to 'obs_tc' (Two-component error for each observed variable)</span> -<span class="r-out co"><span class="r-pr">#></span> function () </span> -<span class="r-out co"><span class="r-pr">#></span> {</span> -<span class="r-out co"><span class="r-pr">#></span> ini({</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 = 99</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 ~ 2.3</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 = -3.9</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M23 ~ 0.55</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 = -4.3</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M27 ~ 0.86</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 = -4.2</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M31 ~ 0.75</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 = -2.2</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 ~ 0.9</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 = -3.8</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k2 ~ 1.6</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis = 0.44</span> -<span class="r-out co"><span class="r-pr">#></span> eta.g_qlogis ~ 3.1</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_1_qlogis = -2.1</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis ~ 0.3</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_2_qlogis = -2.2</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_2_qlogis ~ 0.3</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_3_qlogis = -2.1</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis ~ 0.3</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low_DMTA = 0.7</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high_DMTA = 0.026</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low_M23 = 0.7</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high_M23 = 0.026</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low_M27 = 0.7</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high_M27 = 0.026</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low_M31 = 0.7</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high_M31 = 0.026</span> -<span class="r-out co"><span class="r-pr">#></span> })</span> -<span class="r-out co"><span class="r-pr">#></span> model({</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0_model = DMTA_0 + eta.DMTA_0</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA(0) = DMTA_0_model</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 = exp(log_k_M23 + eta.log_k_M23)</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 = exp(log_k_M27 + eta.log_k_M27)</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 = exp(log_k_M31 + eta.log_k_M31)</span> -<span class="r-out co"><span class="r-pr">#></span> k1 = exp(log_k1 + eta.log_k1)</span> -<span class="r-out co"><span class="r-pr">#></span> k2 = exp(log_k2 + eta.log_k2)</span> -<span class="r-out co"><span class="r-pr">#></span> g = expit(g_qlogis + eta.g_qlogis)</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_1 = expit(f_DMTA_tffm0_1_qlogis + eta.f_DMTA_tffm0_1_qlogis)</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_2 = expit(f_DMTA_tffm0_2_qlogis + eta.f_DMTA_tffm0_2_qlogis)</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_3 = expit(f_DMTA_tffm0_3_qlogis + eta.f_DMTA_tffm0_3_qlogis)</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 = f_DMTA_tffm0_1</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 = f_DMTA_tffm0_2 * (1 - f_DMTA_tffm0_1)</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 = f_DMTA_tffm0_3 * (1 - f_DMTA_tffm0_2) * </span> -<span class="r-out co"><span class="r-pr">#></span> (1 - f_DMTA_tffm0_1)</span> -<span class="r-out co"><span class="r-pr">#></span> d/dt(DMTA) = -((k1 * g * exp(-k1 * time) + k2 * (1 - </span> -<span class="r-out co"><span class="r-pr">#></span> g) * exp(-k2 * time))/(g * exp(-k1 * time) + (1 - </span> -<span class="r-out co"><span class="r-pr">#></span> g) * exp(-k2 * time))) * DMTA</span> -<span class="r-out co"><span class="r-pr">#></span> d/dt(M23) = +f_DMTA_to_M23 * ((k1 * g * exp(-k1 * time) + </span> -<span class="r-out co"><span class="r-pr">#></span> k2 * (1 - g) * exp(-k2 * time))/(g * exp(-k1 * time) + </span> -<span class="r-out co"><span class="r-pr">#></span> (1 - g) * exp(-k2 * time))) * DMTA - k_M23 * M23</span> -<span class="r-out co"><span class="r-pr">#></span> d/dt(M27) = +f_DMTA_to_M27 * ((k1 * g * exp(-k1 * time) + </span> -<span class="r-out co"><span class="r-pr">#></span> k2 * (1 - g) * exp(-k2 * time))/(g * exp(-k1 * time) + </span> -<span class="r-out co"><span class="r-pr">#></span> (1 - g) * exp(-k2 * time))) * DMTA - k_M27 * M27 + </span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 * M31</span> -<span class="r-out co"><span class="r-pr">#></span> d/dt(M31) = +f_DMTA_to_M31 * ((k1 * g * exp(-k1 * time) + </span> -<span class="r-out co"><span class="r-pr">#></span> k2 * (1 - g) * exp(-k2 * time))/(g * exp(-k1 * time) + </span> -<span class="r-out co"><span class="r-pr">#></span> (1 - g) * exp(-k2 * time))) * DMTA - k_M31 * M31</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA ~ add(sigma_low_DMTA) + prop(rsd_high_DMTA)</span> -<span class="r-out co"><span class="r-pr">#></span> M23 ~ add(sigma_low_M23) + prop(rsd_high_M23)</span> -<span class="r-out co"><span class="r-pr">#></span> M27 ~ add(sigma_low_M27) + prop(rsd_high_M27)</span> -<span class="r-out co"><span class="r-pr">#></span> M31 ~ add(sigma_low_M31) + prop(rsd_high_M31)</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> <environment: 0x555560091f40></span> +<span class="r-in"><span class="fu">nlmixr_model</span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span><span class="op">)</span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmixr_model(f_dmta_mkin_tc):</span> could not find function "nlmixr_model"</span> <span class="r-in"><span class="co"># The focei fit takes about four minutes on my system</span></span> <span class="r-in"><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> -<span class="r-in"> <span class="va">f_dmta_nlmixr_focei</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlmixr/man/nlmixr.html" class="external-link">nlmixr</a></span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span>, est <span class="op">=</span> <span class="st">"focei"</span>,</span> +<span class="r-in"> <span class="va">f_dmta_nlmixr_focei</span> <span class="op"><-</span> <span class="fu">nlmixr</span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span>, est <span class="op">=</span> <span class="st">"focei"</span>,</span> <span class="r-in"> control <span class="op">=</span> <span class="fu">nlmixr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/nlmixr/man/foceiControl.html" class="external-link">foceiControl</a></span><span class="op">(</span>print <span class="op">=</span> <span class="fl">500</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Need to run with the source intact to parse comments</span> -<span class="r-msg co"><span class="r-pr">#></span> → creating full model...</span> -<span class="r-msg co"><span class="r-pr">#></span> → pruning branches (`if`/`else`)...</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> → loading into <span style="color: #0000BB;">symengine</span> environment...</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> → creating full model...</span> -<span class="r-msg co"><span class="r-pr">#></span> → pruning branches (`if`/`else`)...</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> → loading into <span style="color: #0000BB;">symengine</span> environment...</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> → calculate jacobian</span> -<span class="r-out co"><span class="r-pr">#></span> [====|====|====|====|====|====|====|====|====|====] 0:00:02 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → calculate sensitivities</span> -<span class="r-out co"><span class="r-pr">#></span> [====|====|====|====|====|====|====|====|====|====] 0:00:04 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → calculate ∂(f)/∂(η)</span> -<span class="r-out co"><span class="r-pr">#></span> [====|====|====|====|====|====|====|====|====|====] 0:00:01 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → calculate ∂(R²)/∂(η)</span> -<span class="r-out co"><span class="r-pr">#></span> [====|====|====|====|====|====|====|====|====|====] 0:00:08 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → finding duplicate expressions in inner model...</span> -<span class="r-out co"><span class="r-pr">#></span> [====|====|====|====|====|====|====|====|====|====] 0:00:07 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → optimizing duplicate expressions in inner model...</span> -<span class="r-out co"><span class="r-pr">#></span> [====|====|====|====|====|====|====|====|====|====] 0:00:07 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → finding duplicate expressions in EBE model...</span> -<span class="r-out co"><span class="r-pr">#></span> [====|====|====|====|====|====|====|====|====|====] 0:00:00 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → optimizing duplicate expressions in EBE model...</span> -<span class="r-out co"><span class="r-pr">#></span> [====|====|====|====|====|====|====|====|====|====] 0:00:00 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → compiling inner model...</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> → finding duplicate expressions in FD model...</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → optimizing duplicate expressions in FD model...</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → compiling EBE model...</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> → compiling events FD model...</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> Needed Covariates:</span> -<span class="r-out co"><span class="r-pr">#></span> [1] "CMT"</span> -<span class="r-msg co"><span class="r-pr">#></span> RxODE 1.1.4 using 8 threads (see ?getRxThreads)</span> -<span class="r-msg co"><span class="r-pr">#></span> no cache: create with `rxCreateCache()`</span> -<span class="r-out co"><span class="r-pr">#></span> <span style="font-weight: bold;">Key:</span> U: Unscaled Parameters; X: Back-transformed parameters; G: Gill difference gradient approximation</span> -<span class="r-out co"><span class="r-pr">#></span> F: Forward difference gradient approximation</span> -<span class="r-out co"><span class="r-pr">#></span> C: Central difference gradient approximation</span> -<span class="r-out co"><span class="r-pr">#></span> M: Mixed forward and central difference gradient approximation</span> -<span class="r-out co"><span class="r-pr">#></span> Unscaled parameters for Omegas=chol(solve(omega));</span> -<span class="r-out co"><span class="r-pr">#></span> Diagonals are transformed, as specified by foceiControl(diagXform=)</span> -<span class="r-out co"><span class="r-pr">#></span> |-----+---------------+-----------+-----------+-----------+-----------|</span> -<span class="r-out co"><span class="r-pr">#></span> | #| Objective Fun | DMTA_0 | log_k_M23 | log_k_M27 | log_k_M31 |</span> -<span class="r-out co"><span class="r-pr">#></span> |.....................| log_k1 | log_k2 | g_qlogis |f_DMTA_tffm0_1_qlogis |</span> -<span class="r-out co"><span class="r-pr">#></span> |.....................|f_DMTA_tffm0_2_qlogis |f_DMTA_tffm0_3_qlogis | sigma_low | rsd_high |</span> -<span class="r-out co"><span class="r-pr">#></span> |.....................| o1 | o2 | o3 | o4 |</span> -<span class="r-out co"><span class="r-pr">#></span> |.....................| o5 | o6 | o7 | o8 |</span> -<span class="r-out co"><span class="r-pr">#></span> <span style="text-decoration: underline;">|.....................| o9 | o10 |...........|...........|</span></span> -<span class="r-out co"><span class="r-pr">#></span> calculating covariance matrix</span> -<span class="r-out co"><span class="r-pr">#></span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> Calculating residuals/tables</span> -<span class="r-msg co"><span class="r-pr">#></span> done</span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))</span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>ETAs were reset to zero during optimization; (Can control by foceiControl(resetEtaP=.))</span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>last objective function was not at minimum, possible problems in optimization</span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>S matrix non-positive definite</span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>using R matrix to calculate covariance</span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>gradient problems with initial estimate and covariance; see $scaleInfo</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> 553.721 10.570 564.258 </span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmixr(f_dmta_mkin_tc, est = "focei", control = nlmixr::foceiControl(print = 500)):</span> could not find function "nlmixr"</span> +<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 0 0 0</span> <span class="r-in"><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_nlmixr_focei</span><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> nlmixr version used for fitting: 2.0.6 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Mar 2 13:27:22 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Mar 2 13:27:22 2022 </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 = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> -<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> -<span class="r-out co"><span class="r-pr">#></span> * DMTA</span> -<span class="r-out co"><span class="r-pr">#></span> d_M23/dt = + f_DMTA_to_M23 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> -<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> -<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * DMTA - k_M23 * M23</span> -<span class="r-out co"><span class="r-pr">#></span> d_M27/dt = + f_DMTA_to_M27 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> -<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> -<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * DMTA - k_M27 * M27 + k_M31 * M31</span> -<span class="r-out co"><span class="r-pr">#></span> d_M31/dt = + f_DMTA_to_M31 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> -<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> -<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * DMTA - k_M31 * M31</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> 563 observations of 4 variable(s) grouped in 6 datasets</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Degradation model predictions using RxODE</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 564.08 s</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> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 log_k_M23 log_k_M27 log_k_M31 f_DMTA_ilr_1 f_DMTA_ilr_2 </span> -<span class="r-out co"><span class="r-pr">#></span> 98.7132 -3.9216 -4.3306 -4.2442 0.1376 0.1388 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 log_k1 log_k2 g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> -1.7554 -2.2352 -3.7758 0.4363 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for error model parameters:</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> 0.70012 0.02577 </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> -<span class="r-out co"><span class="r-pr">#></span> </span> -<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 calculated by focei </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> 1857 1952 -906.5</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> DMTA_0 98.0116 95.243 100.780</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0184 -5.213 -2.824</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -4.2033 -5.013 -3.394</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -4.1728 -4.999 -3.347</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.4831 -3.398 -1.568</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.8423 -5.450 -2.235</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.4682 -2.188 3.124</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_1_qlogis -2.0823 -2.591 -1.574</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_2_qlogis -2.1265 -2.686 -1.567</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_3_qlogis -2.0795 -2.735 -1.424</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 lg__M23 lg__M27 lg__M31 log_k1 log_k2 g_qlogs</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0154 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0164 0.0031 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0131 0.0018 0.0541 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -0.0306 0.0045 0.0019 0.0011 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0527 -0.0043 -0.0037 -0.0003 0.0375 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1005 0.0076 0.0074 0.0013 0.0910 0.1151 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_1_qlogis -0.0308 0.0362 0.0024 0.0021 0.0058 -0.0070 0.0145</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_2_qlogis -0.0309 0.0062 0.0353 -0.0229 0.0047 -0.0082 0.0146</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_3_qlogis -0.0308 0.0061 0.0419 0.0547 0.0033 -0.0055 0.0104</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_0_1 f_DMTA_0_2</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_1_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_2_qlogis 0.0118 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_3_qlogis 0.0086 -0.0057 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Random effects (omega):</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 eta.log_k_M23 eta.log_k_M27 eta.log_k_M31</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 4.224 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M23 0.000 1.041 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M27 0.000 0.000 0.4609 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M31 0.000 0.000 0.0000 0.4728</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k2 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.g_qlogis 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_2_qlogis 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 eta.log_k2 eta.g_qlogis</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 0.000 0.000 0.00</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M23 0.000 0.000 0.00</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M27 0.000 0.000 0.00</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M31 0.000 0.000 0.00</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 0.635 0.000 0.00</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k2 0.000 1.662 0.00</span> -<span class="r-out co"><span class="r-pr">#></span> eta.g_qlogis 0.000 0.000 4.36</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis 0.000 0.000 0.00</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_2_qlogis 0.000 0.000 0.00</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis 0.000 0.000 0.00</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis eta.f_DMTA_tffm0_2_qlogis</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M23 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M27 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M31 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k2 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.g_qlogis 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis 0.1909 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_2_qlogis 0.0000 0.2232</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M23 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M27 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M31 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k2 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.g_qlogis 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_2_qlogis 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis 0.3149</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> sigma_low rsd_high </span> -<span class="r-out co"><span class="r-pr">#></span> 0.82408 0.03045 </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 98.01163 95.243379 100.77988</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01798 0.005443 0.05940</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.01495 0.006652 0.03358</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01541 0.006746 0.03520</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.11083 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.09474 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.08827 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.08348 0.033429 0.20848</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.02144 0.004296 0.10704</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.61496 0.100857 0.95788</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 0.11083</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.09474</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.08827</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.70616</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> DMTA 12.96 64.24 19.34 8.303 32.32</span> -<span class="r-out co"><span class="r-pr">#></span> M23 38.55 128.06 NA NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> M27 46.38 154.06 NA NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> M31 44.98 149.43 NA NA NA</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in summary(f_dmta_nlmixr_focei):</span> object 'f_dmta_nlmixr_focei' not found</span> <span class="r-in"><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_dmta_nlmixr_focei</span><span class="op">)</span></span> -<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in plot(f_dmta_nlmixr_focei):</span> object 'f_dmta_nlmixr_focei' not found</span> <span class="r-in"><span class="co"># Using saemix takes about 18 minutes</span></span> <span class="r-in"><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> <span class="r-in"> <span class="va">f_dmta_saemix</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> @@ -496,8 +194,8 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 55.3899, R2 = nan</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in out[available, var]:</span> (subscript) logical subscript too long</span> -<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 12.58 0 12.58</span> -<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 12.99 0.008 13</span> +<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 12.76 3.069 11.79</span> +<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 13.77 4.719 12.37</span> <span class="r-in"></span> <span class="r-in"><span class="co"># nlmixr with est = "saem" is pretty fast with default iteration numbers, most</span></span> <span class="r-in"><span class="co"># of the time (about 2.5 minutes) is spent for calculating the log likelihood at the end</span></span> @@ -506,203 +204,17 @@ specific pieces of information in the comments.</p> <span class="r-in"><span class="co"># convincing for the parent. It seems we are fitting an overparameterised</span></span> <span class="r-in"><span class="co"># model, so the result we get strongly depends on starting parameters and control settings.</span></span> <span class="r-in"><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> -<span class="r-in"> <span class="va">f_dmta_nlmixr_saem</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlmixr/man/nlmixr.html" class="external-link">nlmixr</a></span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span>, est <span class="op">=</span> <span class="st">"saem"</span>,</span> +<span class="r-in"> <span class="va">f_dmta_nlmixr_saem</span> <span class="op"><-</span> <span class="fu">nlmixr</span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span>, est <span class="op">=</span> <span class="st">"saem"</span>,</span> <span class="r-in"> control <span class="op">=</span> <span class="fu">nlmixr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/nlmixr/man/saemControl.html" class="external-link">saemControl</a></span><span class="op">(</span>print <span class="op">=</span> <span class="fl">500</span>, logLik <span class="op">=</span> <span class="cn">TRUE</span>, nmc <span class="op">=</span> <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> With est = 'saem', a different error model is required for each observed variableChanging the error model to 'obs_tc' (Two-component error for each observed variable)</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Need to run with the source intact to parse comments</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → generate SAEM model</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-out co"><span class="r-pr">#></span> 1: 98.7179 -3.4492 -3.2592 -3.6952 -2.1629 -2.7824 0.8990 -2.8080 -2.7380 -2.8041 2.7789 0.6848 0.8170 0.7125 0.8550 1.5200 2.9882 0.3073 0.2850 0.2877 4.0480 0.4153 4.5214 0.3775 4.4419 0.4181 3.7069 0.5935</span> -<span class="r-out co"><span class="r-pr">#></span> 500: 97.8519 -4.3891 -4.0888 -4.1247 -2.9246 -4.2755 2.6294 -2.1212 -2.1380 -2.0739 3.1293 1.2665 0.2763 0.3429 0.5743 1.5561 4.4991 0.1499 0.1551 0.3103 0.9514 0.0341 0.4846 0.1068 0.6597 0.0767 0.7836 0.0360</span> -<span class="r-msg co"><span class="r-pr">#></span> Calculating covariance matrix</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> Calculating -2LL by Gaussian quadrature (nnodes=3,nsd=1.6)</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> → creating full model...</span> -<span class="r-msg co"><span class="r-pr">#></span> → pruning branches (`if`/`else`)...</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> → loading into <span style="color: #0000BB;">symengine</span> environment...</span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> → compiling EBE model...</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">✔</span> done</span> -<span class="r-msg co"><span class="r-pr">#></span> Needed Covariates:</span> -<span class="r-out co"><span class="r-pr">#></span> [1] "CMT"</span> -<span class="r-msg co"><span class="r-pr">#></span> Calculating residuals/tables</span> -<span class="r-msg co"><span class="r-pr">#></span> done</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> 785.825 3.841 153.598 </span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmixr(f_dmta_mkin_tc, est = "saem", control = nlmixr::saemControl(print = 500, logLik = TRUE, nmc = 9)):</span> could not find function "nlmixr"</span> +<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 0 0 0.001</span> <span class="r-in"><span class="fu">traceplot</span><span class="op">(</span><span class="va">f_dmta_nlmixr_saem</span><span class="op">$</span><span class="va">nm</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in traceplot(f_dmta_nlmixr_saem$nm):</span> could not find function "traceplot"</span> <span class="r-in"><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_nlmixr_saem</span><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> nlmixr version used for fitting: 2.0.6 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Mar 2 13:30:09 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Mar 2 13:30:09 2022 </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 = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> -<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> -<span class="r-out co"><span class="r-pr">#></span> * DMTA</span> -<span class="r-out co"><span class="r-pr">#></span> d_M23/dt = + f_DMTA_to_M23 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> -<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> -<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * DMTA - k_M23 * M23</span> -<span class="r-out co"><span class="r-pr">#></span> d_M27/dt = + f_DMTA_to_M27 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> -<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> -<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * DMTA - k_M27 * M27 + k_M31 * M31</span> -<span class="r-out co"><span class="r-pr">#></span> d_M31/dt = + f_DMTA_to_M31 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> -<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> -<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * DMTA - k_M31 * M31</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> 563 observations of 4 variable(s) grouped in 6 datasets</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Degradation model predictions using RxODE</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 153.313 s</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> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 log_k_M23 log_k_M27 log_k_M31 f_DMTA_ilr_1 f_DMTA_ilr_2 </span> -<span class="r-out co"><span class="r-pr">#></span> 98.7132 -3.9216 -4.3306 -4.2442 0.1376 0.1388 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 log_k1 log_k2 g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> -1.7554 -2.2352 -3.7758 0.4363 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for error model parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low_DMTA rsd_high_DMTA sigma_low_M23 rsd_high_M23 sigma_low_M27 </span> -<span class="r-out co"><span class="r-pr">#></span> 0.70012 0.02577 0.70012 0.02577 0.70012 </span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high_M27 sigma_low_M31 rsd_high_M31 </span> -<span class="r-out co"><span class="r-pr">#></span> 0.02577 0.70012 0.02577 </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> -<span class="r-out co"><span class="r-pr">#></span> </span> -<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 calculated by focei </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> 1966 2088 -955.2</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> DMTA_0 97.852 95.86386 99.840</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.389 -5.35084 -3.427</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -4.089 -4.54432 -3.633</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -4.125 -4.63280 -3.617</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.925 -3.54158 -2.308</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.275 -5.81760 -2.733</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis 2.629 -0.01785 5.277</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_1_qlogis -2.121 -2.44462 -1.798</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_2_qlogis -2.138 -2.47804 -1.798</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_3_qlogis -2.074 -2.53581 -1.612</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 lg__M23 lg__M27 lg__M31 log_k1 log_k2 g_qlogs</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0164 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0267 0.0028 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0179 0.0023 0.0755 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 0.0385 -0.0034 -0.0054 -0.0029 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0381 0.0115 0.0087 0.0093 0.0786 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0656 0.0021 0.0051 0.0001 -0.1177 -0.4389 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_1_qlogis -0.0604 0.0554 0.0054 0.0039 -0.0082 -0.0022 0.0119</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_2_qlogis -0.0601 0.0091 0.0577 -0.0350 -0.0081 -0.0057 0.0137</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_3_qlogis -0.0515 0.0083 0.0569 0.0729 -0.0059 0.0005 0.0073</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_0_1 f_DMTA_0_2</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_1_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_2_qlogis 0.0167 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_tffm0_3_qlogis 0.0145 -0.0060 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Random effects (omega):</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 eta.log_k_M23 eta.log_k_M27 eta.log_k_M31</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 3.129 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M23 0.000 1.266 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M27 0.000 0.000 0.2763 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M31 0.000 0.000 0.0000 0.3429</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k2 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.g_qlogis 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_2_qlogis 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis 0.000 0.000 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 eta.log_k2 eta.g_qlogis</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 0.0000 0.000 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M23 0.0000 0.000 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M27 0.0000 0.000 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M31 0.0000 0.000 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 0.5743 0.000 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k2 0.0000 1.556 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.g_qlogis 0.0000 0.000 4.499</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis 0.0000 0.000 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_2_qlogis 0.0000 0.000 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis 0.0000 0.000 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis eta.f_DMTA_tffm0_2_qlogis</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M23 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M27 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M31 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k2 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.g_qlogis 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis 0.1499 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_2_qlogis 0.0000 0.1551</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis 0.0000 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis</span> -<span class="r-out co"><span class="r-pr">#></span> eta.DMTA_0 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M23 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M27 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k_M31 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k1 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.log_k2 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.g_qlogis 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_1_qlogis 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_2_qlogis 0.0000</span> -<span class="r-out co"><span class="r-pr">#></span> eta.f_DMTA_tffm0_3_qlogis 0.3103</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> sigma_low_DMTA rsd_high_DMTA sigma_low_M23 rsd_high_M23 sigma_low_M27 </span> -<span class="r-out co"><span class="r-pr">#></span> 0.95135 0.03412 0.48455 0.10682 0.65969 </span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high_M27 sigma_low_M31 rsd_high_M31 </span> -<span class="r-out co"><span class="r-pr">#></span> 0.07670 0.78365 0.03598 </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 97.85189 95.863863 99.83992</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01241 0.004744 0.03247</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.01676 0.010627 0.02643</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01617 0.009727 0.02687</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.10705 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.09417 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.08919 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.05369 0.028968 0.09950</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01391 0.002975 0.06500</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.93273 0.495538 0.99492</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 0.10705</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.09417</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.08919</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.70959</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> DMTA 13.81 49.3 14.84 12.91 49.85</span> -<span class="r-out co"><span class="r-pr">#></span> M23 55.85 185.5 NA NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> M27 41.36 137.4 NA NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> M31 42.87 142.4 NA NA NA</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in summary(f_dmta_nlmixr_saem):</span> object 'f_dmta_nlmixr_saem' not found</span> <span class="r-in"><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_dmta_nlmixr_saem</span><span class="op">)</span></span> -<span class="r-plt img"><img src="dimethenamid_2018-2.png" alt="" width="700" height="433"></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in plot(f_dmta_nlmixr_saem):</span> object 'f_dmta_nlmixr_saem' not found</span> <span class="r-in"><span class="co"># }</span></span> </code></pre></div> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 1476eed8..f764b742 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -32,7 +32,7 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax - <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -104,8 +104,8 @@ advantage that the SFORB model can also be used for metabolites.</p> <div id="arguments"> <h2>Arguments</h2> <dl><dt>fit</dt> -<dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a>, <a href="saem.html">saem.mmkin</a> or -<a href="nlmixr.mmkin.html">nlmixr.mmkin</a>. Or another object that has list components +<dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a> or <a href="saem.html">saem.mmkin</a>, +or another object that has list components mkinmod containing an <a href="mkinmod.html">mkinmod</a> degradation model, and two numeric vectors, bparms.optim and bparms.fixed, that contain parameter values for that model.</p></dd> diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 862c63e4..e87105b6 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -54,7 +54,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index 4bec2bd5..eb0e6f73 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -27,7 +27,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- mathjax <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 726f87c4..9189ef76 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -27,7 +27,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><!-- mathjax --><script <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 55d325f5..130e786a 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 5322c41e..d0cb6372 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -27,7 +27,7 @@ transformations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/index.html b/docs/reference/index.html index 552829bf..90387a56 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -180,10 +180,6 @@ of an mmkin object</p></td> </td> <td><p>Fit nonlinear mixed models with SAEM</p></td> </tr><tr><td> - <p><code><a href="nlmixr.mmkin.html">nlmixr(<i><mmkin></i>)</a></code> <code><a href="nlmixr.mmkin.html">print(<i><nlmixr.mmkin></i>)</a></code> <code><a href="nlmixr.mmkin.html">nlmixr_model()</a></code> <code><a href="nlmixr.mmkin.html">nlmixr_data()</a></code> </p> - </td> - <td><p>Fit nonlinear mixed models using nlmixr</p></td> - </tr><tr><td> <p><code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></i>)</a></code> </p> </td> <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td> @@ -192,10 +188,6 @@ of an mmkin object</p></td> </td> <td><p>Summary method for class "nlme.mmkin"</p></td> </tr><tr><td> - <p><code><a href="summary.nlmixr.mmkin.html">summary(<i><nlmixr.mmkin></i>)</a></code> <code><a href="summary.nlmixr.mmkin.html">print(<i><summary.nlmixr.mmkin></i>)</a></code> </p> - </td> - <td><p>Summary method for class "nlmixr.mmkin"</p></td> - </tr><tr><td> <p><code><a href="summary.saem.mmkin.html">summary(<i><saem.mmkin></i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i><summary.saem.mmkin></i>)</a></code> </p> </td> <td><p>Summary method for class "saem.mmkin"</p></td> @@ -219,10 +211,6 @@ of an mmkin object</p></td> <p><code><a href="intervals.saem.mmkin.html">intervals(<i><saem.mmkin></i>)</a></code> </p> </td> <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td> - </tr><tr><td> - <p><code><a href="intervals.nlmixr.mmkin.html">intervals(<i><nlmixr.mmkin></i>)</a></code> </p> - </td> - <td><p>Confidence intervals for parameters in nlmixr.mmkin objects</p></td> </tr></tbody><tbody><tr><th colspan="2"> <h2 id="datasets-and-known-results">Datasets and known results <a href="#datasets-and-known-results" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> @@ -345,10 +333,6 @@ kinetic models fitted with mkinfit</p></td> </td> <td><p>Function to perform isometric log-ratio transformation</p></td> </tr><tr><td> - <p><code><a href="tffm0.html">tffm0()</a></code> <code><a href="tffm0.html">invtffm0()</a></code> </p> - </td> - <td><p>Transform formation fractions as in the first published mkin version</p></td> - </tr><tr><td> <p><code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> </p> </td> <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td> diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index d2eb31de..ddc565b3 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index 75578cbe..a96e6932 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -29,7 +29,7 @@ lrtest.default from the lmtest package."><!-- mathjax --><script src="https://cd <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index dc1bfbba..c41950a3 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -30,7 +30,7 @@ the error model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 5c3c2b42..ed6e29dc 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -27,7 +27,7 @@ an increasing rate constant, supposedly caused by microbial growth"><!-- mathjax <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index d4355c43..6adc1245 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -30,7 +30,7 @@ and can be expressed by fixing the parameters of the other."><!-- mathjax --><sc <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 03b0263d..29b17d1a 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -32,7 +32,7 @@ soil section of the FOCUS guidance."><!-- mathjax --><script src="https://cdnjs. <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 94cd1450..9b698e64 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -28,7 +28,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index c31e310c..aaeb44ea 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index dc0d1681..af73f22a 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index be37f095..ed0abedd 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -28,7 +28,7 @@ variable and several dependent variables as columns."><!-- mathjax --><script sr <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 06bea7e7..37c84761 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -28,7 +28,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 25edbf38..73a14840 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -29,7 +29,7 @@ provided by this package come as mkinds objects nevertheless."><!-- mathjax -->< <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index bae7488f..7f4ff290 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -29,7 +29,7 @@ dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.clo <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index b72017fe..dc2cdab8 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -27,7 +27,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."><!-- ma <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 5dc188fe..95206b61 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -30,7 +30,7 @@ using the argument show_errplot = TRUE."><!-- mathjax --><script src="https://cd <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index a0644947..c006ddab 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -34,7 +34,7 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -331,15 +331,15 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"><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 class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Mar 2 13:30:39 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Mar 2 13:30:39 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:11:56 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:11:56 2022 </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> <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 222 model solutions performed in 0.046 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.045 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> @@ -480,9 +480,9 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"><span class="op">}</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 0.699</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.595 1.115</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.252 1.574</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.573</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.642 0.941</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.517 1.442</span> <span class="r-in"><span class="co"># }</span></span> <span class="r-in"></span> <span class="r-in"><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span> @@ -508,8 +508,8 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"><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.FOMC_SFO.tc</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Mar 2 13:30:53 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Mar 2 13:30:53 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:12:07 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:12:07 2022 </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> @@ -518,7 +518,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <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 2.916 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.67 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> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index a5cc3d7a..72a9ea52 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -30,7 +30,7 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -267,7 +267,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span> <span class="r-in"> 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 class="r-in"> 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 class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpNObdrK/filecabc85d9446.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/Rtmp1TiIZY/file1180516cafe4a2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span class="co"># Now we can save the model and restore it in a new session</span></span> <span class="r-in"><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 class="r-in"><span class="co"># Terminate the R session here if you would like to check, and then do</span></span> @@ -319,7 +319,7 @@ 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: 0x5555673b8fd0></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f6c4cd8></span> <span class="r-in"></span> <span class="r-in"><span class="co"># If we have several parallel metabolites</span></span> <span class="r-in"><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 2d7f6228..2e787240 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -27,7 +27,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 896c30a0..79599787 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -27,7 +27,7 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index b52d9ece..c197e6dc 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -28,7 +28,7 @@ kinetic parameters and initial values for the state variables."><!-- mathjax --> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -337,10 +337,10 @@ as these always return mapped output.</p></dd> <span class="r-in"> 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 class="r-in"><span class="op">}</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> 4 analytical 1.0 0.005</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.2 0.006</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.2 0.021</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 40.8 0.204</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.00 0.004</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.50 0.006</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 5.25 0.021</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 52.00 0.208</span> <span class="r-in"></span> <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"> <span class="co"># Predict from a fitted model</span></span> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 54d612ef..cd3b4009 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -29,7 +29,7 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 4012df67..1ca0190a 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -29,7 +29,7 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -167,10 +167,10 @@ plotting.</p></div> <span class="r-in"></span> <span class="r-in"><span class="va">time_default</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> 6.055 1.405 2.191 </span> +<span class="r-out co"><span class="r-pr">#></span> 4.710 0.665 1.757 </span> <span class="r-in"><span class="va">time_1</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> 6.746 0.004 6.750 </span> +<span class="r-out co"><span class="r-pr">#></span> 5.644 0.001 5.645 </span> <span class="r-in"></span> <span class="r-in"><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 class="r-out co"><span class="r-pr">#></span> $ff</span> diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 28e44864..0711886a 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -30,7 +30,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><! <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 5eebecaa..746cc6aa 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -29,7 +29,7 @@ datasets. They are used internally by the nlme.mmkin() method."><!-- mathjax --> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 56770856..4b59afed 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -28,7 +28,7 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index 0fc1ca7c..34da24d9 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 00726a1d..1ddd3eb9 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -28,7 +28,7 @@ considering the error structure that was assumed for the fit."><!-- mathjax -->< <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png Binary files differnew file mode 100644 index 00000000..0840c7da --- /dev/null +++ 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 differnew file mode 100644 index 00000000..a78087bb --- /dev/null +++ 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 da382eb9..b405b84a 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -197,9 +197,8 @@ corresponding model prediction lines for the different datasets.</p></dd> <span class="r-plt img"><img src="plot.mixed.mmkin-2.png" alt="" width="700" height="433"></span> <span class="r-in"></span> <span class="r-in"><span class="va">f_saem</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in saem(f, transformations = "saemix"):</span> unused argument (transformations = "saemix")</span> <span class="r-in"><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_saem</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in plot(f_saem):</span> object 'f_saem' not found</span> +<span class="r-plt img"><img src="plot.mixed.mmkin-3.png" alt="" width="700" height="433"></span> <span class="r-in"></span> <span class="r-in"><span class="va">f_obs</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/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span> <span class="r-in"><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> @@ -213,7 +212,7 @@ corresponding model prediction lines for the different datasets.</p></dd> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="va">f_nlme</span><span class="op">$</span><span class="va">bparms.optim</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, A1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">180</span>, by <span class="op">=</span> <span class="fl">0.2</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"><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_saem</span>, pred_over <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>nlme <span class="op">=</span> <span class="va">pred_nlme</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in plot(f_saem, pred_over = list(nlme = pred_nlme)):</span> object 'f_saem' not found</span> +<span class="r-plt img"><img src="plot.mixed.mmkin-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="co"># }</span></span> </code></pre></div> </div> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 0ad6ffc0..4c2ff570 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -28,7 +28,7 @@ observed data together with the solution of the fitted model."><!-- mathjax -->< <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 0994c4b6..d7ad89dc 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -30,7 +30,7 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index d3407a24..a14ed303 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -27,7 +27,7 @@ function (SFO, then IORE, then DFOP)."><!-- mathjax --><script src="https://cdnj <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 22180913..1367ccf5 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -10,10 +10,6 @@ lrtest intervals, nlme - nlmixr -nlmixr - - "><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> @@ -41,7 +37,7 @@ nlmixr <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -93,7 +89,7 @@ nlmixr <div class="col-md-9 contents"> <div class="page-header"> <h1>Objects exported from other packages</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/intervals.R" class="external-link"><code>R/intervals.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/lrtest.mkinfit.R" class="external-link"><code>R/lrtest.mkinfit.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.mmkin.R" class="external-link"><code>R/nlme.mmkin.R</code></a>, and 1 more</small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/intervals.R" class="external-link"><code>R/intervals.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/lrtest.mkinfit.R" class="external-link"><code>R/lrtest.mkinfit.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.mmkin.R" class="external-link"><code>R/nlme.mmkin.R</code></a></small> <div class="hidden name"><code>reexports.Rd</code></div> </div> @@ -108,10 +104,6 @@ below to see their documentation.</p> <dd><p><code><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></code>, <code><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></code></p></dd> - <dt>nlmixr</dt> -<dd><p><code><a href="https://rdrr.io/pkg/nlmixr/man/nlmixr.html" class="external-link">nlmixr</a></code></p></dd> - - </dl></div> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index 19e077c5..c27cea76 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/saem-1.png b/docs/reference/saem-1.png Binary files differnew file mode 100644 index 00000000..08939d4f --- /dev/null +++ b/docs/reference/saem-1.png diff --git a/docs/reference/saem-2.png b/docs/reference/saem-2.png Binary files differnew file mode 100644 index 00000000..b737db03 --- /dev/null +++ b/docs/reference/saem-2.png diff --git a/docs/reference/saem-3.png b/docs/reference/saem-3.png Binary files differnew file mode 100644 index 00000000..99f2a2d6 --- /dev/null +++ b/docs/reference/saem-3.png diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png Binary files differnew file mode 100644 index 00000000..5f65ba2e --- /dev/null +++ b/docs/reference/saem-4.png diff --git a/docs/reference/saem.html b/docs/reference/saem.html index 8b86b5a2..cc597665 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -28,7 +28,7 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -203,29 +203,16 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span class="va">f_mmkin_parent_p0_fixed</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">ds</span>,</span> <span class="r-in"> state.ini <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>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, fixed_initials <span class="op">=</span> <span class="st">"parent"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_saem_p0_fixed</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_p0_fixed</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"></span> <span class="r-in"><span class="va">f_mmkin_parent</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 class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_saem_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="va">f_saem_fomc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="va">f_saem_dfop</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"></span> <span class="r-in"><span class="co"># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span></span> <span class="r-in"><span class="co"># functions from saemix</span></span> <span class="r-in"><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">saemix</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: npde</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘npde’</span> -<span class="r-msg co"><span class="r-pr">#></span> The following object is masked from ‘package:nlmixr’:</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> warfarin</span> <span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.0</span> <span class="r-msg co"><span class="r-pr">#></span> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span> <span class="r-msg co"><span class="r-pr">#></span> </span> @@ -233,26 +220,30 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-msg co"><span class="r-pr">#></span> The following objects are masked from ‘package:npde’:</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> kurtosis, skewness</span> -<span class="r-msg co"><span class="r-pr">#></span> The following object is masked from ‘package:RxODE’:</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> phi</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_sfo</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_dfop</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in compare.saemix(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so):</span> object 'f_saem_sfo' not found</span> +<span class="r-msg co"><span class="r-pr">#></span> Likelihoods calculated by importance sampling</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC</span> +<span class="r-out co"><span class="r-pr">#></span> 1 624.2598 622.3070</span> +<span class="r-out co"><span class="r-pr">#></span> 2 467.8664 465.1324</span> +<span class="r-out co"><span class="r-pr">#></span> 3 493.9811 490.4660</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> +<span class="r-plt img"><img src="saem-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"individual.fit"</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> +<span class="r-plt img"><img src="saem-2.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"npde"</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> +<span class="r-out co"><span class="r-pr">#></span> Simulating data using nsim = 1000 simulated datasets</span> +<span class="r-out co"><span class="r-pr">#></span> Computing WRES and npde .</span> +<span class="r-msg co"><span class="r-pr">#></span> Please use npdeSaemix to obtain VPC and npde</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"vpc"</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> +<span class="r-plt img"><img src="saem-3.png" alt="" width="700" height="433"></span> <span class="r-in"></span> <span class="r-in"><span class="va">f_mmkin_parent_tc</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_mmkin_parent</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_saem_fomc_tc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_tc</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in compare.saemix(f_saem_fomc$so, f_saem_fomc_tc$so):</span> object 'f_saem_fomc' not found</span> +<span class="r-msg co"><span class="r-pr">#></span> Likelihoods calculated by importance sampling</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC</span> +<span class="r-out co"><span class="r-pr">#></span> 1 467.8664 465.1324</span> +<span class="r-out co"><span class="r-pr">#></span> 2 469.9096 466.7851</span> <span class="r-in"></span> <span class="r-in"><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 class="r-in"> 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> @@ -273,18 +264,303 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span class="co"># When using the analytical solutions written for mkin this took around</span></span> <span class="r-in"><span class="co"># four minutes</span></span> <span class="r-in"><span class="va">f_saem_sfo_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="va">f_saem_dfop_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="co"># We can use print, plot and summary methods to check the results</span></span> <span class="r-in"><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_saem_dfop_sfo</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'print': object 'f_saem_dfop_sfo' not found</span> +<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by SAEM</span> +<span class="r-out co"><span class="r-pr">#></span> Structural model:</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> +<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> +<span class="r-out co"><span class="r-pr">#></span> * parent</span> +<span class="r-out co"><span class="r-pr">#></span> d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> +<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> +<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * parent - k_A1 * A1</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> 170 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> 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> 842 836.9 -408</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 93.7701 91.1458 96.3945</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.8116 -7.5998 -4.0234</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.8856 1.6676 2.1037</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_dfop_sfo' not found</span> +<span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><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 class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'object' in selecting a method for function 'summary': object 'f_saem_dfop_sfo' not found</span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:26 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:26 2022 </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> +<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> +<span class="r-out co"><span class="r-pr">#></span> * parent</span> +<span class="r-out co"><span class="r-pr">#></span> d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> +<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> +<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * parent - k_A1 * A1</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> 170 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> 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 8.741 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> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 </span> +<span class="r-out co"><span class="r-pr">#></span> 93.8102 -5.3734 -0.9711 -1.8799 -4.2708 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> +<span class="r-out co"><span class="r-pr">#></span> 0.1356 </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> +<span class="r-out co"><span class="r-pr">#></span> </span> +<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> 842 836.9 -408</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 93.7701 91.1458 96.3945</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.8116 -7.5998 -4.0234</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</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_A1 f_prnt_ log_k1 log_k2 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -0.0160 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.0263 0.0612 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.0100 -0.0014 -0.0033 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0131 0.0050 -0.0011 0.0071 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0419 -0.0199 0.0026 -0.0765 -0.0707</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.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</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 1.886 1.668 2.104</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 93.770115 9.115e+01 96.39447</span> +<span class="r-out co"><span class="r-pr">#></span> k_A1 0.002993 5.005e-04 0.01789</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_A1 0.276720 2.034e-01 0.36443</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.075467 2.503e-02 0.22753</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.029516 4.867e-03 0.17902</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.474353 2.949e-01 0.66073</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_A1 0.2767</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7233</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 14.56 58.26 17.54 9.185 23.48</span> +<span class="r-out co"><span class="r-pr">#></span> A1 231.62 769.41 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> Dataset 6 parent 0 97.2 95.78623 1.41377 1.886 0.749758</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 0 96.4 95.78623 0.61377 1.886 0.325498</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 3 71.1 71.34666 -0.24666 1.886 -0.130812</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 3 69.2 71.34666 -2.14666 1.886 -1.138429</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 6 58.1 56.49768 1.60232 1.886 0.849749</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 6 56.6 56.49768 0.10232 1.886 0.054262</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 10 44.4 44.53511 -0.13511 1.886 -0.071650</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 10 43.4 44.53511 -1.13511 1.886 -0.601974</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 20 33.3 29.77451 3.52549 1.886 1.869656</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 20 29.2 29.77451 -0.57451 1.886 -0.304675</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 34 17.6 19.32540 -1.72540 1.886 -0.915023</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 34 18.0 19.32540 -1.32540 1.886 -0.702894</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 55 10.5 10.42781 0.07219 1.886 0.038282</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 55 9.3 10.42781 -1.12781 1.886 -0.598107</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 90 4.5 3.74190 0.75810 1.886 0.402037</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 90 4.7 3.74190 0.95810 1.886 0.508102</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 112 3.0 1.96485 1.03515 1.886 0.548966</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 112 3.4 1.96485 1.43515 1.886 0.761096</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 132 2.3 1.09395 1.20605 1.886 0.639596</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 132 2.7 1.09395 1.60605 1.886 0.851726</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 3 4.3 4.72702 -0.42702 1.886 -0.226458</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 3 4.6 4.72702 -0.12702 1.886 -0.067361</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 6 7.0 7.51314 -0.51314 1.886 -0.272128</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 6 7.2 7.51314 -0.31314 1.886 -0.166063</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 10 8.2 9.63719 -1.43719 1.886 -0.762179</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 10 8.0 9.63719 -1.63719 1.886 -0.868244</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 20 11.0 11.84931 -0.84931 1.886 -0.450409</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 20 13.7 11.84931 1.85069 1.886 0.981468</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 34 11.5 12.82336 -1.32336 1.886 -0.701808</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 34 12.7 12.82336 -0.12336 1.886 -0.065418</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 55 14.9 12.89456 2.00544 1.886 1.063533</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 55 14.5 12.89456 1.60544 1.886 0.851403</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 90 12.1 11.55919 0.54081 1.886 0.286806</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 90 12.3 11.55919 0.74081 1.886 0.392871</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 112 9.9 10.42334 -0.52334 1.886 -0.277539</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 112 10.2 10.42334 -0.22334 1.886 -0.118442</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 132 8.8 9.37987 -0.57987 1.886 -0.307519</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 132 7.8 9.37987 -1.57987 1.886 -0.837844</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 0 93.6 90.95702 2.64298 1.886 1.401639</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 0 92.3 90.95702 1.34298 1.886 0.712217</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 3 87.0 84.77506 2.22494 1.886 1.179942</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 3 82.2 84.77506 -2.57506 1.886 -1.365616</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 7 74.0 77.60962 -3.60962 1.886 -1.914268</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 7 73.9 77.60962 -3.70962 1.886 -1.967301</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 14 64.2 67.50646 -3.30646 1.886 -1.753499</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 14 69.5 67.50646 1.99354 1.886 1.057221</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 30 54.0 52.48909 1.51091 1.886 0.801271</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 30 54.6 52.48909 2.11091 1.886 1.119465</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 60 41.1 39.54372 1.55628 1.886 0.825335</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 60 38.4 39.54372 -1.14372 1.886 -0.606542</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 90 32.5 33.87968 -1.37968 1.886 -0.731676</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 90 35.5 33.87968 1.62032 1.886 0.859298</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 120 28.1 30.41071 -2.31071 1.886 -1.225427</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 120 29.0 30.41071 -1.41071 1.886 -0.748135</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 180 26.5 25.36386 1.13614 1.886 0.602524</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 180 27.6 25.36386 2.23614 1.886 1.185881</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 3 3.9 2.74863 1.15137 1.886 0.610600</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 3 3.1 2.74863 0.35137 1.886 0.186341</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 7 6.9 5.92686 0.97314 1.886 0.516081</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 7 6.6 5.92686 0.67314 1.886 0.356983</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 14 10.4 10.38800 0.01200 1.886 0.006362</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 14 8.3 10.38800 -2.08800 1.886 -1.107320</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 30 14.4 16.93529 -2.53529 1.886 -1.344524</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 30 13.7 16.93529 -3.23529 1.886 -1.715751</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 60 22.1 22.33044 -0.23044 1.886 -0.122209</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 60 22.3 22.33044 -0.03044 1.886 -0.016144</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 90 27.5 24.42300 3.07700 1.886 1.631809</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 90 25.4 24.42300 0.97700 1.886 0.518127</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 120 28.0 25.51140 2.48860 1.886 1.319768</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 120 26.6 25.51140 1.08860 1.886 0.577313</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 180 25.8 26.80282 -1.00282 1.886 -0.531818</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 180 25.3 26.80282 -1.50282 1.886 -0.796981</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 0 91.9 91.08733 0.81267 1.886 0.430980</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 0 90.8 91.08733 -0.28733 1.886 -0.152377</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 1 64.9 67.55332 -2.65332 1.886 -1.407123</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 1 66.2 67.55332 -1.35332 1.886 -0.717701</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 3 43.5 41.65811 1.84189 1.886 0.976800</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 3 44.1 41.65811 2.44189 1.886 1.294994</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 8 18.3 19.65773 -1.35773 1.886 -0.720038</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 8 18.1 19.65773 -1.55773 1.886 -0.826103</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 14 10.2 10.65118 -0.45118 1.886 -0.239269</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 14 10.8 10.65118 0.14882 1.886 0.078925</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 27 4.9 3.11694 1.78306 1.886 0.945601</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 27 3.3 3.11694 0.18306 1.886 0.097082</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 48 1.6 0.43165 1.16835 1.886 0.619603</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 48 1.5 0.43165 1.06835 1.886 0.566570</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 70 1.1 0.05441 1.04559 1.886 0.554503</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 70 0.9 0.05441 0.84559 1.886 0.448438</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 1 9.6 7.66431 1.93569 1.886 1.026546</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 1 7.7 7.66431 0.03569 1.886 0.018930</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 3 15.0 15.57948 -0.57948 1.886 -0.307311</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 3 15.1 15.57948 -0.47948 1.886 -0.254279</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 8 21.2 20.38988 0.81012 1.886 0.429625</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 8 21.1 20.38988 0.71012 1.886 0.376593</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 14 19.7 20.16439 -0.46439 1.886 -0.246276</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 14 18.9 20.16439 -1.26439 1.886 -0.670535</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 27 17.5 16.40918 1.09082 1.886 0.578489</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 27 15.9 16.40918 -0.50918 1.886 -0.270030</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 48 9.5 10.12011 -0.62011 1.886 -0.328861</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 48 9.8 10.12011 -0.32011 1.886 -0.169764</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 70 6.2 5.79080 0.40920 1.886 0.217011</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 70 6.1 5.79080 0.30920 1.886 0.163979</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 0 99.8 97.38786 2.41214 1.886 1.279218</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 0 98.3 97.38786 0.91214 1.886 0.483731</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 1 77.1 79.25431 -2.15431 1.886 -1.142481</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 1 77.2 79.25431 -2.05431 1.886 -1.089449</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 3 59.0 55.69866 3.30134 1.886 1.750781</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 3 58.1 55.69866 2.40134 1.886 1.273489</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 8 27.4 31.64893 -4.24893 1.886 -2.253314</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 8 29.2 31.64893 -2.44893 1.886 -1.298729</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 14 19.1 22.57316 -3.47316 1.886 -1.841901</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 14 29.6 22.57316 7.02684 1.886 3.726507</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 27 10.1 14.11345 -4.01345 1.886 -2.128430</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 27 18.2 14.11345 4.08655 1.886 2.167199</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 48 4.5 6.95586 -2.45586 1.886 -1.302400</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 48 9.1 6.95586 2.14414 1.886 1.137093</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 70 2.3 3.31753 -1.01753 1.886 -0.539619</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 70 2.9 3.31753 -0.41753 1.886 -0.221424</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 91 2.0 1.63642 0.36358 1.886 0.192816</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 91 1.8 1.63642 0.16358 1.886 0.086751</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 120 2.0 0.61667 1.38333 1.886 0.733614</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 120 2.2 0.61667 1.58333 1.886 0.839679</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 1 4.2 3.67247 0.52753 1.886 0.279763</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 1 3.9 3.67247 0.22753 1.886 0.120666</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 3 7.4 8.36240 -0.96240 1.886 -0.510385</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 3 7.9 8.36240 -0.46240 1.886 -0.245223</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 8 14.5 12.80590 1.69410 1.886 0.898422</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 8 13.7 12.80590 0.89410 1.886 0.474162</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 14 14.2 13.99625 0.20375 1.886 0.108053</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 14 12.2 13.99625 -1.79625 1.886 -0.952596</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 27 13.7 14.22730 -0.52730 1.886 -0.279641</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 27 13.2 14.22730 -1.02730 1.886 -0.544803</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 48 13.6 13.33713 0.26287 1.886 0.139406</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 48 15.4 13.33713 2.06287 1.886 1.093991</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 70 10.4 11.84008 -1.44008 1.886 -0.763708</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 70 11.6 11.84008 -0.24008 1.886 -0.127318</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 91 10.0 10.30732 -0.30732 1.886 -0.162980</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 91 9.5 10.30732 -0.80732 1.886 -0.428142</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 120 9.1 8.33981 0.76019 1.886 0.403149</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 120 9.0 8.33981 0.66019 1.886 0.350117</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 0 96.1 93.70349 2.39651 1.886 1.270926</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 0 94.3 93.70349 0.59651 1.886 0.316342</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 8 73.9 77.86253 -3.96253 1.886 -2.101429</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 8 73.9 77.86253 -3.96253 1.886 -2.101429</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 14 69.4 70.18665 -0.78665 1.886 -0.417182</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 14 73.1 70.18665 2.91335 1.886 1.545019</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 21 65.6 64.03245 1.56755 1.886 0.831308</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 21 65.3 64.03245 1.26755 1.886 0.672210</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 41 55.9 54.71491 1.18509 1.886 0.628480</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 41 54.4 54.71491 -0.31491 1.886 -0.167007</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 63 47.0 49.63436 -2.63436 1.886 -1.397065</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 63 49.3 49.63436 -0.33436 1.886 -0.177319</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 91 44.7 45.08853 -0.38853 1.886 -0.206049</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 91 46.7 45.08853 1.61147 1.886 0.854600</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 120 42.1 41.07653 1.02347 1.886 0.542772</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 120 41.3 41.07653 0.22347 1.886 0.118513</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 8 3.3 4.08295 -0.78295 1.886 -0.415218</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 8 3.4 4.08295 -0.68295 1.886 -0.362186</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 14 3.9 6.04367 -2.14367 1.886 -1.136841</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 14 2.9 6.04367 -3.14367 1.886 -1.667165</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 6.4 7.59693 -1.19693 1.886 -0.634761</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 7.2 7.59693 -0.39693 1.886 -0.210502</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 9.1 9.86436 -0.76436 1.886 -0.405361</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 8.5 9.86436 -1.36436 1.886 -0.723555</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 11.7 10.99397 0.70603 1.886 0.374425</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 12.0 10.99397 1.00603 1.886 0.533522</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.3 11.91274 1.38726 1.886 0.735696</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.2 11.91274 1.28726 1.886 0.682663</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 14.3 12.66519 1.63481 1.886 0.866981</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 12.1 12.66519 -0.56519 1.886 -0.299733</span> <span class="r-in"></span> <span class="r-in"><span class="co"># The following takes about 6 minutes</span></span> <span class="r-in"><span class="co">#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 8c39ca1b..e1032453 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -28,7 +28,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 63e23326..7fef34e4 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -27,7 +27,7 @@ dependence of the measured value \(y\):"><!-- mathjax --><script src="https://cd <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index b4d25f4f..f01d1048 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -30,7 +30,7 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -180,15 +180,15 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-in"> <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="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Mar 2 13:42:12 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Mar 2 13:42:12 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:30 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:30 2022 </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 0.029 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.028 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.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 2bc50dac..d2ed2a86 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -30,7 +30,7 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -201,8 +201,8 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.155 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Mar 2 13:42:16 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Mar 2 13:42:16 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:33 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:33 2022 </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> @@ -212,7 +212,7 @@ 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 0.545 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.528 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> diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index 2fe81023..26ece42d 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -30,7 +30,7 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -196,10 +196,269 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-in"><span class="va">f_mmkin_dfop_sfo</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/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds_syn_dfop_sfo</span>,</span> <span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">5</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_saem_dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin_dfop_sfo</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><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 class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'object' in selecting a method for function 'summary': object 'f_saem_dfop_sfo' not found</span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:47 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:47 2022 </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> +<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> +<span class="r-out co"><span class="r-pr">#></span> * parent</span> +<span class="r-out co"><span class="r-pr">#></span> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> +<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> +<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * parent - k_m1 * m1</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> 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> 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 12.164 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> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual 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> 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> </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> +<span class="r-out co"><span class="r-pr">#></span> </span> +<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> 828.1 822.7 -400.1</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_0 100.74378 97.813 103.6747</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06168 -4.171 -3.9523</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.92584 -1.313 -0.5389</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.81914 -3.602 -2.0362</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.63916 -4.327 -2.9516</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02927 -1.152 1.0939</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 -0.3571 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2190 0.2189 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1248 -0.1042 -0.0514 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0130 0.0043 -0.0049 0.0883 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0643 0.0437 0.0354 -0.3477 -0.2589</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.parent_0 0.73313 -7.46512 8.9314</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.06488 -0.06041 0.1902</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.41955 0.15206 0.6870</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.81750 0.29140 1.3436</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.75265 0.27939 1.2259</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.34411 -1.70964 2.3979</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 0.86164 0.67928 1.04400</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07973 0.06437 0.09509</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_0 100.74378 97.81291 103.67465</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01722 0.01544 0.01921</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28377 0.21203 0.36843</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.05966 0.02727 0.13052</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.02627 0.01321 0.05226</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.49268 0.24004 0.74912</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 0.2838</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7162</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 17.17 65.72 19.78 11.62 26.38</span> +<span class="r-out co"><span class="r-pr">#></span> m1 40.25 133.71 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 1.005e+02 -1.069e+01 8.0584 -1.327e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.005e+02 3.607e+00 8.0584 4.476e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.580e+01 -7.103e+00 7.6867 -9.241e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.580e+01 -3.030e-01 7.6867 -3.942e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.722e+01 -5.418e+00 7.0070 -7.733e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.722e+01 7.282e+00 7.0070 1.039e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.278e+01 -1.282e+00 5.8665 -2.186e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.278e+01 -2.482e+00 5.8665 -4.231e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.418e+01 2.128e-02 4.4047 4.831e-03</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.418e+01 -4.579e+00 4.4047 -1.040e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.235e+01 -8.510e-01 2.7194 -3.129e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.235e+01 -3.551e+00 2.7194 -1.306e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.282e+01 -7.213e-01 1.3369 -5.395e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.282e+01 7.787e-01 1.3369 5.825e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.184e+00 1.593e-02 0.9927 1.605e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.184e+00 2.116e+00 0.9927 2.131e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.092e+00 -8.915e-01 0.8962 -9.948e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.092e+00 -6.915e-01 0.8962 -7.716e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.147e+00 -8.468e-01 0.8665 -9.773e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.147e+00 -9.468e-01 0.8665 -1.093e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.190e+00 -9.901e-01 0.8984 -1.102e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.190e+00 -1.901e-01 0.8984 -2.116e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.422e+00 7.828e-02 1.0023 7.811e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.422e+00 -1.422e+00 1.0023 -1.418e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.002e+01 1.782e-01 1.1751 1.517e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.002e+01 -5.218e-01 1.1751 -4.440e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.265e+01 -4.548e-01 1.3268 -3.428e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.265e+01 7.452e-01 1.3268 5.617e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.093e+01 8.735e-01 1.2253 7.129e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.093e+01 2.273e+00 1.2253 1.855e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.845e+00 -1.245e+00 1.0647 -1.170e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.845e+00 1.455e+00 1.0647 1.366e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.322e+00 -1.822e+00 0.9605 -1.897e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.322e+00 7.779e-02 0.9605 8.099e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.008e+02 1.724e+01 8.0794 2.134e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.008e+02 -9.578e-01 8.0794 -1.185e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.538e+01 -5.183e+00 7.6535 -6.773e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.538e+01 -7.834e-01 7.6535 -1.024e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.604e+01 1.006e+01 6.9134 1.456e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.604e+01 -7.635e+00 6.9134 -1.104e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.170e+01 6.196e+00 5.7814 1.072e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.170e+01 5.996e+00 5.7814 1.037e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.556e+01 4.370e-01 4.5130 9.683e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.556e+01 -8.630e-01 4.5130 -1.912e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.869e+01 -2.085e+00 3.2024 -6.512e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.869e+01 -1.885e+00 3.2024 -5.888e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.103e+01 1.072e+00 1.8850 5.688e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.103e+01 3.672e+00 1.8850 1.948e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.231e+01 8.760e-02 1.3062 6.707e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.231e+01 -1.512e+00 1.3062 -1.158e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.222e+00 -4.220e-01 1.0363 -4.072e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.222e+00 6.780e-01 1.0363 6.542e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.431e+00 -1.313e-01 0.8692 -1.510e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.849e+00 -1.486e-01 0.9146 -1.624e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.849e+00 8.514e-01 0.9146 9.309e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.298e+00 8.021e-01 1.0397 7.715e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.298e+00 6.021e-01 1.0397 5.791e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.051e+01 -4.109e-01 1.2020 -3.418e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.051e+01 -2.109e-01 1.2020 -1.755e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.218e+01 -1.476e+00 1.2980 -1.137e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.218e+01 2.421e-02 1.2980 1.865e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.043e+01 2.682e-01 1.1976 2.240e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.043e+01 2.068e+00 1.1976 1.727e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 7.931e+00 1.169e+00 1.0688 1.094e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 7.931e+00 -5.310e-01 1.0688 -4.969e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.717e+00 3.829e-01 0.9748 3.928e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.717e+00 -1.217e+00 0.9748 -1.249e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.010e+02 5.220e+00 8.0970 6.447e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.010e+02 5.920e+00 8.0970 7.312e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.352e+01 1.388e+01 7.5058 1.849e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.352e+01 2.581e+00 7.5058 3.439e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.127e+01 -1.866e+00 6.5363 -2.855e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.127e+01 1.334e+00 6.5363 2.041e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.441e+01 -5.112e-01 5.2072 -9.818e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.441e+01 -2.011e+00 5.2072 -3.862e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.843e+01 2.573e+00 3.9560 6.505e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.843e+01 -1.327e+00 3.9560 -3.353e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.447e+01 1.631e+00 2.8801 5.664e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.447e+01 2.131e+00 2.8801 7.400e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.974e+01 3.570e-01 1.7945 1.989e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.974e+01 5.700e-02 1.7945 3.176e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.193e+01 -6.276e-01 1.2833 -4.891e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.193e+01 -1.228e+00 1.2833 -9.567e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.208e+00 9.920e-01 1.0357 9.578e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.208e+00 9.200e-02 1.0357 8.883e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 -6.821e-13 8.000e-01 0.8616 9.285e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.796e+00 4.189e-03 0.8735 4.795e-03</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.796e+00 5.042e-01 0.8735 5.772e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.656e+00 -4.556e-01 0.9382 -4.856e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.656e+00 -5.556e-01 0.9382 -5.922e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.280e+00 -1.480e+00 1.0854 -1.363e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.280e+00 1.820e+00 1.0854 1.677e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.094e+01 4.571e-01 1.2262 3.728e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.094e+01 1.857e+00 1.2262 1.515e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.150e+01 1.650e-05 1.2582 1.311e-05</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.150e+01 -9.000e-01 1.2582 -7.153e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.187e+00 -1.687e+00 1.1309 -1.492e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.187e+00 -5.875e-01 1.1309 -5.194e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 6.854e+00 4.461e-01 1.0203 4.372e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 6.854e+00 1.246e+00 1.0203 1.221e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 4.908e+00 3.917e-01 0.9463 4.139e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 4.908e+00 -1.108e+00 0.9463 -1.171e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.006e+02 4.116e+00 8.0656 5.104e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.006e+02 -1.228e+01 8.0656 -1.523e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.733e+01 -3.133e+00 7.8079 -4.012e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.733e+01 -2.733e+00 7.8079 -3.500e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.122e+01 -1.312e+01 7.3237 -1.791e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 96.5 9.122e+01 5.280e+00 7.3237 7.209e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 76.2 8.039e+01 -4.193e+00 6.4673 -6.484e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 77.8 8.039e+01 -2.593e+00 6.4673 -4.010e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 70.8 6.513e+01 5.670e+00 5.2637 1.077e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 67.3 6.513e+01 2.170e+00 5.2637 4.123e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 43.1 4.437e+01 -1.272e+00 3.6411 -3.493e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 45.1 4.437e+01 7.281e-01 3.6411 2.000e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 21.3 2.129e+01 7.295e-03 1.9038 3.832e-03</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 23.5 2.129e+01 2.207e+00 1.9038 1.159e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.187e+01 -6.922e-02 1.2798 -5.409e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.187e+01 2.308e-01 1.2798 1.803e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 6.901e+00 9.863e-02 1.0223 9.648e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 6.901e+00 -7.014e-01 1.0223 -6.860e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 7.958e-13 1.600e+00 0.8616 1.857e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 6.965e-01 2.035e-01 0.8634 2.357e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 1.970e+00 1.730e+00 0.8758 1.976e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 1.970e+00 3.043e-02 0.8758 3.474e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.090e+00 -4.896e-01 0.9213 -5.315e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.090e+00 -2.896e-01 0.9213 -3.144e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.699e+00 4.006e-01 1.0138 3.952e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.699e+00 -9.938e-02 1.0138 -9.803e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.139e+00 3.609e-01 1.1284 3.198e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.139e+00 1.609e-01 1.1284 1.426e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.777e+00 -4.772e-01 1.1100 -4.299e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.777e+00 2.228e-01 1.1100 2.007e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.654e+00 -5.373e-02 1.0119 -5.310e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.654e+00 1.046e+00 1.0119 1.034e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.695e+00 -9.950e-01 0.9394 -1.059e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.695e+00 -1.195e+00 0.9394 -1.272e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.012e+02 9.182e+00 8.1159 1.131e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.012e+02 1.088e+01 8.1159 1.341e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.450e+01 -9.992e-01 7.5834 -1.318e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.450e+01 -3.499e+00 7.5834 -4.614e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.289e+01 -1.189e+01 6.6644 -1.784e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.289e+01 6.814e+00 6.6644 1.022e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 60.4 6.541e+01 -5.014e+00 5.2861 -9.486e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 59.1 6.541e+01 -6.314e+00 5.2861 -1.195e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 56.5 4.682e+01 9.684e+00 3.8308 2.528e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 47.0 4.682e+01 1.835e-01 3.8308 4.791e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 30.2 3.039e+01 -1.888e-01 2.5715 -7.343e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 23.9 3.039e+01 -6.489e+00 2.5715 -2.523e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.783e+01 -8.306e-01 1.6623 -4.996e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.783e+01 8.694e-01 1.6623 5.230e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.186e+01 -5.608e-01 1.2793 -4.383e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.186e+01 3.924e-02 1.2793 3.067e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.932e+00 1.068e+00 1.0688 9.997e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.932e+00 1.684e-01 1.0688 1.576e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 4.974e-14 7.000e-01 0.8616 8.124e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.106e+00 -1.063e-01 0.8965 -1.186e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.106e+00 -5.063e-01 0.8965 -5.648e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.331e+00 -3.231e+00 1.0879 -2.970e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.331e+00 -8.307e-01 1.0879 -7.636e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.568e+01 8.233e-01 1.5181 5.424e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.568e+01 3.323e+00 1.5181 2.189e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.214e+01 7.593e-01 1.9643 3.865e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.214e+01 1.059e+00 1.9643 5.393e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.436e+01 -2.163e+00 2.1250 -1.018e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.436e+01 3.673e-02 2.1250 1.728e-02</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.887e+01 -3.367e+00 1.7335 -1.942e+00</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.887e+01 9.335e-01 1.7335 5.385e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.376e+01 1.139e+00 1.3951 8.162e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.376e+01 4.387e-01 1.3951 3.144e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.886e+00 1.014e+00 1.1677 8.687e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.886e+00 5.144e-01 1.1677 4.405e-01</span> <span class="r-in"><span class="co"># }</span></span> <span class="r-in"></span> </code></pre></div> diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index 7d79341c..39a92dd1 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -41,7 +41,7 @@ Compare also the code in the example section to see the degradation models."><!- <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -248,8 +248,8 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-in"> <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 class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Mar 2 13:44:06 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Mar 2 13:44:06 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:49 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:49 2022 </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> @@ -258,7 +258,7 @@ 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 0.756 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 833 model solutions performed in 0.624 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/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 39b9becb..327e8ae9 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -27,7 +27,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 25d0e76b..95e8c6b6 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -31,7 +31,7 @@ the ilr transformation is used."><!-- mathjax --><script src="https://cdnjs.clou <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index 036283d5..ff175937 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -29,7 +29,7 @@ override these starting values."><!-- mathjax --><script src="https://cdnjs.clou <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> |
