diff options
Diffstat (limited to 'docs/reference')
90 files changed, 234 insertions, 188 deletions
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 516e6009..5bc4200f 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -9,7 +9,7 @@ same dataset."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 3dd5cafe..b54920c7 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -9,7 +9,7 @@ specified as well."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/D24_2014-1.png b/docs/reference/D24_2014-1.png Binary files differnew file mode 100644 index 00000000..3f04f216 --- /dev/null +++ b/docs/reference/D24_2014-1.png diff --git a/docs/reference/D24_2014-2.png b/docs/reference/D24_2014-2.png Binary files differnew file mode 100644 index 00000000..316bfd3a --- /dev/null +++ b/docs/reference/D24_2014-2.png diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index 8bb74b1d..a0b17969 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014 • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014"><meta name="description" content="The five datasets were extracted from the active substance evaluation dossier +<!-- Generated by pkgdown: do not edit by hand --><html lang="en-GB"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014 • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014"><meta name="description" content="The five datasets were extracted from the active substance evaluation dossier published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance kinetic modelling. The fact that these data and some results are shown here does not imply a license to use them in the @@ -17,7 +17,7 @@ constrained by data protection regulations."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -38,7 +38,7 @@ constrained by data protection regulations."></head><body> <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> - <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/web_only/mesotrione_parent_2023.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> @@ -97,7 +97,9 @@ https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811</p> </div> <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> - <p>Data for the first dataset are from p. 685. Data for the other four + <p>The acronyms used for the 2,4-D transformation products are DCP for +2,4-dichlorophenol and DCA for 2,4-dichloroanisole.</p> +<p>Data for the first dataset are from p. 685. Data for the other four datasets were used in the preprocessed versions given in the kinetics section (p. 761ff.), with the exception of residues smaller than 1 for DCP in the soil from Site I2, where the values given on p. 694 were used.</p> @@ -193,6 +195,53 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2</span> <span class="r-out co"><span class="r-pr">#></span> * time))) * D24 - k_DCP * DCP</span> <span class="r-out co"><span class="r-pr">#></span> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</span> +<span class="r-in"><span><span class="va">D24_2014_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">D24_2014_data</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_D24_2014_const</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> models <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></span> +<span class="r-in"><span> <span class="st">"SFO-SFO-SFO"</span> <span class="op">=</span> <span class="va">m_D24</span>, </span></span> +<span class="r-in"><span> <span class="st">"DFOP-SFO-SFO"</span> <span class="op">=</span> <span class="va">m_D24_2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> data <span class="op">=</span> <span class="va">D24_2014_data</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_D24_2014_const</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model Mississippi Fayette RefSol 03-G Site E1 Site I2</span> +<span class="r-out co"><span class="r-pr">#></span> SFO-SFO-SFO OK Z Z Z Z </span> +<span class="r-out co"><span class="r-pr">#></span> DFOP-SFO-SFO OK Z Z Z Z </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Z: Observations with value of zero were removed from the data</span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_D24_2014_const</span><span class="op">[</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="D24_2014-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="va">f_D24_2014_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_D24_2014_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_D24_2014_tc</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model Mississippi Fayette RefSol 03-G Site E1 Site I2</span> +<span class="r-out co"><span class="r-pr">#></span> SFO-SFO-SFO OK Z Z Z Z </span> +<span class="r-out co"><span class="r-pr">#></span> DFOP-SFO-SFO OK Z Z Z Z </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Z: Observations with value of zero were removed from the data</span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_D24_2014_tc</span><span class="op">[</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="D24_2014-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># For dataset 3, the best fit is obtained using constant </span></span></span> +<span class="r-in"><span><span class="co"># variance and the DFOP-SFO-SFO model</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="va">f_D24_2014_const</span><span class="op">[[</span><span class="st">"SFO-SFO-SFO"</span>, <span class="fl">3</span><span class="op">]</span><span class="op">]</span>, </span></span> +<span class="r-in"><span> <span class="va">f_D24_2014_const</span><span class="op">[[</span><span class="st">"DFOP-SFO-SFO"</span>, <span class="fl">3</span><span class="op">]</span><span class="op">]</span>, </span></span> +<span class="r-in"><span> <span class="va">f_D24_2014_tc</span><span class="op">[[</span><span class="st">"SFO-SFO-SFO"</span>, <span class="fl">3</span><span class="op">]</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="va">f_D24_2014_tc</span><span class="op">[[</span><span class="st">"DFOP-SFO-SFO"</span>, <span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> f_D24_2014_const[["SFO-SFO-SFO", 3]] 7 220.4991</span> +<span class="r-out co"><span class="r-pr">#></span> f_D24_2014_const[["DFOP-SFO-SFO", 3]] 9 179.8933</span> +<span class="r-out co"><span class="r-pr">#></span> f_D24_2014_tc[["SFO-SFO-SFO", 3]] 8 200.7663</span> +<span class="r-out co"><span class="r-pr">#></span> f_D24_2014_tc[["DFOP-SFO-SFO", 3]] 10 181.8933</span> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> @@ -205,7 +254,7 @@ specific pieces of information in the comments.</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index ab31d4e1..895754a7 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -9,7 +9,7 @@ two exponential decline functions."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index d0af31c7..77d2516f 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> 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 1b9f38ac..696e3c3d 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -15,7 +15,7 @@ in this fit."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> 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 568bb125..a167281b 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -15,7 +15,7 @@ in this fit."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> 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 73d2cc42..4ad992fa 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -15,7 +15,7 @@ in this fit."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> 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 69b92c4f..af504715 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -15,7 +15,7 @@ in this fit."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index f6283e46..b4dd6b79 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 4878da60..51dba054 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -9,7 +9,7 @@ a decreasing rate constant."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 0420545d..b95b3595 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -9,7 +9,7 @@ between them."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 13aacdce..26f3b828 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -9,7 +9,7 @@ a concentration dependent rate constant."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index ebe30cbf..39a8e4ad 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index f922430b..9bb0b8f1 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 8e8deb83..00d4987f 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 50d15ac2..112d696c 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -15,7 +15,7 @@ and no substance in the bound fraction."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 4fd6326c..bd9ac98c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -11,7 +11,7 @@ may depend on the predicted value and is specified as a standard deviation."></h <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/anova.saem.mmkin.html b/docs/reference/anova.saem.mmkin.html index 9fb05d5c..97dc3b3c 100644 --- a/docs/reference/anova.saem.mmkin.html +++ b/docs/reference/anova.saem.mmkin.html @@ -13,7 +13,7 @@ the model on the previous line."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 3405e6f2..3fd67e42 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -11,7 +11,7 @@ by Burnham and Anderson (2004)."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/check_failed.html b/docs/reference/check_failed.html index d6fd6dfe..73cf02ec 100644 --- a/docs/reference/check_failed.html +++ b/docs/reference/check_failed.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 195ad75b..67007b32 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -21,7 +21,7 @@ method of Venzon and Moolgavkar (1988)."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -217,7 +217,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.206 0.000 1.206 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.194 0.000 1.194 </span> <span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> <span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> <span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> @@ -225,7 +225,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 0.406 0.172 0.317 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.439 0.119 0.304 </span> <span class="r-in"><span><span class="va">ci_profile</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index be11b498..ea4f7f41 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -104,8 +104,8 @@ <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.24 1.000 0.240 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.31 1.292 0.309 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.239 1.000 0.239 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.297 1.243 0.297 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> @@ -118,8 +118,8 @@ <span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.403 1.000 0.402 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.539 1.337 0.538 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.389 1.000 0.388 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.513 1.319 0.513 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 2311a67e..703b49dd 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -17,7 +17,7 @@ constrained by data protection regulations."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -183,10 +183,10 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.3 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.9 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 14:56:10 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 14:56:10 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.5.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon May 12 20:21:22 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon May 12 20:21:22 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -199,7 +199,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 295.43 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 303.226 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> diff --git a/docs/reference/ds_mixed.html b/docs/reference/ds_mixed.html index 37c49191..5208f9a4 100644 --- a/docs/reference/ds_mixed.html +++ b/docs/reference/ds_mixed.html @@ -9,7 +9,7 @@ the 'dataset_generation' directory."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 23c550ca..502b0603 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -15,7 +15,7 @@ advantage that the SFORB model can also be used for metabolites."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index d1329e21..8556fcfb 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -63,7 +63,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index c318b762..9e688da7 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -9,7 +9,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."></head><body <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 3b07a5ea..305aa407 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -9,7 +9,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 6b296b87..ad1b1c82 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html index 85cd2644..5c59b749 100644 --- a/docs/reference/hierarchical_kinetics.html +++ b/docs/reference/hierarchical_kinetics.html @@ -21,7 +21,7 @@ includes them.'></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html index cbe48623..f79ee876 100644 --- a/docs/reference/illparms.html +++ b/docs/reference/illparms.html @@ -15,7 +15,7 @@ without parameter transformations is used."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 7aa6379f..cd817e3e 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -9,7 +9,7 @@ transformations."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/index.html b/docs/reference/index.html index 191fbe04..ab9bbb13 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Package index • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en-GB"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Package index • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -28,7 +28,7 @@ <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> - <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/web_only/mesotrione_parent_2023.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> @@ -722,7 +722,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index 3a8cdb5d..08f65cfc 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/llhist.html b/docs/reference/llhist.html index 01299b04..a739c846 100644 --- a/docs/reference/llhist.html +++ b/docs/reference/llhist.html @@ -9,7 +9,7 @@ original fit is shown as a red vertical line."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index 97b48751..136256f7 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -13,7 +13,7 @@ lrtest.default from the lmtest package."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index eddf1f8f..04f38684 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -15,7 +15,7 @@ the error model."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/logLik.saem.mmkin.html b/docs/reference/logLik.saem.mmkin.html index 8cc985a8..b32d2f9a 100644 --- a/docs/reference/logLik.saem.mmkin.html +++ b/docs/reference/logLik.saem.mmkin.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index f03f0c70..00af94e9 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -9,7 +9,7 @@ an increasing rate constant, supposedly caused by microbial growth"></head><body <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 17ed11c6..bffae5f3 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -15,7 +15,7 @@ and can be expressed by fixing the parameters of the other."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 453f801a..6af12d05 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -15,7 +15,7 @@ soil section of the FOCUS guidance."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index bb0e36cf..866b093a 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -11,7 +11,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index e9c78767..9320abbd 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html index 26bfd34b..8b249f77 100644 --- a/docs/reference/mhmkin.html +++ b/docs/reference/mhmkin.html @@ -13,7 +13,7 @@ mixed-effects model fitting functions."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index 9bdd620d..089635f6 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 4bdbbc64..9f4dcfb0 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -11,7 +11,7 @@ variable and several dependent variables as columns."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index bcc303d1..37963f44 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -11,7 +11,7 @@ mkinfit."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 488c0c2f..c45a1b0b 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -1,10 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>A dataset class for mkin — mkinds • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A dataset class for mkin — mkinds"><meta name="description" content="At the moment this dataset class is hardly used in mkin. For example, +<!-- Generated by pkgdown: do not edit by hand --><html lang="en-GB"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>A dataset class for mkin — mkinds • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A dataset class for mkin — mkinds"><meta name="description" content="At the moment this dataset class is hardly used in mkin. For example, mkinfit does not take mkinds datasets as argument, but works with dataframes -such as the on contained in the data field of mkinds objects. Some datasets +such as the one contained in the data field of mkinds objects. Some datasets provided by this package come as mkinds objects nevertheless."><meta property="og:description" content="At the moment this dataset class is hardly used in mkin. For example, mkinfit does not take mkinds datasets as argument, but works with dataframes -such as the on contained in the data field of mkinds objects. Some datasets +such as the one contained in the data field of mkinds objects. Some datasets provided by this package come as mkinds objects nevertheless."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -13,7 +13,7 @@ provided by this package come as mkinds objects nevertheless."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -34,7 +34,7 @@ provided by this package come as mkinds objects nevertheless."></head><body> <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> - <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/web_only/mesotrione_parent_2023.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> @@ -69,7 +69,7 @@ provided by this package come as mkinds objects nevertheless."></head><body> <div class="ref-description section level2"> <p>At the moment this dataset class is hardly used in mkin. For example, mkinfit does not take mkinds datasets as argument, but works with dataframes -such as the on contained in the data field of mkinds objects. Some datasets +such as the one contained in the data field of mkinds objects. Some datasets provided by this package come as mkinds objects nevertheless.</p> </div> @@ -206,7 +206,7 @@ and value in order to be compatible with mkinfit</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index b314a5f8..6ab6f2f1 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>A class for dataset groups for mkin — mkindsg • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A class for dataset groups for mkin — mkindsg"><meta name="description" content="A container for working with datasets that share at least one compound, +<!-- Generated by pkgdown: do not edit by hand --><html lang="en-GB"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>A class for dataset groups for mkin — mkindsg • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A class for dataset groups for mkin — mkindsg"><meta name="description" content="A container for working with datasets that share at least one compound, so that combined evaluations are desirable. Time normalisation factors are initialised with a value of 1 for each dataset if no data are supplied."><meta property="og:description" content="A container for working with datasets that share at least one compound, @@ -13,7 +13,7 @@ dataset if no data are supplied."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -34,7 +34,7 @@ dataset if no data are supplied."></head><body> <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> - <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/web_only/mesotrione_parent_2023.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> @@ -100,6 +100,12 @@ dataset if no data are supplied.</p> </dl></div> <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> + <p>Currently, no functions making use of the defined class structure +are available in this package. Refer to <a href="D24_2014.html">D24_2014</a> for an example +dataset in this structure, with some example evaluations.</p> + </div> + <div class="section level2"> <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2> <p></p><div class="r6-fields"><dl><dt><code>title</code></dt> <dd><p>A title for the dataset group</p></dd> @@ -394,7 +400,7 @@ or covariates like soil pH).</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 26cc19f7..3dbcc4b8 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -9,7 +9,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."></head> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index bcd4285b..b217c154 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -15,7 +15,7 @@ using the argument show_errplot = TRUE."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 5af8eaaf..bc27e81f 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -23,7 +23,7 @@ likelihood function."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -366,17 +366,17 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.9 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 14:56:49 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 14:56:49 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.5.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon May 12 20:22:04 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon May 12 20:22:04 2025 </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 0.014 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.027 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> @@ -517,9 +517,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.227</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 1.930 0.438</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.991 0.452</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.256</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 1.898 0.486</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 2.000 0.512</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -545,10 +545,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.FOMC_SFO.tc</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(V) had non-positive or NA entries; the non-finite result may be dubious</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.9 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 14:56:53 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 14:56:53 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.5.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon May 12 20:22:10 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon May 12 20:22:10 2025 </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> @@ -557,7 +557,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 0.751 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 0.809 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 9ddbdc59..b4b303a5 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -15,7 +15,7 @@ components."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -290,7 +290,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpUBdk0y/file210eb9601bdd53.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/Rtmph4D0tb/file1385e349a06fa9.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> @@ -303,6 +303,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> <span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Setting PKG_CPPFLAGS to -DR_NO_REMAP </span> <span class="r-out co"><span class="r-pr">#></span> Program source:</span> <span class="r-out co"><span class="r-pr">#></span> 1: #include <R.h></span> <span class="r-out co"><span class="r-pr">#></span> 2: </span> @@ -343,7 +344,7 @@ 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: 0x55555a37aab8></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x5555585b89c0></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 57f536e0..6a081056 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -9,7 +9,7 @@ mkinfit."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index b5c84645..40478f12 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -9,7 +9,7 @@ plot.mkinfit."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index fc656e43..8dc08187 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -11,7 +11,7 @@ kinetic parameters and initial values for the state variables."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -353,10 +353,10 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1 0.002</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1 0.002</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4 0.008</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 32 0.064</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.5 0.009</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 35.0 0.070</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 97b24dbf..d1d37b44 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -13,7 +13,7 @@ argument show_residuals = TRUE."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 66ea275d..4675a9d3 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -9,7 +9,7 @@ datasets specified in its first two arguments."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -158,10 +158,10 @@ plotting.</p></div> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">time_default</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.608 0.866 0.732 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.423 1.112 1.111 </span> <span class="r-in"><span><span class="va">time_1</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.964 0.016 1.980 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.655 0.036 2.691 </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> diff --git a/docs/reference/multistart.html b/docs/reference/multistart.html index af5f614e..825e3210 100644 --- a/docs/reference/multistart.html +++ b/docs/reference/multistart.html @@ -17,7 +17,7 @@ mixed-effects models by Duchesne et al (2021)."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 07dc0f42..aa2ab7ca 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -15,7 +15,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."></ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 8bf352af..190ac359 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -13,7 +13,7 @@ datasets. They are used internally by the nlme.mmkin() method."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 4f124b07..ba0b0f16 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -11,7 +11,7 @@ have been obtained by fitting the same model to a list of datasets."></head><bod <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index 3cdfc619..d94f4a34 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 46b0bb31..f51455c9 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -11,7 +11,7 @@ without considering the error structure that was assumed for the fit."></head><b <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html index 30523983..54e3880f 100644 --- a/docs/reference/parplot.html +++ b/docs/reference/parplot.html @@ -11,7 +11,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."></head> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 838265d8..1c3abcaa 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 4ce5a914..10c21e2c 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -11,7 +11,7 @@ observed data together with the solution of the fitted model."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 572731a7..7f35d790 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -11,7 +11,7 @@ the fit of at least one model to the same dataset is shown."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 2b2338c6..170599a4 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -9,7 +9,7 @@ function (SFO, then IORE, then DFOP)."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/read_spreadsheet.html b/docs/reference/read_spreadsheet.html index 173ee608..069b8403 100644 --- a/docs/reference/read_spreadsheet.html +++ b/docs/reference/read_spreadsheet.html @@ -17,7 +17,7 @@ factors can be given in columns named 'Temperature' and 'Moisture'."></head><bod <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 94ee6f14..f7cacc84 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -29,7 +29,7 @@ intervals, nlme <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index cf2f62bb..4da7194c 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/saem-3.png b/docs/reference/saem-3.png Binary files differindex 09eb2d40..8ba8700d 100644 --- a/docs/reference/saem-3.png +++ b/docs/reference/saem-3.png diff --git a/docs/reference/saem.html b/docs/reference/saem.html index 7146875f..4e81388b 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -1,5 +1,5 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fit nonlinear mixed models with SAEM — saem • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fit nonlinear mixed models with SAEM — saem"><meta name="description" content="This function uses saemix::saemix() as a backend for fitting nonlinear mixed +<!-- Generated by pkgdown: do not edit by hand --><html lang="en-GB"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fit nonlinear mixed models with SAEM — saem • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fit nonlinear mixed models with SAEM — saem"><meta name="description" content="This function uses saemix::saemix() as a backend for fitting nonlinear mixed effects models created from mmkin row objects using the Stochastic Approximation Expectation Maximisation algorithm (SAEM)."><meta property="og:description" content="This function uses saemix::saemix() as a backend for fitting nonlinear mixed effects models created from mmkin row objects using the Stochastic Approximation @@ -11,7 +11,7 @@ Expectation Maximisation algorithm (SAEM)."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -32,7 +32,7 @@ Expectation Maximisation algorithm (SAEM)."></head><body> <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> - <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/web_only/mesotrione_parent_2023.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> @@ -87,6 +87,7 @@ Expectation Maximisation algorithm (SAEM).</p> <span> omega.init <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> center_covariates <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="cn">NA</span>, <span class="st">"median"</span>, <span class="st">"mean"</span><span class="op">)</span>,</span> <span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> error.init <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span>,</span> <span> nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">300</span>, <span class="fl">100</span><span class="op">)</span>,</span> @@ -195,6 +196,12 @@ variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available in the 'covariates' data frame.</p></dd> +<dt id="arg-center-covariates">center_covariates<a class="anchor" aria-label="anchor" href="#arg-center-covariates"></a></dt> +<dd><p>Either NA, for no centering, or your +preferred function for calculating the center, currently either +median or mean.</p></dd> + + <dt id="arg-no-random-effect">no_random_effect<a class="anchor" aria-label="anchor" href="#arg-no-random-effect"></a></dt> <dd><p>Character vector of degradation parameters for which there should be no variability over the groups. Only used @@ -303,7 +310,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="co"># functions from saemix</span></span></span> <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></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> Package saemix, version 3.3, March 2024</span> +<span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.4, March 2024</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> <span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘saemix’</span> @@ -394,11 +401,11 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.3 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.9 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 14:59:07 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 14:59:07 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.4 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.5.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Nov 28 09:18:42 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Nov 28 09:18:42 2025 </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> @@ -413,7 +420,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 3.96 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 3.833 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> @@ -675,28 +682,11 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 14.3 12.79238 1.50762 1.882 0.80111</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 12.1 12.79238 -0.69238 1.882 -0.36791</span> <span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># The following takes about 6 minutes</span></span></span> -<span class="r-in"><span><span class="va">f_saem_dfop_sfo_deSolve</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>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span></span> -<span class="r-in"><span> nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">200</span>, <span class="fl">80</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> DINTDY- T (=R1) illegal </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 70</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> T not in interval TCUR - HU (= R1) to TCUR (=R2) </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1042, R2 = 56.6326</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> DINTDY- T (=R1) illegal </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 91</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> T not in interval TCUR - HU (= R1) to TCUR (=R2) </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1042, R2 = 56.6326</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> DLSODA- Trouble in DINTDY. ITASK = I1, TOUT = R1</span> -<span class="r-out co"><span class="r-pr">#></span> In above message, I1 = 1</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 91</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Error in deSolve::lsoda(y = odeini, times = outtimes, func = lsoda_func, : </span> -<span class="r-out co"><span class="r-pr">#></span> illegal input detected before taking any integration steps - see written message</span> +<span class="r-in"><span><span class="co"># The following took about 6 minutes and currently fails with</span></span></span> +<span class="r-in"><span><span class="co"># "Error in deSolve::lsoda(y = odeini, times = outtimes_deSolve, func = lsoda_func, : </span></span></span> +<span class="r-in"><span><span class="co"># illegal input detected before taking any integration steps - see written message"</span></span></span> +<span class="r-in"><span><span class="co">#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span></span> +<span class="r-in"><span><span class="co"># nbiter.saemix = c(200, 80))</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co">#anova(</span></span></span> <span class="r-in"><span><span class="co"># f_saem_dfop_sfo,</span></span></span> @@ -718,7 +708,7 @@ using <a href="mmkin.html">mmkin</a>.</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> </div> </footer></div> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index c11e4ec5..732b71ff 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -11,7 +11,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html index 3ee21a41..238a2f6f 100644 --- a/docs/reference/set_nd_nq.html +++ b/docs/reference/set_nd_nq.html @@ -15,7 +15,7 @@ it automates the proposal of Boesten et al (2015)."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 5c9fb8b8..b3be95e9 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -9,7 +9,7 @@ dependence of the measured value \(y\):"></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/status.html b/docs/reference/status.html index bf77c36d..d7a6d669 100644 --- a/docs/reference/status.html +++ b/docs/reference/status.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 86663890..aa3f6bf0 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -15,7 +15,7 @@ values."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -191,10 +191,10 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.9 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 15:01:12 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 15:01:12 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.5.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon May 12 20:26:43 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon May 12 20:26:43 2025 </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> diff --git a/docs/reference/summary.mmkin.html b/docs/reference/summary.mmkin.html index bf48a2a6..d1f90296 100644 --- a/docs/reference/summary.mmkin.html +++ b/docs/reference/summary.mmkin.html @@ -9,7 +9,7 @@ and gives an overview of ill-defined parameters calculated by illparms."></head> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -113,7 +113,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.478 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.533 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 22cecb0d..c4f53a23 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -15,7 +15,7 @@ endpoints such as formation fractions and DT50 values. Optionally <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -211,11 +211,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> <span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.166 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.9 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 15:01:14 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 15:01:14 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.168 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.5.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon May 12 20:26:45 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon May 12 20:26:45 2025 </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> @@ -225,7 +225,7 @@ 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 0.185 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.193 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 4c9f0d17..39cdb471 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -15,7 +15,7 @@ endpoints such as formation fractions and DT50 values. Optionally <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -288,10 +288,10 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> b.1 0.06522297 0.07920531 0.09318766</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.3 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.9 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 15:01:30 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 15:01:30 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.5.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon May 12 20:27:02 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon May 12 20:27:02 2025 </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> @@ -306,7 +306,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.035 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.206 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> diff --git a/docs/reference/summary_listing.html b/docs/reference/summary_listing.html index 01ddec57..8d0c6da5 100644 --- a/docs/reference/summary_listing.html +++ b/docs/reference/summary_listing.html @@ -9,7 +9,7 @@ option results = "asis".'></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index b81bbea4..630fade6 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -37,7 +37,7 @@ Compare also the code in the example section to see the degradation models."></h <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -240,10 +240,10 @@ Compare also the code in the example section to see the degradation models."></h <span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.9 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 15:01:40 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 15:01:40 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.5.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon May 12 20:27:12 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon May 12 20:27:12 2025 </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> @@ -252,7 +252,7 @@ Compare also the code in the example section to see the degradation models."></h <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 848 model solutions performed in 0.165 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 848 model solutions performed in 0.176 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 2ebbbd96..70608d65 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -9,7 +9,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index feaf0917..94a9b6a8 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -17,7 +17,7 @@ the ilr transformation is used."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index e4a2de34..24467b43 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -13,7 +13,7 @@ override these starting values."></head><body> <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> |
