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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 2eee55fa..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 @@ -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/index.html b/docs/reference/index.html index f63ec3f2..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> @@ -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/web_only/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/mkinds.html b/docs/reference/mkinds.html index 3c905b02..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> @@ -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 92d5cd12..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, @@ -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/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 2d02fd77..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 @@ -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> 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: 4.5.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon May 12 20:24:36 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon May 12 20:24:36 2025 </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 3.747 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_deSolve, 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> |
