diff options
| author | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-11-28 09:20:07 +0100 |
|---|---|---|
| committer | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-11-28 09:20:07 +0100 |
| commit | fe411af3dbed474d9e5b3cc1d509f66bd76f7319 (patch) | |
| tree | 8b1a3a355c0aa6e0a59ec192e315e96c99640ff2 /docs/reference | |
| parent | a5a73e8d76faff5983399386de571431e8824636 (diff) | |
Example evaluation of D24_2014, improve docs
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/D24_2014-1.png | bin | 0 -> 88185 bytes | |||
| -rw-r--r-- | docs/reference/D24_2014.html | 27 | ||||
| -rw-r--r-- | docs/reference/index.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinds.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkindsg.html | 12 | ||||
| -rw-r--r-- | docs/reference/saem.html | 39 |
6 files changed, 51 insertions, 41 deletions
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.html b/docs/reference/D24_2014.html index 2eee55fa..fed830e6 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> @@ -193,6 +193,27 @@ 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</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</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</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="co"># }</span></span></span> </code></pre></div> </div> @@ -205,7 +226,7 @@ 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 57af6079..ab9bbb13 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.11</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 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.html b/docs/reference/saem.html index 159bc00f..4e81388b 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -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-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.11</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"> @@ -402,10 +402,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.4 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.11 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.5.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 12 20:34:55 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 12 20:34:55 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: 4.5.2 </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> @@ -420,7 +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 4.017 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> @@ -682,28 +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> |
