diff options
| author | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-09-12 22:16:13 +0200 |
|---|---|---|
| committer | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-09-12 22:16:13 +0200 |
| commit | 17af45b984d348505527140470c7fff204748ea6 (patch) | |
| tree | 4a7409236626c86e07746f7dfc736745f83a99d6 /docs/reference/saem.html | |
| parent | 3ae975f6039da0edc3ae6298bcac388e7346e73f (diff) | |
Facilitate centering covariates
The motivation for this is to obtain confidence intervals for
covariate dependent parameters that are valid for a median/mean
value of the covariate.
Implementation by adding an argument to the 'saem' function, and
adapting the relevant functions working with 'saem' objects.
Vignettes, the template and tests were updated to use the new functionality.
Diffstat (limited to 'docs/reference/saem.html')
| -rw-r--r-- | docs/reference/saem.html | 29 |
1 files changed, 18 insertions, 11 deletions
diff --git a/docs/reference/saem.html b/docs/reference/saem.html index 2d02fd77..159bc00f 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-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.11</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: 1.2.10 </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> 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> </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 4.017 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> @@ -718,7 +725,7 @@ 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> |