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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> |