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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 09:47:33 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 09:47:33 +0100 |
| commit | 17258b37e7f22008298d350a2dc954d71d2fd496 (patch) | |
| tree | d6e7ad679cca1581fc25e9a839abda6e20d93b77 /docs/dev | |
| parent | 82c8b014c537c0634615c3c007aa4a3fa672307f (diff) | |
Remove outdated doc page
Diffstat (limited to 'docs/dev')
| -rw-r--r-- | docs/dev/reference/saemix.html | 1202 |
1 files changed, 0 insertions, 1202 deletions
diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html deleted file mode 100644 index 5dacefc9..00000000 --- a/docs/dev/reference/saemix.html +++ /dev/null @@ -1,1202 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Create saemix models from mmkin row objects — saemix_model • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Create saemix models from mmkin row objects — saemix_model" /> -<meta property="og:description" content="This function sets up a nonlinear mixed effects model for an mmkin row -object for use with the saemix package. An mmkin row object is essentially a -list of mkinfit objects that have been obtained by fitting the same model to -a list of datasets." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body data-spy="scroll" data-target="#toc"> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../reference/index.html">Functions and data</a> -</li> -<li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> - Articles - - <span class="caret"></span> - </a> - <ul class="dropdown-menu" role="menu"> - <li> - <a href="../articles/mkin.html">Introduction to mkin</a> - </li> - <li> - <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - </li> - <li> - <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </li> - <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> - </ul> -</li> -<li> - <a href="../news/index.html">News</a> -</li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Create saemix models from mmkin row objects</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small> - <div class="hidden name"><code>saemix.Rd</code></div> - </div> - - <div class="ref-description"> - <p>This function sets up a nonlinear mixed effects model for an mmkin row -object for use with the saemix package. An mmkin row object is essentially a -list of mkinfit objects that have been obtained by fitting the same model to -a list of datasets.</p> - </div> - - <pre class="usage"><span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>object</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> - -<span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An mmkin row object containing several fits of the same model -to different datasets</p></td> - </tr> - <tr> - <th>cores</th> - <td><p>The number of cores to be used for multicore processing using -<code><a href='https://rdrr.io/r/parallel/mclapply.html'>parallel::mclapply()</a></code>. Using more than 1 core is experimental and may -lead to uncontrolled forking, apparently depending on the BLAS version -used.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixData.html'>saemix::saemixData</a></p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> object.</p> -<p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a> object.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>Starting values for the fixed effects (population mean parameters, argument psi0 of -<code><a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel()</a></code> are the mean values of the parameters found using -mmkin. Starting variances of the random effects (argument omega.init) are the -variances of the deviations of the parameters from these mean values.</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Package saemix, version 3.1.9000</span> -#> <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, - <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span> -<span class='va'>f_mmkin_parent_p0_fixed</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>ds</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, - state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>m_saemix_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> -#> -#> The following SaemixModel object was successfully created: -#> -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> odeini_fixed/(xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, -#> 1]) -#> } -#> <bytecode: 0x5555599945b8> -#> <environment: 0x555559984388> -#> Nb of parameters: 2 -#> parameter names: log_alpha log_beta -#> distribution: -#> Parameter Distribution Estimated -#> [1,] log_alpha normal Estimated -#> [2,] log_beta normal Estimated -#> Variance-covariance matrix: -#> log_alpha log_beta -#> log_alpha 1 0 -#> log_beta 0 1 -#> Error model: constant , initial values: a.1=2.95893806804889 -#> No covariate in the model. -#> Initial values -#> log_alpha log_beta -#> Pop.CondInit -0.347996 1.66788</div><div class='input'><span class='va'>d_saemix_parent</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> -</div><div class='output co'>#> -#> -#> The following SaemixData object was successfully created: -#> -#> Object of class SaemixData -#> longitudinal data for use with the SAEM algorithm -#> Dataset ds_saemix -#> Structured data: value ~ time + name | ds -#> X variable for graphs: time () </div><div class='input'><span class='va'>saemix_options</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>seed <span class='op'>=</span> <span class='fl'>123456</span>, displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, - save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span> <span class='cn'>FALSE</span>, nbiter.saemix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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 class='va'>f_saemix_p0_fixed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_p0_fixed</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> -</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Thu Nov 5 23:53:29 2020" -#> .. -#> Minimisation finished -#> [1] "Thu Nov 5 23:53:30 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm -#> ----------------------------------- -#> ---- Data ---- -#> ----------------------------------- -#> Object of class SaemixData -#> longitudinal data for use with the SAEM algorithm -#> Dataset ds_saemix -#> Structured data: value ~ time + name | ds -#> X variable for graphs: time () -#> Dataset characteristics: -#> number of subjects: 5 -#> number of observations: 90 -#> average/min/max nb obs: 18.00 / 16 / 20 -#> First 10 lines of data: -#> ds time name value mdv cens occ ytype -#> 1 Dataset 6 0 parent 97.2 0 0 1 1 -#> 2 Dataset 6 0 parent 96.4 0 0 1 1 -#> 3 Dataset 6 3 parent 71.1 0 0 1 1 -#> 4 Dataset 6 3 parent 69.2 0 0 1 1 -#> 5 Dataset 6 6 parent 58.1 0 0 1 1 -#> 6 Dataset 6 6 parent 56.6 0 0 1 1 -#> 7 Dataset 6 10 parent 44.4 0 0 1 1 -#> 8 Dataset 6 10 parent 43.4 0 0 1 1 -#> 9 Dataset 6 20 parent 33.3 0 0 1 1 -#> 10 Dataset 6 20 parent 29.2 0 0 1 1 -#> ----------------------------------- -#> ---- Model ---- -#> ----------------------------------- -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> odeini_fixed/(xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, -#> 1]) -#> } -#> <bytecode: 0x5555599945b8> -#> <environment: 0x555559984388> -#> Nb of parameters: 2 -#> parameter names: log_alpha log_beta -#> distribution: -#> Parameter Distribution Estimated -#> [1,] log_alpha normal Estimated -#> [2,] log_beta normal Estimated -#> Variance-covariance matrix: -#> log_alpha log_beta -#> log_alpha 1 0 -#> log_beta 0 1 -#> Error model: constant , initial values: a.1=2.95893806804889 -#> No covariate in the model. -#> Initial values -#> log_alpha log_beta -#> Pop.CondInit -0.347996 1.66788 -#> ----------------------------------- -#> ---- Key algorithm options ---- -#> ----------------------------------- -#> Estimation of individual parameters (MAP) -#> Estimation of standard errors and linearised log-likelihood -#> Estimation of log-likelihood by importance sampling -#> Number of iterations: K1=200, K2=80 -#> Number of chains: 10 -#> Seed: 123456 -#> Number of MCMC iterations for IS: 5000 -#> Simulations: -#> nb of simulated datasets used for npde: 1000 -#> nb of simulated datasets used for VPC: 100 -#> Input/output -#> save the results to a file: FALSE -#> save the graphs to files: FALSE -#> ---------------------------------------------------- -#> ---- Results ---- -#> ---------------------------------------------------- -#> ----------------- Fixed effects ------------------ -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> log_alpha -0.33 0.30 91.6 -#> log_beta 1.70 0.21 12.4 -#> a a.1 3.15 0.25 7.9 -#> ---------------------------------------------------- -#> ----------- Variance of random effects ----------- -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> log_alpha omega2.log_alpha 0.44 0.28 65 -#> log_beta omega2.log_beta 0.18 0.14 79 -#> ---------------------------------------------------- -#> ------ Correlation matrix of random effects ------ -#> ---------------------------------------------------- -#> omega2.log_alpha omega2.log_beta -#> omega2.log_alpha 1 0 -#> omega2.log_beta 0 1 -#> ---------------------------------------------------- -#> --------------- Statistical criteria ------------- -#> ---------------------------------------------------- -#> Likelihood computed by linearisation -#> -2LL= 501.6082 -#> AIC = 511.6082 -#> BIC = 509.6554 -#> -#> Likelihood computed by importance sampling -#> -2LL= 501.7 -#> AIC = 511.7 -#> BIC = 509.7472 -#> ----------------------------------------------------</div><div class='input'> -<span class='va'>f_mmkin_parent</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>m_saemix_sfo</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> -#> -#> The following SaemixModel object was successfully created: -#> -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> psi[id, 1] * exp(-exp(psi[id, 2]) * xidep[, "time"]) -#> } -#> <bytecode: 0x55555998d588> -#> <environment: 0x55555c0f4ae8> -#> Nb of parameters: 2 -#> parameter names: parent_0 log_k_parent -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k_parent normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_k_parent -#> parent_0 1 0 -#> log_k_parent 0 1 -#> Error model: constant , initial values: a.1=5.76827561471585 -#> No covariate in the model. -#> Initial values -#> parent_0 log_k_parent -#> Pop.CondInit 86.39406 -3.215063</div><div class='input'><span class='va'>m_saemix_fomc</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> -#> -#> The following SaemixModel object was successfully created: -#> -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> psi[id, 1]/(xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, -#> 2]) -#> } -#> <bytecode: 0x55555998dc50> -#> <environment: 0x5555595d7668> -#> Nb of parameters: 3 -#> parameter names: parent_0 log_alpha log_beta -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_alpha normal Estimated -#> [3,] log_beta normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_alpha log_beta -#> parent_0 1 0 0 -#> log_alpha 0 1 0 -#> log_beta 0 0 1 -#> Error model: constant , initial values: a.1=1.91976382242696 -#> No covariate in the model. -#> Initial values -#> parent_0 log_alpha log_beta -#> Pop.CondInit 94.43884 -0.2226095 2.048192</div><div class='input'><span class='va'>m_saemix_dfop</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> -#> -#> The following SaemixModel object was successfully created: -#> -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> g <- plogis(psi[id, 4]) -#> t = xidep[, "time"] -#> psi[id, 1] * (g * exp(-exp(psi[id, 2]) * t) + (1 - g) * exp(-exp(psi[id, -#> 3]) * t)) -#> } -#> <bytecode: 0x55555998e548> -#> <environment: 0x555558225bf0> -#> Nb of parameters: 4 -#> parameter names: parent_0 log_k1 log_k2 g_qlogis -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k1 normal Estimated -#> [3,] log_k2 normal Estimated -#> [4,] g_qlogis normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_k1 log_k2 g_qlogis -#> parent_0 1 0 0 0 -#> log_k1 0 1 0 0 -#> log_k2 0 0 1 0 -#> g_qlogis 0 0 0 1 -#> Error model: constant , initial values: a.1=1.94671278396371 -#> No covariate in the model. -#> Initial values -#> parent_0 log_k1 log_k2 g_qlogis -#> Pop.CondInit 94.08322 -1.834163 -4.210797 0.11002</div><div class='input'><span class='va'>d_saemix_parent</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> -#> -#> The following SaemixData object was successfully created: -#> -#> Object of class SaemixData -#> longitudinal data for use with the SAEM algorithm -#> Dataset ds_saemix -#> Structured data: value ~ time + name | ds -#> X variable for graphs: time () </div><div class='input'><span class='va'>f_saemix_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_sfo</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> -</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Thu Nov 5 23:53:31 2020" -#> .. -#> Minimisation finished -#> [1] "Thu Nov 5 23:53:32 2020"</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm -#> ----------------------------------- -#> ---- Data ---- -#> ----------------------------------- -#> Object of class SaemixData -#> longitudinal data for use with the SAEM algorithm -#> Dataset ds_saemix -#> Structured data: value ~ time + name | ds -#> X variable for graphs: time () -#> Dataset characteristics: -#> number of subjects: 5 -#> number of observations: 90 -#> average/min/max nb obs: 18.00 / 16 / 20 -#> First 10 lines of data: -#> ds time name value mdv cens occ ytype -#> 1 Dataset 6 0 parent 97.2 0 0 1 1 -#> 2 Dataset 6 0 parent 96.4 0 0 1 1 -#> 3 Dataset 6 3 parent 71.1 0 0 1 1 -#> 4 Dataset 6 3 parent 69.2 0 0 1 1 -#> 5 Dataset 6 6 parent 58.1 0 0 1 1 -#> 6 Dataset 6 6 parent 56.6 0 0 1 1 -#> 7 Dataset 6 10 parent 44.4 0 0 1 1 -#> 8 Dataset 6 10 parent 43.4 0 0 1 1 -#> 9 Dataset 6 20 parent 33.3 0 0 1 1 -#> 10 Dataset 6 20 parent 29.2 0 0 1 1 -#> ----------------------------------- -#> ---- Model ---- -#> ----------------------------------- -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> psi[id, 1] * exp(-exp(psi[id, 2]) * xidep[, "time"]) -#> } -#> <bytecode: 0x55555998d588> -#> <environment: 0x55555c0f4ae8> -#> Nb of parameters: 2 -#> parameter names: parent_0 log_k_parent -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k_parent normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_k_parent -#> parent_0 1 0 -#> log_k_parent 0 1 -#> Error model: constant , initial values: a.1=5.76827561471585 -#> No covariate in the model. -#> Initial values -#> parent_0 log_k_parent -#> Pop.CondInit 86.39406 -3.215063 -#> ----------------------------------- -#> ---- Key algorithm options ---- -#> ----------------------------------- -#> Estimation of individual parameters (MAP) -#> Estimation of standard errors and linearised log-likelihood -#> Estimation of log-likelihood by importance sampling -#> Number of iterations: K1=200, K2=80 -#> Number of chains: 10 -#> Seed: 123456 -#> Number of MCMC iterations for IS: 5000 -#> Simulations: -#> nb of simulated datasets used for npde: 1000 -#> nb of simulated datasets used for VPC: 100 -#> Input/output -#> save the results to a file: FALSE -#> save the graphs to files: FALSE -#> ---------------------------------------------------- -#> ---- Results ---- -#> ---------------------------------------------------- -#> ----------------- Fixed effects ------------------ -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 85.8 1.85 2.2 -#> log_k_parent -3.2 0.59 18.3 -#> a a.1 6.2 0.49 7.9 -#> ---------------------------------------------------- -#> ----------- Variance of random effects ----------- -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 omega2.parent_0 7.8 10.7 138 -#> log_k_parent omega2.log_k_parent 1.7 1.1 64 -#> ---------------------------------------------------- -#> ------ Correlation matrix of random effects ------ -#> ---------------------------------------------------- -#> omega2.parent_0 omega2.log_k_parent -#> omega2.parent_0 1 0 -#> omega2.log_k_parent 0 1 -#> ---------------------------------------------------- -#> --------------- Statistical criteria ------------- -#> ---------------------------------------------------- -#> Likelihood computed by linearisation -#> -2LL= 615.4074 -#> AIC = 625.4074 -#> BIC = 623.4546 -#> -#> Likelihood computed by importance sampling -#> -2LL= 614.4911 -#> AIC = 624.4911 -#> BIC = 622.5382 -#> ----------------------------------------------------</div><div class='input'><span class='va'>f_saemix_fomc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_fomc</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> -</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Thu Nov 5 23:53:33 2020" -#> .. -#> Minimisation finished -#> [1] "Thu Nov 5 23:53:34 2020"</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm -#> ----------------------------------- -#> ---- Data ---- -#> ----------------------------------- -#> Object of class SaemixData -#> longitudinal data for use with the SAEM algorithm -#> Dataset ds_saemix -#> Structured data: value ~ time + name | ds -#> X variable for graphs: time () -#> Dataset characteristics: -#> number of subjects: 5 -#> number of observations: 90 -#> average/min/max nb obs: 18.00 / 16 / 20 -#> First 10 lines of data: -#> ds time name value mdv cens occ ytype -#> 1 Dataset 6 0 parent 97.2 0 0 1 1 -#> 2 Dataset 6 0 parent 96.4 0 0 1 1 -#> 3 Dataset 6 3 parent 71.1 0 0 1 1 -#> 4 Dataset 6 3 parent 69.2 0 0 1 1 -#> 5 Dataset 6 6 parent 58.1 0 0 1 1 -#> 6 Dataset 6 6 parent 56.6 0 0 1 1 -#> 7 Dataset 6 10 parent 44.4 0 0 1 1 -#> 8 Dataset 6 10 parent 43.4 0 0 1 1 -#> 9 Dataset 6 20 parent 33.3 0 0 1 1 -#> 10 Dataset 6 20 parent 29.2 0 0 1 1 -#> ----------------------------------- -#> ---- Model ---- -#> ----------------------------------- -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> psi[id, 1]/(xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, -#> 2]) -#> } -#> <bytecode: 0x55555998dc50> -#> <environment: 0x5555595d7668> -#> Nb of parameters: 3 -#> parameter names: parent_0 log_alpha log_beta -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_alpha normal Estimated -#> [3,] log_beta normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_alpha log_beta -#> parent_0 1 0 0 -#> log_alpha 0 1 0 -#> log_beta 0 0 1 -#> Error model: constant , initial values: a.1=1.91976382242696 -#> No covariate in the model. -#> Initial values -#> parent_0 log_alpha log_beta -#> Pop.CondInit 94.43884 -0.2226095 2.048192 -#> ----------------------------------- -#> ---- Key algorithm options ---- -#> ----------------------------------- -#> Estimation of individual parameters (MAP) -#> Estimation of standard errors and linearised log-likelihood -#> Estimation of log-likelihood by importance sampling -#> Number of iterations: K1=200, K2=80 -#> Number of chains: 10 -#> Seed: 123456 -#> Number of MCMC iterations for IS: 5000 -#> Simulations: -#> nb of simulated datasets used for npde: 1000 -#> nb of simulated datasets used for VPC: 100 -#> Input/output -#> save the results to a file: FALSE -#> save the graphs to files: FALSE -#> ---------------------------------------------------- -#> ---- Results ---- -#> ---------------------------------------------------- -#> ----------------- Fixed effects ------------------ -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 94.49 1.18 1.2 -#> log_alpha -0.21 0.30 142.0 -#> log_beta 2.06 0.21 10.4 -#> a a.1 2.28 0.19 8.2 -#> ---------------------------------------------------- -#> ----------- Variance of random effects ----------- -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 omega2.parent_0 4.66 4.34 93 -#> log_alpha omega2.log_alpha 0.45 0.29 65 -#> log_beta omega2.log_beta 0.19 0.14 75 -#> ---------------------------------------------------- -#> ------ Correlation matrix of random effects ------ -#> ---------------------------------------------------- -#> omega2.parent_0 omega2.log_alpha omega2.log_beta -#> omega2.parent_0 1 0 0 -#> omega2.log_alpha 0 1 0 -#> omega2.log_beta 0 0 1 -#> ---------------------------------------------------- -#> --------------- Statistical criteria ------------- -#> ---------------------------------------------------- -#> Likelihood computed by linearisation -#> -2LL= 454.0598 -#> AIC = 468.0598 -#> BIC = 465.3259 -#> -#> Likelihood computed by importance sampling -#> -2LL= 453.7499 -#> AIC = 467.7499 -#> BIC = 465.016 -#> ----------------------------------------------------</div><div class='input'><span class='va'>f_saemix_dfop</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_dfop</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> -</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Thu Nov 5 23:53:35 2020" -#> .. -#> Minimisation finished -#> [1] "Thu Nov 5 23:53:37 2020"</div><div class='img'><img src='saemix-4.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm -#> ----------------------------------- -#> ---- Data ---- -#> ----------------------------------- -#> Object of class SaemixData -#> longitudinal data for use with the SAEM algorithm -#> Dataset ds_saemix -#> Structured data: value ~ time + name | ds -#> X variable for graphs: time () -#> Dataset characteristics: -#> number of subjects: 5 -#> number of observations: 90 -#> average/min/max nb obs: 18.00 / 16 / 20 -#> First 10 lines of data: -#> ds time name value mdv cens occ ytype -#> 1 Dataset 6 0 parent 97.2 0 0 1 1 -#> 2 Dataset 6 0 parent 96.4 0 0 1 1 -#> 3 Dataset 6 3 parent 71.1 0 0 1 1 -#> 4 Dataset 6 3 parent 69.2 0 0 1 1 -#> 5 Dataset 6 6 parent 58.1 0 0 1 1 -#> 6 Dataset 6 6 parent 56.6 0 0 1 1 -#> 7 Dataset 6 10 parent 44.4 0 0 1 1 -#> 8 Dataset 6 10 parent 43.4 0 0 1 1 -#> 9 Dataset 6 20 parent 33.3 0 0 1 1 -#> 10 Dataset 6 20 parent 29.2 0 0 1 1 -#> ----------------------------------- -#> ---- Model ---- -#> ----------------------------------- -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> g <- plogis(psi[id, 4]) -#> t = xidep[, "time"] -#> psi[id, 1] * (g * exp(-exp(psi[id, 2]) * t) + (1 - g) * exp(-exp(psi[id, -#> 3]) * t)) -#> } -#> <bytecode: 0x55555998e548> -#> <environment: 0x555558225bf0> -#> Nb of parameters: 4 -#> parameter names: parent_0 log_k1 log_k2 g_qlogis -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k1 normal Estimated -#> [3,] log_k2 normal Estimated -#> [4,] g_qlogis normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_k1 log_k2 g_qlogis -#> parent_0 1 0 0 0 -#> log_k1 0 1 0 0 -#> log_k2 0 0 1 0 -#> g_qlogis 0 0 0 1 -#> Error model: constant , initial values: a.1=1.94671278396371 -#> No covariate in the model. -#> Initial values -#> parent_0 log_k1 log_k2 g_qlogis -#> Pop.CondInit 94.08322 -1.834163 -4.210797 0.11002 -#> ----------------------------------- -#> ---- Key algorithm options ---- -#> ----------------------------------- -#> Estimation of individual parameters (MAP) -#> Estimation of standard errors and linearised log-likelihood -#> Estimation of log-likelihood by importance sampling -#> Number of iterations: K1=200, K2=80 -#> Number of chains: 10 -#> Seed: 123456 -#> Number of MCMC iterations for IS: 5000 -#> Simulations: -#> nb of simulated datasets used for npde: 1000 -#> nb of simulated datasets used for VPC: 100 -#> Input/output -#> save the results to a file: FALSE -#> save the graphs to files: FALSE -#> ---------------------------------------------------- -#> ---- Results ---- -#> ---------------------------------------------------- -#> ----------------- Fixed effects ------------------ -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 93.97 1.35 1.4 -#> log_k1 -2.37 0.58 24.5 -#> log_k2 -3.63 0.87 24.0 -#> g_qlogis -0.14 0.34 246.1 -#> a a.1 2.32 0.19 8.3 -#> ---------------------------------------------------- -#> ----------- Variance of random effects ----------- -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 omega2.parent_0 6.97 5.72 82 -#> log_k1 omega2.log_k1 1.63 1.06 65 -#> log_k2 omega2.log_k2 3.73 2.39 64 -#> g_qlogis omega2.g_qlogis 0.16 0.27 173 -#> ---------------------------------------------------- -#> ------ Correlation matrix of random effects ------ -#> ---------------------------------------------------- -#> omega2.parent_0 omega2.log_k1 omega2.log_k2 omega2.g_qlogis -#> omega2.parent_0 1 0 0 0 -#> omega2.log_k1 0 1 0 0 -#> omega2.log_k2 0 0 1 0 -#> omega2.g_qlogis 0 0 0 1 -#> ---------------------------------------------------- -#> --------------- Statistical criteria ------------- -#> ---------------------------------------------------- -#> Likelihood computed by linearisation -#> -2LL= 485.4627 -#> AIC = 503.4627 -#> BIC = 499.9477 -#> -#> Likelihood computed by importance sampling -#> -2LL= 473.563 -#> AIC = 491.563 -#> BIC = 488.048 -#> ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saemix_sfo</span>, <span class='va'>f_saemix_fomc</span>, <span class='va'>f_saemix_dfop</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC -#> 1 624.4911 622.5382 -#> 2 467.7499 465.0160 -#> 3 491.5630 488.0480</div><div class='input'><span class='va'>f_mmkin_parent_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> -<span class='va'>m_saemix_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> -#> -#> The following SaemixModel object was successfully created: -#> -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> psi[id, 1]/(xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, -#> 2]) -#> } -#> <bytecode: 0x55555998dc50> -#> <environment: 0x555559a957f8> -#> Nb of parameters: 3 -#> parameter names: parent_0 log_alpha log_beta -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_alpha normal Estimated -#> [3,] log_beta normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_alpha log_beta -#> parent_0 1 0 0 -#> log_alpha 0 1 0 -#> log_beta 0 0 1 -#> Error model: combined , initial values: a.1=1.10728182011691 b.1=0.024889924291374 -#> No covariate in the model. -#> Initial values -#> parent_0 log_alpha log_beta -#> Pop.CondInit 93.13042 -0.1215336 2.230815</div><div class='input'><span class='va'>f_saemix_fomc_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_fomc_tc</span>, <span class='va'>d_saemix_parent</span>, <span class='va'>saemix_options</span><span class='op'>)</span> -</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Thu Nov 5 23:53:38 2020" -#> .. -#> Minimisation finished -#> [1] "Thu Nov 5 23:53:42 2020"</div><div class='img'><img src='saemix-5.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm -#> ----------------------------------- -#> ---- Data ---- -#> ----------------------------------- -#> Object of class SaemixData -#> longitudinal data for use with the SAEM algorithm -#> Dataset ds_saemix -#> Structured data: value ~ time + name | ds -#> X variable for graphs: time () -#> Dataset characteristics: -#> number of subjects: 5 -#> number of observations: 90 -#> average/min/max nb obs: 18.00 / 16 / 20 -#> First 10 lines of data: -#> ds time name value mdv cens occ ytype -#> 1 Dataset 6 0 parent 97.2 0 0 1 1 -#> 2 Dataset 6 0 parent 96.4 0 0 1 1 -#> 3 Dataset 6 3 parent 71.1 0 0 1 1 -#> 4 Dataset 6 3 parent 69.2 0 0 1 1 -#> 5 Dataset 6 6 parent 58.1 0 0 1 1 -#> 6 Dataset 6 6 parent 56.6 0 0 1 1 -#> 7 Dataset 6 10 parent 44.4 0 0 1 1 -#> 8 Dataset 6 10 parent 43.4 0 0 1 1 -#> 9 Dataset 6 20 parent 33.3 0 0 1 1 -#> 10 Dataset 6 20 parent 29.2 0 0 1 1 -#> ----------------------------------- -#> ---- Model ---- -#> ----------------------------------- -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> psi[id, 1]/(xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, -#> 2]) -#> } -#> <bytecode: 0x55555998dc50> -#> <environment: 0x555559a957f8> -#> Nb of parameters: 3 -#> parameter names: parent_0 log_alpha log_beta -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_alpha normal Estimated -#> [3,] log_beta normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_alpha log_beta -#> parent_0 1 0 0 -#> log_alpha 0 1 0 -#> log_beta 0 0 1 -#> Error model: combined , initial values: a.1=1.10728182011691 b.1=0.024889924291374 -#> No covariate in the model. -#> Initial values -#> parent_0 log_alpha log_beta -#> Pop.CondInit 93.13042 -0.1215336 2.230815 -#> ----------------------------------- -#> ---- Key algorithm options ---- -#> ----------------------------------- -#> Estimation of individual parameters (MAP) -#> Estimation of standard errors and linearised log-likelihood -#> Estimation of log-likelihood by importance sampling -#> Number of iterations: K1=200, K2=80 -#> Number of chains: 10 -#> Seed: 123456 -#> Number of MCMC iterations for IS: 5000 -#> Simulations: -#> nb of simulated datasets used for npde: 1000 -#> nb of simulated datasets used for VPC: 100 -#> Input/output -#> save the results to a file: FALSE -#> save the graphs to files: FALSE -#> ---------------------------------------------------- -#> ---- Results ---- -#> ---------------------------------------------------- -#> ----------------- Fixed effects ------------------ -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 94.4481 1.2052 1.3 -#> log_alpha -0.2088 0.3059 146.5 -#> log_beta 2.0668 0.2182 10.6 -#> a a.1 2.4273 0.3178 13.1 -#> b b.1 -0.0037 0.0062 168.3 -#> ---------------------------------------------------- -#> ----------- Variance of random effects ----------- -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 omega2.parent_0 5.34 4.58 86 -#> log_alpha omega2.log_alpha 0.46 0.29 65 -#> log_beta omega2.log_beta 0.20 0.15 74 -#> ---------------------------------------------------- -#> ------ Correlation matrix of random effects ------ -#> ---------------------------------------------------- -#> omega2.parent_0 omega2.log_alpha omega2.log_beta -#> omega2.parent_0 1 0 0 -#> omega2.log_alpha 0 1 0 -#> omega2.log_beta 0 0 1 -#> ---------------------------------------------------- -#> --------------- Statistical criteria ------------- -#> ---------------------------------------------------- -#> Likelihood computed by linearisation -#> -2LL= 453.7703 -#> AIC = 469.7703 -#> BIC = 466.6458 -#> -#> Likelihood computed by importance sampling -#> -2LL= 453.6186 -#> AIC = 469.6186 -#> BIC = 466.4942 -#> ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saemix_fomc</span>, <span class='va'>f_saemix_fomc_tc</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC -#> 1 467.7499 465.0160 -#> 2 469.6186 466.4942</div><div class='input'> -<span class='va'>dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>f_mmkin</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>m_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> -</div><div class='output co'>#> -#> -#> The following SaemixModel object was successfully created: -#> -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> uid <- unique(id) -#> res_list <- parallel::mclapply(uid, function(i) { -#> transparms_optim <- psi[i, ] -#> names(transparms_optim) <- names(degparms_optim) -#> odeini_optim <- transparms_optim[odeini_optim_parm_names] -#> names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names) -#> odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] -#> ode_transparms_optim_names <- setdiff(names(transparms_optim), -#> odeini_optim_parm_names) -#> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], -#> mkin_model, transform_rates = object[[1]]$transform_rates, -#> transform_fractions = object[[1]]$transform_fractions) -#> odeparms <- c(odeparms_optim, odeparms_fixed) -#> xidep_i <- subset(xidep, id == i) -#> if (solution_type == "analytical") { -#> out_values <- mkin_model$deg_func(xidep_i, odeini, -#> odeparms) -#> } -#> else { -#> i_time <- xidep_i$time -#> i_name <- xidep_i$name -#> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, -#> odeini = odeini, solution_type = solution_type, -#> outtimes = sort(unique(i_time))) -#> out_index <- cbind(as.character(i_time), as.character(i_name)) -#> out_values <- out_wide[out_index] -#> } -#> return(out_values) -#> }, mc.cores = cores) -#> res <- unlist(res_list) -#> return(res) -#> } -#> <bytecode: 0x55555998cba0> -#> <environment: 0x55555bd1fee8> -#> Nb of parameters: 6 -#> parameter names: parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k_A1 normal Estimated -#> [3,] f_parent_qlogis normal Estimated -#> [4,] log_k1 normal Estimated -#> [5,] log_k2 normal Estimated -#> [6,] g_qlogis normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis -#> parent_0 1 0 0 0 0 0 -#> log_k_A1 0 1 0 0 0 0 -#> f_parent_qlogis 0 0 1 0 0 0 -#> log_k1 0 0 0 1 0 0 -#> log_k2 0 0 0 0 1 0 -#> g_qlogis 0 0 0 0 0 1 -#> Error model: constant , initial values: a.1=1.64723790168612 -#> No covariate in the model. -#> Initial values -#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis -#> Pop.CondInit 93.81015 -9.764746 -0.9711148 -1.879937 -4.270814 0.1356441</div><div class='input'><span class='va'>d_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> -</div><div class='output co'>#> -#> -#> The following SaemixData object was successfully created: -#> -#> Object of class SaemixData -#> longitudinal data for use with the SAEM algorithm -#> Dataset ds_saemix -#> Structured data: value ~ time + name | ds -#> X variable for graphs: time () </div><div class='input'><span class='va'>f_saemix</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix</span>, <span class='va'>d_saemix</span>, <span class='va'>saemix_options</span><span class='op'>)</span> -</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Thu Nov 5 23:53:43 2020" -#> .. -#> Minimisation finished -#> [1] "Thu Nov 5 23:56:33 2020"</div><div class='img'><img src='saemix-6.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm -#> ----------------------------------- -#> ---- Data ---- -#> ----------------------------------- -#> Object of class SaemixData -#> longitudinal data for use with the SAEM algorithm -#> Dataset ds_saemix -#> Structured data: value ~ time + name | ds -#> X variable for graphs: time () -#> Dataset characteristics: -#> number of subjects: 5 -#> number of observations: 170 -#> average/min/max nb obs: 34.00 / 30 / 38 -#> First 10 lines of data: -#> ds time name value mdv cens occ ytype -#> 1 Dataset 6 0 parent 97.2 0 0 1 1 -#> 2 Dataset 6 0 parent 96.4 0 0 1 1 -#> 3 Dataset 6 3 parent 71.1 0 0 1 1 -#> 4 Dataset 6 3 parent 69.2 0 0 1 1 -#> 5 Dataset 6 6 parent 58.1 0 0 1 1 -#> 6 Dataset 6 6 parent 56.6 0 0 1 1 -#> 7 Dataset 6 10 parent 44.4 0 0 1 1 -#> 8 Dataset 6 10 parent 43.4 0 0 1 1 -#> 9 Dataset 6 20 parent 33.3 0 0 1 1 -#> 10 Dataset 6 20 parent 29.2 0 0 1 1 -#> ----------------------------------- -#> ---- Model ---- -#> ----------------------------------- -#> Nonlinear mixed-effects model -#> Model function: Mixed model generated from mmkin object Model type: structural -#> function (psi, id, xidep) -#> { -#> uid <- unique(id) -#> res_list <- parallel::mclapply(uid, function(i) { -#> transparms_optim <- psi[i, ] -#> names(transparms_optim) <- names(degparms_optim) -#> odeini_optim <- transparms_optim[odeini_optim_parm_names] -#> names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names) -#> odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] -#> ode_transparms_optim_names <- setdiff(names(transparms_optim), -#> odeini_optim_parm_names) -#> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], -#> mkin_model, transform_rates = object[[1]]$transform_rates, -#> transform_fractions = object[[1]]$transform_fractions) -#> odeparms <- c(odeparms_optim, odeparms_fixed) -#> xidep_i <- subset(xidep, id == i) -#> if (solution_type == "analytical") { -#> out_values <- mkin_model$deg_func(xidep_i, odeini, -#> odeparms) -#> } -#> else { -#> i_time <- xidep_i$time -#> i_name <- xidep_i$name -#> out_wide <- mkinpredict(mkin_model, odeparms = odeparms, -#> odeini = odeini, solution_type = solution_type, -#> outtimes = sort(unique(i_time))) -#> out_index <- cbind(as.character(i_time), as.character(i_name)) -#> out_values <- out_wide[out_index] -#> } -#> return(out_values) -#> }, mc.cores = cores) -#> res <- unlist(res_list) -#> return(res) -#> } -#> <bytecode: 0x55555998cba0> -#> <environment: 0x55555bd1fee8> -#> Nb of parameters: 6 -#> parameter names: parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis -#> distribution: -#> Parameter Distribution Estimated -#> [1,] parent_0 normal Estimated -#> [2,] log_k_A1 normal Estimated -#> [3,] f_parent_qlogis normal Estimated -#> [4,] log_k1 normal Estimated -#> [5,] log_k2 normal Estimated -#> [6,] g_qlogis normal Estimated -#> Variance-covariance matrix: -#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis -#> parent_0 1 0 0 0 0 0 -#> log_k_A1 0 1 0 0 0 0 -#> f_parent_qlogis 0 0 1 0 0 0 -#> log_k1 0 0 0 1 0 0 -#> log_k2 0 0 0 0 1 0 -#> g_qlogis 0 0 0 0 0 1 -#> Error model: constant , initial values: a.1=1.64723790168612 -#> No covariate in the model. -#> Initial values -#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis -#> Pop.CondInit 93.81015 -9.764746 -0.9711148 -1.879937 -4.270814 0.1356441 -#> ----------------------------------- -#> ---- Key algorithm options ---- -#> ----------------------------------- -#> Estimation of individual parameters (MAP) -#> Estimation of standard errors and linearised log-likelihood -#> Estimation of log-likelihood by importance sampling -#> Number of iterations: K1=200, K2=80 -#> Number of chains: 10 -#> Seed: 123456 -#> Number of MCMC iterations for IS: 5000 -#> Simulations: -#> nb of simulated datasets used for npde: 1000 -#> nb of simulated datasets used for VPC: 100 -#> Input/output -#> save the results to a file: FALSE -#> save the graphs to files: FALSE -#> ---------------------------------------------------- -#> ---- Results ---- -#> ---------------------------------------------------- -#> ----------------- Fixed effects ------------------ -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 93.78 1.35 1.4 -#> log_k_A1 -6.05 1.12 18.5 -#> f_parent_qlogis -0.97 0.20 21.1 -#> log_k1 -2.46 0.51 20.7 -#> log_k2 -3.63 0.95 26.3 -#> g_qlogis -0.08 0.36 447.7 -#> a a.1 1.88 0.11 5.9 -#> ---------------------------------------------------- -#> ----------- Variance of random effects ----------- -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 omega2.parent_0 7.85 5.76 73 -#> log_k_A1 omega2.log_k_A1 4.27 3.44 80 -#> f_parent_qlogis omega2.f_parent_qlogis 0.20 0.13 65 -#> log_k1 omega2.log_k1 1.08 0.77 72 -#> log_k2 omega2.log_k2 4.24 2.83 67 -#> g_qlogis omega2.g_qlogis 0.21 0.26 123 -#> ---------------------------------------------------- -#> ------ Correlation matrix of random effects ------ -#> ---------------------------------------------------- -#> omega2.parent_0 omega2.log_k_A1 omega2.f_parent_qlogis -#> omega2.parent_0 1 0 0 -#> omega2.log_k_A1 0 1 0 -#> omega2.f_parent_qlogis 0 0 1 -#> omega2.log_k1 0 0 0 -#> omega2.log_k2 0 0 0 -#> omega2.g_qlogis 0 0 0 -#> omega2.log_k1 omega2.log_k2 omega2.g_qlogis -#> omega2.parent_0 0 0 0 -#> omega2.log_k_A1 0 0 0 -#> omega2.f_parent_qlogis 0 0 0 -#> omega2.log_k1 1 0 0 -#> omega2.log_k2 0 1 0 -#> omega2.g_qlogis 0 0 1 -#> ---------------------------------------------------- -#> --------------- Statistical criteria ------------- -#> ---------------------------------------------------- -#> Likelihood computed by linearisation -#> -2LL= 879.7721 -#> AIC = 905.7721 -#> BIC = 900.6948 -#> -#> Likelihood computed by importance sampling -#> -2LL= 816.8276 -#> AIC = 842.8276 -#> BIC = 837.7503 -#> ----------------------------------------------------</div><div class='input'> -<span class='co'># }</span> -</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> - - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> -</div> - - </footer> - </div> - - - - - 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