<!-- 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." /> <!-- 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</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="http://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='http://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='no'>object</span>) <span class='fu'>saemix_data</span>(<span class='no'>object</span>, <span class='no'>...</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>...</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="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)])) <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>) <span class='no'>sfo_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"A1"</span>), <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</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='no'>f_mmkin</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>sfo_sfo</span>), <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>5</span>) <span class='co'># \dontrun{</span> <span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>saemix</span>)) { <span class='no'>m_saemix</span> <span class='kw'><-</span> <span class='fu'>saemix_model</span>(<span class='no'>f_mmkin</span>) <span class='no'>d_saemix</span> <span class='kw'><-</span> <span class='fu'>saemix_data</span>(<span class='no'>f_mmkin</span>) <span class='no'>saemix_options</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>, <span class='kw'>save</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>save.graphs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span>(<span class='no'>m_saemix</span>, <span class='no'>d_saemix</span>, <span class='no'>saemix_options</span>) }</div><div class='output co'>#> <span class='message'>Loading required package: saemix</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='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]]$transform_fractions) #> odeparms <- c(odeparms_optim, odeparms_fixed) #> xidep_i <- subset(xidep, id == i) #> if (analytical) { #> out_values <- mkin_model$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 = object[[1]]$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 = 15) #> res <- unlist(res_list) #> return(res) #> } #> <bytecode: 0x555559875398> #> <environment: 0x55555973a248> #> Nb of parameters: 4 #> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> distribution: #> Parameter Distribution Estimated #> [1,] parent_0 normal Estimated #> [2,] log_k_parent normal Estimated #> [3,] log_k_A1 normal Estimated #> [4,] f_parent_ilr_1 normal Estimated #> Variance-covariance matrix: #> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> parent_0 1 0 0 0 #> log_k_parent 0 1 0 0 #> log_k_A1 0 0 1 0 #> f_parent_ilr_1 0 0 0 1 #> Error model: constant , initial values: a.1=1 #> No covariate in the model. #> Initial values #> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449 #> #> #> 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 () #> Running main SAEM algorithm #> [1] "Mon May 25 12:48:51 2020" #> .</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> .</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='output co'>#> .</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#> .</div><div class='img'><img src='saemix-4.png' alt='' width='700' height='433' /></div><div class='output co'>#> #> Minimisation finished #> [1] "Mon May 25 12:56:39 2020"</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]]$transform_fractions) #> odeparms <- c(odeparms_optim, odeparms_fixed) #> xidep_i <- subset(xidep, id == i) #> if (analytical) { #> out_values <- mkin_model$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 = object[[1]]$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 = 15) #> res <- unlist(res_list) #> return(res) #> } #> <bytecode: 0x555559875398> #> <environment: 0x55555973a248> #> Nb of parameters: 4 #> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> distribution: #> Parameter Distribution Estimated #> [1,] parent_0 normal Estimated #> [2,] log_k_parent normal Estimated #> [3,] log_k_A1 normal Estimated #> [4,] f_parent_ilr_1 normal Estimated #> Variance-covariance matrix: #> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> parent_0 1 0 0 0 #> log_k_parent 0 1 0 0 #> log_k_A1 0 0 1 0 #> f_parent_ilr_1 0 0 0 1 #> Error model: constant , initial values: a.1=1 #> No covariate in the model. #> Initial values #> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449 #> ----------------------------------- #> ---- 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=300, K2=100 #> 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(%) #> [1,] parent_0 86.21 1.51 1.7 #> [2,] log_k_parent -3.21 0.59 18.5 #> [3,] log_k_A1 -4.64 0.29 6.3 #> [4,] f_parent_ilr_1 -0.32 0.30 93.2 #> [5,] a.1 4.69 0.27 5.8 #> ---------------------------------------------------- #> ----------- Variance of random effects ----------- #> ---------------------------------------------------- #> Parameter Estimate SE CV(%) #> parent_0 omega2.parent_0 6.07 7.08 117 #> log_k_parent omega2.log_k_parent 1.75 1.11 63 #> log_k_A1 omega2.log_k_A1 0.26 0.26 101 #> f_parent_ilr_1 omega2.f_parent_ilr_1 0.38 0.27 71 #> ---------------------------------------------------- #> ------ Correlation matrix of random effects ------ #> ---------------------------------------------------- #> omega2.parent_0 omega2.log_k_parent omega2.log_k_A1 #> omega2.parent_0 1 0 0 #> omega2.log_k_parent 0 1 0 #> omega2.log_k_A1 0 0 1 #> omega2.f_parent_ilr_1 0 0 0 #> omega2.f_parent_ilr_1 #> omega2.parent_0 0 #> omega2.log_k_parent 0 #> omega2.log_k_A1 0 #> omega2.f_parent_ilr_1 1 #> ---------------------------------------------------- #> --------------- Statistical criteria ------------- #> ---------------------------------------------------- #> Likelihood computed by linearisation #> -2LL= 1064.397 #> AIC = 1082.397 #> BIC = 1078.882 #> #> Likelihood computed by importance sampling #> -2LL= 1063.161 #> AIC = 1081.161 #> BIC = 1077.646 #> ----------------------------------------------------</div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm #> ----------------------------------------- #> ---- Data and Model ---- #> ----------------------------------------- #> Data #> Dataset ds_saemix #> Longitudinal data: value ~ time + name | ds #> #> Model: #> Mixed model generated from mmkin object #> 4 parameters: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> error model: constant #> No covariate #> #> Key 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=300, K2=100 #> Number of chains: 10 #> Seed: 123456 #> Number of MCMC iterations for IS: 5000 #> Input/output #> results not saved #> no graphs #> ---------------------------------------------------- #> ---- Results ---- #> Fixed effects #> Parameter Estimate SE CV(%) #> parent_0 86.214 1.506 1.75 #> log_k_parent -3.210 0.593 18.47 #> log_k_A1 -4.643 0.294 6.34 #> f_parent_ilr_1 -0.322 0.300 93.24 #> a.1 4.689 0.270 5.76 #> #> Variance of random effects #> Parameter Estimate SE CV(%) #> omega2.parent_0 6.068 7.078 116.7 #> omega2.log_k_parent 1.752 1.111 63.4 #> omega2.log_k_A1 0.256 0.257 100.5 #> omega2.f_parent_ilr_1 0.385 0.273 70.8 #> #> Statistical criteria #> Likelihood computed by linearisation #> -2LL= 1064.397 #> AIC= 1082.397 #> BIC= 1078.882 #> Likelihood computed by importance sampling #> -2LL= 1063.161 #> AIC= 1081.161 #> BIC= 1077.646 </div><div class='input'># } </div><div class='img'><img src='saemix-5.png' alt='' width='700' height='433' /></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 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