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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 07:12:51 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 07:12:51 +0200 |
| commit | b5ee48a86e4b1d4c05aaadb80b44954e2e994ebc (patch) | |
| tree | aeeeaf623e4a6102b9ca2440cf0e32ff7a7a1d25 /docs/reference/saemix.html | |
| parent | a77a10ea6c607346778ba0700b3b66ac393101a2 (diff) | |
Add docs generated using released version 0.9.52
Diffstat (limited to 'docs/reference/saemix.html')
| -rw-r--r-- | docs/reference/saemix.html | 446 |
1 files changed, 0 insertions, 446 deletions
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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='kw'>cores</span> <span class='kw'>=</span> <span class='kw pkg'>parallel</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></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>cores</th> - <td><p>The number of cores to be used for multicore processing. -On Windows machines, cores > 1 is currently not supported.</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='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='co'># \dontrun{</span> -<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='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>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='input'><span class='no'>m_saemix</span> <span class='kw'><-</span> <span class='fu'>saemix_model</span>(<span class='no'>f_mmkin</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 = cores) -#> res <- unlist(res_list) -#> return(res) -#> } -#> <bytecode: 0x555559668108> -#> <environment: 0x555559677c08> -#> 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</div><div class='input'><span class='no'>d_saemix</span> <span class='kw'><-</span> <span class='fu'>saemix_data</span>(<span class='no'>f_mmkin</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='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='kw'>displayProgress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>nbiter.saemix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>200</span>, <span class='fl'>80</span>)) -<span class='no'>f_saemix</span> <span class='kw'><-</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'>#> Running main SAEM algorithm -#> [1] "Tue May 26 18:25:16 2020" -#> .. -#> Minimisation finished -#> [1] "Tue May 26 18:31:09 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: 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 = cores) -#> res <- unlist(res_list) -#> return(res) -#> } -#> <bytecode: 0x555559668108> -#> <environment: 0x555559677c08> -#> 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=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(%) -#> [1,] parent_0 86.14 1.61 1.9 -#> [2,] log_k_parent -3.21 0.59 18.5 -#> [3,] log_k_A1 -4.66 0.30 6.4 -#> [4,] f_parent_ilr_1 -0.33 0.30 91.7 -#> [5,] a.1 4.68 0.27 5.8 -#> ---------------------------------------------------- -#> ----------- Variance of random effects ----------- -#> ---------------------------------------------------- -#> Parameter Estimate SE CV(%) -#> parent_0 omega2.parent_0 7.71 8.14 106 -#> log_k_parent omega2.log_k_parent 1.76 1.12 63 -#> log_k_A1 omega2.log_k_A1 0.26 0.26 101 -#> f_parent_ilr_1 omega2.f_parent_ilr_1 0.39 0.28 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= 1064.364 -#> AIC = 1082.364 -#> BIC = 1078.848 -#> -#> Likelihood computed by importance sampling -#> -2LL= 1063.462 -#> AIC = 1081.462 -#> BIC = 1077.947 -#> ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span>(<span class='no'>f_saemix</span>, <span class='kw'>plot.type</span> <span class='kw'>=</span> <span class='st'>"convergence"</span>)</div><div class='output co'>#> Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'># } -</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> 1.5.1.</p> -</div> - - </footer> - </div> - - - - - </body> -</html> - - |