diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-25 13:01:23 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-25 13:01:23 +0200 |
| commit | 9f9336d59e68690472888bfdeb12944176d7d272 (patch) | |
| tree | 0d50debb2a06daa506e8c45925637ccb862a8787 /docs/reference/saemix.html | |
| parent | f345762ddcdac65b0d565c7a622d32c1f849e7c7 (diff) | |
First working version of saemix helper functions
saemix_data depends on a development version of saemix, see
pull request saemixdevelopment/saemixextension#2
Diffstat (limited to 'docs/reference/saemix.html')
| -rw-r--r-- | docs/reference/saemix.html | 489 |
1 files changed, 489 insertions, 0 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='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 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> + + |