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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.</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"> -      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