diff options
Diffstat (limited to 'docs/dev/reference')
| -rw-r--r-- | docs/dev/reference/Rplot001.png | bin | 27839 -> 19782 bytes | |||
| -rw-r--r-- | docs/dev/reference/Rplot002.png | bin | 57363 -> 16877 bytes | |||
| -rw-r--r-- | docs/dev/reference/Rplot003.png | bin | 56909 -> 28593 bytes | |||
| -rw-r--r-- | docs/dev/reference/index.html | 12 | ||||
| -rw-r--r-- | docs/dev/reference/nlme.mmkin-1.png | bin | 119649 -> 119655 bytes | |||
| -rw-r--r-- | docs/dev/reference/nlme.mmkin-3.png | bin | 158930 -> 158883 bytes | |||
| -rw-r--r-- | docs/dev/reference/nlme.mmkin-4.png | bin | 163000 -> 162990 bytes | |||
| -rw-r--r-- | docs/dev/reference/nlme.mmkin.html | 61 | ||||
| -rw-r--r-- | docs/dev/reference/plot.mixed.mmkin-1.png | bin | 0 -> 86076 bytes | |||
| -rw-r--r-- | docs/dev/reference/plot.mixed.mmkin-2.png | bin | 0 -> 164488 bytes | |||
| -rw-r--r-- | docs/dev/reference/plot.mixed.mmkin-3.png | bin | 0 -> 164014 bytes | |||
| -rw-r--r-- | docs/dev/reference/plot.mixed.mmkin.html | 313 | ||||
| -rw-r--r-- | docs/dev/reference/saem.html | 39 |
13 files changed, 370 insertions, 55 deletions
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex cfc5bc2b..fc26276a 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex 8ada7133..48e8698c 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png Binary files differindex cd2014eb..b4581e35 100644 --- a/docs/dev/reference/Rplot003.png +++ b/docs/dev/reference/Rplot003.png diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 5ed2044b..ada9fb24 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -325,21 +325,21 @@ of an mmkin object</p></td> </tr><tr> <td> - <p><code><a href="plot_mixed.html">plot(<i><saem.mmkin></i>)</a></code> <code><a href="plot_mixed.html">plot(<i><nlme.mmkin></i>)</a></code> </p> + <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p> </td> - <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td> + <td><p>Fit nonlinear mixed models with SAEM</p></td> </tr><tr> <td> - <p><code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> </p> + <p><code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></i>)</a></code> </p> </td> - <td><p>Summary method for class "nlme.mmkin"</p></td> + <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td> </tr><tr> <td> - <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p> + <p><code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> </p> </td> - <td><p>Fit nonlinear mixed models with SAEM</p></td> + <td><p>Summary method for class "nlme.mmkin"</p></td> </tr><tr> <td> diff --git a/docs/dev/reference/nlme.mmkin-1.png b/docs/dev/reference/nlme.mmkin-1.png Binary files differindex 04d8b234..25bebeca 100644 --- a/docs/dev/reference/nlme.mmkin-1.png +++ b/docs/dev/reference/nlme.mmkin-1.png diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png Binary files differindex 281d6024..46846067 100644 --- a/docs/dev/reference/nlme.mmkin-3.png +++ b/docs/dev/reference/nlme.mmkin-3.png diff --git a/docs/dev/reference/nlme.mmkin-4.png b/docs/dev/reference/nlme.mmkin-4.png Binary files differindex d504e8f0..6724163f 100644 --- a/docs/dev/reference/nlme.mmkin-4.png +++ b/docs/dev/reference/nlme.mmkin-4.png diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index c3cc53ff..defef75d 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -152,7 +152,7 @@ have been obtained by fitting the same model to a list of datasets.</p> </div> <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'>nlme</span><span class='op'>(</span> +<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span> <span class='va'>model</span>, data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>fixed</span>, @@ -253,8 +253,8 @@ parameters taken from the mmkin object are used</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Upon success, a fitted nlme.mmkin object, which is an nlme object -with additional elements</p> + <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object +with additional elements. It also inherits from 'mixed.mmkin'.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of @@ -262,7 +262,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <code><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>nlme::intervals()</a></code>, <code><a href='https://rdrr.io/pkg/nlme/man/anova.lme.html'>nlme::anova.lme()</a></code> and <code><a href='https://rdrr.io/pkg/nlme/man/coef.lme.html'>nlme::coef.lme()</a></code>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code></p></div> + <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code>, <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a>, <a href='summary.nlme.mmkin.html'>summary.nlme.mmkin</a>, +parms.nlme.mmkin</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><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>, @@ -288,21 +289,21 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Log-likelihood: -238.5635 #> #> Fixed effects: -#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) -#> parent_0 log_k1 log_k2 g_ilr -#> 94.17015133 -1.80015306 -4.14738870 0.02290935 +#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) +#> parent_0 log_k1 log_k2 g_qlogis +#> 94.17015185 -1.80015278 -4.14738834 0.03239833 #> #> Random effects: -#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_ilr Residual -#> StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364 +#> parent_0 log_k1 log_k2 g_qlogis Residual +#> StdDev: 2.488249 0.8447275 1.32965 0.4651789 2.321364 #> </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 10.79857 100.7937 30.34193 4.193938 43.85443 +#> parent 10.79857 100.7937 30.34192 4.193937 43.85442 #> </div><div class='input'> <span class='co'># \dontrun{</span> <span class='va'>f_nlme_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, log_k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span> @@ -353,35 +354,35 @@ methods that will automatically work on 'nlme.mmkin' objects, such as control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> #> **Iteration 1 -#> LME step: Loglik: -404.9582, nlminb iterations: 1 +#> LME step: Loglik: -404.9583, nlminb iterations: 1 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.4114355 0.9798697 1.6990037 0.7293315 0.3354323 1.7113046 +#> -0.4114356 0.9798646 1.3524300 0.7293315 0.3354323 1.3647313 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3644 -#> fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.05532828 +#> PNLS step: RSS = 630.3633 +#> fixed effects: 93.82269 -5.455993 -0.9601037 -1.862196 -4.199671 0.07824609 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 0.7885368 0.5822683 +#> 0.7897284 0.5822782 #> #> **Iteration 2 #> LME step: Loglik: -407.7755, nlminb iterations: 11 #> reStruct parameters: -#> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.371224133 0.003056179 1.789939402 0.724671158 0.301602977 1.754200729 +#> ds1 ds2 ds3 ds4 ds5 ds6 +#> -0.37122411 0.00305562 1.44336560 0.72467122 0.30160310 1.40762692 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3633 -#> fixed effects: 93.82269 -5.455992 -0.6788958 -1.862196 -4.199671 0.05532831 +#> PNLS step: RSS = 630.3637 +#> fixed effects: 93.82269 -5.455992 -0.9601036 -1.862196 -4.199671 0.0782462 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 4.789774e-07 2.200661e-05 </div><div class='input'> +#> 1.375673e-06 9.758294e-06 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> </div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273 +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 #> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> </div><div class='output co'>#> $ff @@ -400,7 +401,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 11.07091 104.6320 31.49738 4.462384 46.20825 -#> A1 162.30536 539.1667 NA NA NA +#> A1 162.30523 539.1663 NA NA NA #> </div><div class='input'> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span> <span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span> @@ -425,23 +426,23 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Log-likelihood: -238.4298 #> #> Fixed effects: -#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) -#> parent_0 log_k1 log_k2 g_ilr -#> 94.04774463 -1.82339924 -4.16715509 0.04020161 +#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) +#> parent_0 log_k1 log_k2 g_qlogis +#> 94.04774566 -1.82339808 -4.16715311 0.05685186 #> #> Random effects: -#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_ilr Residual -#> StdDev: 2.473883 0.8499901 1.337187 0.3294411 1 +#> parent_0 log_k1 log_k2 g_qlogis Residual +#> StdDev: 2.473881 0.8499884 1.337185 0.4659005 1 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 2.23222625 0.01262414 </div><div class='input'> +#> 2.23224114 0.01262341 </div><div class='input'> <span class='va'>f_2_obs</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'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>, <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> diff --git a/docs/dev/reference/plot.mixed.mmkin-1.png b/docs/dev/reference/plot.mixed.mmkin-1.png Binary files differnew file mode 100644 index 00000000..5cb33214 --- /dev/null +++ b/docs/dev/reference/plot.mixed.mmkin-1.png diff --git a/docs/dev/reference/plot.mixed.mmkin-2.png b/docs/dev/reference/plot.mixed.mmkin-2.png Binary files differnew file mode 100644 index 00000000..c0d67204 --- /dev/null +++ b/docs/dev/reference/plot.mixed.mmkin-2.png diff --git a/docs/dev/reference/plot.mixed.mmkin-3.png b/docs/dev/reference/plot.mixed.mmkin-3.png Binary files differnew file mode 100644 index 00000000..67058e6c --- /dev/null +++ b/docs/dev/reference/plot.mixed.mmkin-3.png diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html new file mode 100644 index 00000000..4108aea3 --- /dev/null +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -0,0 +1,313 @@ +<!-- 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>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin • 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="Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin" /> +<meta property="og:description" content="Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object" /> + + +<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>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mixed.mmkin.R'><code>R/plot.mixed.mmkin.R</code></a></small> + <div class="hidden name"><code>plot.mixed.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p> + </div> + + <pre class="usage"><span class='co'># S3 method for mixed.mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> + <span class='va'>x</span>, + i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>, + obs_vars <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'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, + standardized <span class='op'>=</span> <span class='cn'>TRUE</span>, + xlab <span class='op'>=</span> <span class='st'>"Time"</span>, + xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</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='va'>time</span><span class='op'>)</span>, + resplot <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'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>, + ymax <span class='op'>=</span> <span class='st'>"auto"</span>, + maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, + ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'><=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'><=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>, + nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>, + rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>, + rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>, + pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>, + col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>, + lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>, + frame <span class='op'>=</span> <span class='cn'>TRUE</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>x</th> + <td><p>An object of class <a href='saem.html'>saem.mmkin</a> or <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td> + </tr> + <tr> + <th>i</th> + <td><p>A numeric index to select datasets for which to plot the individual predictions, +in case plots get too large</p></td> + </tr> + <tr> + <th>obs_vars</th> + <td><p>A character vector of names of the observed variables for +which the data and the model should be plotted. Defauls to all observed +variables in the model.</p></td> + </tr> + <tr> + <th>standardized</th> + <td><p>Should the residuals be standardized? Only takes effect if +<code>resplot = "time"</code>.</p></td> + </tr> + <tr> + <th>xlab</th> + <td><p>Label for the x axis.</p></td> + </tr> + <tr> + <th>xlim</th> + <td><p>Plot range in x direction.</p></td> + </tr> + <tr> + <th>resplot</th> + <td><p>Should the residuals plotted against time or against +predicted values?</p></td> + </tr> + <tr> + <th>ymax</th> + <td><p>Vector of maximum y axis values</p></td> + </tr> + <tr> + <th>maxabs</th> + <td><p>Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".</p></td> + </tr> + <tr> + <th>ncol.legend</th> + <td><p>Number of columns to use in the legend</p></td> + </tr> + <tr> + <th>nrow.legend</th> + <td><p>Number of rows to use in the legend</p></td> + </tr> + <tr> + <th>rel.height.legend</th> + <td><p>The relative height of the legend shown on top</p></td> + </tr> + <tr> + <th>rel.height.bottom</th> + <td><p>The relative height of the bottom plot row</p></td> + </tr> + <tr> + <th>pch_ds</th> + <td><p>Symbols to be used for plotting the data.</p></td> + </tr> + <tr> + <th>col_ds</th> + <td><p>Colors used for plotting the observed data and the +corresponding model prediction lines for the different datasets.</p></td> + </tr> + <tr> + <th>lty_ds</th> + <td><p>Line types to be used for the model predictions.</p></td> + </tr> + <tr> + <th>frame</th> + <td><p>Should a frame be drawn around the plots?</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The function is called for its side effect.</p> + <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + + <p>Johannes Ranke</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><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='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='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'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span> +<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>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='co'># \dontrun{</span> +<span class='va'>f</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='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mixed.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span> +<span class='co'># tolerance in order to speed up the fit for this example evaluation</span> +<span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='va'>f_saem</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Mon Nov 9 17:18:17 2020" +#> .... +#> Minimisation finished +#> [1] "Mon Nov 9 17:18:26 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></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> + + + + + </body> +</html> + + diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 26f4c3e3..f1b4c421 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -206,7 +206,8 @@ by the saemix function?</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>An S3 object of class 'saem.mmkin', containing the fitted -<a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a> as a list component named 'so'.</p> +<a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a> as a list component named 'so'. The +object also inherits from 'mixed.mmkin'.</p> <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> @@ -218,7 +219,7 @@ psi0 of <code><a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix:: using <a href='mmkin.html'>mmkin</a>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <div class='dont-index'><p><a href='summary.saem.mmkin.html'>summary.saem.mmkin</a></p></div> + <div class='dont-index'><p><a href='summary.saem.mmkin.html'>summary.saem.mmkin</a> <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a></p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> @@ -229,27 +230,27 @@ using <a href='mmkin.html'>mmkin</a>.</p> 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'>f_saem_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:11 2020" +#> [1] "Mon Nov 9 17:18:28 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:13 2020"</div><div class='input'> +#> [1] "Mon Nov 9 17:18:30 2020"</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'>f_saem_sfo</span> <span class='op'><-</span> <span class='fu'>saem</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'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:14 2020" +#> [1] "Mon Nov 9 17:18:31 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:16 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</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> +#> [1] "Mon Nov 9 17:18:33 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</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'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:16 2020" +#> [1] "Mon Nov 9 17:18:33 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:18 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</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> +#> [1] "Mon Nov 9 17:18:35 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</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'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:19 2020" +#> [1] "Mon Nov 9 17:18:36 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:22 2020"</div><div class='input'> +#> [1] "Mon Nov 9 17:18:39 2020"</div><div class='input'> <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span> <span class='co'># functions from saemix</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> @@ -295,10 +296,10 @@ using <a href='mmkin.html'>mmkin</a>.</p> <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'>f_saem_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saem</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'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:24 2020" +#> [1] "Mon Nov 9 17:18:41 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:29 2020"</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_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +#> [1] "Mon Nov 9 17:18:46 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</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 #> 1 467.7644 465.0305 #> 2 469.4862 466.3617</div><div class='input'> @@ -318,20 +319,20 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='co'># solutions written for mkin this took around four minutes</span> <span class='va'>f_saem_sfo_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:31 2020" +#> [1] "Mon Nov 9 17:18:48 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:36 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Nov 9 17:18:53 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:37 2020" +#> [1] "Mon Nov 9 17:18:54 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:46 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> +#> [1] "Mon Nov 9 17:19:03 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Nov 9 09:03:47 2020 -#> Date of summary: Mon Nov 9 09:03:47 2020 +#> Date of fit: Mon Nov 9 17:19:04 2020 +#> Date of summary: Mon Nov 9 17:19:04 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -346,7 +347,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.758 s using 300, 100 iterations +#> Fitted in 9.941 s using 300, 100 iterations #> #> Variance model: Constant variance #> |
