diff options
Diffstat (limited to 'docs/dev/reference')
| -rw-r--r-- | docs/dev/reference/endpoints.html | 30 | ||||
| -rw-r--r-- | docs/dev/reference/index.html | 4 | ||||
| -rw-r--r-- | docs/dev/reference/saemix-1.png | bin | 31551 -> 50490 bytes | |||
| -rw-r--r-- | docs/dev/reference/saemix-2.png | bin | 58815 -> 60503 bytes | |||
| -rw-r--r-- | docs/dev/reference/saemix-3.png | bin | 0 -> 16942 bytes | |||
| -rw-r--r-- | docs/dev/reference/saemix-4.png | bin | 0 -> 65995 bytes | |||
| -rw-r--r-- | docs/dev/reference/saemix.html | 323 |
7 files changed, 299 insertions, 58 deletions
diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index 1858e243..5a20a34c 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> </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">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -126,7 +126,7 @@ advantage that the SFORB model can also be used for metabolites." /> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -146,7 +146,7 @@ advantage that the SFORB model can also be used for metabolites." /> <div class="page-header"> <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/endpoints.R'><code>R/endpoints.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/endpoints.R'><code>R/endpoints.R</code></a></small> <div class="hidden name"><code>endpoints.Rd</code></div> </div> @@ -158,7 +158,7 @@ are equivalent to the rate constants of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites.</p> </div> - <pre class="usage"><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</pre> + <pre class="usage"><span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -179,20 +179,26 @@ of these SFORB models, equivalent to DFOP rate constants</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</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='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $distimes + <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> +</div><div class='output co'>#> $distimes #> DT50 DT90 DT50back #> parent 1.785233 15.1479 4.559973 #> </div><div class='input'> <span class='co'># \dontrun{</span> - <span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>endpoints</span>(<span class='no'>fit_2</span>)</div><div class='output co'>#> $distimes + <span class='va'>fit_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit_2</span><span class='op'>)</span> +</div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 1.886925 21.25106 6.397207 1.508293 38.83438 -#> </div><div class='input'> <span class='no'>fit_3</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>endpoints</span>(<span class='no'>fit_3</span>)</div><div class='output co'>#> $ff +#> </div><div class='input'> <span class='va'>fit_3</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFORB"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> + <span class='fu'>endpoints</span><span class='op'>(</span><span class='va'>fit_3</span><span class='op'>)</span> +</div><div class='output co'>#> $ff #> parent_free #> 1 #> @@ -203,7 +209,7 @@ of these SFORB models, equivalent to DFOP rate constants</p> #> $distimes #> DT50 DT90 DT50back DT50_parent_b1 DT50_parent_b2 #> parent 1.886925 21.25106 6.397208 1.508293 38.83438 -#> </div><div class='input'> # } +#> </div><div class='input'> <span class='co'># }</span> </div></pre> </div> @@ -221,7 +227,7 @@ of these SFORB models, equivalent to DFOP rate constants</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index a5cd6663..5d70a450 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -71,7 +71,7 @@ </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">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -678,7 +678,7 @@ kinetic models fitted with mkinfit</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/reference/saemix-1.png b/docs/dev/reference/saemix-1.png Binary files differindex 0d79300d..696fa7d9 100644 --- a/docs/dev/reference/saemix-1.png +++ b/docs/dev/reference/saemix-1.png diff --git a/docs/dev/reference/saemix-2.png b/docs/dev/reference/saemix-2.png Binary files differindex 04de70b5..6525a36c 100644 --- a/docs/dev/reference/saemix-2.png +++ b/docs/dev/reference/saemix-2.png diff --git a/docs/dev/reference/saemix-3.png b/docs/dev/reference/saemix-3.png Binary files differnew file mode 100644 index 00000000..13157f91 --- /dev/null +++ b/docs/dev/reference/saemix-3.png diff --git a/docs/dev/reference/saemix-4.png b/docs/dev/reference/saemix-4.png Binary files differnew file mode 100644 index 00000000..1e717cb2 --- /dev/null +++ b/docs/dev/reference/saemix-4.png diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html index da28bff1..5b160959 100644 --- a/docs/dev/reference/saemix.html +++ b/docs/dev/reference/saemix.html @@ -75,7 +75,7 @@ a list of datasets." /> </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">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -123,7 +123,7 @@ a list of datasets." /> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -142,7 +142,7 @@ a list of datasets." /> <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> + <small class="dont-index">Source: <a href='https://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> @@ -153,9 +153,9 @@ 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>()) + <pre class="usage"><span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>object</span>, cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> -<span class='fu'>saemix_data</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre> +<span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>object</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"> @@ -187,14 +187,17 @@ 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'>#> + <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='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</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='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='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'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span> +<span class='va'>sfo_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'>"SFO"</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><span class='op'>)</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='va'>f_mmkin</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'>sfo_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='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> +</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='va'>m_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +</div><div class='output co'>#> #> #> The following SaemixModel object was successfully created: #> @@ -234,8 +237,8 @@ variances of the deviations of the parameters from these mean values.</p> #> res <- unlist(res_list) #> return(res) #> } -#> <bytecode: 0x55555bbf17c0> -#> <environment: 0x55555bbec4e0> +#> <bytecode: 0x55555c1e7720> +#> <environment: 0x55555c1eff38> #> Nb of parameters: 4 #> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> distribution: @@ -250,11 +253,12 @@ variances of the deviations of the parameters from these mean values.</p> #> 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 +#> Error model: constant , initial values: a.1=4.97259024646577 #> 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'>#> +#> Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449</div><div class='input'><span class='va'>d_saemix</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> +</div><div class='output co'>#> #> #> The following SaemixData object was successfully created: #> @@ -262,14 +266,15 @@ variances of the deviations of the parameters from these mean values.</p> #> 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] "Wed May 27 07:45:07 2020" +#> X variable for graphs: time () </div><div class='input'><span class='va'>saemix_options</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>seed <span class='op'>=</span> <span class='fl'>123456</span>, + save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span> <span class='cn'>FALSE</span>, displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, + nbiter.saemix <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='fl'>200</span>, <span class='fl'>80</span><span class='op'>)</span><span class='op'>)</span> +<span class='va'>f_saemix</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix</span>, <span class='va'>d_saemix</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Thu Oct 15 11:55:14 2020" #> .. #> Minimisation finished -#> [1] "Wed May 27 07:51:24 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 +#> [1] "Thu Oct 15 11:57:07 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 ---- #> ----------------------------------- @@ -333,8 +338,8 @@ variances of the deviations of the parameters from these mean values.</p> #> res <- unlist(res_list) #> return(res) #> } -#> <bytecode: 0x55555bbf17c0> -#> <environment: 0x55555bbec4e0> +#> <bytecode: 0x55555c1e7720> +#> <environment: 0x55555c1eff38> #> Nb of parameters: 4 #> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1 #> distribution: @@ -349,7 +354,7 @@ variances of the deviations of the parameters from these mean values.</p> #> 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 +#> Error model: constant , initial values: a.1=4.97259024646577 #> No covariate in the model. #> Initial values #> parent_0 log_k_parent log_k_A1 f_parent_ilr_1 @@ -375,20 +380,20 @@ variances of the deviations of the parameters from these mean values.</p> #> ---------------------------------------------------- #> ----------------- 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 +#> Parameter Estimate SE CV(%) +#> parent_0 86.09 1.57 1.8 +#> log_k_parent -3.21 0.59 18.5 +#> log_k_A1 -4.69 0.31 6.6 +#> f_parent_ilr_1 -0.34 0.30 89.2 +#> a a.1 4.69 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 +#> parent_0 omega2.parent_0 7.07 7.72 109 +#> log_k_parent omega2.log_k_parent 1.75 1.11 63 +#> log_k_A1 omega2.log_k_A1 0.28 0.28 99 +#> f_parent_ilr_1 omega2.f_parent_ilr_1 0.39 0.27 71 #> ---------------------------------------------------- #> ------ Correlation matrix of random effects ------ #> ---------------------------------------------------- @@ -406,15 +411,245 @@ variances of the deviations of the parameters from these mean values.</p> #> --------------- Statistical criteria ------------- #> ---------------------------------------------------- #> Likelihood computed by linearisation -#> -2LL= 1064.364 -#> AIC = 1082.364 -#> BIC = 1078.848 +#> -2LL= 1064.35 +#> AIC = 1082.35 +#> BIC = 1078.835 #> #> 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'># } +#> -2LL= 1063.475 +#> AIC = 1081.475 +#> BIC = 1077.96 +#> ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saemix</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</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'><span class='co'># }</span> +<span class='co'># Synthetic data with two-component error</span> +<span class='va'>sampling_times</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='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> +<span class='va'>dt50_sfo_in</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='fl'>800</span>, <span class='fl'>900</span>, <span class='fl'>1000</span>, <span class='fl'>1111.11</span>, <span class='fl'>1250</span><span class='op'>)</span> +<span class='va'>k_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in</span> + +<span class='va'>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'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> + +<span class='va'>pred_sfo</span> <span class='op'><-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</span><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>, <span class='va'>sampling_times</span><span class='op'>)</span> +<span class='op'>}</span> + +<span class='va'>ds_sfo_mean</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'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456L</span><span class='op'>)</span> +<span class='va'>ds_sfo_syn</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'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>, sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>, + n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> + <span class='op'>}</span><span class='op'>)</span> +<span class='va'>f_mmkin_syn</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>m_saemix_tc</span> <span class='op'><-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</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: 0x55555c1e7720> +#> <environment: 0x55555be5b848> +#> Nb of parameters: 2 +#> parameter names: parent_0 log_k_parent +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_parent normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_k_parent +#> parent_0 1 0 +#> log_k_parent 0 1 +#> Error model: combined , initial values: a.1=2.4206146215511 b.1=0.03831266409084 +#> No covariate in the model. +#> Initial values +#> parent_0 log_k_parent +#> Pop.CondInit 100.2498 -9.33922</div><div class='input'><span class='va'>d_saemix_tc</span> <span class='op'><-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span><span class='op'>)</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='va'>f_saemix_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_tc</span>, <span class='va'>d_saemix_tc</span>, <span class='va'>saemix_options</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Thu Oct 15 11:57:25 2020" +#> .. +#> Minimisation finished +#> [1] "Thu Oct 15 11:58:16 2020" +#> Error in solve.default(Fth) : +#> Lapack routine dgesv: system is exactly singular: U[2,2] = 0 +#> Error computing the Fisher Information Matrix: singular system. +#> Error in solve.default(FO) : +#> Lapack routine dgesv: system is exactly singular: U[2,2] = 0 +#> Error computing the Fisher Information Matrix: singular system.</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: 90 +#> average/min/max nb obs: 18.00 / 18 / 18 +#> First 10 lines of data: +#> ds time name value mdv cens occ ytype +#> 1 1 0 parent 105.9 0 0 1 1 +#> 2 1 0 parent 98.0 0 0 1 1 +#> 3 1 1 parent 97.4 0 0 1 1 +#> 4 1 1 parent 100.5 0 0 1 1 +#> 5 1 3 parent 115.6 0 0 1 1 +#> 6 1 3 parent 105.6 0 0 1 1 +#> 7 1 7 parent 108.6 0 0 1 1 +#> 8 1 7 parent 117.0 0 0 1 1 +#> 9 1 14 parent 107.0 0 0 1 1 +#> 10 1 14 parent 95.8 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: 0x55555c1e7720> +#> <environment: 0x55555be5b848> +#> Nb of parameters: 2 +#> parameter names: parent_0 log_k_parent +#> distribution: +#> Parameter Distribution Estimated +#> [1,] parent_0 normal Estimated +#> [2,] log_k_parent normal Estimated +#> Variance-covariance matrix: +#> parent_0 log_k_parent +#> parent_0 1 0 +#> log_k_parent 0 1 +#> Error model: combined , initial values: a.1=2.4206146215511 b.1=0.03831266409084 +#> No covariate in the model. +#> Initial values +#> parent_0 log_k_parent +#> Pop.CondInit 100.2498 -9.33922 +#> ----------------------------------- +#> ---- 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(%) +#> parent_0 97.44 <NA> <NA> +#> log_k_parent -56.97 <NA> <NA> +#> a a.1 -7.12 <NA> <NA> +#> b b.1 0.15 <NA> <NA> +#> ---------------------------------------------------- +#> ----------- Variance of random effects ----------- +#> ---------------------------------------------------- +#> Parameter Estimate SE CV(%) +#> parent_0 omega2.parent_0 2.8 NA NA +#> log_k_parent omega2.log_k_parent 750.3 NA NA +#> ---------------------------------------------------- +#> ------ Correlation matrix of random effects ------ +#> ---------------------------------------------------- +#> omega2.parent_0 omega2.log_k_parent +#> omega2.parent_0 1 0 +#> omega2.log_k_parent 0 1 +#> ---------------------------------------------------- +#> --------------- Statistical criteria ------------- +#> ---------------------------------------------------- +#> Likelihood computed by linearisation +#> -2LL= 623.7744 +#> AIC = 635.7744 +#> BIC = 633.431 +#> +#> Likelihood computed by importance sampling +#> -2LL= 621.1909 +#> AIC = 633.1909 +#> BIC = 630.8475 +#> ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saemix_tc</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> +</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#> Plotting convergence plots</div><div class='img'><img src='saemix-4.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"> @@ -431,7 +666,7 @@ variances of the deviations of the parameters from these mean values.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> |
