diff options
| -rw-r--r-- | docs/dev/404.html | 2 | ||||
| -rw-r--r-- | docs/dev/articles/index.html | 2 | ||||
| -rw-r--r-- | docs/dev/authors.html | 2 | ||||
| -rw-r--r-- | docs/dev/index.html | 2 | ||||
| -rw-r--r-- | docs/dev/news/index.html | 18 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/endpoints.html | 2 | ||||
| -rw-r--r-- | docs/dev/reference/index.html | 2 | ||||
| -rw-r--r-- | docs/dev/reference/plot.mixed.mmkin.html | 6 | ||||
| -rw-r--r-- | docs/dev/reference/saem.html | 38 | ||||
| -rw-r--r-- | docs/dev/reference/summary.saem.mmkin.html | 14 |
11 files changed, 49 insertions, 41 deletions
diff --git a/docs/dev/404.html b/docs/dev/404.html index 5f29faf2..ea547a2a 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 441d49c0..57d0c0eb 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/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">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 9641eec0..8ffb9f97 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.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">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> diff --git a/docs/dev/index.html b/docs/dev/index.html index 8888633d..ff9b201f 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -38,7 +38,7 @@ </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">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 998917f2..eab75984 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/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">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> @@ -141,9 +141,9 @@ <small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small> </div> - <div id="mkin-1019000" class="section level1"> -<h1 class="page-header" data-toc-text="1.0.1.9000"> -<a href="#mkin-1019000" class="anchor"></a>mkin 1.0.1.9000<small> Unreleased </small> + <div id="mkin-1029000" class="section level1"> +<h1 class="page-header" data-toc-text="1.0.2.9000"> +<a href="#mkin-1029000" class="anchor"></a>mkin 1.0.2.9000<small> Unreleased </small> </h1> <ul> <li><p>Switch to a versioning scheme where the fourth version component indicates development versions</p></li> @@ -152,9 +152,17 @@ <li><p>‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods</p></li> </ul> </div> + <div id="mkin-102" class="section level1"> +<h1 class="page-header" data-toc-text="1.0.2"> +<a href="#mkin-102" class="anchor"></a>mkin 1.0.2<small> Unreleased </small> +</h1> +<ul> +<li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li> +</ul> +</div> <div id="mkin-101" class="section level1"> <h1 class="page-header" data-toc-text="1.0.1"> -<a href="#mkin-101" class="anchor"></a>mkin 1.0.1<small> Unreleased </small> +<a href="#mkin-101" class="anchor"></a>mkin 1.0.1<small> 2021-02-10 </small> </h1> <ul> <li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index f9b16e29..8921a1e4 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-02-06T17:26Z +last_built: 2021-02-13T11:32Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index a13e11a7..301b454f 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">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 7e98aa50..b52ecb22 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">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 601e1554..ef169074 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ </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">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> @@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.</p></td> </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>, transformations <span class='op'>=</span> <span class='st'>"saemix"</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:17 2021" +#> [1] "Sat Feb 13 12:33:07 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:23 2021"</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> +#> [1] "Sat Feb 13 12:33:13 2021"</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'># We can overlay the two variants if we generate predictions</span> <span class='va'>pred_nlme</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>, diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 4578db2a..02483bec 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." /> </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">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> @@ -261,27 +261,27 @@ 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] "Sat Feb 6 18:29:26 2021" +#> [1] "Sat Feb 13 12:33:16 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:27 2021"</div><div class='input'> +#> [1] "Sat Feb 13 12:33:18 2021"</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] "Sat Feb 6 18:29:28 2021" +#> [1] "Sat Feb 13 12:33:19 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:30 2021"</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] "Sat Feb 13 12:33:20 2021"</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] "Sat Feb 6 18:29:30 2021" +#> [1] "Sat Feb 13 12:33:20 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:32 2021"</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] "Sat Feb 13 12:33:22 2021"</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] "Sat Feb 6 18:29:32 2021" +#> [1] "Sat Feb 13 12:33:23 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:35 2021"</div><div class='input'> +#> [1] "Sat Feb 13 12:33:25 2021"</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> @@ -324,10 +324,10 @@ 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] "Sat Feb 6 18:29:37 2021" +#> [1] "Sat Feb 13 12:33:28 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:42 2021"</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] "Sat Feb 13 12:33:32 2021"</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'>#> <span class='error'>Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'> <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='mkinmod.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='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> @@ -346,15 +346,15 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='co'># 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] "Sat Feb 6 18:29:44 2021" +#> [1] "Sat Feb 13 12:33:35 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:48 2021"</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] "Sat Feb 13 12:33:39 2021"</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] "Sat Feb 6 18:29:49 2021" +#> [1] "Sat Feb 13 12:33:40 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:57 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [1] "Sat Feb 13 12:33:48 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -395,10 +395,10 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> SD.g_qlogis 0.44771 -0.86417 1.7596</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_saem_dfop_sfo</span><span class='op'>)</span> </div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></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'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:29:57 2021 -#> Date of summary: Sat Feb 6 18:29:58 2021 +#> Date of fit: Sat Feb 13 12:33:48 2021 +#> Date of summary: Sat Feb 13 12:33:48 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -413,7 +413,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 8.539 s using 300, 100 iterations +#> Fitted in 8.875 s using 300, 100 iterations #> #> Variance model: Constant variance #> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 93e1365d..81054813 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally </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">1.0.1.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span> </span> </div> @@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.</p> quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span> <span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:30:00 2021" +#> [1] "Sat Feb 13 12:33:52 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:30:11 2021"</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'>TRUE</span><span class='op'>)</span> +#> [1] "Sat Feb 13 12:34:03 2021"</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'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:30:12 2021 -#> Date of summary: Sat Feb 6 18:30:12 2021 +#> Date of fit: Sat Feb 13 12:34:04 2021 +#> Date of summary: Sat Feb 13 12:34:04 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 11.769 s using 300, 100 iterations +#> Fitted in 11.899 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> |