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Diffstat (limited to 'docs/dev/reference')
| -rw-r--r-- | docs/dev/reference/Rplot001.png | bin | 19395 -> 1011 bytes | |||
| -rw-r--r-- | docs/dev/reference/mccall81_245T-1.png | bin | 0 -> 65341 bytes | |||
| -rw-r--r-- | docs/dev/reference/mccall81_245T.html | 77 | ||||
| -rw-r--r-- | docs/dev/reference/saem.html | 50 | ||||
| -rw-r--r-- | docs/dev/reference/summary.saem.mmkin.html | 432 |
5 files changed, 296 insertions, 263 deletions
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex bca41e2c..17a35806 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/mccall81_245T-1.png b/docs/dev/reference/mccall81_245T-1.png Binary files differnew file mode 100644 index 00000000..5daa5f18 --- /dev/null +++ b/docs/dev/reference/mccall81_245T-1.png diff --git a/docs/dev/reference/mccall81_245T.html b/docs/dev/reference/mccall81_245T.html index fa352d0a..255c3568 100644 --- a/docs/dev/reference/mccall81_245T.html +++ b/docs/dev/reference/mccall81_245T.html @@ -74,7 +74,7 @@ </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> @@ -122,7 +122,7 @@ </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> @@ -151,12 +151,12 @@ extracts.</p> </div> - <pre class="usage"><span class='no'>mccall81_245T</span></pre> + <pre class="usage"><span class='va'>mccall81_245T</span></pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A dataframe containing the following variables.</p><dl'> + <p>A dataframe containing the following variables.</p><dl> <dt><code>name</code></dt><dd><p>the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is a legitimate object name in R, which is necessary for specifying models using @@ -174,46 +174,71 @@ <a href='http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), - <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</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'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) -#> T245_0 1.038550e+02 2.184707514 47.537272 4.472189e-18 -#> k_T245 4.337042e-02 0.001898397 22.845818 2.276912e-13 -#> k_phenol 4.050581e-01 0.298699428 1.356073 9.756994e-02 -#> k_anisole 6.678742e-03 0.000802144 8.326114 2.623179e-07 -#> f_T245_to_phenol 6.227599e-01 0.398534167 1.562626 6.949418e-02 -#> f_phenol_to_anisole 1.000000e+00 0.671844168 1.488440 7.867794e-02 -#> sigma 2.514628e+00 0.490755943 5.123989 6.233164e-05 + <pre class="examples"><div class='input'> <span class='va'>SFO_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>, + phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span><span class='op'>)</span>, + anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <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'>fit.1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) +#> T245_0 1.038550e+02 2.1847074888 47.537272 4.472189e-18 +#> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13 +#> k_phenol 4.050581e-01 0.2986993400 1.356073 9.756988e-02 +#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07 +#> f_T245_to_phenol 6.227599e-01 0.3985340295 1.562627 6.949412e-02 +#> f_phenol_to_anisole 1.000000e+00 0.6718439378 1.488441 7.867787e-02 +#> sigma 2.514628e+00 0.4907558750 5.123989 6.233156e-05 #> Lower Upper -#> T245_0 99.246061371 1.084640e+02 +#> T245_0 99.246061370 1.084640e+02 #> k_T245 0.039631621 4.746194e-02 #> k_phenol 0.218013878 7.525762e-01 #> k_anisole 0.005370739 8.305299e-03 -#> f_T245_to_phenol 0.547559082 6.924813e-01 +#> f_T245_to_phenol 0.547559083 6.924813e-01 #> f_phenol_to_anisole 0.000000000 1.000000e+00 -#> sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff +#> sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> +</div><div class='output co'>#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 1.748047e-10 +#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 #> anisole 103.784092 344.76329 -#> </div><div class='input'> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span> - <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), - <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), - <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Initial parameter(s) k_phenol_sink not used in the model</span></div><div class='output co'>#> <span class='error'>Error in data.frame(value = c(state.ini.fixed, parms.fixed)): row names contain missing values</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff +#> </div><div class='input'> <span class='co'># formation fraction from phenol to anisol is practically 1. As we cannot</span> + <span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span> + <span class='co'># the sink in the model generation</span> + <span class='va'>SFO_SFO_SFO_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>, + phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, + anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <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='va'>fit.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO_2</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, + quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> +</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> T245_0 1.038550e+02 2.1623653027 48.028439 4.993108e-19 99.271020526 +#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573555e-14 0.039650977 +#> k_phenol 4.050582e-01 0.1177237248 3.440752 1.679252e-03 0.218746585 +#> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 +#> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198825 2.039410e-12 0.547975628 +#> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 +#> Upper +#> T245_0 108.43904097 +#> k_T245 0.04743877 +#> k_phenol 0.75005577 +#> k_anisole 0.00829550 +#> f_T245_to_phenol 0.69212306 +#> sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> +</div><div class='output co'>#> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 1.748047e-10 +#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 #> anisole 103.784092 344.76329 -#> </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#> <span class='error'>Error in identical(fit$err_mod, "const"): object 'fit.2' not found</span></div><div class='input'> # } +#> </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> +</div><div class='img'><img src='mccall81_245T-1.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"> @@ -230,7 +255,7 @@ </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/saem.html b/docs/dev/reference/saem.html index bc54e1e1..d0c3495a 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -141,7 +141,7 @@ Expectation Maximisation algorithm (SAEM)." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit nonlinear mixed models with SAEM</h1> - <small class="dont-index">Source: <a href='https://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/saem.R'><code>R/saem.R</code></a></small> <div class="hidden name"><code>saem.Rd</code></div> </div> @@ -161,6 +161,7 @@ Expectation Maximisation algorithm (SAEM).</p> cores <span class='op'>=</span> <span class='fl'>1</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, suppressPlot <span class='op'>=</span> <span class='cn'>TRUE</span>, + quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span> <span class='op'>)</span> @@ -185,19 +186,19 @@ Expectation Maximisation algorithm (SAEM).</p> </tr> <tr> <th>...</th> - <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixData.html'>saemix::saemixData</a> -and <a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel</a>.</p></td> + <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel</a>.</p></td> </tr> <tr> <th>cores</th> <td><p>The number of cores to be used for multicore processing using <code><a href='https://rdrr.io/r/parallel/mclapply.html'>parallel::mclapply()</a></code>. Using more than 1 core is experimental and may -lead to uncontrolled forking, apparently depending on the BLAS version +lead to excessive forking, apparently depending on the BLAS version used.</p></td> </tr> <tr> <th>verbose</th> - <td><p>Should we print information about created objects?</p></td> + <td><p>Should we print information about created objects of +type <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> and <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a>?</p></td> </tr> <tr> <th>suppressPlot</th> @@ -205,6 +206,11 @@ used.</p></td> by the saemix function?</p></td> </tr> <tr> + <th>quiet</th> + <td><p>Should we suppress the messages saemix prints at the beginning +and the end of the optimisation process?</p></td> + </tr> + <tr> <th>x</th> <td><p>An saem.mmkin object to print</p></td> </tr> @@ -241,27 +247,27 @@ 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] "Wed Nov 11 09:36:41 2020" +#> [1] "Wed Nov 11 19:47:58 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:43 2020"</div><div class='input'> +#> [1] "Wed Nov 11 19:48:00 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] "Wed Nov 11 09:36:44 2020" +#> [1] "Wed Nov 11 19:48:01 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:45 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] "Wed Nov 11 19:48:03 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] "Wed Nov 11 09:36:46 2020" +#> [1] "Wed Nov 11 19:48:03 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:48 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] "Wed Nov 11 19:48:05 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] "Wed Nov 11 09:36:48 2020" +#> [1] "Wed Nov 11 19:48:06 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:51 2020"</div><div class='input'> +#> [1] "Wed Nov 11 19:48:08 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> @@ -307,10 +313,10 @@ 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] "Wed Nov 11 09:36:54 2020" +#> [1] "Wed Nov 11 19:48:11 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:59 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] "Wed Nov 11 19:48:16 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 #> 1 467.7096 464.9757 #> 2 469.5208 466.3963</div><div class='input'> @@ -330,15 +336,15 @@ 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] "Wed Nov 11 09:37:01 2020" +#> [1] "Wed Nov 11 19:48:18 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:37:06 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] "Wed Nov 11 19:48:23 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] "Wed Nov 11 09:37:06 2020" +#> [1] "Wed Nov 11 19:48:23 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:37:15 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [1] "Wed Nov 11 19:48:32 2020"</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: @@ -384,8 +390,8 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> LL by is "-407.78 (df=13)"</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: Wed Nov 11 09:37:16 2020 -#> Date of summary: Wed Nov 11 09:37:16 2020 +#> Date of fit: Wed Nov 11 19:48:33 2020 +#> Date of summary: Wed Nov 11 19:48:33 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -400,7 +406,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.691 s using 300, 100 iterations +#> Fitted in 9.564 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 e718806e..8a5d001a 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -156,7 +156,7 @@ endpoints such as formation fractions and DT50 values. Optionally </div> <pre class="usage"><span class='co'># S3 method for saem.mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span> <span class='co'># S3 method for summary.saem.mmkin</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>verbose</span>, <span class='va'>...</span><span class='op'>)</span></pre> @@ -256,18 +256,20 @@ saemix authors for the parts inherited from saemix.</p> <span class='co'># \dontrun{</span> <span class='co'># Evaluate using mmkin and saem</span> -<span class='va'>f_mmkin_dfop_sfo</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='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_syn_dfop_sfo</span>, 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_mmkin_dfop_sfo</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='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_syn_dfop_sfo</span>, + 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] "Mon Nov 9 09:24:08 2020" +#> [1] "Wed Nov 11 19:48:36 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:24:21 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.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 +#> [1] "Wed Nov 11 19:48:48 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'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> +#> LL by is "-401.01 (df=14)"</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 09:24:22 2020 -#> Date of summary: Mon Nov 9 09:24:22 2020 +#> Date of fit: Wed Nov 11 19:48:49 2020 +#> Date of summary: Wed Nov 11 19:48:49 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -282,7 +284,7 @@ saemix authors for the parts inherited from saemix.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 13.457 s using 300, 100 iterations +#> Fitted in 13.272 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> @@ -298,232 +300,232 @@ saemix authors for the parts inherited from saemix.</p> #> Results: #> #> Likelihood computed by importance sampling -#> AIC BIC logLik -#> 828.8639 823.396 -400.432 +#> AIC BIC logLik +#> 830 824.5 -401 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> est. lower upper -#> parent_0 101.35835807 97.8846505 104.8320657 -#> log_k_m1 -4.06644838 -4.1861445 -3.9467523 -#> f_parent_qlogis -0.94818070 -1.3124706 -0.5838908 -#> log_k1 -2.92096208 -3.7684319 -2.0734922 -#> log_k2 -3.54529352 -4.2532018 -2.8373852 -#> g_qlogis -0.09254475 -0.9675848 0.7824953 +#> est. lower upper +#> parent_0 101.4423 97.862 105.0224 +#> log_k_m1 -4.0703 -4.191 -3.9495 +#> f_parent_qlogis -0.9539 -1.313 -0.5949 +#> log_k1 -2.9724 -3.811 -2.1342 +#> log_k2 -3.4977 -4.206 -2.7895 +#> g_qlogis -0.0449 -1.116 1.0262 #> #> Correlation: #> prnt_0 lg_k_1 f_prn_ log_k1 log_k2 -#> log_k_m1 -0.217 -#> f_parent_qlogis -0.153 0.203 -#> log_k1 0.066 -0.067 -0.035 -#> log_k2 0.002 0.010 0.001 -0.041 -#> g_qlogis -0.014 0.005 0.015 -0.163 -0.106 +#> log_k_m1 -0.207 +#> f_parent_qlogis -0.148 0.202 +#> log_k1 0.040 -0.038 -0.022 +#> log_k2 0.022 -0.015 -0.009 0.001 +#> g_qlogis -0.012 0.005 0.011 -0.173 -0.130 #> #> Random effects: -#> est. lower upper -#> SD.parent_0 2.70034095 -0.7003441 6.1010260 -#> SD.log_k_m1 0.08269959 -0.0456860 0.2110852 -#> SD.f_parent_qlogis 0.39452161 0.1376650 0.6513782 -#> SD.log_k1 0.90605744 0.2946394 1.5174755 -#> SD.log_k2 0.77604374 0.2646031 1.2874844 -#> SD.g_qlogis 0.37531563 -0.6836568 1.4342881 +#> est. lower upper +#> SD.parent_0 2.88564 -0.5163 6.2876 +#> SD.log_k_m1 0.08502 -0.0427 0.2127 +#> SD.f_parent_qlogis 0.38857 0.1350 0.6421 +#> SD.log_k1 0.92338 0.3296 1.5172 +#> SD.log_k2 0.78644 0.2817 1.2912 +#> SD.g_qlogis 0.34614 -0.8727 1.5650 #> #> Variance model: -#> est. lower upper -#> a.1 0.65736042 0.48750246 0.82721839 -#> b.1 0.06424086 0.05011127 0.07837046 +#> est. lower upper +#> a.1 0.65859 0.49250 0.82469 +#> b.1 0.06411 0.05006 0.07817 #> #> Backtransformed parameters with asymmetric confidence intervals: -#> est. lower upper -#> parent_0 101.35835807 97.88465048 104.83206565 -#> k_m1 0.01713815 0.01520479 0.01931734 -#> f_parent_to_m1 0.27925085 0.21207372 0.35803781 -#> k1 0.05388182 0.02308824 0.12574588 -#> k2 0.02886015 0.01421864 0.05857864 -#> g 0.47688031 0.27536216 0.68621766 +#> est. lower upper +#> parent_0 101.44231 97.86220 105.02241 +#> k_m1 0.01707 0.01513 0.01926 +#> f_parent_to_m1 0.27811 0.21201 0.35551 +#> k1 0.05118 0.02213 0.11834 +#> k2 0.03027 0.01491 0.06145 +#> g 0.48878 0.24675 0.73618 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.2793 -#> parent_sink 0.7207 +#> parent_m1 0.2781 +#> parent_sink 0.7219 #> #> Estimated disappearance times: #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 17.57 63.28 19.05 12.86 24.02 -#> m1 40.44 134.35 NA NA NA +#> parent 17.53 61.64 18.55 13.54 22.9 +#> m1 40.60 134.88 NA NA NA #> #> Data: -#> ds name time observed predicted residual standardized -#> ds 1 parent 0 89.8 9.848e+01 -8.68339 1.243323 -#> ds 1 parent 0 104.1 9.848e+01 5.61661 -0.804209 -#> ds 1 parent 1 88.7 9.403e+01 -5.32943 0.795687 -#> ds 1 parent 1 95.5 9.403e+01 1.47057 -0.219557 -#> ds 1 parent 3 81.8 8.584e+01 -4.04129 0.654791 -#> ds 1 parent 3 94.5 8.584e+01 8.65871 -1.402929 -#> ds 1 parent 7 71.5 7.196e+01 -0.46034 0.087182 -#> ds 1 parent 7 70.3 7.196e+01 -1.66034 0.314448 -#> ds 1 parent 14 54.2 5.384e+01 0.36125 -0.087766 -#> ds 1 parent 14 49.6 5.384e+01 -4.23875 1.029821 -#> ds 1 parent 28 31.5 3.220e+01 -0.69922 0.256514 -#> ds 1 parent 28 28.8 3.220e+01 -3.39922 1.247025 -#> ds 1 parent 60 12.1 1.264e+01 -0.53539 0.364441 -#> ds 1 parent 60 13.6 1.264e+01 0.96461 -0.656614 -#> ds 1 parent 90 6.2 6.081e+00 0.11929 -0.113824 -#> ds 1 parent 90 8.3 6.081e+00 2.21929 -2.117659 -#> ds 1 parent 120 2.2 3.055e+00 -0.85531 1.001955 -#> ds 1 parent 120 2.4 3.055e+00 -0.65531 0.767664 -#> ds 1 m1 1 0.3 1.115e+00 -0.81540 1.118502 -#> ds 1 m1 1 0.2 1.115e+00 -0.91540 1.255673 -#> ds 1 m1 3 2.2 3.111e+00 -0.91095 1.062691 -#> ds 1 m1 3 3.0 3.111e+00 -0.11095 0.129432 -#> ds 1 m1 7 6.5 6.292e+00 0.20799 -0.195930 -#> ds 1 m1 7 5.0 6.292e+00 -1.29201 1.217079 -#> ds 1 m1 14 10.2 9.886e+00 0.31362 -0.242650 -#> ds 1 m1 14 9.5 9.886e+00 -0.38638 0.298948 -#> ds 1 m1 28 12.2 1.259e+01 -0.39388 0.268603 -#> ds 1 m1 28 13.4 1.259e+01 0.80612 -0.549726 -#> ds 1 m1 60 11.8 1.092e+01 0.87659 -0.644982 -#> ds 1 m1 60 13.2 1.092e+01 2.27659 -1.675083 -#> ds 1 m1 90 6.6 7.814e+00 -1.21445 1.047509 -#> ds 1 m1 90 9.3 7.814e+00 1.48555 -1.281347 -#> ds 1 m1 120 3.5 5.275e+00 -1.77526 1.781944 -#> ds 1 m1 120 5.4 5.275e+00 0.12474 -0.125213 -#> ds 2 parent 0 118.0 1.045e+02 13.54366 -1.838241 -#> ds 2 parent 0 99.8 1.045e+02 -4.65634 0.631992 -#> ds 2 parent 1 90.2 9.872e+01 -8.51733 1.216927 -#> ds 2 parent 1 94.6 9.872e+01 -4.11733 0.588270 -#> ds 2 parent 3 96.1 8.872e+01 7.38009 -1.160975 -#> ds 2 parent 3 78.4 8.872e+01 -10.31991 1.623443 -#> ds 2 parent 7 77.9 7.337e+01 4.52584 -0.842647 -#> ds 2 parent 7 77.7 7.337e+01 4.32584 -0.805409 -#> ds 2 parent 14 56.0 5.616e+01 -0.15795 0.037034 -#> ds 2 parent 14 54.7 5.616e+01 -1.45795 0.341841 -#> ds 2 parent 28 36.6 3.859e+01 -1.99435 0.635813 -#> ds 2 parent 28 36.8 3.859e+01 -1.79435 0.572052 -#> ds 2 parent 60 22.1 2.113e+01 0.97273 -0.482843 -#> ds 2 parent 60 24.7 2.113e+01 3.57273 -1.773425 -#> ds 2 parent 90 12.4 1.258e+01 -0.17909 0.122205 -#> ds 2 parent 90 10.8 1.258e+01 -1.77909 1.214019 -#> ds 2 parent 120 6.8 7.509e+00 -0.70864 0.621767 -#> ds 2 parent 120 7.9 7.509e+00 0.39136 -0.343380 -#> ds 2 m1 1 1.3 1.466e+00 -0.16566 0.220431 -#> ds 2 m1 3 3.7 3.947e+00 -0.24719 0.271357 -#> ds 2 m1 3 4.7 3.947e+00 0.75281 -0.826421 -#> ds 2 m1 7 8.1 7.501e+00 0.59910 -0.525881 -#> ds 2 m1 7 7.9 7.501e+00 0.39910 -0.350323 -#> ds 2 m1 14 10.1 1.082e+01 -0.71564 0.529253 -#> ds 2 m1 14 10.3 1.082e+01 -0.51564 0.381342 -#> ds 2 m1 28 10.7 1.248e+01 -1.78322 1.221977 -#> ds 2 m1 28 12.2 1.248e+01 -0.28322 0.194082 -#> ds 2 m1 60 10.7 1.058e+01 0.12295 -0.091967 -#> ds 2 m1 60 12.5 1.058e+01 1.92295 -1.438427 -#> ds 2 m1 90 9.1 8.029e+00 1.07074 -0.912688 -#> ds 2 m1 90 7.4 8.029e+00 -0.62926 0.536381 -#> ds 2 m1 120 6.1 5.816e+00 0.28391 -0.275375 -#> ds 2 m1 120 4.5 5.816e+00 -1.31609 1.276529 -#> ds 3 parent 0 106.2 1.048e+02 1.43237 -0.193885 -#> ds 3 parent 0 106.9 1.048e+02 2.13237 -0.288636 -#> ds 3 parent 1 107.4 9.616e+01 11.23530 -1.643774 -#> ds 3 parent 1 96.1 9.616e+01 -0.06470 0.009466 -#> ds 3 parent 3 79.4 8.238e+01 -2.97800 0.500554 -#> ds 3 parent 3 82.6 8.238e+01 0.22200 -0.037315 -#> ds 3 parent 7 63.9 6.427e+01 -0.36601 0.076477 -#> ds 3 parent 7 62.4 6.427e+01 -1.86601 0.389900 -#> ds 3 parent 14 51.0 4.825e+01 2.74941 -0.731807 -#> ds 3 parent 14 47.1 4.825e+01 -1.15059 0.306250 -#> ds 3 parent 28 36.1 3.501e+01 1.09474 -0.376700 -#> ds 3 parent 28 36.6 3.501e+01 1.59474 -0.548750 -#> ds 3 parent 60 20.1 2.050e+01 -0.40214 0.203675 -#> ds 3 parent 60 19.8 2.050e+01 -0.70214 0.355617 -#> ds 3 parent 90 11.3 1.257e+01 -1.27210 0.868328 -#> ds 3 parent 90 10.7 1.257e+01 -1.87210 1.277883 -#> ds 3 parent 120 8.2 7.710e+00 0.48984 -0.424960 -#> ds 3 parent 120 7.3 7.710e+00 -0.41016 0.355837 -#> ds 3 m1 0 0.8 -1.421e-13 0.80000 -1.216988 -#> ds 3 m1 1 1.8 1.928e+00 -0.12842 0.164382 -#> ds 3 m1 1 2.3 1.928e+00 0.37158 -0.475623 -#> ds 3 m1 3 4.2 4.925e+00 -0.72511 0.744654 -#> ds 3 m1 3 4.1 4.925e+00 -0.82511 0.847349 -#> ds 3 m1 7 6.8 8.542e+00 -1.74215 1.444429 -#> ds 3 m1 7 10.1 8.542e+00 1.55785 -1.291627 -#> ds 3 m1 14 11.4 1.096e+01 0.44492 -0.326877 -#> ds 3 m1 14 12.8 1.096e+01 1.84492 -1.355438 -#> ds 3 m1 28 11.5 1.122e+01 0.27920 -0.202587 -#> ds 3 m1 28 10.6 1.122e+01 -0.62080 0.450442 -#> ds 3 m1 60 7.5 8.912e+00 -1.41171 1.147867 -#> ds 3 m1 60 8.6 8.912e+00 -0.31171 0.253453 -#> ds 3 m1 90 7.3 6.683e+00 0.61657 -0.567369 -#> ds 3 m1 90 8.1 6.683e+00 1.41657 -1.303536 -#> ds 3 m1 120 5.3 4.825e+00 0.47527 -0.491339 -#> ds 3 m1 120 3.8 4.825e+00 -1.02473 1.059361 -#> ds 4 parent 0 104.7 9.956e+01 5.14415 -0.729366 -#> ds 4 parent 0 88.3 9.956e+01 -11.25585 1.595915 -#> ds 4 parent 1 94.2 9.639e+01 -2.19462 0.320391 -#> ds 4 parent 1 94.6 9.639e+01 -1.79462 0.261995 -#> ds 4 parent 3 78.1 9.044e+01 -12.34368 1.908558 -#> ds 4 parent 3 96.5 9.044e+01 6.05632 -0.936418 -#> ds 4 parent 7 76.2 7.988e+01 -3.67799 0.635364 -#> ds 4 parent 7 77.8 7.988e+01 -2.07799 0.358968 -#> ds 4 parent 14 70.8 6.492e+01 5.88059 -1.218059 -#> ds 4 parent 14 67.3 6.492e+01 2.38059 -0.493097 -#> ds 4 parent 28 43.1 4.442e+01 -1.32411 0.377111 -#> ds 4 parent 28 45.1 4.442e+01 0.67589 -0.192494 -#> ds 4 parent 60 21.3 2.136e+01 -0.06143 0.030267 -#> ds 4 parent 60 23.5 2.136e+01 2.13857 -1.053671 -#> ds 4 parent 90 11.8 1.187e+01 -0.06548 0.046122 -#> ds 4 parent 90 12.1 1.187e+01 0.23452 -0.165204 -#> ds 4 parent 120 7.0 6.864e+00 0.13645 -0.124240 -#> ds 4 parent 120 6.2 6.864e+00 -0.66355 0.604171 -#> ds 4 m1 0 1.6 8.811e-13 1.60000 -2.433977 -#> ds 4 m1 1 0.9 6.943e-01 0.20568 -0.293006 -#> ds 4 m1 3 3.7 1.964e+00 1.73568 -2.215152 -#> ds 4 m1 3 2.0 1.964e+00 0.03568 -0.045539 -#> ds 4 m1 7 3.6 4.082e+00 -0.48184 0.523977 -#> ds 4 m1 7 3.8 4.082e+00 -0.28184 0.306486 -#> ds 4 m1 14 7.1 6.694e+00 0.40571 -0.373099 -#> ds 4 m1 14 6.6 6.694e+00 -0.09429 0.086710 -#> ds 4 m1 28 9.5 9.147e+00 0.35343 -0.283895 -#> ds 4 m1 28 9.3 9.147e+00 0.15343 -0.123245 -#> ds 4 m1 60 8.3 8.788e+00 -0.48803 0.399399 -#> ds 4 m1 60 9.0 8.788e+00 0.21197 -0.173474 -#> ds 4 m1 90 6.6 6.644e+00 -0.04431 0.040866 -#> ds 4 m1 90 7.7 6.644e+00 1.05569 -0.973711 -#> ds 4 m1 120 3.7 4.667e+00 -0.96735 1.010605 -#> ds 4 m1 120 3.5 4.667e+00 -1.16735 1.219548 -#> ds 5 parent 0 110.4 1.020e+02 8.37855 -1.161863 -#> ds 5 parent 0 112.1 1.020e+02 10.07855 -1.397604 -#> ds 5 parent 1 93.5 9.494e+01 -1.43722 0.212725 -#> ds 5 parent 1 91.0 9.494e+01 -3.93722 0.582755 -#> ds 5 parent 3 71.0 8.280e+01 -11.80256 1.974773 -#> ds 5 parent 3 89.7 8.280e+01 6.89744 -1.154061 -#> ds 5 parent 7 60.4 6.485e+01 -4.45291 0.923157 -#> ds 5 parent 7 59.1 6.485e+01 -5.75291 1.192667 -#> ds 5 parent 14 56.5 4.626e+01 10.24038 -2.821727 -#> ds 5 parent 14 47.0 4.626e+01 0.74038 -0.204011 -#> ds 5 parent 28 30.2 3.034e+01 -0.13506 0.051824 -#> ds 5 parent 28 23.9 3.034e+01 -6.43506 2.469220 -#> ds 5 parent 60 17.0 1.795e+01 -0.95206 0.525822 -#> ds 5 parent 60 18.7 1.795e+01 0.74794 -0.413085 -#> ds 5 parent 90 11.3 1.186e+01 -0.56163 0.395692 -#> ds 5 parent 90 11.9 1.186e+01 0.03837 -0.027033 -#> ds 5 parent 120 9.0 7.866e+00 1.13427 -0.975579 -#> ds 5 parent 120 8.1 7.866e+00 0.23427 -0.201493 -#> ds 5 m1 0 0.7 -4.263e-14 0.70000 -1.064865 -#> ds 5 m1 1 3.0 3.169e+00 -0.16908 0.196384 -#> ds 5 m1 1 2.6 3.169e+00 -0.56908 0.660990 -#> ds 5 m1 3 5.1 8.455e+00 -3.35479 2.794486 -#> ds 5 m1 3 7.5 8.455e+00 -0.95479 0.795325 -#> ds 5 m1 7 16.5 1.577e+01 0.73235 -0.438460 -#> ds 5 m1 7 19.0 1.577e+01 3.23235 -1.935208 -#> ds 5 m1 14 22.9 2.202e+01 0.88393 -0.426673 -#> ds 5 m1 14 23.2 2.202e+01 1.18393 -0.571482 -#> ds 5 m1 28 22.2 2.399e+01 -1.79091 0.814583 -#> ds 5 m1 28 24.4 2.399e+01 0.40909 -0.186073 -#> ds 5 m1 60 15.5 1.872e+01 -3.21988 1.731175 -#> ds 5 m1 60 19.8 1.872e+01 1.08012 -0.580725 -#> ds 5 m1 90 14.9 1.383e+01 1.06749 -0.690500 -#> ds 5 m1 90 14.2 1.383e+01 0.36749 -0.237710 -#> ds 5 m1 120 10.9 1.004e+01 0.85568 -0.656897 -#> ds 5 m1 120 10.4 1.004e+01 0.35568 -0.273054</div><div class='input'><span class='co'># }</span> +#> ds name time observed predicted residual standardized +#> ds 1 parent 0 89.8 9.869e+01 -8.894553 1.273163 +#> ds 1 parent 0 104.1 9.869e+01 5.405447 -0.773734 +#> ds 1 parent 1 88.7 9.413e+01 -5.426448 0.810727 +#> ds 1 parent 1 95.5 9.413e+01 1.373552 -0.205213 +#> ds 1 parent 3 81.8 8.576e+01 -3.961821 0.643463 +#> ds 1 parent 3 94.5 8.576e+01 8.738179 -1.419220 +#> ds 1 parent 7 71.5 7.168e+01 -0.184828 0.035175 +#> ds 1 parent 7 70.3 7.168e+01 -1.384828 0.263550 +#> ds 1 parent 14 54.2 5.351e+01 0.688235 -0.168298 +#> ds 1 parent 14 49.6 5.351e+01 -3.911765 0.956565 +#> ds 1 parent 28 31.5 3.209e+01 -0.590445 0.217395 +#> ds 1 parent 28 28.8 3.209e+01 -3.290445 1.211502 +#> ds 1 parent 60 12.1 1.272e+01 -0.618158 0.419377 +#> ds 1 parent 60 13.6 1.272e+01 0.881842 -0.598269 +#> ds 1 parent 90 6.2 6.085e+00 0.115212 -0.109861 +#> ds 1 parent 90 8.3 6.085e+00 2.215212 -2.112329 +#> ds 1 parent 120 2.2 3.009e+00 -0.809439 0.950563 +#> ds 1 parent 120 2.4 3.009e+00 -0.609439 0.715693 +#> ds 1 m1 1 0.3 1.129e+00 -0.828817 1.133869 +#> ds 1 m1 1 0.2 1.129e+00 -0.928817 1.270675 +#> ds 1 m1 3 2.2 3.141e+00 -0.940880 1.094093 +#> ds 1 m1 3 3.0 3.141e+00 -0.140880 0.163821 +#> ds 1 m1 7 6.5 6.326e+00 0.174162 -0.163662 +#> ds 1 m1 7 5.0 6.326e+00 -1.325838 1.245901 +#> ds 1 m1 14 10.2 9.883e+00 0.317417 -0.245642 +#> ds 1 m1 14 9.5 9.883e+00 -0.382583 0.296072 +#> ds 1 m1 28 12.2 1.251e+01 -0.309856 0.212138 +#> ds 1 m1 28 13.4 1.251e+01 0.890144 -0.609422 +#> ds 1 m1 60 11.8 1.086e+01 0.940009 -0.693807 +#> ds 1 m1 60 13.2 1.086e+01 2.340009 -1.727126 +#> ds 1 m1 90 6.6 7.823e+00 -1.222977 1.054158 +#> ds 1 m1 90 9.3 7.823e+00 1.477023 -1.273135 +#> ds 1 m1 120 3.5 5.315e+00 -1.815201 1.816354 +#> ds 1 m1 120 5.4 5.315e+00 0.084799 -0.084853 +#> ds 2 parent 0 118.0 1.031e+02 14.876736 -2.046284 +#> ds 2 parent 0 99.8 1.031e+02 -3.323264 0.457112 +#> ds 2 parent 1 90.2 9.757e+01 -7.371379 1.066126 +#> ds 2 parent 1 94.6 9.757e+01 -2.971379 0.429752 +#> ds 2 parent 3 96.1 8.788e+01 8.222746 -1.306721 +#> ds 2 parent 3 78.4 8.788e+01 -9.477254 1.506081 +#> ds 2 parent 7 77.9 7.293e+01 4.972272 -0.932149 +#> ds 2 parent 7 77.7 7.293e+01 4.772272 -0.894656 +#> ds 2 parent 14 56.0 5.602e+01 -0.016773 0.003947 +#> ds 2 parent 14 54.7 5.602e+01 -1.316773 0.309830 +#> ds 2 parent 28 36.6 3.855e+01 -1.945779 0.621680 +#> ds 2 parent 28 36.8 3.855e+01 -1.745779 0.557779 +#> ds 2 parent 60 22.1 2.101e+01 1.086693 -0.541771 +#> ds 2 parent 60 24.7 2.101e+01 3.686693 -1.838002 +#> ds 2 parent 90 12.4 1.246e+01 -0.058759 0.040319 +#> ds 2 parent 90 10.8 1.246e+01 -1.658759 1.138195 +#> ds 2 parent 120 6.8 7.406e+00 -0.606226 0.534861 +#> ds 2 parent 120 7.9 7.406e+00 0.493774 -0.435647 +#> ds 2 m1 1 1.3 1.438e+00 -0.138236 0.184118 +#> ds 2 m1 3 3.7 3.879e+00 -0.178617 0.196874 +#> ds 2 m1 3 4.7 3.879e+00 0.821383 -0.905344 +#> ds 2 m1 7 8.1 7.389e+00 0.710951 -0.627868 +#> ds 2 m1 7 7.9 7.389e+00 0.510951 -0.451240 +#> ds 2 m1 14 10.1 1.069e+01 -0.593533 0.441556 +#> ds 2 m1 14 10.3 1.069e+01 -0.393533 0.292767 +#> ds 2 m1 28 10.7 1.240e+01 -1.703647 1.171837 +#> ds 2 m1 28 12.2 1.240e+01 -0.203647 0.140077 +#> ds 2 m1 60 10.7 1.055e+01 0.147672 -0.110605 +#> ds 2 m1 60 12.5 1.055e+01 1.947672 -1.458786 +#> ds 2 m1 90 9.1 8.010e+00 1.090041 -0.929963 +#> ds 2 m1 90 7.4 8.010e+00 -0.609959 0.520383 +#> ds 2 m1 120 6.1 5.793e+00 0.306797 -0.297858 +#> ds 2 m1 120 4.5 5.793e+00 -1.293203 1.255523 +#> ds 3 parent 0 106.2 1.035e+02 2.712344 -0.371886 +#> ds 3 parent 0 106.9 1.035e+02 3.412344 -0.467862 +#> ds 3 parent 1 107.4 9.548e+01 11.924044 -1.758752 +#> ds 3 parent 1 96.1 9.548e+01 0.624044 -0.092044 +#> ds 3 parent 3 79.4 8.246e+01 -3.056105 0.514055 +#> ds 3 parent 3 82.6 8.246e+01 0.143895 -0.024204 +#> ds 3 parent 7 63.9 6.489e+01 -0.991141 0.205676 +#> ds 3 parent 7 62.4 6.489e+01 -2.491141 0.516947 +#> ds 3 parent 14 51.0 4.869e+01 2.306824 -0.610198 +#> ds 3 parent 14 47.1 4.869e+01 -1.593176 0.421425 +#> ds 3 parent 28 36.1 3.480e+01 1.304261 -0.451388 +#> ds 3 parent 28 36.6 3.480e+01 1.804261 -0.624431 +#> ds 3 parent 60 20.1 1.988e+01 0.221952 -0.114821 +#> ds 3 parent 60 19.8 1.988e+01 -0.078048 0.040376 +#> ds 3 parent 90 11.3 1.194e+01 -0.642458 0.451083 +#> ds 3 parent 90 10.7 1.194e+01 -1.242458 0.872355 +#> ds 3 parent 120 8.2 7.176e+00 1.023847 -0.915231 +#> ds 3 parent 120 7.3 7.176e+00 0.123847 -0.110709 +#> ds 3 m1 0 0.8 8.527e-13 0.800000 -1.214712 +#> ds 3 m1 1 1.8 1.856e+00 -0.055925 0.071921 +#> ds 3 m1 1 2.3 1.856e+00 0.444075 -0.571099 +#> ds 3 m1 3 4.2 4.780e+00 -0.580164 0.601168 +#> ds 3 m1 3 4.1 4.780e+00 -0.680164 0.704788 +#> ds 3 m1 7 6.8 8.410e+00 -1.609920 1.344090 +#> ds 3 m1 7 10.1 8.410e+00 1.690080 -1.411014 +#> ds 3 m1 14 11.4 1.098e+01 0.424444 -0.311572 +#> ds 3 m1 14 12.8 1.098e+01 1.824444 -1.339271 +#> ds 3 m1 28 11.5 1.142e+01 0.079336 -0.057043 +#> ds 3 m1 28 10.6 1.142e+01 -0.820664 0.590065 +#> ds 3 m1 60 7.5 9.110e+00 -1.610231 1.295778 +#> ds 3 m1 60 8.6 9.110e+00 -0.510231 0.410591 +#> ds 3 m1 90 7.3 6.799e+00 0.501085 -0.457825 +#> ds 3 m1 90 8.1 6.799e+00 1.301085 -1.188759 +#> ds 3 m1 120 5.3 4.868e+00 0.431505 -0.444518 +#> ds 3 m1 120 3.8 4.868e+00 -1.068495 1.100718 +#> ds 4 parent 0 104.7 9.926e+01 5.444622 -0.775351 +#> ds 4 parent 0 88.3 9.926e+01 -10.955378 1.560119 +#> ds 4 parent 1 94.2 9.618e+01 -1.978413 0.289883 +#> ds 4 parent 1 94.6 9.618e+01 -1.578413 0.231274 +#> ds 4 parent 3 78.1 9.037e+01 -12.268550 1.901399 +#> ds 4 parent 3 96.5 9.037e+01 6.131450 -0.950262 +#> ds 4 parent 7 76.2 7.999e+01 -3.794958 0.655739 +#> ds 4 parent 7 77.8 7.999e+01 -2.194958 0.379272 +#> ds 4 parent 14 70.8 6.518e+01 5.624996 -1.162874 +#> ds 4 parent 14 67.3 6.518e+01 2.124996 -0.439307 +#> ds 4 parent 28 43.1 4.462e+01 -1.517860 0.431312 +#> ds 4 parent 28 45.1 4.462e+01 0.482140 -0.137004 +#> ds 4 parent 60 21.3 2.130e+01 0.003305 -0.001633 +#> ds 4 parent 60 23.5 2.130e+01 2.203305 -1.088598 +#> ds 4 parent 90 11.8 1.180e+01 -0.002834 0.002002 +#> ds 4 parent 90 12.1 1.180e+01 0.297166 -0.209966 +#> ds 4 parent 120 7.0 6.868e+00 0.132251 -0.120348 +#> ds 4 parent 120 6.2 6.868e+00 -0.667749 0.607650 +#> ds 4 m1 0 1.6 0.000e+00 1.600000 -2.429424 +#> ds 4 m1 1 0.9 6.826e-01 0.217363 -0.309476 +#> ds 4 m1 3 3.7 1.935e+00 1.765082 -2.255277 +#> ds 4 m1 3 2.0 1.935e+00 0.065082 -0.083157 +#> ds 4 m1 7 3.6 4.035e+00 -0.434805 0.474018 +#> ds 4 m1 7 3.8 4.035e+00 -0.234805 0.255981 +#> ds 4 m1 14 7.1 6.652e+00 0.448187 -0.413053 +#> ds 4 m1 14 6.6 6.652e+00 -0.051813 0.047751 +#> ds 4 m1 28 9.5 9.156e+00 0.343805 -0.276011 +#> ds 4 m1 28 9.3 9.156e+00 0.143805 -0.115448 +#> ds 4 m1 60 8.3 8.848e+00 -0.547762 0.446843 +#> ds 4 m1 60 9.0 8.848e+00 0.152238 -0.124190 +#> ds 4 m1 90 6.6 6.674e+00 -0.073979 0.068090 +#> ds 4 m1 90 7.7 6.674e+00 1.026021 -0.944353 +#> ds 4 m1 120 3.7 4.668e+00 -0.967537 1.010122 +#> ds 4 m1 120 3.5 4.668e+00 -1.167537 1.218925 +#> ds 5 parent 0 110.4 1.022e+02 8.170986 -1.132847 +#> ds 5 parent 0 112.1 1.022e+02 9.870986 -1.368539 +#> ds 5 parent 1 93.5 9.513e+01 -1.630764 0.241319 +#> ds 5 parent 1 91.0 9.513e+01 -4.130764 0.611268 +#> ds 5 parent 3 71.0 8.296e+01 -11.964279 2.001495 +#> ds 5 parent 3 89.7 8.296e+01 6.735721 -1.126813 +#> ds 5 parent 7 60.4 6.495e+01 -4.547441 0.942951 +#> ds 5 parent 7 59.1 6.495e+01 -5.847441 1.212518 +#> ds 5 parent 14 56.5 4.626e+01 10.241319 -2.825682 +#> ds 5 parent 14 47.0 4.626e+01 0.741319 -0.204537 +#> ds 5 parent 28 30.2 3.026e+01 -0.058478 0.022504 +#> ds 5 parent 28 23.9 3.026e+01 -6.358478 2.446932 +#> ds 5 parent 60 17.0 1.792e+01 -0.919046 0.508481 +#> ds 5 parent 60 18.7 1.792e+01 0.780954 -0.432079 +#> ds 5 parent 90 11.3 1.187e+01 -0.573917 0.404206 +#> ds 5 parent 90 11.9 1.187e+01 0.026083 -0.018370 +#> ds 5 parent 120 9.0 7.898e+00 1.102089 -0.946039 +#> ds 5 parent 120 8.1 7.898e+00 0.202089 -0.173474 +#> ds 5 m1 0 0.7 -1.421e-14 0.700000 -1.062873 +#> ds 5 m1 1 3.0 3.144e+00 -0.143526 0.166865 +#> ds 5 m1 1 2.6 3.144e+00 -0.543526 0.631910 +#> ds 5 m1 3 5.1 8.390e+00 -3.290265 2.749870 +#> ds 5 m1 3 7.5 8.390e+00 -0.890265 0.744048 +#> ds 5 m1 7 16.5 1.566e+01 0.841368 -0.506082 +#> ds 5 m1 7 19.0 1.566e+01 3.341368 -2.009830 +#> ds 5 m1 14 22.9 2.188e+01 1.017753 -0.493689 +#> ds 5 m1 14 23.2 2.188e+01 1.317753 -0.639212 +#> ds 5 m1 28 22.2 2.386e+01 -1.655914 0.756794 +#> ds 5 m1 28 24.4 2.386e+01 0.544086 -0.248661 +#> ds 5 m1 60 15.5 1.859e+01 -3.091124 1.670405 +#> ds 5 m1 60 19.8 1.859e+01 1.208876 -0.653262 +#> ds 5 m1 90 14.9 1.372e+01 1.176815 -0.764948 +#> ds 5 m1 90 14.2 1.372e+01 0.476815 -0.309937 +#> ds 5 m1 120 10.9 9.961e+00 0.938796 -0.723690 +#> ds 5 m1 120 10.4 9.961e+00 0.438796 -0.338255</div><div class='input'><span class='co'># }</span> </div></pre> </div> |
