diff options
Diffstat (limited to 'docs/dev/reference')
| -rw-r--r-- | docs/dev/reference/Rplot001.png | bin | 18113 -> 1011 bytes | |||
| -rw-r--r-- | docs/dev/reference/Rplot002.png | bin | 38732 -> 16953 bytes | |||
| -rw-r--r-- | docs/dev/reference/illparms.html | 15 | ||||
| -rw-r--r-- | docs/dev/reference/parplot.html | 9 | ||||
| -rw-r--r-- | docs/dev/reference/saem.html | 21 | ||||
| -rw-r--r-- | docs/dev/reference/summary.saem.mmkin.html | 508 |
6 files changed, 321 insertions, 232 deletions
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex 8a77fc7f..17a35806 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex c1621707..27feab09 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/illparms.html b/docs/dev/reference/illparms.html index 8fe71568..9c498e1c 100644 --- a/docs/dev/reference/illparms.html +++ b/docs/dev/reference/illparms.html @@ -116,7 +116,14 @@ without parameter transformations is used.</p> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for saem.mmkin</span></span> -<span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, errmod <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> +<span><span class="fu">illparms</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> conf.level <span class="op">=</span> <span class="fl">0.95</span>,</span> +<span> random <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> errmod <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> slopes <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for illparms.saem.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> @@ -154,6 +161,12 @@ without parameter transformations is used.</p> <dd><p>For hierarchical fits, should error model parameters be tested?</p></dd> + +<dt>slopes</dt> +<dd><p>For hierarchical <a href="saem.html">saem</a> fits using saemix as backend, +should slope parameters in the covariate model(starting with 'beta_') be +tested?</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> diff --git a/docs/dev/reference/parplot.html b/docs/dev/reference/parplot.html index 9852b694..720c0b2a 100644 --- a/docs/dev/reference/parplot.html +++ b/docs/dev/reference/parplot.html @@ -103,6 +103,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).</p> <span><span class="fu">parplot</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> llmin <span class="op">=</span> <span class="op">-</span><span class="cn">Inf</span>,</span> +<span> llquant <span class="op">=</span> <span class="cn">NA</span>,</span> <span> scale <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"best"</span>, <span class="st">"median"</span><span class="op">)</span>,</span> <span> lpos <span class="op">=</span> <span class="st">"bottomleft"</span>,</span> <span> main <span class="op">=</span> <span class="st">""</span>,</span> @@ -124,8 +125,14 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).</p> <dd><p>The minimum likelihood of objects to be shown</p></dd> +<dt>llquant</dt> +<dd><p>Fractional value for selecting only the fits with higher +likelihoods. Overrides 'llmin'.</p></dd> + + <dt>scale</dt> -<dd><p>By default, scale parameters using the best available fit. +<dd><p>By default, scale parameters using the best +available fit. If 'median', parameters are scaled using the median parameters from all fits.</p></dd> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index d18cb848..131b168b 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -432,8 +432,8 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:00 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:01 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Dec 7 16:22:26 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Dec 7 16:22:26 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -448,12 +448,12 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.778 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.508 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for degradation parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 </span> <span class="r-out co"><span class="r-pr">#></span> 93.8102 -5.3734 -0.9711 -1.8799 -4.2708 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> @@ -462,6 +462,19 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for random effects (square root of initial entries in omega):</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 4.941 0.000 0.0000 0.000 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 0.000 2.551 0.0000 0.000 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.000 0.000 0.7251 0.000 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.000 0.000 0.0000 1.449 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.000 0.000 0.0000 0.000 2.228 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.000 0.000 0.0000 0.000 0.000 0.7814</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for error model parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 </span> +<span class="r-out co"><span class="r-pr">#></span> 1 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Results:</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index a4150959..3b5869f1 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -102,7 +102,7 @@ endpoints such as formation fractions and DT50 values. Optionally <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> -<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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> +<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">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> <span></span> <span><span class="co"># S3 method for summary.saem.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">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" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">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></span></code></pre></div> @@ -266,36 +266,38 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.37478 0.04490 0.70467</span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] "sd(parent_0)" "sd(log_k_m1)"</span> -<span class="r-in"><span><span class="va">f_saem_dfop_sfo_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_dfop_sfo_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>,</span></span> +<span class="r-in"><span> no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"parent_0"</span>, <span class="st">"log_k_m1"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Approximate 95% confidence intervals</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 97.57609542 100.73343868 103.89078195</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01549292 0.01714893 0.01898194</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20720315 0.28358738 0.37481744</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.06149334 0.08733164 0.12402670</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01448390 0.01699942 0.01995184</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.45084762 0.51075839 0.57036168</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 98.36731429 101.42508066 104.48284703</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01513234 0.01670094 0.01843214</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20221431 0.27608850 0.36461630</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.06915073 0.09759718 0.13774560</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01487068 0.01740389 0.02036863</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.37365671 0.48384821 0.59563299</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.16606767 0.4479731 0.7298784</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.12284609 0.3588446 0.5948430</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.05379723 0.1548780 0.2559588</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.16439770 0.4427585 0.7211193</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.08304243 0.3345213 0.5860002</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.03146410 0.1490210 0.2665779</span> +<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.06216385 0.4023430 0.7425221</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.6811490 0.88503409 1.08891921</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.0676515 0.08336272 0.09907394</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.67696663 0.87777355 1.07858048</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.06363957 0.07878001 0.09392044</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:52 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:52 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Dec 15 14:47:14 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Dec 15 14:47:14 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -310,12 +312,12 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 26.242 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.623 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for degradation parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 </span> <span class="r-out co"><span class="r-pr">#></span> 101.65645 -4.05368 -0.94311 -2.35943 -4.07006 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> @@ -324,237 +326,291 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for random effects (square root of initial entries in omega):</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 6.742 0.0000 0.0000 0.0000 0.0000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.000 0.2236 0.0000 0.0000 0.0000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.000 0.0000 0.5572 0.0000 0.0000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.000 0.0000 0.0000 0.8031 0.0000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.000 0.0000 0.0000 0.0000 0.2931 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.000 0.0000 0.0000 0.0000 0.0000 0.807</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for error model parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 b.1 </span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Results:</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 809.5 805.2 -393.7</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 807 802.3 -391.5</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.73344 97.57610 103.89078</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06582 -4.16737 -3.96427</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.92674 -1.34187 -0.51160</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.43804 -2.78883 -2.08726</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.07458 -4.23472 -3.91443</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.04304 -0.19725 0.28333</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.88503 0.68115 1.08892</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.08336 0.06765 0.09907</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44797 0.16607 0.72988</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.35884 0.12285 0.59484</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.15488 0.05380 0.25596</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.42508 98.36731 104.48285</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.09229 -4.19092 -3.99366</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.96395 -1.37251 -0.55538</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.32691 -2.67147 -1.98235</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.05106 -4.20836 -3.89376</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.06463 -0.51656 0.38730</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87777 0.67697 1.07858</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07878 0.06364 0.09392</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44276 0.16440 0.72112</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.33452 0.08304 0.58600</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.14902 0.03146 0.26658</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.40234 0.06216 0.74252</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4698 </span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2461 0.2709 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1572 -0.1517 -0.0648 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -0.0023 0.0835 0.0125 0.1420 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.2314 -0.2337 -0.0755 -0.2762 -0.4797</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4693 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2378 0.2595 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1720 -0.1593 -0.0669 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0179 0.0594 0.0035 0.1995 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.1073 -0.1060 -0.0322 -0.2299 -0.3168</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4480 0.1661 0.7299</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.3588 0.1228 0.5948</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.1549 0.0538 0.2560</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4428 0.16440 0.7211</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.3345 0.08304 0.5860</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.1490 0.03146 0.2666</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4023 0.06216 0.7425</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.88503 0.68115 1.08892</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.08336 0.06765 0.09907</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87777 0.67697 1.07858</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07878 0.06364 0.09392</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.73344 97.57610 103.89078</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01715 0.01549 0.01898</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28359 0.20720 0.37482</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.08733 0.06149 0.12403</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01700 0.01448 0.01995</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.51076 0.45085 0.57036</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.4251 98.36731 104.48285</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0167 0.01513 0.01843</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.2761 0.20221 0.36462</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.0976 0.06915 0.13775</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.0174 0.01487 0.02037</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.4838 0.37366 0.59563</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2836</span> -<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7164</span> +<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2761</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7239</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 15.94 93.48 28.14 7.937 40.77</span> -<span class="r-out co"><span class="r-pr">#></span> m1 40.42 134.27 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> parent 15.54 94.33 28.4 7.102 39.83</span> +<span class="r-out co"><span class="r-pr">#></span> m1 41.50 137.87 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 89.8 1.007e+02 -10.93344 8.4439 -1.29483</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.007e+02 3.36656 8.4439 0.39870</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.591e+01 -7.20789 8.0440 -0.89606</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.591e+01 -0.40789 8.0440 -0.05071</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.712e+01 -5.31561 7.3159 -0.72658</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.712e+01 7.38439 7.3159 1.00936</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.246e+01 -0.95675 6.1047 -0.15672</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.246e+01 -2.15675 6.1047 -0.35329</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.382e+01 0.38143 4.5729 0.08341</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.382e+01 -4.21857 4.5729 -0.92251</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.230e+01 -0.80120 2.8344 -0.28267</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.230e+01 -3.50120 2.8344 -1.23524</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.307e+01 -0.97165 1.4038 -0.69215</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.307e+01 0.52835 1.4038 0.37637</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.353e+00 -0.15285 1.0314 -0.14820</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.353e+00 1.94715 1.0314 1.88790</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.175e+00 -0.97462 0.9238 -1.05506</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.175e+00 -0.77462 0.9238 -0.83855</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.183e+00 -0.88350 0.8905 -0.99212</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.183e+00 -0.98350 0.8905 -1.10441</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.281e+00 -1.08106 0.9263 -1.16703</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.281e+00 -0.28106 0.9263 -0.30341</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.564e+00 -0.06353 1.0405 -0.06106</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.564e+00 -1.56353 1.0405 -1.50266</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.015e+01 0.05147 1.2243 0.04204</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.015e+01 -0.64853 1.2243 -0.52970</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.265e+01 -0.44824 1.3766 -0.32561</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.265e+01 0.75176 1.3766 0.54610</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.078e+01 1.02355 1.2611 0.81165</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.078e+01 2.42355 1.2611 1.92181</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.698e+00 -1.09840 1.0932 -1.00474</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.698e+00 1.60160 1.0932 1.46502</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.199e+00 -1.69853 0.9854 -1.72363</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.199e+00 0.20147 0.9854 0.20445</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.007e+02 17.26656 8.4439 2.04485</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.007e+02 -0.93344 8.4439 -0.11055</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.584e+01 -5.63852 8.0382 -0.70146</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.584e+01 -1.23852 8.0382 -0.15408</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.706e+01 9.04068 7.3113 1.23654</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.706e+01 -8.65932 7.3113 -1.18438</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.286e+01 5.04438 6.1376 0.82188</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.286e+01 4.84438 6.1376 0.78930</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.567e+01 0.33336 4.7242 0.07057</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.567e+01 -0.96664 4.7242 -0.20462</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.705e+01 -0.44800 3.2127 -0.13944</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.705e+01 -0.24800 3.2127 -0.07719</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.008e+01 2.01984 1.8935 1.06672</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.008e+01 4.61984 1.8935 2.43984</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.253e+01 -0.12814 1.3689 -0.09360</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.253e+01 -1.72814 1.3689 -1.26238</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.916e+00 -1.11595 1.1040 -1.01085</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.916e+00 -0.01595 1.1040 -0.01445</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.317e+00 -0.01669 0.8918 -0.01871</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.613e+00 0.08699 0.9349 0.09305</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.613e+00 1.08699 0.9349 1.16270</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.092e+00 1.00781 1.0643 0.94688</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.092e+00 0.80781 1.0643 0.75897</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.066e+01 -0.56458 1.2545 -0.45006</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.066e+01 -0.36458 1.2545 -0.29063</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.281e+01 -2.11106 1.3870 -1.52201</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.281e+01 -0.61106 1.3870 -0.44055</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.078e+01 -0.08464 1.2616 -0.06709</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.078e+01 1.71536 1.2616 1.35970</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.013e+00 1.08684 1.1088 0.98016</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.013e+00 -0.61316 1.1088 -0.55298</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.749e+00 0.35063 1.0065 0.34838</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.749e+00 -1.24937 1.0065 -1.24133</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.007e+02 5.46656 8.4439 0.64740</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.007e+02 6.16656 8.4439 0.73030</span> -<span class="r-out co"><span 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1.3365 -0.51843</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.279e+01 0.80713 1.3365 0.60392</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.397e+00 -0.19718 1.0122 -0.19481</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.397e+00 1.90282 1.0122 1.87996</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.323e+00 -1.12320 0.9160 -1.22623</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.323e+00 -0.92320 0.9160 -1.00788</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.179e+00 -0.87919 0.8827 -0.99605</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.179e+00 -0.97919 0.8827 -1.10935</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.273e+00 -1.07272 0.9149 -1.17256</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.273e+00 -0.27272 0.9149 -0.29811</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.559e+00 -0.05872 1.0186 -0.05765</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.559e+00 -1.55872 1.0186 -1.53032</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.016e+01 0.03787 1.1880 0.03188</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.016e+01 -0.66213 1.1880 -0.55734</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.268e+01 -0.47913 1.3297 -0.36032</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.268e+01 0.72087 1.3297 0.54211</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.078e+01 1.02493 1.2211 0.83936</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.078e+01 2.42493 1.2211 1.98588</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.705e+00 -1.10464 1.0672 -1.03509</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.705e+00 1.59536 1.0672 1.49491</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.236e+00 -1.73617 0.9699 -1.79010</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.236e+00 0.16383 0.9699 0.16892</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.014e+02 16.57492 8.0383 2.06198</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.014e+02 -1.62508 8.0383 -0.20217</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.599e+01 -5.79045 7.6129 -0.76061</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.599e+01 -1.39045 7.6129 -0.18264</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.652e+01 9.57931 6.8724 1.39388</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.652e+01 -8.12069 6.8724 -1.18164</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.197e+01 5.93429 5.7370 1.03439</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.197e+01 5.73429 5.7370 0.99953</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.555e+01 0.44657 4.4637 0.10005</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.555e+01 -0.85343 4.4637 -0.19120</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.853e+01 -1.93170 3.1599 -0.61132</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.853e+01 -1.73170 3.1599 -0.54803</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.110e+01 1.00360 1.8795 0.53396</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.110e+01 3.60360 1.8795 1.91728</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.250e+01 -0.09712 1.3190 -0.07363</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.250e+01 -1.69712 1.3190 -1.28667</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.419e+00 -0.61913 1.0546 -0.58709</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.419e+00 0.48087 1.0546 0.45599</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.422e+00 -0.12194 0.8849 -0.13781</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.831e+00 -0.13149 0.9282 -0.14166</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.831e+00 0.86851 0.9282 0.93567</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.292e+00 0.80812 1.0490 0.77034</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.292e+00 0.60812 1.0490 0.57969</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.055e+01 -0.45332 1.2090 -0.37495</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.055e+01 -0.25332 1.2090 -0.20953</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.230e+01 -1.59960 1.3074 -1.22347</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.230e+01 -0.09960 1.3074 -0.07618</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.065e+01 0.05342 1.2141 0.04400</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.065e+01 1.85342 1.2141 1.52661</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.196e+00 0.90368 1.0897 0.82930</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.196e+00 -0.79632 1.0897 -0.73078</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.997e+00 0.10252 0.9969 0.10284</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.997e+00 -1.49748 0.9969 -1.50220</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.014e+02 4.77492 8.0383 0.59402</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.014e+02 5.47492 8.0383 0.68110</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.390e+01 13.49935 7.4494 1.81214</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.390e+01 2.19935 7.4494 0.29524</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.152e+01 -2.12307 6.4821 -0.32753</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.152e+01 1.07693 6.4821 0.16614</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.446e+01 -0.55834 5.1533 -0.10834</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.446e+01 -2.05834 5.1533 -0.39942</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.826e+01 2.74073 3.9019 0.70241</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.826e+01 -1.15927 3.9019 -0.29711</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.424e+01 1.86399 2.8364 0.65718</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.424e+01 2.36399 2.8364 0.83346</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.968e+01 0.42172 1.7815 0.23672</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.968e+01 0.12172 1.7815 0.06833</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.195e+01 -0.64633 1.2869 -0.50222</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.195e+01 -1.24633 1.2869 -0.96844</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.255e+00 0.94532 1.0474 0.90251</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.255e+00 0.04532 1.0474 0.04327</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 2.956e-11 0.80000 0.8778 0.91140</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.758e+00 0.04187 0.8886 0.04712</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.758e+00 0.54187 0.8886 0.60978</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.567e+00 -0.36697 0.9486 -0.38683</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.567e+00 -0.46697 0.9486 -0.49224</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.151e+00 -1.35124 1.0876 -1.24242</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.151e+00 1.94876 1.0876 1.79182</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.083e+01 0.57098 1.2240 0.46647</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.083e+01 1.97098 1.2240 1.61022</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.147e+01 0.03175 1.2597 0.02520</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.147e+01 -0.86825 1.2597 -0.68928</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.298e+00 -1.79834 1.1433 -1.57298</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.298e+00 -0.69834 1.1433 -0.61083</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 7.038e+00 0.26249 1.0382 0.25283</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 7.038e+00 1.06249 1.0382 1.02340</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 5.116e+00 0.18417 0.9659 0.19068</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 5.116e+00 -1.31583 0.9659 -1.36232</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.014e+02 3.27492 8.0383 0.40741</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.014e+02 -13.12508 8.0383 -1.63281</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.781e+01 -3.61183 7.7555 -0.46572</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.781e+01 -3.21183 7.7555 -0.41414</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.110e+01 -13.00467 7.2307 -1.79853</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 96.5 9.110e+01 5.39533 7.2307 0.74617</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 76.2 7.951e+01 -3.30511 6.3246 -0.52258</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 77.8 7.951e+01 -1.70511 6.3246 -0.26960</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 70.8 6.376e+01 7.03783 5.0993 1.38016</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 67.3 6.376e+01 3.53783 5.0993 0.69379</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 43.1 4.340e+01 -0.30456 3.5303 -0.08627</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 45.1 4.340e+01 1.69544 3.5303 0.48026</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 21.3 2.142e+01 -0.12077 1.9022 -0.06349</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 23.5 2.142e+01 2.07923 1.9022 1.09308</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.207e+01 -0.26813 1.2940 -0.20721</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.207e+01 0.03187 1.2940 0.02463</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 6.954e+00 0.04554 1.0347 0.04402</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 6.954e+00 -0.75446 1.0347 -0.72914</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 1.990e-13 1.60000 0.8778 1.82279</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 7.305e-01 0.16949 0.8797 0.19267</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 2.051e+00 1.64896 0.8925 1.84753</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 2.051e+00 -0.05104 0.8925 -0.05719</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.204e+00 -0.60375 0.9382 -0.64354</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.204e+00 -0.40375 0.9382 -0.43036</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.760e+00 0.34021 1.0267 0.33137</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.760e+00 -0.15979 1.0267 -0.15563</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.011e+00 0.48856 1.1289 0.43277</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.011e+00 0.28856 1.1289 0.25561</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.611e+00 -0.31077 1.1093 -0.28014</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.611e+00 0.38923 1.1093 0.35086</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.678e+00 -0.07753 1.0233 -0.07576</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.678e+00 1.02247 1.0233 0.99915</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.847e+00 -1.14679 0.9572 -1.19804</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.847e+00 -1.34679 0.9572 -1.40698</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.014e+02 8.97492 8.0383 1.11651</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.014e+02 10.67492 8.0383 1.32800</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.466e+01 -1.16118 7.5089 -0.15464</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.466e+01 -3.66118 7.5089 -0.48758</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.302e+01 -12.01844 6.5988 -1.82130</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.302e+01 6.68156 6.5988 1.01254</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 60.4 6.563e+01 -5.22574 5.2440 -0.99652</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 59.1 6.563e+01 -6.52574 5.2440 -1.24442</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 56.5 4.727e+01 9.22621 3.8263 2.41128</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 47.0 4.727e+01 -0.27379 3.8263 -0.07156</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 30.2 3.103e+01 -0.83405 2.5977 -0.32108</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 23.9 3.103e+01 -7.13405 2.5977 -2.74634</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.800e+01 -0.99696 1.6675 -0.59787</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.800e+01 0.70304 1.6675 0.42161</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.167e+01 -0.36809 1.2710 -0.28961</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.167e+01 0.23191 1.2710 0.18246</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.595e+00 1.40496 1.0623 1.32256</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.595e+00 0.50496 1.0623 0.47535</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 0.000e+00 0.70000 0.8778 0.79747</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.158e+00 -0.15799 0.9123 -0.17317</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.158e+00 -0.55799 0.9123 -0.61160</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.443e+00 -3.34286 1.1013 -3.03535</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.443e+00 -0.94286 1.1013 -0.85613</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.580e+01 0.69781 1.5232 0.45811</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.580e+01 3.19781 1.5232 2.09935</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.216e+01 0.73604 1.9543 0.37663</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.216e+01 1.03604 1.9543 0.53014</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.423e+01 -2.03128 2.1011 -0.96678</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.423e+01 0.16872 2.1011 0.08030</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.876e+01 -3.25610 1.7187 -1.89455</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.876e+01 1.04390 1.7187 0.60739</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.366e+01 1.23585 1.3890 0.88976</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.366e+01 0.53585 1.3890 0.38579</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.761e+00 1.13911 1.1670 0.97613</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.761e+00 0.63911 1.1670 0.54767</span> +<span class="r-in"><span><span class="co"># Add a correlation between random effects of g and k2</span></span></span> +<span class="r-in"><span><span class="va">cov_model_3</span> <span class="op"><-</span> <span class="va">f_saem_dfop_sfo_2</span><span class="op">$</span><span class="va">so</span><span class="op">@</span><span class="va">model</span><span class="op">@</span><span class="va">covariance.model</span></span></span> +<span class="r-in"><span><span class="va">cov_model_3</span><span class="op">[</span><span class="st">"log_k2"</span>, <span class="st">"g_qlogis"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="va">cov_model_3</span><span class="op">[</span><span class="st">"g_qlogis"</span>, <span class="st">"log_k2"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="va">f_saem_dfop_sfo_3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>,</span></span> +<span class="r-in"><span> covariance.model <span class="op">=</span> <span class="va">cov_model_3</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Approximate 95% confidence intervals</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 98.39888363 101.48951337 104.58014311</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01508704 0.01665986 0.01839665</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20141557 0.27540583 0.36418131</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.07708759 0.10430866 0.14114200</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01476621 0.01786384 0.02161129</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.33679867 0.45083525 0.57028162</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.38085375 0.4441841 0.5075145</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.04774819 0.2660384 0.4843286</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) -0.63842736 0.1977024 1.0338321</span> +<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.22711289 0.4502227 0.6733326</span> +<span class="r-out co"><span class="r-pr">#></span> corr(log_k2,g_qlogis) -0.83271473 -0.6176939 -0.4026730</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.67347568 0.87437392 1.07527216</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.06393032 0.07912417 0.09431802</span> +<span class="r-in"><span><span class="co"># The correlation does not improve the fit judged by AIC and BIC, although</span></span></span> +<span class="r-in"><span><span class="co"># the likelihood is higher with the additional parameter</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, <span class="va">f_saem_dfop_sfo_2</span>, <span class="va">f_saem_dfop_sfo_3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 171 observations of 2 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_2 12 806.96 802.27 -391.48</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_3 13 807.99 802.91 -391.00</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo 14 810.83 805.36 -391.42</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> </code></pre></div> |
