diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-16 14:42:30 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-16 14:42:30 +0100 |
| commit | e48c1f2ef990a622722e416c8d301430db4f5081 (patch) | |
| tree | cca6412417798973277072f858514fcaea268c71 /docs/reference | |
| parent | 0cf759e7d878817fd4c25411c4e93b036bc5596b (diff) | |
Use saemix in help page, typo in vignette
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/Rplot001.png | bin | 1011 -> 90922 bytes | |||
| -rw-r--r-- | docs/reference/Rplot002.png | bin | 57977 -> 90653 bytes | |||
| -rw-r--r-- | docs/reference/Rplot003.png | bin | 59128 -> 20189 bytes | |||
| -rw-r--r-- | docs/reference/Rplot004.png | bin | 59260 -> 19212 bytes | |||
| -rw-r--r-- | docs/reference/dimethenamid_2018-1.png | bin | 264424 -> 254862 bytes | |||
| -rw-r--r-- | docs/reference/dimethenamid_2018-2.png | bin | 243268 -> 254236 bytes | |||
| -rw-r--r-- | docs/reference/dimethenamid_2018-3.png | bin | 0 -> 7629 bytes | |||
| -rw-r--r-- | docs/reference/dimethenamid_2018.html | 203 |
8 files changed, 145 insertions, 58 deletions
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex 17a35806..26efcdd2 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex ddd3a0d7..065f21f6 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex fa29fc43..50a52a1c 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 69fdb09d..0f3d8214 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/dimethenamid_2018-1.png b/docs/reference/dimethenamid_2018-1.png Binary files differindex 338076a5..be59fc90 100644 --- a/docs/reference/dimethenamid_2018-1.png +++ b/docs/reference/dimethenamid_2018-1.png diff --git a/docs/reference/dimethenamid_2018-2.png b/docs/reference/dimethenamid_2018-2.png Binary files differindex 1f41a3a8..0bbb14d8 100644 --- a/docs/reference/dimethenamid_2018-2.png +++ b/docs/reference/dimethenamid_2018-2.png diff --git a/docs/reference/dimethenamid_2018-3.png b/docs/reference/dimethenamid_2018-3.png Binary files differnew file mode 100644 index 00000000..71087e85 --- /dev/null +++ b/docs/reference/dimethenamid_2018-3.png diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index f0bc23ee..85e954ac 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -156,65 +156,152 @@ specific pieces of information in the comments.</p> <span class="r-in"><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span> <span class="r-in"><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span> <span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">dfop_sfo3_plus</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> DMTA <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</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">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> M23 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M27 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M31 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span></span> +<span class="r-in"><span class="co"># We don't use DFOP for the parent compound, as this gives numerical</span></span> +<span class="r-in"><span class="co"># instabilities in the fits</span></span> +<span class="r-in"><span class="va">sfo_sfo3p</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span class="r-in"> DMTA <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span> +<span class="r-in"> M23 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span class="r-in"> M27 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span class="r-in"> M31 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span></span> <span class="r-in"><span class="op">)</span></span> -<span class="r-in"><span class="va">f_dmta_mkin_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO3+"</span> <span class="op">=</span> <span class="va">dfop_sfo3_plus</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">dmta_ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> -<span class="r-in"><span class="fu">nlmixr_model</span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmixr_model(f_dmta_mkin_tc):</span> could not find function "nlmixr_model"</span> -<span class="r-in"><span class="co"># The focei fit takes about four minutes on my system</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span></span> -<span class="r-in"> <span class="va">f_dmta_nlmixr_focei</span> <span class="op"><-</span> <span class="fu">nlmixr</span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span>, est <span class="op">=</span> <span class="st">"focei"</span>,</span> -<span class="r-in"> control <span class="op">=</span> <span class="fu">nlmixr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/nlmixr/man/foceiControl.html" class="external-link">foceiControl</a></span><span class="op">(</span>print <span class="op">=</span> <span class="fl">500</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmixr(f_dmta_mkin_tc, est = "focei", control = nlmixr::foceiControl(print = 500)):</span> could not find function "nlmixr"</span> -<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 0 0 0</span> -<span class="r-in"><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_dmta_nlmixr_focei</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in summary(f_dmta_nlmixr_focei):</span> object 'f_dmta_nlmixr_focei' not found</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_dmta_nlmixr_focei</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in plot(f_dmta_nlmixr_focei):</span> object 'f_dmta_nlmixr_focei' not found</span> -<span class="r-in"><span class="co"># Using saemix takes about 18 minutes</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span></span> -<span class="r-in"> <span class="va">f_dmta_saemix</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> DINTDY- T (=R1) illegal </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 115.507</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> T not in interval TCUR - HU (= R1) to TCUR (=R2) </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 112.133, R2 = 113.577</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> DLSODA- At T (=R1), too much accuracy requested </span> -<span class="r-out co"><span class="r-pr">#></span> for precision of machine.. See TOLSF (=R2) </span> -<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 55.3899, R2 = nan</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in out[available, var]:</span> (subscript) logical subscript too long</span> -<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 12.76 3.069 11.79</span> -<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 13.77 4.719 12.37</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># nlmixr with est = "saem" is pretty fast with default iteration numbers, most</span></span> -<span class="r-in"><span class="co"># of the time (about 2.5 minutes) is spent for calculating the log likelihood at the end</span></span> -<span class="r-in"><span class="co"># The likelihood calculated for the nlmixr fit is much lower than that found by saemix</span></span> -<span class="r-in"><span class="co"># Also, the trace plot and the plot of the individual predictions is not</span></span> -<span class="r-in"><span class="co"># convincing for the parent. It seems we are fitting an overparameterised</span></span> -<span class="r-in"><span class="co"># model, so the result we get strongly depends on starting parameters and control settings.</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span></span> -<span class="r-in"> <span class="va">f_dmta_nlmixr_saem</span> <span class="op"><-</span> <span class="fu">nlmixr</span><span class="op">(</span><span class="va">f_dmta_mkin_tc</span>, est <span class="op">=</span> <span class="st">"saem"</span>,</span> -<span class="r-in"> control <span class="op">=</span> <span class="fu">nlmixr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/nlmixr/man/saemControl.html" class="external-link">saemControl</a></span><span class="op">(</span>print <span class="op">=</span> <span class="fl">500</span>, logLik <span class="op">=</span> <span class="cn">TRUE</span>, nmc <span class="op">=</span> <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmixr(f_dmta_mkin_tc, est = "saem", control = nlmixr::saemControl(print = 500, logLik = TRUE, nmc = 9)):</span> could not find function "nlmixr"</span> -<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 0 0 0.001</span> -<span class="r-in"><span class="fu">traceplot</span><span class="op">(</span><span class="va">f_dmta_nlmixr_saem</span><span class="op">$</span><span class="va">nm</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in traceplot(f_dmta_nlmixr_saem$nm):</span> could not find function "traceplot"</span> -<span class="r-in"><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_dmta_nlmixr_saem</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in summary(f_dmta_nlmixr_saem):</span> object 'f_dmta_nlmixr_saem' not found</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_dmta_nlmixr_saem</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in plot(f_dmta_nlmixr_saem):</span> object 'f_dmta_nlmixr_saem' not found</span> +<span class="r-in"><span class="va">dmta_sfo_sfo3p_tc</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" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO3+"</span> <span class="op">=</span> <span class="va">sfo_sfo3p</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><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">dmta_sfo_sfo3p_tc</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot</span> +<span class="r-out co"><span class="r-pr">#></span> SFO-SFO3+ OK OK OK OK OK OK </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span class="co"># The default (test_log_parms = FALSE) gives an undue</span></span> +<span class="r-in"><span class="co"># influence of ill-defined rate constants that have</span></span> +<span class="r-in"><span class="co"># extremely small values:</span></span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span class="co"># If we disregards ill-defined rate constants, the results</span></span> +<span class="r-in"><span class="co"># look more plausible, but the truth is likely to be in</span></span> +<span class="r-in"><span class="co"># between these variants</span></span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-plt img"><img src="dimethenamid_2018-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span class="co"># Therefore we use nonlinear mixed-effects models</span></span> +<span class="r-in"><span class="co"># f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc)</span></span> +<span class="r-in"><span class="co"># nlme reaches maxIter = 50 without convergence</span></span> +<span class="r-in"><span class="va">f_dmta_saem_tc</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span></span> +<span class="r-in"><span class="co"># I am commenting out the convergence plot as rendering them</span></span> +<span class="r-in"><span class="co"># with pkgdown fails (at least without further tweaks to the </span></span> +<span class="r-in"><span class="co"># graphics device used)</span></span> +<span class="r-in"><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span> +<span class="r-in"><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_dmta_saem_tc</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.3 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Mar 16 14:32:04 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Mar 16 14:32:04 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_DMTA/dt = - k_DMTA * DMTA</span> +<span class="r-out co"><span class="r-pr">#></span> d_M23/dt = + f_DMTA_to_M23 * k_DMTA * DMTA - k_M23 * M23</span> +<span class="r-out co"><span class="r-pr">#></span> d_M27/dt = + f_DMTA_to_M27 * k_DMTA * DMTA - k_M27 * M27 + k_M31 * M31</span> +<span class="r-out co"><span class="r-pr">#></span> d_M31/dt = + f_DMTA_to_M31 * k_DMTA * DMTA - k_M31 * M31</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> 563 observations of 4 variable(s) grouped in 6 datasets</span> +<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 deSolve </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 927.963 s</span> +<span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 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> DMTA_0 log_k_DMTA log_k_M23 log_k_M27 log_k_M31 f_DMTA_ilr_1 </span> +<span class="r-out co"><span class="r-pr">#></span> 95.5662 -2.9048 -3.8130 -4.1600 -4.1486 0.1341 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 f_DMTA_ilr_3 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.1385 -1.6700 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<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> 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> 2276 2272 -1120</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> DMTA_0 88.5943 84.3961 92.7925</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0466 -3.5609 -2.5322</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0684 -4.9340 -3.2029</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8628 -4.2627 -3.4628</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9803 -4.4804 -3.4801</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1304 -0.2186 0.4795</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1490 -0.2559 0.5540</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3970 -1.6976 -1.0964</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> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0309 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0231 -0.0031 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0381 -0.0048 0.0039 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0251 -0.0031 0.0021 0.0830 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0417 -0.0437 0.0328 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0270 -0.0909 -0.0361 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1832 -0.0135 0.0434 0.0804 0.0395 -0.0070 0.0059 </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.DMTA_0 3.3651 -0.9655 7.6956</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6415 0.2774 1.0055</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0176 0.3809 1.6543</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4538 0.1522 0.7554</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5684 0.1905 0.9464</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4111 0.1524 0.6699</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4788 0.1808 0.7768</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3501 0.1316 0.5685</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 0.9349 0.8395 1.0302</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1344 0.1176 0.1512</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> DMTA_0 88.59431 84.396147 92.79246</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04752 0.028413 0.07948</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01710 0.007198 0.04064</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02101 0.014084 0.03134</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01868 0.011329 0.03080</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14498 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12056 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11015 NA NA</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> DMTA_M23 0.1450</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1206</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1101</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6243</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</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA 14.59 48.45</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.52 134.62</span> +<span class="r-out co"><span class="r-pr">#></span> M27 32.99 109.60</span> +<span class="r-out co"><span class="r-pr">#></span> M31 37.11 123.26</span> +<span class="r-in"><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span> +<span class="r-in"><span class="co"># includes zero, we could try an alternative model without</span></span> +<span class="r-in"><span class="co"># such random effects</span></span> +<span class="r-in"><span class="co"># f_dmta_saem_tc_2 <- saem(dmta_sfo_sfo3p_tc,</span></span> +<span class="r-in"><span class="co"># covariance.model = diag(c(0, rep(1, 7))))</span></span> +<span class="r-in"><span class="co"># saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence")</span></span> +<span class="r-in"><span class="co"># This does not perform better judged by AIC and BIC</span></span> +<span class="r-in"><span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_dmta_saem_tc_2</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so):</span> object 'f_dmta_saem_tc_2' not found</span> <span class="r-in"><span class="co"># }</span></span> </code></pre></div> </div> |
