diff options
Diffstat (limited to 'docs/reference')
92 files changed, 549 insertions, 539 deletions
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index a049850d..c46824e6 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -123,6 +123,8 @@ dataframe if there are several fits in the column).</p> <span class="r-in"> <span class="va">f</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" class="external-link">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> <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">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span> <span class="r-in"> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"> <span class="co"># We get a warning because the FOMC model does not converge for the</span></span> <span class="r-in"> <span class="co"># FOCUS A dataset, as it is well described by SFO</span></span> <span class="r-in"></span> @@ -136,17 +138,17 @@ dataframe if there are several fits in the column).</p> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 55.28197</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28222</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28198</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.28197</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span>, k <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># If we do not penalize additional parameters, we get nearly the same</span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 49.28197</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28222</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28198</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 49.28197</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># Comparing the BIC gives a very similar picture</span></span> <span class="r-out co"><span class="r-pr">#></span> df BIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 55.52030</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59999</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59975</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.67918</span> <span class="r-in"></span> <span class="r-in"> <span class="co"># For FOCUS C, the more complex models fit better</span></span> @@ -176,7 +178,7 @@ dataframe if there are several fits in the column).</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index f16a9e6c..4a0b599b 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -161,7 +161,7 @@ compatible with CAKE.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index 1c47c7f7..6e2ec0ba 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -224,7 +224,7 @@ specific pieces of information in the comments.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 86df2efc..41a7d256 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -154,7 +154,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 7193e0f9..e00391e8 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -155,7 +155,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-in"> <span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $par</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma </span> -<span class="r-out co"><span class="r-pr">#></span> 99.666192 2.549850 5.050586 1.890202 </span> +<span class="r-out co"><span class="r-pr">#></span> 99.666193 2.549849 5.050586 1.890202 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $objective</span> <span class="r-out co"><span class="r-pr">#></span> [1] 28.58291</span> @@ -168,7 +168,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $evaluations</span> <span class="r-out co"><span class="r-pr">#></span> function gradient </span> -<span class="r-out co"><span class="r-pr">#></span> 25 78 </span> +<span class="r-out co"><span class="r-pr">#></span> 25 72 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $message</span> <span class="r-out co"><span class="r-pr">#></span> [1] "both X-convergence and relative convergence (5)"</span> @@ -187,7 +187,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 1e0e270e..aeeaf723 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -144,7 +144,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index d507b9c8..7274cadc 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -167,7 +167,7 @@ Technology</em> <b>24</b>, 1032-1038</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index d30c4e8a..03b30958 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -155,7 +155,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index fec06e0a..0116760d 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -144,7 +144,7 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <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="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore.deS</span><span class="op">$</span><span class="va">par</span>, </span> <span class="r-in"> row.names <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"model par"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> fit.fomc.par fit.iore.par fit.iore.deS.par</span> -<span class="r-out co"><span class="r-pr">#></span> model par 1 85.87489063 85.874890 85.874890</span> +<span class="r-out co"><span class="r-pr">#></span> model par 1 85.87489063 85.874890 85.874891</span> <span class="r-out co"><span class="r-pr">#></span> model par 2 0.05192238 -4.826631 -4.826631</span> <span class="r-out co"><span class="r-pr">#></span> model par 3 0.65096665 1.949403 1.949403</span> <span class="r-out co"><span class="r-pr">#></span> model par 4 1.85744396 1.857444 1.857444</span> @@ -170,7 +170,7 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index ab3ae7b8..06b5bd6f 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -178,7 +178,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png Binary files differindex 48f5bbd8..bc6979e9 100644 --- a/docs/reference/Rplot006.png +++ b/docs/reference/Rplot006.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index dfae0f69..3607a5ac 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -147,7 +147,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 40ed1338..9b4c391c 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -161,7 +161,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index de773982..3a129533 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -208,7 +208,7 @@ https://jrwb.de/posters/piacenza_2015.pdf</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 1182ab8c..1694d5f7 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -151,7 +151,7 @@ Inference: Understanding AIC and BIC in Model Selection. </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 806e94ca..5469f8f8 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -206,7 +206,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span class="va">f_d_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</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</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/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 4.361 0.964 3.998 </span> +<span class="r-out co"><span class="r-pr">#></span> 3.409 0.000 3.411 </span> <span class="r-in"><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span> <span class="r-in"><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span> <span class="r-in"><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span> @@ -214,7 +214,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"> <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">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.473 0.118 0.917 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.317 0.152 0.847 </span> <span class="r-in"><span class="va">ci_profile</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> @@ -281,7 +281,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span class="va">ci_quadratic_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> <span class="r-in"><span class="va">ci_quadratic_transformed_ff</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833578 102.79311649</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833565 102.79311648</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090823771 0.10725430</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.004012219 0.00689755</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469118824 0.55959615</span> @@ -289,7 +289,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span class="va">ci_quadratic_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span class="r-in"><span class="va">ci_quadratic_untransformed_ff</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833583 1.027931e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833570 1.027931e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090491913 1.069035e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.003835485 6.685823e-03</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469113477 5.598387e-01</span> @@ -309,17 +309,17 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-out co"><span class="r-pr">#></span> sigma TRUE FALSE</span> <span class="r-in"><span class="va">rel_diffs_transformed_ff</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408690 0.0002217233</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598532 0.0009001864</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283041 0.0290588361</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881769 0.0027780063</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408691 0.0002217232</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598534 0.0009001862</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283050 0.0290588375</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881765 0.0027780058</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> <span class="r-in"><span class="va">rel_diffs_untransformed_ff</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408689 0.0002217232</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102156 0.0023732281</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740690 0.0025291820</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995211 0.0023457712</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408691 0.0002217231</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102157 0.0023732283</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740682 0.0025291807</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995207 0.0023457708</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> <span class="r-in"></span> <span class="r-in"><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span> @@ -333,19 +333,19 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"> error_model_algorithm <span class="op">=</span> <span class="st">"direct"</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/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596039609 106.19954892</span> -<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605368 0.04490762</span> -<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568731 0.01087676</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021462489 0.62023882</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015165617 0.37975348</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.273897348 0.33388101</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.018614554 0.02250378</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.671943411 0.73583305</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283495 0.83992077</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411024 0.07662008</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596210088 106.19935874</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605436 0.04490756</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568746 0.01087674</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021466645 0.62023879</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015168549 0.37975352</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.273897574 0.33388069</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.018614555 0.02250379</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.671943815 0.73583258</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283808 0.83992121</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411010 0.07662004</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, <span class="st">"parent_0"</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59604 106.1995</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59621 106.1994</span> <span class="r-in"><span class="co"># }</span></span> </code></pre></div> </div> @@ -361,7 +361,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 1c70a094..b85acb7a 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -114,7 +114,7 @@ <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"><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</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span> +<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span></span> <span class="r-in"> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> @@ -129,7 +129,7 @@ <span class="r-in"> parent <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="st">"m1"</span><span class="op">)</span>,</span> <span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span> +<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span></span> <span class="r-in"> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> @@ -154,7 +154,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/dimethenamid_2018-1.png b/docs/reference/dimethenamid_2018-1.png Binary files differindex 4300b0c0..6e5d357d 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 36db063c..cf5f03f7 100644 --- a/docs/reference/dimethenamid_2018-2.png +++ b/docs/reference/dimethenamid_2018-2.png diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index e913fa27..431e5c34 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -239,65 +239,65 @@ specific pieces of information in the comments.</p> <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> DMTA_0 88.3098 84.1383 92.4813</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0510 -3.5659 -2.5361</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0567 -4.9178 -3.1955</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8592 -4.2571 -3.4614</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9685 -4.4683 -3.4686</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1382 -0.2120 0.4885</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1429 -0.2616 0.5473</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3889 -1.6943 -1.0836</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> log_k_DMTA 0.0315 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0237 -0.0031 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0392 -0.0048 0.0040 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0257 -0.0032 0.0022 0.0821 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0048 -0.0007 0.0415 -0.0435 0.0333 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0007 -0.0002 0.0214 -0.0270 -0.0900 -0.0372 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1861 -0.0136 0.0431 0.0797 0.0382 -0.0072 0.0066 </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> SD.DMTA_0 3.2733 -1.1098 7.6564</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6422 0.2777 1.0066</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0131 0.3797 1.6465</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4511 0.1510 0.7513</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5695 0.1923 0.9466</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4123 0.1526 0.6720</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1804 0.7757</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3559 0.1344 0.5775</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> a.1 0.9255 0.8288 1.0221</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1365 0.1191 0.1538</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> DMTA_0 88.30980 84.138334 92.48126</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04731 0.028272 0.07918</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01731 0.007315 0.04095</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02108 0.014164 0.03139</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01890 0.011467 0.03116</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14626 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12029 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11135 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> DMTA_M23 0.1463</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1203</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1113</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6221</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-out co"><span class="r-pr">#></span> DMTA 14.65 48.67</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.05 133.05</span> +<span class="r-out co"><span class="r-pr">#></span> M27 32.88 109.21</span> +<span class="r-out co"><span class="r-pr">#></span> M31 36.67 121.81</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> @@ -321,7 +321,7 @@ specific pieces of information in the comments.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index f764b742..883c9e5d 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -178,7 +178,7 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png Binary files differindex b7b4d63b..50c09278 100644 --- a/docs/reference/experimental_data_for_UBA-1.png +++ b/docs/reference/experimental_data_for_UBA-1.png diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index e87105b6..69a8baf4 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -238,7 +238,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index eb0e6f73..27da5718 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -194,7 +194,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 9189ef76..6b64ba73 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -133,7 +133,7 @@ Version 2.2, May 2014 <a href="https://esdac.jrc.ec.europa.eu/projects/ground-wa </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 130e786a..c63a968c 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -108,7 +108,7 @@ nlme.mmkin</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index d0cb6372..58ae56b0 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -170,7 +170,7 @@ Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 90387a56..4d657918 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -429,7 +429,7 @@ kinetic models fitted with mkinfit</p></td> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index ddc565b3..ae621adc 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -123,7 +123,7 @@ class attribute</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex d897c363..a1a65a61 100644 --- a/docs/reference/loftest-3.png +++ b/docs/reference/loftest-3.png diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png Binary files differindex 0847bbec..c441f2ed 100644 --- a/docs/reference/loftest-5.png +++ b/docs/reference/loftest-5.png diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index a96e6932..ee9b37e4 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -302,7 +302,7 @@ of replicate samples.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index c41950a3..9c34d890 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -162,7 +162,7 @@ and the fitted error model parameters.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index ed6e29dc..b09d3a69 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -176,20 +176,20 @@ Version 1.1, 18 December 2014 <span class="r-plt img"><img src="logistic.solution-2.png" alt="" width="700" height="433"></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">m</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-16 1.016451e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02</span> <span class="r-out co"><span class="r-pr">#></span> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08</span> -<span class="r-out co"><span class="r-pr">#></span> r 2.263946e-01 0.1718110662 1.317695 1.061043e-01 4.335843e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846685e-08</span> +<span class="r-out co"><span class="r-pr">#></span> r 2.263946e-01 0.1718110773 1.317695 1.061044e-01 4.335843e-02</span> <span class="r-out co"><span class="r-pr">#></span> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00</span> <span class="r-out co"><span class="r-pr">#></span> Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 109.9341588</span> <span class="r-out co"><span class="r-pr">#></span> kmax 0.1041853</span> -<span class="r-out co"><span class="r-pr">#></span> k0 0.4448749</span> -<span class="r-out co"><span class="r-pr">#></span> r 1.1821120</span> +<span class="r-out co"><span class="r-pr">#></span> k0 0.4448750</span> +<span class="r-out co"><span class="r-pr">#></span> r 1.1821121</span> <span class="r-out co"><span class="r-pr">#></span> sigma 7.3256566</span> <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span></span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_k0 DT50_kmax</span> -<span class="r-out co"><span class="r-pr">#></span> parent 36.86533 62.41511 4297.853 10.83349</span> +<span class="r-out co"><span class="r-pr">#></span> parent 36.86533 62.41511 4297.854 10.83349</span> <span class="r-in"></span> </code></pre></div> </div> @@ -205,7 +205,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 6adc1245..bc8dab67 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -191,7 +191,7 @@ lower number of fitted parameters (null hypothesis).</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 29b17d1a..69da881b 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -179,7 +179,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 9b698e64..97ac647e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -117,7 +117,7 @@ <div id="source"> <h2>Source</h2> <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 - doi: <a href="https://doi.org/10.1021/jf00103a026" class="external-link">10.1021/jf00103a026</a></p> + <a href="https://doi.org/10.1021/jf00103a026" class="external-link">doi:10.1021/jf00103a026</a></p> </div> <div id="ref-examples"> @@ -128,19 +128,20 @@ <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"> <span class="co"># \dontrun{</span></span> <span class="r-in"> <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" class="external-link">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></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</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">fit.1</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t)</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074929 47.537272 4.472189e-18</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02</span> -<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993439 1.356073 9.756988e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340365 1.562627 6.949413e-02</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718439498 1.488441 7.867788e-02</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558786 5.123989 6.233156e-05</span> <span class="r-out co"><span class="r-pr">#></span> Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061385 1.084640e+02</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061401 1.084640e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 0.039631621 4.746194e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013879 7.525762e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013878 7.525762e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_anisole 0.005370739 8.305299e-03</span> <span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.547559081 6.924813e-01</span> <span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 0.000000000 1.000000e+00</span> @@ -148,13 +149,13 @@ <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.195366e-10 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> <span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> -<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784092 344.76329</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"> <span class="co"># formation fraction from phenol to anisol is practically 1. As we cannot</span></span> <span class="r-in"> <span class="co"># fix formation fractions when using the ilr transformation, we can turn of</span></span> @@ -165,31 +166,32 @@ <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"> <span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO_2</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>,</span> <span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284</span> -<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587</span> -<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653038 48.028439 4.993108e-19 99.271020197</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343667 23.643268 3.573556e-14 0.039650977</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050583e-01 0.1177237899 3.440751 1.679257e-03 0.218746592</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872895e-08 0.005377082</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198824 2.039410e-12 0.547975622</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655</span> <span class="r-out co"><span class="r-pr">#></span> Upper</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 108.43904074</span> -<span class="r-out co"><span class="r-pr">#></span> k_T245 0.04743877</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.75005585</span> -<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.00829550</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.69212308</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.31827222</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.084390e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.743877e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 7.500560e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 8.295499e-03</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.921231e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.318272e+00</span> <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.195366e-10 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> <span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> -<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784092 344.76329</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"> <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></span> <span class="r-plt img"><img src="mccall81_245T-1.png" alt="" width="700" height="433"></span> @@ -208,7 +210,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index efe91b6f..bea9f2d8 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -134,7 +134,7 @@ nlme for the case of a single grouping variable ds.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png Binary files differindex 54b81b70..fe7e6c47 100644 --- a/docs/reference/mixed-1.png +++ b/docs/reference/mixed-1.png diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index af73f22a..dfc7a731 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -177,9 +177,9 @@ single dataframe which is convenient for plotting</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Mean fitted 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> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 </span> +<span class="r-out co"><span class="r-pr">#></span> 100.674757 -8.762456 -0.004347 -3.348812 -3.986853 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> -0.087392 </span> +<span class="r-out co"><span class="r-pr">#></span> -0.087391 </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_mixed</span><span class="op">)</span></span> <span class="r-plt img"><img src="mixed-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="co"># }</span></span> @@ -197,7 +197,7 @@ single dataframe which is convenient for plotting</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index ed0abedd..ba00a80a 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -157,7 +157,7 @@ observed values called "value".</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 37c84761..0cb9ebca 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -139,7 +139,7 @@ column of observed values.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 73a14840..bef3be93 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -145,9 +145,9 @@ and value in order to be compatible with mkinfit</p></dd> <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> -<ul><li><p><a href="#method-new"><code>mkinds$new()</code></a></p></li> -<li><p><a href="#method-clone"><code>mkinds$clone()</code></a></p></li> -</ul></div><p></p><hr><a id="method-new"></a><div class="section"> +<ul><li><p><a href="#method-mkinds-new"><code>mkinds$new()</code></a></p></li> +<li><p><a href="#method-mkinds-clone"><code>mkinds$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-mkinds-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> <p>Create a new mkinds object</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> @@ -175,7 +175,7 @@ and value in order to be compatible with mkinfit</p></dd> </dl><p></p></div> </div> -</div><p></p><hr><a id="method-clone"></a><div class="section"> +</div><p></p><hr><a id="method-mkinds-clone"></a><div class="section"> <h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> <p>The objects of this class are cloneable with this method.</p><div class="section"> <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> @@ -220,7 +220,7 @@ and value in order to be compatible with mkinfit</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 7f4ff290..ceee4f37 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -142,9 +142,9 @@ or covariates like soil pH).</p></dd> <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> -<ul><li><p><a href="#method-new"><code>mkindsg$new()</code></a></p></li> -<li><p><a href="#method-clone"><code>mkindsg$clone()</code></a></p></li> -</ul></div><p></p><hr><a id="method-new"></a><div class="section"> +<ul><li><p><a href="#method-mkindsg-new"><code>mkindsg$new()</code></a></p></li> +<li><p><a href="#method-mkindsg-clone"><code>mkindsg$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-mkindsg-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> <p>Create a new mkindsg object</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> @@ -172,7 +172,7 @@ or covariates like soil pH).</p></dd> </dl><p></p></div> </div> -</div><p></p><hr><a id="method-clone"></a><div class="section"> +</div><p></p><hr><a id="method-mkindsg-clone"></a><div class="section"> <h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> <p>The objects of this class are cloneable with this method.</p><div class="section"> <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> @@ -406,7 +406,7 @@ or covariates like soil pH).</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index dc2cdab8..b6051ab8 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -139,6 +139,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"></span> <span class="r-in"><span class="va">fit_FOCUS_D</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_D</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> <span class="r-out co"><span class="r-pr">#></span> All data 0.0640 4 15</span> @@ -167,7 +168,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png Binary files differindex 49bb1c0e..852da18d 100644 --- a/docs/reference/mkinerrplot-1.png +++ b/docs/reference/mkinerrplot-1.png diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 95206b61..4b78f6eb 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -164,6 +164,7 @@ lines of the mkinfit object.</p></div> <span class="r-in"><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</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-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu">mkinerrplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-plt img"><img src="mkinerrplot-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="co"># }</span></span> @@ -182,7 +183,7 @@ lines of the mkinfit object.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index c006ddab..e5bf1203 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -307,7 +307,7 @@ internal rate transformation.</p> for measurement error in analytical chemistry. <em>Technometrics</em> 37(2), 176-184.</p> <p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. <em>Environments</em> 6(12) 124 -doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link">10.3390/environments6120124</a> +<a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a> .</p> </div> <div id="see-also"> @@ -330,16 +330,16 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <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">fit</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:11:56 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:11:56 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:37:57 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:37:57 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 = - (alpha/beta) * 1/((time/beta) + 1) * parent</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 analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.045 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.041 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -374,10 +374,10 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00</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> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -462,7 +462,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> parent 6.89313 22.89848</span> -<span class="r-out co"><span class="r-pr">#></span> m1 134.15634 445.65772</span> +<span class="r-out co"><span class="r-pr">#></span> m1 134.15634 445.65770</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"></span> <span class="r-in"><span class="co"># We can show a quick (only one replication) benchmark for this case, as we</span></span> @@ -471,7 +471,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"><span class="co"># benchmark vignette</span></span> <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <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">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <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">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> <span class="r-in"> deSolve_compiled <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> <span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> eigen <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> @@ -479,10 +479,8 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"> analytical <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> <span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</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> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.573</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.642 0.941</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.517 1.442</span> +<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there is no package called ‘rbenchmark’</span> <span class="r-in"><span class="co"># }</span></span> <span class="r-in"></span> <span class="r-in"><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span> @@ -506,10 +504,13 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"><span class="co"># Also, the missing standard error for log_beta and the t-tests for alpha</span></span> <span class="r-in"><span class="co"># and beta indicate overparameterisation</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">fit.FOMC_SFO.tc</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:12:07 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:12:07 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:38:07 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:38:07 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 = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -518,12 +519,12 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <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 using 3729 model solutions performed in 2.67 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 3924 model solutions performed in 7.107 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error 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> Error model algorithm: d_3 </span> -<span class="r-out co"><span class="r-pr">#></span> Direct fitting and three-step fitting yield approximately the same likelihood </span> +<span class="r-out co"><span class="r-pr">#></span> Three-step fitting yielded a higher likelihood than direct fitting </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 parameters to be optimised:</span> <span class="r-out co"><span class="r-pr">#></span> value type</span> @@ -558,7 +559,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 101.600000 2.6400000 96.240000 107.000000</span> <span class="r-out co"><span class="r-pr">#></span> log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.001426 0.0766900 -0.155000 0.157800</span> <span class="r-out co"><span class="r-pr">#></span> log_alpha 5.522000 0.0077320 5.506000 5.538000</span> <span class="r-out co"><span class="r-pr">#></span> log_beta 7.806000 NaN NaN NaN</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low 0.002488 0.0002431 0.001992 0.002984</span> @@ -566,31 +567,31 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000000 -0.095145 -0.76674 0.70541 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.095145 1.000000 0.51428 -0.14381 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.766743 0.514278 1.00000 -0.61392 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.705413 -0.143809 -0.61392 1.00000 NaN</span> <span class="r-out co"><span class="r-pr">#></span> log_beta NaN NaN NaN NaN 1</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.016073 0.001586 0.01548 5.87007 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.016077 0.001586 0.01548 5.87034 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.006617 -0.011694 -0.05356 0.04848 NaN</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low rsd_high</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.016073 0.006626</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.001586 -0.011700</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.015476 -0.053566</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha 5.870075 0.048487</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.016077 0.006617</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.001586 -0.011694</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.015476 -0.053560</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha 5.870339 0.048481</span> <span class="r-out co"><span class="r-pr">#></span> log_beta NaN NaN</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 1.000000 -0.652558</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high -0.652558 1.000000</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 1.000000 -0.652555</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high -0.652555 1.000000</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> Confidence intervals for internally transformed parameters are asymmetric.</span> <span class="r-out co"><span class="r-pr">#></span> t-test (unrealistically) based on the assumption of normal distribution</span> <span class="r-out co"><span class="r-pr">#></span> for estimators of untransformed parameters.</span> <span class="r-out co"><span class="r-pr">#></span> Estimate t value Pr(>t) Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.016e+02 32.7800 6.312e-26 9.624e+01 1.070e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01</span> -<span class="r-out co"><span class="r-pr">#></span> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 5.004e-01 20.8300 4.318e-20 4.613e-01 5.394e-01</span> +<span class="r-out co"><span class="r-pr">#></span> alpha 2.502e+02 0.5624 2.890e-01 2.463e+02 2.542e+02</span> <span class="r-out co"><span class="r-pr">#></span> beta 2.455e+03 0.5549 2.915e-01 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03</span> <span class="r-out co"><span class="r-pr">#></span> rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02</span> @@ -630,7 +631,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 72a9ea52..3a29b39b 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -258,6 +258,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"></span> <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"></span> <span class="r-in"> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span> <span class="r-in"> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span> @@ -267,13 +268,14 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span> <span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span> <span class="r-in"> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmp1TiIZY/file1180516cafe4a2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpkcKjUM/file8dd657f864c2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span class="co"># Now we can save the model and restore it in a new session</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> <span class="r-in"><span class="co"># Terminate the R session here if you would like to check, and then do</span></span> <span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> <span class="r-in"><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> <span class="r-in"><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"></span> <span class="r-in"><span class="co"># Show details of creating the C function</span></span> <span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> @@ -319,7 +321,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f6c4cd8></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55cc1a5f8ad8></span> <span class="r-in"></span> <span class="r-in"><span class="co"># If we have several parallel metabolites</span></span> <span class="r-in"><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span> @@ -348,7 +350,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex fff98391..69d9ac75 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 2e787240..b9eda413 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -117,6 +117,7 @@ effect, namely to produce a plot.</p> <span class="r-in"> anisole <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>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">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></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-plt img"><img src="mkinparplot-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="co"># }</span></span> @@ -134,7 +135,7 @@ effect, namely to produce a plot.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 79599787..cad5b35f 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -120,7 +120,7 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index c197e6dc..d888bb25 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -318,7 +318,7 @@ as these always return mapped output.</p></dd> <span class="r-in"> m1 <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>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">10</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <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">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">10</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <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">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> <span class="r-in"> eigen <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> @@ -336,11 +336,8 @@ as these always return mapped output.</p></dd> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> <span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</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> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.00 0.004</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.50 0.006</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 5.25 0.021</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 52.00 0.208</span> +<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there is no package called ‘rbenchmark’</span> <span class="r-in"></span> <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"> <span class="co"># Predict from a fitted model</span></span> @@ -370,7 +367,7 @@ as these always return mapped output.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index cd3b4009..654b93d8 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -166,6 +166,7 @@ combining the plot of the fit and the residual plot.</p></div> <span class="r-in"><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu">mkinresplot</span><span class="op">(</span><span class="va">fit</span>, <span class="st">"m1"</span><span class="op">)</span></span> <span class="r-plt img"><img src="mkinresplot-1.png" alt="" width="700" height="433"></span> <span class="r-in"></span> @@ -183,7 +184,7 @@ combining the plot of the fit and the residual plot.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 8ad9c11d..75cbc054 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex da2a48a8..76f42b73 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex 10d3f35b..e92d81b2 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 132380a8..8d747ffe 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex 4bfcc55e..ffd7640d 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 1ca0190a..cbb46ab0 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -167,10 +167,10 @@ plotting.</p></div> <span class="r-in"></span> <span class="r-in"><span class="va">time_default</span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 4.710 0.665 1.757 </span> +<span class="r-out co"><span class="r-pr">#></span> 35.152 1.185 8.439 </span> <span class="r-in"><span class="va">time_1</span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 5.644 0.001 5.645 </span> +<span class="r-out co"><span class="r-pr">#></span> 14.744 0.008 14.768 </span> <span class="r-in"></span> <span class="r-in"><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> @@ -180,8 +180,8 @@ plotting.</p></div> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> parent 0.877769 2.915885</span> -<span class="r-out co"><span class="r-pr">#></span> M1 2.325744 7.725956</span> -<span class="r-out co"><span class="r-pr">#></span> M2 33.720100 112.015749</span> +<span class="r-out co"><span class="r-pr">#></span> M1 2.325744 7.725955</span> +<span class="r-out co"><span class="r-pr">#></span> M2 33.720111 112.015785</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"></span> <span class="r-in"><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</span></span> @@ -214,10 +214,12 @@ plotting.</p></div> <span class="r-out co"><span class="r-pr">#></span> dataset</span> <span class="r-out co"><span class="r-pr">#></span> model A B C D </span> <span class="r-out co"><span class="r-pr">#></span> SFO OK OK OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC C OK OK OK</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 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-out co"><span class="r-pr">#></span> C: Optimisation did not converge:</span> +<span class="r-out co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span> <span class="r-in"><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span> @@ -237,7 +239,7 @@ plotting.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 0711886a..1d22b617 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -209,7 +209,7 @@ list element "data" contains the dataset used in the fits.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex 67cc7f3c..0b6cb78d 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex bb1e6f81..ef152270 100644 --- a/docs/reference/nlme-2.png +++ b/docs/reference/nlme-2.png diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 746cc6aa..ff8de9f3 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -202,7 +202,7 @@ A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external- </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 1f071ffa..c8bd28e9 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -97,7 +97,7 @@ have been obtained by fitting the same model to a list of datasets.</p> data <span class="op">=</span> <span class="st">"auto"</span>, fixed <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, - random <span class="op">=</span> <span class="fu">pdDiag</span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>, + random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>, <span class="va">groups</span>, start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, correlation <span class="op">=</span> <span class="cn">NULL</span>, @@ -196,7 +196,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"> <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_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001</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">f_nlme_dfop</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -227,7 +227,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $distimes</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 10.79857 100.7937 30.34193 4.193938 43.85443</span> +<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34192 4.193936 43.85441</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"></span> <span class="r-in"> <span class="va">ds_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span> @@ -278,12 +278,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 0.2768574 0.7231426 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.2768575 0.7231425 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</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 11.07091 104.6320 31.49737 4.462383 46.20825</span> -<span class="r-out co"><span class="r-pr">#></span> A1 162.30519 539.1662 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> A1 162.30524 539.1663 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"></span> <span class="r-in"> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span> @@ -311,7 +311,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> 94.04774 -1.82340 -4.16716 0.05686 </span> +<span class="r-out co"><span class="r-pr">#></span> 94.04775 -1.82340 -4.16715 0.05685 </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> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span> @@ -325,7 +325,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 2.23223147 0.01262395 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.23223513 0.01262371 </span> <span class="r-in"></span> <span class="r-in"> <span class="va">f_2_obs</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_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span> <span class="r-in"> <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> @@ -358,7 +358,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~1 | name </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> parent A1 </span> -<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049995 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049985 </span> <span class="r-in"> <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span> <span class="r-in"> control <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>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"></span> @@ -370,7 +370,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"> <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_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32091</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32092</span> <span class="r-out co"><span class="r-pr">#></span> p-value</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo </span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs <.0001</span> @@ -390,7 +390,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index 34da24d9..e37fff64 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -115,7 +115,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 1ddd3eb9..18f3566e 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -157,10 +157,10 @@ such matrices is returned.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 7</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971589</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971599</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.044946770</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.002868336</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.526942415</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.526942414</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.221302196</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span> @@ -179,10 +179,10 @@ such matrices is returned.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971599 90.34509493 98.14858821 94.311323732</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> @@ -222,7 +222,7 @@ such matrices is returned.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png Binary files differindex 8678c166..b35f28d6 100644 --- a/docs/reference/plot.mixed.mmkin-2.png +++ b/docs/reference/plot.mixed.mmkin-2.png diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png Binary files differindex 9bd01852..c981538f 100644 --- a/docs/reference/plot.mixed.mmkin-3.png +++ b/docs/reference/plot.mixed.mmkin-3.png diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png Binary files differindex d2fa1ae1..ccbe5861 100644 --- a/docs/reference/plot.mixed.mmkin-4.png +++ b/docs/reference/plot.mixed.mmkin-4.png diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 52971427..2af2328d 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -232,7 +232,7 @@ corresponding model prediction lines for the different datasets.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex cef94cb8..39098648 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex f90b3f54..3545b8d8 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png Binary files differindex 3e5d828e..daf43033 100644 --- a/docs/reference/plot.mkinfit-7.png +++ b/docs/reference/plot.mkinfit-7.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index b74d1e7b..23cf27b5 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -279,7 +279,7 @@ latex is being used for the formatting of the chi2 error level, if </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex 7af84edf..f5768c40 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 56bfac50..c3f77d3d 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 5da05f40..29439156 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png Binary files differindex 3ec224f4..89a111b0 100644 --- a/docs/reference/plot.mmkin-5.png +++ b/docs/reference/plot.mmkin-5.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index d7ad89dc..3dd0203b 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -173,6 +173,8 @@ latex is being used for the formatting of the chi2 error level.</p> <span class="r-in"> <span class="va">fits</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" class="external-link">c</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"HS"</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">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span> <span class="r-in"> cores <span class="op">=</span> <span class="fl">1</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-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</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">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span> <span class="r-plt img"><img src="plot.mmkin-1.png" alt="" width="700" height="433"></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">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> @@ -205,7 +207,7 @@ latex is being used for the formatting of the chi2 error level.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index a14ed303..af65d8eb 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -129,7 +129,7 @@ function (SFO, then IORE, then DFOP).</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 1367ccf5..4da7092a 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -120,7 +120,7 @@ below to see their documentation.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index c27cea76..7d9e50de 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -125,7 +125,7 @@ standard deviation obtained from the fitted error model?</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/saem.html b/docs/reference/saem.html index f9e6565f..e9898a73 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -291,13 +291,13 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> <span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 1.8856 1.6676 2.1037</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.8856 1.6770 2.0943</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7669 4.7695</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> <span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3068 1.1946</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><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</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> @@ -359,16 +359,16 @@ 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> 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.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7669 4.7695</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> <span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3068 1.1946</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 1.886 1.668 2.104</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.886 1.677 2.094</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> @@ -554,7 +554,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 6.4 7.59693 -1.19693 1.886 -0.634761</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 7.2 7.59693 -0.39693 1.886 -0.210502</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 9.1 9.86436 -0.76436 1.886 -0.405361</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 8.5 9.86436 -1.36436 1.886 -0.723555</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 8.5 9.86436 -1.36436 1.886 -0.723556</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 11.7 10.99397 0.70603 1.886 0.374425</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 12.0 10.99397 1.00603 1.886 0.533522</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.3 11.91274 1.38726 1.886 0.735696</span> @@ -589,7 +589,7 @@ using <a href="mmkin.html">mmkin</a>.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 7fef34e4..23102f17 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -125,7 +125,7 @@ Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> <p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. <em>Environments</em> 6(12) 124 -doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link">10.3390/environments6120124</a> +<a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a> .</p> </div> @@ -172,7 +172,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f01d1048..6d816366 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -179,16 +179,16 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> <span class="r-in"> <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="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:30 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:30 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:42:00 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:42:00 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 = - k_parent * parent</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 analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.028 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.027 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -220,9 +220,9 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 5.428e-01 1.642e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent 5.428e-01 1.000e+00 2.507e-07</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 1.642e-07 2.507e-07 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 5.428e-01 1.648e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 5.428e-01 1.000e+00 2.514e-07</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.648e-07 2.514e-07 1.000e+00</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> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -267,7 +267,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 4879269e..ff014cc1 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -197,8 +197,6 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-in"><span class="co"># Evaluate using mmkin and nlme</span></span> <span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> <span class="r-in"><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo_syn</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">1</span><span class="op">)</span></span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> -<span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> <span class="r-in"><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span> <span class="r-in"><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_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> @@ -222,7 +220,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <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> parent_0 log_k_parent </span> -<span class="r-out co"><span class="r-pr">#></span> 101.569 -4.454 </span> +<span class="r-out co"><span class="r-pr">#></span> 101.612 -4.454 </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> @@ -246,18 +244,18 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.924e-05 0.5863 1</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.904e-05 0.5863 1</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance function:</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Constant plus proportion of variance covariate</span> <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> -<span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 0.0001208853 0.0789968036 </span> +<span class="r-out co"><span class="r-pr">#></span> const prop </span> +<span class="r-out co"><span class="r-pr">#></span> 0.000121099 0.078996777 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters with asymmetric confidence intervals:</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 99.370882 101.59243 103.81398</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.370886 101.59243 103.81398</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.006923 0.01168 0.01972</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> @@ -268,48 +266,48 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <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 0 104.1 101.592 2.50757 8.0255 0.312451</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288314</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788813</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389080</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401988</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958481</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561253</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063244</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585875</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667252</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007681</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249487</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964200</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572173</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901593</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669544</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485010</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668740</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 109.9 99.218 10.68195 7.8379 1.362858</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 97.8 99.218 -1.41805 7.8379 -0.180921</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305361</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 78.3 86.093 -7.79273 6.8010 -1.145814</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 90.3 86.093 4.20727 6.8010 0.618620</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842</span> @@ -317,45 +315,45 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206778</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323283</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535204</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260887</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 98.1 98.362 -0.26191 7.7703 -0.033706</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 87.8 98.362 -10.56191 7.7703 -1.359271</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 97.9 95.234 2.66589 7.5232 0.354356</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 104.8 95.234 9.56589 7.5232 1.271521</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 85.0 89.274 -4.27373 7.0523 -0.606002</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 77.2 89.274 -12.07373 7.0523 -1.712019</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18659 6.0838 0.852523</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08659 6.0838 1.493568</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 70.5 67.053 3.44690 5.2970 0.650729</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 61.7 67.053 -5.35310 5.2970 -1.010595</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 60.0 58.381 1.61902 4.6119 0.351052</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 56.4 58.381 -1.98098 4.6119 -0.429535</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120486</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024412</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935383</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273296</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 20.8 22.692 -1.89165 1.7926 -1.055273</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.4 13.768 -0.36790 1.0876 -0.338259</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.8 13.768 0.03210 1.0876 0.029517</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802063</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 38.3 37.399 0.90062 2.9544 0.304836</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 40.7 37.399 3.30062 2.9544 1.117176</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 22.5 22.692 -0.19164 1.7926 -0.106910</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 20.8 22.692 -1.89164 1.7926 -1.055271</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.4 13.768 -0.36789 1.0876 -0.338255</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.8 13.768 0.03211 1.0876 0.029520</span> <span class="r-in"><span class="co"># }</span></span> <span class="r-in"></span> </code></pre></div> @@ -372,7 +370,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index 26ece42d..c2f9490e 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -199,9 +199,9 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-in"><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</span>, data <span class="op">=</span> <span class="cn">TRUE</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: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:47 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:47 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:42:18 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:42:18 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> @@ -216,7 +216,7 @@ 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 12.164 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 12.833 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> @@ -225,7 +225,7 @@ saemix authors for the parts inherited from saemix.</p> <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> -<span class="r-out co"><span class="r-pr">#></span> -0.01132 </span> +<span class="r-out co"><span class="r-pr">#></span> -0.01133 </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> @@ -234,231 +234,231 @@ 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> 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> 828.1 822.7 -400.1</span> +<span class="r-out co"><span class="r-pr">#></span> 829.3 823.8 -400.6</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_0 100.74378 97.813 103.6747</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06168 -4.171 -3.9523</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.92584 -1.313 -0.5389</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.81914 -3.602 -2.0362</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.63916 -4.327 -2.9516</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02927 -1.152 1.0939</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.26516 98.412 104.1188</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.07510 -4.168 -3.9819</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.94320 -1.350 -0.5364</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.87697 -3.703 -2.0510</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.58133 -4.313 -2.8492</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.03174 -1.564 1.5008</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 -0.3571 </span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2190 0.2189 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1248 -0.1042 -0.0514 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0130 0.0043 -0.0049 0.0883 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0643 0.0437 0.0354 -0.3477 -0.2589</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4167 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2084 0.2383 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1324 -0.1242 -0.0500 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0173 0.0001 -0.0067 0.1137 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0849 0.0691 0.0399 -0.3916 -0.3012</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.parent_0 0.73313 -7.46512 8.9314</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.06488 -0.06041 0.1902</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.41955 0.15206 0.6870</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.81750 0.29140 1.3436</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.75265 0.27939 1.2259</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.34411 -1.70964 2.3979</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.parent_0 0.16032 -34.0484 34.3690</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.01463 -0.3605 0.3898</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44391 0.1646 0.7232</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.84861 0.3044 1.3928</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.79185 0.2944 1.2893</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.34997 -3.0572 3.7572</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 0.86164 0.67928 1.04400</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.07973 0.06437 0.09509</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 0.87200 0.69118 1.0528</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07963 0.06435 0.0949</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_0 100.74378 97.81291 103.67465</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01722 0.01544 0.01921</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28377 0.21203 0.36843</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.05966 0.02727 0.13052</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.02627 0.01321 0.05226</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.49268 0.24004 0.74912</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.26516 98.41151 104.11881</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01699 0.01548 0.01865</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28025 0.20588 0.36902</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.05630 0.02465 0.12861</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.02784 0.01339 0.05789</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.49207 0.17303 0.81770</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 0.2838</span> -<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7162</span> +<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2803</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7197</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 17.17 65.72 19.78 11.62 26.38</span> -<span class="r-out co"><span class="r-pr">#></span> m1 40.25 133.71 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> parent 17.28 63.65 19.16 12.31 24.9</span> +<span class="r-out co"><span class="r-pr">#></span> m1 40.80 135.52 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 1.005e+02 -1.069e+01 8.0584 -1.327e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.005e+02 3.607e+00 8.0584 4.476e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.580e+01 -7.103e+00 7.6867 -9.241e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.580e+01 -3.030e-01 7.6867 -3.942e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.722e+01 -5.418e+00 7.0070 -7.733e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.722e+01 7.282e+00 7.0070 1.039e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.278e+01 -1.282e+00 5.8665 -2.186e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.278e+01 -2.482e+00 5.8665 -4.231e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.418e+01 2.128e-02 4.4047 4.831e-03</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.418e+01 -4.579e+00 4.4047 -1.040e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.235e+01 -8.510e-01 2.7194 -3.129e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.235e+01 -3.551e+00 2.7194 -1.306e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.282e+01 -7.213e-01 1.3369 -5.395e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.282e+01 7.787e-01 1.3369 5.825e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.184e+00 1.593e-02 0.9927 1.605e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.184e+00 2.116e+00 0.9927 2.131e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.092e+00 -8.915e-01 0.8962 -9.948e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.092e+00 -6.915e-01 0.8962 -7.716e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.147e+00 -8.468e-01 0.8665 -9.773e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.147e+00 -9.468e-01 0.8665 -1.093e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.190e+00 -9.901e-01 0.8984 -1.102e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.190e+00 -1.901e-01 0.8984 -2.116e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.422e+00 7.828e-02 1.0023 7.811e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.422e+00 -1.422e+00 1.0023 -1.418e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.002e+01 1.782e-01 1.1751 1.517e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.002e+01 -5.218e-01 1.1751 -4.440e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.265e+01 -4.548e-01 1.3268 -3.428e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.265e+01 7.452e-01 1.3268 5.617e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.093e+01 8.735e-01 1.2253 7.129e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.093e+01 2.273e+00 1.2253 1.855e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.845e+00 -1.245e+00 1.0647 -1.170e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.845e+00 1.455e+00 1.0647 1.366e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.322e+00 -1.822e+00 0.9605 -1.897e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.322e+00 7.779e-02 0.9605 8.099e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.008e+02 1.724e+01 8.0794 2.134e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.008e+02 -9.578e-01 8.0794 -1.185e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.538e+01 -5.183e+00 7.6535 -6.773e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.538e+01 -7.834e-01 7.6535 -1.024e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.604e+01 1.006e+01 6.9134 1.456e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.604e+01 -7.635e+00 6.9134 -1.104e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.170e+01 6.196e+00 5.7814 1.072e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.170e+01 5.996e+00 5.7814 1.037e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.556e+01 4.370e-01 4.5130 9.683e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.556e+01 -8.630e-01 4.5130 -1.912e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.869e+01 -2.085e+00 3.2024 -6.512e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.869e+01 -1.885e+00 3.2024 -5.888e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.103e+01 1.072e+00 1.8850 5.688e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.103e+01 3.672e+00 1.8850 1.948e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.231e+01 8.760e-02 1.3062 6.707e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.231e+01 -1.512e+00 1.3062 -1.158e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.222e+00 -4.220e-01 1.0363 -4.072e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.222e+00 6.780e-01 1.0363 6.542e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.431e+00 -1.313e-01 0.8692 -1.510e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.849e+00 -1.486e-01 0.9146 -1.624e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.849e+00 8.514e-01 0.9146 9.309e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.298e+00 8.021e-01 1.0397 7.715e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.298e+00 6.021e-01 1.0397 5.791e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.051e+01 -4.109e-01 1.2020 -3.418e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.051e+01 -2.109e-01 1.2020 -1.755e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.218e+01 -1.476e+00 1.2980 -1.137e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.218e+01 2.421e-02 1.2980 1.865e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.043e+01 2.682e-01 1.1976 2.240e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.043e+01 2.068e+00 1.1976 1.727e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 7.931e+00 1.169e+00 1.0688 1.094e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 7.931e+00 -5.310e-01 1.0688 -4.969e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.717e+00 3.829e-01 0.9748 3.928e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.717e+00 -1.217e+00 0.9748 -1.249e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.010e+02 5.220e+00 8.0970 6.447e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.010e+02 5.920e+00 8.0970 7.312e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.352e+01 1.388e+01 7.5058 1.849e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.352e+01 2.581e+00 7.5058 3.439e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.127e+01 -1.866e+00 6.5363 -2.855e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.127e+01 1.334e+00 6.5363 2.041e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.441e+01 -5.112e-01 5.2072 -9.818e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.441e+01 -2.011e+00 5.2072 -3.862e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.843e+01 2.573e+00 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class="r-pr">#></span> ds 5 parent 28 23.9 3.077e+01 -6.874817 2.6010 -2.643147</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.796e+01 -0.957722 1.6748 -0.571838</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.796e+01 0.742278 1.6748 0.443201</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.186e+01 -0.560382 1.2854 -0.435957</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.186e+01 0.039618 1.2854 0.030821</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.875e+00 1.125373 1.0740 1.047800</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.875e+00 0.225373 1.0740 0.209838</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 7.105e-15 0.700000 0.8720 0.802748</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.133e+00 -0.132776 0.9070 -0.146393</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.133e+00 -0.532776 0.9070 -0.587416</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.401e+00 -3.300544 1.0990 -3.003203</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.401e+00 -0.900544 1.0990 -0.819415</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.580e+01 0.697935 1.5309 0.455905</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.580e+01 3.197935 1.5309 2.088955</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.230e+01 0.604922 1.9779 0.305846</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.230e+01 0.904922 1.9779 0.457525</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.446e+01 -2.255019 2.1336 -1.056917</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.446e+01 -0.055019 2.1336 -0.025787</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.874e+01 -3.242459 1.7285 -1.875916</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.874e+01 1.057541 1.7285 0.611838</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.352e+01 1.376176 1.3856 0.993173</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.352e+01 0.676176 1.3856 0.487989</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.609e+00 1.291013 1.1601 1.112858</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.609e+00 0.791013 1.1601 0.681856</span> <span class="r-in"><span class="co"># }</span></span> <span class="r-in"></span> </code></pre></div> @@ -475,7 +475,7 @@ saemix authors for the parts inherited from saemix.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 132380a8..8d747ffe 100644 --- a/docs/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index 39a92dd1..e9251de3 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -247,9 +247,9 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></span> <span class="r-in"> <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">fit</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:49 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:49 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:42:21 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:42:21 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 = - k_parent * parent</span> @@ -258,7 +258,7 @@ Compare also the code in the example section to see the degradation models."><!- <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 using 833 model solutions performed in 0.624 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 830 model solutions performed in 1.716 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -310,15 +310,15 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01</span> -<span class="r-out co"><span class="r-pr">#></span> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.063e-07 -1.980e-07 1.088e-07 1.041e-07 7.820e-09</span> <span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 -2.900e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 -8.030e-09</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 -2.741e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 3.938e-08</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 -2.681e-08</span> -<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 4.971e-08</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 4.971e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 2.063e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 -1.980e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 1.088e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 1.041e-07</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 7.820e-09</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 -6.495e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma -6.495e-08 1.000e+00</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> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -355,8 +355,8 @@ Compare also the code in the example section to see the degradation models."><!- <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> time variable observed predicted residual</span> -<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.5 1.021e+02 -0.56248</span> -<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.2 1.021e+02 -0.86248</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.5 1.021e+02 -0.56249</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.2 1.021e+02 -0.86249</span> <span class="r-out co"><span class="r-pr">#></span> 1 parent 53.9 4.873e+01 5.17118</span> <span class="r-out co"><span class="r-pr">#></span> 1 parent 47.5 4.873e+01 -1.22882</span> <span class="r-out co"><span class="r-pr">#></span> 3 parent 10.4 1.111e+01 -0.70773</span> @@ -365,8 +365,8 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> 7 parent 0.3 5.772e-01 -0.27717</span> <span class="r-out co"><span class="r-pr">#></span> 14 parent 3.5 3.264e-03 3.49674</span> <span class="r-out co"><span class="r-pr">#></span> 28 parent 3.2 1.045e-07 3.20000</span> -<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.530e-10 0.60000</span> -<span class="r-out co"><span class="r-pr">#></span> 120 parent 3.5 -5.940e-10 3.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.534e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 parent 3.5 -5.941e-10 3.50000</span> <span class="r-out co"><span class="r-pr">#></span> 1 M1 36.4 3.479e+01 1.61088</span> <span class="r-out co"><span class="r-pr">#></span> 1 M1 37.4 3.479e+01 2.61088</span> <span class="r-out co"><span class="r-pr">#></span> 3 M1 34.3 3.937e+01 -5.07027</span> @@ -376,9 +376,9 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> 14 M1 5.8 1.995e+00 3.80469</span> <span class="r-out co"><span class="r-pr">#></span> 14 M1 1.2 1.995e+00 -0.79531</span> <span class="r-out co"><span class="r-pr">#></span> 60 M1 0.5 2.111e-06 0.50000</span> -<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.670e-10 3.20000</span> -<span class="r-out co"><span class="r-pr">#></span> 120 M1 1.5 7.670e-10 1.50000</span> -<span class="r-out co"><span class="r-pr">#></span> 120 M1 0.6 7.670e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.675e-10 3.20000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 1.5 7.671e-10 1.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 0.6 7.671e-10 0.60000</span> <span class="r-out co"><span class="r-pr">#></span> 1 M2 4.8 4.455e+00 0.34517</span> <span class="r-out co"><span class="r-pr">#></span> 3 M2 20.9 2.153e+01 -0.62527</span> <span class="r-out co"><span class="r-pr">#></span> 3 M2 19.3 2.153e+01 -2.22527</span> @@ -409,7 +409,7 @@ Compare also the code in the example section to see the degradation models."><!- </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 95e8c6b6..2da09efe 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -288,7 +288,7 @@ This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index ff175937..48bf1d7f 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -115,7 +115,7 @@ remove arguments given in the original call</p></dd> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</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="parms.html">parms</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma </span> -<span class="r-out co"><span class="r-pr">#></span> 99.44423885 0.09793574 3.39632469 </span> +<span class="r-out co"><span class="r-pr">#></span> 99.44423886 0.09793574 3.39632469 </span> <span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-plt img"><img src="update.mkinfit-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="va">fit_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">fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> @@ -139,7 +139,7 @@ remove arguments given in the original call</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> |
