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-rw-r--r--docs/reference/nlme.mmkin.html79
1 files changed, 38 insertions, 41 deletions
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 2ada9501..c0fb499d 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.2</span>
</span>
</div>
@@ -111,9 +111,6 @@ have been obtained by fitting the same model to a list of datasets." />
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
- <li>
- <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
- </li>
</ul>
</li>
<li>
@@ -184,7 +181,7 @@ have been obtained by fitting the same model to a list of datasets.</p>
</tr>
<tr>
<th>data</th>
- <td><p>Ignored, data are taken from the mmkin model</p></td>
+ <td><p>Should the data be printed?</p></td>
</tr>
<tr>
<th>fixed</th>
@@ -274,19 +271,19 @@ with additional elements</p>
#&gt; Log-likelihood: -307.5269
#&gt; Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#&gt; parent_0 log_k_parent_sink
-#&gt; 85.541149 -3.229596
+#&gt; 85.540979 -3.229602
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#&gt; Level: ds
#&gt; Structure: Diagonal
#&gt; parent_0 log_k_parent_sink Residual
-#&gt; StdDev: 1.30857 1.288591 6.304906
+#&gt; StdDev: 1.308245 1.288586 6.304923
#&gt;
#&gt; Number of Observations: 90
#&gt; Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#&gt; $distimes
#&gt; DT50 DT90
-#&gt; parent 17.51545 58.18505
+#&gt; parent 17.51556 58.18543
#&gt; </div><div class='input'><span class='co'># \dontrun{</span>
<span class='no'>f_nlme_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))
<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
@@ -300,7 +297,7 @@ with additional elements</p>
#&gt; Random effects:
#&gt; Formula: parent_0 ~ 1 | ds
#&gt; parent_0 Residual
-#&gt; StdDev: 0.002416792 21.63027
+#&gt; StdDev: 0.002416802 21.63027
#&gt;
#&gt; Number of Observations: 90
#&gt; Number of Groups: 5 </div><div class='input'> <span class='co'># Test on some real data</span>
@@ -332,88 +329,88 @@ with additional elements</p>
<span class='no'>f_nlme_fomc_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ],
<span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt;
#&gt; **Iteration 1
-#&gt; LME step: Loglik: -394.1603, nlminb iterations: 3
+#&gt; LME step: Loglik: -394.1603, nlminb iterations: 2
#&gt; reStruct parameters:
#&gt; ds1 ds2 ds3 ds4 ds5
-#&gt; -0.2079793 0.8563830 1.7454105 1.0917354 1.2756825
+#&gt; -0.2079863 0.8563823 1.7454253 1.0917707 1.2756955
#&gt; Beginning PNLS step: .. completed fit_nlme() step.
-#&gt; PNLS step: RSS = 643.8803
-#&gt; fixed effects: 94.17379 -5.473193 -0.6970236 -0.2025091 2.103883
+#&gt; PNLS step: RSS = 643.8814
+#&gt; fixed effects: 94.17379 -5.473189 -0.6970234 -0.202509 2.103883
#&gt; iterations: 100
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
#&gt; fixed reStruct
-#&gt; 0.7960134 0.1447728
+#&gt; 0.7959873 0.1447512
#&gt;
#&gt; **Iteration 2
#&gt; LME step: Loglik: -396.3824, nlminb iterations: 7
#&gt; reStruct parameters:
#&gt; ds1 ds2 ds3 ds4 ds5
-#&gt; -1.712404e-01 -2.432655e-05 1.842120e+00 1.073975e+00 1.322925e+00
+#&gt; -1.712406e-01 -2.278541e-05 1.842120e+00 1.073975e+00 1.322924e+00
#&gt; Beginning PNLS step: .. completed fit_nlme() step.
-#&gt; PNLS step: RSS = 643.8035
-#&gt; fixed effects: 94.17385 -5.473487 -0.6970404 -0.2025137 2.103871
+#&gt; PNLS step: RSS = 643.8025
+#&gt; fixed effects: 94.17385 -5.473491 -0.6970406 -0.2025139 2.103871
#&gt; iterations: 100
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
-#&gt; fixed reStruct
-#&gt; 5.382757e-05 1.236667e-03
+#&gt; fixed reStruct
+#&gt; 5.51758e-05 1.26861e-03
#&gt;
#&gt; **Iteration 3
#&gt; LME step: Loglik: -396.3825, nlminb iterations: 7
#&gt; reStruct parameters:
#&gt; ds1 ds2 ds3 ds4 ds5
-#&gt; -0.1712499044 -0.0001499831 1.8420971364 1.0739799123 1.3229167796
+#&gt; -0.1712500923 -0.0001515734 1.8420972550 1.0739796967 1.3229177241
#&gt; Beginning PNLS step: .. completed fit_nlme() step.
-#&gt; PNLS step: RSS = 643.7948
-#&gt; fixed effects: 94.17386 -5.473521 -0.6970422 -0.2025144 2.10387
+#&gt; PNLS step: RSS = 643.7941
+#&gt; fixed effects: 94.17386 -5.473523 -0.6970424 -0.2025146 2.103869
#&gt; iterations: 100
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
#&gt; fixed reStruct
-#&gt; 6.072817e-06 1.400857e-04
+#&gt; 5.792621e-06 1.335434e-04
#&gt;
#&gt; **Iteration 4
#&gt; LME step: Loglik: -396.3825, nlminb iterations: 7
#&gt; reStruct parameters:
#&gt; ds1 ds2 ds3 ds4 ds5
-#&gt; -0.1712529502 -0.0001641277 1.8420957542 1.0739797181 1.3229173076
+#&gt; -0.1712517206 -0.0001651603 1.8420950864 1.0739800294 1.3229173529
#&gt; Beginning PNLS step: .. completed fit_nlme() step.
-#&gt; PNLS step: RSS = 643.7936
-#&gt; fixed effects: 94.17386 -5.473526 -0.6970426 -0.2025146 2.103869
+#&gt; PNLS step: RSS = 643.7949
+#&gt; fixed effects: 94.17386 -5.473521 -0.6970423 -0.2025145 2.10387
#&gt; iterations: 100
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
#&gt; fixed reStruct
-#&gt; 1.027451e-06 2.275704e-05 </div><div class='input'> <span class='no'>f_nlme_dfop_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, ],
+#&gt; 4.025781e-07 9.628656e-06 </div><div class='input'> <span class='no'>f_nlme_dfop_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, ],
<span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>120</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>5e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt;
#&gt; **Iteration 1
-#&gt; LME step: Loglik: -404.9582, nlminb iterations: 1
+#&gt; LME step: Loglik: -404.9583, nlminb iterations: 1
#&gt; reStruct parameters:
#&gt; ds1 ds2 ds3 ds4 ds5 ds6
-#&gt; -0.4114355 0.9798697 1.6990037 0.7293315 0.3354323 1.7113046
+#&gt; -0.4114357 0.9798641 1.6990035 0.7293314 0.3354323 1.7113047
#&gt; Beginning PNLS step: .. completed fit_nlme() step.
-#&gt; PNLS step: RSS = 630.3644
-#&gt; fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.05532828
+#&gt; PNLS step: RSS = 630.3642
+#&gt; fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.0553284
#&gt; iterations: 120
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
#&gt; fixed reStruct
-#&gt; 0.7885368 0.5822683
+#&gt; 0.7879730 0.5822574
#&gt;
#&gt; **Iteration 2
#&gt; LME step: Loglik: -407.7755, nlminb iterations: 11
#&gt; reStruct parameters:
#&gt; ds1 ds2 ds3 ds4 ds5 ds6
-#&gt; -0.371224133 0.003056179 1.789939402 0.724671158 0.301602977 1.754200729
+#&gt; -0.371224105 0.003056163 1.789939431 0.724671132 0.301602942 1.754200482
#&gt; Beginning PNLS step: .. completed fit_nlme() step.
-#&gt; PNLS step: RSS = 630.3633
-#&gt; fixed effects: 93.82269 -5.455992 -0.6788958 -1.862196 -4.199671 0.05532831
+#&gt; PNLS step: RSS = 630.364
+#&gt; fixed effects: 93.82269 -5.455991 -0.6788958 -1.862196 -4.199671 0.05532834
#&gt; iterations: 120
#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
#&gt; fixed reStruct
-#&gt; 4.789774e-07 2.200661e-05 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'>
+#&gt; 9.814652e-07 1.059239e-05 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-6.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-7.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#&gt; Model df AIC BIC logLik Test L.Ratio p-value
-#&gt; f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273
-#&gt; f_nlme_fomc_sfo 2 11 818.5149 853.0087 -398.2575 1 vs 2 21.33975 &lt;.0001
-#&gt; f_nlme_sfo_sfo 3 9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66716 &lt;.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#&gt; Model df AIC BIC logLik Test L.Ratio p-value
-#&gt; f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273
+#&gt; f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274
+#&gt; f_nlme_fomc_sfo 2 11 818.5151 853.0089 -398.2576 1 vs 2 21.33957 &lt;.0001
+#&gt; f_nlme_sfo_sfo 3 9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66697 &lt;.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#&gt; Model df AIC BIC logLik Test L.Ratio p-value
+#&gt; f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274
#&gt; f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 &lt;.0001</div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_A1 A1_sink
@@ -430,7 +427,7 @@ with additional elements</p>
#&gt; $distimes
#&gt; DT50 DT90 DT50_k1 DT50_k2
#&gt; parent 11.07091 104.6320 4.462384 46.20825
-#&gt; A1 162.30536 539.1667 NA NA
+#&gt; A1 162.30518 539.1661 NA NA
#&gt; </div><div class='input'># }
</div></pre>
</div>

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