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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-15 17:36:12 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-15 17:36:12 +0100
commitb9be19af5e3085216d0cd5af439332f631fa8b92 (patch)
treee10511f60e7f1713b781d5ea2acf885f3d1e6767 /docs/dev/reference/nlme.html
parent11c7f26dd6c532d977d9875f3c16952c7bba37ca (diff)
Fully rebuild docs, rerun tests and check
Diffstat (limited to 'docs/dev/reference/nlme.html')
-rw-r--r--docs/dev/reference/nlme.html28
1 files changed, 14 insertions, 14 deletions
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index b3e88428..b850eb3d 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -124,7 +124,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -224,37 +224,37 @@ nlme for the case of a single grouping variable ds.</p>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>m_nlme</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
#&gt; Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
-#&gt; Data: grouped_data
+#&gt; Data: grouped_data
#&gt; AIC BIC logLik
-#&gt; 252.7798 262.1358 -121.3899
+#&gt; 300.6824 310.2426 -145.3412
#&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: 0.0006768135 0.6800777 2.489397
+#&gt; parent_0 log_k_parent_sink Residual
+#&gt; StdDev: 1.697361 0.6801209 3.666073
#&gt;
-#&gt; Fixed effects: parent_0 + log_k_parent_sink ~ 1
-#&gt; Value Std.Error DF t-value p-value
-#&gt; parent_0 101.74884 0.6456014 44 157.60321 0
-#&gt; log_k_parent_sink -3.05575 0.4015811 44 -7.60929 0
+#&gt; Fixed effects: parent_0 + log_k_parent_sink ~ 1
+#&gt; Value Std.Error DF t-value p-value
+#&gt; parent_0 100.99378 1.3890416 46 72.70753 0
+#&gt; log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0
#&gt; Correlation:
#&gt; prnt_0
-#&gt; log_k_parent_sink 0.026
+#&gt; log_k_parent_sink 0.027
#&gt;
#&gt; Standardized Within-Group Residuals:
#&gt; Min Q1 Med Q3 Max
-#&gt; -2.1317488 -0.6878121 0.0828385 0.8592270 2.9529864
+#&gt; -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781
#&gt;
-#&gt; Number of Observations: 48
+#&gt; Number of Observations: 50
#&gt; Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span><span class='op'>(</span><span class='va'>m_nlme</span>, level <span class='op'>=</span> <span class='fl'>0</span><span class='op'>:</span><span class='fl'>1</span><span class='op'>)</span>, layout <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># augPred does not work on fits with more than one state</span>
<span class='co'># variable</span>
<span class='co'>#</span>
<span class='co'># The procedure is greatly simplified by the nlme.mmkin function</span>
<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
</div><div class='img'><img src='nlme-2.png' alt='' width='700' height='433' /></div></pre>
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