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authorJohannes Ranke <jranke@uni-bremen.de>2021-03-09 17:35:47 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-03-09 17:35:47 +0100
commitc73b2f30ec836c949885784ab576e814eb8070a9 (patch)
tree7cfff70c5dae646fb464f4071e4ec444bbf40de1 /docs/dev/reference/nlme.html
parent9a414d01985f9177745ce0ad234ef7fc1b9822bb (diff)
Some improvements for borderline cases
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
Diffstat (limited to 'docs/dev/reference/nlme.html')
-rw-r--r--docs/dev/reference/nlme.html33
1 files changed, 22 insertions, 11 deletions
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index b850eb3d..78d132e9 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">1.0.3.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span>
</span>
</div>
@@ -155,7 +155,7 @@ datasets. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.m
<pre class="usage"><span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span>
-<span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>object</span>, random <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+<span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>object</span>, random <span class='op'>=</span> <span class='cn'>FALSE</span>, test_log_parms <span class='op'>=</span> <span class='cn'>FALSE</span>, conf.level <span class='op'>=</span> <span class='fl'>0.6</span><span class='op'>)</span>
<span class='fu'>nlme_data</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre>
@@ -170,6 +170,17 @@ datasets. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.m
<th>random</th>
<td><p>Should a list with fixed and random effects be returned?</p></td>
</tr>
+ <tr>
+ <th>test_log_parms</th>
+ <td><p>If TRUE, log parameters are only considered in
+the mean calculations if their untransformed counterparts (most likely
+rate constants) pass the t-test for significant difference from zero.</p></td>
+ </tr>
+ <tr>
+ <th>conf.level</th>
+ <td><p>Possibility to adjust the required confidence level
+for parameter that are tested if requested by 'test_log_parms'.</p></td>
+ </tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -211,7 +222,7 @@ nlme for the case of a single grouping variable ds.</p>
<span class='va'>nlme_f</span> <span class='op'>&lt;-</span> <span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
<span class='co'># These assignments are necessary for these objects to be</span>
<span class='co'># visible to nlme and augPred when evaluation is done by</span>
-<span class='co'># pkgdown to generated the html docs.</span>
+<span class='co'># pkgdown to generate the html docs.</span>
<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='st'>"nlme_f"</span>, <span class='va'>nlme_f</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='st'>"grouped_data"</span>, <span class='va'>grouped_data</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
@@ -226,28 +237,28 @@ nlme for the case of a single grouping variable ds.</p>
#&gt; Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#&gt; Data: grouped_data
#&gt; AIC BIC logLik
-#&gt; 300.6824 310.2426 -145.3412
+#&gt; 298.2781 307.7372 -144.1391
#&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: 1.697361 0.6801209 3.666073
+#&gt; StdDev: 0.937473 0.7098105 3.83543
#&gt;
#&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; parent_0 101.76838 1.1445443 45 88.91607 0
+#&gt; log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0
#&gt; Correlation:
#&gt; prnt_0
-#&gt; log_k_parent_sink 0.027
+#&gt; log_k_parent_sink 0.034
#&gt;
#&gt; Standardized Within-Group Residuals:
-#&gt; Min Q1 Med Q3 Max
-#&gt; -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781
+#&gt; Min Q1 Med Q3 Max
+#&gt; -2.61693595 -0.21853231 0.05740682 0.57209372 3.04598764
#&gt;
-#&gt; Number of Observations: 50
+#&gt; Number of Observations: 49
#&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>

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