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authorJohannes Ranke <jranke@uni-bremen.de>2020-10-27 15:34:14 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-10-27 15:36:46 +0100
commita5874ab7fce4616e80be69366ff0685332f47bf1 (patch)
tree17f36842de8ff457879be152779f8704f06a4787 /docs/dev/reference/nlme.mmkin.html
parentca1b4c8cdb1de72b44df0ee8cebe11e10814efdf (diff)
Add summary method for nlme.mmkin objects
Improve and update docs
Diffstat (limited to 'docs/dev/reference/nlme.mmkin.html')
-rw-r--r--docs/dev/reference/nlme.mmkin.html96
1 files changed, 63 insertions, 33 deletions
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index 90aec9be..3fa4d97b 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -152,7 +152,7 @@ have been obtained by fitting the same model to a list of datasets.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mmkin</span>
-<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span>
+<span class='fu'>nlme</span><span class='op'>(</span>
<span class='va'>model</span>,
data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>,
<span class='va'>fixed</span>,
@@ -255,6 +255,11 @@ parameters taken from the mmkin object are used</p></td>
<p>Upon success, a fitted nlme.mmkin object, which is an nlme object
with additional elements</p>
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of
+methods that will automatically work on 'nlme.mmkin' objects, such as
+<code><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>nlme::intervals()</a></code>, <code><a href='https://rdrr.io/pkg/nlme/man/anova.lme.html'>nlme::anova.lme()</a></code> and <code><a href='https://rdrr.io/pkg/nlme/man/coef.lme.html'>nlme::coef.lme()</a></code>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function</a></code></p></div>
@@ -270,11 +275,20 @@ with additional elements</p>
</div><div class='output co'>#&gt; df AIC
#&gt; f_nlme_sfo 5 625.0539
#&gt; f_nlme_dfop 9 495.1270</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
-#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k1, log_k2, g_ilr)
-#&gt; Data: "Not shown"
-#&gt; Log-likelihood: -238.5635
-#&gt; Fixed: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
+</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
+#&gt;
+#&gt; Structural model:
+#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+#&gt; * parent
+#&gt;
+#&gt; Data:
+#&gt; 90 observations of 1 variable(s) grouped in 5 datasets
+#&gt;
+#&gt; Log-likelihood: -238.5635
+#&gt;
+#&gt; Fixed effects:
+#&gt; list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
#&gt; parent_0 log_k1 log_k2 g_ilr
#&gt; 94.17015133 -1.80015306 -4.14738870 0.02290935
#&gt;
@@ -284,9 +298,7 @@ with additional elements</p>
#&gt; Structure: Diagonal
#&gt; parent_0 log_k1 log_k2 g_ilr Residual
#&gt; StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364
-#&gt;
-#&gt; Number of Observations: 90
-#&gt; Number of Groups: 5 </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_dfop</span><span class='op'>)</span>
+#&gt; </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_dfop</span><span class='op'>)</span>
</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><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>
</div><div class='output co'>#&gt; $distimes
#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
@@ -295,11 +307,18 @@ with additional elements</p>
<span class='co'># \dontrun{</span>
<span class='va'>f_nlme_2</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><span class='st'>"SFO"</span>, <span class='op'>]</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, log_k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nlme_2</span>, random <span class='op'>=</span> <span class='va'>parent_0</span> <span class='op'>~</span> <span class='fl'>1</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
-#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent)
-#&gt; Data: "Not shown"
-#&gt; Log-likelihood: -404.3729
-#&gt; Fixed: list(parent_0 ~ 1, log_k_parent ~ 1)
+</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
+#&gt;
+#&gt; Structural model:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt;
+#&gt; Data:
+#&gt; observations of 0 variable(s) grouped in 0 datasets
+#&gt;
+#&gt; Log-likelihood: -404.3729
+#&gt;
+#&gt; Fixed effects:
+#&gt; list(parent_0 ~ 1, log_k_parent ~ 1)
#&gt; parent_0 log_k_parent
#&gt; 75.933480 -3.555983
#&gt;
@@ -307,9 +326,7 @@ with additional elements</p>
#&gt; Formula: parent_0 ~ 1 | ds
#&gt; parent_0 Residual
#&gt; StdDev: 0.002416792 21.63027
-#&gt;
-#&gt; Number of Observations: 90
-#&gt; Number of Groups: 5 </div><div class='input'> <span class='va'>ds_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>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>,
+#&gt; </div><div class='input'> <span class='va'>ds_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>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 class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><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='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
<span class='va'>m_sfo_sfo</span> <span class='op'>&lt;-</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.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'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@@ -395,11 +412,20 @@ with additional elements</p>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_sfo_tc</span>, <span class='va'>f_nlme_dfop</span>, <span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
<span class='op'>}</span>
-</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
-#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k1, log_k2, g_ilr)
-#&gt; Data: "Not shown"
-#&gt; Log-likelihood: -238.4298
-#&gt; Fixed: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
+</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
+#&gt;
+#&gt; Structural model:
+#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+#&gt; * parent
+#&gt;
+#&gt; Data:
+#&gt; 90 observations of 1 variable(s) grouped in 5 datasets
+#&gt;
+#&gt; Log-likelihood: -238.4298
+#&gt;
+#&gt; Fixed effects:
+#&gt; list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
#&gt; parent_0 log_k1 log_k2 g_ilr
#&gt; 94.04774463 -1.82339924 -4.16715509 0.04020161
#&gt;
@@ -415,19 +441,25 @@ with additional elements</p>
#&gt; Formula: ~fitted(.)
#&gt; Parameter estimates:
#&gt; const prop
-#&gt; 2.23222625 0.01262414
-#&gt; Number of Observations: 90
-#&gt; Number of Groups: 5 </div><div class='input'>
+#&gt; 2.23222625 0.01262414 </div><div class='input'>
<span class='va'>f_2_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
<span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
<span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
<span class='va'>f_nlme_sfo_sfo_obs</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_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
-#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink, log_k_parent_A1, log_k_A1_sink)
-#&gt; Data: "Not shown"
-#&gt; Log-likelihood: -472.976
-#&gt; Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1)
+</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by maximum likelihood
+#&gt;
+#&gt; Structural model:
+#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_A1 * parent
+#&gt; d_A1/dt = + k_parent_A1 * parent - k_A1_sink * A1
+#&gt;
+#&gt; Data:
+#&gt; 170 observations of 2 variable(s) grouped in 5 datasets
+#&gt;
+#&gt; Log-likelihood: -472.976
+#&gt;
+#&gt; Fixed effects:
+#&gt; list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1)
#&gt; parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink
#&gt; 87.975536 -3.669816 -4.164127 -4.645073
#&gt;
@@ -443,9 +475,7 @@ with additional elements</p>
#&gt; Formula: ~1 | name
#&gt; Parameter estimates:
#&gt; parent A1
-#&gt; 1.0000000 0.2050003
-#&gt; Number of Observations: 170
-#&gt; Number of Groups: 5 </div><div class='input'> <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span>
+#&gt; 1.0000000 0.2050003 </div><div class='input'> <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span>
<span class='co'># parent and A1 are too similar in this case, so that the model is</span>
<span class='co'># overparameterised</span>
<span class='co'>#f_nlme_dfop_sfo_obs &lt;- nlme(f_2_obs["DFOP-SFO", ], control = list(maxIter = 100))</span>

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