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-rw-r--r--docs/reference/confint.mkinfit.html20
1 files changed, 10 insertions, 10 deletions
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
index 13662adf..ea69c3bb 100644
--- a/docs/reference/confint.mkinfit.html
+++ b/docs/reference/confint.mkinfit.html
@@ -40,10 +40,10 @@
the curvature of the likelihood function at the maximum likelihood parameter
estimates.
The alternative method 'profile' is based on the profile likelihood for each
-parameter. The method uses two nested optimisations and can take a very long
-time, even if parallelized by specifying 'cores' on unixoid platforms. The
-speed of the method could likely be improved by using the method of Venzon
-and Moolgavkar (1988)." />
+parameter. The 'profile' method uses two nested optimisations and can take a
+very long time, even if parallelized by specifying 'cores' on unixoid
+platforms. The speed of the method could likely be improved by using the
+method of Venzon and Moolgavkar (1988)." />
<meta name="twitter:card" content="summary" />
@@ -144,10 +144,10 @@ and Moolgavkar (1988)." />
the curvature of the likelihood function at the maximum likelihood parameter
estimates.
The alternative method 'profile' is based on the profile likelihood for each
-parameter. The method uses two nested optimisations and can take a very long
-time, even if parallelized by specifying 'cores' on unixoid platforms. The
-speed of the method could likely be improved by using the method of Venzon
-and Moolgavkar (1988).</p>
+parameter. The 'profile' method uses two nested optimisations and can take a
+very long time, even if parallelized by specifying 'cores' on unixoid
+platforms. The speed of the method could likely be improved by using the
+method of Venzon and Moolgavkar (1988).</p>
</div>
<pre class="usage"><span class='co'># S3 method for mkinfit</span>
@@ -254,13 +254,13 @@ On Windows machines, cores &gt; 1 is currently not supported.</p></td>
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>f_d_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 51.341 0.000 51.370 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
+#&gt; 51.058 0.000 51.088 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span>
<span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span>
<span class='co'># minor interest), we get a nice performance improvement from about 50</span>
<span class='co'># seconds to about 12 seconds if we use at least four cores</span>
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile_no_parent_0</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>,
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.001 0.007 11.432 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; 0.005 0.004 11.349 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003650 1.027703e+02
#&gt; k_parent_sink 0.040762501 5.549764e-02
#&gt; k_parent_m1 0.046786482 5.500879e-02

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