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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-15 14:08:13 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-15 15:20:53 +0100
commita9427a09abdf7ce9aaeae7c7190f90c8f2e5ef52 (patch)
treea9ecf25af6657e70d8f1faabd88fb6e2f6334b07 /docs/reference/confint.mkinfit.html
parentb4582fc7d3f1d395bfd9d870137b705469d9eab2 (diff)
Improve README, introductory vignette and some other docsv1.0.3
Also bump version to 1.0.3.
Diffstat (limited to 'docs/reference/confint.mkinfit.html')
-rw-r--r--docs/reference/confint.mkinfit.html44
1 files changed, 22 insertions, 22 deletions
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
index b71e039a..06e78459 100644
--- a/docs/reference/confint.mkinfit.html
+++ b/docs/reference/confint.mkinfit.html
@@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." />
</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">1.0.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.3</span>
</span>
</div>
@@ -285,13 +285,13 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<span class='va'>f_d_1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 4.324 0.980 3.960 </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; 4.255 1.029 3.937 </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 if we use at least 4 cores</span>
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>,
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</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='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 1.480 0.109 0.905 </div><div class='input'><span class='va'>ci_profile</span>
+#&gt; 1.469 0.092 0.911 </div><div class='input'><span class='va'>ci_profile</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003640 1.027703e+02
#&gt; k_parent_sink 0.040762501 5.549764e-02
@@ -349,14 +349,14 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
<span class='va'>ci_quadratic_transformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833585 102.79311650
+#&gt; parent_0 96.403833578 102.79311649
#&gt; k_parent 0.090823771 0.10725430
#&gt; k_m1 0.004012219 0.00689755
#&gt; f_parent_to_m1 0.469118824 0.55959615
#&gt; sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='va'>ci_quadratic_untransformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403833589 1.027931e+02
+#&gt; parent_0 96.403833583 1.027931e+02
#&gt; k_parent 0.090491913 1.069035e-01
#&gt; k_m1 0.003835485 6.685823e-03
#&gt; f_parent_to_m1 0.469113477 5.598387e-01
@@ -374,15 +374,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
#&gt; f_parent_to_m1 TRUE FALSE
#&gt; sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408689 0.0002217234
+#&gt; parent_0 0.0005408690 0.0002217233
#&gt; k_parent 0.0009598532 0.0009001864
-#&gt; k_m1 0.0307283044 0.0290588365
-#&gt; f_parent_to_m1 0.0046881768 0.0027780063
+#&gt; k_m1 0.0307283041 0.0290588361
+#&gt; f_parent_to_m1 0.0046881769 0.0027780063
#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408689 0.0002217233
-#&gt; k_parent 0.0046102155 0.0023732281
-#&gt; k_m1 0.0146740688 0.0025291817
+#&gt; parent_0 0.0005408689 0.0002217232
+#&gt; k_parent 0.0046102156 0.0023732281
+#&gt; k_m1 0.0146740690 0.0025291820
#&gt; f_parent_to_m1 0.0046995211 0.0023457712
#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'>
<span class='co'># The profiling for the following fit does not finish in a reasonable time,</span>
@@ -396,18 +396,18 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
error_model_algorithm <span class='op'>=</span> <span class='st'>"direct"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 94.596126334 106.19944007
-#&gt; k_M1 0.037605408 0.04490759
-#&gt; k_M2 0.008568739 0.01087675
-#&gt; f_parent_to_M1 0.021463787 0.62023881
-#&gt; f_parent_to_M2 0.015166531 0.37975349
-#&gt; k1 0.273897467 0.33388084
-#&gt; k2 0.018614555 0.02250379
-#&gt; g 0.671943606 0.73583278
-#&gt; sigma_low 0.251283766 0.83992113
-#&gt; rsd_high 0.040411014 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
+#&gt; parent_0 94.596039609 106.19954892
+#&gt; k_M1 0.037605368 0.04490762
+#&gt; k_M2 0.008568731 0.01087676
+#&gt; f_parent_to_M1 0.021462489 0.62023882
+#&gt; f_parent_to_M2 0.015165617 0.37975348
+#&gt; k1 0.273897348 0.33388101
+#&gt; k2 0.018614554 0.02250378
+#&gt; g 0.671943411 0.73583305
+#&gt; sigma_low 0.251283495 0.83992077
+#&gt; rsd_high 0.040411024 0.07662008</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 94.59613 106.1994</div><div class='input'><span class='co'># }</span>
+#&gt; parent_0 94.59604 106.1995</div><div class='input'><span class='co'># }</span>
</div></pre>
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