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authorJohannes Ranke <jranke@uni-bremen.de>2020-10-08 09:31:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-10-08 09:31:35 +0200
commitbc3825ae2d12c18ea3d3caf17eb23c93fef180b8 (patch)
tree112e70a29db2fb35dd624af20f4d400c579b0283 /docs/dev/reference/confint.mkinfit.html
parentc7635af214729d2dc15dd8fbee2ebe6bc64493a4 (diff)
Fix issues for release
Diffstat (limited to 'docs/dev/reference/confint.mkinfit.html')
-rw-r--r--docs/dev/reference/confint.mkinfit.html86
1 files changed, 42 insertions, 44 deletions
diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html
index 074bed3e..5b683355 100644
--- a/docs/dev/reference/confint.mkinfit.html
+++ b/docs/dev/reference/confint.mkinfit.html
@@ -258,15 +258,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 71.8242430 93.1600766
-#&gt; k_parent_sink 0.2109541 0.4440528
-#&gt; sigma 1.9778868 7.3681380</div><div class='input'>
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 71.8242430 93.1600766
+#&gt; k_parent 0.2109541 0.4440528
+#&gt; sigma 1.9778868 7.3681380</div><div class='input'>
<span class='co'># \dontrun{</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>)</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 73.0641834 92.1392181
-#&gt; k_parent_sink 0.2170293 0.4235348
-#&gt; sigma 3.1307772 8.0628314</div><div class='input'>
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>)</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 73.0641834 92.1392181
+#&gt; k_parent 0.2170293 0.4235348
+#&gt; sigma 3.1307772 8.0628314</div><div class='input'>
<span class='co'># Set the number of cores for the profiling method for further examples</span>
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span>(<span class='st'>"NOT_CRAN"</span>), <span class='st'>"true"</span>)) {
<span class='no'>n_cores</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>parallel</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span>() - <span class='fl'>1</span>
@@ -279,30 +279,29 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
<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 elapsed
-#&gt; 3.610 1.071 3.378 </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='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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><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 elapsed
+#&gt; 3.810 0.964 3.430 </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; <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.005 0.04 0.206</span></div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#&gt; 2.5% 97.5%
+ <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; <span class='warning'>Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#&gt; <span class='error'>Error in dimnames(x) &lt;- dn: length of 'dimnames' [2] not equal to array extent</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.015 0.029 0.198</span></div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003640 1.027703e+02
#&gt; k_parent 0.090911032 1.071578e-01
#&gt; k_m1 0.003892605 6.702778e-03
#&gt; f_parent_to_m1 0.471328495 5.611550e-01
#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed</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'>"quadratic"</span>)
<span class='no'>ci_quadratic_transformed</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403839476 1.027931e+02
+#&gt; parent_0 96.403839460 1.027931e+02
#&gt; k_parent 0.090823790 1.072543e-01
#&gt; k_m1 0.004012216 6.897547e-03
#&gt; f_parent_to_m1 0.469118713 5.595960e-01
#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed</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'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='no'>ci_quadratic_untransformed</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403839429 1.027931e+02
+#&gt; parent_0 96.403839413 1.027931e+02
#&gt; k_parent 0.090491931 1.069035e-01
#&gt; k_m1 0.003835483 6.685819e-03
-#&gt; f_parent_to_m1 0.469113364 5.598386e-01
+#&gt; f_parent_to_m1 0.469113365 5.598386e-01
#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span>
<span class='co'># intervals based on the internal parameter transformation are less</span>
<span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span>
@@ -314,7 +313,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
#&gt; k_parent TRUE TRUE
#&gt; k_m1 FALSE FALSE
#&gt; f_parent_to_m1 TRUE FALSE
-#&gt; sigma FALSE TRUE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 0.000541 0.000222
#&gt; k_parent 0.000960 0.000900
#&gt; k_m1 0.030700 0.029100
@@ -327,24 +326,23 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
#&gt; sigma 0.055000 0.032700</div><div class='input'>
<span class='co'># Investigate a case with formation fractions</span>
-<span class='no'>f_d_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</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='no'>ci_profile_ff</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_2</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='no'>n_cores</span>)</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='input'><span class='no'>ci_profile_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
+<span class='no'>f_d_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>ci_profile_ff</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_2</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='no'>n_cores</span>)</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='input'><span class='no'>ci_profile_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003640 1.027703e+02
#&gt; k_parent 0.090911032 1.071578e-01
#&gt; k_m1 0.003892605 6.702778e-03
#&gt; f_parent_to_m1 0.471328495 5.611550e-01
#&gt; sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed_ff</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_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)
<span class='no'>ci_quadratic_transformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403839476 1.027931e+02
+#&gt; parent_0 96.403839460 1.027931e+02
#&gt; k_parent 0.090823790 1.072543e-01
#&gt; k_m1 0.004012216 6.897547e-03
#&gt; f_parent_to_m1 0.469118713 5.595960e-01
#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed_ff</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_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='no'>ci_quadratic_untransformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 96.403839429 1.027931e+02
+#&gt; parent_0 96.403839413 1.027931e+02
#&gt; k_parent 0.090491931 1.069035e-01
#&gt; k_m1 0.003835483 6.685819e-03
-#&gt; f_parent_to_m1 0.469113364 5.598386e-01
+#&gt; f_parent_to_m1 0.469113365 5.598386e-01
#&gt; sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>)
<span class='no'>rel_diffs_untransformed_ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>)
<span class='co'># While the confidence interval for the parent rate constant is closer to</span>
@@ -356,17 +354,17 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
#&gt; k_parent TRUE TRUE
#&gt; k_m1 FALSE FALSE
#&gt; f_parent_to_m1 TRUE FALSE
-#&gt; sigma FALSE TRUE</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408078 0.0002217796
+#&gt; sigma FALSE FALSE</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 0.0005408080 0.0002217794
#&gt; k_parent 0.0009596417 0.0009003876
-#&gt; k_m1 0.0307277372 0.0290579184
-#&gt; f_parent_to_m1 0.0046884131 0.0027782558
-#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'><span class='no'>rel_diffs_untransformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 0.0005408083 0.000221780
-#&gt; k_parent 0.0046100096 0.002373023
-#&gt; k_m1 0.0146746467 0.002530101
-#&gt; f_parent_to_m1 0.0046997600 0.002346022
-#&gt; sigma 0.0550252516 0.032706684</div><div class='input'>
+#&gt; k_m1 0.0307277370 0.0290579182
+#&gt; f_parent_to_m1 0.0046884130 0.0027782556
+#&gt; sigma 0.0550252516 0.0327066836</div><div class='input'><span class='no'>rel_diffs_untransformed_ff</span></div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 0.0005408085 0.0002217799
+#&gt; k_parent 0.0046100096 0.0023730229
+#&gt; k_m1 0.0146746469 0.0025301011
+#&gt; f_parent_to_m1 0.0046997599 0.0023460223
+#&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>
<span class='co'># therefore we use the quadratic approximation</span>
<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
@@ -375,19 +373,19 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
<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'>DFOP_par_c</span> <span class='kw'>&lt;-</span> <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>
<span class='no'>f_tc_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, <span class='no'>DFOP_par_c</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>,
- <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='st'>"direct"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
-#&gt; <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 95.654015524 105.79279749
-#&gt; k_M1 0.037723773 0.04447598
-#&gt; k_M2 0.008586438 0.01078076
-#&gt; f_parent_to_M1 0.230403596 0.61953014
-#&gt; f_parent_to_M2 0.162909765 0.38019017
-#&gt; k1 0.275434628 0.33331386
-#&gt; k2 0.018602188 0.02249211
-#&gt; g 0.675149759 0.73520889
-#&gt; sigma_low 0.251416929 0.84272023
-#&gt; rsd_high 0.040371818 0.07666540</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
-#&gt; parent_0 95.65402 105.7928</div><div class='input'># }
+ <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='st'>"direct"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 94.59613833 106.19939215
+#&gt; k_M1 0.03760542 0.04490759
+#&gt; k_M2 0.00856874 0.01087675
+#&gt; f_parent_to_M1 0.02146166 0.62023888
+#&gt; f_parent_to_M2 0.01516502 0.37975343
+#&gt; k1 0.27389751 0.33388078
+#&gt; k2 0.01861456 0.02250379
+#&gt; g 0.67194349 0.73583256
+#&gt; sigma_low 0.25128383 0.83992146
+#&gt; rsd_high 0.04041100 0.07662001</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 94.59614 106.1994</div><div class='input'># }
</div></pre>
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