diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-05-19 17:08:43 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-05-19 17:10:16 +0200 |
| commit | cf54ccca37d27480dbf8d59eb027300518f7ad75 (patch) | |
| tree | 81a9d5955f716a74822ecb65dc83daeeb7efbba6 /docs/reference/confint.mkinfit.html | |
| parent | c931057ce8f05d3a0dfefea72b73903efb82e900 (diff) | |
Prepare release of v1.2.4v1.2.4
- Update DESCRIPTION
- Update Makefile to document how to use R-patched
- Remove markup from two URLs to avoid CRAN NOTE
- Switch two vignettes from html_document to html_vignette to save space
in the docs directory, also avoiding a CRAN NOTE
- Complete rebuild of pkgdown docs for release
Diffstat (limited to 'docs/reference/confint.mkinfit.html')
| -rw-r--r-- | docs/reference/confint.mkinfit.html | 44 |
1 files changed, 22 insertions, 22 deletions
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index dd6409b6..33c4a939 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -24,7 +24,7 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -254,7 +254,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">f_d_1</span> <span class="op"><-</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" class="external-link">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></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.26 0.00 1.26 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.086 0.000 1.086 </span> <span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> <span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> <span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> @@ -262,7 +262,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 0.417 0.103 0.291 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.396 0.065 0.263 </span> <span class="r-in"><span><span class="va">ci_profile</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> @@ -329,7 +329,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">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></span> <span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833578 102.79311649</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833581 102.79311649</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090823771 0.10725430</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.004012219 0.00689755</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469118824 0.55959615</span> @@ -337,7 +337,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">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></span> <span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833583 1.027931e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833586 1.027931e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090491913 1.069035e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.003835485 6.685823e-03</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469113477 5.598387e-01</span> @@ -359,15 +359,15 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408690 0.0002217233</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598532 0.0009001864</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283041 0.0290588361</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881769 0.0027780063</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283045 0.0290588367</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881768 0.0027780062</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> <span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408689 0.0002217232</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102156 0.0023732281</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740690 0.0025291820</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995211 0.0023457712</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408689 0.0002217233</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102155 0.0023732280</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740687 0.0025291815</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995210 0.0023457712</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span></span> @@ -381,19 +381,19 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span> 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></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596039609 106.19954892</span> -<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605368 0.04490762</span> -<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568731 0.01087676</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021462489 0.62023882</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015165617 0.37975348</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.273897348 0.33388101</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.018614554 0.02250378</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.671943411 0.73583305</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283495 0.83992077</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411024 0.07662008</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596181875 106.19936592</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605432 0.04490757</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568745 0.01087675</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021464676 0.62023880</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015167158 0.37975350</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.273897535 0.33388072</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.018614555 0.02250379</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.671943738 0.73583261</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283679 0.83992102</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411022 0.07662008</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">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></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59604 106.1995</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59618 106.1994</span> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> |