diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-11 05:15:19 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-11 05:18:32 +0200 |
| commit | 234c9059a95e104917e488a6ddd2313234a96cdc (patch) | |
| tree | f6e54098f79d94578434ef727b62f7cc5d5e79b7 /docs/articles/FOCUS_D.html | |
| parent | d113cd79b178fdc91aecb894707ed356129dfb75 (diff) | |
Avoid merge() and data.frame() in cost function
also for deSolve and eigenvalue based solutions. This noticeably increases
performance for these methods, see test.log and benchmark vignette.
Diffstat (limited to 'docs/articles/FOCUS_D.html')
| -rw-r--r-- | docs/articles/FOCUS_D.html | 110 |
1 files changed, 54 insertions, 56 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index e9c6b005..0a9ddf4a 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -31,7 +31,7 @@ </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">0.9.49.11</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> </span> </div> @@ -97,7 +97,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-07</h4> + <h4 class="date">2020-05-11</h4> <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.Rmd"><code>vignettes/FOCUS_D.Rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -159,10 +159,10 @@ <div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/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="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<span class="no">diffs</span>)</pre></body></html></div> -<pre><code>## parent -## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" -## m1 -## "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre> +<pre><code>## parent +## "d_parent = - k_parent * parent" +## m1 +## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</code></pre> <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> <div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">fit</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div> <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value @@ -175,85 +175,83 @@ <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div> -<pre><code>## mkin version used for fitting: 0.9.49.11 +<pre><code>## mkin version used for fitting: 0.9.50 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 7 08:59:27 2020 -## Date of summary: Thu May 7 08:59:27 2020 +## Date of fit: Mon May 11 05:14:41 2020 +## Date of summary: Mon May 11 05:14:41 2020 ## ## Equations: -## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent -## d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 +## d_parent/dt = - k_parent * parent +## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 ## -## Model predictions using solution type deSolve +## Model predictions using solution type analytical ## -## Fitted using 389 model solutions performed in 1.031 s +## Fitted using 421 model solutions performed in 0.167 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 100.7500 state -## k_parent_sink 0.1000 deparm -## k_parent_m1 0.1001 deparm -## k_m1_sink 0.1002 deparm +## value type +## parent_0 100.7500 state +## k_parent 0.1000 deparm +## k_m1 0.1001 deparm +## f_parent_to_m1 0.5000 deparm ## ## Starting values for the transformed parameters actually optimised: -## value lower upper -## parent_0 100.750000 -Inf Inf -## log_k_parent_sink -2.302585 -Inf Inf -## log_k_parent_m1 -2.301586 -Inf Inf -## log_k_m1_sink -2.300587 -Inf Inf +## value lower upper +## parent_0 100.750000 -Inf Inf +## log_k_parent -2.302585 -Inf Inf +## log_k_m1 -2.301586 -Inf Inf +## f_parent_ilr_1 0.000000 -Inf Inf ## ## Fixed parameter values: ## value type ## m1_0 0 state ## +## Results: +## +## AIC BIC logLik +## 204.4486 212.6365 -97.22429 +## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 99.600 1.57000 96.400 102.800 -## log_k_parent_sink -3.038 0.07626 -3.193 -2.883 -## log_k_parent_m1 -2.980 0.04033 -3.062 -2.898 -## log_k_m1_sink -5.248 0.13320 -5.518 -4.977 -## sigma 3.126 0.35850 2.396 3.855 +## Estimate Std. Error Lower Upper +## parent_0 99.60000 1.57000 96.40000 102.8000 +## log_k_parent -2.31600 0.04087 -2.39900 -2.2330 +## log_k_m1 -5.24800 0.13320 -5.51800 -4.9770 +## f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694 +## sigma 3.12600 0.35850 2.39600 3.8550 ## ## Parameter correlation: -## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -## parent_0 1.000e+00 6.067e-01 -6.372e-02 -1.688e-01 -## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02 -6.252e-01 -## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00 4.731e-01 -## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01 1.000e+00 -## sigma 5.287e-10 3.306e-09 4.421e-08 -3.319e-10 -## sigma -## parent_0 5.287e-10 -## log_k_parent_sink 3.306e-09 -## log_k_parent_m1 4.421e-08 -## log_k_m1_sink -3.319e-10 -## sigma 1.000e+00 +## parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma +## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.214e-07 +## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.168e-07 +## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.410e-07 +## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 5.093e-10 +## sigma -3.214e-07 3.168e-07 -1.410e-07 5.093e-10 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. -## Estimate t value Pr(>t) Lower Upper -## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02 -## k_parent_sink 0.047920 13.110 6.126e-15 0.041030 5.596e-02 -## k_parent_m1 0.050780 24.800 3.269e-23 0.046780 5.512e-02 -## k_m1_sink 0.005261 7.510 6.165e-09 0.004012 6.898e-03 -## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 +## Estimate t value Pr(>t) Lower Upper +## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02 +## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01 +## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03 +## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01 +## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 6.398 4 15 -## parent 6.827 3 6 -## m1 4.490 1 9 +## parent 6.459 2 7 +## m1 4.690 2 8 ## ## Resulting formation fractions: ## ff -## parent_sink 0.4855 ## parent_m1 0.5145 -## m1_sink 1.0000 +## parent_sink 0.4855 ## ## Estimated disappearance times: ## DT50 DT90 @@ -266,10 +264,10 @@ ## 0 parent 102.04 99.59848 2.442e+00 ## 1 parent 93.50 90.23787 3.262e+00 ## 1 parent 92.50 90.23787 2.262e+00 -## 3 parent 63.23 74.07320 -1.084e+01 -## 3 parent 68.99 74.07320 -5.083e+00 -## 7 parent 52.32 49.91207 2.408e+00 -## 7 parent 55.13 49.91207 5.218e+00 +## 3 parent 63.23 74.07319 -1.084e+01 +## 3 parent 68.99 74.07319 -5.083e+00 +## 7 parent 52.32 49.91206 2.408e+00 +## 7 parent 55.13 49.91206 5.218e+00 ## 14 parent 27.27 25.01257 2.257e+00 ## 14 parent 26.64 25.01257 1.627e+00 ## 21 parent 11.50 12.53462 -1.035e+00 @@ -279,7 +277,7 @@ ## 50 parent 0.69 0.71624 -2.624e-02 ## 50 parent 0.63 0.71624 -8.624e-02 ## 75 parent 0.05 0.06074 -1.074e-02 -## 75 parent 0.06 0.06074 -7.382e-04 +## 75 parent 0.06 0.06074 -7.381e-04 ## 1 m1 4.84 4.80296 3.704e-02 ## 1 m1 5.64 4.80296 8.370e-01 ## 3 m1 12.91 13.02400 -1.140e-01 |