diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-12-08 09:23:22 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-12-08 09:26:47 +0100 |
| commit | 9733b1ae5596228c50b3acdfdd78fe96ab1e0533 (patch) | |
| tree | e486ce3225a3d2d955940d17c6fec1bd3aca4ab3 | |
| parent | cc72aa3422eb6cb51b47da32e2cccca6afd4d271 (diff) | |
Static documentation articles rebuilt by pkgdown::build_articles()
37 files changed, 165 insertions, 78 deletions
@@ -1,4 +1,4 @@ -docs/articles/cache/ +docs/articles/*_cache/ install.log mkin*.tar.gz mkin.Rcheck diff --git a/GNUmakefile b/GNUmakefile index f41c2d3f..0ce9e64c 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -96,8 +96,9 @@ pd_articles: git commit -m 'Static documentation articles rebuilt by pkgdown::build_articles()' -e r-forge: - rm -rf $(SDDIR)/* + rm -r $(SDDIR)/* cp -a docs/* $(SDDIR) + rm -r $(SDDIR)/articles/cache cd $(SDDIR) && svn add --force . git archive master > $(HOME)/mkin.tar;\ cd $(RFDIR) && rm -r `ls` && tar -xf $(HOME)/mkin.tar;\ diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 9640c62f..de1e1072 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -37,6 +37,9 @@ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> @@ -127,10 +130,10 @@ <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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div> -<pre><code>## mkin version: 0.9.44.9000 +<pre><code>## mkin version: 0.9.45 ## R version: 3.3.2 -## Date of fit: Fri Nov 18 16:48:11 2016 -## Date of summary: Fri Nov 18 16:48:11 2016 +## Date of fit: Thu Dec 8 09:23:12 2016 +## Date of summary: Thu Dec 8 09:23:13 2016 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -138,7 +141,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.638 s +## Fitted with method Port using 153 model solutions performed in 0.639 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_D_cache/html/__packages b/docs/articles/FOCUS_D_cache/html/__packages index f8bbf624..c8b1e877 100644 --- a/docs/articles/FOCUS_D_cache/html/__packages +++ b/docs/articles/FOCUS_D_cache/html/__packages @@ -1,12 +1,8 @@ base -colorout -setwidth -nvimcom +knitr minpack.lm rootSolve inline mkin -rmarkdown -knitr microbenchmark ggplot2 diff --git a/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData Binary files differindex f670208c..f5ad0de0 100644 --- a/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData +++ b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData Binary files differindex 9a067af3..5dab0855 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a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData Binary files differindex ca6eff0e..a90e3de4 100644 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData +++ b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index feceab6f..a6ec5532 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -37,6 +37,9 @@ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> @@ -74,17 +77,17 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_2006_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>) <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> -<pre><code>## mkin version: 0.9.44.9000 +<pre><code>## mkin version: 0.9.45 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 08:18:47 2016 -## Date of summary: Thu Dec 8 08:18:47 2016 +## Date of fit: Thu Dec 8 09:23:13 2016 +## Date of summary: Thu Dec 8 09:23:13 2016 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.084 s +## Fitted with method Port using 37 model solutions performed in 0.088 s ## ## Weighting: none ## @@ -167,10 +170,10 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.44.9000 +<pre><code>## mkin version: 0.9.45 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 08:18:47 2016 -## Date of summary: Thu Dec 8 08:18:47 2016 +## Date of fit: Thu Dec 8 09:23:14 2016 +## Date of summary: Thu Dec 8 09:23:14 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -182,7 +185,7 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.462 s +## Fitted with method Port using 188 model solutions performed in 0.427 s ## ## Weighting: none ## @@ -264,17 +267,17 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.44.9000 +<pre><code>## mkin version: 0.9.45 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 08:18:48 2016 -## Date of summary: Thu Dec 8 08:18:48 2016 +## Date of fit: Thu Dec 8 09:23:14 2016 +## Date of summary: Thu Dec 8 09:23:14 2016 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.201 s +## Fitted with method Port using 81 model solutions performed in 0.185 s ## ## Weighting: none ## @@ -334,10 +337,10 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.44.9000 +<pre><code>## mkin version: 0.9.45 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 08:18:49 2016 -## Date of summary: Thu Dec 8 08:18:49 2016 +## Date of fit: Thu Dec 8 09:23:15 2016 +## Date of summary: Thu Dec 8 09:23:15 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -346,7 +349,7 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.767 s +## Fitted with method Port using 336 model solutions performed in 0.765 s ## ## Weighting: none ## @@ -423,10 +426,10 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div> -<pre><code>## mkin version: 0.9.44.9000 +<pre><code>## mkin version: 0.9.45 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 08:18:50 2016 -## Date of summary: Thu Dec 8 08:18:51 2016 +## Date of fit: Thu Dec 8 09:23:17 2016 +## Date of summary: Thu Dec 8 09:23:17 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -435,7 +438,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.311 s +## Fitted with method Port using 137 model solutions performed in 0.309 s ## ## Weighting: none ## @@ -523,17 +526,17 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.44.9000 +<pre><code>## mkin version: 0.9.45 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 08:18:51 2016 -## Date of summary: Thu Dec 8 08:18:51 2016 +## Date of fit: Thu Dec 8 09:23:17 2016 +## Date of summary: Thu Dec 8 09:23:17 2016 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.118 s +## Fitted with method Port using 46 model solutions performed in 0.106 s ## ## Weighting: none ## @@ -583,17 +586,17 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## DT50 DT90 ## parent 106 352</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> -<pre><code>## mkin version: 0.9.44.9000 +<pre><code>## mkin version: 0.9.45 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 08:18:51 2016 -## Date of summary: Thu Dec 8 08:18:51 2016 +## Date of fit: Thu Dec 8 09:23:17 2016 +## Date of summary: Thu Dec 8 09:23:17 2016 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.151 s +## Fitted with method Port using 66 model solutions performed in 0.148 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R index eacefa90..0d5f0940 100644 --- a/docs/articles/FOCUS_Z.R +++ b/docs/articles/FOCUS_Z.R @@ -3,20 +3,96 @@ require(knitr) opts_chunk$set(engine='R', tidy = FALSE, cache = TRUE) options(width=70) -## ----FOCUS_2006_Z_data, echo=TRUE, eval=TRUE------------------------ -require(mkin) -LOD = 0.5 -FOCUS_2006_Z = data.frame( - t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21, - 42, 61, 96, 124), - Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8, - 2.9, 3.5, 5.3, 4.4, 1.2, 0.7), - Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1, - 1.6, 0.6, 0.5 * LOD, NA, NA, NA), - Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5, - 0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA), - Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5, - 25.2, 17.2, 4.8, 4.5, 2.8, 4.4)) - -FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z) +## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6------------------- +Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"), + Z1 = mkinsub("SFO")) +m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.2a) +summary(m.Z.2a, data = FALSE)$bpar + +## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6------------------- +Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"), + Z1 = mkinsub("SFO"), + use_of_ff = "max") + +m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.2a.ff) +summary(m.Z.2a.ff, data = FALSE)$bpar + +## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6------------------- +Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO"), use_of_ff = "max") +m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.3) +summary(m.Z.3, data = FALSE)$bpar + +## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7------------------- +Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO"), use_of_ff = "max") +m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.5) + +## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8------------------- +Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFO"), + use_of_ff = "max") +m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, + parms.ini = m.Z.5$bparms.ode, + quiet = TRUE) +plot_sep(m.Z.FOCUS) +summary(m.Z.FOCUS, data = FALSE)$bpar +endpoints(m.Z.FOCUS) + +## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8------------------- +Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFORB")) +m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.mkin.1) +summary(m.Z.mkin.1, data = FALSE)$cov.unscaled + +## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8------------------- +Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO")) +m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE) +plot_sep(m.Z.mkin.3) + +## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8------------------ +Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFO")) +m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, + parms.ini = m.Z.mkin.3$bparms.ode, + quiet = TRUE) +plot_sep(m.Z.mkin.4) + +## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8------------------ +Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), + Z1 = mkinsub("SFO", "Z2", sink = FALSE), + Z2 = mkinsub("SFO", "Z3"), + Z3 = mkinsub("SFORB")) +m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, + parms.ini = m.Z.mkin.4$bparms.ode[1:4], + quiet = TRUE) +plot_sep(m.Z.mkin.5) + +## ----FOCUS_2006_Z_fits_11a, echo=TRUE------------------------------- +m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, + parms.ini = c(m.Z.mkin.5$bparms.ode[1:7], + k_Z3_bound_free = 0), + fixed_parms = "k_Z3_bound_free", + quiet = TRUE) +plot_sep(m.Z.mkin.5a) + +## ----FOCUS_2006_Z_fits_11b, echo=TRUE------------------------------- +mkinparplot(m.Z.mkin.5a) + +## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE--------------------- +endpoints(m.Z.mkin.5a) diff --git a/docs/articles/FOCUS_Z.pdf b/docs/articles/FOCUS_Z.pdf Binary files differindex d8bfd68c..fd313555 100644 --- a/docs/articles/FOCUS_Z.pdf +++ b/docs/articles/FOCUS_Z.pdf diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 2850a9ae..660af1d1 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -37,6 +37,9 @@ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> @@ -96,21 +99,21 @@ mb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">micr <span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div> <pre><code>## Unit: milliseconds ## expr min lq mean median uq -## deSolve, not compiled 4973.8901 4975.2320 5000.4065 4976.5739 5013.6648 -## Eigenvalue based 848.4335 859.7111 886.9766 870.9887 906.2481 -## deSolve, compiled 702.8916 705.1930 706.2696 707.4944 707.9587 +## deSolve, not compiled 5006.3815 5014.4629 5112.7115 5022.5443 5165.8765 +## Eigenvalue based 840.3027 874.3549 892.0593 908.4071 917.9376 +## deSolve, compiled 706.9909 712.8031 723.4380 718.6154 731.6615 ## max neval cld -## 5050.7556 3 c -## 941.5075 3 b -## 708.4229 3 a</code></pre> +## 5309.2087 3 b +## 927.4680 3 a +## 744.7077 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p> <p>We see that using the compiled model is by a factor of 7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) <-<span class="st"> </span>smb<span class="fl">.1</span>$expr smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median -## deSolve, not compiled 7.034082 -## Eigenvalue based 1.231089 +## deSolve, not compiled 6.989197 +## Eigenvalue based 1.264108 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -131,20 +134,20 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">summary</span>(mb<span class="fl">.2</span>) <span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div> <pre><code>## Unit: seconds -## expr min lq mean median uq -## deSolve, not compiled 10.819486 10.846433 10.863732 10.873381 10.885855 -## deSolve, compiled 1.300192 1.301168 1.304769 1.302144 1.307058 +## expr min lq mean median uq +## deSolve, not compiled 11.015990 11.17783 11.24827 11.339674 11.364403 +## deSolve, compiled 1.285264 1.29794 1.32988 1.310616 1.352189 ## max neval cld -## 10.898330 3 b -## 1.311972 3 a</code></pre> +## 11.389132 3 b +## 1.393762 3 a</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div> <pre><code>## median ## 1 NA ## 2 NA</code></pre> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div> <p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p> -<p>Here we get a performance benefit of a factor of 8.4 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.44.9000 on</p> +<p>Here we get a performance benefit of a factor of 8.7 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 0.9.45 on</p> <pre><code>## R version 3.3.2 (2016-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 8 (jessie)</code></pre> diff --git 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FALSE---------------------------------------------------- -require(knitr) -opts_chunk$set(engine='R', tidy=FALSE) - diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index c70f8ddf..4159c427 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -37,6 +37,9 @@ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages index ff62e6df..45ea9824 100644 --- a/docs/articles/mkin_cache/html/__packages +++ b/docs/articles/mkin_cache/html/__packages @@ -1,12 +1,15 @@ base +datasets +utils +grDevices +graphics +stats knitr minpack.lm rootSolve +methods inline +parallel mkin -colorout -setwidth -nvimcom -rmarkdown 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