diff options
15 files changed, 69 insertions, 64 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 2244a359..4c3e5c9b 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -63,15 +63,15 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 16:56:21 2016 -## Date of summary: Fri Nov 4 16:56:21 2016 +## Date of fit: Fri Nov 4 17:13:56 2016 +## Date of summary: Fri Nov 4 17:13:56 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.087 s +## Fitted with method Port using 37 model solutions performed in 0.089 s ## ## Weighting: none ## @@ -156,8 +156,8 @@ 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">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 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 16:56:21 2016 -## Date of summary: Fri Nov 4 16:56:21 2016 +## Date of fit: Fri Nov 4 17:13:57 2016 +## Date of summary: Fri Nov 4 17:13:57 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -169,7 +169,7 @@ 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 0.46 s +## Fitted with method Port using 188 model solutions performed in 0.444 s ## ## Weighting: none ## @@ -253,15 +253,15 @@ FOCUS_2006_L2_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">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 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 16:56:22 2016 -## Date of summary: Fri Nov 4 16:56:22 2016 +## Date of fit: Fri Nov 4 17:13:58 2016 +## Date of summary: Fri Nov 4 17:13:58 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.199 s +## Fitted with method Port using 81 model solutions performed in 0.194 s ## ## Weighting: none ## @@ -323,8 +323,8 @@ FOCUS_2006_L2_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">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 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 16:56:23 2016 -## Date of summary: Fri Nov 4 16:56:23 2016 +## Date of fit: Fri Nov 4 17:13:59 2016 +## Date of summary: Fri Nov 4 17:13:59 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -333,7 +333,7 @@ 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 0.81 s +## Fitted with method Port using 336 model solutions performed in 0.82 s ## ## Weighting: none ## @@ -412,8 +412,8 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 16:56:24 2016 -## Date of summary: Fri Nov 4 16:56:25 2016 +## Date of fit: Fri Nov 4 17:14:00 2016 +## Date of summary: Fri Nov 4 17:14:00 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -422,7 +422,7 @@ 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 0.335 s +## Fitted with method Port using 137 model solutions performed in 0.336 s ## ## Weighting: none ## @@ -512,15 +512,15 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 16:56:25 2016 -## Date of summary: Fri Nov 4 16:56:25 2016 +## Date of fit: Fri Nov 4 17:14:01 2016 +## Date of summary: Fri Nov 4 17:14:01 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.109 s +## Fitted with method Port using 46 model solutions performed in 0.114 s ## ## Weighting: none ## @@ -572,15 +572,15 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <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 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 16:56:25 2016 -## Date of summary: Fri Nov 4 16:56:25 2016 +## Date of fit: Fri Nov 4 17:14:01 2016 +## Date of summary: Fri Nov 4 17:14:01 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.16 s +## Fitted with method Port using 66 model solutions performed in 0.162 s ## ## Weighting: none ## diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index e1572b17..153841ae 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -78,21 +78,21 @@ 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 6326.4518 6378.7429 6476.2219 6431.0341 6551.1069 -## Eigenvalue based 925.7797 935.9924 939.8725 946.2051 946.9189 -## deSolve, compiled 740.2821 750.0017 767.8440 759.7212 781.6249 +## deSolve, not compiled 6282.2220 6293.7637 6323.0479 6305.3053 6343.4608 +## Eigenvalue based 873.2553 886.5949 903.6178 899.9345 918.7990 +## deSolve, compiled 737.7899 738.8794 752.3343 739.9689 759.6065 ## max neval cld -## 6671.1797 3 b -## 947.6327 3 a -## 803.5287 3 a</code></pre> +## 6381.6162 3 c +## 937.6634 3 b +## 779.2441 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 8.5 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 8.464993 -## Eigenvalue based 1.245464 +## deSolve, not compiled 8.521041 +## Eigenvalue based 1.216179 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -114,18 +114,18 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <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 13.619556 13.761382 13.825679 13.903207 13.928741 -## deSolve, compiled 1.316871 1.322577 1.358847 1.328283 1.379834 +## deSolve, not compiled 13.644880 13.648332 13.835874 13.651784 13.931372 +## deSolve, compiled 1.422381 1.448574 1.495091 1.474767 1.531446 ## max neval cld -## 13.954275 3 b -## 1.431386 3 a</code></pre> +## 14.210959 3 b +## 1.588125 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 10.5 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 9.3 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> <pre><code>## R version 3.3.2 (2016-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png Binary files differindex 57730131..c52ccd5d 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png Binary files differindex 50adff32..c89ef9a5 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages index c8b1e877..03ece635 100644 --- a/docs/articles/mkin_cache/html/__packages +++ b/docs/articles/mkin_cache/html/__packages @@ -1,8 +1,13 @@ base +datasets +utils +grDevices +graphics +stats knitr minpack.lm rootSolve +methods inline +parallel mkin -microbenchmark -ggplot2 diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData Binary files differnew file mode 100644 index 00000000..d11ccf31 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb Binary files differnew file mode 100644 index 00000000..5ac4f484 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx Binary files differnew file mode 100644 index 00000000..8983f69e --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex d34e3805..2e7e2244 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index ad4614fb..4b6545db 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -193,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.264 0.000 0.262 +#> 0.260 0.000 0.261 #> #> $mkinmod #> <mkinmod> model generated with @@ -379,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x50d32d0> +#> <environment: 0x5bbb4a8> #> #> $cost_notrans #> function (P) @@ -401,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x50d32d0> +#> <environment: 0x5bbb4a8> #> #> $hessian_notrans #> parent_0 alpha beta @@ -467,7 +467,7 @@ #> 99.66619 #> #> $date -#> [1] "Fri Nov 4 17:08:52 2016" +#> [1] "Fri Nov 4 17:12:26 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset @@ -546,7 +546,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.067 +#> 0.068 0.000 0.071 #> #> $mkinmod #> <mkinmod> model generated with @@ -733,7 +733,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4f17408> +#> <environment: 0x5719c08> #> #> $cost_notrans #> function (P) @@ -755,7 +755,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4f17408> +#> <environment: 0x5719c08> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -818,7 +818,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 17:08:51 2016" +#> [1] "Fri Nov 4 17:12:26 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] @@ -894,7 +894,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.067 +#> 0.068 0.000 0.071 #> #> $mkinmod #> <mkinmod> model generated with @@ -1081,7 +1081,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4f17408> +#> <environment: 0x5719c08> #> #> $cost_notrans #> function (P) @@ -1103,7 +1103,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4f17408> +#> <environment: 0x5719c08> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1166,7 +1166,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 17:08:51 2016" +#> [1] "Fri Nov 4 17:12:26 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 6eb4741b..40c21d3c 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -122,8 +122,8 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 17:08:59 2016 -#> Date of summary: Fri Nov 4 17:08:59 2016 +#> Date of fit: Fri Nov 4 17:12:32 2016 +#> Date of summary: Fri Nov 4 17:12:32 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -133,7 +133,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.497 s +#> Fitted with method Port using 246 model solutions performed in 1.502 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 93185eff..32083843 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -359,15 +359,15 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</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'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 17:09:01 2016 -#> Date of summary: Fri Nov 4 17:09:01 2016 +#> Date of fit: Fri Nov 4 17:12:35 2016 +#> Date of summary: Fri Nov 4 17:12:35 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.156 s +#> Fitted with method Port using 64 model solutions performed in 0.147 s #> #> Weighting: none #> @@ -436,7 +436,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 1.256 1.216 0.946 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.208 1.256 0.935 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 9f00dab7..e8302508 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -275,17 +275,17 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.004 0.028 0.004 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.008 0.016 0.005 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.000 0.020 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.000 0.016 0.002 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.052 0.000 0.052 </div></pre> +#> 0.036 0.000 0.035 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f67bc1d1..60f7cdf6 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -142,15 +142,15 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 17:09:10 2016 -#> Date of summary: Fri Nov 4 17:09:10 2016 +#> Date of fit: Fri Nov 4 17:12:43 2016 +#> Date of summary: Fri Nov 4 17:12:43 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.086 s +#> Fitted with method Port using 35 model solutions performed in 0.084 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 60208ff4..f455951d 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -149,8 +149,8 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='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>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 17:09:11 2016 -#> Date of summary: Fri Nov 4 17:09:11 2016 +#> Date of fit: Fri Nov 4 17:12:44 2016 +#> Date of summary: Fri Nov 4 17:12:44 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -158,7 +158,7 @@ #> #> 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 0.656 s #> #> Weighting: none #> |
