diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-12-08 07:59:20 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-12-08 07:59:20 +0100 |
| commit | 8ec45cd4a89fe8493fd688a0d34e25f279ad95b7 (patch) | |
| tree | 98b08f8af8ee9f5bb06b13e277dd9b929a45f6ad | |
| parent | 0e57bfcf262a2b2a6a4c8148353cdaed7dc91c9c (diff) | |
Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)
22 files changed, 116 insertions, 189 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 782a789d..9640c62f 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -54,7 +54,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-18</h4> + <h4 class="date">2016-12-08</h4> </div> diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 68054ec1..6a25282b 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -54,7 +54,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-18</h4> + <h4 class="date">2016-12-08</h4> </div> @@ -76,15 +76,15 @@ 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 18 22:54:43 2016 -## Date of summary: Fri Nov 18 22:54:43 2016 +## Date of fit: Thu Dec 8 07:59:15 2016 +## Date of summary: Thu Dec 8 07:59:15 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 0.09 s +## Fitted with method Port using 37 model solutions performed in 0.087 s ## ## Weighting: none ## @@ -169,8 +169,8 @@ 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 18 22:54:44 2016 -## Date of summary: Fri Nov 18 22:54:44 2016 +## Date of fit: Thu Dec 8 07:59:15 2016 +## Date of summary: Thu Dec 8 07:59:15 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -182,7 +182,7 @@ 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 0.43 s +## Fitted with method Port using 188 model solutions performed in 0.436 s ## ## Weighting: none ## @@ -266,15 +266,15 @@ 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 18 22:54:44 2016 -## Date of summary: Fri Nov 18 22:54:44 2016 +## Date of fit: Thu Dec 8 07:59:16 2016 +## Date of summary: Thu Dec 8 07:59:16 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 0.184 s +## Fitted with method Port using 81 model solutions performed in 0.19 s ## ## Weighting: none ## @@ -336,8 +336,8 @@ 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 18 22:54:45 2016 -## Date of summary: Fri Nov 18 22:54:46 2016 +## Date of fit: Thu Dec 8 07:59:17 2016 +## Date of summary: Thu Dec 8 07:59:17 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -346,7 +346,7 @@ 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 0.784 s +## Fitted with method Port using 336 model solutions performed in 0.785 s ## ## Weighting: none ## @@ -425,8 +425,8 @@ 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 18 22:54:47 2016 -## Date of summary: Fri Nov 18 22:54:47 2016 +## Date of fit: Thu Dec 8 07:59:18 2016 +## Date of summary: Thu Dec 8 07:59:18 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -435,7 +435,7 @@ 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 0.328 s +## Fitted with method Port using 137 model solutions performed in 0.319 s ## ## Weighting: none ## @@ -525,15 +525,15 @@ 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 18 22:54:47 2016 -## Date of summary: Fri Nov 18 22:54:48 2016 +## Date of fit: Thu Dec 8 07:59:19 2016 +## Date of summary: Thu Dec 8 07:59:19 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 0.108 s +## Fitted with method Port using 46 model solutions performed in 0.107 s ## ## Weighting: none ## @@ -585,15 +585,15 @@ 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 18 22:54:47 2016 -## Date of summary: Fri Nov 18 22:54:48 2016 +## Date of fit: Thu Dec 8 07:59:19 2016 +## Date of summary: Thu Dec 8 07:59:19 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 0.145 s +## Fitted with method Port using 66 model solutions performed in 0.152 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R index 5c70b57e..eacefa90 100644 --- a/docs/articles/FOCUS_Z.R +++ b/docs/articles/FOCUS_Z.R @@ -20,96 +20,3 @@ FOCUS_2006_Z = data.frame( 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/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData Binary files differnew file mode 100644 index 00000000..282678c3 --- /dev/null +++ b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb Binary files differnew file mode 100644 index 00000000..9c88c526 --- /dev/null +++ b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx Binary files differnew file mode 100644 index 00000000..5f5be10e --- /dev/null +++ b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx diff --git a/docs/articles/cache/__packages b/docs/articles/cache/__packages new file mode 100644 index 00000000..03ece635 --- /dev/null +++ b/docs/articles/cache/__packages @@ -0,0 +1,13 @@ +base +datasets +utils +grDevices +graphics +stats +knitr +minpack.lm +rootSolve +methods +inline +parallel +mkin diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 87913685..d39caf12 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -54,7 +54,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-18</h4> + <h4 class="date">2016-12-08</h4> </div> @@ -91,21 +91,21 @@ 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 6126.4954 6152.1764 6170.8152 6177.8573 6192.9751 -## Eigenvalue based 864.8441 891.7069 902.0212 918.5697 920.6098 -## deSolve, compiled 706.9115 711.1015 714.9195 715.2915 718.9235 +## deSolve, not compiled 6263.2932 6273.5107 6286.8574 6283.7283 6298.6394 +## Eigenvalue based 865.5257 872.4146 892.2705 879.3036 905.6429 +## deSolve, compiled 716.7534 717.9075 724.6869 719.0617 728.6537 ## max neval cld -## 6208.0929 3 c -## 922.6498 3 b -## 722.5556 3 a</code></pre> +## 6313.5506 3 c +## 931.9821 3 b +## 738.2457 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 8.6 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> +<p>We see that using the compiled model is by a factor of 8.7 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 8.636839 -## Eigenvalue based 1.284189 +## deSolve, not compiled 8.738789 +## Eigenvalue based 1.222849 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -127,18 +127,18 @@ 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 13.163796 13.205491 13.478255 13.247187 13.635484 -## deSolve, compiled 1.267154 1.268198 1.272722 1.269242 1.275506 +## deSolve, not compiled 13.487097 13.492149 13.528060 13.497201 13.548541 +## deSolve, compiled 1.307845 1.318979 1.322967 1.330114 1.330528 ## max neval cld -## 14.023782 3 b -## 1.281771 3 a</code></pre> +## 13.599881 3 b +## 1.330941 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 10.4 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 10.1 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 55aca8fa..d881a0a2 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 90ac9cbc..b3faa16f 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.html b/docs/articles/mkin.html index 1292480b..c70f8ddf 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -54,7 +54,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-18</h4> + <h4 class="date">2016-12-08</h4> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 2bba63eb..4ef3bb00 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -239,7 +239,7 @@ #> #> $time #> user system elapsed -#> 0.08 0.00 0.08 +#> 0.064 0.000 0.065 #> #> $mkinmod #> <mkinmod> model generated with @@ -428,7 +428,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4807c50> +#> <environment: 0x5ce33e0> #> #> $cost_notrans #> function (P) @@ -450,7 +450,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4807c50> +#> <environment: 0x5ce33e0> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -513,7 +513,7 @@ #> 99.17407 #> #> $date -#> [1] "Mon Nov 21 16:07:10 2016" +#> [1] "Thu Dec 8 07:56:34 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 1a8170ff..123af096 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -130,8 +130,8 @@ <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Optimisation by method Port did not converge.</span> #> <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='fu'>summary</span>(<span class='no'>fit.1</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: Mon Nov 21 16:07:20 2016 -#> Date of summary: Mon Nov 21 16:07:20 2016 +#> Date of fit: Thu Dec 8 07:56:42 2016 +#> Date of summary: Thu Dec 8 07:56:42 2016 #> #> #> Warning: Optimisation by method Port did not converge. @@ -146,7 +146,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 590 model solutions performed in 3.627 s +#> Fitted with method Port using 590 model solutions performed in 3.474 s #> #> Weighting: none #> @@ -225,8 +225,8 @@ <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: Mon Nov 21 16:07:22 2016 -#> Date of summary: Mon Nov 21 16:07:22 2016 +#> Date of fit: Thu Dec 8 07:56:44 2016 +#> Date of summary: Thu Dec 8 07:56:44 2016 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -236,7 +236,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.475 s +#> Fitted with method Port using 246 model solutions performed in 1.44 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index a992db8e..3dd701d3 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -374,15 +374,15 @@ <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: Mon Nov 21 16:07:24 2016 -#> Date of summary: Mon Nov 21 16:07:24 2016 +#> Date of fit: Thu Dec 8 07:56:46 2016 +#> Date of summary: Thu Dec 8 07:56:46 2016 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.162 s +#> Fitted with method Port using 64 model solutions performed in 0.145 s #> #> Weighting: none #> @@ -451,7 +451,7 @@ <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 -#> 1.368 1.244 1.029 </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 +#> 1.172 1.232 0.904 </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 @@ -528,7 +528,7 @@ #> Model cost at call 152 : 371.2134 #> Optimisation by method Port successfully terminated. #> user system elapsed -#> 0.784 0.032 0.773 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.712 0.044 0.709 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</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.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -571,8 +571,8 @@ <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>)</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='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</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'>f.noweight</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Mon Nov 21 16:07:35 2016 -#> Date of summary: Mon Nov 21 16:07:35 2016 +#> Date of fit: Thu Dec 8 07:56:57 2016 +#> Date of summary: Thu Dec 8 07:56:57 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -580,7 +580,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.808 s +#> Fitted with method Port using 185 model solutions performed in 0.77 s #> #> Weighting: none #> @@ -692,8 +692,8 @@ #> 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Mon Nov 21 16:07:37 2016 -#> Date of summary: Mon Nov 21 16:07:37 2016 +#> Date of fit: Thu Dec 8 07:56:59 2016 +#> Date of summary: Thu Dec 8 07:56:59 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -701,7 +701,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 486 model solutions performed in 2.071 s +#> Fitted with method Port using 486 model solutions performed in 2.019 s #> #> Weighting: none then iterative reweighting method obs #> @@ -813,8 +813,8 @@ #> 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Mon Nov 21 16:07:38 2016 -#> Date of summary: Mon Nov 21 16:07:38 2016 +#> Date of fit: Thu Dec 8 07:57:00 2016 +#> Date of summary: Thu Dec 8 07:57:00 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -822,7 +822,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.645 s +#> Fitted with method Port using 155 model solutions performed in 0.65 s #> #> Weighting: mean #> @@ -935,8 +935,8 @@ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Mon Nov 21 16:07:39 2016 -#> Date of summary: Mon Nov 21 16:07:39 2016 +#> Date of fit: Thu Dec 8 07:57:01 2016 +#> Date of summary: Thu Dec 8 07:57:01 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -944,7 +944,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.724 s +#> Fitted with method Port using 174 model solutions performed in 0.713 s #> #> Weighting: manual #> @@ -1057,8 +1057,8 @@ <span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Mon Nov 21 16:07:40 2016 -#> Date of summary: Mon Nov 21 16:07:40 2016 +#> Date of fit: Thu Dec 8 07:57:02 2016 +#> Date of summary: Thu Dec 8 07:57:02 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1066,7 +1066,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 316 model solutions performed in 1.306 s +#> Fitted with method Port using 316 model solutions performed in 1.322 s #> #> Weighting: manual #> @@ -1179,8 +1179,8 @@ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) <span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Mon Nov 21 16:07:43 2016 -#> Date of summary: Mon Nov 21 16:07:43 2016 +#> Date of fit: Thu Dec 8 07:57:05 2016 +#> Date of summary: Thu Dec 8 07:57:05 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1188,7 +1188,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 648 model solutions performed in 2.758 s +#> Fitted with method Port using 648 model solutions performed in 2.818 s #> #> Weighting: manual then iterative reweighting method obs #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index dce23299..1044af6b 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -188,7 +188,7 @@ <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file40bc52407fe7.c 2> file40bc52407fe7.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file386742883b12.c 2> file386742883b12.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index d4d7caff..766b6613 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -290,17 +290,17 @@ <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 -#> 0.000 0.028 0.004 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.012 0.020 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 -#> 0.016 0.004 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.000 0.020 0.003 </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> +#> 0.032 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/mmkin.html b/docs/reference/mmkin.html index 5ff63336..0127f114 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -158,8 +158,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</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>)) <span class='no'>time_default</span></div><div class='output co'>#> user system elapsed -#> 16.488 0.116 9.046 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed -#> 22.788 0.004 22.795 </div><div class='input'> +#> 16.776 0.108 9.353 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed +#> 22.696 0.000 22.701 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340479 0.2659521 0.7505687 0.2494313 diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index f34ef5e5..9969e198 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -99,6 +99,10 @@ <p>Solves the differential equations with the optimised and fixed parameters from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots the observed data together with the solution of the fitted model.</p> + + <p>If the current plot device is a <code><a href='http://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device, + then latex is being used for the formatting of the chi2 error level, + if <code>show_errmin = TRUE</code>.</p> <pre># S3 method for mkinfit diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 8fd98372..1d5d0574 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -99,6 +99,9 @@ <p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), the same model fitted for at least one dataset is shown. When it is a column, the fit of at least one model to the same dataset is shown.</p> + + <p>If the current plot device is a <code><a href='http://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device, + then latex is being used for the formatting of the chi2 error level.</p> <pre><span class='co'># S3 method for mmkin</span> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 139fd061..b305410d 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -157,15 +157,15 @@ <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'><a href='mkinsub.html'>mkinsub</a></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: Mon Nov 21 16:08:34 2016 -#> Date of summary: Mon Nov 21 16:08:34 2016 +#> Date of fit: Thu Dec 8 07:57:55 2016 +#> Date of summary: Thu Dec 8 07:57:55 2016 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.082 s +#> Fitted with method Port using 35 model solutions performed in 0.079 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index b050eb25..bc2bb02b 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -155,8 +155,8 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><img src='synthetic_data_for_UBA_2014-10.png' alt='' width='540' height='400' /><div class='input'><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: Mon Nov 21 16:08:37 2016 -#> Date of summary: Mon Nov 21 16:08:37 2016 +#> Date of fit: Thu Dec 8 07:57:58 2016 +#> Date of summary: Thu Dec 8 07:57:58 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -165,7 +165,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 351 model solutions performed in 2.261 s +#> Fitted with method Port using 351 model solutions performed in 2.152 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 2fc74a5a..e1fb0437 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -164,8 +164,8 @@ <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: Mon Nov 21 16:08:38 2016 -#> Date of summary: Mon Nov 21 16:08:38 2016 +#> Date of fit: Thu Dec 8 07:57:59 2016 +#> Date of summary: Thu Dec 8 07:57:59 2016 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -173,7 +173,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.637 s +#> Fitted with method Port using 153 model solutions performed in 0.621 s #> #> Weighting: none #> @@ -241,8 +241,8 @@ <span class='no'>fit.2</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'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</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: Mon Nov 21 16:08:39 2016 -#> Date of summary: Mon Nov 21 16:08:39 2016 +#> Date of fit: Thu Dec 8 07:58:01 2016 +#> Date of summary: Thu Dec 8 07:58:01 2016 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -250,7 +250,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 327 model solutions performed in 1.357 s +#> Fitted with method Port using 327 model solutions performed in 1.419 s #> #> Weighting: none #> @@ -331,8 +331,8 @@ <span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</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.ff</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: Mon Nov 21 16:08:40 2016 -#> Date of summary: Mon Nov 21 16:08:40 2016 +#> Date of fit: Thu Dec 8 07:58:02 2016 +#> Date of summary: Thu Dec 8 07:58:02 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -340,7 +340,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.816 s +#> Fitted with method Port using 185 model solutions performed in 0.814 s #> #> Weighting: none #> @@ -415,8 +415,8 @@ <span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</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.ff.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: Mon Nov 21 16:08:41 2016 -#> Date of summary: Mon Nov 21 16:08:41 2016 +#> Date of fit: Thu Dec 8 07:58:03 2016 +#> Date of summary: Thu Dec 8 07:58:03 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -424,7 +424,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.428 s +#> Fitted with method Port using 104 model solutions performed in 0.436 s #> #> Weighting: none #> |
