diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 17:20:20 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 17:45:46 +0200 |
| commit | b2cbfc35e4c2b3f8dbb2e9d83ab1f4b358427896 (patch) | |
| tree | 65e737d3d79cc5875f18822e1cbc26a680b9a244 | |
| parent | 70d158c4dd919f4f77bc12f8ace333d29d249b79 (diff) | |
Update NEWS
Static documentation rebuilt by pkgdown
| -rw-r--r-- | NEWS.md | 10 | ||||
| -rw-r--r-- | R/mkinfit.R | 6 | ||||
| -rw-r--r-- | build.log | 2 | ||||
| -rw-r--r-- | check.log | 2 | ||||
| -rw-r--r-- | docs/articles/FOCUS_D.html | 6 | ||||
| -rw-r--r-- | docs/articles/FOCUS_L.html | 38 | ||||
| -rw-r--r-- | docs/articles/web_only/compiled_models.html | 12 | ||||
| -rw-r--r-- | docs/news/index.html | 22 | ||||
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 12 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 46 | ||||
| -rw-r--r-- | docs/reference/mkinmod.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 2 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 6 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 24 |
16 files changed, 112 insertions, 94 deletions
@@ -1,8 +1,14 @@ -# mkin 0.9.47.4 (2018-09-14) +# mkin 0.9.47.5 (2018-09-14) + +- Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows + +- Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times) + +# mkin 0.9.47.4 - Exclude more example code from testing on CRAN to avoid NOTES from long execution times -# mkin 0.9.47.3 (not released to CRAN) +# mkin 0.9.47.3 - 'mkinfit': Improve fitting the error model for reweight.method = 'tc'. Add 'manual' to possible arguments for 'weight' diff --git a/R/mkinfit.R b/R/mkinfit.R index 2c4e3268..dec55a4e 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -415,8 +415,10 @@ mkinfit <- function(mkinmod, observed, # We need unweighted residuals to update the weighting
cost_tmp <- cost(fit$par)
- p_tmp <- cor.test(abs(cost_tmp$residuals$res.unweighted),
- cost_tmp$residuals$obs, method = "kendall")$p.value
+ # We need to supress warnings as we may have ties
+ p_tmp <- suppressWarnings(cor.test(abs(cost_tmp$residuals$res.unweighted),
+ cost_tmp$residuals$obs, method = "kendall")$p.value)
+
if (p_tmp > 0.1) {
stop("No correlation of absolute residuals with observed values found.\n",
"Try without reweighting or with reweight.method = 'obs'.")
@@ -6,5 +6,5 @@ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added -* building ‘mkin_0.9.47.4.tar.gz’ +* building ‘mkin_0.9.47.5.tar.gz’ @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘0.9.47.4’ +* this is package ‘mkin’ version ‘0.9.47.5’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 6dde02d4..a90cb7fb 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -162,8 +162,8 @@ <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw">summary</span>(fit)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 16:50:31 2018 -## Date of summary: Fri Sep 14 16:50:31 2018 +## Date of fit: Fri Sep 14 17:17:43 2018 +## Date of summary: Fri Sep 14 17:17:44 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -171,7 +171,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.728 s +## Fitted with method Port using 153 model solutions performed in 0.645 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 1087c0ed..8b06f072 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -110,15 +110,15 @@ <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 16:54:49 2018 -## Date of summary: Fri Sep 14 16:54:49 2018 +## Date of fit: Fri Sep 14 17:43:07 2018 +## Date of summary: Fri Sep 14 17:43:07 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.088 s +## Fitted with method Port using 37 model solutions performed in 0.091 s ## ## Weighting: none ## @@ -201,15 +201,15 @@ <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 16:54:51 2018 -## Date of summary: Fri Sep 14 16:54:51 2018 +## Date of fit: Fri Sep 14 17:43:09 2018 +## Date of summary: Fri Sep 14 17:43:09 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.349 s +## Fitted with method Port using 611 model solutions performed in 1.398 s ## ## Weighting: none ## @@ -296,8 +296,8 @@ <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 16:54:51 2018 -## Date of summary: Fri Sep 14 16:54:51 2018 +## Date of fit: Fri Sep 14 17:43:10 2018 +## Date of summary: Fri Sep 14 17:43:10 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -367,8 +367,8 @@ <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 16:54:52 2018 -## Date of summary: Fri Sep 14 16:54:52 2018 +## Date of fit: Fri Sep 14 17:43:11 2018 +## Date of summary: Fri Sep 14 17:43:11 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -377,7 +377,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.754 s +## Fitted with method Port using 336 model solutions performed in 0.782 s ## ## Weighting: none ## @@ -459,8 +459,8 @@ <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 16:54:53 2018 -## Date of summary: Fri Sep 14 16:54:53 2018 +## Date of fit: Fri Sep 14 17:43:12 2018 +## Date of summary: Fri Sep 14 17:43:12 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -560,15 +560,15 @@ <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><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>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 16:54:54 2018 -## Date of summary: Fri Sep 14 16:54:54 2018 +## Date of fit: Fri Sep 14 17:43:12 2018 +## Date of summary: Fri Sep 14 17:43:12 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.098 s +## Fitted with method Port using 46 model solutions performed in 0.106 s ## ## Weighting: none ## @@ -620,15 +620,15 @@ <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><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>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 16:54:54 2018 -## Date of summary: Fri Sep 14 16:54:54 2018 +## Date of fit: Fri Sep 14 17:43:12 2018 +## Date of summary: Fri Sep 14 17:43:12 2018 ## ## 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 0.153 s +## Fitted with method Port using 66 model solutions performed in 0.15 s ## ## Weighting: none ## diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index e941bea3..0d91a50c 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -125,9 +125,9 @@ <a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.120 1.000 2.118 0.000 -## 1 deSolve, not compiled 3 17.195 8.111 17.187 0.000 -## 2 Eigenvalue based 3 2.589 1.221 2.582 0.004 +## 3 deSolve, compiled 3 2.174 1.000 2.172 0 +## 1 deSolve, not compiled 3 16.745 7.702 16.737 0 +## 2 Eigenvalue based 3 2.652 1.220 2.650 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -156,12 +156,12 @@ <a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 3.761 1.000 3.758 0.000 -## 1 deSolve, not compiled 3 36.462 9.695 36.441 0.004 +## 2 deSolve, compiled 3 4.012 1.000 4.010 0 +## 1 deSolve, not compiled 3 35.620 8.878 35.604 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 10 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 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.47.5 on</p> <pre><code>## R version 3.5.1 (2018-07-02) ## Platform: x86_64-pc-linux-gnu (64-bit) diff --git a/docs/news/index.html b/docs/news/index.html index 4bd93964..cbfcdde0 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -117,17 +117,26 @@ </div> - <div id="mkin-0-9-47-4-2018-09-14" class="section level1"> + <div id="mkin-0-9-47-5-2018-09-14" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-47-4-2018-09-14" class="anchor"></a>mkin 0.9.47.4 (2018-09-14)<small> Unreleased </small> +<a href="#mkin-0-9-47-5-2018-09-14" class="anchor"></a>mkin 0.9.47.5 (2018-09-14)<small> Unreleased </small> +</h1> +<ul> +<li><p>Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows</p></li> +<li><p>Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)</p></li> +</ul> +</div> + <div id="mkin-0-9-47-4" class="section level1"> +<h1 class="page-header"> +<a href="#mkin-0-9-47-4" class="anchor"></a>mkin 0.9.47.4<small> Unreleased </small> </h1> <ul> <li>Exclude more example code from testing on CRAN to avoid NOTES from long execution times</li> </ul> </div> - <div id="mkin-0-9-47-3-not-released-to-cran" class="section level1"> + <div id="mkin-0-9-47-3" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-47-3-not-released-to-cran" class="anchor"></a>mkin 0.9.47.3 (not released to CRAN)<small> Unreleased </small> +<a href="#mkin-0-9-47-3" class="anchor"></a>mkin 0.9.47.3<small> Unreleased </small> </h1> <ul> <li><p>‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’</p></li> @@ -656,8 +665,9 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0-9-47-4-2018-09-14">0.9.47.4</a></li> - <li><a href="#mkin-0-9-47-3-not-released-to-cran">0.9.47.3</a></li> + <li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li> + <li><a href="#mkin-0-9-47-4">0.9.47.4</a></li> + <li><a href="#mkin-0-9-47-3">0.9.47.3</a></li> <li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li> <li><a href="#mkin-0-9-47-1-2018-02-06">0.9.47.1</a></li> <li><a href="#mkin-0-9-46-3-2017-11-16">0.9.46.3</a></li> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 9d49313c..8cf55860 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.169 0.000 0.169 +#> 0.174 0.000 0.173 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bd4a710> -#> <environment: 0x55555bd3c748> +#> <bytecode: 0x55555bd78ed0> +#> <environment: 0x55555bc7eda8> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555c9b4488> -#> <environment: 0x55555bd3c748> +#> <bytecode: 0x55555ca99e50> +#> <environment: 0x55555bc7eda8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Sep 14 16:53:13 2018" +#> [1] "Fri Sep 14 17:41:26 2018" #> #> $version #> [1] "0.9.47.5" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 86f3c07e..902f1224 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -158,8 +158,8 @@ <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'> </div><div class='input'> <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>) <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:53:25 2018 -#> Date of summary: Fri Sep 14 16:53:25 2018 +#> Date of fit: Fri Sep 14 17:41:38 2018 +#> Date of summary: Fri Sep 14 17:41:38 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -169,7 +169,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.403 s +#> Fitted with method Port using 574 model solutions performed in 3.566 s #> #> Weighting: none #> @@ -247,8 +247,8 @@ <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:53:27 2018 -#> Date of summary: Fri Sep 14 16:53:27 2018 +#> Date of fit: Fri Sep 14 17:41:39 2018 +#> Date of summary: Fri Sep 14 17:41:40 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -258,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.46 s +#> Fitted with method Port using 246 model solutions performed in 1.577 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 0f2bb875..2d5ed97f 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -434,15 +434,15 @@ <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:53:29 2018 -#> Date of summary: Fri Sep 14 16:53:29 2018 +#> Date of fit: Fri Sep 14 17:41:42 2018 +#> Date of summary: Fri Sep 14 17:41:42 2018 #> #> 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 0.158 s +#> Fitted with method Port using 64 model solutions performed in 0.153 s #> #> Weighting: none #> @@ -511,7 +511,7 @@ <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 verstrichen -#> 0.909 0.000 0.910 </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 +#> 0.946 0.000 0.947 </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 @@ -586,7 +586,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.749 0.000 0.749 </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 +#> 0.762 0.000 0.763 </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 @@ -624,8 +624,8 @@ <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:53:40 2018 -#> Date of summary: Fri Sep 14 16:53:40 2018 +#> Date of fit: Fri Sep 14 17:41:54 2018 +#> Date of summary: Fri Sep 14 17:41:54 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -633,7 +633,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.79 s +#> Fitted with method Port using 186 model solutions performed in 0.874 s #> #> Weighting: none #> @@ -741,8 +741,8 @@ #> 120 m1 33.31 28.78984 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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:53:43 2018 -#> Date of summary: Fri Sep 14 16:53:43 2018 +#> Date of fit: Fri Sep 14 17:41:56 2018 +#> Date of summary: Fri Sep 14 17:41:56 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -750,7 +750,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.278 s +#> Fitted with method Port using 551 model solutions performed in 2.493 s #> #> Weighting: none #> @@ -863,8 +863,8 @@ #> 120 m1 33.31 28.80898 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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:53:43 2018 -#> Date of summary: Fri Sep 14 16:53:43 2018 +#> Date of fit: Fri Sep 14 17:41:57 2018 +#> Date of summary: Fri Sep 14 17:41:57 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -872,7 +872,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.643 s +#> Fitted with method Port using 155 model solutions performed in 0.692 s #> #> Weighting: mean #> @@ -981,8 +981,8 @@ <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:53:44 2018 -#> Date of summary: Fri Sep 14 16:53:44 2018 +#> Date of fit: Fri Sep 14 17:41:58 2018 +#> Date of summary: Fri Sep 14 17:41:58 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -990,7 +990,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.722 s +#> Fitted with method Port using 174 model solutions performed in 0.749 s #> #> Weighting: manual #> @@ -1101,8 +1101,8 @@ <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:53:45 2018 -#> Date of summary: Fri Sep 14 16:53:45 2018 +#> Date of fit: Fri Sep 14 17:41:59 2018 +#> Date of summary: Fri Sep 14 17:41:59 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1110,7 +1110,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.11 s +#> Fitted with method Port using 270 model solutions performed in 1.155 s #> #> Weighting: manual #> @@ -1219,8 +1219,8 @@ <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:53:49 2018 -#> Date of summary: Fri Sep 14 16:53:49 2018 +#> Date of fit: Fri Sep 14 17:42:03 2018 +#> Date of summary: Fri Sep 14 17:42:03 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1228,7 +1228,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 2.945 s +#> Fitted with method Port using 692 model solutions performed in 3.154 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 3633686e..fa2880ec 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -229,7 +229,7 @@ For the definition of model types and their parameters, the equations given <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 file7b505448f8a5.c 2> file7b505448f8a5.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file2cf4aedfaf6.c 2> file2cf4aedfaf6.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 6c30d7a8..fc90757d 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -331,7 +331,7 @@ <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 verstrichen -#> 0.035 0.000 0.035 </div></pre> +#> 0.04 0.00 0.04 </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 a656ef65..768e836c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -189,8 +189,8 @@ <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 verstrichen -#> 0.054 0.029 6.762 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 20.495 0.004 20.512 </div><div class='input'> +#> 0.044 0.034 7.567 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 22.374 0.000 22.397 </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 #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index bb701470..01c0d330 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,15 +206,15 @@ <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:54:36 2018 -#> Date of summary: Fri Sep 14 16:54:36 2018 +#> Date of fit: Fri Sep 14 17:42:54 2018 +#> Date of summary: Fri Sep 14 17:42:54 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.077 s +#> Fitted with method Port using 35 model solutions performed in 0.078 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 38c3fe9d..55640a7f 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:54:43 2018 -#> Date of summary: Fri Sep 14 16:54:43 2018 +#> Date of fit: Fri Sep 14 17:43:01 2018 +#> Date of summary: Fri Sep 14 17:43:01 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.629 s +#> Fitted with method Port using 153 model solutions performed in 0.739 s #> #> Weighting: none #> @@ -276,8 +276,8 @@ The transformation of sets of formation fractions is fragile, as it supposes </div><div class='input'><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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:54:45 2018 -#> Date of summary: Fri Sep 14 16:54:45 2018 +#> Date of fit: Fri Sep 14 17:43:03 2018 +#> Date of summary: Fri Sep 14 17:43:03 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -285,7 +285,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 350 model solutions performed in 1.426 s +#> Fitted with method Port using 350 model solutions performed in 1.457 s #> #> Weighting: none #> @@ -364,8 +364,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:54:46 2018 -#> Date of summary: Fri Sep 14 16:54:46 2018 +#> Date of fit: Fri Sep 14 17:43:04 2018 +#> Date of summary: Fri Sep 14 17:43:04 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -373,7 +373,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.766 s +#> Fitted with method Port using 186 model solutions performed in 0.785 s #> #> Weighting: none #> @@ -448,8 +448,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 16:54:46 2018 -#> Date of summary: Fri Sep 14 16:54:46 2018 +#> Date of fit: Fri Sep 14 17:43:05 2018 +#> Date of summary: Fri Sep 14 17:43:05 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -457,7 +457,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.42 s +#> Fitted with method Port using 104 model solutions performed in 0.429 s #> #> Weighting: none #> |