diff options
| -rw-r--r-- | build.log | 7 | ||||
| -rw-r--r-- | check.log | 12 | ||||
| -rw-r--r-- | test.R | 10 | ||||
| -rw-r--r-- | vignettes/FOCUS_D.html | 10 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 64 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 226064 -> 225027 bytes | |||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160258 -> 160258 bytes |
7 files changed, 61 insertions, 42 deletions
@@ -2,4 +2,9 @@ * preparing ‘mkin’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes -* creating vignettes ...
\ No newline at end of file +* creating vignettes ... OK +* checking for LF line-endings in source and make files +* checking for empty or unneeded directories +* looking to see if a ‘data/datalist’ file should be added +* building ‘mkin_0.9-40.tar.gz’ + @@ -1,6 +1,6 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 3.2.1 (2015-06-18) -* using platform: x86_64-pc-linux-gnu (64-bit) +* using R Under development (unstable) (2015-07-19 r68700) +* using platform: x86_64-unknown-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK @@ -33,7 +33,6 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK -* checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK @@ -66,4 +65,9 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ ‘FOCUS_Z.Rnw’ using ‘UTF-8’ ... OK ‘mkin.Rnw’ using ‘UTF-8’ ... OK OK -* checking re-building of vignette outputs ...
\ No newline at end of file +* checking re-building of vignette outputs ... OK +* checking PDF version of manual ... OK +* DONE + +Status: OK + @@ -0,0 +1,10 @@ +devtools::document("~/git/staticdocs") +devtools::install("~/git/staticdocs") +library(staticdocs) + +debug(staticdocs:::to_html.list) +debug(staticdocs:::to_html.Rd_doc) +debug(staticdocs:::to_html.examples) +debug(staticdocs:::replay_html) +debug(staticdocs:::replay_html.recordedplot) +build_site("~/git/mkin", site_path = "~/svn/kinfit.r-forge/www/mkin_static") diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index f5b8f22a..800186f2 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -10,7 +10,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2015-07-18" /> +<meta name="date" content="2015-07-20" /> <title>Example evaluation of FOCUS Example Dataset D</title> @@ -64,7 +64,7 @@ img { <div id="header"> <h1 class="title">Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2015-07-18</em></h4> +<h4 class="date"><em>2015-07-20</em></h4> </div> @@ -137,8 +137,8 @@ print(FOCUS_2006_D)</code></pre> <pre class="r"><code>summary(fit)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:50:58 2015 -## Date of summary: Sat Jul 18 16:50:59 2015 +## Date of fit: Mon Jul 20 14:51:06 2015 +## Date of summary: Mon Jul 20 14:51:06 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -146,7 +146,7 @@ print(FOCUS_2006_D)</code></pre> ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.604 s +## Fitted with method Port using 153 model solutions performed in 0.66 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 963dff0c..c84d6c83 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -10,7 +10,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2015-07-18" /> +<meta name="date" content="2015-07-20" /> <title>Example evaluation of FOCUS Laboratory Data L1 to L3</title> @@ -65,7 +65,7 @@ img { <div id="header"> <h1 class="title">Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2015-07-18</em></h4> +<h4 class="date"><em>2015-07-20</em></h4> </div> <div id="TOC"> @@ -93,15 +93,15 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)</code></pre> summary(m.L1.SFO)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:50:59 2015 -## Date of summary: Sat Jul 18 16:50:59 2015 +## Date of fit: Mon Jul 20 14:51:06 2015 +## Date of summary: Mon Jul 20 14:51:07 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.083 s +## Fitted with method Port using 37 model solutions performed in 0.087 s ## ## Weighting: none ## @@ -183,8 +183,8 @@ summary(m.L1.SFO)</code></pre> <pre class="r"><code>summary(m.L1.FOMC, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:51:00 2015 -## Date of summary: Sat Jul 18 16:51:00 2015 +## Date of fit: Mon Jul 20 14:51:07 2015 +## Date of summary: Mon Jul 20 14:51:07 2015 ## ## ## Warning: Optimisation by method Port did not converge. @@ -196,7 +196,7 @@ summary(m.L1.SFO)</code></pre> ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.414 s +## Fitted with method Port using 188 model solutions performed in 0.43 s ## ## Weighting: none ## @@ -263,15 +263,15 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)</code></pre> summary(m.L2.SFO)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:51:00 2015 -## Date of summary: Sat Jul 18 16:51:00 2015 +## Date of fit: Mon Jul 20 14:51:07 2015 +## Date of summary: Mon Jul 20 14:51:07 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 41 model solutions performed in 0.089 s +## Fitted with method Port using 41 model solutions performed in 0.094 s ## ## Weighting: none ## @@ -351,15 +351,15 @@ mkinresplot(m.L2.FOMC)</code></pre> <pre class="r"><code>summary(m.L2.FOMC, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:51:01 2015 -## Date of summary: Sat Jul 18 16:51:01 2015 +## Date of fit: Mon Jul 20 14:51:08 2015 +## Date of summary: Mon Jul 20 14:51:08 2015 ## ## 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 0.177 s +## Fitted with method Port using 81 model solutions performed in 0.18 s ## ## Weighting: none ## @@ -423,8 +423,8 @@ plot(m.L2.DFOP)</code></pre> <pre class="r"><code>summary(m.L2.DFOP, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:51:03 2015 -## Date of summary: Sat Jul 18 16:51:03 2015 +## Date of fit: Mon Jul 20 14:51:10 2015 +## Date of summary: Mon Jul 20 14:51:10 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -433,7 +433,7 @@ plot(m.L2.DFOP)</code></pre> ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.791 s +## Fitted with method Port using 336 model solutions performed in 0.793 s ## ## Weighting: none ## @@ -500,15 +500,15 @@ plot(m.L3.SFO)</code></pre> <pre class="r"><code>summary(m.L3.SFO)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:51:03 2015 -## Date of summary: Sat Jul 18 16:51:03 2015 +## Date of fit: Mon Jul 20 14:51:10 2015 +## Date of summary: Mon Jul 20 14:51:10 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 43 model solutions performed in 0.093 s +## Fitted with method Port using 43 model solutions performed in 0.103 s ## ## Weighting: none ## @@ -576,15 +576,15 @@ plot(m.L3.FOMC)</code></pre> <pre class="r"><code>summary(m.L3.FOMC, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:51:03 2015 -## Date of summary: Sat Jul 18 16:51:03 2015 +## Date of fit: Mon Jul 20 14:51:11 2015 +## Date of summary: Mon Jul 20 14:51:11 2015 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 83 model solutions performed in 0.173 s +## Fitted with method Port using 83 model solutions performed in 0.187 s ## ## Weighting: none ## @@ -642,8 +642,8 @@ plot(m.L3.DFOP)</code></pre> <pre class="r"><code>summary(m.L3.DFOP, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:51:04 2015 -## Date of summary: Sat Jul 18 16:51:04 2015 +## Date of fit: Mon Jul 20 14:51:11 2015 +## Date of summary: Mon Jul 20 14:51:11 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -652,7 +652,7 @@ plot(m.L3.DFOP)</code></pre> ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.303 s +## Fitted with method Port using 137 model solutions performed in 0.322 s ## ## Weighting: none ## @@ -724,15 +724,15 @@ plot(m.L4.SFO)</code></pre> <pre class="r"><code>summary(m.L4.SFO, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:51:04 2015 -## Date of summary: Sat Jul 18 16:51:04 2015 +## Date of fit: Mon Jul 20 14:51:12 2015 +## Date of summary: Mon Jul 20 14:51:12 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.104 s +## Fitted with method Port using 46 model solutions performed in 0.101 s ## ## Weighting: none ## @@ -789,15 +789,15 @@ plot(m.L4.FOMC)</code></pre> <pre class="r"><code>summary(m.L4.FOMC, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.40 ## R version: 3.2.1 -## Date of fit: Sat Jul 18 16:51:04 2015 -## Date of summary: Sat Jul 18 16:51:04 2015 +## Date of fit: Mon Jul 20 14:51:12 2015 +## Date of summary: Mon Jul 20 14:51:12 2015 ## ## 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 0.148 s +## Fitted with method Port using 66 model solutions performed in 0.146 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 3745234a..580c0e4d 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex d5183527..710a9534 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |