diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-10-06 10:47:45 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-10-06 10:47:45 +0200 |
| commit | d106bebafe070cb803dd7205b1581b20eaf61cb5 (patch) | |
| tree | d3e83a26cf0978912151bdc264b75ece195d9bd6 | |
| parent | 7c62da1269e8910a210ba1917d4dc62d186d5606 (diff) | |
Static documentation rebuilt by pkgdown::build_site()
| -rw-r--r-- | GNUmakefile | 2 | ||||
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 24 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 6 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 8 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 6 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 6 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 6 |
7 files changed, 29 insertions, 29 deletions
diff --git a/GNUmakefile b/GNUmakefile index 7cddc15d..3cb2e40f 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -92,7 +92,7 @@ sd: git commit -m 'Static documentation rebuilt by staticdocs::build_site()' -e pd: - "$(RBIN)/Rscript" -e "pkgdown::build_site()" + "$(RBIN)/Rscript" -e "pkgdown::build_site(articles = FALSE)" git add -A git commit -m 'Static documentation rebuilt by pkgdown::build_site()' -e diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 1802e260..b513fac1 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -192,7 +192,7 @@ #> #> $time #> user system elapsed -#> 0.256 0.000 0.256 +#> 0.252 0.000 0.253 #> #> $mkinmod #> <mkinmod> model generated with @@ -378,7 +378,7 @@ #> } #> return(mC) #> } -#> <environment: 0x435ac28> +#> <environment: 0x3e9c368> #> #> $cost_notrans #> function (P) @@ -400,7 +400,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x435ac28> +#> <environment: 0x3e9c368> #> #> $hessian_notrans #> parent_0 alpha beta @@ -466,7 +466,7 @@ #> 99.66619 #> #> $date -#> [1] "Thu Oct 6 09:39:06 2016" +#> [1] "Thu Oct 6 10:47:28 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -547,7 +547,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.068 +#> 0.064 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -734,7 +734,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4da08d0> +#> <environment: 0x3c1a660> #> #> $cost_notrans #> function (P) @@ -756,7 +756,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4da08d0> +#> <environment: 0x3c1a660> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -819,7 +819,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Oct 6 09:39:06 2016" +#> [1] "Thu Oct 6 10:47:28 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -896,7 +896,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.068 +#> 0.064 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -1083,7 +1083,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4da08d0> +#> <environment: 0x3c1a660> #> #> $cost_notrans #> function (P) @@ -1105,7 +1105,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4da08d0> +#> <environment: 0x3c1a660> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1168,7 +1168,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Oct 6 09:39:06 2016" +#> [1] "Thu Oct 6 10:47:28 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 17e900a4..63635f9a 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -122,8 +122,8 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 09:39:12 2016 -#> Date of summary: Thu Oct 6 09:39:12 2016 +#> Date of fit: Thu Oct 6 10:47:34 2016 +#> Date of summary: Thu Oct 6 10:47:34 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -133,7 +133,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.544 s +#> Fitted with method Port using 246 model solutions performed in 1.492 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 14c1b364..7acbbe5a 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -363,15 +363,15 @@ <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: 3.3.1 -#> Date of fit: Thu Oct 6 09:39:14 2016 -#> Date of summary: Thu Oct 6 09:39:14 2016 +#> Date of fit: Thu Oct 6 10:47:36 2016 +#> Date of summary: Thu Oct 6 10:47:36 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.16 s +#> Fitted with method Port using 64 model solutions performed in 0.152 s #> #> Weighting: none #> @@ -441,7 +441,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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 -#> 1.204 1.224 0.917 +#> 1.240 1.280 0.973 #> </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'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index b0899a3e..5b7cdb32 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -284,21 +284,21 @@ <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 -#> 0.008 0.024 0.004 +#> 0.008 0.020 0.004 #> </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 0.002 +#> 0.016 0.004 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 -#> 0.032 0.000 0.033 +#> 0.032 0.000 0.034 #> </div></pre> </div> <div class="col-md-3"> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 001852a5..acbf36dc 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -142,15 +142,15 @@ <h2 id="examples">Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'>mkinfit</span>(<span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 09:39:22 2016 -#> Date of summary: Thu Oct 6 09:39:22 2016 +#> Date of fit: Thu Oct 6 10:47:44 2016 +#> Date of summary: Thu Oct 6 10:47:44 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.078 s +#> Fitted with method Port using 35 model solutions performed in 0.079 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 2b736098..66253bba 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -147,8 +147,8 @@ <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'>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: 3.3.1 -#> Date of fit: Thu Oct 6 09:39:23 2016 -#> Date of summary: Thu Oct 6 09:39:23 2016 +#> Date of fit: Thu Oct 6 10:47:45 2016 +#> Date of summary: Thu Oct 6 10:47:45 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -156,7 +156,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.63 s +#> Fitted with method Port using 153 model solutions performed in 0.638 s #> #> Weighting: none #> |