diff options
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 8 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 12 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 48 | ||||
| -rw-r--r-- | docs/reference/mkinmod.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinplot.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 8 | ||||
| -rw-r--r-- | docs/reference/mkinresplot.html | 2 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 6 | ||||
| -rw-r--r-- | docs/reference/plot.mkinfit.html | 2 | ||||
| -rw-r--r-- | docs/reference/plot.mmkin.html | 2 | ||||
| -rw-r--r-- | docs/reference/print.mkinds.html | 2 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 8 | ||||
| -rw-r--r-- | docs/reference/synthetic_data_for_UBA.html | 6 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 24 |
14 files changed, 66 insertions, 66 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index bcf11173..2bba63eb 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -239,7 +239,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.065 +#> 0.08 0.00 0.08 #> #> $mkinmod #> <mkinmod> model generated with @@ -428,7 +428,7 @@ #> } #> return(mC) #> } -#> <environment: 0x58e8e58> +#> <environment: 0x4807c50> #> #> $cost_notrans #> function (P) @@ -450,7 +450,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x58e8e58> +#> <environment: 0x4807c50> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -513,7 +513,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 18 22:52:07 2016" +#> [1] "Mon Nov 21 16:07:10 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 8eac2a55..1a8170ff 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: Fri Nov 18 22:52:15 2016 -#> Date of summary: Fri Nov 18 22:52:15 2016 +#> Date of fit: Mon Nov 21 16:07:20 2016 +#> Date of summary: Mon Nov 21 16:07:20 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 3.397 s +#> Fitted with method Port using 590 model solutions performed in 3.627 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: Fri Nov 18 22:52:16 2016 -#> Date of summary: Fri Nov 18 22:52:16 2016 +#> Date of fit: Mon Nov 21 16:07:22 2016 +#> Date of summary: Mon Nov 21 16:07:22 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 1.471 s +#> Fitted with method Port using 246 model solutions performed in 1.475 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 2f32348e..a992db8e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -336,7 +336,7 @@ <dd> Should a trace of the parameter values be listed? </dd> - <dt>&#8230;</dt> + <dt>…</dt> <dd> Further arguments that will be passed to <code>modFit</code>. </dd> @@ -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: Fri Nov 18 22:52:19 2016 -#> Date of summary: Fri Nov 18 22:52:19 2016 +#> Date of fit: Mon Nov 21 16:07:24 2016 +#> Date of summary: Mon Nov 21 16:07:24 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 0.145 s +#> Fitted with method Port using 64 model solutions performed in 0.162 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 -#> 1.244 1.176 0.911 </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 +#> 1.368 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 #> 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 -#> 0.724 0.040 0.713 </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 +#> 0.784 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 #> 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: Fri Nov 18 22:52:29 2016 -#> Date of summary: Fri Nov 18 22:52:29 2016 +#> Date of fit: Mon Nov 21 16:07:35 2016 +#> Date of summary: Mon Nov 21 16:07:35 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 0.757 s +#> Fitted with method Port using 185 model solutions performed in 0.808 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: Fri Nov 18 22:52:31 2016 -#> Date of summary: Fri Nov 18 22:52:31 2016 +#> Date of fit: Mon Nov 21 16:07:37 2016 +#> Date of summary: Mon Nov 21 16:07:37 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 2.046 s +#> Fitted with method Port using 486 model solutions performed in 2.071 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: Fri Nov 18 22:52:32 2016 -#> Date of summary: Fri Nov 18 22:52:32 2016 +#> Date of fit: Mon Nov 21 16:07:38 2016 +#> Date of summary: Mon Nov 21 16:07:38 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 0.64 s +#> Fitted with method Port using 155 model solutions performed in 0.645 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: Fri Nov 18 22:52:33 2016 -#> Date of summary: Fri Nov 18 22:52:33 2016 +#> Date of fit: Mon Nov 21 16:07:39 2016 +#> Date of summary: Mon Nov 21 16:07:39 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 0.752 s +#> Fitted with method Port using 174 model solutions performed in 0.724 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: Fri Nov 18 22:52:34 2016 -#> Date of summary: Fri Nov 18 22:52:34 2016 +#> Date of fit: Mon Nov 21 16:07:40 2016 +#> Date of summary: Mon Nov 21 16:07:40 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 1.28 s +#> Fitted with method Port using 316 model solutions performed in 1.306 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: Fri Nov 18 22:52:37 2016 -#> Date of summary: Fri Nov 18 22:52:37 2016 +#> Date of fit: Mon Nov 21 16:07:43 2016 +#> Date of summary: Mon Nov 21 16:07:43 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 2.631 s +#> Fitted with method Port using 648 model solutions performed in 2.758 s #> #> Weighting: manual then iterative reweighting method obs #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 0ec62a2b..dce23299 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 file2d971c8bce81.c 2> file2d971c8bce81.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file40bc52407fe7.c 2> file40bc52407fe7.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index cfd4b396..1b8a9828 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -107,7 +107,7 @@ <dd> an object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> - <dt>&#8230;</dt> + <dt>…</dt> <dd> further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>. </dd> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index a36e485b..d4d7caff 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -161,7 +161,7 @@ Boolean to specify if the output should list values for the observed variables (default) or for all state variables (if set to FALSE). </dd> - <dt>&#8230;</dt> + <dt>…</dt> <dd> Further arguments passed to the ode solver in case such a solver is used. </dd> @@ -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 -#> 0.008 0.020 0.005 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.000 0.028 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 -#> 0.012 0.004 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 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 -#> 0.036 0.000 0.034 </div></pre> +#> 0.052 0.000 0.052 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index c11038b6..4a061ecb 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -144,7 +144,7 @@ <dd> Where should the legend be placed? Default is "topright". Will be passed on to <code>legend</code>. </dd> - <dt>&#8230;</dt> + <dt>…</dt> <dd> further arguments passed to <code>plot</code>. </dd> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 76cf7bd5..5ff63336 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -126,7 +126,7 @@ A cluster as returned by <code>makeCluster</code> to be used for parallel execution. </dd> - <dt>&#8230;</dt> + <dt>…</dt> <dd> Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> @@ -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 -#> 16.184 0.108 9.158 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed -#> 21.764 0.000 21.764 </div><div class='input'> +#> 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'> <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 a19ee195..f34ef5e5 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -206,7 +206,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <dd> The number of significant digits for rounding the FOCUS chi2 error percentage. </dd> - <dt>&#8230;</dt> + <dt>…</dt> <dd> Further arguments passed to <code>plot</code>. </dd> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 71b1cac5..8fd98372 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -135,7 +135,7 @@ <dd> The relative height of the middle plot, if more than two rows of plots are shown. </dd> - <dt>&#8230;</dt> + <dt>…</dt> <dd> Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. </dd> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 7796b0dd..a102410a 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -108,7 +108,7 @@ <dd> An <code><a href='mkinds.html'>mkinds</a></code> object. </dd> - <dt>&#8230;</dt> + <dt>…</dt> <dd> Not used. </dd> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 9c22b621..139fd061 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -133,7 +133,7 @@ <dd> Number of digits to use for printing </dd> - <dt>&#8230;</dt> + <dt>…</dt> <dd> optional arguments passed to methods like <code>print</code>. </dd> @@ -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: Fri Nov 18 22:53:26 2016 -#> Date of summary: Fri Nov 18 22:53:26 2016 +#> Date of fit: Mon Nov 21 16:08:34 2016 +#> Date of summary: Mon Nov 21 16:08:34 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 0.078 s +#> Fitted with method Port using 35 model solutions performed in 0.082 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 7eb4b193..b050eb25 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: Fri Nov 18 22:53:29 2016 -#> Date of summary: Fri Nov 18 22:53:29 2016 +#> Date of fit: Mon Nov 21 16:08:37 2016 +#> Date of summary: Mon Nov 21 16:08:37 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 2.1 s +#> Fitted with method Port using 351 model solutions performed in 2.261 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 84d3d0e1..2fc74a5a 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: Fri Nov 18 22:53:30 2016 -#> Date of summary: Fri Nov 18 22:53:30 2016 +#> Date of fit: Mon Nov 21 16:08:38 2016 +#> Date of summary: Mon Nov 21 16:08:38 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 0.618 s +#> Fitted with method Port using 153 model solutions performed in 0.637 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: Fri Nov 18 22:53:31 2016 -#> Date of summary: Fri Nov 18 22:53:31 2016 +#> Date of fit: Mon Nov 21 16:08:39 2016 +#> Date of summary: Mon Nov 21 16:08:39 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 1.335 s +#> Fitted with method Port using 327 model solutions performed in 1.357 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: Fri Nov 18 22:53:32 2016 -#> Date of summary: Fri Nov 18 22:53:32 2016 +#> Date of fit: Mon Nov 21 16:08:40 2016 +#> Date of summary: Mon Nov 21 16:08:40 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 0.749 s +#> Fitted with method Port using 185 model solutions performed in 0.816 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: Fri Nov 18 22:53:33 2016 -#> Date of summary: Fri Nov 18 22:53:33 2016 +#> Date of fit: Mon Nov 21 16:08:41 2016 +#> Date of summary: Mon Nov 21 16:08:41 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 0.426 s +#> Fitted with method Port using 104 model solutions performed in 0.428 s #> #> Weighting: none #> |