diff options
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 14 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 8 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 10 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 4 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 8 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 8 |
7 files changed, 29 insertions, 27 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index e554432f..2a3b1c78 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -263,7 +263,7 @@ #> #> $time #> user system elapsed -#> 0.234 0.000 0.234 +#> 0.242 0.000 0.244 #> #> $mkinmod #> <mkinmod> model generated with @@ -452,8 +452,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x5555578e66e0> -#> <environment: 0x555559cd9780> +#> <bytecode: 0x5555578ff9d0> +#> <environment: 0x555559a0da40> #> #> $cost_notrans #> function (P) @@ -475,8 +475,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555acf3f50> -#> <environment: 0x555559cd9780> +#> <bytecode: 0x555559b90d60> +#> <environment: 0x555559a0da40> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -543,13 +543,13 @@ #> 99.17407 #> #> $date -#> [1] "Sun Mar 11 22:10:21 2018" +#> [1] "Wed Mar 21 18:14:20 2018" #> #> $version #> [1] "0.9.47.1" #> #> $Rversion -#> [1] "3.4.3" +#> [1] "3.4.4" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 80cac442..cb70e68c 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -150,9 +150,9 @@ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <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: 0.9.47.1 -#> R version used for fitting: 3.4.3 -#> Date of fit: Sun Mar 11 22:10:30 2018 -#> Date of summary: Sun Mar 11 22:10:30 2018 +#> R version used for fitting: 3.4.4 +#> Date of fit: Wed Mar 21 18:14:30 2018 +#> Date of summary: Wed Mar 21 18:14:30 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -162,7 +162,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.318 s +#> Fitted with method Port using 246 model solutions performed in 1.403 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 991df1cc..8ac8295f 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -413,16 +413,16 @@ <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <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: 0.9.47.1 -#> R version used for fitting: 3.4.3 -#> Date of fit: Sun Mar 11 22:10:32 2018 -#> Date of summary: Sun Mar 11 22:10:32 2018 +#> R version used for fitting: 3.4.4 +#> Date of fit: Wed Mar 21 18:14:33 2018 +#> Date of summary: Wed Mar 21 18:14:33 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 0.135 s +#> Fitted with method Port using 64 model solutions performed in 0.14 s #> #> Weighting: none #> @@ -491,7 +491,7 @@ <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 -#> 0.829 0.000 0.829 </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 +#> 0.834 0.000 0.835 </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 diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 044b2d92..4768215b 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -306,7 +306,7 @@ <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'>"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 -#> 0.002 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.003 0.000 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='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 @@ -316,7 +316,7 @@ <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 elapsed -#> 0.029 0.000 0.029 </div></pre> +#> 0.033 0.000 0.032 </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 65c37898..6c99f07b 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -134,7 +134,9 @@ <tr> <th>cores</th> <td><p>The number of cores to be used for multicore processing. This is only - used when the <code>cluster</code> argument is <code>NULL</code>.</p></td> + used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines, + cores > 1 is not supported, you need to use the <code>cluster</code> argument + to use multiple logical processors.</p></td> </tr> <tr> <th>cluster</th> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index e462fd17..37b8fff8 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -190,16 +190,16 @@ <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: 0.9.47.1 -#> R version used for fitting: 3.4.3 -#> Date of fit: Sun Mar 11 22:10:41 2018 -#> Date of summary: Sun Mar 11 22:10:41 2018 +#> R version used for fitting: 3.4.4 +#> Date of fit: Wed Mar 21 18:14:42 2018 +#> Date of summary: Wed Mar 21 18:14:42 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 0.07 s +#> Fitted with method Port using 35 model solutions performed in 0.072 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 5c89f8e2..fb03cdac 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -184,9 +184,9 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>m1</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'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <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: 0.9.47.1 -#> R version used for fitting: 3.4.3 -#> Date of fit: Sun Mar 11 22:10:42 2018 -#> Date of summary: Sun Mar 11 22:10:42 2018 +#> R version used for fitting: 3.4.4 +#> Date of fit: Wed Mar 21 18:14:43 2018 +#> Date of summary: Wed Mar 21 18:14:43 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -194,7 +194,7 @@ 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 0.564 s +#> Fitted with method Port using 153 model solutions performed in 0.585 s #> #> Weighting: none #> |