diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-02 13:17:05 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-02 13:17:05 +0200 |
| commit | 70591022c07f0e8fb4dd67789b7c8d78af8ebc18 (patch) | |
| tree | acaecfce5ae304cfc48b111c6db24a3f2ed5c83d /docs/reference | |
| parent | 380a29e81f88cd80c9c6915200ddc7054c8a085a (diff) | |
Better initials for error model parameters
- Also make it possible to specify initial values for error model
parameters.
- Run tests
- Rebuild docs
Diffstat (limited to 'docs/reference')
31 files changed, 183 insertions, 175 deletions
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index d5386145..c797567c 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -169,10 +169,10 @@ <span class='co'># of parameters, the higher (worse) the AIC</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>])</div><div class='output co'>#> df AIC #> SFO 3 55.28197 -#> FOMC 4 57.28198 +#> FOMC 4 57.28202 #> DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>], <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>0</span>) <span class='co'># If we do not penalize additional parameters, we get nearly the same</span></div><div class='output co'>#> df AIC #> SFO 3 49.28197 -#> FOMC 4 49.28198 +#> FOMC 4 49.28202 #> DFOP 5 49.28197</div><div class='input'> <span class='co'># For FOCUS C, the more complex models fit better</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#> df AIC diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 77eff52e..3b7209b1 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -189,7 +189,7 @@ <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]] )</div><div class='output co'>#> $par #> parent_0 log_alpha log_beta sigma -#> 99.666193 2.549849 5.050586 1.890202 +#> 99.666193 2.549850 5.050586 1.890202 #> #> $objective #> [1] 28.58291 diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png Binary files differindex c4f9f048..bcf5d12c 100644 --- a/docs/reference/NAFTA_SOP_2015-1.png +++ b/docs/reference/NAFTA_SOP_2015-1.png diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 513cb128..84341a17 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -192,7 +192,7 @@ #> DFOP 429 2380 841 #> #> Representative half-life: -#> [1] 841.4094</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre> +#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png Binary files differindex 7c6c723f..87068d7c 100644 --- a/docs/reference/NAFTA_SOP_Attachment-1.png +++ b/docs/reference/NAFTA_SOP_Attachment-1.png diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index ead06a54..48a1495f 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -189,7 +189,7 @@ #> DFOP 55.5 3.70e+11 2.03e+11 #> #> Representative half-life: -#> [1] 321.5119</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre> +#> [1] 321.51</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex e2107cc2..2f60fdf7 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 6e6592a5..06f877c2 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index a336a840..1f0f6b50 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -160,14 +160,14 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1508106806 48.286460 3.542223e-18 99.246062186 -#> k_T245_sink 1.636106e-02 NaN NaN NaN 0.012661557 -#> k_T245_phenol 2.700936e-02 NaN NaN NaN 0.024487315 -#> k_phenol_sink 1.054519e-10 NaN NaN NaN 0.000000000 -#> k_phenol_anisole 4.050581e-01 0.1053797258 3.843795 7.969973e-04 0.218013983 -#> k_anisole_sink 6.678742e-03 0.0006205825 10.762053 9.427693e-09 0.005370739 -#> sigma 2.514628e+00 0.3383657682 7.431685 1.054052e-06 1.706607296 + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> T245_0 1.038550e+02 2.150809526 48.286486 3.542195e-18 99.246062243 +#> k_T245_sink 1.636106e-02 NaN NaN NaN 0.012661558 +#> k_T245_phenol 2.700936e-02 NaN NaN NaN 0.024487315 +#> k_phenol_sink 1.187912e-10 NaN NaN NaN 0.000000000 +#> k_phenol_anisole 4.050581e-01 0.105378416 3.843843 7.969195e-04 0.218013983 +#> k_anisole_sink 6.678742e-03 0.000620576 10.762166 9.426361e-09 0.005370739 +#> sigma 2.514628e+00 0.338361458 7.431780 1.053891e-06 1.706607296 #> Upper #> T245_0 1.084640e+02 #> k_T245_sink 2.114150e-02 @@ -177,7 +177,7 @@ #> k_anisole_sink 8.305299e-03 #> sigma 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff #> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink -#> 3.772401e-01 6.227599e-01 2.603376e-10 1.000000e+00 1.000000e+00 +#> 3.772401e-01 6.227599e-01 2.932696e-10 1.000000e+00 1.000000e+00 #> #> $SFORB #> logical(0) @@ -205,7 +205,7 @@ #> k_anisole_sink 8.295501e-03 #> sigma 3.318272e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff #> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink -#> 3.772401e-01 6.227599e-01 2.603376e-10 1.000000e+00 1.000000e+00 +#> 3.772401e-01 6.227599e-01 2.932696e-10 1.000000e+00 1.000000e+00 #> #> $SFORB #> logical(0) diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index d3a826b9..7693287e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -151,6 +151,7 @@ Per default, parameters in the kinetic models are internally transformed in <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>), @@ -210,6 +211,13 @@ Per default, parameters in the kinetic models are internally transformed in If this variable has no time zero observations, its initial value is set to 100.</p></td> </tr> <tr> + <th>err.ini</th> + <td><p>A named vector of initial values for the error model parameters to be + optimised. If set to "auto", initial values are set to default values. + Otherwise, inital values for all error model parameters must be + given.</p></td> + </tr> + <tr> <th>fixed_parms</th> <td><p>The names of parameters that should not be optimised but rather kept at the values specified in <code>parms.ini</code>.</p></td> @@ -353,19 +361,19 @@ Per default, parameters in the kinetic models are internally transformed in <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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:10:01 2019 -#> Date of summary: Wed Apr 10 10:10:01 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:38:56 2019 +#> Date of summary: Thu May 2 12:38:56 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method using 221 model solutions performed in 0.508 s +#> Fitted using 221 model solutions performed in 0.455 s #> #> Error model: -#> NULL +#> Constant variance #> #> Starting values for parameters to be optimised: #> value type @@ -393,10 +401,10 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 -1.313e-07 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 -2.634e-07 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 -2.200e-07 -#> sigma -1.313e-07 -2.634e-07 -2.200e-07 1.000e+00 +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 -1.317e-07 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 -2.640e-07 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 -2.205e-07 +#> sigma -1.317e-07 -2.640e-07 -2.205e-07 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -408,7 +416,7 @@ Per default, parameters in the kinetic models are internally transformed in #> beta 1.917 4.373 3.601e-03 1.0650 3.451 #> sigma 1.857 4.243 4.074e-03 0.7320 2.983 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.657 3 6 #> parent 6.657 3 6 @@ -435,7 +443,7 @@ Per default, parameters in the kinetic models are internally transformed in <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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 1.653 0.000 1.653 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</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 +#> 1.551 0.000 1.552 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</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 #> @@ -448,71 +456,71 @@ Per default, parameters in the kinetic models are internally transformed in #> m1 131.760715 437.69962 #> </div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit.deSolve</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'>"deSolve"</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> Negative log-likelihood at call 1: 18915.53 -#> Negative log-likelihood at call 2: 18915.53 -#> Negative log-likelihood at call 6: 11424.02 -#> Negative log-likelihood at call 10: 11424 -#> Negative log-likelihood at call 13: 2367.052 -#> Negative log-likelihood at call 14: 2367.05 -#> Negative log-likelihood at call 19: 1314.716 -#> Negative log-likelihood at call 22: 1314.714 -#> Negative log-likelihood at call 25: 991.8311 -#> Negative log-likelihood at call 28: 991.8305 -#> Negative log-likelihood at call 30: 893.6462 -#> Negative log-likelihood at call 33: 893.6457 -#> Negative log-likelihood at call 35: 569.4049 -#> Negative log-likelihood at call 38: 569.4047 -#> Negative log-likelihood at call 40: 565.0651 -#> Negative log-likelihood at call 41: 565.065 -#> Negative log-likelihood at call 42: 565.0637 -#> Negative log-likelihood at call 45: 428.0188 -#> Negative log-likelihood at call 46: 428.0185 -#> Negative log-likelihood at call 50: 406.732 -#> Negative log-likelihood at call 52: 406.732 -#> Negative log-likelihood at call 55: 398.9115 -#> Negative log-likelihood at call 57: 398.9113 -#> Negative log-likelihood at call 60: 394.5943 -#> Negative log-likelihood at call 62: 394.5943 -#> Negative log-likelihood at call 66: 385.26 -#> Negative log-likelihood at call 67: 385.2599 -#> Negative log-likelihood at call 69: 385.2599 -#> Negative log-likelihood at call 70: 385.2597 -#> Negative log-likelihood at call 71: 374.7604 -#> Negative log-likelihood at call 72: 374.7603 -#> Negative log-likelihood at call 76: 373.199 -#> Negative log-likelihood at call 79: 373.199 -#> Negative log-likelihood at call 80: 373.199 -#> Negative log-likelihood at call 81: 372.3772 -#> Negative log-likelihood at call 84: 372.3772 -#> Negative log-likelihood at call 86: 371.2615 -#> Negative log-likelihood at call 89: 371.2615 -#> Negative log-likelihood at call 90: 371.2615 -#> Negative log-likelihood at call 92: 371.2439 -#> Negative log-likelihood at call 93: 371.2439 -#> Negative log-likelihood at call 94: 371.2439 -#> Negative log-likelihood at call 97: 371.2198 -#> Negative log-likelihood at call 98: 371.2198 -#> Negative log-likelihood at call 102: 371.2174 -#> Negative log-likelihood at call 104: 371.2174 -#> Negative log-likelihood at call 107: 371.2147 -#> Negative log-likelihood at call 110: 371.2147 -#> Negative log-likelihood at call 111: 371.2147 -#> Negative log-likelihood at call 112: 371.2145 -#> Negative log-likelihood at call 113: 371.2145 -#> Negative log-likelihood at call 116: 371.2145 -#> Negative log-likelihood at call 119: 371.2135 -#> Negative log-likelihood at call 121: 371.2135 -#> Negative log-likelihood at call 124: 371.2135 -#> Negative log-likelihood at call 126: 371.2135 -#> Negative log-likelihood at call 127: 371.2135 -#> Negative log-likelihood at call 133: 371.2134 -#> Negative log-likelihood at call 135: 371.2134 -#> Negative log-likelihood at call 138: 371.2134 -#> Negative log-likelihood at call 142: 371.2134 + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> Sum of squared residuals at call 1: 18915.53 +#> Sum of squared residuals at call 2: 18915.53 +#> Sum of squared residuals at call 6: 11424.02 +#> Sum of squared residuals at call 10: 11424 +#> Sum of squared residuals at call 13: 2367.052 +#> Sum of squared residuals at call 14: 2367.05 +#> Sum of squared residuals at call 19: 1314.716 +#> Sum of squared residuals at call 22: 1314.714 +#> Sum of squared residuals at call 25: 991.8311 +#> Sum of squared residuals at call 28: 991.8305 +#> Sum of squared residuals at call 30: 893.6462 +#> Sum of squared residuals at call 33: 893.6457 +#> Sum of squared residuals at call 35: 569.4049 +#> Sum of squared residuals at call 38: 569.4047 +#> Sum of squared residuals at call 40: 565.0651 +#> Sum of squared residuals at call 41: 565.065 +#> Sum of squared residuals at call 42: 565.0637 +#> Sum of squared residuals at call 45: 428.0188 +#> Sum of squared residuals at call 46: 428.0185 +#> Sum of squared residuals at call 50: 406.732 +#> Sum of squared residuals at call 52: 406.732 +#> Sum of squared residuals at call 55: 398.9115 +#> Sum of squared residuals at call 57: 398.9113 +#> Sum of squared residuals at call 60: 394.5943 +#> Sum of squared residuals at call 62: 394.5943 +#> Sum of squared residuals at call 66: 385.26 +#> Sum of squared residuals at call 67: 385.2599 +#> Sum of squared residuals at call 69: 385.2599 +#> Sum of squared residuals at call 70: 385.2597 +#> Sum of squared residuals at call 71: 374.7604 +#> Sum of squared residuals at call 72: 374.7603 +#> Sum of squared residuals at call 76: 373.199 +#> Sum of squared residuals at call 79: 373.199 +#> Sum of squared residuals at call 80: 373.199 +#> Sum of squared residuals at call 81: 372.3772 +#> Sum of squared residuals at call 84: 372.3772 +#> Sum of squared residuals at call 86: 371.2615 +#> Sum of squared residuals at call 89: 371.2615 +#> Sum of squared residuals at call 90: 371.2615 +#> Sum of squared residuals at call 92: 371.2439 +#> Sum of squared residuals at call 93: 371.2439 +#> Sum of squared residuals at call 94: 371.2439 +#> Sum of squared residuals at call 97: 371.2198 +#> Sum of squared residuals at call 98: 371.2198 +#> Sum of squared residuals at call 102: 371.2174 +#> Sum of squared residuals at call 104: 371.2174 +#> Sum of squared residuals at call 107: 371.2147 +#> Sum of squared residuals at call 110: 371.2147 +#> Sum of squared residuals at call 111: 371.2147 +#> Sum of squared residuals at call 112: 371.2145 +#> Sum of squared residuals at call 113: 371.2145 +#> Sum of squared residuals at call 116: 371.2145 +#> Sum of squared residuals at call 119: 371.2135 +#> Sum of squared residuals at call 121: 371.2135 +#> Sum of squared residuals at call 124: 371.2135 +#> Sum of squared residuals at call 126: 371.2135 +#> Sum of squared residuals at call 127: 371.2135 +#> Sum of squared residuals at call 133: 371.2134 +#> Sum of squared residuals at call 135: 371.2134 +#> Sum of squared residuals at call 138: 371.2134 +#> Sum of squared residuals at call 142: 371.2134 #> Negative log-likelihood at call 152: 97.22429 #> Optimisation successfully terminated. #> User System verstrichen -#> 1.136 0.000 1.135 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</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 +#> 1.152 0.000 1.153 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</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 #> @@ -543,9 +551,9 @@ Per default, parameters in the kinetic models are internally transformed in </div><div class='input'><span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</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='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'>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>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:10:17 2019 -#> Date of summary: Wed Apr 10 10:10:17 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:39:13 2019 +#> Date of summary: Thu May 2 12:39:13 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -553,10 +561,10 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted with method using 404 model solutions performed in 1.105 s +#> Fitted using 404 model solutions performed in 1.178 s #> #> Error model: -#> NULL +#> Constant variance #> #> Starting values for parameters to be optimised: #> value type @@ -605,7 +613,7 @@ Per default, parameters in the kinetic models are internally transformed in #> f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01 #> sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.398 4 15 #> parent 6.459 2 7 @@ -661,9 +669,9 @@ Per default, parameters in the kinetic models are internally transformed in #> 100 m1 33.13 31.98163 1.148e+00 #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:10:19 2019 -#> Date of summary: Wed Apr 10 10:10:19 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:39:14 2019 +#> Date of summary: Thu May 2 12:39:14 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -671,10 +679,10 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted with method using 558 model solutions performed in 1.602 s +#> Fitted using 558 model solutions performed in 1.518 s #> #> Error model: -#> NULL +#> Variance unique to each observed variable #> #> Starting values for parameters to be optimised: #> value type @@ -735,7 +743,7 @@ Per default, parameters in the kinetic models are internally transformed in #> sigma_parent 3.401000 5.985 5.662e-07 2.244000 4.559e+00 #> sigma_m1 2.855000 6.311 2.215e-07 1.934000 3.777e+00 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.398 4 15 #> parent 6.464 2 7 @@ -791,9 +799,9 @@ Per default, parameters in the kinetic models are internally transformed in #> 100 m1 33.13 31.98774 1.142e+00 #> 120 m1 25.15 28.80430 -3.654e+00 #> 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:10:22 2019 -#> Date of summary: Wed Apr 10 10:10:22 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:39:18 2019 +#> Date of summary: Thu May 2 12:39:18 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -801,10 +809,10 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted with method using 756 model solutions performed in 3.222 s +#> Fitted using 844 model solutions performed in 3.501 s #> #> Error model: -#> NULL +#> Two-component variance function #> #> Starting values for parameters to be optimised: #> value type @@ -812,8 +820,8 @@ Per default, parameters in the kinetic models are internally transformed in #> k_parent 0.1000 deparm #> k_m1 0.1001 deparm #> f_parent_to_m1 0.5000 deparm -#> sigma_low 0.5000 error -#> rsd_high 0.0700 error +#> sigma_low 3.0000 error +#> rsd_high 0.0100 error #> #> Starting values for the transformed parameters actually optimised: #> value lower upper @@ -821,8 +829,8 @@ Per default, parameters in the kinetic models are internally transformed in #> log_k_parent -2.302585 -Inf Inf #> log_k_m1 -2.301586 -Inf Inf #> f_parent_ilr_1 0.000000 -Inf Inf -#> sigma_low 0.500000 0 Inf -#> rsd_high 0.070000 0 Inf +#> sigma_low 3.000000 0 Inf +#> rsd_high 0.010000 0 Inf #> #> Fixed parameter values: #> value type @@ -858,7 +866,7 @@ Per default, parameters in the kinetic models are internally transformed in #> sigma_low 3.050e-03 0.6314 2.661e-01 -0.006786 1.289e-02 #> rsd_high 7.928e-02 8.4170 6.418e-10 0.060100 9.847e-02 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.475 4 15 #> parent 6.573 2 7 @@ -876,18 +884,18 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Data: #> time variable observed predicted residual -#> 0 parent 99.46 100.73434 -1.274340 -#> 0 parent 102.04 100.73434 1.305660 +#> 0 parent 99.46 100.73434 -1.274339 +#> 0 parent 102.04 100.73434 1.305661 #> 1 parent 93.50 91.09751 2.402486 #> 1 parent 92.50 91.09751 1.402486 #> 3 parent 63.23 74.50141 -11.271410 #> 3 parent 68.99 74.50141 -5.511410 -#> 7 parent 52.32 49.82880 2.491200 -#> 7 parent 55.13 49.82880 5.301200 +#> 7 parent 52.32 49.82880 2.491201 +#> 7 parent 55.13 49.82880 5.301201 #> 14 parent 27.27 24.64809 2.621908 #> 14 parent 26.64 24.64809 1.991908 -#> 21 parent 11.50 12.19232 -0.692316 -#> 21 parent 11.64 12.19232 -0.552316 +#> 21 parent 11.50 12.19232 -0.692315 +#> 21 parent 11.64 12.19232 -0.552315 #> 35 parent 2.85 2.98327 -0.133266 #> 35 parent 2.91 2.98327 -0.073266 #> 50 parent 0.69 0.66013 0.029874 @@ -900,20 +908,20 @@ Per default, parameters in the kinetic models are internally transformed in #> 3 m1 12.96 13.22867 -0.268669 #> 7 m1 22.97 25.36417 -2.394167 #> 7 m1 24.47 25.36417 -0.894167 -#> 14 m1 41.69 37.00974 4.680262 -#> 14 m1 33.21 37.00974 -3.799738 +#> 14 m1 41.69 37.00974 4.680263 +#> 14 m1 33.21 37.00974 -3.799737 #> 21 m1 44.37 41.90133 2.468668 #> 21 m1 46.44 41.90133 4.538668 #> 35 m1 41.22 43.45691 -2.236914 #> 35 m1 37.95 43.45691 -5.506914 #> 50 m1 41.19 41.34199 -0.151986 #> 50 m1 40.01 41.34199 -1.331986 -#> 75 m1 40.09 36.61470 3.475295 -#> 75 m1 33.85 36.61470 -2.764705 -#> 100 m1 31.04 32.20082 -1.160823 -#> 100 m1 33.13 32.20082 0.929177 -#> 120 m1 25.15 29.04130 -3.891303 -#> 120 m1 33.31 29.04130 4.268697</div><div class='input'> +#> 75 m1 40.09 36.61471 3.475294 +#> 75 m1 33.85 36.61471 -2.764706 +#> 100 m1 31.04 32.20082 -1.160824 +#> 100 m1 33.13 32.20082 0.929176 +#> 120 m1 25.15 29.04130 -3.891305 +#> 120 m1 33.31 29.04130 4.268695</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index b100f251..b545dad1 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -234,7 +234,7 @@ 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 file27ad440ff595.c 2> file27ad440ff595.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file35fe67db2b2a.c 2> file35fe67db2b2a.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 82b9c212..798722a2 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 56c1ed27..4b75603f 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -328,7 +328,7 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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 verstrichen -#> 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( +#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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 @@ -338,34 +338,34 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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 -#> 0.04 0.00 0.04 </div><div class='input'> +#> 0.021 0.000 0.021 </div><div class='input'> </div><div class='input'> <span class='co'># Predict from a fitted model</span> - <span class='no'>f</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_C</span>)</div><div class='output co'>#> Negative log-likelihood at call 1: 552.5739 -#> Negative log-likelihood at call 3: 552.5739 -#> Negative log-likelihood at call 4: 552.5739 -#> Negative log-likelihood at call 6: 279.9345 -#> Negative log-likelihood at call 7: 279.9344 -#> Negative log-likelihood at call 8: 279.9294 -#> Negative log-likelihood at call 9: 279.9294 -#> Negative log-likelihood at call 12: 200.3629 -#> Negative log-likelihood at call 13: 200.3629 -#> Negative log-likelihood at call 18: 197.9039 -#> Negative log-likelihood at call 25: 196.6754 -#> Negative log-likelihood at call 27: 196.6754 -#> Negative log-likelihood at call 32: 196.5742 -#> Negative log-likelihood at call 33: 196.5742 -#> Negative log-likelihood at call 34: 196.5742 -#> Negative log-likelihood at call 38: 196.5361 -#> Negative log-likelihood at call 40: 196.5361 -#> Negative log-likelihood at call 44: 196.5336 -#> Negative log-likelihood at call 45: 196.5336 -#> Negative log-likelihood at call 50: 196.5334 -#> Negative log-likelihood at call 51: 196.5334 -#> Negative log-likelihood at call 52: 196.5334 -#> Negative log-likelihood at call 56: 196.5334 -#> Negative log-likelihood at call 58: 196.5334 -#> Negative log-likelihood at call 59: 196.5334 -#> Negative log-likelihood at call 65: 196.5334 + <span class='no'>f</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_C</span>)</div><div class='output co'>#> Sum of squared residuals at call 1: 552.5739 +#> Sum of squared residuals at call 3: 552.5739 +#> Sum of squared residuals at call 4: 552.5739 +#> Sum of squared residuals at call 6: 279.9345 +#> Sum of squared residuals at call 7: 279.9344 +#> Sum of squared residuals at call 8: 279.9294 +#> Sum of squared residuals at call 9: 279.9294 +#> Sum of squared residuals at call 12: 200.3629 +#> Sum of squared residuals at call 13: 200.3629 +#> Sum of squared residuals at call 18: 197.9039 +#> Sum of squared residuals at call 25: 196.6754 +#> Sum of squared residuals at call 27: 196.6754 +#> Sum of squared residuals at call 32: 196.5742 +#> Sum of squared residuals at call 33: 196.5742 +#> Sum of squared residuals at call 34: 196.5742 +#> Sum of squared residuals at call 38: 196.5361 +#> Sum of squared residuals at call 40: 196.5361 +#> Sum of squared residuals at call 44: 196.5336 +#> Sum of squared residuals at call 45: 196.5336 +#> Sum of squared residuals at call 50: 196.5334 +#> Sum of squared residuals at call 51: 196.5334 +#> Sum of squared residuals at call 52: 196.5334 +#> Sum of squared residuals at call 56: 196.5334 +#> Sum of squared residuals at call 58: 196.5334 +#> Sum of squared residuals at call 59: 196.5334 +#> Sum of squared residuals at call 65: 196.5334 #> Negative log-likelihood at call 75: 26.64668 #> Negative log-likelihood at call 103: 26.64668 #> Optimisation successfully terminated.</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#> time parent m1 diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 6f24b369..9d86a2df 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex 1ed2b216..c66b0beb 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex 4743eabd..761778f8 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex cad6ee11..89048ea3 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex 5e1527fa..0c81649c 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 68451ca6..a16cb6d7 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -194,8 +194,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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 -#> 0.034 0.041 5.124 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 19.594 0.000 19.605 </div><div class='input'> +#> 0.040 0.035 7.515 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 21.597 0.000 21.609 </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 #> 0.7340481 0.2659519 0.7505683 0.2494317 diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png Binary files differindex c4f9f048..bcf5d12c 100644 --- a/docs/reference/nafta-1.png +++ b/docs/reference/nafta-1.png diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 93bc3955..a9ee2f76 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -219,7 +219,7 @@ #> DFOP 429 2380 841 #> #> Representative half-life: -#> [1] 841.4094</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div></pre> +#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex 9a074f31..52de09bd 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex f8ae39c2..a832ede2 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex 60e602d4..03d334f7 100644 --- a/docs/reference/plot.mmkin-1.png +++ b/docs/reference/plot.mmkin-1.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex f1e4318c..555cb7d6 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 04762756..412c7244 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index fec2a187..f645e6a7 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -167,7 +167,7 @@ <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</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'> </div><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</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='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></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_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809619 0.1954667 0.4235714 0.0000000 0.4479605 0.5520395 +#> 0.3809619 0.1954667 0.4235714 0.0000000 0.4479603 0.5520397 #> #> $SFORB #> logical(0) @@ -175,10 +175,10 @@ #> $distimes #> DT50 DT90 #> parent 13.95078 46.34350 -#> A1 49.75344 165.27734 -#> B1 37.26908 123.80520 -#> C1 11.23130 37.30958 -#> A2 28.50644 94.69634 +#> A1 49.75343 165.27733 +#> B1 37.26907 123.80518 +#> C1 11.23131 37.30959 +#> A2 28.50644 94.69635 #> </div><div class='input'> </div><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#> compound parameter KinGUI ModelMaker deviation #> 1 parent degradation rate 0.0496 0.0506 2.0 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index e5565990..1a08132f 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -210,19 +210,19 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:11:15 2019 -#> Date of summary: Wed Apr 10 10:11:15 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:40:14 2019 +#> Date of summary: Thu May 2 12:40:14 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method using 131 model solutions performed in 0.284 s +#> Fitted using 131 model solutions performed in 0.269 s #> #> Error model: -#> NULL +#> Constant variance #> #> Starting values for parameters to be optimised: #> value type @@ -260,7 +260,7 @@ #> k_parent_sink 0.03722 10.90 5.650e-05 0.0294 0.04712 #> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 8.385 2 6 #> parent 8.385 2 6 diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differindex 9157a6a1..a9aeea21 100644 --- a/docs/reference/test_data_from_UBA_2014-1.png +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differindex 528f3987..f6c91bff 100644 --- a/docs/reference/test_data_from_UBA_2014-2.png +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index dfb49619..688baf32 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -184,25 +184,25 @@ <span class='kw'>M3</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_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 76.55425584 0.859186614 89.1008479 1.113866e-26 74.755959751 -#> k_parent 0.12081956 0.004601922 26.2541548 1.077373e-16 0.111561582 -#> k_M1 0.84258651 0.806231481 1.0450925 1.545475e-01 0.113839756 +#> parent_0 76.55425583 0.859186612 89.1008482 1.113866e-26 74.755959748 +#> k_parent 0.12081956 0.004601921 26.2541551 1.077372e-16 0.111561582 +#> k_M1 0.84258650 0.806231456 1.0450926 1.545475e-01 0.113839804 #> k_M2 0.04210878 0.017083049 2.4649452 1.170195e-02 0.018013807 #> k_M3 0.01122919 0.007245890 1.5497322 6.885127e-02 0.002909463 -#> f_parent_to_M1 0.32240199 0.240803570 1.3388589 9.820821e-02 NA +#> f_parent_to_M1 0.32240199 0.240803564 1.3388589 9.820820e-02 NA #> f_parent_to_M2 0.16099854 0.033691991 4.7785403 6.531225e-05 NA -#> f_M1_to_M3 0.27921500 0.269443517 1.0362654 1.565440e-01 0.022992921 -#> f_M2_to_M3 0.55641333 0.595125456 0.9349513 1.807725e-01 0.008003316 +#> f_M1_to_M3 0.27921500 0.269443517 1.0362654 1.565440e-01 0.022992933 +#> f_M2_to_M3 0.55641333 0.595125466 0.9349513 1.807725e-01 0.008003317 #> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 #> Upper #> parent_0 78.35255192 #> k_parent 0.13084582 -#> k_M1 6.23641562 +#> k_M1 6.23641283 #> k_M2 0.09843279 #> k_M3 0.04333950 #> f_parent_to_M1 NA #> f_parent_to_M2 NA -#> f_M1_to_M3 0.86443090 +#> f_M1_to_M3 0.86443084 #> f_M2_to_M3 0.99489847 #> sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.09649963 9 20 |
