diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-03 19:14:15 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-03 19:14:15 +0200 |
| commit | 1ef7008be2a72a0847064ad9c2ddcfa16b055482 (patch) | |
| tree | ecc3f90e5d18c75aea14ad774aad9214039c0674 /docs/reference | |
| parent | de7b6acdd75a0f95f2a9522c22625810f4aa329a (diff) | |
Improve error model fitting
Now we have a three stage fitting process for
nonconstant error models:
- Unweighted least squares
- Only optimize the error model
- Optimize both
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/reference')
22 files changed, 282 insertions, 277 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 3b7209b1..652dfee0 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 2.549850 5.050586 1.890202 +#> 99.666193 2.549849 5.050586 1.890202 #> #> $objective #> [1] 28.58291 @@ -202,7 +202,7 @@ #> #> $evaluations #> function gradient -#> 25 76 +#> 25 72 #> #> $message #> [1] "both X-convergence and relative convergence (5)" diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index c9b79512..c67c2a37 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -182,9 +182,9 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='no'>fit.fomc</span>$<span class='no'>par</span>, <span class='no'>fit.iore</span>$<span class='no'>par</span>, <span class='no'>fit.iore.deS</span>$<span class='no'>par</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>4</span>)))</div><div class='output co'>#> fit.fomc.par fit.iore.par fit.iore.deS.par -#> model par 1 85.87488995 85.874890 85.874890 -#> model par 2 0.05192228 -4.826631 -4.826631 -#> model par 3 0.65096650 1.949403 1.949403 +#> model par 1 85.87489063 85.874890 85.874890 +#> model par 2 0.05192238 -4.826631 -4.826631 +#> model par 3 0.65096665 1.949403 1.949403 #> model par 4 1.85744396 1.857444 1.857444</div><div class='input'> <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/cbind'>rbind</a></span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back #> fomc 1.785233 15.1479 4.559973 diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png Binary files differindex 87068d7c..a40cb689 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 48a1495f..76d91c40 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -177,7 +177,7 @@ #> Estimate Pr(>t) Lower Upper #> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 #> k1 2.67e-02 5.05e-06 0.0243 0.0295 -#> k2 3.41e-12 5.00e-01 0.0000 Inf +#> k2 2.86e-12 5.00e-01 0.0000 Inf #> g 6.47e-01 3.67e-06 0.6248 0.6677 #> sigma 1.27e+00 8.91e-06 0.8395 1.6929 #> @@ -186,7 +186,7 @@ #> DT50 DT90 DT50_rep #> SFO 67.7 2.25e+02 6.77e+01 #> IORE 58.2 1.07e+03 3.22e+02 -#> DFOP 55.5 3.70e+11 2.03e+11 +#> DFOP 55.5 4.42e+11 2.42e+11 #> #> Representative half-life: #> [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> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 2f60fdf7..61f00d9b 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 0184d573..f5844a8e 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -180,7 +180,7 @@ The total number of estimated parameters returned with the value <span class='no'>f_nw</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># no weighting (weights are unity)</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='no'>f_obs</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</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='no'>f_tc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</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/stats/topics/AIC'>AIC</a></span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>)</div><div class='output co'>#> df AIC #> f_nw 5 204.4486 #> f_obs 6 205.8727 -#> f_tc 6 141.9656</div><div class='input'> </div></pre> +#> f_tc 6 148.1802</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 4ce03e83..3b45b14f 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -206,18 +206,18 @@ <span class='no'>m</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</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'>m</span>)</div><div class='img'><img src='logistic.solution-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'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 1.057896e+02 1.9023449643 55.610120 3.768361e-16 1.016451e+02 +#> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02 #> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02 -#> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846687e-08 -#> r 2.263946e-01 0.1718110718 1.317695 1.061044e-01 4.335843e-02 +#> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846685e-08 +#> r 2.263946e-01 0.1718110773 1.317695 1.061044e-01 4.335843e-02 #> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00 #> Upper #> parent_0 109.9341588 #> kmax 0.1041853 -#> k0 0.4448749 +#> k0 0.4448750 #> r 1.1821121 #> sigma 7.3256566</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#> DT50 DT90 DT50_k0 DT50_kmax -#> parent 36.86533 62.41511 4297.853 10.83349</div></pre> +#> parent 36.86533 62.41511 4297.854 10.83349</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 1f0f6b50..1db9a9d9 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 2.150809526 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 + <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 2.1508110557 48.286452 3.542232e-18 99.246062215 +#> 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 1.788604e-10 NaN NaN NaN 0.000000000 +#> k_phenol_anisole 4.050581e-01 0.1053801116 3.843781 7.970202e-04 0.218013982 +#> k_anisole_sink 6.678742e-03 0.0006205844 10.762020 9.428076e-09 0.005370739 +#> sigma 2.514628e+00 0.3383670685 7.431657 1.054101e-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 2.932696e-10 1.000000e+00 1.000000e+00 +#> 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00 #> #> $SFORB #> logical(0) @@ -191,21 +191,21 @@ <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1623652988 48.028441 4.993105e-19 99.271024566 -#> k_T245_sink 1.636106e-02 0.0019676253 8.315129 1.673677e-07 0.012679144 -#> k_T245_phenol 2.700936e-02 0.0012421965 21.743225 1.314080e-13 0.024500318 -#> k_phenol_anisole 4.050581e-01 0.1177235385 3.440757 1.679236e-03 0.218746681 -#> k_anisole_sink 6.678743e-03 0.0006829745 9.778904 1.872891e-08 0.005377084 +#> T245_0 1.038550e+02 2.1623653063 48.028441 4.993105e-19 99.271025146 +#> k_T245_sink 1.636106e-02 0.0019676255 8.315130 1.673674e-07 0.012679148 +#> k_T245_phenol 2.700936e-02 0.0012421966 21.743224 1.314080e-13 0.024500319 +#> k_phenol_anisole 4.050581e-01 0.1177235488 3.440757 1.679237e-03 0.218746679 +#> k_anisole_sink 6.678742e-03 0.0006829745 9.778904 1.872892e-08 0.005377084 #> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 #> Upper -#> T245_0 1.084390e+02 -#> k_T245_sink 2.111217e-02 -#> k_T245_phenol 2.977534e-02 -#> k_phenol_anisole 7.500550e-01 -#> 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_0 108.43904395 +#> k_T245_sink 0.02111217 +#> k_T245_phenol 0.02977535 +#> k_phenol_anisole 0.75005504 +#> k_anisole_sink 0.00829550 +#> sigma 3.31827222</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 2.932696e-10 1.000000e+00 1.000000e+00 +#> 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00 #> #> $SFORB #> logical(0) diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 545ed8ab..8c14fc9d 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -362,15 +362,15 @@ Per default, parameters in the kinetic models are internally transformed in <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: 3.6.0 -#> Date of fit: Thu May 2 18:47:43 2019 -#> Date of summary: Thu May 2 18:47:43 2019 +#> Date of fit: Fri May 3 19:07:19 2019 +#> Date of summary: Fri May 3 19:07:19 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 221 model solutions performed in 0.458 s +#> Fitted using 222 model solutions performed in 0.463 s #> #> Error model: #> Constant variance @@ -400,11 +400,11 @@ Per default, parameters in the kinetic models are internally transformed in #> sigma 1.85700 0.4378 0.73200 2.9830 #> #> Parameter correlation: -#> parent_0 log_alpha log_beta sigma -#> 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 +#> parent_0 log_alpha log_beta sigma +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08 +#> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -443,7 +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 -#> 1.524 0.000 1.525 </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 +#> 1.493 0.000 1.494 </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 #> @@ -452,75 +452,72 @@ Per default, parameters in the kinetic models are internally transformed in #> #> $distimes #> DT50 DT90 -#> parent 7.022928 23.32966 -#> m1 131.760715 437.69962 +#> parent 7.022929 23.32967 +#> m1 131.760712 437.69961 #> </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'>#> Sum of squared residuals at call 1: 18915.53 + <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'>#> <span class='message'>Ordinary least squares optimisation</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 12: 4094.396 +#> Sum of squared residuals at call 16: 4094.396 +#> Sum of squared residuals at call 19: 1340.595 +#> Sum of squared residuals at call 20: 1340.593 +#> Sum of squared residuals at call 25: 1072.239 +#> Sum of squared residuals at call 28: 1072.236 +#> Sum of squared residuals at call 30: 874.2615 +#> Sum of squared residuals at call 33: 874.2611 +#> Sum of squared residuals at call 35: 616.2375 +#> Sum of squared residuals at call 37: 616.237 +#> Sum of squared residuals at call 40: 467.4386 +#> Sum of squared residuals at call 42: 467.438 +#> Sum of squared residuals at call 46: 398.2913 +#> Sum of squared residuals at call 48: 398.2913 +#> Sum of squared residuals at call 49: 398.2912 +#> Sum of squared residuals at call 51: 395.0711 +#> Sum of squared residuals at call 54: 395.071 +#> Sum of squared residuals at call 56: 378.3298 +#> Sum of squared residuals at call 59: 378.3298 +#> Sum of squared residuals at call 62: 376.9812 +#> Sum of squared residuals at call 64: 376.9811 +#> Sum of squared residuals at call 67: 375.2085 +#> Sum of squared residuals at call 69: 375.2085 +#> Sum of squared residuals at call 70: 375.2085 +#> Sum of squared residuals at call 71: 375.2085 +#> Sum of squared residuals at call 72: 374.5723 +#> Sum of squared residuals at call 74: 374.5723 +#> Sum of squared residuals at call 77: 374.0075 +#> Sum of squared residuals at call 79: 374.0075 +#> Sum of squared residuals at call 80: 374.0075 +#> Sum of squared residuals at call 82: 373.1711 +#> Sum of squared residuals at call 84: 373.1711 +#> Sum of squared residuals at call 87: 372.6445 +#> Sum of squared residuals at call 88: 372.1615 +#> Sum of squared residuals at call 90: 372.1615 +#> Sum of squared residuals at call 91: 372.1615 +#> Sum of squared residuals at call 94: 371.6464 +#> Sum of squared residuals at call 99: 371.4299 +#> Sum of squared residuals at call 101: 371.4299 +#> Sum of squared residuals at call 104: 371.4071 +#> Sum of squared residuals at call 106: 371.4071 +#> Sum of squared residuals at call 107: 371.4071 +#> Sum of squared residuals at call 109: 371.2524 +#> Sum of squared residuals at call 113: 371.2524 +#> Sum of squared residuals at call 114: 371.2136 +#> Sum of squared residuals at call 115: 371.2136 +#> Sum of squared residuals at call 116: 371.2136 +#> Sum of squared residuals at call 119: 371.2134 +#> Sum of squared residuals at call 120: 371.2134 +#> Sum of squared residuals at call 122: 371.2134 +#> Sum of squared residuals at call 123: 371.2134 +#> Sum of squared residuals at call 125: 371.2134 +#> Sum of squared residuals at call 126: 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 +#> Negative log-likelihood at call 145: 97.22429 #> Optimisation successfully terminated. #> User System verstrichen -#> 1.095 0.000 1.096 </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 +#> 1.082 0.000 1.083 </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 #> @@ -529,8 +526,8 @@ Per default, parameters in the kinetic models are internally transformed in #> #> $distimes #> DT50 DT90 -#> parent 7.022928 23.32966 -#> m1 131.760710 437.69961 +#> parent 7.022929 23.32967 +#> m1 131.760712 437.69961 #> </div><div class='input'> # Use stepwise fitting, using optimised parameters from parent only fit, FOMC </div><div class='input'><span class='no'>FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( @@ -552,8 +549,8 @@ Per default, parameters in the kinetic models are internally transformed in <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: 3.6.0 -#> Date of fit: Thu May 2 18:47:59 2019 -#> Date of summary: Thu May 2 18:47:59 2019 +#> Date of fit: Fri May 3 19:07:35 2019 +#> Date of summary: Fri May 3 19:07:35 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -561,7 +558,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 404 model solutions performed in 1.047 s +#> Fitted using 421 model solutions performed in 1.099 s #> #> Error model: #> Constant variance @@ -596,11 +593,11 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Parameter correlation: #> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma -#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -5.940e-09 -#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -1.406e-08 -#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -2.306e-08 -#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -6.664e-09 -#> sigma -5.940e-09 -1.406e-08 -2.306e-08 -6.664e-09 1.000e+00 +#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -2.265e-07 +#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.785e-07 +#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.386e-07 +#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -3.641e-08 +#> sigma -2.265e-07 3.785e-07 -1.386e-07 -3.641e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -635,10 +632,10 @@ Per default, parameters in the kinetic models are internally transformed in #> 0 parent 102.04 99.59848 2.442e+00 #> 1 parent 93.50 90.23787 3.262e+00 #> 1 parent 92.50 90.23787 2.262e+00 -#> 3 parent 63.23 74.07320 -1.084e+01 -#> 3 parent 68.99 74.07320 -5.083e+00 -#> 7 parent 52.32 49.91207 2.408e+00 -#> 7 parent 55.13 49.91207 5.218e+00 +#> 3 parent 63.23 74.07319 -1.084e+01 +#> 3 parent 68.99 74.07319 -5.083e+00 +#> 7 parent 52.32 49.91206 2.408e+00 +#> 7 parent 55.13 49.91206 5.218e+00 #> 14 parent 27.27 25.01257 2.257e+00 #> 14 parent 26.64 25.01257 1.627e+00 #> 21 parent 11.50 12.53462 -1.035e+00 @@ -648,7 +645,7 @@ Per default, parameters in the kinetic models are internally transformed in #> 50 parent 0.69 0.71624 -2.624e-02 #> 50 parent 0.63 0.71624 -8.624e-02 #> 75 parent 0.05 0.06074 -1.074e-02 -#> 75 parent 0.06 0.06074 -7.382e-04 +#> 75 parent 0.06 0.06074 -7.381e-04 #> 1 m1 4.84 4.80296 3.704e-02 #> 1 m1 5.64 4.80296 8.370e-01 #> 3 m1 12.91 13.02400 -1.140e-01 @@ -670,8 +667,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 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: 3.6.0 -#> Date of fit: Thu May 2 18:48:00 2019 -#> Date of summary: Thu May 2 18:48:00 2019 +#> Date of fit: Fri May 3 19:07:37 2019 +#> Date of summary: Fri May 3 19:07:37 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -679,7 +676,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 558 model solutions performed in 1.45 s +#> Fitted using 756 model solutions performed in 1.973 s #> #> Error model: #> Variance unique to each observed variable @@ -717,17 +714,17 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Parameter correlation: #> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_parent -#> parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035671 -#> log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069834 -#> log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026158 -#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041369 -#> sigma_parent 0.03567 0.06983 -0.02616 -0.04137 1.000000 -#> sigma_m1 -0.03385 -0.06627 0.02482 0.03926 -0.004628 +#> parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035685 +#> log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069840 +#> log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026160 +#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041377 +#> sigma_parent 0.03569 0.06984 -0.02616 -0.04138 1.000000 +#> sigma_m1 -0.03385 -0.06626 0.02482 0.03925 -0.004628 #> sigma_m1 #> parent_0 -0.033847 -#> log_k_parent -0.066265 +#> log_k_parent -0.066264 #> log_k_m1 0.024822 -#> f_parent_ilr_1 0.039256 +#> f_parent_ilr_1 0.039254 #> sigma_parent -0.004628 #> sigma_m1 1.000000 #> @@ -761,47 +758,47 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Data: #> time variable observed predicted residual -#> 0 parent 99.46 99.65417 -1.942e-01 -#> 0 parent 102.04 99.65417 2.386e+00 -#> 1 parent 93.50 90.26333 3.237e+00 -#> 1 parent 92.50 90.26333 2.237e+00 -#> 3 parent 63.23 74.05306 -1.082e+01 -#> 3 parent 68.99 74.05306 -5.063e+00 -#> 7 parent 52.32 49.84325 2.477e+00 -#> 7 parent 55.13 49.84325 5.287e+00 -#> 14 parent 27.27 24.92971 2.340e+00 -#> 14 parent 26.64 24.92971 1.710e+00 -#> 21 parent 11.50 12.46890 -9.689e-01 -#> 21 parent 11.64 12.46890 -8.289e-01 -#> 35 parent 2.85 3.11925 -2.692e-01 -#> 35 parent 2.91 3.11925 -2.092e-01 -#> 50 parent 0.69 0.70679 -1.679e-02 -#> 50 parent 0.63 0.70679 -7.679e-02 -#> 75 parent 0.05 0.05952 -9.523e-03 -#> 75 parent 0.06 0.05952 4.772e-04 +#> 0 parent 99.46 99.65425 -1.942e-01 +#> 0 parent 102.04 99.65425 2.386e+00 +#> 1 parent 93.50 90.26338 3.237e+00 +#> 1 parent 92.50 90.26338 2.237e+00 +#> 3 parent 63.23 74.05309 -1.082e+01 +#> 3 parent 68.99 74.05309 -5.063e+00 +#> 7 parent 52.32 49.84326 2.477e+00 +#> 7 parent 55.13 49.84326 5.287e+00 +#> 14 parent 27.27 24.92970 2.340e+00 +#> 14 parent 26.64 24.92970 1.710e+00 +#> 21 parent 11.50 12.46888 -9.689e-01 +#> 21 parent 11.64 12.46888 -8.289e-01 +#> 35 parent 2.85 3.11924 -2.692e-01 +#> 35 parent 2.91 3.11924 -2.092e-01 +#> 50 parent 0.69 0.70678 -1.678e-02 +#> 50 parent 0.63 0.70678 -7.678e-02 +#> 75 parent 0.05 0.05952 -9.522e-03 +#> 75 parent 0.06 0.05952 4.776e-04 #> 1 m1 4.84 4.81075 2.925e-02 #> 1 m1 5.64 4.81075 8.292e-01 #> 3 m1 12.91 13.04197 -1.320e-01 #> 3 m1 12.96 13.04197 -8.197e-02 -#> 7 m1 22.97 25.06847 -2.098e+00 -#> 7 m1 24.47 25.06847 -5.985e-01 +#> 7 m1 22.97 25.06848 -2.098e+00 +#> 7 m1 24.47 25.06848 -5.985e-01 #> 14 m1 41.69 36.70308 4.987e+00 #> 14 m1 33.21 36.70308 -3.493e+00 #> 21 m1 44.37 41.65115 2.719e+00 #> 21 m1 46.44 41.65115 4.789e+00 -#> 35 m1 41.22 43.29465 -2.075e+00 -#> 35 m1 37.95 43.29465 -5.345e+00 -#> 50 m1 41.19 41.19948 -9.482e-03 -#> 50 m1 40.01 41.19948 -1.189e+00 -#> 75 m1 40.09 36.44036 3.650e+00 -#> 75 m1 33.85 36.44036 -2.590e+00 -#> 100 m1 31.04 31.98774 -9.477e-01 -#> 100 m1 33.13 31.98774 1.142e+00 +#> 35 m1 41.22 43.29464 -2.075e+00 +#> 35 m1 37.95 43.29464 -5.345e+00 +#> 50 m1 41.19 41.19947 -9.473e-03 +#> 50 m1 40.01 41.19947 -1.189e+00 +#> 75 m1 40.09 36.44035 3.650e+00 +#> 75 m1 33.85 36.44035 -2.590e+00 +#> 100 m1 31.04 31.98773 -9.477e-01 +#> 100 m1 33.13 31.98773 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 +#> 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'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Thu May 2 18:48:04 2019 -#> Date of summary: Thu May 2 18:48:04 2019 +#> Date of fit: Fri May 3 19:07:40 2019 +#> Date of summary: Fri May 3 19:07:40 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -809,7 +806,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 844 model solutions performed in 3.407 s +#> Fitted using 888 model solutions performed in 3.579 s #> #> Error model: #> Two-component variance function @@ -820,8 +817,8 @@ 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 3.0000 error -#> rsd_high 0.0100 error +#> sigma_low 0.1000 error +#> rsd_high 0.1000 error #> #> Starting values for the transformed parameters actually optimised: #> value lower upper @@ -829,99 +826,106 @@ 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 3.000000 0 Inf -#> rsd_high 0.010000 0 Inf +#> sigma_low 0.100000 0 Inf +#> rsd_high 0.100000 0 Inf #> #> Fixed parameter values: #> value type #> m1_0 0 state #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 100.70000 2.621000 95.400000 106.10000 -#> log_k_parent -2.29700 0.008862 -2.315000 -2.27900 -#> log_k_m1 -5.26600 0.091310 -5.452000 -5.08000 -#> f_parent_ilr_1 0.02374 0.055300 -0.088900 0.13640 -#> sigma_low 0.00305 0.004829 -0.006786 0.01289 -#> rsd_high 0.07928 0.009418 0.060100 0.09847 +#> Estimate Std. Error Lower Upper +#> parent_0 100.30000 3.06400 94.08000 106.60000 +#> log_k_parent -2.31100 0.02913 -2.37100 -2.25200 +#> log_k_m1 -5.27800 0.10890 -5.49900 -5.05600 +#> f_parent_ilr_1 0.02128 0.07223 -0.12590 0.16840 +#> sigma_low 0.99650 NaN NaN NaN +#> rsd_high 0.07560 0.01059 0.05402 0.09717 #> #> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low rsd_high -#> parent_0 1.00000 0.67644 -0.10215 -0.76822 0.14294 -0.08783 -#> log_k_parent 0.67644 1.00000 -0.15102 -0.59491 0.34611 -0.08125 -#> log_k_m1 -0.10215 -0.15102 1.00000 0.51808 -0.05236 0.01240 -#> f_parent_ilr_1 -0.76822 -0.59491 0.51808 1.00000 -0.13900 0.03248 -#> sigma_low 0.14294 0.34611 -0.05236 -0.13900 1.00000 -0.16546 -#> rsd_high -0.08783 -0.08125 0.01240 0.03248 -0.16546 1.00000 +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low +#> parent_0 1.00000 0.64703 -0.220160 -0.79035 NaN +#> log_k_parent 0.64703 1.00000 -0.339633 -0.67982 NaN +#> log_k_m1 -0.22016 -0.33963 1.000000 0.62815 NaN +#> f_parent_ilr_1 -0.79035 -0.67982 0.628148 1.00000 NaN +#> sigma_low NaN NaN NaN NaN 1 +#> rsd_high -0.05745 -0.01123 0.003502 0.00568 NaN +#> rsd_high +#> parent_0 -0.057450 +#> log_k_parent -0.011230 +#> log_k_m1 0.003502 +#> f_parent_ilr_1 0.005680 +#> sigma_low NaN +#> rsd_high 1.000000 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 1.007e+02 38.4300 1.180e-28 95.400000 1.061e+02 -#> k_parent 1.006e-01 112.8000 1.718e-43 0.098760 1.024e-01 -#> k_m1 5.167e-03 10.9500 1.171e-12 0.004290 6.223e-03 -#> f_parent_to_m1 5.084e-01 26.0100 2.146e-23 0.468600 5.481e-01 -#> 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 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 1.003e+02 32.740 1.759e-26 94.080000 1.066e+02 +#> k_parent 9.914e-02 34.330 4.045e-27 0.093430 1.052e-01 +#> k_m1 5.105e-03 9.186 8.682e-11 0.004089 6.372e-03 +#> f_parent_to_m1 5.075e-01 19.880 7.143e-20 0.455600 5.593e-01 +#> sigma_low 9.965e-01 NaN NaN NaN NaN +#> rsd_high 7.560e-02 7.137 2.114e-08 0.054020 9.717e-02 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df -#> All data 6.475 4 15 -#> parent 6.573 2 7 -#> m1 4.671 2 8 +#> All data 6.433 4 15 +#> parent 6.506 2 7 +#> m1 4.692 2 8 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.5084 -#> parent_sink 0.4916 +#> parent_m1 0.5075 +#> parent_sink 0.4925 #> #> Estimated disappearance times: -#> DT50 DT90 -#> parent 6.893 22.9 -#> m1 134.156 445.7 +#> DT50 DT90 +#> parent 6.992 23.23 +#> m1 135.787 451.08 #> #> Data: #> time variable observed predicted residual -#> 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 2.491201 -#> 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 -0.692315 -#> 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 -#> 50 parent 0.63 0.66013 -0.030126 -#> 75 parent 0.05 0.05344 -0.003438 -#> 75 parent 0.06 0.05344 0.006562 -#> 1 m1 4.84 4.88645 -0.046451 -#> 1 m1 5.64 4.88645 0.753549 -#> 3 m1 12.91 13.22867 -0.318669 -#> 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 4.680263 -#> 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 36.61471 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'> +#> 0 parent 99.46 100.32122 -0.861220 +#> 0 parent 102.04 100.32122 1.718780 +#> 1 parent 93.50 90.85266 2.647340 +#> 1 parent 92.50 90.85266 1.647340 +#> 3 parent 63.23 74.51219 -11.282190 +#> 3 parent 68.99 74.51219 -5.522190 +#> 7 parent 52.32 50.11950 2.200504 +#> 7 parent 55.13 50.11950 5.010504 +#> 14 parent 27.27 25.03921 2.230792 +#> 14 parent 26.64 25.03921 1.600792 +#> 21 parent 11.50 12.50934 -1.009342 +#> 21 parent 11.64 12.50934 -0.869342 +#> 35 parent 2.85 3.12221 -0.272211 +#> 35 parent 2.91 3.12221 -0.212211 +#> 50 parent 0.69 0.70572 -0.015724 +#> 50 parent 0.63 0.70572 -0.075724 +#> 75 parent 0.05 0.05919 -0.009191 +#> 75 parent 0.06 0.05919 0.000809 +#> 1 m1 4.84 4.79307 0.046928 +#> 1 m1 5.64 4.79307 0.846928 +#> 3 m1 12.91 12.99398 -0.083980 +#> 3 m1 12.96 12.99398 -0.033980 +#> 7 m1 22.97 24.97744 -2.007441 +#> 7 m1 24.47 24.97744 -0.507441 +#> 14 m1 41.69 36.57917 5.110827 +#> 14 m1 33.21 36.57917 -3.369173 +#> 21 m1 44.37 41.52931 2.840692 +#> 21 m1 46.44 41.52931 4.910692 +#> 35 m1 41.22 43.22614 -2.006138 +#> 35 m1 37.95 43.22614 -5.276138 +#> 50 m1 41.19 41.20972 -0.019717 +#> 50 m1 40.01 41.20972 -1.199717 +#> 75 m1 40.09 36.57312 3.516882 +#> 75 m1 33.85 36.57312 -2.723118 +#> 100 m1 31.04 32.21655 -1.176546 +#> 100 m1 33.13 32.21655 0.913454 +#> 120 m1 25.15 29.09181 -3.941814 +#> 120 m1 33.31 29.09181 4.218186</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 23139c0f..9ba463e3 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 file26cc3b169ccf.c 2> file26cc3b169ccf.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file2b304be466d0.c 2> file2b304be466d0.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 798722a2..65918d53 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index c90acf4a..8cfb9374 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -154,8 +154,7 @@ <pre class="examples"><div class='input'><span class='no'>model</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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"anisole"</span>)), - <span class='kw'>anisole</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'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</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='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>false convergence (8)</span></div><div class='input'><span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div></pre> + <span class='kw'>anisole</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'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</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'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-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/mkinpredict.html b/docs/reference/mkinpredict.html index 7b75b85d..074ac3ac 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -333,14 +333,14 @@ <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 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.002 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( +#> 0.002 0.000 0.001 </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='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 -#> 0.021 0.000 0.021 </div><div class='input'> +#> 0.022 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'>#> Sum of squared residuals at call 1: 552.5739 + <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'>#> <span class='message'>Ordinary least squares optimisation</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 @@ -350,6 +350,7 @@ #> 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 23: 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 @@ -366,15 +367,16 @@ #> 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 +#> Sum of squared residuals at call 73: 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 #> 1 0.0 82.49216 0.000000 -#> 2 0.1 80.00563 1.179956 -#> 3 0.2 77.59404 2.312583 -#> 4 0.3 75.25515 3.399424 -#> 5 0.4 72.98675 4.441974 -#> 6 0.5 70.78673 5.441685</div><div class='input'> </div></pre> +#> 2 0.1 80.00563 1.179955 +#> 3 0.2 77.59404 2.312580 +#> 4 0.3 75.25515 3.399419 +#> 5 0.4 72.98675 4.441969 +#> 6 0.5 70.78673 5.441679</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png Binary files differindex 5b7180ee..344561de 100644 --- a/docs/reference/mkinresplot-1.png +++ b/docs/reference/mkinresplot-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex c66b0beb..59d293d5 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 761778f8..a947ac65 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 49d41270..c730ecb0 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -194,11 +194,11 @@ <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 -#> 0.047 0.041 7.417 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 21.251 0.000 21.263 </div><div class='input'> +#> 0.042 0.028 5.095 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 19.29 0.00 19.30 </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 +#> 0.7340481 0.2659519 0.7505684 0.2494316 #> #> $SFORB #> logical(0) @@ -206,8 +206,8 @@ #> $distimes #> DT50 DT90 #> parent 0.8777689 2.915885 -#> M1 2.3257442 7.725955 -#> M2 33.7200941 112.015728 +#> M1 2.3257449 7.725957 +#> M2 33.7200958 112.015734 #> </div><div class='input'> <span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png Binary files differindex 115792db..e7b3bac7 100644 --- a/docs/reference/plot.mkinfit-1.png +++ b/docs/reference/plot.mkinfit-1.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 412c7244..7f32afe2 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 f645e6a7..09f6d1e2 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 0.4479603 0.5520397 +#> 0.3809619 0.1954667 0.4235714 0.0000000 0.4479620 0.5520380 #> #> $SFORB #> logical(0) @@ -175,10 +175,10 @@ #> $distimes #> DT50 DT90 #> parent 13.95078 46.34350 -#> A1 49.75343 165.27733 -#> B1 37.26907 123.80518 -#> C1 11.23131 37.30959 -#> A2 28.50644 94.69635 +#> A1 49.75344 165.27737 +#> B1 37.26907 123.80517 +#> C1 11.23131 37.30960 +#> A2 28.50627 94.69577 #> </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 89a8b9a6..351d7a7e 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -211,15 +211,15 @@ <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: 3.6.0 -#> Date of fit: Thu May 2 18:48:59 2019 -#> Date of summary: Thu May 2 18:48:59 2019 +#> Date of fit: Fri May 3 19:08:31 2019 +#> Date of summary: Fri May 3 19:08:31 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.274 s +#> Fitted using 131 model solutions performed in 0.27 s #> #> Error model: #> Constant variance @@ -247,9 +247,9 @@ #> #> Parameter correlation: #> parent_0 log_k_parent_sink sigma -#> parent_0 1.000e+00 5.428e-01 1.642e-07 -#> log_k_parent_sink 5.428e-01 1.000e+00 2.507e-07 -#> sigma 1.642e-07 2.507e-07 1.000e+00 +#> parent_0 1.000e+00 5.428e-01 1.648e-07 +#> log_k_parent_sink 5.428e-01 1.000e+00 2.513e-07 +#> sigma 1.648e-07 2.513e-07 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 688baf32..bc988340 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -160,14 +160,14 @@ <span class='no'>m_ws</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>), <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</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_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_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>)</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_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.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_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) -#> parent_w_0 9.598567e+01 2.12352039 4.520120e+01 9.476357e-18 -#> k_parent_w_sink 3.603743e-01 0.03149366 1.144276e+01 4.128096e-09 -#> k_parent_w_parent_s 6.031371e-02 0.01603582 3.761185e+00 9.436293e-04 -#> k_parent_s_sink 7.560341e-11 0.09483761 7.971881e-10 5.000000e-01 -#> k_parent_s_parent_w 7.419672e-02 0.10738374 6.909493e-01 2.500756e-01 -#> sigma 2.982879e+00 0.50546582 5.901247e+00 1.454824e-05 +#> parent_w_0 9.598567e+01 2.12351789 4.520126e+01 9.476190e-18 +#> k_parent_w_sink 3.603743e-01 0.03149282 1.144306e+01 4.126593e-09 +#> k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04 +#> k_parent_s_sink 5.108964e-11 0.09482736 5.387647e-10 5.000000e-01 +#> k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01 +#> sigma 2.982879e+00 0.50545649 5.901356e+00 1.454535e-05 #> Lower Upper -#> parent_w_0 91.48420501 100.4871438 +#> parent_w_0 91.48420503 100.4871438 #> k_parent_w_sink 0.30668904 0.4234571 #> k_parent_w_parent_s 0.03423904 0.1062455 #> k_parent_s_sink 0.00000000 Inf @@ -184,25 +184,25 @@ <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<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 76.55425583 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 +#> parent_0 76.55425584 0.859186619 89.1008474 1.113866e-26 74.755959756 +#> k_parent 0.12081956 0.004601922 26.2541544 1.077373e-16 0.111561582 +#> k_M1 0.84258649 0.806231419 1.0450926 1.545475e-01 0.113839803 +#> k_M2 0.04210878 0.017083049 2.4649453 1.170195e-02 0.018013807 #> k_M3 0.01122919 0.007245890 1.5497322 6.885127e-02 0.002909463 -#> f_parent_to_M1 0.32240199 0.240803564 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 0.022992933 -#> f_M2_to_M3 0.55641333 0.595125466 0.9349513 1.807725e-01 0.008003317 +#> f_parent_to_M1 0.32240199 0.240803555 1.3388589 9.820820e-02 NA +#> f_parent_to_M2 0.16099854 0.033691991 4.7785403 6.531224e-05 NA +#> f_M1_to_M3 0.27921501 0.269443514 1.0362655 1.565440e-01 0.022992937 +#> f_M2_to_M3 0.55641331 0.595125445 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 6.23641283 +#> k_M1 6.23641265 #> k_M2 0.09843279 #> k_M3 0.04333950 #> f_parent_to_M1 NA #> f_parent_to_M2 NA -#> f_M1_to_M3 0.86443084 +#> f_M1_to_M3 0.86443083 #> 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 |
