diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-07 08:12:27 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-07 08:12:27 +0200 |
| commit | 8a3475c59f3d91ce5ce7d980d6de09360617e7fe (patch) | |
| tree | a0a8bf1053e8bab09921b84916f1ace15e8ae8a4 /docs/reference | |
| parent | 1ef7008be2a72a0847064ad9c2ddcfa16b055482 (diff) | |
After the OLS step, use OLS parameter estimates
- Fix the respective error in the code
- Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/NAFTA_SOP_2015.html | 32 | ||||
| -rw-r--r-- | docs/reference/NAFTA_SOP_Attachment.html | 32 | ||||
| -rw-r--r-- | docs/reference/logLik.mkinfit.html | 2 | ||||
| -rw-r--r-- | docs/reference/logistic.solution.html | 18 | ||||
| -rw-r--r-- | docs/reference/mccall81_245T.html | 45 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 339 | ||||
| -rw-r--r-- | docs/reference/mkinmod.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinparplot-1.png | bin | 16549 -> 17306 bytes | |||
| -rw-r--r-- | docs/reference/mkinparplot.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinpredict.html | 8 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/reference/nafta.html | 32 | ||||
| -rw-r--r-- | docs/reference/summary.mkinfit.html | 30 | ||||
| -rw-r--r-- | docs/reference/test_data_from_UBA_2014.html | 54 | ||||
| -rw-r--r-- | docs/reference/transform_odeparms.html | 90 |
15 files changed, 300 insertions, 390 deletions
diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 84341a17..9fbc71c6 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -155,7 +155,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#> Sums of squares: + <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#> Sums of squares: #> SFO IORE DFOP #> 1378.6832 615.7730 517.8836 #> @@ -164,25 +164,25 @@ #> #> Parameters: #> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.7558 1.80e-14 77.18268 90.3288 -#> k_parent_sink 0.0017 7.43e-05 0.00112 0.0026 -#> sigma 8.7518 1.22e-05 5.64278 11.8608 +#> Estimate Pr(>t) Lower Upper +#> parent_0 83.7558 NA NA NA +#> k_parent_sink 0.0017 NA NA NA +#> sigma 8.7518 NA NA NA #> #> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.69e+01 NA 8.88e+01 1.05e+02 -#> k__iore_parent_sink 8.40e-14 NA 1.79e-18 3.94e-09 -#> N_parent 6.68e+00 NA 4.19e+00 9.17e+00 -#> sigma 5.85e+00 NA 3.76e+00 7.94e+00 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.69e+01 NA NA NA +#> k__iore_parent_sink 8.40e-14 NA NA NA +#> N_parent 6.68e+00 NA NA NA +#> sigma 5.85e+00 NA NA NA #> #> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02 -#> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02 -#> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03 -#> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01 -#> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.76e+01 NA NA NA +#> k1 4.24e-02 NA NA NA +#> k2 8.24e-04 NA NA NA +#> g 2.88e-01 NA NA NA +#> sigma 5.36e+00 NA NA NA #> #> #> DTx values: diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 76d91c40..149b4d82 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -152,7 +152,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>nafta_att_p5a</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</span>]], <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='output co'>#> Sums of squares: + <pre class="examples"><div class='input'> <span class='no'>nafta_att_p5a</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</span>]], <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='output co'>#> Sums of squares: #> SFO IORE DFOP #> 465.21753 56.27506 32.06401 #> @@ -161,25 +161,25 @@ #> #> Parameters: #> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 95.8401 4.67e-21 92.245 99.4357 -#> k_parent_sink 0.0102 3.92e-12 0.009 0.0117 -#> sigma 4.8230 3.81e-06 3.214 6.4318 +#> Estimate Pr(>t) Lower Upper +#> parent_0 95.8401 NA NA NA +#> k_parent_sink 0.0102 NA NA NA +#> sigma 4.8230 NA NA NA #> #> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 1.01e+02 NA 9.91e+01 1.02e+02 -#> k__iore_parent_sink 1.54e-05 NA 4.08e-06 5.84e-05 -#> N_parent 2.57e+00 NA 2.25e+00 2.89e+00 -#> sigma 1.68e+00 NA 1.12e+00 2.24e+00 +#> Estimate Pr(>t) Lower Upper +#> parent_0 1.01e+02 NA NA NA +#> k__iore_parent_sink 1.54e-05 NA NA NA +#> N_parent 2.57e+00 NA NA NA +#> sigma 1.68e+00 NA NA NA #> #> $DFOP -#> 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 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 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.99e+01 NA NA NA +#> k1 2.67e-02 NA NA NA +#> k2 2.86e-12 NA NA NA +#> g 6.47e-01 NA NA NA +#> sigma 1.27e+00 NA NA NA #> #> #> DTx values: diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index f5844a8e..0184d573 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 6 148.1802</div><div class='input'> </div></pre> +#> f_tc 6 141.9656</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 3b45b14f..082cd4fb 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -205,18 +205,12 @@ <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]] <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 1.9023449649 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 5.846685e-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 0.4448750 -#> 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>)$<span class='no'>distimes</span></div><div class='output co'>#> DT50 DT90 DT50_k0 DT50_kmax + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 1.057896e+02 NA NA NA NA NA +#> kmax 6.398190e-02 NA NA NA NA NA +#> k0 1.612775e-04 NA NA NA NA NA +#> r 2.263946e-01 NA NA NA NA NA +#> sigma 5.332935e+00 NA NA NA NA NA</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 4297.854 10.83349</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 1db9a9d9..26bbd2ec 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -160,22 +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 2.1508110557 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 -#> k_T245_phenol 2.979116e-02 -#> k_phenol_sink Inf -#> k_phenol_anisole 7.525759e-01 -#> 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'>#> $ff + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> T245_0 1.038550e+02 NA NA NA NA NA +#> k_T245_sink 1.636106e-02 NA NA NA NA NA +#> k_T245_phenol 2.700936e-02 NA NA NA NA NA +#> k_phenol_sink 1.788604e-10 NA NA NA NA NA +#> k_phenol_anisole 4.050581e-01 NA NA NA NA NA +#> k_anisole_sink 6.678742e-03 NA NA NA NA NA +#> sigma 2.514628e+00 NA NA NA NA NA</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'>#> $ff #> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink #> 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00 #> @@ -190,20 +182,13 @@ #> </div><div class='input'> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span> <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), - <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1623653063 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_0 108.43904395 -#> 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'>#> $ff + <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> T245_0 1.038550e+02 NA NA NA NA NA +#> k_T245_sink 1.636106e-02 NA NA NA NA NA +#> k_T245_phenol 2.700936e-02 NA NA NA NA NA +#> k_phenol_anisole 4.050581e-01 NA NA NA NA NA +#> k_anisole_sink 6.678742e-03 NA NA NA NA NA +#> sigma 2.514628e+00 NA NA NA NA NA</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 4.415672e-10 1.000000e+00 1.000000e+00 #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 8c14fc9d..b75b7c95 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -360,17 +360,17 @@ Per default, parameters in the kinetic models are internally transformed in <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <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 +<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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</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: Fri May 3 19:07:19 2019 -#> Date of summary: Fri May 3 19:07:19 2019 +#> Date of fit: Tue May 7 08:08:23 2019 +#> Date of summary: Tue May 7 08:08:23 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.463 s +#> Fitted using 66 model solutions performed in 0.139 s #> #> Error model: #> Constant variance @@ -393,28 +393,23 @@ Per default, parameters in the kinetic models are internally transformed in #> None #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 85.87000 1.8070 81.23000 90.5200 -#> log_alpha 0.05192 0.1353 -0.29580 0.3996 -#> log_beta 0.65100 0.2287 0.06315 1.2390 -#> sigma 1.85700 0.4378 0.73200 2.9830 +#> Estimate Std. Error Lower Upper +#> parent_0 85.87000 NA NA NA +#> log_alpha 0.05192 NA NA NA +#> log_beta 0.65100 NA NA NA +#> sigma 1.85700 NA NA NA #> #> Parameter correlation: -#> 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 -#> +#> No covariance matrix #> 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 85.870 47.530 3.893e-08 81.2300 90.520 -#> alpha 1.053 7.393 3.562e-04 0.7439 1.491 -#> beta 1.917 4.373 3.601e-03 1.0650 3.451 -#> sigma 1.857 4.243 4.074e-03 0.7320 2.983 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 85.870 NA NA NA NA +#> alpha 1.053 NA NA NA NA +#> beta 1.917 NA NA NA NA +#> sigma 1.857 NA NA NA NA #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df @@ -443,7 +438,7 @@ 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 -#> 1.493 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 +#> 0.637 0.000 0.640 </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 #> @@ -514,10 +509,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 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 -#> Negative log-likelihood at call 145: 97.22429 -#> Optimisation successfully terminated. -#> User System verstrichen -#> 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 +#> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen +#> 0.544 0.000 0.550 </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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -547,10 +540,10 @@ Per default, parameters in the kinetic models are internally transformed in <span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</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'> </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 + <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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</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: Fri May 3 19:07:35 2019 -#> Date of summary: Fri May 3 19:07:35 2019 +#> Date of fit: Tue May 7 08:08:30 2019 +#> Date of summary: Tue May 7 08:08:30 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -558,7 +551,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.099 s +#> Fitted using 185 model solutions performed in 0.499 s #> #> Error model: #> Constant variance @@ -584,31 +577,25 @@ Per default, parameters in the kinetic models are internally transformed in #> m1_0 0 state #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.60000 1.57000 96.40000 102.8000 -#> log_k_parent -2.31600 0.04087 -2.39900 -2.2330 -#> log_k_m1 -5.24800 0.13320 -5.51800 -4.9770 -#> f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694 -#> sigma 3.12600 0.35850 2.39600 3.8550 +#> Estimate Std. Error Lower Upper +#> parent_0 99.60000 NA NA NA +#> log_k_parent -2.31600 NA NA NA +#> log_k_m1 -5.24800 NA NA NA +#> f_parent_ilr_1 0.04096 NA NA NA +#> sigma 3.12600 NA NA NA #> #> 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 -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 -#> +#> No covariance matrix #> 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 99.600000 63.430 2.298e-36 96.400000 1.028e+02 -#> k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01 -#> k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03 -#> 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 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.600000 NA NA NA NA +#> k_parent 0.098700 NA NA NA NA +#> k_m1 0.005261 NA NA NA NA +#> f_parent_to_m1 0.514500 NA NA NA NA +#> sigma 3.126000 NA NA NA NA #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df @@ -665,10 +652,10 @@ Per default, parameters in the kinetic models are internally transformed in #> 100 m1 31.04 31.98163 -9.416e-01 #> 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 +#> 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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</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: Fri May 3 19:07:37 2019 -#> Date of summary: Fri May 3 19:07:37 2019 +#> Date of fit: Tue May 7 08:08:32 2019 +#> Date of summary: Tue May 7 08:08:32 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -676,7 +663,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 756 model solutions performed in 1.973 s +#> Fitted using 426 model solutions performed in 1.139 s #> #> Error model: #> Variance unique to each observed variable @@ -704,41 +691,27 @@ Per default, parameters in the kinetic models are internally transformed in #> m1_0 0 state #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.65000 1.70200 96.19000 103.1000 -#> log_k_parent -2.31300 0.04376 -2.40200 -2.2240 -#> log_k_m1 -5.25000 0.12430 -5.50400 -4.9970 -#> f_parent_ilr_1 0.03861 0.06171 -0.08708 0.1643 -#> sigma_parent 3.40100 0.56820 2.24400 4.5590 -#> sigma_m1 2.85500 0.45240 1.93400 3.7770 +#> Estimate Std. Error Lower Upper +#> parent_0 99.65000 NA NA NA +#> log_k_parent -2.31300 NA NA NA +#> log_k_m1 -5.25000 NA NA NA +#> f_parent_ilr_1 0.03861 NA NA NA +#> sigma_parent 3.40100 NA NA NA +#> sigma_m1 2.85500 NA NA NA #> #> 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 0.035685 -#> 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 -0.066264 -#> log_k_m1 0.024822 -#> f_parent_ilr_1 0.039254 -#> sigma_parent -0.004628 -#> sigma_m1 1.000000 -#> +#> No covariance matrix #> 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 99.650000 58.560 2.004e-34 96.190000 1.031e+02 -#> k_parent 0.098970 22.850 1.099e-21 0.090530 1.082e-01 -#> k_m1 0.005245 8.046 1.732e-09 0.004072 6.756e-03 -#> f_parent_to_m1 0.513600 23.560 4.352e-22 0.469300 5.578e-01 -#> 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 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.650000 NA NA NA NA +#> k_parent 0.098970 NA NA NA NA +#> k_m1 0.005245 NA NA NA NA +#> f_parent_to_m1 0.513600 NA NA NA NA +#> sigma_parent 3.401000 NA NA NA NA +#> sigma_m1 2.855000 NA NA NA NA #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df @@ -758,47 +731,47 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Data: #> time variable observed predicted residual -#> 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 +#> 0 parent 99.46 99.65417 -1.942e-01 +#> 0 parent 102.04 99.65417 2.386e+00 +#> 1 parent 93.50 90.26332 3.237e+00 +#> 1 parent 92.50 90.26332 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 #> 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 25.06848 -2.098e+00 -#> 7 m1 24.47 25.06848 -5.985e-01 +#> 3 m1 12.91 13.04196 -1.320e-01 +#> 3 m1 12.96 13.04196 -8.196e-02 +#> 7 m1 22.97 25.06847 -2.098e+00 +#> 7 m1 24.47 25.06847 -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 43.29464 -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 +#> 35 m1 41.22 43.29465 -2.075e+00 +#> 35 m1 37.95 43.29465 -5.345e+00 +#> 50 m1 41.19 41.19948 -9.481e-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 #> 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'>#> <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 +#> 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: Could not calculate correlation; no covariance matrix</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: Fri May 3 19:07:40 2019 -#> Date of summary: Fri May 3 19:07:40 2019 +#> Date of fit: Tue May 7 08:08:34 2019 +#> Date of summary: Tue May 7 08:08:34 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -806,7 +779,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 888 model solutions performed in 3.579 s +#> Fitted using 489 model solutions performed in 2.013 s #> #> Error model: #> Two-component variance function @@ -834,98 +807,84 @@ Per default, parameters in the kinetic models are internally transformed in #> m1_0 0 state #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> 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 +#> Estimate Std. Error Lower Upper +#> parent_0 100.70000 NA NA NA +#> log_k_parent -2.29700 NA NA NA +#> log_k_m1 -5.26600 NA NA NA +#> f_parent_ilr_1 0.02374 NA NA NA +#> sigma_low 0.00305 NA NA NA +#> rsd_high 0.07928 NA NA NA #> #> Parameter correlation: -#> 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 -#> +#> No covariance matrix #> 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 1.003e+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 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 1.007e+02 NA NA NA NA +#> k_parent 1.006e-01 NA NA NA NA +#> k_m1 5.167e-03 NA NA NA NA +#> f_parent_to_m1 5.084e-01 NA NA NA NA +#> sigma_low 3.050e-03 NA NA NA NA +#> rsd_high 7.928e-02 NA NA NA NA #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df -#> All data 6.433 4 15 -#> parent 6.506 2 7 -#> m1 4.692 2 8 +#> All data 6.475 4 15 +#> parent 6.573 2 7 +#> m1 4.671 2 8 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.5075 -#> parent_sink 0.4925 +#> parent_m1 0.5084 +#> parent_sink 0.4916 #> #> Estimated disappearance times: -#> DT50 DT90 -#> parent 6.992 23.23 -#> m1 135.787 451.08 +#> DT50 DT90 +#> parent 6.893 22.9 +#> m1 134.156 445.7 #> #> Data: #> time variable observed predicted residual -#> 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'> +#> 0 parent 99.46 100.73433 -1.274329 +#> 0 parent 102.04 100.73433 1.305671 +#> 1 parent 93.50 91.09750 2.402495 +#> 1 parent 92.50 91.09750 1.402495 +#> 3 parent 63.23 74.50140 -11.271403 +#> 3 parent 68.99 74.50140 -5.511403 +#> 7 parent 52.32 49.82880 2.491205 +#> 7 parent 55.13 49.82880 5.301205 +#> 14 parent 27.27 24.64809 2.621909 +#> 14 parent 26.64 24.64809 1.991909 +#> 21 parent 11.50 12.19231 -0.692315 +#> 21 parent 11.64 12.19231 -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 -0.318668 +#> 3 m1 12.96 13.22867 -0.268668 +#> 7 m1 22.97 25.36416 -2.394164 +#> 7 m1 24.47 25.36416 -0.894164 +#> 14 m1 41.69 37.00974 4.680265 +#> 14 m1 33.21 37.00974 -3.799735 +#> 21 m1 44.37 41.90133 2.468670 +#> 21 m1 46.44 41.90133 4.538670 +#> 35 m1 41.22 43.45691 -2.236914 +#> 35 m1 37.95 43.45691 -5.506914 +#> 50 m1 41.19 41.34199 -0.151988 +#> 50 m1 40.01 41.34199 -1.331988 +#> 75 m1 40.09 36.61471 3.475290 +#> 75 m1 33.85 36.61471 -2.764710 +#> 100 m1 31.04 32.20083 -1.160830 +#> 100 m1 33.13 32.20083 0.929170 +#> 120 m1 25.15 29.04131 -3.891312 +#> 120 m1 33.31 29.04131 4.268688</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 9ba463e3..9f417cf3 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 file2b304be466d0.c 2> file2b304be466d0.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file6d1314eef3d7.c 2> file6d1314eef3d7.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 65918d53..d4e465d4 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 8cfb9374..05af0f15 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -154,7 +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='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='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</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 074ac3ac..8c5c50e4 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -333,12 +333,12 @@ <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 0.001 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( +#> 0.001 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 -#> 0.022 0.000 0.021 </div><div class='input'> +#> 0.021 0.000 0.022 </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'>#> <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 @@ -368,9 +368,7 @@ #> 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 +#> Negative log-likelihood at call 75: 26.64668</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></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 1.179955 #> 3 0.2 77.59404 2.312580 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index c730ecb0..849e619e 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 -#> 0.042 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'> +#> 0.039 0.031 3.113 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 10.445 0.001 10.456 </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 0.7505684 0.2494316 diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index a9ee2f76..62027fab 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -182,7 +182,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'>nafta</span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#> Sums of squares: + <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'>nafta</span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#> Sums of squares: #> SFO IORE DFOP #> 1378.6832 615.7730 517.8836 #> @@ -191,25 +191,25 @@ #> #> Parameters: #> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.7558 1.80e-14 77.18268 90.3288 -#> k_parent_sink 0.0017 7.43e-05 0.00112 0.0026 -#> sigma 8.7518 1.22e-05 5.64278 11.8608 +#> Estimate Pr(>t) Lower Upper +#> parent_0 83.7558 NA NA NA +#> k_parent_sink 0.0017 NA NA NA +#> sigma 8.7518 NA NA NA #> #> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.69e+01 NA 8.88e+01 1.05e+02 -#> k__iore_parent_sink 8.40e-14 NA 1.79e-18 3.94e-09 -#> N_parent 6.68e+00 NA 4.19e+00 9.17e+00 -#> sigma 5.85e+00 NA 3.76e+00 7.94e+00 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.69e+01 NA NA NA +#> k__iore_parent_sink 8.40e-14 NA NA NA +#> N_parent 6.68e+00 NA NA NA +#> sigma 5.85e+00 NA NA NA #> #> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02 -#> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02 -#> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03 -#> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01 -#> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.76e+01 NA NA NA +#> k1 4.24e-02 NA NA NA +#> k2 8.24e-04 NA NA NA +#> g 2.88e-01 NA NA NA +#> sigma 5.36e+00 NA NA NA #> #> #> DTx values: diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 351d7a7e..a4f3d04f 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -209,17 +209,17 @@ <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 + <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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</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: Fri May 3 19:08:31 2019 -#> Date of summary: Fri May 3 19:08:31 2019 +#> Date of fit: Tue May 7 08:09:03 2019 +#> Date of summary: Tue May 7 08:09:03 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.27 s +#> Fitted using 39 model solutions performed in 0.08 s #> #> Error model: #> Constant variance @@ -240,25 +240,21 @@ #> None #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 109.200 3.70400 99.630 118.700 -#> log_k_parent_sink -3.291 0.09176 -3.527 -3.055 -#> sigma 5.266 1.31600 1.882 8.649 +#> Estimate Std. Error Lower Upper +#> parent_0 109.200 NA NA NA +#> log_k_parent_sink -3.291 NA NA NA +#> sigma 5.266 NA NA NA #> #> Parameter correlation: -#> parent_0 log_k_parent_sink sigma -#> 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 -#> +#> No covariance matrix #> 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_0 109.20000 29.47 4.218e-07 99.6300 118.70000 -#> 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 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 109.20000 NA NA NA NA +#> k_parent_sink 0.03722 NA NA NA NA +#> sigma 5.26600 NA NA NA NA #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index bc988340..11cb6420 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -159,20 +159,13 @@ <span class='co'># model).</span> <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>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) -#> parent_w_0 9.598567e+01 2.12351789 4.520126e+01 9.476190e-18 -#> k_parent_w_sink 3.603743e-01 0.03149282 1.144306e+01 4.126593e-09 -#> k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04 -#> k_parent_s_sink 5.108964e-11 0.09482736 5.387647e-10 5.000000e-01 -#> k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01 -#> sigma 2.982879e+00 0.50545649 5.901356e+00 1.454535e-05 -#> Lower Upper -#> parent_w_0 91.48420503 100.4871438 -#> k_parent_w_sink 0.30668904 0.4234571 -#> k_parent_w_parent_s 0.03423904 0.1062455 -#> k_parent_s_sink 0.00000000 Inf -#> k_parent_s_parent_w 0.02289956 0.2404043 -#> sigma 2.00184022 3.9639169</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> err.min n.optim df + <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_w_0 9.598567e+01 NA NA NA NA NA +#> k_parent_w_sink 3.603743e-01 NA NA NA NA NA +#> k_parent_w_parent_s 6.031371e-02 NA NA NA NA NA +#> k_parent_s_sink 5.108964e-11 NA NA NA NA NA +#> k_parent_s_parent_w 7.419672e-02 NA NA NA NA NA +#> sigma 2.982879e+00 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.09246946 5 6 #> parent_w 0.06377096 3 3 #> parent_s 0.20882325 2 3</div><div class='input'> @@ -183,28 +176,17 @@ <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>), <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 0.859186619 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 0.240803555 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 6.23641265 -#> k_M2 0.09843279 -#> k_M3 0.04333950 -#> f_parent_to_M1 NA -#> f_parent_to_M2 NA -#> 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 + <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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 76.55425584 NA NA NA NA NA +#> k_parent 0.12081956 NA NA NA NA NA +#> k_M1 0.84258649 NA NA NA NA NA +#> k_M2 0.04210878 NA NA NA NA NA +#> k_M3 0.01122919 NA NA NA NA NA +#> f_parent_to_M1 0.32240199 NA NA NA NA NA +#> f_parent_to_M2 0.16099854 NA NA NA NA NA +#> f_M1_to_M3 0.27921501 NA NA NA NA NA +#> f_M2_to_M3 0.55641331 NA NA NA NA NA +#> sigma 1.14005399 NA NA NA NA NA</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 #> parent 0.04721283 2 6 #> M1 0.26551209 2 5 diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 7e05480e..c91565b9 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -202,32 +202,30 @@ The transformation of sets of formation fractions is fragile, as it supposes <pre class="examples"><div class='input'><span class='no'>SFO_SFO</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='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'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>m1</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'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</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'>fit.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>) -<span class='co'># Transformed and backtransformed parameters</span> -<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.60 1.5702 96.40 102.79 -#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 -#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 -#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 -#> sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</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'>SFO_SFO</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='no'>fit.s</span> <span class='kw'><-</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'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='input'><span class='co'># Transformed and backtransformed parameters</span> +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.60 NA NA NA +#> log_k_parent_sink -3.04 NA NA NA +#> log_k_parent_m1 -2.98 NA NA NA +#> log_k_m1_sink -5.25 NA NA NA +#> sigma 3.13 NA NA NA</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 NA NA NA NA NA +#> k_parent_sink 0.04792 NA NA NA NA NA +#> k_parent_m1 0.05078 NA NA NA NA NA +#> k_m1_sink 0.00526 NA NA NA NA NA +#> sigma 3.12550 NA NA NA NA NA</div><div class='input'> </div><div class='input'><span class='co'># Compare to the version without transforming rate parameters</span> -<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</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'>fit.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>) -<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.59848 1.57022 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'> +<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</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'>fit.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.59848 NA NA NA +#> k_parent_sink 0.04792 NA NA NA +#> k_parent_m1 0.05078 NA NA NA +#> k_m1_sink 0.00526 NA NA NA +#> sigma 3.12550 NA NA NA</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 NA NA NA NA NA +#> k_parent_sink 0.04792 NA NA NA NA NA +#> k_parent_m1 0.05078 NA NA NA NA NA +#> k_m1_sink 0.00526 NA NA NA NA NA +#> sigma 3.12550 NA NA NA NA NA</div><div class='input'> <span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>) <span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span> @@ -240,18 +238,17 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.ff.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>) -<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.598 1.5702 96.4038 102.793 -#> log_k_parent -2.316 0.0409 -2.3988 -2.233 -#> log_k_m1 -5.248 0.1332 -5.5184 -4.977 -#> f_parent_ilr_1 0.041 0.0631 -0.0875 0.169 -#> sigma 3.126 0.3585 2.3961 3.855</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 -#> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 -#> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) +<span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.ff.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>)</div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.598 NA NA NA +#> log_k_parent -2.316 NA NA NA +#> log_k_m1 -5.248 NA NA NA +#> f_parent_ilr_1 0.041 NA NA NA +#> sigma 3.126 NA NA NA</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 NA NA NA NA NA +#> k_parent 0.09870 NA NA NA NA NA +#> k_m1 0.00526 NA NA NA NA NA +#> f_parent_to_m1 0.51448 NA NA NA NA NA +#> sigma 3.12550 NA NA NA NA NA</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) <span class='no'>transformed</span> <span class='kw'><-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>) <span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#> f_parent_to_m1 #> 0.5 </div><div class='input'> @@ -261,16 +258,15 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>m1</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'> -<span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</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'>fit.ff.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>) -<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 84.79 3.012 78.67 90.91 -#> log_k_parent -2.76 0.082 -2.92 -2.59 -#> log_k_m1 -4.21 0.123 -4.46 -3.96 -#> sigma 8.22 0.943 6.31 10.14</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913 -#> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075 -#> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019 -#> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div></pre> +<span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.ff.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>)</div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 84.79 NA NA NA +#> log_k_parent -2.76 NA NA NA +#> log_k_m1 -4.21 NA NA NA +#> sigma 8.22 NA NA NA</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>fit.ff.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 84.7916 NA NA NA NA NA +#> k_parent 0.0635 NA NA NA NA NA +#> k_m1 0.0148 NA NA NA NA NA +#> sigma 8.2229 NA NA NA NA NA</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |
