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Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 339 |
1 files changed, 149 insertions, 190 deletions
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> 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