diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-03 19:14:15 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-03 19:14:15 +0200 |
| commit | 1ef7008be2a72a0847064ad9c2ddcfa16b055482 (patch) | |
| tree | ecc3f90e5d18c75aea14ad774aad9214039c0674 /docs/reference/mkinfit.html | |
| parent | de7b6acdd75a0f95f2a9522c22625810f4aa329a (diff) | |
Improve error model fitting
Now we have a three stage fitting process for
nonconstant error models:
- Unweighted least squares
- Only optimize the error model
- Optimize both
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 402 |
1 files changed, 203 insertions, 199 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 545ed8ab..8c14fc9d 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -362,15 +362,15 @@ Per default, parameters in the kinetic models are internally transformed in <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Thu May 2 18:47:43 2019 -#> Date of summary: Thu May 2 18:47:43 2019 +#> Date of fit: Fri May 3 19:07:19 2019 +#> Date of summary: Fri May 3 19:07:19 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 221 model solutions performed in 0.458 s +#> Fitted using 222 model solutions performed in 0.463 s #> #> Error model: #> Constant variance @@ -400,11 +400,11 @@ Per default, parameters in the kinetic models are internally transformed in #> sigma 1.85700 0.4378 0.73200 2.9830 #> #> Parameter correlation: -#> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 -1.317e-07 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 -2.640e-07 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 -2.205e-07 -#> sigma -1.317e-07 -2.640e-07 -2.205e-07 1.000e+00 +#> parent_0 log_alpha log_beta sigma +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08 +#> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -443,7 +443,7 @@ Per default, parameters in the kinetic models are internally transformed in <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 1.524 0.000 1.525 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> 1.493 0.000 1.494 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -452,75 +452,72 @@ Per default, parameters in the kinetic models are internally transformed in #> #> $distimes #> DT50 DT90 -#> parent 7.022928 23.32966 -#> m1 131.760715 437.69962 +#> parent 7.022929 23.32967 +#> m1 131.760712 437.69961 #> </div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> Sum of squared residuals at call 1: 18915.53 + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 18915.53 #> Sum of squared residuals at call 2: 18915.53 #> Sum of squared residuals at call 6: 11424.02 #> Sum of squared residuals at call 10: 11424 -#> Sum of squared residuals at call 13: 2367.052 -#> Sum of squared residuals at call 14: 2367.05 -#> Sum of squared residuals at call 19: 1314.716 -#> Sum of squared residuals at call 22: 1314.714 -#> Sum of squared residuals at call 25: 991.8311 -#> Sum of squared residuals at call 28: 991.8305 -#> Sum of squared residuals at call 30: 893.6462 -#> Sum of squared residuals at call 33: 893.6457 -#> Sum of squared residuals at call 35: 569.4049 -#> Sum of squared residuals at call 38: 569.4047 -#> Sum of squared residuals at call 40: 565.0651 -#> Sum of squared residuals at call 41: 565.065 -#> Sum of squared residuals at call 42: 565.0637 -#> Sum of squared residuals at call 45: 428.0188 -#> Sum of squared residuals at call 46: 428.0185 -#> Sum of squared residuals at call 50: 406.732 -#> Sum of squared residuals at call 52: 406.732 -#> Sum of squared residuals at call 55: 398.9115 -#> Sum of squared residuals at call 57: 398.9113 -#> Sum of squared residuals at call 60: 394.5943 -#> Sum of squared residuals at call 62: 394.5943 -#> Sum of squared residuals at call 66: 385.26 -#> Sum of squared residuals at call 67: 385.2599 -#> Sum of squared residuals at call 69: 385.2599 -#> Sum of squared residuals at call 70: 385.2597 -#> Sum of squared residuals at call 71: 374.7604 -#> Sum of squared residuals at call 72: 374.7603 -#> Sum of squared residuals at call 76: 373.199 -#> Sum of squared residuals at call 79: 373.199 -#> Sum of squared residuals at call 80: 373.199 -#> Sum of squared residuals at call 81: 372.3772 -#> Sum of squared residuals at call 84: 372.3772 -#> Sum of squared residuals at call 86: 371.2615 -#> Sum of squared residuals at call 89: 371.2615 -#> Sum of squared residuals at call 90: 371.2615 -#> Sum of squared residuals at call 92: 371.2439 -#> Sum of squared residuals at call 93: 371.2439 -#> Sum of squared residuals at call 94: 371.2439 -#> Sum of squared residuals at call 97: 371.2198 -#> Sum of squared residuals at call 98: 371.2198 -#> Sum of squared residuals at call 102: 371.2174 -#> Sum of squared residuals at call 104: 371.2174 -#> Sum of squared residuals at call 107: 371.2147 -#> Sum of squared residuals at call 110: 371.2147 -#> Sum of squared residuals at call 111: 371.2147 -#> Sum of squared residuals at call 112: 371.2145 -#> Sum of squared residuals at call 113: 371.2145 -#> Sum of squared residuals at call 116: 371.2145 -#> Sum of squared residuals at call 119: 371.2135 -#> Sum of squared residuals at call 121: 371.2135 -#> Sum of squared residuals at call 124: 371.2135 -#> Sum of squared residuals at call 126: 371.2135 -#> Sum of squared residuals at call 127: 371.2135 -#> Sum of squared residuals at call 133: 371.2134 +#> Sum of squared residuals at call 12: 4094.396 +#> Sum of squared residuals at call 16: 4094.396 +#> Sum of squared residuals at call 19: 1340.595 +#> Sum of squared residuals at call 20: 1340.593 +#> Sum of squared residuals at call 25: 1072.239 +#> Sum of squared residuals at call 28: 1072.236 +#> Sum of squared residuals at call 30: 874.2615 +#> Sum of squared residuals at call 33: 874.2611 +#> Sum of squared residuals at call 35: 616.2375 +#> Sum of squared residuals at call 37: 616.237 +#> Sum of squared residuals at call 40: 467.4386 +#> Sum of squared residuals at call 42: 467.438 +#> Sum of squared residuals at call 46: 398.2913 +#> Sum of squared residuals at call 48: 398.2913 +#> Sum of squared residuals at call 49: 398.2912 +#> Sum of squared residuals at call 51: 395.0711 +#> Sum of squared residuals at call 54: 395.071 +#> Sum of squared residuals at call 56: 378.3298 +#> Sum of squared residuals at call 59: 378.3298 +#> Sum of squared residuals at call 62: 376.9812 +#> Sum of squared residuals at call 64: 376.9811 +#> Sum of squared residuals at call 67: 375.2085 +#> Sum of squared residuals at call 69: 375.2085 +#> Sum of squared residuals at call 70: 375.2085 +#> Sum of squared residuals at call 71: 375.2085 +#> Sum of squared residuals at call 72: 374.5723 +#> Sum of squared residuals at call 74: 374.5723 +#> Sum of squared residuals at call 77: 374.0075 +#> Sum of squared residuals at call 79: 374.0075 +#> Sum of squared residuals at call 80: 374.0075 +#> Sum of squared residuals at call 82: 373.1711 +#> Sum of squared residuals at call 84: 373.1711 +#> Sum of squared residuals at call 87: 372.6445 +#> Sum of squared residuals at call 88: 372.1615 +#> Sum of squared residuals at call 90: 372.1615 +#> Sum of squared residuals at call 91: 372.1615 +#> Sum of squared residuals at call 94: 371.6464 +#> Sum of squared residuals at call 99: 371.4299 +#> Sum of squared residuals at call 101: 371.4299 +#> Sum of squared residuals at call 104: 371.4071 +#> Sum of squared residuals at call 106: 371.4071 +#> Sum of squared residuals at call 107: 371.4071 +#> Sum of squared residuals at call 109: 371.2524 +#> Sum of squared residuals at call 113: 371.2524 +#> Sum of squared residuals at call 114: 371.2136 +#> Sum of squared residuals at call 115: 371.2136 +#> Sum of squared residuals at call 116: 371.2136 +#> Sum of squared residuals at call 119: 371.2134 +#> Sum of squared residuals at call 120: 371.2134 +#> Sum of squared residuals at call 122: 371.2134 +#> Sum of squared residuals at call 123: 371.2134 +#> Sum of squared residuals at call 125: 371.2134 +#> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 -#> Sum of squared residuals at call 138: 371.2134 -#> Sum of squared residuals at call 142: 371.2134 -#> Negative log-likelihood at call 152: 97.22429 +#> Negative log-likelihood at call 145: 97.22429 #> Optimisation successfully terminated. #> User System verstrichen -#> 1.095 0.000 1.096 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff +#> 1.082 0.000 1.083 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -529,8 +526,8 @@ Per default, parameters in the kinetic models are internally transformed in #> #> $distimes #> DT50 DT90 -#> parent 7.022928 23.32966 -#> m1 131.760710 437.69961 +#> parent 7.022929 23.32967 +#> m1 131.760712 437.69961 #> </div><div class='input'> # Use stepwise fitting, using optimised parameters from parent only fit, FOMC </div><div class='input'><span class='no'>FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( @@ -552,8 +549,8 @@ Per default, parameters in the kinetic models are internally transformed in <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Thu May 2 18:47:59 2019 -#> Date of summary: Thu May 2 18:47:59 2019 +#> Date of fit: Fri May 3 19:07:35 2019 +#> Date of summary: Fri May 3 19:07:35 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -561,7 +558,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 404 model solutions performed in 1.047 s +#> Fitted using 421 model solutions performed in 1.099 s #> #> Error model: #> Constant variance @@ -596,11 +593,11 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Parameter correlation: #> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma -#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -5.940e-09 -#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -1.406e-08 -#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -2.306e-08 -#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -6.664e-09 -#> sigma -5.940e-09 -1.406e-08 -2.306e-08 -6.664e-09 1.000e+00 +#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -2.265e-07 +#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.785e-07 +#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.386e-07 +#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -3.641e-08 +#> sigma -2.265e-07 3.785e-07 -1.386e-07 -3.641e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -635,10 +632,10 @@ Per default, parameters in the kinetic models are internally transformed in #> 0 parent 102.04 99.59848 2.442e+00 #> 1 parent 93.50 90.23787 3.262e+00 #> 1 parent 92.50 90.23787 2.262e+00 -#> 3 parent 63.23 74.07320 -1.084e+01 -#> 3 parent 68.99 74.07320 -5.083e+00 -#> 7 parent 52.32 49.91207 2.408e+00 -#> 7 parent 55.13 49.91207 5.218e+00 +#> 3 parent 63.23 74.07319 -1.084e+01 +#> 3 parent 68.99 74.07319 -5.083e+00 +#> 7 parent 52.32 49.91206 2.408e+00 +#> 7 parent 55.13 49.91206 5.218e+00 #> 14 parent 27.27 25.01257 2.257e+00 #> 14 parent 26.64 25.01257 1.627e+00 #> 21 parent 11.50 12.53462 -1.035e+00 @@ -648,7 +645,7 @@ Per default, parameters in the kinetic models are internally transformed in #> 50 parent 0.69 0.71624 -2.624e-02 #> 50 parent 0.63 0.71624 -8.624e-02 #> 75 parent 0.05 0.06074 -1.074e-02 -#> 75 parent 0.06 0.06074 -7.382e-04 +#> 75 parent 0.06 0.06074 -7.381e-04 #> 1 m1 4.84 4.80296 3.704e-02 #> 1 m1 5.64 4.80296 8.370e-01 #> 3 m1 12.91 13.02400 -1.140e-01 @@ -670,8 +667,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Thu May 2 18:48:00 2019 -#> Date of summary: Thu May 2 18:48:00 2019 +#> Date of fit: Fri May 3 19:07:37 2019 +#> Date of summary: Fri May 3 19:07:37 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -679,7 +676,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 558 model solutions performed in 1.45 s +#> Fitted using 756 model solutions performed in 1.973 s #> #> Error model: #> Variance unique to each observed variable @@ -717,17 +714,17 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Parameter correlation: #> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_parent -#> parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035671 -#> log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069834 -#> log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026158 -#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041369 -#> sigma_parent 0.03567 0.06983 -0.02616 -0.04137 1.000000 -#> sigma_m1 -0.03385 -0.06627 0.02482 0.03926 -0.004628 +#> parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035685 +#> log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069840 +#> log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026160 +#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041377 +#> sigma_parent 0.03569 0.06984 -0.02616 -0.04138 1.000000 +#> sigma_m1 -0.03385 -0.06626 0.02482 0.03925 -0.004628 #> sigma_m1 #> parent_0 -0.033847 -#> log_k_parent -0.066265 +#> log_k_parent -0.066264 #> log_k_m1 0.024822 -#> f_parent_ilr_1 0.039256 +#> f_parent_ilr_1 0.039254 #> sigma_parent -0.004628 #> sigma_m1 1.000000 #> @@ -761,47 +758,47 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Data: #> time variable observed predicted residual -#> 0 parent 99.46 99.65417 -1.942e-01 -#> 0 parent 102.04 99.65417 2.386e+00 -#> 1 parent 93.50 90.26333 3.237e+00 -#> 1 parent 92.50 90.26333 2.237e+00 -#> 3 parent 63.23 74.05306 -1.082e+01 -#> 3 parent 68.99 74.05306 -5.063e+00 -#> 7 parent 52.32 49.84325 2.477e+00 -#> 7 parent 55.13 49.84325 5.287e+00 -#> 14 parent 27.27 24.92971 2.340e+00 -#> 14 parent 26.64 24.92971 1.710e+00 -#> 21 parent 11.50 12.46890 -9.689e-01 -#> 21 parent 11.64 12.46890 -8.289e-01 -#> 35 parent 2.85 3.11925 -2.692e-01 -#> 35 parent 2.91 3.11925 -2.092e-01 -#> 50 parent 0.69 0.70679 -1.679e-02 -#> 50 parent 0.63 0.70679 -7.679e-02 -#> 75 parent 0.05 0.05952 -9.523e-03 -#> 75 parent 0.06 0.05952 4.772e-04 +#> 0 parent 99.46 99.65425 -1.942e-01 +#> 0 parent 102.04 99.65425 2.386e+00 +#> 1 parent 93.50 90.26338 3.237e+00 +#> 1 parent 92.50 90.26338 2.237e+00 +#> 3 parent 63.23 74.05309 -1.082e+01 +#> 3 parent 68.99 74.05309 -5.063e+00 +#> 7 parent 52.32 49.84326 2.477e+00 +#> 7 parent 55.13 49.84326 5.287e+00 +#> 14 parent 27.27 24.92970 2.340e+00 +#> 14 parent 26.64 24.92970 1.710e+00 +#> 21 parent 11.50 12.46888 -9.689e-01 +#> 21 parent 11.64 12.46888 -8.289e-01 +#> 35 parent 2.85 3.11924 -2.692e-01 +#> 35 parent 2.91 3.11924 -2.092e-01 +#> 50 parent 0.69 0.70678 -1.678e-02 +#> 50 parent 0.63 0.70678 -7.678e-02 +#> 75 parent 0.05 0.05952 -9.522e-03 +#> 75 parent 0.06 0.05952 4.776e-04 #> 1 m1 4.84 4.81075 2.925e-02 #> 1 m1 5.64 4.81075 8.292e-01 #> 3 m1 12.91 13.04197 -1.320e-01 #> 3 m1 12.96 13.04197 -8.197e-02 -#> 7 m1 22.97 25.06847 -2.098e+00 -#> 7 m1 24.47 25.06847 -5.985e-01 +#> 7 m1 22.97 25.06848 -2.098e+00 +#> 7 m1 24.47 25.06848 -5.985e-01 #> 14 m1 41.69 36.70308 4.987e+00 #> 14 m1 33.21 36.70308 -3.493e+00 #> 21 m1 44.37 41.65115 2.719e+00 #> 21 m1 46.44 41.65115 4.789e+00 -#> 35 m1 41.22 43.29465 -2.075e+00 -#> 35 m1 37.95 43.29465 -5.345e+00 -#> 50 m1 41.19 41.19948 -9.482e-03 -#> 50 m1 40.01 41.19948 -1.189e+00 -#> 75 m1 40.09 36.44036 3.650e+00 -#> 75 m1 33.85 36.44036 -2.590e+00 -#> 100 m1 31.04 31.98774 -9.477e-01 -#> 100 m1 33.13 31.98774 1.142e+00 +#> 35 m1 41.22 43.29464 -2.075e+00 +#> 35 m1 37.95 43.29464 -5.345e+00 +#> 50 m1 41.19 41.19947 -9.473e-03 +#> 50 m1 40.01 41.19947 -1.189e+00 +#> 75 m1 40.09 36.44035 3.650e+00 +#> 75 m1 33.85 36.44035 -2.590e+00 +#> 100 m1 31.04 31.98773 -9.477e-01 +#> 100 m1 33.13 31.98773 1.142e+00 #> 120 m1 25.15 28.80430 -3.654e+00 -#> 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 +#> 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Thu May 2 18:48:04 2019 -#> Date of summary: Thu May 2 18:48:04 2019 +#> Date of fit: Fri May 3 19:07:40 2019 +#> Date of summary: Fri May 3 19:07:40 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -809,7 +806,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 844 model solutions performed in 3.407 s +#> Fitted using 888 model solutions performed in 3.579 s #> #> Error model: #> Two-component variance function @@ -820,8 +817,8 @@ Per default, parameters in the kinetic models are internally transformed in #> k_parent 0.1000 deparm #> k_m1 0.1001 deparm #> f_parent_to_m1 0.5000 deparm -#> sigma_low 3.0000 error -#> rsd_high 0.0100 error +#> sigma_low 0.1000 error +#> rsd_high 0.1000 error #> #> Starting values for the transformed parameters actually optimised: #> value lower upper @@ -829,99 +826,106 @@ Per default, parameters in the kinetic models are internally transformed in #> log_k_parent -2.302585 -Inf Inf #> log_k_m1 -2.301586 -Inf Inf #> f_parent_ilr_1 0.000000 -Inf Inf -#> sigma_low 3.000000 0 Inf -#> rsd_high 0.010000 0 Inf +#> sigma_low 0.100000 0 Inf +#> rsd_high 0.100000 0 Inf #> #> Fixed parameter values: #> value type #> m1_0 0 state #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 100.70000 2.621000 95.400000 106.10000 -#> log_k_parent -2.29700 0.008862 -2.315000 -2.27900 -#> log_k_m1 -5.26600 0.091310 -5.452000 -5.08000 -#> f_parent_ilr_1 0.02374 0.055300 -0.088900 0.13640 -#> sigma_low 0.00305 0.004829 -0.006786 0.01289 -#> rsd_high 0.07928 0.009418 0.060100 0.09847 +#> Estimate Std. Error Lower Upper +#> parent_0 100.30000 3.06400 94.08000 106.60000 +#> log_k_parent -2.31100 0.02913 -2.37100 -2.25200 +#> log_k_m1 -5.27800 0.10890 -5.49900 -5.05600 +#> f_parent_ilr_1 0.02128 0.07223 -0.12590 0.16840 +#> sigma_low 0.99650 NaN NaN NaN +#> rsd_high 0.07560 0.01059 0.05402 0.09717 #> #> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low rsd_high -#> parent_0 1.00000 0.67644 -0.10215 -0.76822 0.14294 -0.08783 -#> log_k_parent 0.67644 1.00000 -0.15102 -0.59491 0.34611 -0.08125 -#> log_k_m1 -0.10215 -0.15102 1.00000 0.51808 -0.05236 0.01240 -#> f_parent_ilr_1 -0.76822 -0.59491 0.51808 1.00000 -0.13900 0.03248 -#> sigma_low 0.14294 0.34611 -0.05236 -0.13900 1.00000 -0.16546 -#> rsd_high -0.08783 -0.08125 0.01240 0.03248 -0.16546 1.00000 +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low +#> parent_0 1.00000 0.64703 -0.220160 -0.79035 NaN +#> log_k_parent 0.64703 1.00000 -0.339633 -0.67982 NaN +#> log_k_m1 -0.22016 -0.33963 1.000000 0.62815 NaN +#> f_parent_ilr_1 -0.79035 -0.67982 0.628148 1.00000 NaN +#> sigma_low NaN NaN NaN NaN 1 +#> rsd_high -0.05745 -0.01123 0.003502 0.00568 NaN +#> rsd_high +#> parent_0 -0.057450 +#> log_k_parent -0.011230 +#> log_k_m1 0.003502 +#> f_parent_ilr_1 0.005680 +#> sigma_low NaN +#> rsd_high 1.000000 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 1.007e+02 38.4300 1.180e-28 95.400000 1.061e+02 -#> k_parent 1.006e-01 112.8000 1.718e-43 0.098760 1.024e-01 -#> k_m1 5.167e-03 10.9500 1.171e-12 0.004290 6.223e-03 -#> f_parent_to_m1 5.084e-01 26.0100 2.146e-23 0.468600 5.481e-01 -#> sigma_low 3.050e-03 0.6314 2.661e-01 -0.006786 1.289e-02 -#> rsd_high 7.928e-02 8.4170 6.418e-10 0.060100 9.847e-02 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 1.003e+02 32.740 1.759e-26 94.080000 1.066e+02 +#> k_parent 9.914e-02 34.330 4.045e-27 0.093430 1.052e-01 +#> k_m1 5.105e-03 9.186 8.682e-11 0.004089 6.372e-03 +#> f_parent_to_m1 5.075e-01 19.880 7.143e-20 0.455600 5.593e-01 +#> sigma_low 9.965e-01 NaN NaN NaN NaN +#> rsd_high 7.560e-02 7.137 2.114e-08 0.054020 9.717e-02 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df -#> All data 6.475 4 15 -#> parent 6.573 2 7 -#> m1 4.671 2 8 +#> All data 6.433 4 15 +#> parent 6.506 2 7 +#> m1 4.692 2 8 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.5084 -#> parent_sink 0.4916 +#> parent_m1 0.5075 +#> parent_sink 0.4925 #> #> Estimated disappearance times: -#> DT50 DT90 -#> parent 6.893 22.9 -#> m1 134.156 445.7 +#> DT50 DT90 +#> parent 6.992 23.23 +#> m1 135.787 451.08 #> #> Data: #> time variable observed predicted residual -#> 0 parent 99.46 100.73434 -1.274339 -#> 0 parent 102.04 100.73434 1.305661 -#> 1 parent 93.50 91.09751 2.402486 -#> 1 parent 92.50 91.09751 1.402486 -#> 3 parent 63.23 74.50141 -11.271410 -#> 3 parent 68.99 74.50141 -5.511410 -#> 7 parent 52.32 49.82880 2.491201 -#> 7 parent 55.13 49.82880 5.301201 -#> 14 parent 27.27 24.64809 2.621908 -#> 14 parent 26.64 24.64809 1.991908 -#> 21 parent 11.50 12.19232 -0.692315 -#> 21 parent 11.64 12.19232 -0.552315 -#> 35 parent 2.85 2.98327 -0.133266 -#> 35 parent 2.91 2.98327 -0.073266 -#> 50 parent 0.69 0.66013 0.029874 -#> 50 parent 0.63 0.66013 -0.030126 -#> 75 parent 0.05 0.05344 -0.003438 -#> 75 parent 0.06 0.05344 0.006562 -#> 1 m1 4.84 4.88645 -0.046451 -#> 1 m1 5.64 4.88645 0.753549 -#> 3 m1 12.91 13.22867 -0.318669 -#> 3 m1 12.96 13.22867 -0.268669 -#> 7 m1 22.97 25.36417 -2.394167 -#> 7 m1 24.47 25.36417 -0.894167 -#> 14 m1 41.69 37.00974 4.680263 -#> 14 m1 33.21 37.00974 -3.799737 -#> 21 m1 44.37 41.90133 2.468668 -#> 21 m1 46.44 41.90133 4.538668 -#> 35 m1 41.22 43.45691 -2.236914 -#> 35 m1 37.95 43.45691 -5.506914 -#> 50 m1 41.19 41.34199 -0.151986 -#> 50 m1 40.01 41.34199 -1.331986 -#> 75 m1 40.09 36.61471 3.475294 -#> 75 m1 33.85 36.61471 -2.764706 -#> 100 m1 31.04 32.20082 -1.160824 -#> 100 m1 33.13 32.20082 0.929176 -#> 120 m1 25.15 29.04130 -3.891305 -#> 120 m1 33.31 29.04130 4.268695</div><div class='input'> +#> 0 parent 99.46 100.32122 -0.861220 +#> 0 parent 102.04 100.32122 1.718780 +#> 1 parent 93.50 90.85266 2.647340 +#> 1 parent 92.50 90.85266 1.647340 +#> 3 parent 63.23 74.51219 -11.282190 +#> 3 parent 68.99 74.51219 -5.522190 +#> 7 parent 52.32 50.11950 2.200504 +#> 7 parent 55.13 50.11950 5.010504 +#> 14 parent 27.27 25.03921 2.230792 +#> 14 parent 26.64 25.03921 1.600792 +#> 21 parent 11.50 12.50934 -1.009342 +#> 21 parent 11.64 12.50934 -0.869342 +#> 35 parent 2.85 3.12221 -0.272211 +#> 35 parent 2.91 3.12221 -0.212211 +#> 50 parent 0.69 0.70572 -0.015724 +#> 50 parent 0.63 0.70572 -0.075724 +#> 75 parent 0.05 0.05919 -0.009191 +#> 75 parent 0.06 0.05919 0.000809 +#> 1 m1 4.84 4.79307 0.046928 +#> 1 m1 5.64 4.79307 0.846928 +#> 3 m1 12.91 12.99398 -0.083980 +#> 3 m1 12.96 12.99398 -0.033980 +#> 7 m1 22.97 24.97744 -2.007441 +#> 7 m1 24.47 24.97744 -0.507441 +#> 14 m1 41.69 36.57917 5.110827 +#> 14 m1 33.21 36.57917 -3.369173 +#> 21 m1 44.37 41.52931 2.840692 +#> 21 m1 46.44 41.52931 4.910692 +#> 35 m1 41.22 43.22614 -2.006138 +#> 35 m1 37.95 43.22614 -5.276138 +#> 50 m1 41.19 41.20972 -0.019717 +#> 50 m1 40.01 41.20972 -1.199717 +#> 75 m1 40.09 36.57312 3.516882 +#> 75 m1 33.85 36.57312 -2.723118 +#> 100 m1 31.04 32.21655 -1.176546 +#> 100 m1 33.13 32.21655 0.913454 +#> 120 m1 25.15 29.09181 -3.941814 +#> 120 m1 33.31 29.09181 4.218186</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |