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Diffstat (limited to 'docs/dev/reference/summary.saem.mmkin.html')
| -rw-r--r-- | docs/dev/reference/summary.saem.mmkin.html | 270 |
1 files changed, 3 insertions, 267 deletions
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 722415fb..fe537320 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> </span> </div> @@ -259,272 +259,8 @@ saemix authors for the parts inherited from saemix.</p> <span class='va'>f_mmkin_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_syn_dfop_sfo</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span> <span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span> -</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:40 2021" -#> .... -#> Minimisation finished -#> [1] "Mon Jan 11 12:42:53 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 0.9.50.4 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Jan 11 12:42:54 2021 -#> Date of summary: Mon Jan 11 12:42:54 2021 -#> -#> Equations: -#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * -#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) -#> * parent -#> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) -#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * -#> exp(-k2 * time))) * parent - k_m1 * m1 -#> -#> Data: -#> 171 observations of 2 variable(s) grouped in 5 datasets -#> -#> Model predictions using solution type analytical -#> -#> Fitted in 13.298 s using 300, 100 iterations -#> -#> Variance model: Two-component variance function -#> -#> Mean of starting values for individual parameters: -#> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 -#> 101.65645 -4.05368 -0.94311 -2.35943 -4.07006 -#> g_qlogis -#> -0.01133 -#> -#> Fixed degradation parameter values: -#> None -#> -#> Results: -#> -#> Likelihood computed by importance sampling -#> AIC BIC logLik -#> 830 824.5 -401 -#> -#> Optimised parameters: -#> est. lower upper -#> parent_0 101.4423 97.862 105.0224 -#> log_k_m1 -4.0703 -4.191 -3.9495 -#> f_parent_qlogis -0.9539 -1.313 -0.5949 -#> log_k1 -2.9724 -3.811 -2.1342 -#> log_k2 -3.4977 -4.206 -2.7895 -#> g_qlogis -0.0449 -1.116 1.0262 -#> -#> Correlation: -#> prnt_0 lg_k_1 f_prn_ log_k1 log_k2 -#> log_k_m1 -0.207 -#> f_parent_qlogis -0.148 0.202 -#> log_k1 0.040 -0.038 -0.022 -#> log_k2 0.022 -0.015 -0.009 0.001 -#> g_qlogis -0.012 0.005 0.011 -0.173 -0.130 -#> -#> Random effects: -#> est. lower upper -#> SD.parent_0 2.88564 -0.5163 6.2876 -#> SD.log_k_m1 0.08502 -0.0427 0.2127 -#> SD.f_parent_qlogis 0.38857 0.1350 0.6421 -#> SD.log_k1 0.92338 0.3296 1.5172 -#> SD.log_k2 0.78644 0.2817 1.2912 -#> SD.g_qlogis 0.34614 -0.8727 1.5650 -#> -#> Variance model: -#> est. lower upper -#> a.1 0.65859 0.49250 0.82469 -#> b.1 0.06411 0.05006 0.07817 -#> -#> Backtransformed parameters: -#> est. lower upper -#> parent_0 101.44231 97.86220 105.02241 -#> k_m1 0.01707 0.01513 0.01926 -#> f_parent_to_m1 0.27811 0.21201 0.35551 -#> k1 0.05118 0.02213 0.11834 -#> k2 0.03027 0.01491 0.06145 -#> g 0.48878 0.24675 0.73618 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.2781 -#> parent_sink 0.7219 -#> -#> Estimated disappearance times: -#> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 17.53 61.64 18.55 13.54 22.9 -#> m1 40.60 134.88 NA NA NA -#> -#> Data: -#> ds name time observed predicted residual std standardized -#> ds 1 parent 0 89.8 9.869e+01 8.894553 6.3618 1.398124 -#> ds 1 parent 0 104.1 9.869e+01 -5.405447 6.3618 -0.849676 -#> ds 1 parent 1 88.7 9.413e+01 5.426448 6.0706 0.893897 -#> ds 1 parent 1 95.5 9.413e+01 -1.373552 6.0706 -0.226265 -#> ds 1 parent 3 81.8 8.576e+01 3.961821 5.5377 0.715422 -#> ds 1 parent 3 94.5 8.576e+01 -8.738179 5.5377 -1.577932 -#> ds 1 parent 7 71.5 7.168e+01 0.184828 4.6429 0.039809 -#> ds 1 parent 7 70.3 7.168e+01 1.384828 4.6429 0.298270 -#> ds 1 parent 14 54.2 5.351e+01 -0.688235 3.4934 -0.197008 -#> ds 1 parent 14 49.6 5.351e+01 3.911765 3.4934 1.119747 -#> ds 1 parent 28 31.5 3.209e+01 0.590445 2.1603 0.273322 -#> ds 1 parent 28 28.8 3.209e+01 3.290445 2.1603 1.523177 -#> ds 1 parent 60 12.1 1.272e+01 0.618158 1.0481 0.589761 -#> ds 1 parent 60 13.6 1.272e+01 -0.881842 1.0481 -0.841332 -#> ds 1 parent 90 6.2 6.085e+00 -0.115212 0.7655 -0.150512 -#> ds 1 parent 90 8.3 6.085e+00 -2.215212 0.7655 -2.893953 -#> ds 1 parent 120 2.2 3.009e+00 0.809439 0.6863 1.179470 -#> ds 1 parent 120 2.4 3.009e+00 0.609439 0.6863 0.888041 -#> ds 1 m1 1 0.3 1.129e+00 0.828817 0.6626 1.250938 -#> ds 1 m1 1 0.2 1.129e+00 0.928817 0.6626 1.401869 -#> ds 1 m1 3 2.2 3.141e+00 0.940880 0.6887 1.366187 -#> ds 1 m1 3 3.0 3.141e+00 0.140880 0.6887 0.204562 -#> ds 1 m1 7 6.5 6.326e+00 -0.174162 0.7735 -0.225175 -#> ds 1 m1 7 5.0 6.326e+00 1.325838 0.7735 1.714181 -#> ds 1 m1 14 10.2 9.883e+00 -0.317417 0.9139 -0.347326 -#> ds 1 m1 14 9.5 9.883e+00 0.382583 0.9139 0.418631 -#> ds 1 m1 28 12.2 1.251e+01 0.309856 1.0378 0.298572 -#> ds 1 m1 28 13.4 1.251e+01 -0.890144 1.0378 -0.857726 -#> ds 1 m1 60 11.8 1.086e+01 -0.940009 0.9584 -0.980812 -#> ds 1 m1 60 13.2 1.086e+01 -2.340009 0.9584 -2.441581 -#> ds 1 m1 90 6.6 7.823e+00 1.222977 0.8278 1.477332 -#> ds 1 m1 90 9.3 7.823e+00 -1.477023 0.8278 -1.784214 -#> ds 1 m1 120 3.5 5.315e+00 1.815201 0.7415 2.447906 -#> ds 1 m1 120 5.4 5.315e+00 -0.084799 0.7415 -0.114356 -#> ds 2 parent 0 118.0 1.031e+02 -14.876736 6.6443 -2.239038 -#> ds 2 parent 0 99.8 1.031e+02 3.323264 6.6443 0.500171 -#> ds 2 parent 1 90.2 9.757e+01 7.371379 6.2902 1.171891 -#> ds 2 parent 1 94.6 9.757e+01 2.971379 6.2902 0.472386 -#> ds 2 parent 3 96.1 8.788e+01 -8.222746 5.6724 -1.449599 -#> ds 2 parent 3 78.4 8.788e+01 9.477254 5.6724 1.670758 -#> ds 2 parent 7 77.9 7.293e+01 -4.972272 4.7218 -1.053054 -#> ds 2 parent 7 77.7 7.293e+01 -4.772272 4.7218 -1.010697 -#> ds 2 parent 14 56.0 5.602e+01 0.016773 3.6513 0.004594 -#> ds 2 parent 14 54.7 5.602e+01 1.316773 3.6513 0.360633 -#> ds 2 parent 28 36.6 3.855e+01 1.945779 2.5575 0.760803 -#> ds 2 parent 28 36.8 3.855e+01 1.745779 2.5575 0.682603 -#> ds 2 parent 60 22.1 2.101e+01 -1.086693 1.4996 -0.724663 -#> ds 2 parent 60 24.7 2.101e+01 -3.686693 1.4996 -2.458475 -#> ds 2 parent 90 12.4 1.246e+01 0.058759 1.0353 0.056757 -#> ds 2 parent 90 10.8 1.246e+01 1.658759 1.0353 1.602256 -#> ds 2 parent 120 6.8 7.406e+00 0.606226 0.8119 0.746659 -#> ds 2 parent 120 7.9 7.406e+00 -0.493774 0.8119 -0.608157 -#> ds 2 m1 1 1.3 1.438e+00 0.138236 0.6650 0.207869 -#> ds 2 m1 3 3.7 3.879e+00 0.178617 0.7040 0.253726 -#> ds 2 m1 3 4.7 3.879e+00 -0.821383 0.7040 -1.166780 -#> ds 2 m1 7 8.1 7.389e+00 -0.710951 0.8113 -0.876337 -#> ds 2 m1 7 7.9 7.389e+00 -0.510951 0.8113 -0.629812 -#> ds 2 m1 14 10.1 1.069e+01 0.593533 0.9507 0.624328 -#> ds 2 m1 14 10.3 1.069e+01 0.393533 0.9507 0.413951 -#> ds 2 m1 28 10.7 1.240e+01 1.703647 1.0325 1.649956 -#> ds 2 m1 28 12.2 1.240e+01 0.203647 1.0325 0.197229 -#> ds 2 m1 60 10.7 1.055e+01 -0.147672 0.9442 -0.156405 -#> ds 2 m1 60 12.5 1.055e+01 -1.947672 0.9442 -2.062848 -#> ds 2 m1 90 9.1 8.010e+00 -1.090041 0.8351 -1.305210 -#> ds 2 m1 90 7.4 8.010e+00 0.609959 0.8351 0.730362 -#> ds 2 m1 120 6.1 5.793e+00 -0.306797 0.7561 -0.405759 -#> ds 2 m1 120 4.5 5.793e+00 1.293203 0.7561 1.710347 -#> ds 3 parent 0 106.2 1.035e+02 -2.712344 6.6675 -0.406801 -#> ds 3 parent 0 106.9 1.035e+02 -3.412344 6.6675 -0.511788 -#> ds 3 parent 1 107.4 9.548e+01 -11.924044 6.1566 -1.936801 -#> ds 3 parent 1 96.1 9.548e+01 -0.624044 6.1566 -0.101362 -#> ds 3 parent 3 79.4 8.246e+01 3.056105 5.3274 0.573662 -#> ds 3 parent 3 82.6 8.246e+01 -0.143895 5.3274 -0.027010 -#> ds 3 parent 7 63.9 6.489e+01 0.991141 4.2122 0.235304 -#> ds 3 parent 7 62.4 6.489e+01 2.491141 4.2122 0.591416 -#> ds 3 parent 14 51.0 4.869e+01 -2.306824 3.1906 -0.723013 -#> ds 3 parent 14 47.1 4.869e+01 1.593176 3.1906 0.499338 -#> ds 3 parent 28 36.1 3.480e+01 -1.304261 2.3260 -0.560722 -#> ds 3 parent 28 36.6 3.480e+01 -1.804261 2.3260 -0.775679 -#> ds 3 parent 60 20.1 1.988e+01 -0.221952 1.4346 -0.154719 -#> ds 3 parent 60 19.8 1.988e+01 0.078048 1.4346 0.054406 -#> ds 3 parent 90 11.3 1.194e+01 0.642458 1.0099 0.636132 -#> ds 3 parent 90 10.7 1.194e+01 1.242458 1.0099 1.230224 -#> ds 3 parent 120 8.2 7.176e+00 -1.023847 0.8034 -1.274423 -#> ds 3 parent 120 7.3 7.176e+00 -0.123847 0.8034 -0.154158 -#> ds 3 m1 0 0.8 8.527e-13 -0.800000 0.6586 -1.214712 -#> ds 3 m1 1 1.8 1.856e+00 0.055925 0.6693 0.083562 -#> ds 3 m1 1 2.3 1.856e+00 -0.444075 0.6693 -0.663537 -#> ds 3 m1 3 4.2 4.780e+00 0.580164 0.7264 0.798676 -#> ds 3 m1 3 4.1 4.780e+00 0.680164 0.7264 0.936340 -#> ds 3 m1 7 6.8 8.410e+00 1.609920 0.8512 1.891455 -#> ds 3 m1 7 10.1 8.410e+00 -1.690080 0.8512 -1.985633 -#> ds 3 m1 14 11.4 1.098e+01 -0.424444 0.9638 -0.440389 -#> ds 3 m1 14 12.8 1.098e+01 -1.824444 0.9638 -1.892979 -#> ds 3 m1 28 11.5 1.142e+01 -0.079336 0.9848 -0.080558 -#> ds 3 m1 28 10.6 1.142e+01 0.820664 0.9848 0.833311 -#> ds 3 m1 60 7.5 9.110e+00 1.610231 0.8803 1.829222 -#> ds 3 m1 60 8.6 9.110e+00 0.510231 0.8803 0.579622 -#> ds 3 m1 90 7.3 6.799e+00 -0.501085 0.7898 -0.634463 -#> ds 3 m1 90 8.1 6.799e+00 -1.301085 0.7898 -1.647404 -#> ds 3 m1 120 5.3 4.868e+00 -0.431505 0.7288 -0.592064 -#> ds 3 m1 120 3.8 4.868e+00 1.068495 0.7288 1.466073 -#> ds 4 parent 0 104.7 9.926e+01 -5.444622 6.3975 -0.851049 -#> ds 4 parent 0 88.3 9.926e+01 10.955378 6.3975 1.712436 -#> ds 4 parent 1 94.2 9.618e+01 1.978413 6.2013 0.319030 -#> ds 4 parent 1 94.6 9.618e+01 1.578413 6.2013 0.254527 -#> ds 4 parent 3 78.1 9.037e+01 12.268550 5.8311 2.103985 -#> ds 4 parent 3 96.5 9.037e+01 -6.131450 5.8311 -1.051508 -#> ds 4 parent 7 76.2 7.999e+01 3.794958 5.1708 0.733918 -#> ds 4 parent 7 77.8 7.999e+01 2.194958 5.1708 0.424489 -#> ds 4 parent 14 70.8 6.518e+01 -5.624996 4.2301 -1.329742 -#> ds 4 parent 14 67.3 6.518e+01 -2.124996 4.2301 -0.502346 -#> ds 4 parent 28 43.1 4.462e+01 1.517860 2.9354 0.517085 -#> ds 4 parent 28 45.1 4.462e+01 -0.482140 2.9354 -0.164249 -#> ds 4 parent 60 21.3 2.130e+01 -0.003305 1.5159 -0.002180 -#> ds 4 parent 60 23.5 2.130e+01 -2.203305 1.5159 -1.453435 -#> ds 4 parent 90 11.8 1.180e+01 0.002834 1.0032 0.002825 -#> ds 4 parent 90 12.1 1.180e+01 -0.297166 1.0032 -0.296226 -#> ds 4 parent 120 7.0 6.868e+00 -0.132251 0.7922 -0.166937 -#> ds 4 parent 120 6.2 6.868e+00 0.667749 0.7922 0.842879 -#> ds 4 m1 0 1.6 0.000e+00 -1.600000 0.6586 -2.429424 -#> ds 4 m1 1 0.9 6.826e-01 -0.217363 0.6600 -0.329315 -#> ds 4 m1 3 3.7 1.935e+00 -1.765082 0.6702 -2.633768 -#> ds 4 m1 3 2.0 1.935e+00 -0.065082 0.6702 -0.097112 -#> ds 4 m1 7 3.6 4.035e+00 0.434805 0.7076 0.614501 -#> ds 4 m1 7 3.8 4.035e+00 0.234805 0.7076 0.331845 -#> ds 4 m1 14 7.1 6.652e+00 -0.448187 0.7846 -0.571220 -#> ds 4 m1 14 6.6 6.652e+00 0.051813 0.7846 0.066036 -#> ds 4 m1 28 9.5 9.156e+00 -0.343805 0.8822 -0.389696 -#> ds 4 m1 28 9.3 9.156e+00 -0.143805 0.8822 -0.163000 -#> ds 4 m1 60 8.3 8.848e+00 0.547762 0.8692 0.630185 -#> ds 4 m1 60 9.0 8.848e+00 -0.152238 0.8692 -0.175146 -#> ds 4 m1 90 6.6 6.674e+00 0.073979 0.7854 0.094194 -#> ds 4 m1 90 7.7 6.674e+00 -1.026021 0.7854 -1.306390 -#> ds 4 m1 120 3.7 4.668e+00 0.967537 0.7234 1.337503 -#> ds 4 m1 120 3.5 4.668e+00 1.167537 0.7234 1.613979 -#> ds 5 parent 0 110.4 1.022e+02 -8.170986 6.5872 -1.240433 -#> ds 5 parent 0 112.1 1.022e+02 -9.870986 6.5872 -1.498509 -#> ds 5 parent 1 93.5 9.513e+01 1.630764 6.1346 0.265832 -#> ds 5 parent 1 91.0 9.513e+01 4.130764 6.1346 0.673359 -#> ds 5 parent 3 71.0 8.296e+01 11.964279 5.3597 2.232268 -#> ds 5 parent 3 89.7 8.296e+01 -6.735721 5.3597 -1.256735 -#> ds 5 parent 7 60.4 6.495e+01 4.547441 4.2157 1.078684 -#> ds 5 parent 7 59.1 6.495e+01 5.847441 4.2157 1.387053 -#> ds 5 parent 14 56.5 4.626e+01 -10.241319 3.0380 -3.371047 -#> ds 5 parent 14 47.0 4.626e+01 -0.741319 3.0380 -0.244014 -#> ds 5 parent 28 30.2 3.026e+01 0.058478 2.0487 0.028544 -#> ds 5 parent 28 23.9 3.026e+01 6.358478 2.0487 3.103661 -#> ds 5 parent 60 17.0 1.792e+01 0.919046 1.3242 0.694024 -#> ds 5 parent 60 18.7 1.792e+01 -0.780954 1.3242 -0.589742 -#> ds 5 parent 90 11.3 1.187e+01 0.573917 1.0066 0.570144 -#> ds 5 parent 90 11.9 1.187e+01 -0.026083 1.0066 -0.025912 -#> ds 5 parent 120 9.0 7.898e+00 -1.102089 0.8307 -1.326622 -#> ds 5 parent 120 8.1 7.898e+00 -0.202089 0.8307 -0.243261 -#> ds 5 m1 0 0.7 -1.421e-14 -0.700000 0.6586 -1.062873 -#> ds 5 m1 1 3.0 3.144e+00 0.143526 0.6887 0.208390 -#> ds 5 m1 1 2.6 3.144e+00 0.543526 0.6887 0.789161 -#> ds 5 m1 3 5.1 8.390e+00 3.290265 0.8504 3.869277 -#> ds 5 m1 3 7.5 8.390e+00 0.890265 0.8504 1.046932 -#> ds 5 m1 7 16.5 1.566e+01 -0.841368 1.2007 -0.700751 -#> ds 5 m1 7 19.0 1.566e+01 -3.341368 1.2007 -2.782928 -#> ds 5 m1 14 22.9 2.188e+01 -1.017753 1.5498 -0.656687 -#> ds 5 m1 14 23.2 2.188e+01 -1.317753 1.5498 -0.850257 -#> ds 5 m1 28 22.2 2.386e+01 1.655914 1.6652 0.994399 -#> ds 5 m1 28 24.4 2.386e+01 -0.544086 1.6652 -0.326731 -#> ds 5 m1 60 15.5 1.859e+01 3.091124 1.3618 2.269915 -#> ds 5 m1 60 19.8 1.859e+01 -1.208876 1.3618 -0.887718 -#> ds 5 m1 90 14.9 1.372e+01 -1.176815 1.0990 -1.070784 -#> ds 5 m1 90 14.2 1.372e+01 -0.476815 1.0990 -0.433854 -#> ds 5 m1 120 10.9 9.961e+00 -0.938796 0.9174 -1.023332 -#> ds 5 m1 120 10.4 9.961e+00 -0.438796 0.9174 -0.478308</div><div class='input'><span class='co'># }</span> +</div><div class='output co'>#> <span class='warning'>Warning: argument is not a function</span></div><div class='output co'>#> <span class='message'> </span></div><div class='output co'>#> <span class='error'>Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'f_saem_dfop_sfo' not found</span></div><div class='input'><span class='co'># }</span> </div></pre> </div> |