From 48c463680b51fa767b4cd7bd62865f192d0354ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 18:30:32 +0100 Subject: Reintroduce interface to saemix Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. --- docs/dev/reference/summary.saem.mmkin.html | 426 ++++++++++++++--------------- 1 file changed, 213 insertions(+), 213 deletions(-) (limited to 'docs/dev/reference/summary.saem.mmkin.html') diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 722415fb..93e1365d 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 mkin - 0.9.50.4 + 1.0.1.9000 @@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.

quiet = TRUE, error_model = "tc", cores = 5) f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:40 2021" +#> [1] "Sat Feb 6 18:30:00 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:53 2021"
summary(f_saem_dfop_sfo, data = TRUE) +#> [1] "Sat Feb 6 18:30:11 2021"
summary(f_saem_dfop_sfo, data = TRUE)
#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 0.9.50.4 +#> mkin version used for pre-fitting: 1.0.1.9000 #> 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 +#> Date of fit: Sat Feb 6 18:30:12 2021 +#> Date of summary: Sat Feb 6 18:30:12 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.

#> #> Model predictions using solution type analytical #> -#> Fitted in 13.298 s using 300, 100 iterations +#> Fitted in 11.769 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> @@ -291,7 +291,7 @@ saemix authors for the parts inherited from saemix.

#> 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 +#> -0.01132 #> #> Fixed degradation parameter values: #> None @@ -299,232 +299,232 @@ saemix authors for the parts inherited from saemix.

#> Results: #> #> Likelihood computed by importance sampling -#> AIC BIC logLik -#> 830 824.5 -401 +#> AIC BIC logLik +#> 829.3 823.9 -400.7 #> #> 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 +#> est. lower upper +#> parent_0 101.29457 97.855 104.7344 +#> log_k_m1 -4.06337 -4.182 -3.9445 +#> f_parent_qlogis -0.94546 -1.307 -0.5841 +#> log_k1 -2.98794 -3.844 -2.1321 +#> log_k2 -3.47891 -4.253 -2.7050 +#> g_qlogis -0.03211 -1.157 1.0931 #> #> 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 +#> log_k_m1 -0.202 +#> f_parent_qlogis -0.145 0.195 +#> log_k1 0.094 -0.099 -0.049 +#> log_k2 -0.042 0.056 0.024 -0.097 +#> g_qlogis -0.005 0.000 0.007 -0.160 -0.113 #> #> 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 +#> est. lower upper +#> SD.parent_0 2.70085 -0.64980 6.0515 +#> SD.log_k_m1 0.08408 -0.04023 0.2084 +#> SD.f_parent_qlogis 0.39215 0.13695 0.6473 +#> SD.log_k1 0.89280 0.27466 1.5109 +#> SD.log_k2 0.82387 0.26388 1.3838 +#> SD.g_qlogis 0.36468 -0.86978 1.5991 #> #> Variance model: #> est. lower upper -#> a.1 0.65859 0.49250 0.82469 -#> b.1 0.06411 0.05006 0.07817 +#> a.1 0.65724 0.49361 0.82086 +#> b.1 0.06434 0.05034 0.07835 #> #> 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 +#> parent_0 101.29457 97.85477 104.73437 +#> k_m1 0.01719 0.01526 0.01936 +#> f_parent_to_m1 0.27980 0.21302 0.35798 +#> k1 0.05039 0.02141 0.11859 +#> k2 0.03084 0.01422 0.06687 +#> g 0.49197 0.23916 0.74896 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.2781 -#> parent_sink 0.7219 +#> parent_m1 0.2798 +#> parent_sink 0.7202 #> #> 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 +#> parent 17.49 61.05 18.38 13.76 22.47 +#> m1 40.32 133.94 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
# } +#> ds name time observed predicted residual std standardized +#> ds 1 parent 0 89.8 9.878e+01 8.98039 6.3899 1.40541 +#> ds 1 parent 0 104.1 9.878e+01 -5.31961 6.3899 -0.83251 +#> ds 1 parent 1 88.7 9.422e+01 5.52084 6.0981 0.90533 +#> ds 1 parent 1 95.5 9.422e+01 -1.27916 6.0981 -0.20976 +#> ds 1 parent 3 81.8 8.587e+01 4.06752 5.5641 0.73103 +#> ds 1 parent 3 94.5 8.587e+01 -8.63248 5.5641 -1.55147 +#> ds 1 parent 7 71.5 7.180e+01 0.29615 4.6662 0.06347 +#> ds 1 parent 7 70.3 7.180e+01 1.49615 4.6662 0.32063 +#> ds 1 parent 14 54.2 5.360e+01 -0.59602 3.5112 -0.16975 +#> ds 1 parent 14 49.6 5.360e+01 4.00398 3.5112 1.14035 +#> ds 1 parent 28 31.5 3.213e+01 0.62529 2.1691 0.28828 +#> ds 1 parent 28 28.8 3.213e+01 3.32529 2.1691 1.53306 +#> ds 1 parent 60 12.1 1.271e+01 0.60718 1.0490 0.57879 +#> ds 1 parent 60 13.6 1.271e+01 -0.89282 1.0490 -0.85108 +#> ds 1 parent 90 6.2 6.080e+00 -0.12020 0.7649 -0.15716 +#> ds 1 parent 90 8.3 6.080e+00 -2.22020 0.7649 -2.90279 +#> ds 1 parent 120 2.2 3.011e+00 0.81059 0.6852 1.18302 +#> ds 1 parent 120 2.4 3.011e+00 0.61059 0.6852 0.89113 +#> ds 1 m1 1 0.3 1.131e+00 0.83071 0.6613 1.25628 +#> ds 1 m1 1 0.2 1.131e+00 0.93071 0.6613 1.40750 +#> ds 1 m1 3 2.2 3.147e+00 0.94691 0.6877 1.37688 +#> ds 1 m1 3 3.0 3.147e+00 0.14691 0.6877 0.21361 +#> ds 1 m1 7 6.5 6.341e+00 -0.15949 0.7736 -0.20618 +#> ds 1 m1 7 5.0 6.341e+00 1.34051 0.7736 1.73290 +#> ds 1 m1 14 10.2 9.910e+00 -0.28991 0.9157 -0.31659 +#> ds 1 m1 14 9.5 9.910e+00 0.41009 0.9157 0.44783 +#> ds 1 m1 28 12.2 1.255e+01 0.34690 1.0410 0.33323 +#> ds 1 m1 28 13.4 1.255e+01 -0.85310 1.0410 -0.81949 +#> ds 1 m1 60 11.8 1.087e+01 -0.92713 0.9599 -0.96586 +#> ds 1 m1 60 13.2 1.087e+01 -2.32713 0.9599 -2.42434 +#> ds 1 m1 90 6.6 7.813e+00 1.21254 0.8274 1.46541 +#> ds 1 m1 90 9.3 7.813e+00 -1.48746 0.8274 -1.79766 +#> ds 1 m1 120 3.5 5.295e+00 1.79489 0.7403 2.42457 +#> ds 1 m1 120 5.4 5.295e+00 -0.10511 0.7403 -0.14198 +#> ds 2 parent 0 118.0 1.074e+02 -10.63436 6.9396 -1.53242 +#> ds 2 parent 0 99.8 1.074e+02 7.56564 6.9396 1.09021 +#> ds 2 parent 1 90.2 1.012e+02 10.96486 6.5425 1.67594 +#> ds 2 parent 1 94.6 1.012e+02 6.56486 6.5425 1.00342 +#> ds 2 parent 3 96.1 9.054e+01 -5.56014 5.8627 -0.94839 +#> ds 2 parent 3 78.4 9.054e+01 12.13986 5.8627 2.07069 +#> ds 2 parent 7 77.9 7.468e+01 -3.21805 4.8501 -0.66350 +#> ds 2 parent 7 77.7 7.468e+01 -3.01805 4.8501 -0.62226 +#> ds 2 parent 14 56.0 5.748e+01 1.47774 3.7563 0.39340 +#> ds 2 parent 14 54.7 5.748e+01 2.77774 3.7563 0.73948 +#> ds 2 parent 28 36.6 3.996e+01 3.36317 2.6541 1.26717 +#> ds 2 parent 28 36.8 3.996e+01 3.16317 2.6541 1.19182 +#> ds 2 parent 60 22.1 2.132e+01 -0.78225 1.5210 -0.51430 +#> ds 2 parent 60 24.7 2.132e+01 -3.38225 1.5210 -2.22369 +#> ds 2 parent 90 12.4 1.215e+01 -0.25010 1.0213 -0.24487 +#> ds 2 parent 90 10.8 1.215e+01 1.34990 1.0213 1.32169 +#> ds 2 parent 120 6.8 6.931e+00 0.13105 0.7943 0.16500 +#> ds 2 parent 120 7.9 6.931e+00 -0.96895 0.7943 -1.21994 +#> ds 2 m1 1 1.3 1.519e+00 0.21924 0.6645 0.32995 +#> ds 2 m1 3 3.7 4.049e+00 0.34891 0.7070 0.49351 +#> ds 2 m1 3 4.7 4.049e+00 -0.65109 0.7070 -0.92094 +#> ds 2 m1 7 8.1 7.565e+00 -0.53526 0.8179 -0.65448 +#> ds 2 m1 7 7.9 7.565e+00 -0.33526 0.8179 -0.40993 +#> ds 2 m1 14 10.1 1.071e+01 0.60614 0.9521 0.63663 +#> ds 2 m1 14 10.3 1.071e+01 0.40614 0.9521 0.42657 +#> ds 2 m1 28 10.7 1.224e+01 1.54440 1.0260 1.50526 +#> ds 2 m1 28 12.2 1.224e+01 0.04440 1.0260 0.04327 +#> ds 2 m1 60 10.7 1.056e+01 -0.14005 0.9453 -0.14815 +#> ds 2 m1 60 12.5 1.056e+01 -1.94005 0.9453 -2.05226 +#> ds 2 m1 90 9.1 8.089e+00 -1.01088 0.8384 -1.20577 +#> ds 2 m1 90 7.4 8.089e+00 0.68912 0.8384 0.82197 +#> ds 2 m1 120 6.1 5.855e+00 -0.24463 0.7576 -0.32292 +#> ds 2 m1 120 4.5 5.855e+00 1.35537 0.7576 1.78911 +#> ds 3 parent 0 106.2 1.095e+02 3.30335 7.0765 0.46680 +#> ds 3 parent 0 106.9 1.095e+02 2.60335 7.0765 0.36788 +#> ds 3 parent 1 107.4 9.939e+01 -8.01282 6.4287 -1.24641 +#> ds 3 parent 1 96.1 9.939e+01 3.28718 6.4287 0.51133 +#> ds 3 parent 3 79.4 8.365e+01 4.24698 5.4222 0.78326 +#> ds 3 parent 3 82.6 8.365e+01 1.04698 5.4222 0.19309 +#> ds 3 parent 7 63.9 6.405e+01 0.14704 4.1732 0.03523 +#> ds 3 parent 7 62.4 6.405e+01 1.64704 4.1732 0.39467 +#> ds 3 parent 14 51.0 4.795e+01 -3.04985 3.1546 -0.96681 +#> ds 3 parent 14 47.1 4.795e+01 0.85015 3.1546 0.26950 +#> ds 3 parent 28 36.1 3.501e+01 -1.09227 2.3465 -0.46549 +#> ds 3 parent 28 36.6 3.501e+01 -1.59227 2.3465 -0.67858 +#> ds 3 parent 60 20.1 2.012e+01 0.02116 1.4520 0.01457 +#> ds 3 parent 60 19.8 2.012e+01 0.32116 1.4520 0.22119 +#> ds 3 parent 90 11.3 1.206e+01 0.76096 1.0170 0.74826 +#> ds 3 parent 90 10.7 1.206e+01 1.36096 1.0170 1.33825 +#> ds 3 parent 120 8.2 7.230e+00 -0.97022 0.8052 -1.20493 +#> ds 3 parent 120 7.3 7.230e+00 -0.07022 0.8052 -0.08721 +#> ds 3 m1 0 0.8 -5.684e-13 -0.80000 0.6572 -1.21722 +#> ds 3 m1 1 1.8 2.045e+00 0.24538 0.6703 0.36608 +#> ds 3 m1 1 2.3 2.045e+00 -0.25462 0.6703 -0.37987 +#> ds 3 m1 3 4.2 5.136e+00 0.93594 0.7356 1.27228 +#> ds 3 m1 3 4.1 5.136e+00 1.03594 0.7356 1.40822 +#> ds 3 m1 7 6.8 8.674e+00 1.87438 0.8623 2.17381 +#> ds 3 m1 7 10.1 8.674e+00 -1.42562 0.8623 -1.65335 +#> ds 3 m1 14 11.4 1.083e+01 -0.56746 0.9580 -0.59233 +#> ds 3 m1 14 12.8 1.083e+01 -1.96746 0.9580 -2.05369 +#> ds 3 m1 28 11.5 1.098e+01 -0.51762 0.9651 -0.53637 +#> ds 3 m1 28 10.6 1.098e+01 0.38238 0.9651 0.39623 +#> ds 3 m1 60 7.5 8.889e+00 1.38911 0.8713 1.59436 +#> ds 3 m1 60 8.6 8.889e+00 0.28911 0.8713 0.33183 +#> ds 3 m1 90 7.3 6.774e+00 -0.52608 0.7886 -0.66708 +#> ds 3 m1 90 8.1 6.774e+00 -1.32608 0.7886 -1.68150 +#> ds 3 m1 120 5.3 4.954e+00 -0.34584 0.7305 -0.47345 +#> ds 3 m1 120 3.8 4.954e+00 1.15416 0.7305 1.58004 +#> ds 4 parent 0 104.7 9.957e+01 -5.13169 6.4403 -0.79681 +#> ds 4 parent 0 88.3 9.957e+01 11.26831 6.4403 1.74966 +#> ds 4 parent 1 94.2 9.644e+01 2.23888 6.2400 0.35879 +#> ds 4 parent 1 94.6 9.644e+01 1.83888 6.2400 0.29469 +#> ds 4 parent 3 78.1 9.054e+01 12.43946 5.8627 2.12180 +#> ds 4 parent 3 96.5 9.054e+01 -5.96054 5.8627 -1.01669 +#> ds 4 parent 7 76.2 8.004e+01 3.83771 5.1918 0.73919 +#> ds 4 parent 7 77.8 8.004e+01 2.23771 5.1918 0.43101 +#> ds 4 parent 14 70.8 6.511e+01 -5.69246 4.2406 -1.34238 +#> ds 4 parent 14 67.3 6.511e+01 -2.19246 4.2406 -0.51702 +#> ds 4 parent 28 43.1 4.454e+01 1.43744 2.9401 0.48890 +#> ds 4 parent 28 45.1 4.454e+01 -0.56256 2.9401 -0.19134 +#> ds 4 parent 60 21.3 2.132e+01 0.02005 1.5211 0.01318 +#> ds 4 parent 60 23.5 2.132e+01 -2.17995 1.5211 -1.43310 +#> ds 4 parent 90 11.8 1.182e+01 0.02167 1.0053 0.02156 +#> ds 4 parent 90 12.1 1.182e+01 -0.27833 1.0053 -0.27687 +#> ds 4 parent 120 7.0 6.852e+00 -0.14780 0.7914 -0.18675 +#> ds 4 parent 120 6.2 6.852e+00 0.65220 0.7914 0.82408 +#> ds 4 m1 0 1.6 -5.684e-14 -1.60000 0.6572 -2.43444 +#> ds 4 m1 1 0.9 6.918e-01 -0.20821 0.6587 -0.31607 +#> ds 4 m1 3 3.7 1.959e+00 -1.74131 0.6692 -2.60204 +#> ds 4 m1 3 2.0 1.959e+00 -0.04131 0.6692 -0.06173 +#> ds 4 m1 7 3.6 4.076e+00 0.47590 0.7076 0.67252 +#> ds 4 m1 7 3.8 4.076e+00 0.27590 0.7076 0.38989 +#> ds 4 m1 14 7.1 6.698e+00 -0.40189 0.7859 -0.51135 +#> ds 4 m1 14 6.6 6.698e+00 0.09811 0.7859 0.12483 +#> ds 4 m1 28 9.5 9.175e+00 -0.32492 0.8835 -0.36779 +#> ds 4 m1 28 9.3 9.175e+00 -0.12492 0.8835 -0.14141 +#> ds 4 m1 60 8.3 8.818e+00 0.51810 0.8683 0.59671 +#> ds 4 m1 60 9.0 8.818e+00 -0.18190 0.8683 -0.20949 +#> ds 4 m1 90 6.6 6.645e+00 0.04480 0.7841 0.05713 +#> ds 4 m1 90 7.7 6.645e+00 -1.05520 0.7841 -1.34581 +#> ds 4 m1 120 3.7 4.648e+00 0.94805 0.7221 1.31293 +#> ds 4 m1 120 3.5 4.648e+00 1.14805 0.7221 1.58991 +#> ds 5 parent 0 110.4 1.026e+02 -7.81752 6.6333 -1.17853 +#> ds 5 parent 0 112.1 1.026e+02 -9.51752 6.6333 -1.43482 +#> ds 5 parent 1 93.5 9.560e+01 2.10274 6.1865 0.33989 +#> ds 5 parent 1 91.0 9.560e+01 4.60274 6.1865 0.74399 +#> ds 5 parent 3 71.0 8.356e+01 12.55799 5.4165 2.31846 +#> ds 5 parent 3 89.7 8.356e+01 -6.14201 5.4165 -1.13394 +#> ds 5 parent 7 60.4 6.550e+01 5.09732 4.2653 1.19506 +#> ds 5 parent 7 59.1 6.550e+01 6.39732 4.2653 1.49984 +#> ds 5 parent 14 56.5 4.641e+01 -10.09145 3.0576 -3.30044 +#> ds 5 parent 14 47.0 4.641e+01 -0.59145 3.0576 -0.19344 +#> ds 5 parent 28 30.2 2.982e+01 -0.37647 2.0284 -0.18560 +#> ds 5 parent 28 23.9 2.982e+01 5.92353 2.0284 2.92028 +#> ds 5 parent 60 17.0 1.754e+01 0.53981 1.3060 0.41332 +#> ds 5 parent 60 18.7 1.754e+01 -1.16019 1.3060 -0.88834 +#> ds 5 parent 90 11.3 1.175e+01 0.45050 1.0018 0.44969 +#> ds 5 parent 90 11.9 1.175e+01 -0.14950 1.0018 -0.14923 +#> ds 5 parent 120 9.0 7.915e+00 -1.08476 0.8315 -1.30462 +#> ds 5 parent 120 8.1 7.915e+00 -0.18476 0.8315 -0.22220 +#> ds 5 m1 0 0.7 0.000e+00 -0.70000 0.6572 -1.06507 +#> ds 5 m1 1 3.0 3.062e+00 0.06170 0.6861 0.08992 +#> ds 5 m1 1 2.6 3.062e+00 0.46170 0.6861 0.67290 +#> ds 5 m1 3 5.1 8.209e+00 3.10938 0.8432 3.68760 +#> ds 5 m1 3 7.5 8.209e+00 0.70938 0.8432 0.84130 +#> ds 5 m1 7 16.5 1.544e+01 -1.05567 1.1914 -0.88605 +#> ds 5 m1 7 19.0 1.544e+01 -3.55567 1.1914 -2.98436 +#> ds 5 m1 14 22.9 2.181e+01 -1.08765 1.5498 -0.70181 +#> ds 5 m1 14 23.2 2.181e+01 -1.38765 1.5498 -0.89539 +#> ds 5 m1 28 22.2 2.404e+01 1.83624 1.6805 1.09270 +#> ds 5 m1 28 24.4 2.404e+01 -0.36376 1.6805 -0.21647 +#> ds 5 m1 60 15.5 1.875e+01 3.25390 1.3741 2.36805 +#> ds 5 m1 60 19.8 1.875e+01 -1.04610 1.3741 -0.76131 +#> ds 5 m1 90 14.9 1.380e+01 -1.09507 1.1050 -0.99102 +#> ds 5 m1 90 14.2 1.380e+01 -0.39507 1.1050 -0.35753 +#> ds 5 m1 120 10.9 1.002e+01 -0.88429 0.9205 -0.96069 +#> ds 5 m1 120 10.4 1.002e+01 -0.38429 0.9205 -0.41749
# }
-- cgit v1.2.3 From 3dde3b95f1db925c89cd04d19f95c6fc9f68f473 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 13 Feb 2021 12:40:44 +0100 Subject: Update docs --- docs/dev/404.html | 2 +- docs/dev/articles/index.html | 2 +- docs/dev/authors.html | 2 +- docs/dev/index.html | 2 +- docs/dev/news/index.html | 18 ++++++++++---- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/endpoints.html | 2 +- docs/dev/reference/index.html | 2 +- docs/dev/reference/plot.mixed.mmkin.html | 6 ++--- docs/dev/reference/saem.html | 38 +++++++++++++++--------------- docs/dev/reference/summary.saem.mmkin.html | 14 +++++------ 11 files changed, 49 insertions(+), 41 deletions(-) (limited to 'docs/dev/reference/summary.saem.mmkin.html') diff --git a/docs/dev/404.html b/docs/dev/404.html index 5f29faf2..ea547a2a 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 441d49c0..57d0c0eb 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 9641eec0..8ffb9f97 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/index.html b/docs/dev/index.html index 8888633d..ff9b201f 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -38,7 +38,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 998917f2..eab75984 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 @@ -141,9 +141,9 @@ Source: NEWS.md -
-

-mkin 1.0.1.9000 Unreleased +
+

+mkin 1.0.2.9000 Unreleased

  • Switch to a versioning scheme where the fourth version component indicates development versions

    • @@ -151,10 +151,18 @@

  • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

  • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

+
+
+

+mkin 1.0.2 Unreleased +

+
    +
  • ‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’
    • +

-mkin 1.0.1 Unreleased +mkin 1.0.1 2021-02-10

  • ‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults

    • diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index f9b16e29..8921a1e4 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-02-06T17:26Z +last_built: 2021-02-13T11:32Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index a13e11a7..301b454f 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> mkin - 1.0.1.9000 + 1.0.2.9000
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 7e98aa50..b52ecb22 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000

diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 601e1554..ef169074 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 @@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:17 2021" +#> [1] "Sat Feb 13 12:33:07 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:23 2021"
plot(f_saem) +#> [1] "Sat Feb 13 12:33:13 2021"
plot(f_saem)
# We can overlay the two variants if we generate predictions pred_nlme <- mkinpredict(dfop_sfo, diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 4578db2a..02483bec 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." /> mkin - 1.0.1.9000 + 1.0.2.9000
@@ -261,27 +261,27 @@ using mmkin.

state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE) f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:26 2021" +#> [1] "Sat Feb 13 12:33:16 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:27 2021"
+#> [1] "Sat Feb 13 12:33:18 2021"
f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:28 2021" +#> [1] "Sat Feb 13 12:33:19 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:30 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Sat Feb 13 12:33:20 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:30 2021" +#> [1] "Sat Feb 13 12:33:20 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:32 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Sat Feb 13 12:33:22 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:32 2021" +#> [1] "Sat Feb 13 12:33:23 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:35 2021"
+#> [1] "Sat Feb 13 12:33:25 2021"
# The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) @@ -324,10 +324,10 @@ using mmkin.

f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:37 2021" +#> [1] "Sat Feb 13 12:33:28 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:42 2021"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +#> [1] "Sat Feb 13 12:33:32 2021"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
#> Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.
sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), A1 = mkinsub("SFO")) @@ -346,15 +346,15 @@ using mmkin.

# four minutes f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:44 2021" +#> [1] "Sat Feb 13 12:33:35 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:48 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#> [1] "Sat Feb 13 12:33:39 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:49 2021" +#> [1] "Sat Feb 13 12:33:40 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:57 2021"
# We can use print, plot and summary methods to check the results +#> [1] "Sat Feb 13 12:33:48 2021"
# We can use print, plot and summary methods to check the results print(f_saem_dfop_sfo)
#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -395,10 +395,10 @@ using mmkin.

#> SD.g_qlogis 0.44771 -0.86417 1.7596
plot(f_saem_dfop_sfo)
summary(f_saem_dfop_sfo, data = TRUE)
#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:29:57 2021 -#> Date of summary: Sat Feb 6 18:29:58 2021 +#> Date of fit: Sat Feb 13 12:33:48 2021 +#> Date of summary: Sat Feb 13 12:33:48 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -413,7 +413,7 @@ using mmkin.

#> #> Model predictions using solution type analytical #> -#> Fitted in 8.539 s using 300, 100 iterations +#> Fitted in 8.875 s using 300, 100 iterations #> #> Variance model: Constant variance #> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 93e1365d..81054813 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 mkin - 1.0.1.9000 + 1.0.2.9000
@@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.

quiet = TRUE, error_model = "tc", cores = 5) f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:30:00 2021" +#> [1] "Sat Feb 13 12:33:52 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:30:11 2021"
summary(f_saem_dfop_sfo, data = TRUE) +#> [1] "Sat Feb 13 12:34:03 2021"
summary(f_saem_dfop_sfo, data = TRUE)
#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:30:12 2021 -#> Date of summary: Sat Feb 6 18:30:12 2021 +#> Date of fit: Sat Feb 13 12:34:04 2021 +#> Date of summary: Sat Feb 13 12:34:04 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.

#> #> Model predictions using solution type analytical #> -#> Fitted in 11.769 s using 300, 100 iterations +#> Fitted in 11.899 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> -- cgit v1.2.3 From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 17:36:12 +0100 Subject: Fully rebuild docs, rerun tests and check --- GNUmakefile | 2 +- build.log | 3 +- check.log | 4 +- docs/dev/404.html | 2 +- docs/dev/articles/FOCUS_D.html | 23 +-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../articles/FOCUS_D_files/figure-html/plot-1.png | Bin 81432 -> 79176 bytes .../FOCUS_D_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/articles/FOCUS_L.html | 129 ++++++------ .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../figure-html/unnamed-chunk-10-1.png | Bin 43110 -> 42203 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 84605 -> 82006 bytes .../figure-html/unnamed-chunk-13-1.png 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docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js (limited to 'docs/dev/reference/summary.saem.mmkin.html') diff --git a/GNUmakefile b/GNUmakefile index 8604d3b3..d7c68ebf 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -112,7 +112,7 @@ pd: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)" git add -A -pd_release: roxygen +pd_all: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE)" git add -A diff --git a/build.log b/build.log index 293831aa..d50a4860 100644 --- a/build.log +++ b/build.log @@ -6,4 +6,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.0.2.9000.tar.gz’ +* building ‘mkin_1.0.3.9000.tar.gz’ + diff --git a/check.log b/check.log index 2a4d87ad..ac59f6af 100644 --- a/check.log +++ b/check.log @@ -5,12 +5,12 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.0.2.9000’ +* this is package ‘mkin’ version ‘1.0.3.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: ‘Johannes Ranke ’ -Version contains large components (1.0.2.9000) +Version contains large components (1.0.3.9000) Unknown, possibly mis-spelled, fields in DESCRIPTION: ‘Remotes’ diff --git a/docs/dev/404.html b/docs/dev/404.html index ea547a2a..f9e51aa3 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ mkin - 1.0.2.9000 + 1.0.3.9000
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index dd86f677..a35a255a 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -32,7 +32,7 @@ mkin - 0.9.50.4 + 1.0.3.9000 @@ -81,7 +81,7 @@