From ff83d8b2ba623513d92ac90fac4a1b0ec98c2cb5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 5 Oct 2021 17:33:52 +0200 Subject: Update docs --- docs/dev/reference/summary.saem.mmkin.html | 270 +---------------------------- 1 file changed, 3 insertions(+), 267 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 08e3c8f8..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 mkin - 1.0.5 + 1.1.0 @@ -259,272 +259,8 @@ saemix authors for the parts inherited from saemix.

f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, quiet = TRUE, error_model = "tc", cores = 5) f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo) -
#> Running main SAEM algorithm -#> [1] "Wed Aug 4 16:23:26 2021" -#> .... -#> Minimisation finished -#> [1] "Wed Aug 4 16:23:38 2021"
summary(f_saem_dfop_sfo, data = TRUE) -
#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.5 -#> R version used for fitting: 4.1.0 -#> Date of fit: Wed Aug 4 16:23:39 2021 -#> Date of summary: Wed Aug 4 16:23:39 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 12.54 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 -#> -0.01132 -#> -#> Fixed degradation parameter values: -#> None -#> -#> Results: -#> -#> Likelihood computed by importance sampling -#> AIC BIC logLik -#> 825.9 820.4 -398.9 -#> -#> Optimised parameters: -#> est. lower upper -#> parent_0 101.118986 97.368 104.8695 -#> log_k_m1 -4.057591 -4.177 -3.9379 -#> f_parent_qlogis -0.933087 -1.290 -0.5763 -#> log_k1 -2.945520 -3.833 -2.0576 -#> log_k2 -3.531954 -4.310 -2.7542 -#> g_qlogis -0.009584 -1.688 1.6687 -#> -#> Correlation: -#> prnt_0 lg_k_1 f_prn_ log_k1 log_k2 -#> log_k_m1 -0.198 -#> f_parent_qlogis -0.153 0.184 -#> log_k1 0.080 -0.077 -0.045 -#> log_k2 0.005 0.008 -0.003 -0.019 -#> g_qlogis -0.059 0.048 0.041 -0.334 -0.253 -#> -#> Random effects: -#> est. lower upper -#> SD.parent_0 2.97797 -0.62927 6.5852 -#> SD.log_k_m1 0.09235 -0.02448 0.2092 -#> SD.f_parent_qlogis 0.38712 0.13469 0.6396 -#> SD.log_k1 0.88671 0.27052 1.5029 -#> SD.log_k2 0.80497 0.25587 1.3541 -#> SD.g_qlogis 0.36812 -3.56188 4.2981 -#> -#> Variance model: -#> est. lower upper -#> a.1 0.85879 0.68143 1.03615 -#> b.1 0.07787 0.06288 0.09286 -#> -#> Backtransformed parameters: -#> est. lower upper -#> parent_0 101.11899 97.36850 104.86947 -#> k_m1 0.01729 0.01534 0.01949 -#> f_parent_to_m1 0.28230 0.21587 0.35979 -#> k1 0.05257 0.02163 0.12776 -#> k2 0.02925 0.01344 0.06366 -#> g 0.49760 0.15606 0.84140 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.2823 -#> parent_sink 0.7177 -#> -#> Estimated disappearance times: -#> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 17.47 62.31 18.76 13.18 23.7 -#> m1 40.09 133.17 NA NA NA -#> -#> Data: -#> ds name time observed predicted residual std standardized -#> ds 1 parent 0 89.8 9.838e+01 -8.584661 7.7094 -1.113536 -#> ds 1 parent 0 104.1 9.838e+01 5.715339 7.7094 0.741350 -#> ds 1 parent 1 88.7 9.388e+01 -5.182489 7.3611 -0.704041 -#> ds 1 parent 1 95.5 9.388e+01 1.617511 7.3611 0.219739 -#> ds 1 parent 3 81.8 8.563e+01 -3.825382 6.7229 -0.569010 -#> ds 1 parent 3 94.5 8.563e+01 8.874618 6.7229 1.320062 -#> ds 1 parent 7 71.5 7.169e+01 -0.188290 5.6482 -0.033336 -#> ds 1 parent 7 70.3 7.169e+01 -1.388290 5.6482 -0.245795 -#> ds 1 parent 14 54.2 5.361e+01 0.586595 4.2624 0.137621 -#> ds 1 parent 14 49.6 5.361e+01 -4.013405 4.2624 -0.941587 -#> ds 1 parent 28 31.5 3.219e+01 -0.688936 2.6496 -0.260011 -#> ds 1 parent 28 28.8 3.219e+01 -3.388936 2.6496 -1.279016 -#> ds 1 parent 60 12.1 1.278e+01 -0.678998 1.3145 -0.516562 -#> ds 1 parent 60 13.6 1.278e+01 0.821002 1.3145 0.624595 -#> ds 1 parent 90 6.2 6.157e+00 0.043461 0.9835 0.044188 -#> ds 1 parent 90 8.3 6.157e+00 2.143461 0.9835 2.179316 -#> ds 1 parent 120 2.2 3.076e+00 -0.876218 0.8916 -0.982775 -#> ds 1 parent 120 2.4 3.076e+00 -0.676218 0.8916 -0.758453 -#> ds 1 m1 1 0.3 1.134e+00 -0.833749 0.8633 -0.965750 -#> ds 1 m1 1 0.2 1.134e+00 -0.933749 0.8633 -1.081583 -#> ds 1 m1 3 2.2 3.157e+00 -0.957400 0.8933 -1.071763 -#> ds 1 m1 3 3.0 3.157e+00 -0.157400 0.8933 -0.176202 -#> ds 1 m1 7 6.5 6.369e+00 0.130995 0.9917 0.132090 -#> ds 1 m1 7 5.0 6.369e+00 -1.369005 0.9917 -1.380438 -#> ds 1 m1 14 10.2 9.971e+00 0.229362 1.1577 0.198112 -#> ds 1 m1 14 9.5 9.971e+00 -0.470638 1.1577 -0.406513 -#> ds 1 m1 28 12.2 1.265e+01 -0.447735 1.3067 -0.342637 -#> ds 1 m1 28 13.4 1.265e+01 0.752265 1.3067 0.575683 -#> ds 1 m1 60 11.8 1.097e+01 0.832027 1.2112 0.686945 -#> ds 1 m1 60 13.2 1.097e+01 2.232027 1.2112 1.842825 -#> ds 1 m1 90 6.6 7.876e+00 -1.275985 1.0553 -1.209109 -#> ds 1 m1 90 9.3 7.876e+00 1.424015 1.0553 1.349381 -#> ds 1 m1 120 3.5 5.336e+00 -1.835829 0.9540 -1.924292 -#> ds 1 m1 120 5.4 5.336e+00 0.064171 0.9540 0.067263 -#> ds 2 parent 0 118.0 1.092e+02 8.812058 8.5459 1.031142 -#> ds 2 parent 0 99.8 1.092e+02 -9.387942 8.5459 -1.098529 -#> ds 2 parent 1 90.2 1.023e+02 -12.114268 8.0135 -1.511724 -#> ds 2 parent 1 94.6 1.023e+02 -7.714268 8.0135 -0.962654 -#> ds 2 parent 3 96.1 9.066e+01 5.436165 7.1122 0.764344 -#> ds 2 parent 3 78.4 9.066e+01 -12.263835 7.1122 -1.724339 -#> ds 2 parent 7 77.9 7.365e+01 4.245773 5.7995 0.732090 -#> ds 2 parent 7 77.7 7.365e+01 4.045773 5.7995 0.697604 -#> ds 2 parent 14 56.0 5.593e+01 0.073803 4.4389 0.016626 -#> ds 2 parent 14 54.7 5.593e+01 -1.226197 4.4389 -0.276236 -#> ds 2 parent 28 36.6 3.892e+01 -2.320837 3.1502 -0.736737 -#> ds 2 parent 28 36.8 3.892e+01 -2.120837 3.1502 -0.673248 -#> ds 2 parent 60 22.1 2.136e+01 0.741020 1.8719 0.395868 -#> ds 2 parent 60 24.7 2.136e+01 3.341020 1.8719 1.784841 -#> ds 2 parent 90 12.4 1.251e+01 -0.113999 1.2989 -0.087765 -#> ds 2 parent 90 10.8 1.251e+01 -1.713999 1.2989 -1.319575 -#> ds 2 parent 120 6.8 7.338e+00 -0.537708 1.0315 -0.521281 -#> ds 2 parent 120 7.9 7.338e+00 0.562292 1.0315 0.545113 -#> ds 2 m1 1 1.3 1.576e+00 -0.276176 0.8675 -0.318352 -#> ds 2 m1 3 3.7 4.177e+00 -0.476741 0.9183 -0.519146 -#> ds 2 m1 3 4.7 4.177e+00 0.523259 0.9183 0.569801 -#> ds 2 m1 7 8.1 7.724e+00 0.376365 1.0485 0.358970 -#> ds 2 m1 7 7.9 7.724e+00 0.176365 1.0485 0.168214 -#> ds 2 m1 14 10.1 1.077e+01 -0.674433 1.2006 -0.561738 -#> ds 2 m1 14 10.3 1.077e+01 -0.474433 1.2006 -0.395158 -#> ds 2 m1 28 10.7 1.212e+01 -1.416179 1.2758 -1.110010 -#> ds 2 m1 28 12.2 1.212e+01 0.083821 1.2758 0.065699 -#> ds 2 m1 60 10.7 1.041e+01 0.294930 1.1807 0.249793 -#> ds 2 m1 60 12.5 1.041e+01 2.094930 1.1807 1.774316 -#> ds 2 m1 90 9.1 8.079e+00 1.020859 1.0646 0.958929 -#> ds 2 m1 90 7.4 8.079e+00 -0.679141 1.0646 -0.637941 -#> ds 2 m1 120 6.1 5.968e+00 0.131673 0.9765 0.134843 -#> ds 2 m1 120 4.5 5.968e+00 -1.468327 0.9765 -1.503683 -#> ds 3 parent 0 106.2 1.036e+02 2.638248 8.1101 0.325303 -#> ds 3 parent 0 106.9 1.036e+02 3.338248 8.1101 0.411614 -#> ds 3 parent 1 107.4 9.580e+01 11.600063 7.5094 1.544743 -#> ds 3 parent 1 96.1 9.580e+01 0.300063 7.5094 0.039958 -#> ds 3 parent 3 79.4 8.297e+01 -3.574516 6.5182 -0.548391 -#> ds 3 parent 3 82.6 8.297e+01 -0.374516 6.5182 -0.057457 -#> ds 3 parent 7 63.9 6.517e+01 -1.272397 5.1472 -0.247200 -#> ds 3 parent 7 62.4 6.517e+01 -2.772397 5.1472 -0.538618 -#> ds 3 parent 14 51.0 4.821e+01 2.790075 3.8512 0.724475 -#> ds 3 parent 14 47.1 4.821e+01 -1.109925 3.8512 -0.288205 -#> ds 3 parent 28 36.1 3.385e+01 2.250573 2.7723 0.811811 -#> ds 3 parent 28 36.6 3.385e+01 2.750573 2.7723 0.992168 -#> ds 3 parent 60 20.1 1.964e+01 0.455700 1.7543 0.259760 -#> ds 3 parent 60 19.8 1.964e+01 0.155700 1.7543 0.088753 -#> ds 3 parent 90 11.3 1.210e+01 -0.795458 1.2746 -0.624068 -#> ds 3 parent 90 10.7 1.210e+01 -1.395458 1.2746 -1.094792 -#> ds 3 parent 120 8.2 7.451e+00 0.749141 1.0364 0.722816 -#> ds 3 parent 120 7.3 7.451e+00 -0.150859 1.0364 -0.145558 -#> ds 3 m1 0 0.8 3.695e-13 0.800000 0.8588 0.931542 -#> ds 3 m1 1 1.8 1.740e+00 0.059741 0.8694 0.068714 -#> ds 3 m1 1 2.3 1.740e+00 0.559741 0.8694 0.643812 -#> ds 3 m1 3 4.2 4.531e+00 -0.331379 0.9285 -0.356913 -#> ds 3 m1 3 4.1 4.531e+00 -0.431379 0.9285 -0.464618 -#> ds 3 m1 7 6.8 8.113e+00 -1.312762 1.0661 -1.231333 -#> ds 3 m1 7 10.1 8.113e+00 1.987238 1.0661 1.863971 -#> ds 3 m1 14 11.4 1.079e+01 0.613266 1.2013 0.510507 -#> ds 3 m1 14 12.8 1.079e+01 2.013266 1.2013 1.675923 -#> ds 3 m1 28 11.5 1.133e+01 0.174252 1.2310 0.141553 -#> ds 3 m1 28 10.6 1.133e+01 -0.725748 1.2310 -0.589558 -#> ds 3 m1 60 7.5 8.948e+00 -1.448281 1.1059 -1.309561 -#> ds 3 m1 60 8.6 8.948e+00 -0.348281 1.1059 -0.314922 -#> ds 3 m1 90 7.3 6.665e+00 0.634932 1.0034 0.632752 -#> ds 3 m1 90 8.1 6.665e+00 1.434932 1.0034 1.430004 -#> ds 3 m1 120 5.3 4.795e+00 0.504936 0.9365 0.539199 -#> ds 3 m1 120 3.8 4.795e+00 -0.995064 0.9365 -1.062586 -#> ds 4 parent 0 104.7 9.985e+01 4.850494 7.8227 0.620050 -#> ds 4 parent 0 88.3 9.985e+01 -11.549506 7.8227 -1.476402 -#> ds 4 parent 1 94.2 9.676e+01 -2.556304 7.5834 -0.337093 -#> ds 4 parent 1 94.6 9.676e+01 -2.156304 7.5834 -0.284346 -#> ds 4 parent 3 78.1 9.092e+01 -12.817485 7.1318 -1.797230 -#> ds 4 parent 3 96.5 9.092e+01 5.582515 7.1318 0.782764 -#> ds 4 parent 7 76.2 8.050e+01 -4.297338 6.3270 -0.679204 -#> ds 4 parent 7 77.8 8.050e+01 -2.697338 6.3270 -0.426320 -#> ds 4 parent 14 70.8 6.562e+01 5.179989 5.1816 0.999687 -#> ds 4 parent 14 67.3 6.562e+01 1.679989 5.1816 0.324222 -#> ds 4 parent 28 43.1 4.499e+01 -1.886936 3.6069 -0.523140 -#> ds 4 parent 28 45.1 4.499e+01 0.113064 3.6069 0.031346 -#> ds 4 parent 60 21.3 2.151e+01 -0.214840 1.8827 -0.114114 -#> ds 4 parent 60 23.5 2.151e+01 1.985160 1.8827 1.054433 -#> ds 4 parent 90 11.8 1.190e+01 -0.098528 1.2633 -0.077990 -#> ds 4 parent 90 12.1 1.190e+01 0.201472 1.2633 0.159475 -#> ds 4 parent 120 7.0 6.886e+00 0.113832 1.0125 0.112431 -#> ds 4 parent 120 6.2 6.886e+00 -0.686168 1.0125 -0.677724 -#> ds 4 m1 0 1.6 4.263e-14 1.600000 0.8588 1.863085 -#> ds 4 m1 1 0.9 7.140e-01 0.185984 0.8606 0.216112 -#> ds 4 m1 3 3.7 2.022e+00 1.678243 0.8731 1.922160 -#> ds 4 m1 3 2.0 2.022e+00 -0.021757 0.8731 -0.024919 -#> ds 4 m1 7 3.6 4.207e+00 -0.607229 0.9192 -0.660633 -#> ds 4 m1 7 3.8 4.207e+00 -0.407229 0.9192 -0.443044 -#> ds 4 m1 14 7.1 6.912e+00 0.188339 1.0135 0.185828 -#> ds 4 m1 14 6.6 6.912e+00 -0.311661 1.0135 -0.307506 -#> ds 4 m1 28 9.5 9.449e+00 0.050714 1.1309 0.044843 -#> ds 4 m1 28 9.3 9.449e+00 -0.149286 1.1309 -0.132004 -#> ds 4 m1 60 8.3 8.997e+00 -0.697403 1.1083 -0.629230 -#> ds 4 m1 60 9.0 8.997e+00 0.002597 1.1083 0.002343 -#> ds 4 m1 90 6.6 6.697e+00 -0.096928 1.0047 -0.096472 -#> ds 4 m1 90 7.7 6.697e+00 1.003072 1.0047 0.998348 -#> ds 4 m1 120 3.7 4.622e+00 -0.921607 0.9312 -0.989749 -#> ds 4 m1 120 3.5 4.622e+00 -1.121607 0.9312 -1.204537 -#> ds 5 parent 0 110.4 1.045e+02 5.942426 8.1795 0.726502 -#> ds 5 parent 0 112.1 1.045e+02 7.642426 8.1795 0.934338 -#> ds 5 parent 1 93.5 9.739e+01 -3.893915 7.6327 -0.510162 -#> ds 5 parent 1 91.0 9.739e+01 -6.393915 7.6327 -0.837700 -#> ds 5 parent 3 71.0 8.519e+01 -14.188275 6.6891 -2.121098 -#> ds 5 parent 3 89.7 8.519e+01 4.511725 6.6891 0.674487 -#> ds 5 parent 7 60.4 6.684e+01 -6.439546 5.2753 -1.220701 -#> ds 5 parent 7 59.1 6.684e+01 -7.739546 5.2753 -1.467133 -#> ds 5 parent 14 56.5 4.736e+01 9.138979 3.7868 2.413407 -#> ds 5 parent 14 47.0 4.736e+01 -0.361021 3.7868 -0.095338 -#> ds 5 parent 28 30.2 3.033e+01 -0.131178 2.5132 -0.052195 -#> ds 5 parent 28 23.9 3.033e+01 -6.431178 2.5132 -2.558936 -#> ds 5 parent 60 17.0 1.771e+01 -0.705246 1.6243 -0.434177 -#> ds 5 parent 60 18.7 1.771e+01 0.994754 1.6243 0.612409 -#> ds 5 parent 90 11.3 1.180e+01 -0.504856 1.2580 -0.401315 -#> ds 5 parent 90 11.9 1.180e+01 0.095144 1.2580 0.075631 -#> ds 5 parent 120 9.0 7.917e+00 1.083499 1.0571 1.024928 -#> ds 5 parent 120 8.1 7.917e+00 0.183499 1.0571 0.173579 -#> ds 5 m1 0 0.7 3.553e-15 0.700000 0.8588 0.815100 -#> ds 5 m1 1 3.0 3.204e+00 -0.204414 0.8943 -0.228572 -#> ds 5 m1 1 2.6 3.204e+00 -0.604414 0.8943 -0.675845 -#> ds 5 m1 3 5.1 8.586e+00 -3.485889 1.0884 -3.202858 -#> ds 5 m1 3 7.5 8.586e+00 -1.085889 1.0884 -0.997722 -#> ds 5 m1 7 16.5 1.612e+01 0.376855 1.5211 0.247743 -#> ds 5 m1 7 19.0 1.612e+01 2.876855 1.5211 1.891237 -#> ds 5 m1 14 22.9 2.267e+01 0.228264 1.9633 0.116267 -#> ds 5 m1 14 23.2 2.267e+01 0.528264 1.9633 0.269072 -#> ds 5 m1 28 22.2 2.468e+01 -2.480178 2.1050 -1.178211 -#> ds 5 m1 28 24.4 2.468e+01 -0.280178 2.1050 -0.133099 -#> ds 5 m1 60 15.5 1.860e+01 -3.099615 1.6838 -1.840794 -#> ds 5 m1 60 19.8 1.860e+01 1.200385 1.6838 0.712883 -#> ds 5 m1 90 14.9 1.326e+01 1.636345 1.3433 1.218195 -#> ds 5 m1 90 14.2 1.326e+01 0.936345 1.3433 0.697072 -#> ds 5 m1 120 10.9 9.348e+00 1.551535 1.1258 1.378133 -#> ds 5 m1 120 10.4 9.348e+00 1.051535 1.1258 0.934014
# } +
#> Warning: argument is not a function
#>
#> Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].
summary(f_saem_dfop_sfo, data = TRUE) +
#> 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
# }
-- cgit v1.2.1