From a54bd290bc3884d0000c52c1b29bc557825d9eae Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 15 Dec 2022 14:50:28 +0100 Subject: List random effects correlations in output if any Update docs --- docs/dev/reference/summary.saem.mmkin.html | 508 ++++++++++++++++------------- 1 file changed, 282 insertions(+), 226 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 a4150959..3b5869f1 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -102,7 +102,7 @@ endpoints such as formation fractions and DT50 values. Optionally 
# S3 method for saem.mmkin
-summary(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...)
+summary(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...)
 
 # S3 method for summary.saem.mmkin
 print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)
@@ -266,36 +266,38 @@ saemix authors for the parts inherited from saemix.

#> SD.g_qlogis 0.37478 0.04490 0.70467 illparms(f_saem_dfop_sfo) #> [1] "sd(parent_0)" "sd(log_k_m1)" -f_saem_dfop_sfo_2 <- update(f_saem_dfop_sfo, covariance.model = diag(c(0, 0, 1, 1, 1, 0))) +f_saem_dfop_sfo_2 <- update(f_saem_dfop_sfo, + no_random_effect = c("parent_0", "log_k_m1")) illparms(f_saem_dfop_sfo_2) intervals(f_saem_dfop_sfo_2) #> Approximate 95% confidence intervals #> #> Fixed effects: #> lower est. upper -#> parent_0 97.57609542 100.73343868 103.89078195 -#> k_m1 0.01549292 0.01714893 0.01898194 -#> f_parent_to_m1 0.20720315 0.28358738 0.37481744 -#> k1 0.06149334 0.08733164 0.12402670 -#> k2 0.01448390 0.01699942 0.01995184 -#> g 0.45084762 0.51075839 0.57036168 +#> parent_0 98.36731429 101.42508066 104.48284703 +#> k_m1 0.01513234 0.01670094 0.01843214 +#> f_parent_to_m1 0.20221431 0.27608850 0.36461630 +#> k1 0.06915073 0.09759718 0.13774560 +#> k2 0.01487068 0.01740389 0.02036863 +#> g 0.37365671 0.48384821 0.59563299 #> #> Random effects: #> lower est. upper -#> sd(f_parent_qlogis) 0.16606767 0.4479731 0.7298784 -#> sd(log_k1) 0.12284609 0.3588446 0.5948430 -#> sd(log_k2) 0.05379723 0.1548780 0.2559588 +#> sd(f_parent_qlogis) 0.16439770 0.4427585 0.7211193 +#> sd(log_k1) 0.08304243 0.3345213 0.5860002 +#> sd(log_k2) 0.03146410 0.1490210 0.2665779 +#> sd(g_qlogis) 0.06216385 0.4023430 0.7425221 #> #> -#> lower est. upper -#> a.1 0.6811490 0.88503409 1.08891921 -#> b.1 0.0676515 0.08336272 0.09907394 -summary(f_saem_dfop_sfo_2, data = TRUE) +#> lower est. upper +#> a.1 0.67696663 0.87777355 1.07858048 +#> b.1 0.06363957 0.07878001 0.09392044 +summary(f_saem_dfop_sfo_2, data = TRUE) #> saemix version used for fitting: 3.2 #> mkin version used for pre-fitting: 1.2.2 #> R version used for fitting: 4.2.2 -#> Date of fit: Thu Nov 24 08:11:52 2022 -#> Date of summary: Thu Nov 24 08:11:52 2022 +#> Date of fit: Thu Dec 15 14:47:14 2022 +#> Date of summary: Thu Dec 15 14:47:14 2022 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -310,12 +312,12 @@ saemix authors for the parts inherited from saemix.

#> #> Model predictions using solution type analytical #> -#> Fitted in 26.242 s +#> Fitted in 9.623 s #> Using 300, 100 iterations and 10 chains #> #> Variance model: Two-component variance function #> -#> Mean of starting values for individual parameters: +#> Starting values for degradation 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 @@ -324,237 +326,291 @@ saemix authors for the parts inherited from saemix.

#> Fixed degradation parameter values: #> None #> +#> Starting values for random effects (square root of initial entries in omega): +#> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis +#> parent_0 6.742 0.0000 0.0000 0.0000 0.0000 0.000 +#> log_k_m1 0.000 0.2236 0.0000 0.0000 0.0000 0.000 +#> f_parent_qlogis 0.000 0.0000 0.5572 0.0000 0.0000 0.000 +#> log_k1 0.000 0.0000 0.0000 0.8031 0.0000 0.000 +#> log_k2 0.000 0.0000 0.0000 0.0000 0.2931 0.000 +#> g_qlogis 0.000 0.0000 0.0000 0.0000 0.0000 0.807 +#> +#> Starting values for error model parameters: +#> a.1 b.1 +#> 1 1 +#> #> Results: #> #> Likelihood computed by importance sampling -#> AIC BIC logLik -#> 809.5 805.2 -393.7 +#> AIC BIC logLik +#> 807 802.3 -391.5 #> #> Optimised parameters: #> est. lower upper -#> parent_0 100.73344 97.57610 103.89078 -#> log_k_m1 -4.06582 -4.16737 -3.96427 -#> f_parent_qlogis -0.92674 -1.34187 -0.51160 -#> log_k1 -2.43804 -2.78883 -2.08726 -#> log_k2 -4.07458 -4.23472 -3.91443 -#> g_qlogis 0.04304 -0.19725 0.28333 -#> a.1 0.88503 0.68115 1.08892 -#> b.1 0.08336 0.06765 0.09907 -#> SD.f_parent_qlogis 0.44797 0.16607 0.72988 -#> SD.log_k1 0.35884 0.12285 0.59484 -#> SD.log_k2 0.15488 0.05380 0.25596 +#> parent_0 101.42508 98.36731 104.48285 +#> log_k_m1 -4.09229 -4.19092 -3.99366 +#> f_parent_qlogis -0.96395 -1.37251 -0.55538 +#> log_k1 -2.32691 -2.67147 -1.98235 +#> log_k2 -4.05106 -4.20836 -3.89376 +#> g_qlogis -0.06463 -0.51656 0.38730 +#> a.1 0.87777 0.67697 1.07858 +#> b.1 0.07878 0.06364 0.09392 +#> SD.f_parent_qlogis 0.44276 0.16440 0.72112 +#> SD.log_k1 0.33452 0.08304 0.58600 +#> SD.log_k2 0.14902 0.03146 0.26658 +#> SD.g_qlogis 0.40234 0.06216 0.74252 #> #> Correlation: #> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 -#> log_k_m1 -0.4698 -#> f_parent_qlogis -0.2461 0.2709 -#> log_k1 0.1572 -0.1517 -0.0648 -#> log_k2 -0.0023 0.0835 0.0125 0.1420 -#> g_qlogis 0.2314 -0.2337 -0.0755 -0.2762 -0.4797 +#> log_k_m1 -0.4693 +#> f_parent_qlogis -0.2378 0.2595 +#> log_k1 0.1720 -0.1593 -0.0669 +#> log_k2 0.0179 0.0594 0.0035 0.1995 +#> g_qlogis 0.1073 -0.1060 -0.0322 -0.2299 -0.3168 #> #> Random effects: -#> est. lower upper -#> SD.f_parent_qlogis 0.4480 0.1661 0.7299 -#> SD.log_k1 0.3588 0.1228 0.5948 -#> SD.log_k2 0.1549 0.0538 0.2560 +#> est. lower upper +#> SD.f_parent_qlogis 0.4428 0.16440 0.7211 +#> SD.log_k1 0.3345 0.08304 0.5860 +#> SD.log_k2 0.1490 0.03146 0.2666 +#> SD.g_qlogis 0.4023 0.06216 0.7425 #> #> Variance model: #> est. lower upper -#> a.1 0.88503 0.68115 1.08892 -#> b.1 0.08336 0.06765 0.09907 +#> a.1 0.87777 0.67697 1.07858 +#> b.1 0.07878 0.06364 0.09392 #> #> Backtransformed parameters: -#> est. lower upper -#> parent_0 100.73344 97.57610 103.89078 -#> k_m1 0.01715 0.01549 0.01898 -#> f_parent_to_m1 0.28359 0.20720 0.37482 -#> k1 0.08733 0.06149 0.12403 -#> k2 0.01700 0.01448 0.01995 -#> g 0.51076 0.45085 0.57036 +#> est. lower upper +#> parent_0 101.4251 98.36731 104.48285 +#> k_m1 0.0167 0.01513 0.01843 +#> f_parent_to_m1 0.2761 0.20221 0.36462 +#> k1 0.0976 0.06915 0.13775 +#> k2 0.0174 0.01487 0.02037 +#> g 0.4838 0.37366 0.59563 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.2836 -#> parent_sink 0.7164 +#> parent_m1 0.2761 +#> parent_sink 0.7239 #> #> Estimated disappearance times: #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 15.94 93.48 28.14 7.937 40.77 -#> m1 40.42 134.27 NA NA NA +#> parent 15.54 94.33 28.4 7.102 39.83 +#> m1 41.50 137.87 NA NA NA #> #> Data: -#> ds name time observed predicted residual std standardized -#> ds 1 parent 0 89.8 1.007e+02 -10.93344 8.4439 -1.29483 -#> ds 1 parent 0 104.1 1.007e+02 3.36656 8.4439 0.39870 -#> ds 1 parent 1 88.7 9.591e+01 -7.20789 8.0440 -0.89606 -#> ds 1 parent 1 95.5 9.591e+01 -0.40789 8.0440 -0.05071 -#> ds 1 parent 3 81.8 8.712e+01 -5.31561 7.3159 -0.72658 -#> ds 1 parent 3 94.5 8.712e+01 7.38439 7.3159 1.00936 -#> ds 1 parent 7 71.5 7.246e+01 -0.95675 6.1047 -0.15672 -#> ds 1 parent 7 70.3 7.246e+01 -2.15675 6.1047 -0.35329 -#> ds 1 parent 14 54.2 5.382e+01 0.38143 4.5729 0.08341 -#> ds 1 parent 14 49.6 5.382e+01 -4.21857 4.5729 -0.92251 -#> ds 1 parent 28 31.5 3.230e+01 -0.80120 2.8344 -0.28267 -#> ds 1 parent 28 28.8 3.230e+01 -3.50120 2.8344 -1.23524 -#> ds 1 parent 60 12.1 1.307e+01 -0.97165 1.4038 -0.69215 -#> ds 1 parent 60 13.6 1.307e+01 0.52835 1.4038 0.37637 -#> ds 1 parent 90 6.2 6.353e+00 -0.15285 1.0314 -0.14820 -#> ds 1 parent 90 8.3 6.353e+00 1.94715 1.0314 1.88790 -#> ds 1 parent 120 2.2 3.175e+00 -0.97462 0.9238 -1.05506 -#> ds 1 parent 120 2.4 3.175e+00 -0.77462 0.9238 -0.83855 -#> ds 1 m1 1 0.3 1.183e+00 -0.88350 0.8905 -0.99212 -#> ds 1 m1 1 0.2 1.183e+00 -0.98350 0.8905 -1.10441 -#> ds 1 m1 3 2.2 3.281e+00 -1.08106 0.9263 -1.16703 -#> ds 1 m1 3 3.0 3.281e+00 -0.28106 0.9263 -0.30341 -#> ds 1 m1 7 6.5 6.564e+00 -0.06353 1.0405 -0.06106 -#> ds 1 m1 7 5.0 6.564e+00 -1.56353 1.0405 -1.50266 -#> ds 1 m1 14 10.2 1.015e+01 0.05147 1.2243 0.04204 -#> ds 1 m1 14 9.5 1.015e+01 -0.64853 1.2243 -0.52970 -#> ds 1 m1 28 12.2 1.265e+01 -0.44824 1.3766 -0.32561 -#> ds 1 m1 28 13.4 1.265e+01 0.75176 1.3766 0.54610 -#> ds 1 m1 60 11.8 1.078e+01 1.02355 1.2611 0.81165 -#> ds 1 m1 60 13.2 1.078e+01 2.42355 1.2611 1.92181 -#> ds 1 m1 90 6.6 7.698e+00 -1.09840 1.0932 -1.00474 -#> ds 1 m1 90 9.3 7.698e+00 1.60160 1.0932 1.46502 -#> ds 1 m1 120 3.5 5.199e+00 -1.69853 0.9854 -1.72363 -#> ds 1 m1 120 5.4 5.199e+00 0.20147 0.9854 0.20445 -#> ds 2 parent 0 118.0 1.007e+02 17.26656 8.4439 2.04485 -#> ds 2 parent 0 99.8 1.007e+02 -0.93344 8.4439 -0.11055 -#> ds 2 parent 1 90.2 9.584e+01 -5.63852 8.0382 -0.70146 -#> ds 2 parent 1 94.6 9.584e+01 -1.23852 8.0382 -0.15408 -#> ds 2 parent 3 96.1 8.706e+01 9.04068 7.3113 1.23654 -#> ds 2 parent 3 78.4 8.706e+01 -8.65932 7.3113 -1.18438 -#> ds 2 parent 7 77.9 7.286e+01 5.04438 6.1376 0.82188 -#> ds 2 parent 7 77.7 7.286e+01 4.84438 6.1376 0.78930 -#> ds 2 parent 14 56.0 5.567e+01 0.33336 4.7242 0.07057 -#> ds 2 parent 14 54.7 5.567e+01 -0.96664 4.7242 -0.20462 -#> ds 2 parent 28 36.6 3.705e+01 -0.44800 3.2127 -0.13944 -#> ds 2 parent 28 36.8 3.705e+01 -0.24800 3.2127 -0.07719 -#> ds 2 parent 60 22.1 2.008e+01 2.01984 1.8935 1.06672 -#> ds 2 parent 60 24.7 2.008e+01 4.61984 1.8935 2.43984 -#> ds 2 parent 90 12.4 1.253e+01 -0.12814 1.3689 -0.09360 -#> ds 2 parent 90 10.8 1.253e+01 -1.72814 1.3689 -1.26238 -#> ds 2 parent 120 6.8 7.916e+00 -1.11595 1.1040 -1.01085 -#> ds 2 parent 120 7.9 7.916e+00 -0.01595 1.1040 -0.01445 -#> ds 2 m1 1 1.3 1.317e+00 -0.01669 0.8918 -0.01871 -#> ds 2 m1 3 3.7 3.613e+00 0.08699 0.9349 0.09305 -#> ds 2 m1 3 4.7 3.613e+00 1.08699 0.9349 1.16270 -#> ds 2 m1 7 8.1 7.092e+00 1.00781 1.0643 0.94688 -#> ds 2 m1 7 7.9 7.092e+00 0.80781 1.0643 0.75897 -#> ds 2 m1 14 10.1 1.066e+01 -0.56458 1.2545 -0.45006 -#> ds 2 m1 14 10.3 1.066e+01 -0.36458 1.2545 -0.29063 -#> ds 2 m1 28 10.7 1.281e+01 -2.11106 1.3870 -1.52201 -#> ds 2 m1 28 12.2 1.281e+01 -0.61106 1.3870 -0.44055 -#> ds 2 m1 60 10.7 1.078e+01 -0.08464 1.2616 -0.06709 -#> ds 2 m1 60 12.5 1.078e+01 1.71536 1.2616 1.35970 -#> ds 2 m1 90 9.1 8.013e+00 1.08684 1.1088 0.98016 -#> ds 2 m1 90 7.4 8.013e+00 -0.61316 1.1088 -0.55298 -#> ds 2 m1 120 6.1 5.749e+00 0.35063 1.0065 0.34838 -#> ds 2 m1 120 4.5 5.749e+00 -1.24937 1.0065 -1.24133 -#> ds 3 parent 0 106.2 1.007e+02 5.46656 8.4439 0.64740 -#> ds 3 parent 0 106.9 1.007e+02 6.16656 8.4439 0.73030 -#> ds 3 parent 1 107.4 9.369e+01 13.70530 7.8606 1.74354 -#> ds 3 parent 1 96.1 9.369e+01 2.40530 7.8606 0.30599 -#> ds 3 parent 3 79.4 8.185e+01 -2.45363 6.8807 -0.35660 -#> ds 3 parent 3 82.6 8.185e+01 0.74637 6.8807 0.10847 -#> ds 3 parent 7 63.9 6.487e+01 -0.97153 5.4798 -0.17729 -#> ds 3 parent 7 62.4 6.487e+01 -2.47153 5.4798 -0.45103 -#> ds 3 parent 14 51.0 4.791e+01 3.09024 4.0908 0.75542 -#> ds 3 parent 14 47.1 4.791e+01 -0.80976 4.0908 -0.19795 -#> ds 3 parent 28 36.1 3.313e+01 2.97112 2.9001 1.02450 -#> ds 3 parent 28 36.6 3.313e+01 3.47112 2.9001 1.19691 -#> ds 3 parent 60 20.1 1.927e+01 0.83265 1.8339 0.45404 -#> ds 3 parent 60 19.8 1.927e+01 0.53265 1.8339 0.29045 -#> ds 3 parent 90 11.3 1.203e+01 -0.72783 1.3374 -0.54421 -#> ds 3 parent 90 10.7 1.203e+01 -1.32783 1.3374 -0.99284 -#> ds 3 parent 120 8.2 7.516e+00 0.68382 1.0844 0.63061 -#> ds 3 parent 120 7.3 7.516e+00 -0.21618 1.0844 -0.19936 -#> ds 3 m1 0 0.8 -9.948e-14 0.80000 0.8850 0.90392 -#> ds 3 m1 1 1.8 1.682e+00 0.11759 0.8961 0.13123 -#> ds 3 m1 1 2.3 1.682e+00 0.61759 0.8961 0.68921 -#> ds 3 m1 3 4.2 4.431e+00 -0.23052 0.9590 -0.24037 -#> ds 3 m1 3 4.1 4.431e+00 -0.33052 0.9590 -0.34465 -#> ds 3 m1 7 6.8 8.084e+00 -1.28422 1.1124 -1.15445 -#> ds 3 m1 7 10.1 8.084e+00 2.01578 1.1124 1.81208 -#> ds 3 m1 14 11.4 1.100e+01 0.40274 1.2743 0.31606 -#> ds 3 m1 14 12.8 1.100e+01 1.80274 1.2743 1.41474 -#> ds 3 m1 28 11.5 1.176e+01 -0.25977 1.3207 -0.19669 -#> ds 3 m1 28 10.6 1.176e+01 -1.15977 1.3207 -0.87813 -#> ds 3 m1 60 7.5 9.277e+00 -1.77696 1.1753 -1.51190 -#> ds 3 m1 60 8.6 9.277e+00 -0.67696 1.1753 -0.57598 -#> ds 3 m1 90 7.3 6.883e+00 0.41708 1.0548 0.39542 -#> ds 3 m1 90 8.1 6.883e+00 1.21708 1.0548 1.15389 -#> ds 3 m1 120 5.3 4.948e+00 0.35179 0.9764 0.36028 -#> ds 3 m1 120 3.8 4.948e+00 -1.14821 0.9764 -1.17591 -#> ds 4 parent 0 104.7 1.007e+02 3.96656 8.4439 0.46975 -#> ds 4 parent 0 88.3 1.007e+02 -12.43344 8.4439 -1.47247 -#> ds 4 parent 1 94.2 9.738e+01 -3.18358 8.1663 -0.38985 -#> ds 4 parent 1 94.6 9.738e+01 -2.78358 8.1663 -0.34086 -#> ds 4 parent 3 78.1 9.110e+01 -12.99595 7.6454 -1.69984 -#> ds 4 parent 3 96.5 9.110e+01 5.40405 7.6454 0.70684 -#> ds 4 parent 7 76.2 8.000e+01 -3.79797 6.7273 -0.56456 -#> ds 4 parent 7 77.8 8.000e+01 -2.19797 6.7273 -0.32672 -#> ds 4 parent 14 70.8 6.446e+01 6.34396 5.4456 1.16496 -#> ds 4 parent 14 67.3 6.446e+01 2.84396 5.4456 0.52225 -#> ds 4 parent 28 43.1 4.359e+01 -0.48960 3.7400 -0.13091 -#> ds 4 parent 28 45.1 4.359e+01 1.51040 3.7400 0.40385 -#> ds 4 parent 60 21.3 2.095e+01 0.35282 1.9577 0.18022 -#> ds 4 parent 60 23.5 2.095e+01 2.55282 1.9577 1.30400 -#> ds 4 parent 90 11.8 1.188e+01 -0.07874 1.3281 -0.05929 -#> ds 4 parent 90 12.1 1.188e+01 0.22126 1.3281 0.16660 -#> ds 4 parent 120 7.0 7.072e+00 -0.07245 1.0634 -0.06813 -#> ds 4 parent 120 6.2 7.072e+00 -0.87245 1.0634 -0.82041 -#> ds 4 m1 0 1.6 5.684e-14 1.60000 0.8850 1.80784 -#> ds 4 m1 1 0.9 6.960e-01 0.20399 0.8869 0.23000 -#> ds 4 m1 3 3.7 1.968e+00 1.73240 0.9001 1.92466 -#> ds 4 m1 3 2.0 1.968e+00 0.03240 0.9001 0.03599 -#> ds 4 m1 7 3.6 4.083e+00 -0.48287 0.9482 -0.50924 -#> ds 4 m1 7 3.8 4.083e+00 -0.28287 0.9482 -0.29832 -#> ds 4 m1 14 7.1 6.682e+00 0.41836 1.0457 0.40007 -#> ds 4 m1 14 6.6 6.682e+00 -0.08164 1.0457 -0.07807 -#> ds 4 m1 28 9.5 9.103e+00 0.39733 1.1658 0.34082 -#> ds 4 m1 28 9.3 9.103e+00 0.19733 1.1658 0.16926 -#> ds 4 m1 60 8.3 8.750e+00 -0.44979 1.1469 -0.39218 -#> ds 4 m1 60 9.0 8.750e+00 0.25021 1.1469 0.21817 -#> ds 4 m1 90 6.6 6.673e+00 -0.07285 1.0453 -0.06969 -#> ds 4 m1 90 7.7 6.673e+00 1.02715 1.0453 0.98261 -#> ds 4 m1 120 3.7 4.757e+00 -1.05747 0.9698 -1.09036 -#> ds 4 m1 120 3.5 4.757e+00 -1.25747 0.9698 -1.29658 -#> ds 5 parent 0 110.4 1.007e+02 9.66656 8.4439 1.14480 -#> ds 5 parent 0 112.1 1.007e+02 11.36656 8.4439 1.34612 -#> ds 5 parent 1 93.5 9.395e+01 -0.45394 7.8821 -0.05759 -#> ds 5 parent 1 91.0 9.395e+01 -2.95394 7.8821 -0.37477 -#> ds 5 parent 3 71.0 8.245e+01 -11.44783 6.9298 -1.65197 -#> ds 5 parent 3 89.7 8.245e+01 7.25217 6.9298 1.04652 -#> ds 5 parent 7 60.4 6.567e+01 -5.27002 5.5455 -0.95032 -#> ds 5 parent 7 59.1 6.567e+01 -6.57002 5.5455 -1.18475 -#> ds 5 parent 14 56.5 4.847e+01 8.03029 4.1364 1.94139 -#> ds 5 parent 14 47.0 4.847e+01 -1.46971 4.1364 -0.35532 -#> ds 5 parent 28 30.2 3.309e+01 -2.89206 2.8971 -0.99825 -#> ds 5 parent 28 23.9 3.309e+01 -9.19206 2.8971 -3.17281 -#> ds 5 parent 60 17.0 1.891e+01 -1.90623 1.8076 -1.05458 -#> ds 5 parent 60 18.7 1.891e+01 -0.20623 1.8076 -0.11409 -#> ds 5 parent 90 11.3 1.168e+01 -0.38263 1.3160 -0.29076 -#> ds 5 parent 90 11.9 1.168e+01 0.21737 1.3160 0.16518 -#> ds 5 parent 120 9.0 7.230e+00 1.77031 1.0708 1.65333 -#> ds 5 parent 120 8.1 7.230e+00 0.87031 1.0708 0.81280 -#> ds 5 m1 0 0.7 -5.116e-13 0.70000 0.8850 0.79093 -#> ds 5 m1 1 3.0 3.244e+00 -0.24430 0.9254 -0.26398 -#> ds 5 m1 1 2.6 3.244e+00 -0.64430 0.9254 -0.69621 -#> ds 5 m1 3 5.1 8.592e+00 -3.49175 1.1385 -3.06686 -#> ds 5 m1 3 7.5 8.592e+00 -1.09175 1.1385 -0.95890 -#> ds 5 m1 7 16.5 1.583e+01 0.66887 1.5890 0.42093 -#> ds 5 m1 7 19.0 1.583e+01 3.16887 1.5890 1.99424 -#> ds 5 m1 14 22.9 2.181e+01 1.08658 2.0224 0.53728 -#> ds 5 m1 14 23.2 2.181e+01 1.38658 2.0224 0.68562 -#> ds 5 m1 28 22.2 2.364e+01 -1.43659 2.1600 -0.66508 -#> ds 5 m1 28 24.4 2.364e+01 0.76341 2.1600 0.35342 -#> ds 5 m1 60 15.5 1.873e+01 -3.23377 1.7950 -1.80150 -#> ds 5 m1 60 19.8 1.873e+01 1.06623 1.7950 0.59398 -#> ds 5 m1 90 14.9 1.387e+01 1.03117 1.4560 0.70822 -#> ds 5 m1 90 14.2 1.387e+01 0.33117 1.4560 0.22745 -#> ds 5 m1 120 10.9 9.937e+00 0.96270 1.2122 0.79415 -#> ds 5 m1 120 10.4 9.937e+00 0.46270 1.2122 0.38169 +#> ds name time observed predicted residual std standardized +#> ds 1 parent 0 89.8 1.014e+02 -11.62508 8.0383 -1.44620 +#> ds 1 parent 0 104.1 1.014e+02 2.67492 8.0383 0.33277 +#> ds 1 parent 1 88.7 9.650e+01 -7.80311 7.6530 -1.01961 +#> ds 1 parent 1 95.5 9.650e+01 -1.00311 7.6530 -0.13107 +#> ds 1 parent 3 81.8 8.753e+01 -5.72638 6.9510 -0.82382 +#> ds 1 parent 3 94.5 8.753e+01 6.97362 6.9510 1.00326 +#> ds 1 parent 7 71.5 7.254e+01 -1.04133 5.7818 -0.18010 +#> ds 1 parent 7 70.3 7.254e+01 -2.24133 5.7818 -0.38765 +#> ds 1 parent 14 54.2 5.349e+01 0.71029 4.3044 0.16502 +#> ds 1 parent 14 49.6 5.349e+01 -3.88971 4.3044 -0.90366 +#> ds 1 parent 28 31.5 3.167e+01 -0.16616 2.6446 -0.06283 +#> ds 1 parent 28 28.8 3.167e+01 -2.86616 2.6446 -1.08379 +#> ds 1 parent 60 12.1 1.279e+01 -0.69287 1.3365 -0.51843 +#> ds 1 parent 60 13.6 1.279e+01 0.80713 1.3365 0.60392 +#> ds 1 parent 90 6.2 6.397e+00 -0.19718 1.0122 -0.19481 +#> ds 1 parent 90 8.3 6.397e+00 1.90282 1.0122 1.87996 +#> ds 1 parent 120 2.2 3.323e+00 -1.12320 0.9160 -1.22623 +#> ds 1 parent 120 2.4 3.323e+00 -0.92320 0.9160 -1.00788 +#> ds 1 m1 1 0.3 1.179e+00 -0.87919 0.8827 -0.99605 +#> ds 1 m1 1 0.2 1.179e+00 -0.97919 0.8827 -1.10935 +#> ds 1 m1 3 2.2 3.273e+00 -1.07272 0.9149 -1.17256 +#> ds 1 m1 3 3.0 3.273e+00 -0.27272 0.9149 -0.29811 +#> ds 1 m1 7 6.5 6.559e+00 -0.05872 1.0186 -0.05765 +#> ds 1 m1 7 5.0 6.559e+00 -1.55872 1.0186 -1.53032 +#> ds 1 m1 14 10.2 1.016e+01 0.03787 1.1880 0.03188 +#> ds 1 m1 14 9.5 1.016e+01 -0.66213 1.1880 -0.55734 +#> ds 1 m1 28 12.2 1.268e+01 -0.47913 1.3297 -0.36032 +#> ds 1 m1 28 13.4 1.268e+01 0.72087 1.3297 0.54211 +#> ds 1 m1 60 11.8 1.078e+01 1.02493 1.2211 0.83936 +#> ds 1 m1 60 13.2 1.078e+01 2.42493 1.2211 1.98588 +#> ds 1 m1 90 6.6 7.705e+00 -1.10464 1.0672 -1.03509 +#> ds 1 m1 90 9.3 7.705e+00 1.59536 1.0672 1.49491 +#> ds 1 m1 120 3.5 5.236e+00 -1.73617 0.9699 -1.79010 +#> ds 1 m1 120 5.4 5.236e+00 0.16383 0.9699 0.16892 +#> ds 2 parent 0 118.0 1.014e+02 16.57492 8.0383 2.06198 +#> ds 2 parent 0 99.8 1.014e+02 -1.62508 8.0383 -0.20217 +#> ds 2 parent 1 90.2 9.599e+01 -5.79045 7.6129 -0.76061 +#> ds 2 parent 1 94.6 9.599e+01 -1.39045 7.6129 -0.18264 +#> ds 2 parent 3 96.1 8.652e+01 9.57931 6.8724 1.39388 +#> ds 2 parent 3 78.4 8.652e+01 -8.12069 6.8724 -1.18164 +#> ds 2 parent 7 77.9 7.197e+01 5.93429 5.7370 1.03439 +#> ds 2 parent 7 77.7 7.197e+01 5.73429 5.7370 0.99953 +#> ds 2 parent 14 56.0 5.555e+01 0.44657 4.4637 0.10005 +#> ds 2 parent 14 54.7 5.555e+01 -0.85343 4.4637 -0.19120 +#> ds 2 parent 28 36.6 3.853e+01 -1.93170 3.1599 -0.61132 +#> ds 2 parent 28 36.8 3.853e+01 -1.73170 3.1599 -0.54803 +#> ds 2 parent 60 22.1 2.110e+01 1.00360 1.8795 0.53396 +#> ds 2 parent 60 24.7 2.110e+01 3.60360 1.8795 1.91728 +#> ds 2 parent 90 12.4 1.250e+01 -0.09712 1.3190 -0.07363 +#> ds 2 parent 90 10.8 1.250e+01 -1.69712 1.3190 -1.28667 +#> ds 2 parent 120 6.8 7.419e+00 -0.61913 1.0546 -0.58709 +#> ds 2 parent 120 7.9 7.419e+00 0.48087 1.0546 0.45599 +#> ds 2 m1 1 1.3 1.422e+00 -0.12194 0.8849 -0.13781 +#> ds 2 m1 3 3.7 3.831e+00 -0.13149 0.9282 -0.14166 +#> ds 2 m1 3 4.7 3.831e+00 0.86851 0.9282 0.93567 +#> ds 2 m1 7 8.1 7.292e+00 0.80812 1.0490 0.77034 +#> ds 2 m1 7 7.9 7.292e+00 0.60812 1.0490 0.57969 +#> ds 2 m1 14 10.1 1.055e+01 -0.45332 1.2090 -0.37495 +#> ds 2 m1 14 10.3 1.055e+01 -0.25332 1.2090 -0.20953 +#> ds 2 m1 28 10.7 1.230e+01 -1.59960 1.3074 -1.22347 +#> ds 2 m1 28 12.2 1.230e+01 -0.09960 1.3074 -0.07618 +#> ds 2 m1 60 10.7 1.065e+01 0.05342 1.2141 0.04400 +#> ds 2 m1 60 12.5 1.065e+01 1.85342 1.2141 1.52661 +#> ds 2 m1 90 9.1 8.196e+00 0.90368 1.0897 0.82930 +#> ds 2 m1 90 7.4 8.196e+00 -0.79632 1.0897 -0.73078 +#> ds 2 m1 120 6.1 5.997e+00 0.10252 0.9969 0.10284 +#> ds 2 m1 120 4.5 5.997e+00 -1.49748 0.9969 -1.50220 +#> ds 3 parent 0 106.2 1.014e+02 4.77492 8.0383 0.59402 +#> ds 3 parent 0 106.9 1.014e+02 5.47492 8.0383 0.68110 +#> ds 3 parent 1 107.4 9.390e+01 13.49935 7.4494 1.81214 +#> ds 3 parent 1 96.1 9.390e+01 2.19935 7.4494 0.29524 +#> ds 3 parent 3 79.4 8.152e+01 -2.12307 6.4821 -0.32753 +#> ds 3 parent 3 82.6 8.152e+01 1.07693 6.4821 0.16614 +#> ds 3 parent 7 63.9 6.446e+01 -0.55834 5.1533 -0.10834 +#> ds 3 parent 7 62.4 6.446e+01 -2.05834 5.1533 -0.39942 +#> ds 3 parent 14 51.0 4.826e+01 2.74073 3.9019 0.70241 +#> ds 3 parent 14 47.1 4.826e+01 -1.15927 3.9019 -0.29711 +#> ds 3 parent 28 36.1 3.424e+01 1.86399 2.8364 0.65718 +#> ds 3 parent 28 36.6 3.424e+01 2.36399 2.8364 0.83346 +#> ds 3 parent 60 20.1 1.968e+01 0.42172 1.7815 0.23672 +#> ds 3 parent 60 19.8 1.968e+01 0.12172 1.7815 0.06833 +#> ds 3 parent 90 11.3 1.195e+01 -0.64633 1.2869 -0.50222 +#> ds 3 parent 90 10.7 1.195e+01 -1.24633 1.2869 -0.96844 +#> ds 3 parent 120 8.2 7.255e+00 0.94532 1.0474 0.90251 +#> ds 3 parent 120 7.3 7.255e+00 0.04532 1.0474 0.04327 +#> ds 3 m1 0 0.8 2.956e-11 0.80000 0.8778 0.91140 +#> ds 3 m1 1 1.8 1.758e+00 0.04187 0.8886 0.04712 +#> ds 3 m1 1 2.3 1.758e+00 0.54187 0.8886 0.60978 +#> ds 3 m1 3 4.2 4.567e+00 -0.36697 0.9486 -0.38683 +#> ds 3 m1 3 4.1 4.567e+00 -0.46697 0.9486 -0.49224 +#> ds 3 m1 7 6.8 8.151e+00 -1.35124 1.0876 -1.24242 +#> ds 3 m1 7 10.1 8.151e+00 1.94876 1.0876 1.79182 +#> ds 3 m1 14 11.4 1.083e+01 0.57098 1.2240 0.46647 +#> ds 3 m1 14 12.8 1.083e+01 1.97098 1.2240 1.61022 +#> ds 3 m1 28 11.5 1.147e+01 0.03175 1.2597 0.02520 +#> ds 3 m1 28 10.6 1.147e+01 -0.86825 1.2597 -0.68928 +#> ds 3 m1 60 7.5 9.298e+00 -1.79834 1.1433 -1.57298 +#> ds 3 m1 60 8.6 9.298e+00 -0.69834 1.1433 -0.61083 +#> ds 3 m1 90 7.3 7.038e+00 0.26249 1.0382 0.25283 +#> ds 3 m1 90 8.1 7.038e+00 1.06249 1.0382 1.02340 +#> ds 3 m1 120 5.3 5.116e+00 0.18417 0.9659 0.19068 +#> ds 3 m1 120 3.8 5.116e+00 -1.31583 0.9659 -1.36232 +#> ds 4 parent 0 104.7 1.014e+02 3.27492 8.0383 0.40741 +#> ds 4 parent 0 88.3 1.014e+02 -13.12508 8.0383 -1.63281 +#> ds 4 parent 1 94.2 9.781e+01 -3.61183 7.7555 -0.46572 +#> ds 4 parent 1 94.6 9.781e+01 -3.21183 7.7555 -0.41414 +#> ds 4 parent 3 78.1 9.110e+01 -13.00467 7.2307 -1.79853 +#> ds 4 parent 3 96.5 9.110e+01 5.39533 7.2307 0.74617 +#> ds 4 parent 7 76.2 7.951e+01 -3.30511 6.3246 -0.52258 +#> ds 4 parent 7 77.8 7.951e+01 -1.70511 6.3246 -0.26960 +#> ds 4 parent 14 70.8 6.376e+01 7.03783 5.0993 1.38016 +#> ds 4 parent 14 67.3 6.376e+01 3.53783 5.0993 0.69379 +#> ds 4 parent 28 43.1 4.340e+01 -0.30456 3.5303 -0.08627 +#> ds 4 parent 28 45.1 4.340e+01 1.69544 3.5303 0.48026 +#> ds 4 parent 60 21.3 2.142e+01 -0.12077 1.9022 -0.06349 +#> ds 4 parent 60 23.5 2.142e+01 2.07923 1.9022 1.09308 +#> ds 4 parent 90 11.8 1.207e+01 -0.26813 1.2940 -0.20721 +#> ds 4 parent 90 12.1 1.207e+01 0.03187 1.2940 0.02463 +#> ds 4 parent 120 7.0 6.954e+00 0.04554 1.0347 0.04402 +#> ds 4 parent 120 6.2 6.954e+00 -0.75446 1.0347 -0.72914 +#> ds 4 m1 0 1.6 1.990e-13 1.60000 0.8778 1.82279 +#> ds 4 m1 1 0.9 7.305e-01 0.16949 0.8797 0.19267 +#> ds 4 m1 3 3.7 2.051e+00 1.64896 0.8925 1.84753 +#> ds 4 m1 3 2.0 2.051e+00 -0.05104 0.8925 -0.05719 +#> ds 4 m1 7 3.6 4.204e+00 -0.60375 0.9382 -0.64354 +#> ds 4 m1 7 3.8 4.204e+00 -0.40375 0.9382 -0.43036 +#> ds 4 m1 14 7.1 6.760e+00 0.34021 1.0267 0.33137 +#> ds 4 m1 14 6.6 6.760e+00 -0.15979 1.0267 -0.15563 +#> ds 4 m1 28 9.5 9.011e+00 0.48856 1.1289 0.43277 +#> ds 4 m1 28 9.3 9.011e+00 0.28856 1.1289 0.25561 +#> ds 4 m1 60 8.3 8.611e+00 -0.31077 1.1093 -0.28014 +#> ds 4 m1 60 9.0 8.611e+00 0.38923 1.1093 0.35086 +#> ds 4 m1 90 6.6 6.678e+00 -0.07753 1.0233 -0.07576 +#> ds 4 m1 90 7.7 6.678e+00 1.02247 1.0233 0.99915 +#> ds 4 m1 120 3.7 4.847e+00 -1.14679 0.9572 -1.19804 +#> ds 4 m1 120 3.5 4.847e+00 -1.34679 0.9572 -1.40698 +#> ds 5 parent 0 110.4 1.014e+02 8.97492 8.0383 1.11651 +#> ds 5 parent 0 112.1 1.014e+02 10.67492 8.0383 1.32800 +#> ds 5 parent 1 93.5 9.466e+01 -1.16118 7.5089 -0.15464 +#> ds 5 parent 1 91.0 9.466e+01 -3.66118 7.5089 -0.48758 +#> ds 5 parent 3 71.0 8.302e+01 -12.01844 6.5988 -1.82130 +#> ds 5 parent 3 89.7 8.302e+01 6.68156 6.5988 1.01254 +#> ds 5 parent 7 60.4 6.563e+01 -5.22574 5.2440 -0.99652 +#> ds 5 parent 7 59.1 6.563e+01 -6.52574 5.2440 -1.24442 +#> ds 5 parent 14 56.5 4.727e+01 9.22621 3.8263 2.41128 +#> ds 5 parent 14 47.0 4.727e+01 -0.27379 3.8263 -0.07156 +#> ds 5 parent 28 30.2 3.103e+01 -0.83405 2.5977 -0.32108 +#> ds 5 parent 28 23.9 3.103e+01 -7.13405 2.5977 -2.74634 +#> ds 5 parent 60 17.0 1.800e+01 -0.99696 1.6675 -0.59787 +#> ds 5 parent 60 18.7 1.800e+01 0.70304 1.6675 0.42161 +#> ds 5 parent 90 11.3 1.167e+01 -0.36809 1.2710 -0.28961 +#> ds 5 parent 90 11.9 1.167e+01 0.23191 1.2710 0.18246 +#> ds 5 parent 120 9.0 7.595e+00 1.40496 1.0623 1.32256 +#> ds 5 parent 120 8.1 7.595e+00 0.50496 1.0623 0.47535 +#> ds 5 m1 0 0.7 0.000e+00 0.70000 0.8778 0.79747 +#> ds 5 m1 1 3.0 3.158e+00 -0.15799 0.9123 -0.17317 +#> ds 5 m1 1 2.6 3.158e+00 -0.55799 0.9123 -0.61160 +#> ds 5 m1 3 5.1 8.443e+00 -3.34286 1.1013 -3.03535 +#> ds 5 m1 3 7.5 8.443e+00 -0.94286 1.1013 -0.85613 +#> ds 5 m1 7 16.5 1.580e+01 0.69781 1.5232 0.45811 +#> ds 5 m1 7 19.0 1.580e+01 3.19781 1.5232 2.09935 +#> ds 5 m1 14 22.9 2.216e+01 0.73604 1.9543 0.37663 +#> ds 5 m1 14 23.2 2.216e+01 1.03604 1.9543 0.53014 +#> ds 5 m1 28 22.2 2.423e+01 -2.03128 2.1011 -0.96678 +#> ds 5 m1 28 24.4 2.423e+01 0.16872 2.1011 0.08030 +#> ds 5 m1 60 15.5 1.876e+01 -3.25610 1.7187 -1.89455 +#> ds 5 m1 60 19.8 1.876e+01 1.04390 1.7187 0.60739 +#> ds 5 m1 90 14.9 1.366e+01 1.23585 1.3890 0.88976 +#> ds 5 m1 90 14.2 1.366e+01 0.53585 1.3890 0.38579 +#> ds 5 m1 120 10.9 9.761e+00 1.13911 1.1670 0.97613 +#> ds 5 m1 120 10.4 9.761e+00 0.63911 1.1670 0.54767 +# Add a correlation between random effects of g and k2 +cov_model_3 <- f_saem_dfop_sfo_2$so@model@covariance.model +cov_model_3["log_k2", "g_qlogis"] <- 1 +cov_model_3["g_qlogis", "log_k2"] <- 1 +f_saem_dfop_sfo_3 <- update(f_saem_dfop_sfo, + covariance.model = cov_model_3) +intervals(f_saem_dfop_sfo_3) +#> Approximate 95% confidence intervals +#> +#> Fixed effects: +#> lower est. upper +#> parent_0 98.39888363 101.48951337 104.58014311 +#> k_m1 0.01508704 0.01665986 0.01839665 +#> f_parent_to_m1 0.20141557 0.27540583 0.36418131 +#> k1 0.07708759 0.10430866 0.14114200 +#> k2 0.01476621 0.01786384 0.02161129 +#> g 0.33679867 0.45083525 0.57028162 +#> +#> Random effects: +#> lower est. upper +#> sd(f_parent_qlogis) 0.38085375 0.4441841 0.5075145 +#> sd(log_k1) 0.04774819 0.2660384 0.4843286 +#> sd(log_k2) -0.63842736 0.1977024 1.0338321 +#> sd(g_qlogis) 0.22711289 0.4502227 0.6733326 +#> corr(log_k2,g_qlogis) -0.83271473 -0.6176939 -0.4026730 +#> +#> +#> lower est. upper +#> a.1 0.67347568 0.87437392 1.07527216 +#> b.1 0.06393032 0.07912417 0.09431802 +# The correlation does not improve the fit judged by AIC and BIC, although +# the likelihood is higher with the additional parameter +anova(f_saem_dfop_sfo, f_saem_dfop_sfo_2, f_saem_dfop_sfo_3) +#> Data: 171 observations of 2 variable(s) grouped in 5 datasets +#> +#> npar AIC BIC Lik +#> f_saem_dfop_sfo_2 12 806.96 802.27 -391.48 +#> f_saem_dfop_sfo_3 13 807.99 802.91 -391.00 +#> f_saem_dfop_sfo 14 810.83 805.36 -391.42 # }
-- cgit v1.2.1