From cf54ccca37d27480dbf8d59eb027300518f7ad75 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 May 2023 17:08:43 +0200 Subject: Prepare release of v1.2.4 - Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release --- docs/reference/summary.saem.mmkin.html | 522 ++++++++++++++++----------------- 1 file changed, 261 insertions(+), 261 deletions(-) (limited to 'docs/reference/summary.saem.mmkin.html') diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index 6f7b1ac3..d9049ce5 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally mkin - 1.2.3 + 1.2.4 @@ -285,21 +285,21 @@ saemix authors for the parts inherited from saemix.

#> 810.8 805.4 -391.4 #> #> Fitted parameters: -#> estimate lower upper -#> parent_0 100.86947 97.81542 103.92353 -#> log_k_m1 -4.06947 -4.16944 -3.96950 -#> f_parent_qlogis -0.93256 -1.34200 -0.52312 -#> log_k1 -2.37017 -2.72660 -2.01375 -#> log_k2 -4.06264 -4.21344 -3.91184 -#> g_qlogis -0.02174 -0.45898 0.41549 -#> a.1 0.87598 0.67275 1.07922 -#> b.1 0.07949 0.06389 0.09509 -#> SD.parent_0 0.19170 -30.36286 30.74626 -#> SD.log_k_m1 0.01883 -0.28736 0.32502 -#> SD.f_parent_qlogis 0.44300 0.16391 0.72209 -#> SD.log_k1 0.35320 0.09661 0.60978 -#> SD.log_k2 0.13707 0.02359 0.25056 -#> SD.g_qlogis 0.37478 0.04490 0.70467 +#> estimate lower upper +#> parent_0 100.966822 97.90584 104.0278 +#> log_k_m1 -4.076164 -4.17485 -3.9775 +#> f_parent_qlogis -0.940902 -1.35358 -0.5282 +#> log_k1 -2.363988 -2.71690 -2.0111 +#> log_k2 -4.060016 -4.21743 -3.9026 +#> g_qlogis -0.029999 -0.44766 0.3877 +#> a.1 0.876272 0.67308 1.0795 +#> b.1 0.079594 0.06399 0.0952 +#> SD.parent_0 0.076322 -76.47330 76.6259 +#> SD.log_k_m1 0.005052 -1.09071 1.1008 +#> SD.f_parent_qlogis 0.446968 0.16577 0.7282 +#> SD.log_k1 0.348786 0.09502 0.6025 +#> SD.log_k2 0.147456 0.03111 0.2638 +#> SD.g_qlogis 0.348244 0.02794 0.6686 illparms(f_saem_dfop_sfo) #> [1] "sd(parent_0)" "sd(log_k_m1)" f_saem_dfop_sfo_2 <- update(f_saem_dfop_sfo, @@ -310,30 +310,30 @@ saemix authors for the parts inherited from saemix.

#> #> Fixed effects: #> lower est. upper -#> 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 +#> parent_0 98.04247057 101.09950884 104.15654711 +#> k_m1 0.01528983 0.01687734 0.01862969 +#> f_parent_to_m1 0.20447650 0.27932896 0.36887691 +#> k1 0.06779844 0.09638524 0.13702550 +#> k2 0.01495629 0.01741775 0.02028431 +#> g 0.37669311 0.48368409 0.59219202 #> #> Random effects: #> lower est. upper -#> 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 +#> sd(f_parent_qlogis) 0.16515100 0.4448330 0.7245149 +#> sd(log_k1) 0.08982372 0.3447403 0.5996568 +#> sd(log_k2) 0.02806589 0.1419560 0.2558462 +#> sd(g_qlogis) 0.04908160 0.3801993 0.7113170 #> #> #> lower est. upper -#> a.1 0.67696663 0.87777355 1.07858048 -#> b.1 0.06363957 0.07878001 0.09392044 +#> a.1 0.67539922 0.87630147 1.07720371 +#> b.1 0.06401324 0.07920531 0.09439739 summary(f_saem_dfop_sfo_2, data = TRUE) #> saemix version used for fitting: 3.2 -#> mkin version used for pre-fitting: 1.2.3 -#> R version used for fitting: 4.2.3 -#> Date of fit: Thu Apr 20 07:36:59 2023 -#> Date of summary: Thu Apr 20 07:36:59 2023 +#> mkin version used for pre-fitting: 1.2.4 +#> R version used for fitting: 4.3.0 +#> Date of fit: Fri May 19 09:20:09 2023 +#> Date of summary: Fri May 19 09:20:09 2023 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -348,7 +348,7 @@ saemix authors for the parts inherited from saemix.

#> #> Model predictions using solution type analytical #> -#> Fitted in 9.185 s +#> Fitted in 9.513 s #> Using 300, 100 iterations and 10 chains #> #> Variance model: Two-component variance function @@ -357,7 +357,7 @@ 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 -#> -0.01132 +#> -0.01133 #> #> Fixed degradation parameter values: #> None @@ -378,236 +378,236 @@ saemix authors for the parts inherited from saemix.

#> Results: #> #> Likelihood computed by importance sampling -#> AIC BIC logLik -#> 807 802.3 -391.5 +#> AIC BIC logLik +#> 806.9 802.2 -391.5 #> #> Optimised parameters: -#> est. lower upper -#> 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 +#> est. lower upper +#> parent_0 101.09951 98.04247 104.1565 +#> log_k_m1 -4.08178 -4.18057 -3.9830 +#> f_parent_qlogis -0.94779 -1.35855 -0.5370 +#> log_k1 -2.33940 -2.69122 -1.9876 +#> log_k2 -4.05027 -4.20262 -3.8979 +#> g_qlogis -0.06529 -0.50361 0.3730 +#> a.1 0.87630 0.67540 1.0772 +#> b.1 0.07921 0.06401 0.0944 +#> SD.f_parent_qlogis 0.44483 0.16515 0.7245 +#> SD.log_k1 0.34474 0.08982 0.5997 +#> SD.log_k2 0.14196 0.02807 0.2558 +#> SD.g_qlogis 0.38020 0.04908 0.7113 #> #> Correlation: #> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 -#> 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 +#> log_k_m1 -0.4716 +#> f_parent_qlogis -0.2394 0.2617 +#> log_k1 0.1677 -0.1566 -0.0659 +#> log_k2 0.0165 0.0638 0.0045 0.2013 +#> g_qlogis 0.1118 -0.1118 -0.0340 -0.2324 -0.3419 #> #> Random effects: #> 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 +#> SD.f_parent_qlogis 0.4448 0.16515 0.7245 +#> SD.log_k1 0.3447 0.08982 0.5997 +#> SD.log_k2 0.1420 0.02807 0.2558 +#> SD.g_qlogis 0.3802 0.04908 0.7113 #> #> Variance model: -#> est. lower upper -#> a.1 0.87777 0.67697 1.07858 -#> b.1 0.07878 0.06364 0.09392 +#> est. lower upper +#> a.1 0.87630 0.67540 1.0772 +#> b.1 0.07921 0.06401 0.0944 #> #> Backtransformed parameters: -#> 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 +#> est. lower upper +#> parent_0 101.09951 98.04247 104.15655 +#> k_m1 0.01688 0.01529 0.01863 +#> f_parent_to_m1 0.27933 0.20448 0.36888 +#> k1 0.09639 0.06780 0.13703 +#> k2 0.01742 0.01496 0.02028 +#> g 0.48368 0.37669 0.59219 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.2761 -#> parent_sink 0.7239 +#> parent_m1 0.2793 +#> parent_sink 0.7207 #> #> Estimated disappearance times: #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 15.54 94.33 28.4 7.102 39.83 -#> m1 41.50 137.87 NA NA NA +#> parent 15.66 94.28 28.38 7.191 39.8 +#> m1 41.07 136.43 NA NA NA #> #> Data: -#> 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 +#> ds name time observed predicted residual std standardized +#> ds 1 parent 0 89.8 1.011e+02 -11.29951 8.0554 -1.402721 +#> ds 1 parent 0 104.1 1.011e+02 3.00049 8.0554 0.372481 +#> ds 1 parent 1 88.7 9.624e+01 -7.53600 7.6726 -0.982195 +#> ds 1 parent 1 95.5 9.624e+01 -0.73600 7.6726 -0.095925 +#> ds 1 parent 3 81.8 8.736e+01 -5.55672 6.9744 -0.796732 +#> ds 1 parent 3 94.5 8.736e+01 7.14328 6.9744 1.024217 +#> ds 1 parent 7 71.5 7.251e+01 -1.00511 5.8093 -0.173019 +#> ds 1 parent 7 70.3 7.251e+01 -2.20511 5.8093 -0.379585 +#> ds 1 parent 14 54.2 5.356e+01 0.63921 4.3319 0.147560 +#> ds 1 parent 14 49.6 5.356e+01 -3.96079 4.3319 -0.914340 +#> ds 1 parent 28 31.5 3.175e+01 -0.25429 2.6634 -0.095475 +#> ds 1 parent 28 28.8 3.175e+01 -2.95429 2.6634 -1.109218 +#> ds 1 parent 60 12.1 1.281e+01 -0.71388 1.3409 -0.532390 +#> ds 1 parent 60 13.6 1.281e+01 0.78612 1.3409 0.586271 +#> ds 1 parent 90 6.2 6.405e+00 -0.20462 1.0125 -0.202083 +#> ds 1 parent 90 8.3 6.405e+00 1.89538 1.0125 1.871910 +#> ds 1 parent 120 2.2 3.329e+00 -1.12941 0.9151 -1.234165 +#> ds 1 parent 120 2.4 3.329e+00 -0.92941 0.9151 -1.015615 +#> ds 1 m1 1 0.3 1.177e+00 -0.87699 0.8812 -0.995168 +#> ds 1 m1 1 0.2 1.177e+00 -0.97699 0.8812 -1.108644 +#> ds 1 m1 3 2.2 3.268e+00 -1.06821 0.9137 -1.169063 +#> ds 1 m1 3 3.0 3.268e+00 -0.26821 0.9137 -0.293536 +#> ds 1 m1 7 6.5 6.555e+00 -0.05539 1.0186 -0.054377 +#> ds 1 m1 7 5.0 6.555e+00 -1.55539 1.0186 -1.527022 +#> ds 1 m1 14 10.2 1.017e+01 0.03108 1.1902 0.026117 +#> ds 1 m1 14 9.5 1.017e+01 -0.66892 1.1902 -0.562010 +#> ds 1 m1 28 12.2 1.270e+01 -0.50262 1.3342 -0.376708 +#> ds 1 m1 28 13.4 1.270e+01 0.69738 1.3342 0.522686 +#> ds 1 m1 60 11.8 1.078e+01 1.01734 1.2236 0.831403 +#> ds 1 m1 60 13.2 1.078e+01 2.41734 1.2236 1.975530 +#> ds 1 m1 90 6.6 7.686e+00 -1.08586 1.0670 -1.017675 +#> ds 1 m1 90 9.3 7.686e+00 1.61414 1.0670 1.512779 +#> ds 1 m1 120 3.5 5.205e+00 -1.70467 0.9684 -1.760250 +#> ds 1 m1 120 5.4 5.205e+00 0.19533 0.9684 0.201701 +#> ds 2 parent 0 118.0 1.011e+02 16.90049 8.0554 2.098026 +#> ds 2 parent 0 99.8 1.011e+02 -1.29951 8.0554 -0.161321 +#> ds 2 parent 1 90.2 9.574e+01 -5.53784 7.6334 -0.725473 +#> ds 2 parent 1 94.6 9.574e+01 -1.13784 7.6334 -0.149060 +#> ds 2 parent 3 96.1 8.638e+01 9.72233 6.8975 1.409551 +#> ds 2 parent 3 78.4 8.638e+01 -7.97767 6.8975 -1.156610 +#> ds 2 parent 7 77.9 7.194e+01 5.95854 5.7651 1.033547 +#> ds 2 parent 7 77.7 7.194e+01 5.75854 5.7651 0.998856 +#> ds 2 parent 14 56.0 5.558e+01 0.42141 4.4885 0.093888 +#> ds 2 parent 14 54.7 5.558e+01 -0.87859 4.4885 -0.195742 +#> ds 2 parent 28 36.6 3.852e+01 -1.92382 3.1746 -0.605999 +#> ds 2 parent 28 36.8 3.852e+01 -1.72382 3.1746 -0.543000 +#> ds 2 parent 60 22.1 2.108e+01 1.02043 1.8856 0.541168 +#> ds 2 parent 60 24.7 2.108e+01 3.62043 1.8856 1.920034 +#> ds 2 parent 90 12.4 1.250e+01 -0.09675 1.3220 -0.073184 +#> ds 2 parent 90 10.8 1.250e+01 -1.69675 1.3220 -1.283492 +#> ds 2 parent 120 6.8 7.426e+00 -0.62587 1.0554 -0.593027 +#> ds 2 parent 120 7.9 7.426e+00 0.47413 1.0554 0.449242 +#> ds 2 m1 1 1.3 1.417e+00 -0.11735 0.8835 -0.132825 +#> ds 2 m1 3 3.7 3.823e+00 -0.12301 0.9271 -0.132673 +#> ds 2 m1 3 4.7 3.823e+00 0.87699 0.9271 0.945909 +#> ds 2 m1 7 8.1 7.288e+00 0.81180 1.0494 0.773619 +#> ds 2 m1 7 7.9 7.288e+00 0.61180 1.0494 0.583025 +#> ds 2 m1 14 10.1 1.057e+01 -0.46957 1.2119 -0.387459 +#> ds 2 m1 14 10.3 1.057e+01 -0.26957 1.2119 -0.222432 +#> ds 2 m1 28 10.7 1.234e+01 -1.63555 1.3124 -1.246185 +#> ds 2 m1 28 12.2 1.234e+01 -0.13555 1.3124 -0.103281 +#> ds 2 m1 60 10.7 1.065e+01 0.04641 1.2165 0.038151 +#> ds 2 m1 60 12.5 1.065e+01 1.84641 1.2165 1.517773 +#> ds 2 m1 90 9.1 8.177e+00 0.92337 1.0896 0.847403 +#> ds 2 m1 90 7.4 8.177e+00 -0.77663 1.0896 -0.712734 +#> ds 2 m1 120 6.1 5.966e+00 0.13404 0.9956 0.134631 +#> ds 2 m1 120 4.5 5.966e+00 -1.46596 0.9956 -1.472460 +#> ds 3 parent 0 106.2 1.011e+02 5.10049 8.0554 0.633175 +#> ds 3 parent 0 106.9 1.011e+02 5.80049 8.0554 0.720073 +#> ds 3 parent 1 107.4 9.365e+01 13.74627 7.4695 1.840332 +#> ds 3 parent 1 96.1 9.365e+01 2.44627 7.4695 0.327504 +#> ds 3 parent 3 79.4 8.139e+01 -1.99118 6.5059 -0.306058 +#> ds 3 parent 3 82.6 8.139e+01 1.20882 6.5059 0.185803 +#> ds 3 parent 7 63.9 6.445e+01 -0.54666 5.1792 -0.105549 +#> ds 3 parent 7 62.4 6.445e+01 -2.04666 5.1792 -0.395170 +#> ds 3 parent 14 51.0 4.830e+01 2.69944 3.9247 0.687800 +#> ds 3 parent 14 47.1 4.830e+01 -1.20056 3.9247 -0.305896 +#> ds 3 parent 28 36.1 3.426e+01 1.83885 2.8516 0.644839 +#> ds 3 parent 28 36.6 3.426e+01 2.33885 2.8516 0.820177 +#> ds 3 parent 60 20.1 1.968e+01 0.42208 1.7881 0.236053 +#> ds 3 parent 60 19.8 1.968e+01 0.12208 1.7881 0.068273 +#> ds 3 parent 90 11.3 1.194e+01 -0.64013 1.2893 -0.496496 +#> ds 3 parent 90 10.7 1.194e+01 -1.24013 1.2893 -0.961865 +#> ds 3 parent 120 8.2 7.247e+00 0.95264 1.0476 0.909381 +#> ds 3 parent 120 7.3 7.247e+00 0.05264 1.0476 0.050254 +#> ds 3 m1 0 0.8 -2.956e-12 0.80000 0.8763 0.912928 +#> ds 3 m1 1 1.8 1.757e+00 0.04318 0.8873 0.048666 +#> ds 3 m1 1 2.3 1.757e+00 0.54318 0.8873 0.612186 +#> ds 3 m1 3 4.2 4.566e+00 -0.36607 0.9480 -0.386149 +#> ds 3 m1 3 4.1 4.566e+00 -0.46607 0.9480 -0.491634 +#> ds 3 m1 7 6.8 8.157e+00 -1.35680 1.0887 -1.246241 +#> ds 3 m1 7 10.1 8.157e+00 1.94320 1.0887 1.784855 +#> ds 3 m1 14 11.4 1.085e+01 0.55367 1.2272 0.451182 +#> ds 3 m1 14 12.8 1.085e+01 1.95367 1.2272 1.592023 +#> ds 3 m1 28 11.5 1.149e+01 0.01098 1.2633 0.008689 +#> ds 3 m1 28 10.6 1.149e+01 -0.88902 1.2633 -0.703717 +#> ds 3 m1 60 7.5 9.295e+00 -1.79500 1.1445 -1.568351 +#> ds 3 m1 60 8.6 9.295e+00 -0.69500 1.1445 -0.607245 +#> ds 3 m1 90 7.3 7.017e+00 0.28305 1.0377 0.272775 +#> ds 3 m1 90 8.1 7.017e+00 1.08305 1.0377 1.043720 +#> ds 3 m1 120 5.3 5.087e+00 0.21272 0.9645 0.220547 +#> ds 3 m1 120 3.8 5.087e+00 -1.28728 0.9645 -1.334660 +#> ds 4 parent 0 104.7 1.011e+02 3.60049 8.0554 0.446965 +#> ds 4 parent 0 88.3 1.011e+02 -12.79951 8.0554 -1.588930 +#> ds 4 parent 1 94.2 9.755e+01 -3.35176 7.7762 -0.431030 +#> ds 4 parent 1 94.6 9.755e+01 -2.95176 7.7762 -0.379591 +#> ds 4 parent 3 78.1 9.095e+01 -12.85198 7.2570 -1.770981 +#> ds 4 parent 3 96.5 9.095e+01 5.54802 7.2570 0.764508 +#> ds 4 parent 7 76.2 7.949e+01 -3.29267 6.3569 -0.517966 +#> ds 4 parent 7 77.8 7.949e+01 -1.69267 6.3569 -0.266272 +#> ds 4 parent 14 70.8 6.384e+01 6.95621 5.1321 1.355423 +#> ds 4 parent 14 67.3 6.384e+01 3.45621 5.1321 0.673445 +#> ds 4 parent 28 43.1 4.345e+01 -0.35291 3.5515 -0.099370 +#> ds 4 parent 28 45.1 4.345e+01 1.64709 3.5515 0.463771 +#> ds 4 parent 60 21.3 2.137e+01 -0.07478 1.9063 -0.039229 +#> ds 4 parent 60 23.5 2.137e+01 2.12522 1.9063 1.114813 +#> ds 4 parent 90 11.8 1.205e+01 -0.24925 1.2957 -0.192375 +#> ds 4 parent 90 12.1 1.205e+01 0.05075 1.2957 0.039168 +#> ds 4 parent 120 7.0 6.967e+00 0.03315 1.0356 0.032013 +#> ds 4 parent 120 6.2 6.967e+00 -0.76685 1.0356 -0.740510 +#> ds 4 m1 0 1.6 1.421e-13 1.60000 0.8763 1.825856 +#> ds 4 m1 1 0.9 7.250e-01 0.17503 0.8782 0.199310 +#> ds 4 m1 3 3.7 2.038e+00 1.66201 0.8910 1.865236 +#> ds 4 m1 3 2.0 2.038e+00 -0.03799 0.8910 -0.042637 +#> ds 4 m1 7 3.6 4.186e+00 -0.58623 0.9369 -0.625692 +#> ds 4 m1 7 3.8 4.186e+00 -0.38623 0.9369 -0.412230 +#> ds 4 m1 14 7.1 6.752e+00 0.34768 1.0266 0.338666 +#> ds 4 m1 14 6.6 6.752e+00 -0.15232 1.0266 -0.148372 +#> ds 4 m1 28 9.5 9.034e+00 0.46628 1.1313 0.412159 +#> ds 4 m1 28 9.3 9.034e+00 0.26628 1.1313 0.235373 +#> ds 4 m1 60 8.3 8.634e+00 -0.33359 1.1115 -0.300112 +#> ds 4 m1 60 9.0 8.634e+00 0.36641 1.1115 0.329645 +#> ds 4 m1 90 6.6 6.671e+00 -0.07091 1.0233 -0.069295 +#> ds 4 m1 90 7.7 6.671e+00 1.02909 1.0233 1.005691 +#> ds 4 m1 120 3.7 4.823e+00 -1.12301 0.9559 -1.174763 +#> ds 4 m1 120 3.5 4.823e+00 -1.32301 0.9559 -1.383979 +#> ds 5 parent 0 110.4 1.011e+02 9.30049 8.0554 1.154563 +#> ds 5 parent 0 112.1 1.011e+02 11.00049 8.0554 1.365601 +#> ds 5 parent 1 93.5 9.440e+01 -0.90098 7.5282 -0.119681 +#> ds 5 parent 1 91.0 9.440e+01 -3.40098 7.5282 -0.451764 +#> ds 5 parent 3 71.0 8.287e+01 -11.86698 6.6217 -1.792122 +#> ds 5 parent 3 89.7 8.287e+01 6.83302 6.6217 1.031907 +#> ds 5 parent 7 60.4 6.562e+01 -5.22329 5.2711 -0.990936 +#> ds 5 parent 7 59.1 6.562e+01 -6.52329 5.2711 -1.237566 +#> ds 5 parent 14 56.5 4.739e+01 9.10588 3.8548 2.362225 +#> ds 5 parent 14 47.0 4.739e+01 -0.39412 3.8548 -0.102240 +#> ds 5 parent 28 30.2 3.118e+01 -0.98128 2.6206 -0.374451 +#> ds 5 parent 28 23.9 3.118e+01 -7.28128 2.6206 -2.778500 +#> ds 5 parent 60 17.0 1.804e+01 -1.03959 1.6761 -0.620224 +#> ds 5 parent 60 18.7 1.804e+01 0.66041 1.6761 0.394008 +#> ds 5 parent 90 11.3 1.165e+01 -0.35248 1.2727 -0.276958 +#> ds 5 parent 90 11.9 1.165e+01 0.24752 1.2727 0.194488 +#> ds 5 parent 120 9.0 7.556e+00 1.44368 1.0612 1.360449 +#> ds 5 parent 120 8.1 7.556e+00 0.54368 1.0612 0.512338 +#> ds 5 m1 0 0.7 -1.421e-14 0.70000 0.8763 0.798812 +#> ds 5 m1 1 3.0 3.160e+00 -0.15979 0.9113 -0.175340 +#> ds 5 m1 1 2.6 3.160e+00 -0.55979 0.9113 -0.614254 +#> ds 5 m1 3 5.1 8.448e+00 -3.34789 1.1026 -3.036487 +#> ds 5 m1 3 7.5 8.448e+00 -0.94789 1.1026 -0.859720 +#> ds 5 m1 7 16.5 1.581e+01 0.68760 1.5286 0.449839 +#> ds 5 m1 7 19.0 1.581e+01 3.18760 1.5286 2.085373 +#> ds 5 m1 14 22.9 2.218e+01 0.71983 1.9632 0.366658 +#> ds 5 m1 14 23.2 2.218e+01 1.01983 1.9632 0.519469 +#> ds 5 m1 28 22.2 2.425e+01 -2.05105 2.1113 -0.971479 +#> ds 5 m1 28 24.4 2.425e+01 0.14895 2.1113 0.070552 +#> ds 5 m1 60 15.5 1.876e+01 -3.25968 1.7250 -1.889646 +#> ds 5 m1 60 19.8 1.876e+01 1.04032 1.7250 0.603074 +#> ds 5 m1 90 14.9 1.365e+01 1.25477 1.3914 0.901806 +#> ds 5 m1 90 14.2 1.365e+01 0.55477 1.3914 0.398714 +#> ds 5 m1 120 10.9 9.726e+00 1.17443 1.1667 1.006587 +#> ds 5 m1 120 10.4 9.726e+00 0.67443 1.1667 0.578044 # 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 @@ -619,34 +619,34 @@ saemix authors for the parts inherited from saemix.

#> #> 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 +#> parent_0 98.32277831 101.40841461 104.49405092 +#> k_m1 0.01510464 0.01667815 0.01841557 +#> f_parent_to_m1 0.20195605 0.27597108 0.36471512 +#> k1 0.07321367 0.10121120 0.13991523 +#> k2 0.01466928 0.01766483 0.02127208 +#> g 0.35098400 0.46314412 0.57916193 #> #> 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 +#> sd(f_parent_qlogis) 0.3832326 0.4435601 0.5038876 +#> sd(log_k1) 0.1181772 0.2996192 0.4810613 +#> sd(log_k2) -0.6281964 0.1898692 1.0079349 +#> sd(g_qlogis) 0.1885523 0.4250717 0.6615911 +#> corr(log_k2,g_qlogis) -0.8453380 -0.5695240 -0.2937099 #> #> #> lower est. upper -#> a.1 0.67347568 0.87437392 1.07527216 -#> b.1 0.06393032 0.07912417 0.09431802 +#> a.1 0.67302582 0.87410123 1.07517663 +#> b.1 0.06403679 0.07925211 0.09446744 # 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 +#> f_saem_dfop_sfo_2 12 806.91 802.23 -391.46 +#> f_saem_dfop_sfo_3 13 807.91 802.83 -390.95 +#> f_saem_dfop_sfo 14 810.83 805.36 -391.41 # } -- cgit v1.2.1