Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full.
# S3 method for saem.mmkin 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, ...)
| object | an object of class saem.mmkin |
|---|---|
| data | logical, indicating whether the full data should be included in the summary. |
| verbose | Should the summary be verbose? |
| distimes | logical, indicating whether DT50 and DT90 values should be included. |
| ... | optional arguments passed to methods like |
| x | an object of class summary.saem.mmkin |
| digits | Number of digits to use for printing |
The summary function returns a list based on the saemix::SaemixObject obtained in the fit, with at least the following additional components
The saemix, mkin and R versions used
The dates where the fit and the summary were produced
The differential equations used in the degradation model
Was maximum or minimum use made of formation fractions
The data
Transformed parameters as used in the optimisation, with confidence intervals
Backtransformed parameters, with confidence intervals if available
Error model parameters with confidence intervals
The estimated formation fractions derived from the fitted model.
The DT50 and DT90 values for each observed variable.
If applicable, eigenvalues of SFORB components of the model.
Johannes Ranke for the mkin specific parts saemix authors for the parts inherited from saemix.
# Generate five datasets following DFOP-SFO kinetics sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"), m1 = mkinsub("SFO"), quiet = TRUE) set.seed(1234) k1_in <- rlnorm(5, log(0.1), 0.3) k2_in <- rlnorm(5, log(0.02), 0.3) g_in <- plogis(rnorm(5, qlogis(0.5), 0.3)) f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3)) k_m1_in <- rlnorm(5, log(0.02), 0.3) pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) { mkinpredict(dfop_sfo, c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1), c(parent = 100, m1 = 0), sampling_times) } ds_mean_dfop_sfo <- lapply(1:5, function(i) { mkinpredict(dfop_sfo, c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i], f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]), c(parent = 100, m1 = 0), sampling_times) }) names(ds_mean_dfop_sfo) <- paste("ds", 1:5) ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) { add_err(ds, sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), n = 1)[[1]] }) # \dontrun{ # Evaluate using mmkin and saem 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 Nov 11 19:48:36 2020" #> .... #> Minimisation finished #> [1] "Wed Nov 11 19:48:48 2020"#> #> LL by is "-401.01 (df=14)"#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 #> Date of fit: Wed Nov 11 19:48:49 2020 #> Date of summary: Wed Nov 11 19:48:49 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * #> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) #> * parent #> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) #> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * #> exp(-k2 * time))) * parent - k_m1 * m1 #> #> Data: #> 171 observations of 2 variable(s) grouped in 5 datasets #> #> Model predictions using solution type analytical #> #> Fitted in 13.272 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 #> 101.65644697 -4.05368181 -0.94310703 -2.35943247 -4.07006293 #> g_qlogis #> -0.01132621 #> #> Fixed degradation parameter values: #> None #> #> Results: #> #> Likelihood computed by importance sampling #> AIC BIC logLik #> 830 824.5 -401 #> #> Optimised, transformed parameters with symmetric confidence intervals: #> est. lower upper #> parent_0 101.4423 97.862 105.0224 #> log_k_m1 -4.0703 -4.191 -3.9495 #> f_parent_qlogis -0.9539 -1.313 -0.5949 #> log_k1 -2.9724 -3.811 -2.1342 #> log_k2 -3.4977 -4.206 -2.7895 #> g_qlogis -0.0449 -1.116 1.0262 #> #> Correlation: #> prnt_0 lg_k_1 f_prn_ log_k1 log_k2 #> log_k_m1 -0.207 #> f_parent_qlogis -0.148 0.202 #> log_k1 0.040 -0.038 -0.022 #> log_k2 0.022 -0.015 -0.009 0.001 #> g_qlogis -0.012 0.005 0.011 -0.173 -0.130 #> #> Random effects: #> est. lower upper #> SD.parent_0 2.88564 -0.5163 6.2876 #> SD.log_k_m1 0.08502 -0.0427 0.2127 #> SD.f_parent_qlogis 0.38857 0.1350 0.6421 #> SD.log_k1 0.92338 0.3296 1.5172 #> SD.log_k2 0.78644 0.2817 1.2912 #> SD.g_qlogis 0.34614 -0.8727 1.5650 #> #> Variance model: #> est. lower upper #> a.1 0.65859 0.49250 0.82469 #> b.1 0.06411 0.05006 0.07817 #> #> Backtransformed parameters with asymmetric confidence intervals: #> est. lower upper #> parent_0 101.44231 97.86220 105.02241 #> k_m1 0.01707 0.01513 0.01926 #> f_parent_to_m1 0.27811 0.21201 0.35551 #> k1 0.05118 0.02213 0.11834 #> k2 0.03027 0.01491 0.06145 #> g 0.48878 0.24675 0.73618 #> #> Resulting formation fractions: #> ff #> parent_m1 0.2781 #> parent_sink 0.7219 #> #> Estimated disappearance times: #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 17.53 61.64 18.55 13.54 22.9 #> m1 40.60 134.88 NA NA NA #> #> Data: #> ds name time observed predicted residual standardized #> ds 1 parent 0 89.8 9.869e+01 -8.894553 1.273163 #> ds 1 parent 0 104.1 9.869e+01 5.405447 -0.773734 #> ds 1 parent 1 88.7 9.413e+01 -5.426448 0.810727 #> ds 1 parent 1 95.5 9.413e+01 1.373552 -0.205213 #> ds 1 parent 3 81.8 8.576e+01 -3.961821 0.643463 #> ds 1 parent 3 94.5 8.576e+01 8.738179 -1.419220 #> ds 1 parent 7 71.5 7.168e+01 -0.184828 0.035175 #> ds 1 parent 7 70.3 7.168e+01 -1.384828 0.263550 #> ds 1 parent 14 54.2 5.351e+01 0.688235 -0.168298 #> ds 1 parent 14 49.6 5.351e+01 -3.911765 0.956565 #> ds 1 parent 28 31.5 3.209e+01 -0.590445 0.217395 #> ds 1 parent 28 28.8 3.209e+01 -3.290445 1.211502 #> ds 1 parent 60 12.1 1.272e+01 -0.618158 0.419377 #> ds 1 parent 60 13.6 1.272e+01 0.881842 -0.598269 #> ds 1 parent 90 6.2 6.085e+00 0.115212 -0.109861 #> ds 1 parent 90 8.3 6.085e+00 2.215212 -2.112329 #> ds 1 parent 120 2.2 3.009e+00 -0.809439 0.950563 #> ds 1 parent 120 2.4 3.009e+00 -0.609439 0.715693 #> ds 1 m1 1 0.3 1.129e+00 -0.828817 1.133869 #> ds 1 m1 1 0.2 1.129e+00 -0.928817 1.270675 #> ds 1 m1 3 2.2 3.141e+00 -0.940880 1.094093 #> ds 1 m1 3 3.0 3.141e+00 -0.140880 0.163821 #> ds 1 m1 7 6.5 6.326e+00 0.174162 -0.163662 #> ds 1 m1 7 5.0 6.326e+00 -1.325838 1.245901 #> ds 1 m1 14 10.2 9.883e+00 0.317417 -0.245642 #> ds 1 m1 14 9.5 9.883e+00 -0.382583 0.296072 #> ds 1 m1 28 12.2 1.251e+01 -0.309856 0.212138 #> ds 1 m1 28 13.4 1.251e+01 0.890144 -0.609422 #> ds 1 m1 60 11.8 1.086e+01 0.940009 -0.693807 #> ds 1 m1 60 13.2 1.086e+01 2.340009 -1.727126 #> ds 1 m1 90 6.6 7.823e+00 -1.222977 1.054158 #> ds 1 m1 90 9.3 7.823e+00 1.477023 -1.273135 #> ds 1 m1 120 3.5 5.315e+00 -1.815201 1.816354 #> ds 1 m1 120 5.4 5.315e+00 0.084799 -0.084853 #> ds 2 parent 0 118.0 1.031e+02 14.876736 -2.046284 #> ds 2 parent 0 99.8 1.031e+02 -3.323264 0.457112 #> ds 2 parent 1 90.2 9.757e+01 -7.371379 1.066126 #> ds 2 parent 1 94.6 9.757e+01 -2.971379 0.429752 #> ds 2 parent 3 96.1 8.788e+01 8.222746 -1.306721 #> ds 2 parent 3 78.4 8.788e+01 -9.477254 1.506081 #> ds 2 parent 7 77.9 7.293e+01 4.972272 -0.932149 #> ds 2 parent 7 77.7 7.293e+01 4.772272 -0.894656 #> ds 2 parent 14 56.0 5.602e+01 -0.016773 0.003947 #> ds 2 parent 14 54.7 5.602e+01 -1.316773 0.309830 #> ds 2 parent 28 36.6 3.855e+01 -1.945779 0.621680 #> ds 2 parent 28 36.8 3.855e+01 -1.745779 0.557779 #> ds 2 parent 60 22.1 2.101e+01 1.086693 -0.541771 #> ds 2 parent 60 24.7 2.101e+01 3.686693 -1.838002 #> ds 2 parent 90 12.4 1.246e+01 -0.058759 0.040319 #> ds 2 parent 90 10.8 1.246e+01 -1.658759 1.138195 #> ds 2 parent 120 6.8 7.406e+00 -0.606226 0.534861 #> ds 2 parent 120 7.9 7.406e+00 0.493774 -0.435647 #> ds 2 m1 1 1.3 1.438e+00 -0.138236 0.184118 #> ds 2 m1 3 3.7 3.879e+00 -0.178617 0.196874 #> ds 2 m1 3 4.7 3.879e+00 0.821383 -0.905344 #> ds 2 m1 7 8.1 7.389e+00 0.710951 -0.627868 #> ds 2 m1 7 7.9 7.389e+00 0.510951 -0.451240 #> ds 2 m1 14 10.1 1.069e+01 -0.593533 0.441556 #> ds 2 m1 14 10.3 1.069e+01 -0.393533 0.292767 #> ds 2 m1 28 10.7 1.240e+01 -1.703647 1.171837 #> ds 2 m1 28 12.2 1.240e+01 -0.203647 0.140077 #> ds 2 m1 60 10.7 1.055e+01 0.147672 -0.110605 #> ds 2 m1 60 12.5 1.055e+01 1.947672 -1.458786 #> ds 2 m1 90 9.1 8.010e+00 1.090041 -0.929963 #> ds 2 m1 90 7.4 8.010e+00 -0.609959 0.520383 #> ds 2 m1 120 6.1 5.793e+00 0.306797 -0.297858 #> ds 2 m1 120 4.5 5.793e+00 -1.293203 1.255523 #> ds 3 parent 0 106.2 1.035e+02 2.712344 -0.371886 #> ds 3 parent 0 106.9 1.035e+02 3.412344 -0.467862 #> ds 3 parent 1 107.4 9.548e+01 11.924044 -1.758752 #> ds 3 parent 1 96.1 9.548e+01 0.624044 -0.092044 #> ds 3 parent 3 79.4 8.246e+01 -3.056105 0.514055 #> ds 3 parent 3 82.6 8.246e+01 0.143895 -0.024204 #> ds 3 parent 7 63.9 6.489e+01 -0.991141 0.205676 #> ds 3 parent 7 62.4 6.489e+01 -2.491141 0.516947 #> ds 3 parent 14 51.0 4.869e+01 2.306824 -0.610198 #> ds 3 parent 14 47.1 4.869e+01 -1.593176 0.421425 #> ds 3 parent 28 36.1 3.480e+01 1.304261 -0.451388 #> ds 3 parent 28 36.6 3.480e+01 1.804261 -0.624431 #> ds 3 parent 60 20.1 1.988e+01 0.221952 -0.114821 #> ds 3 parent 60 19.8 1.988e+01 -0.078048 0.040376 #> ds 3 parent 90 11.3 1.194e+01 -0.642458 0.451083 #> ds 3 parent 90 10.7 1.194e+01 -1.242458 0.872355 #> ds 3 parent 120 8.2 7.176e+00 1.023847 -0.915231 #> ds 3 parent 120 7.3 7.176e+00 0.123847 -0.110709 #> ds 3 m1 0 0.8 8.527e-13 0.800000 -1.214712 #> ds 3 m1 1 1.8 1.856e+00 -0.055925 0.071921 #> ds 3 m1 1 2.3 1.856e+00 0.444075 -0.571099 #> ds 3 m1 3 4.2 4.780e+00 -0.580164 0.601168 #> ds 3 m1 3 4.1 4.780e+00 -0.680164 0.704788 #> ds 3 m1 7 6.8 8.410e+00 -1.609920 1.344090 #> ds 3 m1 7 10.1 8.410e+00 1.690080 -1.411014 #> ds 3 m1 14 11.4 1.098e+01 0.424444 -0.311572 #> ds 3 m1 14 12.8 1.098e+01 1.824444 -1.339271 #> ds 3 m1 28 11.5 1.142e+01 0.079336 -0.057043 #> ds 3 m1 28 10.6 1.142e+01 -0.820664 0.590065 #> ds 3 m1 60 7.5 9.110e+00 -1.610231 1.295778 #> ds 3 m1 60 8.6 9.110e+00 -0.510231 0.410591 #> ds 3 m1 90 7.3 6.799e+00 0.501085 -0.457825 #> ds 3 m1 90 8.1 6.799e+00 1.301085 -1.188759 #> ds 3 m1 120 5.3 4.868e+00 0.431505 -0.444518 #> ds 3 m1 120 3.8 4.868e+00 -1.068495 1.100718 #> ds 4 parent 0 104.7 9.926e+01 5.444622 -0.775351 #> ds 4 parent 0 88.3 9.926e+01 -10.955378 1.560119 #> ds 4 parent 1 94.2 9.618e+01 -1.978413 0.289883 #> ds 4 parent 1 94.6 9.618e+01 -1.578413 0.231274 #> ds 4 parent 3 78.1 9.037e+01 -12.268550 1.901399 #> ds 4 parent 3 96.5 9.037e+01 6.131450 -0.950262 #> ds 4 parent 7 76.2 7.999e+01 -3.794958 0.655739 #> ds 4 parent 7 77.8 7.999e+01 -2.194958 0.379272 #> ds 4 parent 14 70.8 6.518e+01 5.624996 -1.162874 #> ds 4 parent 14 67.3 6.518e+01 2.124996 -0.439307 #> ds 4 parent 28 43.1 4.462e+01 -1.517860 0.431312 #> ds 4 parent 28 45.1 4.462e+01 0.482140 -0.137004 #> ds 4 parent 60 21.3 2.130e+01 0.003305 -0.001633 #> ds 4 parent 60 23.5 2.130e+01 2.203305 -1.088598 #> ds 4 parent 90 11.8 1.180e+01 -0.002834 0.002002 #> ds 4 parent 90 12.1 1.180e+01 0.297166 -0.209966 #> ds 4 parent 120 7.0 6.868e+00 0.132251 -0.120348 #> ds 4 parent 120 6.2 6.868e+00 -0.667749 0.607650 #> ds 4 m1 0 1.6 0.000e+00 1.600000 -2.429424 #> ds 4 m1 1 0.9 6.826e-01 0.217363 -0.309476 #> ds 4 m1 3 3.7 1.935e+00 1.765082 -2.255277 #> ds 4 m1 3 2.0 1.935e+00 0.065082 -0.083157 #> ds 4 m1 7 3.6 4.035e+00 -0.434805 0.474018 #> ds 4 m1 7 3.8 4.035e+00 -0.234805 0.255981 #> ds 4 m1 14 7.1 6.652e+00 0.448187 -0.413053 #> ds 4 m1 14 6.6 6.652e+00 -0.051813 0.047751 #> ds 4 m1 28 9.5 9.156e+00 0.343805 -0.276011 #> ds 4 m1 28 9.3 9.156e+00 0.143805 -0.115448 #> ds 4 m1 60 8.3 8.848e+00 -0.547762 0.446843 #> ds 4 m1 60 9.0 8.848e+00 0.152238 -0.124190 #> ds 4 m1 90 6.6 6.674e+00 -0.073979 0.068090 #> ds 4 m1 90 7.7 6.674e+00 1.026021 -0.944353 #> ds 4 m1 120 3.7 4.668e+00 -0.967537 1.010122 #> ds 4 m1 120 3.5 4.668e+00 -1.167537 1.218925 #> ds 5 parent 0 110.4 1.022e+02 8.170986 -1.132847 #> ds 5 parent 0 112.1 1.022e+02 9.870986 -1.368539 #> ds 5 parent 1 93.5 9.513e+01 -1.630764 0.241319 #> ds 5 parent 1 91.0 9.513e+01 -4.130764 0.611268 #> ds 5 parent 3 71.0 8.296e+01 -11.964279 2.001495 #> ds 5 parent 3 89.7 8.296e+01 6.735721 -1.126813 #> ds 5 parent 7 60.4 6.495e+01 -4.547441 0.942951 #> ds 5 parent 7 59.1 6.495e+01 -5.847441 1.212518 #> ds 5 parent 14 56.5 4.626e+01 10.241319 -2.825682 #> ds 5 parent 14 47.0 4.626e+01 0.741319 -0.204537 #> ds 5 parent 28 30.2 3.026e+01 -0.058478 0.022504 #> ds 5 parent 28 23.9 3.026e+01 -6.358478 2.446932 #> ds 5 parent 60 17.0 1.792e+01 -0.919046 0.508481 #> ds 5 parent 60 18.7 1.792e+01 0.780954 -0.432079 #> ds 5 parent 90 11.3 1.187e+01 -0.573917 0.404206 #> ds 5 parent 90 11.9 1.187e+01 0.026083 -0.018370 #> ds 5 parent 120 9.0 7.898e+00 1.102089 -0.946039 #> ds 5 parent 120 8.1 7.898e+00 0.202089 -0.173474 #> ds 5 m1 0 0.7 -1.421e-14 0.700000 -1.062873 #> ds 5 m1 1 3.0 3.144e+00 -0.143526 0.166865 #> ds 5 m1 1 2.6 3.144e+00 -0.543526 0.631910 #> ds 5 m1 3 5.1 8.390e+00 -3.290265 2.749870 #> ds 5 m1 3 7.5 8.390e+00 -0.890265 0.744048 #> ds 5 m1 7 16.5 1.566e+01 0.841368 -0.506082 #> ds 5 m1 7 19.0 1.566e+01 3.341368 -2.009830 #> ds 5 m1 14 22.9 2.188e+01 1.017753 -0.493689 #> ds 5 m1 14 23.2 2.188e+01 1.317753 -0.639212 #> ds 5 m1 28 22.2 2.386e+01 -1.655914 0.756794 #> ds 5 m1 28 24.4 2.386e+01 0.544086 -0.248661 #> ds 5 m1 60 15.5 1.859e+01 -3.091124 1.670405 #> ds 5 m1 60 19.8 1.859e+01 1.208876 -0.653262 #> ds 5 m1 90 14.9 1.372e+01 1.176815 -0.764948 #> ds 5 m1 90 14.2 1.372e+01 0.476815 -0.309937 #> ds 5 m1 120 10.9 9.961e+00 0.938796 -0.723690 #> ds 5 m1 120 10.4 9.961e+00 0.438796 -0.338255# }