Summary method for class

- - -

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 nlme.mmkin
-summary(
-  object,
-  data = FALSE,
-  verbose = FALSE,
-  distimes = TRUE,
-  alpha = 0.05,
-  ...
-)
-
-# S3 method for summary.nlme.mmkin
-print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)

- -

Arguments

object: an object of class nlme.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.
alpha: error level for confidence interval estimation from the t -distribution
...: optional arguments passed to methods like print.
x: an object of class summary.nlme.mmkin
digits: Number of digits to use for printing

Value

- - -

The summary function returns a list based on the nlme object -obtained in the fit, with at least the following additional components

nlmeversion, mkinversion, Rversion: The nlme, mkin and R versions used
date.fit, date.summary: The dates where the fit and the summary were -produced
diffs: The differential equations used in the degradation model
use_of_ff: Was maximum or minimum use made of formation fractions
data: The data
confint_trans: Transformed parameters as used in the optimisation, with confidence intervals
confint_back: Backtransformed parameters, with confidence intervals if available
ff: The estimated formation fractions derived from the fitted -model.
distimes: The DT50 and DT90 values for each observed variable.
SFORB: If applicable, eigenvalues of SFORB components of the model.

The print method is called for its side effect, i.e. printing the summary.

Author

Johannes Ranke for the mkin specific parts -José Pinheiro and Douglas Bates for the components inherited from nlme

- -

Examples


-# Generate five datasets following SFO kinetics
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-dt50_sfo_in_pop <- 50
-k_in_pop <- log(2) / dt50_sfo_in_pop
-set.seed(1234)
-k_in <- rlnorm(5, log(k_in_pop), 0.5)
-SFO <- mkinmod(parent = mkinsub("SFO"))
-
-pred_sfo <- function(k) {
-  mkinpredict(SFO,
-    c(k_parent = k),
-    c(parent = 100),
-    sampling_times)
-}
-
-ds_sfo_mean <- lapply(k_in, pred_sfo)
-names(ds_sfo_mean) <- paste("ds", 1:5)
-
-set.seed(12345)
-ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) {
-  add_err(ds,
-    sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),
-    n = 1)[[1]]
-})
-
-# \dontrun{
-# Evaluate using mmkin and nlme
-library(nlme)
-f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
-#> Warning: Optimisation did not converge:
-#> iteration limit reached without convergence (10)
-f_nlme <- nlme(f_mmkin)
-summary(f_nlme, data = TRUE)
-#> nlme version used for fitting:      3.1.162 
-#> mkin version used for pre-fitting:  1.2.3 
-#> R version used for fitting:         4.2.3 
-#> Date of fit:     Sun Apr 16 08:34:41 2023 
-#> Date of summary: Sun Apr 16 08:34:41 2023 
-#> 
-#> Equations:
-#> d_parent/dt = - k_parent * parent
-#> 
-#> Data:
-#> 90 observations of 1 variable(s) grouped in 5 datasets
-#> 
-#> Model predictions using solution type analytical 
-#> 
-#> Fitted in 0.194 s using 4 iterations
-#> 
-#> Variance model: Two-component variance function 
-#> 
-#> Mean of starting values for individual parameters:
-#>     parent_0 log_k_parent 
-#>      101.569       -4.454 
-#> 
-#> Fixed degradation parameter values:
-#> None
-#> 
-#> Results:
-#> 
-#>     AIC   BIC logLik
-#>   584.5 599.5 -286.2
-#> 
-#> Optimised, transformed parameters with symmetric confidence intervals:
-#>               lower    est.   upper
-#> parent_0     99.371 101.592 103.814
-#> log_k_parent -4.973  -4.449  -3.926
-#> 
-#> Correlation: 
-#>              parnt_0
-#> log_k_parent 0.0507 
-#> 
-#> Random effects:
-#>  Formula: list(parent_0 ~ 1, log_k_parent ~ 1)
-#>  Level: ds
-#>  Structure: Diagonal
-#>         parent_0 log_k_parent Residual
-#> StdDev: 6.92e-05       0.5863        1
-#> 
-#> Variance function:
-#>  Structure: Constant plus proportion of variance covariate
-#>  Formula: ~fitted(.) 
-#>  Parameter estimates:
-#>        const         prop 
-#> 0.0001208154 0.0789968021 
-#> 
-#> Backtransformed parameters with asymmetric confidence intervals:
-#>              lower      est.     upper
-#> parent_0 99.370882 101.59243 103.81398
-#> k_parent  0.006923   0.01168   0.01972
-#> 
-#> Estimated disappearance times:
-#>         DT50  DT90
-#> parent 59.32 197.1
-#> 
-#> Data:
-#>    ds   name time observed predicted  residual    std standardized
-#>  ds 1 parent    0    104.1   101.592   2.50757 8.0255     0.312451
-#>  ds 1 parent    0    105.0   101.592   3.40757 8.0255     0.424594
-#>  ds 1 parent    1     98.5   100.796  -2.29571 7.9625    -0.288313
-#>  ds 1 parent    1     96.1   100.796  -4.69571 7.9625    -0.589725
-#>  ds 1 parent    3    101.9    99.221   2.67904 7.8381     0.341796
-#>  ds 1 parent    3     85.2    99.221 -14.02096 7.8381    -1.788812
-#>  ds 1 parent    7     99.1    96.145   2.95512 7.5951     0.389081
-#>  ds 1 parent    7     93.0    96.145  -3.14488 7.5951    -0.414065
-#>  ds 1 parent   14     88.1    90.989  -2.88944 7.1879    -0.401987
-#>  ds 1 parent   14     84.1    90.989  -6.88944 7.1879    -0.958480
-#>  ds 1 parent   28     80.2    81.493  -1.29305 6.4377    -0.200857
-#>  ds 1 parent   28     91.3    81.493   9.80695 6.4377     1.523364
-#>  ds 1 parent   60     65.1    63.344   1.75642 5.0039     0.351008
-#>  ds 1 parent   60     65.8    63.344   2.45642 5.0039     0.490898
-#>  ds 1 parent   90     47.8    50.018  -2.21764 3.9512    -0.561252
-#>  ds 1 parent   90     53.5    50.018   3.48236 3.9512     0.881335
-#>  ds 1 parent  120     37.6    39.495  -1.89515 3.1200    -0.607423
-#>  ds 1 parent  120     39.3    39.495  -0.19515 3.1200    -0.062549
-#>  ds 2 parent    0    107.9   101.592   6.30757 8.0255     0.785943
-#>  ds 2 parent    0    102.1   101.592   0.50757 8.0255     0.063245
-#>  ds 2 parent    1    103.8   100.058   3.74159 7.9043     0.473361
-#>  ds 2 parent    1    108.6   100.058   8.54159 7.9043     1.080626
-#>  ds 2 parent    3     91.0    97.060  -6.05952 7.6674    -0.790297
-#>  ds 2 parent    3     84.9    97.060 -12.15952 7.6674    -1.585874
-#>  ds 2 parent    7     79.3    91.329 -12.02867 7.2147    -1.667251
-#>  ds 2 parent    7    100.9    91.329   9.57133 7.2147     1.326647
-#>  ds 2 parent   14     77.3    82.102  -4.80185 6.4858    -0.740366
-#>  ds 2 parent   14     83.5    82.102   1.39815 6.4858     0.215571
-#>  ds 2 parent   28     66.8    66.351   0.44945 5.2415     0.085748
-#>  ds 2 parent   28     63.3    66.351  -3.05055 5.2415    -0.582002
-#>  ds 2 parent   60     40.8    40.775   0.02474 3.2211     0.007679
-#>  ds 2 parent   60     44.8    40.775   4.02474 3.2211     1.249485
-#>  ds 2 parent   90     27.8    25.832   1.96762 2.0407     0.964198
-#>  ds 2 parent   90     27.0    25.832   1.16762 2.0407     0.572171
-#>  ds 2 parent  120     15.2    16.366  -1.16561 1.2928    -0.901595
-#>  ds 2 parent  120     15.5    16.366  -0.86561 1.2928    -0.669547
-#>  ds 3 parent    0     97.7   101.592  -3.89243 8.0255    -0.485009
-#>  ds 3 parent    0     88.2   101.592 -13.39243 8.0255    -1.668739
-#>  ds 3 parent    1    109.9    99.218  10.68196 7.8379     1.362858
-#>  ds 3 parent    1     97.8    99.218  -1.41804 7.8379    -0.180921
-#>  ds 3 parent    3    100.5    94.634   5.86555 7.4758     0.784603
-#>  ds 3 parent    3     77.4    94.634 -17.23445 7.4758    -2.305360
-#>  ds 3 parent    7     78.3    86.093  -7.79273 6.8011    -1.145813
-#>  ds 3 parent    7     90.3    86.093   4.20727 6.8011     0.618620
-#>  ds 3 parent   14     76.0    72.958   3.04222 5.7634     0.527848
-#>  ds 3 parent   14     79.1    72.958   6.14222 5.7634     1.065722
-#>  ds 3 parent   28     46.0    52.394  -6.39404 4.1390    -1.544842
-#>  ds 3 parent   28     53.4    52.394   1.00596 4.1390     0.243046
-#>  ds 3 parent   60     25.1    24.582   0.51786 1.9419     0.266676
-#>  ds 3 parent   60     21.4    24.582  -3.18214 1.9419    -1.638664
-#>  ds 3 parent   90     11.0    12.092  -1.09202 0.9552    -1.143199
-#>  ds 3 parent   90     14.2    12.092   2.10798 0.9552     2.206776
-#>  ds 3 parent  120      5.8     5.948  -0.14810 0.4699    -0.315178
-#>  ds 3 parent  120      6.1     5.948   0.15190 0.4699     0.323282
-#>  ds 4 parent    0     95.3   101.592  -6.29243 8.0255    -0.784057
-#>  ds 4 parent    0    102.0   101.592   0.40757 8.0255     0.050784
-#>  ds 4 parent    1    104.4   101.125   3.27549 7.9885     0.410025
-#>  ds 4 parent    1    105.4   101.125   4.27549 7.9885     0.535205
-#>  ds 4 parent    3    113.7   100.195  13.50487 7.9151     1.706218
-#>  ds 4 parent    3     82.3   100.195 -17.89513 7.9151    -2.260886
-#>  ds 4 parent    7     98.1    98.362  -0.26190 7.7703    -0.033706
-#>  ds 4 parent    7     87.8    98.362 -10.56190 7.7703    -1.359270
-#>  ds 4 parent   14     97.9    95.234   2.66590 7.5232     0.354357
-#>  ds 4 parent   14    104.8    95.234   9.56590 7.5232     1.271521
-#>  ds 4 parent   28     85.0    89.274  -4.27372 7.0523    -0.606001
-#>  ds 4 parent   28     77.2    89.274 -12.07372 7.0523    -1.712017
-#>  ds 4 parent   60     82.2    77.013   5.18660 6.0838     0.852526
-#>  ds 4 parent   60     86.1    77.013   9.08660 6.0838     1.493571
-#>  ds 4 parent   90     70.5    67.053   3.44692 5.2970     0.650733
-#>  ds 4 parent   90     61.7    67.053  -5.35308 5.2970    -1.010591
-#>  ds 4 parent  120     60.0    58.381   1.61905 4.6119     0.351058
-#>  ds 4 parent  120     56.4    58.381  -1.98095 4.6119    -0.429530
-#>  ds 5 parent    0     92.6   101.592  -8.99243 8.0255    -1.120485
-#>  ds 5 parent    0    116.5   101.592  14.90757 8.0255     1.857531
-#>  ds 5 parent    1    108.0    99.914   8.08560 7.8929     1.024413
-#>  ds 5 parent    1    104.9    99.914   4.98560 7.8929     0.631655
-#>  ds 5 parent    3    100.5    96.641   3.85898 7.6343     0.505477
-#>  ds 5 parent    3     89.5    96.641  -7.14102 7.6343    -0.935383
-#>  ds 5 parent    7     91.7    90.412   1.28752 7.1423     0.180267
-#>  ds 5 parent    7     95.1    90.412   4.68752 7.1423     0.656304
-#>  ds 5 parent   14     82.2    80.463   1.73715 6.3563     0.273295
-#>  ds 5 parent   14     84.5    80.463   4.03715 6.3563     0.635141
-#>  ds 5 parent   28     60.5    63.728  -3.22788 5.0343    -0.641178
-#>  ds 5 parent   28     72.8    63.728   9.07212 5.0343     1.802062
-#>  ds 5 parent   60     38.3    37.399   0.90061 2.9544     0.304835
-#>  ds 5 parent   60     40.7    37.399   3.30061 2.9544     1.117174
-#>  ds 5 parent   90     22.5    22.692  -0.19165 1.7926    -0.106913
-#>  ds 5 parent   90     20.8    22.692  -1.89165 1.7926    -1.055273
-#>  ds 5 parent  120     13.4    13.768  -0.36790 1.0876    -0.338259
-#>  ds 5 parent  120     13.8    13.768   0.03210 1.0876     0.029517
-# }
-
-

- -

Summary method for class "nlme.mmkin"

Arguments

Value

Author

Examples