Lists model equations, initial parameter values, optimised parameters with some uncertainty statistics, the chi2 error levels calculated according to FOCUS guidance (2006) as defined therein, formation fractions, DT50 values and optionally the data, consisting of observed, predicted and residual values.
Arguments
- object
an object of class mkinfit.
- data
logical, indicating whether the data should be included in the summary.
- distimes
logical, indicating whether DT50 and DT90 values should be included.
- alpha
error level for confidence interval estimation from t distribution
- ...
optional arguments passed to methods like
print.- x
an object of class
summary.mkinfit.- digits
Number of digits to use for printing
Value
The summary function returns a list with components, among others
- version, Rversion
The 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 model
- use_of_ff
Was maximum or minimum use made of formation fractions
- bpar
Optimised and backtransformed parameters
- data
The data (see Description above).
- start
The starting values and bounds, if applicable, for optimised parameters.
- fixed
The values of fixed parameters.
- errmin
The chi2 error levels for each observed variable.
- bparms.ode
All backtransformed ODE parameters, for use as starting parameters for related models.
- errparms
Error model parameters.
- ff
The estimated formation fractions derived from the fitted model.
- distimes
The DT50 and DT90 values for each observed variable.
- SFORB
If applicable, eigenvalues and fractional eigenvector component g of SFORB systems in the model.
The print method is called for its side effect, i.e. printing the summary.
References
FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
Examples
summary(mkinfit("SFO", FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting: 1.2.6
#> R version used for fitting: 4.3.2
#> Date of fit: Thu Nov 16 04:19:39 2023
#> Date of summary: Thu Nov 16 04:19:39 2023
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
#>
#> Model predictions using solution type analytical
#>
#> Fitted using 131 model solutions performed in 0.009 s
#>
#> Error model: Constant variance
#>
#> Error model algorithm: OLS
#>
#> Starting values for parameters to be optimised:
#> value type
#> parent_0 101.24 state
#> k_parent 0.10 deparm
#>
#> Starting values for the transformed parameters actually optimised:
#> value lower upper
#> parent_0 101.240000 -Inf Inf
#> log_k_parent -2.302585 -Inf Inf
#>
#> Fixed parameter values:
#> None
#>
#> Results:
#>
#> AIC BIC logLik
#> 55.28197 55.5203 -24.64099
#>
#> Optimised, transformed parameters with symmetric confidence intervals:
#> Estimate Std. Error Lower Upper
#> parent_0 109.200 3.70400 99.630 118.700
#> log_k_parent -3.291 0.09176 -3.527 -3.055
#> sigma 5.266 1.31600 1.882 8.649
#>
#> Parameter correlation:
#> parent_0 log_k_parent sigma
#> parent_0 1.000e+00 5.428e-01 1.642e-07
#> log_k_parent 5.428e-01 1.000e+00 2.507e-07
#> sigma 1.642e-07 2.507e-07 1.000e+00
#>
#> Backtransformed parameters:
#> Confidence intervals for internally transformed parameters are asymmetric.
#> t-test (unrealistically) based on the assumption of normal distribution
#> for estimators of untransformed parameters.
#> Estimate t value Pr(>t) Lower Upper
#> parent_0 109.20000 29.47 4.218e-07 99.6300 118.70000
#> k_parent 0.03722 10.90 5.650e-05 0.0294 0.04712
#> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900
#>
#> FOCUS Chi2 error levels in percent:
#> err.min n.optim df
#> All data 8.385 2 6
#> parent 8.385 2 6
#>
#> Estimated disappearance times:
#> DT50 DT90
#> parent 18.62 61.87
#>
#> Data:
#> time variable observed predicted residual
#> 0 parent 101.24 109.153 -7.9132
#> 3 parent 99.27 97.622 1.6484
#> 7 parent 90.11 84.119 5.9913
#> 14 parent 72.19 64.826 7.3641
#> 30 parent 29.71 35.738 -6.0283
#> 62 parent 5.98 10.862 -4.8818
#> 90 parent 1.54 3.831 -2.2911
#> 118 parent 0.39 1.351 -0.9613