Summary method for class

@@ -155,187 +94,217 @@ and optionally the data, consisting of observed, predicted and residual values.

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

- -

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 +

# S3 method for mkinfit
+summary(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)
+
+# S3 method for summary.mkinfit
+print(x, digits = max(3, getOption("digits") - 3), ...)

+ +

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 + +
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 + +
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 + +
fixed: The values of fixed parameters.
errmin: The chi2 error levels for each observed variable.
bparms.ode: All backtransformed ODE + +
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 + +
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 of SFORB components of the 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.

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, +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

Author

- +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

Author

Johannes Ranke

Examples


-  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
-
#> mkin version used for fitting:    1.0.3.9000 
-#> R version used for fitting:       4.0.3 
-#> Date of fit:     Mon Feb 15 17:13:09 2021 
-#> Date of summary: Mon Feb 15 17:13:09 2021 
-#> 
-#> Equations:
-#> d_parent/dt = - k_parent * parent
-#> 
-#> Model predictions using solution type analytical 
-#> 
-#> Fitted using 131 model solutions performed in 0.027 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

-

Examples


+  summary(mkinfit("SFO", FOCUS_2006_A, quiet = TRUE))
+#> mkin version used for fitting:    1.1.2 
+#> R version used for fitting:       4.2.1 
+#> Date of fit:     Wed Aug 10 15:27:28 2022 
+#> Date of summary: Wed Aug 10 15:27:28 2022 
+#> 
+#> Equations:
+#> d_parent/dt = - k_parent * parent
+#> 
+#> Model predictions using solution type analytical 
+#> 
+#> Fitted using 131 model solutions performed in 0.029 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
+
+

Summary method for class "mkinfit"

Arguments

Value

Arguments

Value

References

References

Author

Author

Examples

Examples